DNA - Deoxyribonucleic Acid - Genes - Genetics
DNA
is a
molecule that
carries the genetic
instructions for growth,
development, functioning and
reproduction, and
delivers the
information in the
correct time and
sequence.
All known living organisms and many viruses have DNA. All
6 billion A, C, G and T letters provides precise
instructions for how our bodies are built, and how they work. Every living
thing exists because the translational system receives
messages from DNA delivered
to it by
RNA and
translates the messages into
proteins. The system centers on a
cellular machine called the
ribosome, which is made of multiple large
molecules of RNA and protein and is ubiquitous in life as we know it. DNA and
RNA
are
nucleic acids; alongside
proteins,
lipids and complex
carbohydrates
(polysaccharides), they are one of the four major types of
macromolecules
that are essential for all known forms of life. Most DNA molecules consist
of two
biopolymer strands coiled around each other to form a
double helix, which refers to the structure formed by
double-stranded
molecules of nucleic acids such as DNA, which contains the
instructions for life,
encoded within genes. Within all
cells,
DNA is organized into very long lengths known as
chromosomes. In animal and plant cells these are double-ended, like
pieces of string or shoelaces, but in bacteria they are circular. Whether
stringy or
circular, these long
chromosomes must be organized and packaged
inside a cell so that the
genes can be switched
on or
off when they are
required.
Hydrogen Bonds.
In every human cell, all of the body's
blueprints
and
instructions are
stored in the form of DNA inside the nucleus. Molecules that need to
travel in and out of the nucleus -- to turn genes
on or
off or retrieve
information -- do so through passageways called
nuclear pore complexes. Traffic through these NPCs must be
tightly controlled in order to prevent DNA hijacking by viruses or faulty
functioning as in
cancer. To travel through NPCs, many molecules must be
attached to proteins called
transport factors, which act as shuttles that the NPC
recognizes. But the NPC faces a challenge: It must accurately recognize
and bind to TFs to let them through without admitting unwanted traffic,
but it must let them through quickly -- in a matter of milliseconds -- in
order for the cell to be able to do its duties. Proteins known to
accurately bind to specific molecules, like
antibodies, normally stay
stuck to their targets for periods of up to months.
Image of DNA (photo)
DNA Diversity
-
DNA Damage -
DNA Repair -
Gene Editing -
CRISPR -
Genetic Modification -
Gene Therapy -
Replication -
Regeneration G-
A-
C-
T stands for the chemicals
Adenine,
Thymine,
Guanine,
and
Cytosine. An
easy way to remember these 4 letters is to visualize
looking at a tag on a shirt. CTAG or See Tag, the Fabric Tag that has the
instructions and materials list.
Glossary.
Mitochondrial DNA
-
Epigenetics
-
Replication -
Twins -
We are all the Same
-
Non-Coding DNA -
ExpressionA DNA molecule consists
of two long polynucleotide chains composed of four types of nucleotide
subunits. Each of these chains is known as a DNA chain, or a DNA strand.
Hydrogen bonds between the base portions of the nucleotides hold the two
chains together.
The DNA molecule is based on the
Golden Ratio. It measures 34
angstroms long by 21 angstroms wide for each full cycle of its double
helix spiral. 34 and 21, of course, are numbers in the Fibonacci series
and their ratio, 1.6190476 closely approximates phi, 1.6180339.
DNA is a Linear Script.
Linear a continuous
long line involving a single dimension.
Vibrations.
The basic
elements that compose DNA are five atoms:
carbon,
nitrogen,
oxygen,
phosphorous, and
hydrogen. A nucleoside is
the combination of these atoms into two structures, a five-carbon sugar
molecule called
deoxyribose, which is responsible for the name of DNA, and one of four
nitrogen bases. DNA is made of chemical building blocks called
nucleotides. These
building blocks
are made of three parts: a phosphate group, a sugar group and one of four
types of nitrogen bases. To form a strand of DNA, nucleotides are linked
into chains, with the phosphate and sugar groups alternating.
Genetic Code is the
set of rules by
which
information encoded within genetic material (DNA or mRNA
sequences)
is
translated into
proteins by living
cells. Translation is accomplished
by the ribosome, which links amino acids in an order specified by
mRNA,
using transfer RNA (tRNA) molecules to carry
amino acids and to read the
mRNA three nucleotides at a time. The genetic code is highly similar among
all organisms and can be expressed in a simple table with 64 entries. The
code defines how
sequences of nucleotide triplets, called
codons, specify
which amino acid will be added next during
protein synthesis. With some
exceptions, a three-nucleotide codon in a nucleic acid sequence specifies
a single amino acid. The vast majority of genes are encoded with a single
scheme (see the RNA codon table). That scheme is often referred to as the
canonical or standard genetic code, or simply the genetic code, though
variant codes (such as in human mitochondria) exist. While the "genetic
code" determines a protein's amino acid sequence, other genomic regions
determine when and where these proteins are produced according to various
"gene regulatory codes".
DNA is a natural quaternary storage model with four bases: A, T,
C, and G. Therefore, a coding method that can generate multi-ary code is
required to make full use of the four bases. However,
Huffman coding is mostly used for binary coding, which does not
directly satisfy this requirement. A = 0 , C = 1 , G = 2 , T = 3.
Quaternary benefits when compared to binary is higher density. Quaternary
can represent more information in a smaller space than binary. This can be
an advantage in some applications where space is limited, such as in
memory devices. Another benefit is resilience. Quaternary encoding is more
resilient to errors in transmission or storage because it uses four
symbols instead of two. This means that it can detect and correct more
errors than binary. Overall, the choice between binary and quaternary
depends on the specific application and the requirements for efficiency,
compatibility, error correction, and data density.
DNA Storage Devices.
Quaternary Numeral System is a numeral system with four as its base.
It uses the digits 0, 1, 2, and 3 to represent any real number. Conversion
from binary is straightforward. Four is the largest number within the
subitizing range and one of two numbers that is both a square and a highly
composite number (the other being thirty-six), making quaternary a
convenient choice for a base at this scale. Despite being twice as large,
its radix economy is equal to that of binary. However, it fares no better
in the localization of prime numbers (the smallest better base being the
primorial base six, senary). Quaternary shares with all fixed-radix
numeral systems many properties, such as the ability to represent any real
number with a canonical representation (almost unique) and the
characteristics of the representations of rational numbers and irrational
numbers. See decimal and binary for a discussion of these properties.
Radix or
base is the number of unique digits, including the digit zero, used to
represent numbers. For example, for the decimal system (the most common
system in use today) the radix is ten, because it uses the ten digits from
0 through 9.
Machine Code -
Memory Proteins -
DNA animations by
wehi.tv for Science-Art exhibition (youtube)
Gene is a
sequence of
nucleotides in DNA or RNA that encodes the synthesis of a gene product,
either RNA or
protein. During
gene
expression, the DNA is first copied into RNA. The RNA can be directly
functional or be the intermediate template for a
protein that performs a
function. The transmission of genes to an organism's
offspring is the
basis of the inheritance of phenotypic trait. These genes make up
different DNA sequences called genotypes.
Genotypes along with
environmental and developmental factors determine what the phenotypes will
be. Most biological traits are under the influence of
polygenes (many
different genes) as well as gene–environment interactions. Some genetic
traits are instantly visible, such as eye color or the number of limbs,
and some are not, such as blood type, risk for specific diseases, or the
thousands of basic biochemical processes that constitute life. Genes can
acquire mutations in their sequence, leading to different variants, known
as alleles, in the population. These alleles encode slightly different
versions of a protein, which cause different
phenotypical traits. Usage of
the term "having a gene" (e.g., "good genes," "hair colour gene")
typically refers to containing a different allele of the same, shared
gene. Genes evolve due to natural selection / survival of the fittest and
genetic drift of the alleles. The concept of gene continues to be refined
as new phenomena are discovered. For example, regulatory regions of a gene
can be far removed from its coding regions, and coding regions can be
split into several exons. Some viruses store their genome in RNA instead
of DNA and some gene products are functional non-coding RNAs. Therefore, a
broad, modern working definition of a gene is any discrete locus of
heritable, genomic sequence which affect an organism's traits by being
expressed as a functional product or by regulation of
gene expression.
Hox Gene -
Transcription.
The Molecular Basis
of Life (youtube) - These animations show cellular biology on the
molecular scale. The structure of chromatin, the processes of
transcription, translation, DNA replication, and
cell division are shown.
All animations are scientifically accurate and derived from molecular
biology and crystallography research.
Genome for a human contains about 3 billion bases and about 20,000 genes
on 23 pairs of chromosomes. The information in DNA is stored as a code
made up of four chemical bases: adenine (A), guanine (G), cytosine (C),
and thymine (T). Human DNA consists of about 3 billion bases, and
more than 99 percent of those bases are the same in all
people. The order, or sequence, of these bases determines what
biological instructions are contained in a strand of DNA. For example, the
sequence ATCGTT might instruct for blue eyes, while ATCGCT might instruct
for brown.
The complete DNA instruction book, or
genome, for a human contains about 3 billion bases and about 20,000 genes
on 23 pairs of chromosomes. DNA contains the instructions needed for an
organism to develop, survive and reproduce. To carry out these functions,
DNA sequences must be converted into messages that
can be used to produce proteins, which are the complex molecules
that do most of the work in our bodies. Each DNA sequence that contains
instructions to make a protein is known as a gene. The size of a gene may
vary greatly, ranging from about 1,000 bases to 1 million bases in humans.
Genes only make up about 1 percent of the DNA sequence. DNA sequences
outside this 1 percent are involved in regulating when, how and how much
of a protein is made. DNA's instructions are used to make proteins in a
two-step process. First, enzymes read the information in a DNA molecule
and transcribe it into an intermediary molecule called messenger
ribonucleic acid, or mRNA. Next, the information contained in the mRNA
molecule is translated into the "language" of amino acids, which are the
building blocks of proteins. This language tells the cell's protein-making
machinery the precise order in which to link the amino acids to produce a
specific protein. This is a major task because there are 20 types of amino
acids, which can be placed in many different orders to form a wide variety
of proteins.
3 Billion
Base Pairs
encoding almost
30,000 Genes in every
cell nucleus. The human genome of
Homo sapiens is stored on
23 chromosome pairs. 22 of these are autosomal
chromosome pairs, while the remaining pair is sex-determining. The haploid
human genome occupies a total of just over 3 billion DNA base pairs that
means 6 billion base pairs per diploid cell. DNA base pairs form the
"rungs" of the twisted, ladder-shaped DNA molecules. only about 1.5% of
the genome codes for proteins, while the rest consists of non-coding RNA
genes, regulatory sequences, introns, and noncoding DNA (once known as
"junk DNA").
Base
Pair is a unit consisting of two nucleobases bound to each other by
hydrogen bonds. They form the building blocks of the DNA double helix and
contribute to the folded structure of both DNA and RNA. Dictated by
specific hydrogen bonding patterns, Watson-Crick base pairs
(guanine-cytosine and adenine-thymine) allow the DNA helix to maintain a
regular helical structure that is subtly dependent on its nucleotide
sequence. The complementary nature of this based-paired structure provides
a redundant copy of the genetic information encoded within each strand of
DNA. The regular structure and data redundancy provided by the DNA double
helix make DNA well suited to the storage of genetic information, while
base-pairing between DNA and incoming nucleotides provides the mechanism
through which DNA polymerase replicates DNA and RNA polymerase transcribes
DNA into RNA. Many DNA-binding
proteins can recognize specific base pairing patterns that identify
particular regulatory regions of genes. Intramolecular base pairs can
occur within single-stranded nucleic acids. This is particularly important
in RNA molecules (e.g., transfer RNA), where Watson-Crick base pairs
(guanine-cytosine and adenine-uracil) permit the formation of short
double-stranded helices, and a wide variety of non-Watson-Crick
interactions (e.g., G-U or A-A) allow RNAs to fold into a vast range of
specific three-dimensional structures. In addition, base-pairing between
transfer RNA (tRNA) and messenger RNA (mRNA) forms the basis for the
molecular recognition events that result in the nucleotide sequence of
mRNA becoming translated into the amino acid sequence of proteins via the
genetic code. The size of an individual gene or an organism's entire
genome is often measured in base pairs because DNA is usually
double-stranded. Hence, the number of total base pairs is equal to the
number of nucleotides in one of the strands (with the exception of
non-coding single-stranded regions of telomeres). The haploid human genome
(23 chromosomes) is estimated to be about 3.2 billion bases long and to
contain 20,000–25,000 distinct protein-coding genes. A kilobase (kb) is a
unit of measurement in molecular biology equal to 1000 base pairs of DNA
or RNA. The total amount of related DNA base pairs on Earth is estimated
at 5.0 × 1037 and weighs 50 billion tonnes. In comparison, the total mass
of the biosphere has been estimated to be as much as 4 TtC (trillion tons
of carbon).
Nucleobase are nitrogen-containing
biological compounds that
form
nucleosides, which in turn are components of nucleotides; all which
are
monomers that are the
basic building blocks of nucleic acids. Often
simply called bases, as in the field of genetics, the ability of nucleobases to form base-pairs and to stack one upon another leads
directly to long-chain helical structures such as ribonucleic acid (RNA)
and deoxyribonucleic acid (DNA).
We all have three billion bases, or
individual pieces, of DNA in every cell. Five nucleobases—adenine (A),
cytosine (C), guanine (G), thymine (T), and uracil (U)—are called primary
or canonical. They function as the fundamental units of the genetic code,
with the bases A, G, C, and T being found in DNA while A, G, C, and U are
found in RNA. Thymine and uracil are identical excepting that T includes a
methyl group that U lacks.
Nucleotide are organic
molecules that
serve as the
monomer units for forming the nucleic acid polymers DNA
(deoxyribonucleic acid) and RNA (ribonucleic acid), both of which are
essential biomolecules in all life-forms on Earth. Nucleotides are the
building blocks of nucleic acids; they are composed of three subunit
molecules: a nitrogenous base, a five-carbon sugar (ribose or deoxyribose),
and at least one phosphate group. They are also known as phosphate
nucleotides. A nucleoside is a nitrogenuous base and a 5-carbon sugar.
Thus a nucleoside plus a phosphate group yields a nucleotide. Nucleotides
also play a central role in life-form metabolism at the fundamental,
cellular level. They carry packets of chemical energy—in the form of the
nucleoside triphosphates ATP, GTP, CTP and UTP—throughout the cell to the
many cellular functions that demand energy, which include synthesizing
amino acids, proteins and cell membranes and parts; moving the cell and
moving cell parts, both internally and intercellularly; dividing the cell,
etc. In addition, nucleotides participate in
cell signaling (cGMP and cAMP),
and are incorporated into important cofactors of enzymatic reactions (e.g.
coenzyme A, FAD, FMN, NAD, and NADP+). In experimental biochemistry,
nucleotides can be radiolabeled with radionuclides to yield
radionucleotides.
DNA is well-known for its double helix shape. But the human genome
also contains more than 50,000 unusual 'knot'-like DNA structures called
i-motifs. I-motifs are DNA structures that differ from the iconic
double helix shape. They form when stretches of cytosine letters on the
same DNA strand pair with each other, creating a four-stranded,
twisted structure protruding from the double helix.
The researchers found that i-motifs are not randomly scattered but
concentrated in key functional areas of the genome, including regions that
control gene activity. We discovered that i-motifs are associated with
genes that are highly active during specific times in the cell cycle. This
suggests they play a dynamic role in regulating gene activity. We also
found that i-motifs form in the promoter region of oncogenes, for instance
the MYC oncogene, which encodes one of cancer's most notorious 'undruggable'
targets.
Human
Genome is the complete set of
nucleic acid
sequences for humans,
encoded as DNA within the
23 chromosome pairs in cell nuclei and in a small DNA molecule found
within individual mitochondria. Human genomes include both protein-coding
DNA genes and noncoding DNA. Haploid human genomes, which are contained in
germ cells (the egg and sperm gamete cells created in the meiosis phase of
sexual reproduction before fertilization creates a zygote) consist of
three billion DNA base pairs, while diploid genomes (found in somatic
cells) have twice the DNA content. While there are significant differences
among the genomes of human individuals (on the order of 0.1%), these are
considerably smaller than the differences between humans and their closest
living relatives, the chimpanzees (approximately 4%) and bonobos. The
Human Genome Project produced the first complete sequences of individual
human genomes, with the first draft sequence and initial analysis being
published on February 12, 2001. The human genome was the first of all
vertebrates to be completely
sequenced. As of 2012, thousands of human
genomes have been completely sequenced, and many more have been mapped at
lower levels of resolution. The resulting data are used worldwide in
biomedical science, anthropology, forensics and other branches of science.
There is a widely held expectation that genomic studies will lead to
advances in the diagnosis and treatment of diseases, and to new insights
in many fields of biology, including human evolution. Although the
sequence of the human genome has been (almost) completely determined by
DNA sequencing, it is not yet fully understood. Most (though probably not
all) genes have been identified by a combination of high throughput
experimental and bioinformatics approaches, yet much work still needs to
be done to further elucidate the biological functions of their protein and
RNA products. Recent results suggest that most of the vast quantities of
noncoding DNA within the genome have associated biochemical activities,
including regulation of gene expression, organization of chromosome
architecture, and signals controlling epigenetic inheritance. There are an
estimated 19,000-20,000 human protein-coding genes. The estimate of the
number of human genes has been repeatedly revised down from initial
predictions of 100,000 or more as genome sequence quality and gene finding
methods have improved, and could continue to drop further. Protein-coding
sequences account for only a very small fraction of the genome
(approximately 1.5%), and the rest is associated with non-coding RNA
molecules, regulatory DNA sequences, LINEs, SINEs, introns, and sequences
for which as yet no function has been determined. In June 2016, scientists
formally announced HGP-Write, a plan to synthesize the human genome.
Pan-Genome is the entire set of genes from all
strains within a clade. More generally, it is the union of all the
genomes of a
clade. The pan-genome can be broken down into a "core pangenome" that
contains genes present in all individuals, a "shell pangenome" that
contains genes present in two or more strains, and a "cloud pangenome"
that contains genes only found in a single strain.
Molecular Biology.
Scientists have published the first complete, gapless sequence of a human
genome. According to researchers, having a complete, gap-free sequence
of the roughly 3 billion bases (or "letters") in our DNA is critical for
understanding the full spectrum of human genomic variation and for
understanding the genetic contributions to certain diseases. The work was
done by the Telomere to Telomere (T2T) consortium, which included
leadership from researchers at the National Human Genome Research
Institute (NHGRI), part of the National Institutes of Health; University
of California, Santa Cruz; and University of Washington, Seattle. NHGRI
was the primary funder of the study.
Genomics is a
discipline in genetics that applies recombinant DNA, DNA sequencing
methods, and bioinformatics to sequence, assemble, and analyze the
function and structure of genomes (the complete set of DNA within a single
cell of an organism).
Genome in modern
molecular biology and genetics, the genome is the genetic material of an
organism. It consists of DNA (or RNA in RNA viruses). The genome includes
both the genes, (the coding regions), the noncoding DNA and the genomes of
the mitochondria and chloroplasts.
Gene is a sequence of nucleotides in DNA
or RNA that encodes the synthesis of a gene product, either RNA or
protein.
Gene Expression
(hereditary traits).
Genetics is the study
of
genes, genetic variation, and heredity
in living organisms.
Longevity.
Geneticist is a biologist who studies
genetics, the science of genes,
heredity, and variation of organisms.
Genomicist
is a scientist whose specialty is genomics.
Molecular Genetics is the field of
biology that studies the structure and function of genes at a molecular
level and thus employs methods of both molecular biology and genetics. The
study of chromosomes and gene expression of an organism can give insight
into heredity, genetic variation, and mutations. This is useful in the
study of developmental biology and in understanding and treating genetic diseases.
Tiny Machines -
Promotor -
Symmetry (math)
Purine is a
heterocyclic aromatic organic compound that consists of a pyrimidine ring
fused to an imidazole ring. Purine gives its name to the wider class of
molecules, purines, which include substituted purines and their tautomers,
are the most widely occurring nitrogen-containing heterocycle in nature.
Purine is water soluble.
Pyrimidine is an
aromatic heterocyclic
organic
compound similar to
pyridine.
One of the three diazines (six-membered heterocyclics with
two nitrogen
atoms in the ring), it has the nitrogen atoms at positions 1 and 3 in the
rings.
Helicase
are a class of
enzymes vital to all living
organisms. Their main function
is to unpackage an organism's genes. They are motor proteins that move
directionally along a nucleic acid phosphodiester backbone, separating two
annealed nucleic acid strands (i.e., DNA, RNA, or RNA-DNA hybrid) using
energy derived from ATP hydrolysis. There are many helicases resulting
from the great variety of processes in which strand separation must be
catalyzed. Approximately 1% of eukaryotic genes code for helicases. The
human genome codes for 95 non-redundant helicases: 64 RNA helicases and 31
DNA helicases. Many cellular processes, such as DNA replication,
transcription, translation, recombination, DNA repair, and ribosome
biogenesis involve the separation of nucleic acid strands that
necessitates the use of helicases.
Histone
are highly alkaline proteins found in
eukaryotic cell nuclei that package
and order the DNA into structural units called nucleosomes. They are the
chief protein components of chromatin, acting as spools around which DNA
winds, and playing a role in gene regulation. Without histones, the
unwound DNA in chromosomes would be very long (a length to width ratio of
more than 10 million to 1 in human DNA). For example, each human diploid
cell (containing 23 pairs of chromosomes) has about 1.8 meters of DNA, but
wound on the histones it has about 90 micrometers (0.09 mm) of chromatin,
which, when duplicated and condensed during mitosis, result in about 120
micrometers of chromosomes.
Chromatin is a complex of macromolecules found in
cells, consisting of
DNA,
protein, and RNA. The primary functions of chromatin are 1) to
package DNA into a more compact, denser shape, 2) to reinforce the DNA
macromolecule to allow mitosis, 3) to prevent DNA damage, and 4) to
control gene expression and DNA replication. The primary protein
components of chromatin are histones that compact the DNA. Chromatin is
only found in eukaryotic cells (cells with defined nuclei). Prokaryotic
cells have a different organization of their DNA (the prokaryotic
chromosome equivalent is called genophore and is localized within the nucleoid region).
Nucleosome is a
basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA
wound in sequence around eight histone protein cores. This structure is
often compared to thread wrapped around a spool.
Nuclear DNA is the DNA contained within each
cell nucleus of a eukaryotic organism.
Nuclear DNA encodes for the majority of the genome in eukaryotes, with
mitochondrial DNA and plastid DNA coding
for the rest. Nuclear DNA adheres to Mendelian inheritance, with
information coming from two parents, one male and one female, rather than
matrilineally (through the mother) as in mitochondrial DNA. Nuclear DNA is
a nucleic acid, a polymeric biomolecule or biopolymer, found in the
nucleus of eukaryotic organisms.
DNA can fold into complex shapes to execute new functions. DNA can
mimic
protein functions by
folding into elaborate, three-dimensional structures, according to a new
study. High-resolution imaging techniques to reveal the novel and complex
structure of a DNA molecule they created that mimics the activity of a
protein called green fluorescent protein (GFP). GFP, which was derived
from jellyfish, has become an important laboratory tool, functioning as a
fluorescent tag or beacon in cells.
Routine test reveals unique divergence in genetic code. Scientists
testing a new method of sequencing single cells have unexpectedly changed
our understanding of the rules of genetics. The genome of a
protist
has revealed a seemingly unique divergence in the DNA code signalling the
end of a gene, suggesting the need for further research to better
understand this group of diverse organisms. The protist Oligohymenophorea
sp. PL0344 turned out to be a novel species with an unlikely change in how
its DNA is translated into proteins. Ciliates are hotspots for genetic
code changes, including reassignment of one or more stop codons -- the
codons TAA, TAG, and TGA. In virtually all organisms, these three stop
codons are used to signal the end of a gene. DNA is like a blueprint of a
building. It does not do anything in and of itself -- it provides
instructions for work to be done. In order for a gene to have an impact,
the blueprint must be "read" and then built into a molecule which has a
physical effect. For DNA to be read, it is first transcribed into an RNA
copy. This copy is taken to another area of the cell where it is
translated into amino acids, which are combined to make a
three-dimensional molecule. The translation process starts at the DNA
start codon (ATG) and finishes at a stop codon (normally TAA, TAG, or
TGA).
The Largest Genome Of Any Organism. Tiny Fern Breaks The World Record.
The New
Caledonian fork fern species
Tmesipteris oblanceolata has a genome that when stretched out would be
taller than Big Ben’s tower, and is now a three-time world record holder.
The New Caledonian fork fern species Tmesipteris oblanceolata has a genome
that when stretched out would be taller than Big Ben’s tower, and is now a
three-time world record holder. Despite holding the world record, T.
oblanceolata is actually at more of a disadvantage than its smaller-genomed
compatriots. Having a big genome and lots of DNA requires big cells,
meaning that the larger-genomed species are more likely to be slower
growing and less efficient at photosynthesis. The bigger your genomes, the
more constraints you have on ecological opportunities and your ability to
grow and compete successfully with other plants. And so, the species with
the biggest genomes, like Paris japonica or Tmesipteris, this fork fern,
tend to be found in very stable environments, which are not competitive,
Translation
Ribosome is a complex molecular machine,
found within all living cells, that
serves as the site of biological
protein
synthesis (translation).
Ribosomes link amino acids together in the order specified by messenger
RNA (mRNA) molecules. Ribosomes consist of two major components: the small
ribosomal subunits, which read the RNA, and the large subunits, which join
amino acids to form a
polypeptide chain. Each subunit comprises one or more ribosomal RNA (rRNA)
molecules and a variety of ribosomal proteins (r-protein or rProtein). The
ribosomes and associated molecules are also known as the translational
apparatus.
Enzymes (catalysis)
-
Epigenetics -
Transcription -
Expression Translation in Genetics
is the process whereby genetic information coded in messenger RNA directs
the formation of a specific protein at a ribosome in the cytoplasm.
Determine the amino-acid sequence of a protein during its synthesis by
using information on the messenger RNA.
Language Translation.
Translation in
biology is the process in which ribosomes in the
cytoplasm or ER synthesize proteins after the process of transcription of
DNA to RNA in the cell's nucleus. The entire process is called
gene expression. In translation,
messenger RNA (mRNA) is decoded in a ribosome to produce a specific amino
acid chain, or polypeptide. The polypeptide later folds into an active
protein and performs its functions in the cell. The ribosome facilitates
decoding by inducing the binding of complementary tRNA anticodon sequences
to mRNA codons. The tRNAs carry specific amino acids that are chained
together into a polypeptide as the mRNA passes through and is "read" by
the ribosome. Translation proceeds in three phases: Initiation: The
ribosome assembles around the target mRNA. The first tRNA is attached at
the start codon. Elongation: The tRNA transfers an amino acid to the tRNA
corresponding to the next codon. The ribosome then moves (translocates) to
the next mRNA codon to continue the process, creating an amino acid chain.
The three phases of translation initiation polymerase binds to the DNA
strand and moves along until the small ribosomal subunit binds to the DNA.
Elongation is initiated when the large subunit attaches and
termination end the process of elongation.
Termination: When a stop codon is reached, the ribosome releases the
polypeptide.
Chromatid is one copy of a newly copied chromosome which is still
joined to the original copy by a single centromere. Before replication,
one chromosome is composed of one DNA molecule. Following replication,
each chromosome is composed of two DNA molecules; in other words, DNA
replication itself increases the amount of DNA but does not increase the
number of chromosomes. The two identical copies—each forming one half
of the replicated chromosome—are called chromatids. During the later
stages of cell division these chromatids separate longitudinally to become
individual chromosomes. Chromatid pairs are normally genetically
identical, and said to be homozygous; however, if mutation(s) occur, they
will present slight differences, in which case they are heterozygous. The
pairing of chromatids should not be confused with the ploidy of an
organism, which is the number of homologous versions of a chromosome.
Chromonema is the fibre-like structure in prophase in the primary stage of DNA condensation. In metaphase, they are called chromatids.
Kinetochore is a
protein structure on chromatids where the spindle
fibers attach during cell division to pull sister chromatids apart. Their
proteins help to hold the sister chromatids together and also play a role
in chromosome editing. The kinetochore forms in eukaryotes, assembles on
the centromere and links the chromosome to microtubule polymers from the
mitotic spindle during mitosis and meiosis.
Polynucleotide
molecule is a
biopolymer
composed of 13 or more nucleotide monomers covalently bonded in a chain.
DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are examples of
polynucleotides with distinct biological function.
Replication
DNA Replication
is the biological process of producing two identical
replicas of DNA from
one original DNA molecule. This process occurs in all living organisms and
is the basis for
biological inheritance.
The cell possesses the distinctive property of
division, which makes
replication of DNA essential.
How one
cell builds an entire organism. Every cell in a developing embryo
carries within it a
copy of the organism's complete genome. Like
construction workers using only the relevant portion of a
blueprint when
laying a building's
foundation, cells must
express the necessary genes at
the appropriate time for the embryo to develop correctly. DNA is made
up of a double helix of two complementary strands. During replication,
these strands are separated. Each strand of the original DNA molecule then
serves as a template for the production of its counterpart, a process
referred to as
semiconservative replication. As a result of semi-conservative
replication, the new helix will be composed of an original DNA strand as
well as a newly synthesized strand. Cellular
proofreading and
error-checking
mechanisms ensure near perfect fidelity for DNA replication. In a cell,
DNA replication begins at specific locations, or origins of replication,
in the genome. Unwinding of DNA at the origin and synthesis of new
strands, accommodated by an enzyme known as helicase, results in
replication forks growing bi-directionally from the origin. A number of
proteins are associated with the replication fork to help in the
initiation and continuation of DNA synthesis. Most prominently, DNA
polymerase synthesizes the new strands by adding nucleotides that
complement each (template) strand.
DNA replication occurs during the
S-stage of interphase. DNA replication (DNA amplification) can also be
performed in vitro (artificially, outside a cell). DNA polymerases
isolated from cells and artificial DNA primers can be used to initiate DNA
synthesis at known sequences in a template DNA molecule. Polymerase chain
reaction (PCR), ligase chain reaction (LCR), and transcription-mediated
amplification (TMA) are examples.
Mutations -
DNA Repair -
Cell Division -
Molecular Machines
DNA
Polymerase is an enzyme that synthesizes DNA molecules from
deoxyribonucleotides, the building blocks of DNA. These enzymes are
essential for DNA replication and usually work in pairs to create two
identical DNA strands from a single original DNA molecule. During this
process, DNA polymerase "reads" the existing DNA strands to create two new
strands that match the existing ones. Every time a cell divides, DNA
polymerases are required to help duplicate the cell's DNA, so that a copy
of the original DNA molecule can be passed to each daughter cell. In this
way, genetic information is passed down from generation to generation. The
main function of DNA polymerase is to synthesize DNA from
deoxyribonucleotides, the building blocks of DNA. The DNA copies are
created by the pairing of nucleotides to bases present on each strand of
the original DNA molecule. This pairing always occurs in specific
combinations, with cytosine along with guanine, and thymine along with
adenine, forming two separate pairs, respectively. By contrast, RNA
polymerases synthesize RNA from ribonucleotides from either RNA or DNA.
Before replication can take place, an enzyme called helicase unwinds the
DNA molecule from its tightly woven form, in the process breaking the
hydrogen bonds between the nucleotide bases. This opens up or "unzips" the
double-stranded DNA to give two single strands of DNA that can be used as
templates for replication. The function of DNA polymerase is not quite
perfect, with the enzyme making about one mistake for every billion base
pairs copied.
Error correction is a
property of some, but not all DNA polymerases. This process corrects
mistakes in newly synthesized DNA. When an incorrect base pair is
recognized, DNA polymerase moves backwards by one base pair of DNA. The
3'–5' exonuclease activity of the enzyme allows the incorrect base pair to
be excised (this activity is known as proofreading). Following base
excision, the polymerase can re-insert the correct base and replication
can continue forwards. This preserves the integrity of the original DNA
strand that is
passed onto the daughter cells.
Fidelity is very important in DNA replication. Mismatches in DNA base
pairing can potentially result in dysfunctional proteins and could lead to
cancer. Many DNA polymerases contain an
exonuclease domain, which acts in detecting base pair mismatches and
further performs in the removal of the incorrect nucleotide to be replaced
by the correct one. Proofreading by DNA polymerase
corrects errors during replication. Some errors are not corrected
during replication, but are instead corrected after replication is
completed; this type of repair is known as mismatch repair.
Origin and Evolution of DNA and DNA Replication Machineries. The
transition from the RNA to the DNA world was a major event in the history
of life. The invention of DNA required the appearance of enzymatic
activities for both synthesis of DNA precursors, retro-transcription
of RNA templates and replication of singleand double-stranded DNA
molecules. Recent data from comparative genomics, structural biology and
traditional
biochemistry have
revealed that several of these enzymatic activities have been invented
independently more than once, indicating that the transition from RNA to
DNA genomes was more complex than previously thought. The distribution of
the different
protein families
corresponding to these activities in the three domains of life (Archaea,
Eukarya, and
Bacteria) is puzzling.
In many cases, Archaea and Eukarya contain the same version of these
proteins, whereas Bacteria contain another version. However, in other
cases, such as thymidylate synthases or type II DNA topoisomerases, the
phylogenetic distributions of these proteins do not follow this simple
pattern. Several hypotheses have been proposed to explain these
observations, including independent invention of DNA and DNA replication
proteins, ancient gene transfer and gene loss, and/or nonorthologous
replacement. We review all of them here, with more emphasis on recent
proposals suggesting that viruses have played a major role in the origin
and evolution of the DNA replication proteins and possibly of DNA itself.
All cellular organisms have double-stranded DNA
genomes. The origin of DNA and DNA replication mechanisms is thus a
critical question for our understanding of early life evolution. For some
time, it was believed by some molecular biologist that life originated
with the appearance of the first DNA molecule! Watson and Crick even
suggested that DNA was possibly replicated without proteins, wondering
“whether a special enzyme would be required to carry out the
polymerization or whether the existing single helical chain could act
effectively as an enzyme”. Such extreme conception was in line with the
idea that DNA was the aperiodic crystal predicted by Schroedinger in his
influential book “What's life”. Times have changed, and several decades
of experimental work have convinced us that DNA synthesis and replication
actually require a plethora of proteins. We are reasonably sure now that
DNA and DNA replication mechanisms appeared late in early life history,
and that DNA originated from RNA in an RNA/protein world. The origin and
evolution of DNA replication mechanisms thus occurred at a critical period
of life evolution that encompasses the late RNA world and the emergence of
the Last Universal Cellular Ancestor (LUCA) to the present three domains
of life (Eukarya, Bacteria and Archaea). It is an exciting time to
learn through comparative genomics and molecular biology about the
details of modern mechanisms for precursor DNA synthesis and DNA
replication, in order to trace their histories. DNA can be considered as a
modified form of RNA, since the “normal” ribose sugar in RNA is reduced
into deoxyribose in DNA, whereas the “simple” base uracil is methylated
into thymidine. In modern cells, the DNA precursors (the four
deoxyribonucleoties, dNTPs) are produced by reduction of ribonucleotides
di- or triphosphate by ribonucleotide reductases. The synthesis
of DNA building blocks from RNA precursors is a major argument in favor of
RNA preceding DNA in evolution. The direct prebiotic origin of is
theoretically plausible (from acetaldehyde and glyceraldehyde-5-phosphate)
but highly unlikely, considering that evolution, as stated by F. Jacob,
works like a tinkerer, not an engineer.
How to build Synthetic DNA and send it across the internet: Dan Gibson
(video and text)
Gene Editing (Crispr) -
Genetic Modification (GMO)
Synthetic
Genomics is a nascent field of
synthetic biology that uses aspects of genetic modification on
pre-existing life forms, or artificial gene synthesis to create new DNA or
entire life forms.
Palindromic Sequence is a nucleic acid sequence in a double-stranded
DNA or RNA molecule whereby reading in a certain direction (e.g. 5' to 3')
on one strand is identical to the sequence in the same direction (e.g. 5'
to 3') on the complementary strand. This definition of palindrome thus
depends on complementary strands being
palindromic of each other. Palindrome in DNA consists of two closely
spaced or adjacent inverted repeats. Certain palindromes have important
biological functions as parts of various cis-acting elements and protein
binding sites. The human genome contains ca. 20,000 genes that are used
for the construction of proteins.
RNA
RNA or
Ribonucleic Acid, is a
polymeric
molecule implicated in various biological roles in
coding,
decoding,
regulation, and
expression of genes.
Uracil
is one of the four nucleobases in the nucleic acid of RNA that are
represented by the letters A, G, C and U. (GACU).
RNA Interference
is a biological process in which RNA molecules inhibit
gene expression or
translation, by neutralizing targeted mRNA molecules.
Transfer RNA is an adaptor molecule composed of RNA, typically 76 to
90 nucleotides in length, that serves as the physical link between the
mRNA and the amino acid sequence of proteins.
tRNA
does this by carrying an amino acid to the protein synthetic machinery of
a cell (ribosome) as directed by a 3-nucleotide sequence (codon) in a
messenger RNA (mRNA). As such, tRNAs are a necessary component of
translation, the biological synthesis of new proteins in accordance with
the genetic code.
Messenger RNA
is a large family of RNA molecules that
convey genetic information from
DNA to the
ribosome, where they specify the amino acid sequence of the
protein products of gene expression. Following transcription of primary
transcript mRNA (known as pre-mRNA) by RNA polymerase, processed, mature
mRNA is translated into a polymer of amino acids: a protein, as summarized
in the central dogma of molecular biology. As in DNA,
mRNA genetic
information is in the sequence of nucleotides, which are arranged into
codons consisting of three base pairs each. Each codon encodes for a
specific
amino acid, except the stop codons, which terminate
protein
synthesis. This process of translation of codons into amino acids requires
two other types of RNA: Transfer RNA (
tRNA), that mediates recognition of
the codon and provides the corresponding amino acid, and ribosomal RNA (rRNA),
that is the central component of the ribosome's protein-manufacturing
machinery. The existence of mRNA was first suggested by Jacques Monod and
François Jacob, and subsequently discovered by Jacob, Sydney Brenner and
Matthew Meselson at the California Institute of Technology in 1961. It
should not be confused with mitochondrial DNA.
MicroRNA is a small
non-coding RNA
molecule containing about 22 nucleotides found in plants, animals and
some viruses, that functions in RNA silencing and post-transcriptional
regulation of gene expression. While the majority of miRNAs are located
within the cell, some miRNAs, commonly known as circulating miRNAs or
extracellular miRNAs, have also been found in extracellular environment,
including various biological fluids and cell culture media.Encoded by
eukaryotic nuclear DNA in plants and animals and by viral DNA in certain
viruses whose genome is based on DNA, miRNAs function via base-pairing
with complementary sequences within mRNA molecules. As a result, these
mRNA molecules are silenced, by one or more of the following processes:
Cleavage of the mRNA strand into two pieces, Destabilization of the mRNA
through shortening of its poly(A) tail, and Less efficient translation of
the mRNA into proteins by ribosomes. miRNAs resemble the small interfering
RNAs (siRNAs) of the RNA interference (RNAi) pathway, except miRNAs derive
from regions of RNA transcripts that fold back on themselves to form short
hairpins, whereas siRNAs derive from longer regions of double-stranded
RNA. The human genome may encode over 1000 miRNAs, which are abundant in
many mammalian cell types and appear to target about 60% of the genes of
humans and other mammals. miRNAs are well conserved in both plants and
animals, and are thought to be a vital and evolutionarily ancient
component of gene regulation. While core components of the microRNA
pathway are conserved between plants and animals, miRNA repertoires in the
two kingdoms appear to have emerged independently with different primary
modes of action. Plant miRNAs usually have near-perfect pairing with their
mRNA targets, which induces gene repression through cleavage of the target
transcripts. In contrast, animal miRNAs are able to recognize their target
mRNAs by using as little as 6–8 nucleotides (the seed region) at the 5'
end of the miRNA, which is not enough pairing to induce cleavage of the
target mRNAs.Combinatorial regulation is a feature of miRNA regulation in
animals. A given miRNA may have hundreds of different mRNA targets, and a
given target might be regulated by multiple miRNAs.
P-site
or peptidyl, is the second binding site for tRNA in the ribosome. The
other two sites are the A-site (aminoacyl), which is the first binding
site in the ribosome, and the E-site (exit), is the third and final
binding site in the ribosome. During Protein translation, the P-site holds
the tRNA which is linked to the growing polypeptide chain. When a stop
codon is reached, the peptidyl-tRNA bond of the tRNA located in the P-site
is cleaved releasing the newly synthesized protein. During the
translocation step of the elongation phase, the mRNA is advanced by one
codon, coupled to movement of the tRNAs from the ribosomal A to P and P to
E sites, catalyzed by elongation factor EF-G. The deacylated tRNA remains
in the P-site and gets released once the peptidyl-tRNA is transferred to
the P-site. Prior to peptide bond formation, an aminoacyl-tRNA is bound in
the A-site, a peptidyl-tRNA is bound in the P-site, and a deacylated tRNA
(ready to exit from the ribosome) is bound to the E-site.
Intron
is any nucleotide sequence within a gene that is removed by RNA splicing
during maturation of the final RNA product. The term intron refers to both
the DNA sequence within a gene and the corresponding sequence in RNA
transcripts. Sequences that are joined together in the final mature RNA
after RNA splicing are exons. Introns are found in the genes of most
organisms and many viruses, and can be located in a wide range of genes,
including those that generate
proteins, ribosomal RNA (rRNA), and transfer
RNA (tRNA). When proteins are generated from intron-containing genes, RNA
splicing takes place as part of the RNA processing pathway that follows
transcription and precedes
translation.
Control Logic.
Exon
is any part of a gene that will
encode a part of the final mature RNA
produced by that gene after introns have been removed by RNA splicing. The
term exon refers to both the DNA sequence within a gene and to the
corresponding sequence in RNA transcripts. In RNA splicing, introns are
removed and exons are covalently joined to one another as part of
generating the mature messenger RNA. Just as the entire set of genes for a
species constitutes the genome, the entire set of exons constitutes the exome.
DNA-Binding Protein are
proteins composed of DNA-binding domains and thus have a specific or
general affinity for either single or double stranded DNA.
Sequence-specific DNA-binding proteins generally interact with the major
groove of B-DNA, because it exposes more functional groups that identify a
base pair. However, there are some known minor groove DNA-binding ligands
such as netropsin, distamycin, Hoechst 33258, pentamidine, DAPI and others.
RNA
Splicing is the editing of the nascent precursor messenger RNA
(pre-mRNA) transcript into a mature messenger RNA (mRNA). After splicing,
introns are removed and exons are joined together (ligated). For
nuclear-encoded genes, splicing takes place within the nucleus either
during or immediately after transcription. For those eukaryotic genes that
contain introns, splicing is usually required in order to create an mRNA
molecule that can be translated into protein. For many eukaryotic introns,
splicing is carried out in a series of reactions which are catalyzed by
the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs).
Self-splicing introns, or ribozymes capable of catalyzing their own
excision from their parent RNA molecule, also exist.
Genotyping is the process of determining differences in the
genetic make-up (genotype) of an individual by examining the individual's
DNA sequence using biological assays and comparing it to another
individual's sequence or a reference sequence. It reveals the alleles an
individual has inherited from their parents. Traditionally genotyping is
the use of DNA sequences to define biological populations by use of
molecular tools. It does not usually involve defining the genes of an individual.
Human cells can write RNA sequences into DNA. In a discovery that
challenges long-held dogma in biology, researchers show that mammalian
cells can convert RNA sequences back into DNA, a feat more common in
viruses than eukaryotic cells. Cells contain machinery that duplicates DNA
into a new set that goes into a newly formed cell. That same class of
machines, called polymerases, also build RNA messages, which are like
notes copied from the central DNA repository of recipes, so they can be
read more efficiently into proteins. But polymerases were thought to only
work in one direction DNA into DNA or RNA. This prevents RNA messages from
being rewritten back into the master recipe book of genomic DNA. Now,
Thomas Jefferson University researchers provide the first evidence that
RNA segments can be written back into DNA, which potentially challenges
the central dogma in biology and could have wide implications affecting
many fields of biology.
Scientists discover dual-function messenger RNA. A new study has
discovered an unprecedented pathway producing telomerase RNA from a
protein-coding messenger RNA (mRNA). The central dogma of molecular
biology specifies the order in which genetic information is transferred
from DNA to make proteins. Messenger RNA molecules carry the genetic
information from the DNA in the nucleus of the cell to the cytoplasm where
the proteins are made. Messenger RNA acts as the messenger to build
proteins. There are many ribonucleic acids that are not used to make
protein. About 70 percent of the human genome is used to make noncoding
RNAs that don't code for protein sequences but have other uses. While
increased telomerase activity could bring youth to aging cells and cure
premature aging-like diseases, too much of a good thing can be damaging
for the individual. Just as youthful stem cells use telomerase to offset
telomere length loss, cancer cells employ telomerase to maintain their
aberrant and destructive growth. Augmenting and regulating telomerase
function will have to be performed with precision, walking a narrow line
between cell rejuvenation and a heightened risk for cancer development.
A molecular machine's secret weapon exposed. Unfortunately, when RNA
malfunctions, it can result in cancer and developmental disorders.
RNAs can wreak havoc on cells if they aren't
removed at the right time. Dis3L2 is a molecular 'machine' that
untangles and chews up RNAs, but scientists have been unable to explain
how. Biochemists have now pieced together the answer. By shape-shifting,
the machine unsheathes a lethal wedge that pries open and chews up RNA
molecules, a behavior previously unseen.
New RNA-based tool can illuminate brain circuits, edit specific cells.
Editing technology is precise and broadly applicable to all tissues and
species. Researchers have developed a customizable, RNA-based platform to
target cells rather than genes. CellREADR enables scientists to add any
protein to a designated cell type. Initial evidence demonstrates the new
technology works for brain tissue in rodents and humans and its design
relies on an enzyme found in every animal cell, suggesting easy adoption
for other creatures and organs. It may provide an effective route to
treating complex diseases like schizophrenia or cancer. Selective cell
monitoring and control system relies on the ADAR enzyme, which is found in
every animal's cells. While these are early days for CellREADR (Cell
access through RNA sensing by Endogenous ADAR), the possible applications
appear to be endless, Huang said, as is its potential to work across the
animal kingdom.
Sequence
DNA Sequencing
is the process of determining the
precise order of nucleotides within a
DNA molecule.
Whole Genome Sequencing
is the process of determining the complete
DNA sequence of an organism's genome at a single time. This entails
sequencing all of an organism's chromosomal DNA as well as DNA contained
in the mitochondria and, for plants, in the chloroplast.
Scientists make leap forward for genetic sequencing. Research to lead
to improved personalized medicine and understanding of evolution.
Researchers reveal new details about a key
enzyme that makes DNA
sequencing possible. The finding is a leap forward into the era of
personalized medicine when doctors will be able to design treatments based
on the genomes of individual patients.
Enzymes make life possible
by catalyzing chemical transformations that otherwise would just take too
long for an organism.
Nucleic Acid are biopolymers, or large
biomolecules, essential
to all known forms of life. They are composed of
monomers,
which are nucleotides made of three components: a
5-carbon sugar, a
phosphate group, and a nitrogenous base. If the sugar is a simple
ribose, the polymer is RNA (ribonucleic acid); if the sugar is derived
from ribose as deoxyribose, the polymer is DNA (deoxyribonucleic acid).
Nucleic acids are arguably the most important of all biomolecules. They
are found in abundance in all living things, where they function to create
and encode and then store information in the nucleus of every living cell
of every life-form organism on Earth. In turn, they function to transmit
and express that information inside and outside the cell nucleus—to the
interior operations of the cell and ultimately to the next generation of
each living organism. The encoded information is contained and conveyed
via the nucleic acid sequence, which provides the 'ladder-step' ordering
of nucleotides within the molecules of RNA and DNA. Strings of nucleotides
are bonded to form helical backbones—typically, one tor RNA, two for
DNA—and assembled into chains of base-pairs selected from the five
primary, or canonical, nucleobases, which are: adenine, cytosine, granine,
thymine, and uracil; note, thymine occurs only in DNA and uracil only in
RNA. Using amino acids and the process known as protein synthesis, the
specific sequencing in DNA of these nucleobase-pairs enables storing and
transmitting coded instructions as genes. In RNA, base-pair sequencing
provides for manufacturing new proteins that determine the frames and
parts and most chemical processes of all life forms.
Nucleic Acid
Sequence is a succession of letters that indicate the order of
nucleotides within a DNA (using GACT) or RNA (GACU) molecule. By
convention, sequences are usually presented from the 5' end to the 3' end.
For DNA, the sense strand is used. Because nucleic acids are normally
linear (unbranched) polymers, specifying the sequence is equivalent to
defining the covalent structure of the entire molecule. For this reason,
the nucleic acid sequence is also termed the
primary structure.
Genetic Testing
-
Heredity -
Genealogy -
Risk
Genetic Marker is a gene or DNA sequence
with a known location on a
chromosome that can be used to identify individuals or species. It can
be described as a variation (which may arise due to mutation or alteration
in the genomic loci) that can be observed. A genetic marker may be a short
DNA sequence, such as a sequence surrounding a single base-pair change
(single nucleotide polymorphism, SNP), or a long one, like
minisatellites).
5' end to the 3' end,
Directionality in molecular biology is the end-to-end chemical
orientation of a single strand of nucleic acid. In a single strand of DNA
or RNA, the chemical convention of naming carbon atoms in the nucleotide
sugar-ring means that there will be a 5'-end, which frequently contains a
phosphate group attached to the 5' carbon of the ribose ring, and a 3'-end
(usually pronounced "five prime end" and "three prime end"), which
typically is unmodified from the ribose -OH substituent. In a DNA double
helix, the strands run in opposite directions to permit base pairing
between them, which is essential for replication or transcription of the
encoded information.
Bioinformatics
is an interdisciplinary field that develops methods and software tools for
understanding biological data.
Metagenomics is the study of genetic material recovered directly from
environmental samples.
New form of four-stranded 'knot' DNA structure called the i-motif found
inside cells. In the knot structure, C letters on the same strand of
DNA bind to each other -- so this is very different from a double helix,
where 'letters' on opposite strands recognize each other, and where Cs
bind to Gs [guanines]. To detect the i-motifs inside cells, the
researchers developed a precise new tool -- a fragment of an antibody
molecule -- that could specifically recognize and attach to i-motifs with
a very high affinity. Crucially, the antibody fragment didn't detect DNA
in helical form, nor did it recognize 'G-quadruplex structures' (a
structurally similar four-stranded DNA arrangement). With the new tool,
researchers uncovered the location of 'i-motifs' in a range of human cell
lines. Using fluorescence techniques to pinpoint where the i-motifs were
located, they identified numerous spots of green within the nucleus, which
indicate the position of i-motifs. The researchers showed that i-motifs
mostly form at a particular point in the cell's 'life cycle' -- the late
G1 phase, when DNA is being actively 'read'. They also showed that
i-motifs appear in some promoter regions (areas of DNA that control
whether genes are switched on or off) and in telomeres, 'end sections' of
chromosomes that are important in the aging process.
Human Genome could contain up to 20 percent fewer genes. Up to 20% of
genes classified as coding (those that produce the proteins that are the
building blocks of all living things) may not be coding after all because
they have characteristics that are typical of non-coding or pseudogenes
(obsolete coding genes). The consequent reduction in the size of the human
genome could have important effects in biomedicine since the number of
genes that produce proteins and their identification is of vital
importance for the investigation of multiple diseases, including cancer,
cardiovascular diseases, etc.. The researchers analyzed the genes
cataloged as protein coding in the main reference human proteomes: the
detailed comparison of the reference proteomes from GENCODE/Ensembl,
RefSeq and UniProtKB found 22,210 coding genes, but only 19,446 of these
genes were present in all 3 annotations. When they analyzed the 2,764
genes that were present in only one or two of these reference annotations,
they were surprised to discover that experimental evidence and manual
annotations suggested that almost all of these genes were more likely to
be non-coding genes or pseudogenes. In fact, these genes, together with
another 1,470 coding genes that are present in the three reference
catalogs, were not evolving like typical protein coding genes. The
conclusion of the study is that most of these 4,234 genes probably do not
code for proteins.
Pseudogene are segments of DNA that are related to real genes.
Pseudogenes have lost at least some functionality, relative to the
complete gene, in cellular gene expression or protein-coding ability.
Pseudogenes often result from the accumulation of multiple mutations
within a gene whose product is not required for the survival of the
organism, but can also be caused by genomic copy number variation (CNV)
where segments of 1+ kb are duplicated or deleted. Although not fully
functional, pseudogenes may be functional, similar to other kinds of
noncoding DNA, which can perform regulatory functions. The "pseudo" in "pseudogene"
implies a variation in sequence relative to the parent coding gene, but
does not necessarily indicate pseudo-function. Despite being non-coding,
many pseudogenes have important roles in normal physiology and abnormal pathology.
Non-Coding DNA
Non-Coding DNA sequences are components of an organism's DNA that
do
not encode protein sequences. Some noncoding DNA is transcribed into
functional
non-coding RNA molecules (e.g. transfer RNA, ribosomal RNA, and
regulatory RNAs). Other functions of noncoding DNA include the
transcriptional and translational regulation of protein-coding sequences,
scaffold attachment regions, origins of
DNA replication, centromeres and
telomeres. The amount of noncoding DNA varies greatly among species.
Often, only a small percentage of the genome is responsible for coding
proteins, but a rising percentage is being shown to have regulatory
functions. When there is much non-coding DNA, a large proportion appears
to have no biological function, as predicted in the 1960s. Since that
time, this non-functional portion has controversially been called "
junk DNA".
Only about
1 percent of DNA is made up of
protein-coding genes, the other
99 percent
is noncoding.
Spacer
DNA is a region of non-coding DNA between genes. The terms intergenic
spacer (IGS) or non-transcribed spacer (NTS) are used particularly for the
spacer DNA between the many tandemly repeated copies of the ribosomal RNA
genes. In bacteria, spacer DNA sequences are only a few nucleotides long.
In eukaryotes, they can be extensive and include repetitive DNA,
comprising the majority of the DNA of the genome. In ribosomal DNA, there
are spacers within and between gene clusters, called internal transcribed
spacer (ITS) and external transcribed spacers (ETS), respectively. In
animals, the mitochondrial DNA genes generally have very short spacers. In
fungi, mitochondrial DNA spacers are common and variable in length, and
they may also be mobile. Due to the non-coding nature of spacer DNA, its
nucleotide sequence changes much more rapidly over time than nucleotide
sequences coding for genes that are subject to selective forces. Although
spacer DNA might not have a function that depends on its nucleotide
sequence, it may have sequence-independent functions. Spacer DNA has
practical applications that enable researchers and scientists to examine
interactions between
CRISPR proteins and bacteriophages.
Repeated Sequences are patterns of nucleic acids that occur in
multiple copies throughout the genome in DNA or RNA. Repetitive DNA was
first detected because of its rapid re-association kinetics. In many
organisms, a significant fraction of the genomic DNA is highly repetitive,
with over two-thirds of the sequence consisting of repetitive elements in
humans. Repetitive elements found in genomes fall into different classes,
depending on their structure and/or the mode of multiplication. The
disposition of repetitive elements consists either in arrays of tandemly
repeated sequences, or in repeats dispersed throughout the genome.
Repeated sequences are also known as repetitive elements, repeating units
or repeats.
Coding Strand is the DNA strand whose
base sequence corresponds to the base sequence of the
RNA transcript
produced (although with thymine replaced by uracil). It is this strand
which contains codons, while the non-coding strand contains anticodons.
During transcription, RNA Pol II binds the non-coding strand, reads the
anti-codons, and transcribes their sequence to synthesize an RNA
transcript with complementary bases. By convention, the coding strand is
the strand used when displaying a DNA sequence. It is presented in the 5'
to 3' direction.
Single-Nucleotide Polymorphism is a
variation in a single nucleotide that occurs at a specific position in the
genome, where each variation is present to some appreciable degree within
a population (e.g. > 1%).
Biological Dark Matter is an informal
term for genetic material or microorganisms that are unclassified or
poorly understood. Biological dark matter includes non-coding DNA (
junk
DNA) and non-coding RNA. Much of the genomic dark matter is thought to
originate from ancient transposable elements and from other low-complexity
repetitive elements. Uncategorized genetic material is found in humans and
in several other organisms. Their phylogenetic novelty could indicate the
cellular organisms or viruses from which they evolved. Biologists are
unable to culture and grow 99% of all living microorganisms, so few
functional insights exist about the metabolic potential of these organisms.
Gene Therapy
Gene Therapy is the
therapeutic delivery
of nucleic acid polymers into a patient's cells as a drug to treat
disease. Gene therapy involves the transfer of genetic material
into the appropriate cells. Cell therapy is the transfer of cells to a
patient. For treatment of most diseases by cell therapy,
Stem Cells are chosen because their
establishment in the patient leads to continual production of the
appropriate specialized cells. The first attempt at
modifying human DNA was performed in 1980 by
Martin Cline, but the first successful nuclear gene transfer in humans,
approved by the National Institutes of Health, was performed in May 1989.
The first therapeutic use of gene transfer as well as the first direct
insertion of human DNA into the nuclear genome was performed by French
Anderson in a trial starting in September 1990. Between 1989 and February
2016, over 2,300 clinical trials had been conducted, more than half of
them in phase I. It should be noted that not all medical procedures that
introduce alterations to a patient's genetic makeup can be considered gene
therapy. Bone marrow transplantation and organ transplants in general have
been found to introduce foreign DNA into patients. Gene therapy is defined
by the precision of the procedure and the intention of direct therapeutic
effects.
Gene Therapy -
Gene Therapy (youtube) -
Stem Cell Therapy -
Microbes
When added to gene therapy, plant-based compound may enable faster, more
effective treatments. The gene therapy treatment process currently
requires isolating a very small population of hemopoietic stem cells from
the blood of patients; these young cells can self-renew and give rise to
all other types of blood cells. Therapeutic genes are then delivered to
these cells via specially engineered viruses, called "lentiviral vectors,"
which leverage viruses' natural knack for inserting new genetic
information into living cells.However, hemopoietic stem cells are highly
resilient to viral attacks. They protect themselves with structures known
as interferon-induced transmembrane (IFITM) proteins, which intercept
lentiviral vectors.
Luxturna gene therapy to treat patients with a rare form of
inherited
vision loss.
Androgen Receptor is a type of nuclear
receptor that is activated by
binding either of the androgenic hormones,
testosterone, or dihydrotestosterone in the cytoplasm and then
translocating into the nucleus. The androgen receptor is most closely
related to the progesterone receptor, and progestins in higher dosages can
block the androgen receptor. The main function of the androgen receptor is
as a DNA-binding transcription factor that regulates gene expression;
however, the androgen receptor has other functions as well. Androgen
regulated genes are critical for the development and maintenance of the male sexual phenotype.
A new gene therapy strategy, courtesy of nature. Scientists turn a
natural cellular process into a drug-delivery system. Scientists have
developed a new gene-therapy technique by transforming human cells into
mass producers of tiny nano-sized particles full of genetic material that
has the potential to reverse disease processes.
Films about DNA
DNA - PBS Film, 5 Episodes (youtube)
Animations of Biology (video)
Nathan Wolfe
(video) -
Knome
Jennifer Doudna: Editing DNA (video and text)
Journey of Man (youtube)
Cloning the First Human (video)
GATTACA
DNA Resources
The Genetic Atlas
Responsible Genetics
DNA Learning Center
Genetics
Genetics Society of America
Genomes Project
Genome.gov
Genomics
Cambrian Genomics
Hap Map
ENCODE is a public research project
launched by the US National Human Genome Research Institute (NHGRI) in
September 2003. Intended as a follow-up to the Human Genome Project
(Genomic Research), the ENCODE project aims to identify all functional
elements in the human genome.
DNA Variations - Genetic Diversity
Genetic Diversity is the total number of
genetic characteristics in the genetic makeup of a species. It is
distinguished from genetic variability, which describes the tendency of
genetic characteristics to vary. Genetic
diversity serves as a way for
populations to adapt to changing environments. With more variation, it is
more likely that some individuals in a population will possess variations
of alleles that are suited for the environment. Those individuals are more
likely to survive to produce offspring bearing that allele. The population
will continue for more generations because of the success of these
individuals. The academic field of population genetics includes several
hypotheses and theories regarding genetic diversity. The neutral theory of
evolution proposes that diversity is the result of the accumulation of
neutral substitutions. Diversifying selection is the hypothesis that two
subpopulations of a species live in different environments that select for
different alleles at a particular locus. This may occur, for instance, if
a species has a large range relative to the mobility of individuals within
it. Frequency-dependent selection is the hypothesis that as alleles become
more common, they become more vulnerable. This occurs in host–pathogen
interactions, where a high frequency of a defensive allele among the host
means that it is more likely that a pathogen will spread if it is able to
overcome that allele.
We Are 99% The Same, but not
totally
similar.
Genetic
Variation means that biological
systems – individuals and populations – are different over space. Each
gene pool includes various alleles of genes. The variation occurs both
within and among populations, supported by individual carriers of the
variant genes. Genetic variation is brought about, fundamentally, by
random mutation, which is a permanent change in the chemical structure of
chromosomes. Genetic recombination also produces changes within alleles.
Genetic
Variability (vary + liable - to or
capable of change) is the ability,
i.e. capability of a biological system – individual and population – that
is changing over time. The base of the genetic variability is genetic
variation of different biological systems in space.
Human Genetic Variation is the genetic
differences both within and among populations. There may be multiple
variants of any given gene in the human population (genes), leading to
polymorphism. Many genes are not polymorphic, meaning that only a single
allele is present in the population: the gene is then said to be fixed. On
average, in terms of DNA sequence
all humans are 99.5% similar to any
other humans.
No two humans are genetically identical. Even monozygotic
twins, who develop from one zygote, have infrequent genetic differences
due to mutations occurring during development and gene copy-number
variation. Differences between individuals, even closely related
individuals, are the key to techniques such as genetic fingerprinting.
Alleles occur at different frequencies in different human populations,
with populations that are more geographically and ancestrally remote
tending to differ more. Causes of differences between individuals include
independent assortment, the exchange of genes (crossing over and
recombination) during meiosis and various mutational events. There are at
least two reasons why genetic variation exists between populations.
Natural selection may confer an adaptive advantage to individuals in a
specific environment if an allele provides a competitive advantage.
Alleles under selection are likely to occur only in those geographic
regions where they confer an advantage. The second main cause of genetic
variation is due to the high degree of neutrality of most mutations. Most
mutations do not appear to have any selective effect one way or the other
on the organism. The main cause is genetic drift, this is the effect of
random changes in the gene pool. In humans, founder effect and past small
population size (increasing the likelihood of genetic drift) may have had
an important influence in neutral differences between populations. The
theory that humans recently migrated out of Africa supports this. The
study of human genetic variation has both evolutionary significance and
medical applications. It can help scientists understand ancient human
population migrations as well as how different human groups are
biologically related to one another. For medicine, study of human genetic
variation may be important because some disease-causing alleles occur more
often in people from specific geographic regions. New findings show that
each human has on average 60 new mutations compared to their parents.
Apart from mutations, many genes that may have aided humans in ancient
times plague humans today. For example, it is suspected that genes that
allow humans to more efficiently process food are those that make people
susceptible to obesity and diabetes today.
Twins -
DNA Code Printed out on Paper
Astronaut's DNA no longer matches that of his identical twin, NASA finds.
Spending a year in space not only changes your outlook, it transforms your
genes. Preliminary results from NASA's Twins Study reveal that 7% of
astronaut Scott Kelly's genes did not return to normal after his return to
Earth two years ago. Mason's team also saw changes in the length of
Scott's
telomeres, caps at the end of chromosomes
that are considered a marker of biological aging. First, there was a
significant increase in average length while he was in space, and then
there was a decrease in length within about 48 hours of his landing on
Earth that stabilized to nearly preflight levels. Scientists believe that
these telomere changes, along with the DNA damage and DNA repair measured
in Scott's cells, were caused by both radiation and calorie restrictions.
Space Genes -
Body in
Space. Why do Humans have Genes in their DNA that changes the body for
space travel?
Intelligent design?
Damaged DNA
DNA Damage is an alteration in the
chemical structure of DNA, such as a break in a strand of DNA, a base
missing from the backbone of DNA, or a chemically changed base as 8-OHdG.
Damage to DNA that occurs naturally can result from metabolic or
hydrolytic processes.
Metabolism
releases compounds that damage DNA including
reactive oxygen species,
reactive nitrogen species, reactive carbonyl species, lipid peroxidation
products and alkylating agents, among others, while hydrolysis cleaves
chemical bonds in DNA. Naturally occurring oxidative
DNA damages arise at
least 10,000 times per cell per day in humans and 50,000 times or more per
cell per day in rats. DNA damage is distinctly
different from
mutation, although both are types of error in DNA. DNA
damage is an abnormal chemical structure in DNA, while a mutation is a
change in the sequence of standard base pairs. DNA damage and
Mutation have different biological
consequences. While most DNA damages can undergo
DNA Repair, such repair
is not 100% efficient. Un-repaired DNA damages accumulate in
non-replicating cells, such as cells in the brains or muscles of adult
mammals and can cause aging. (Also see DNA damage theory of aging.) In
replicating cells, such as cells lining the colon, errors occur upon
replication of past damages in the template strand of DNA or during repair
of DNA damages. These errors can give rise to mutations or epigenetic
alterations. Both of these types of alteration can be replicated and
passed on to subsequent cell generations. These alterations can change
gene function or regulation of gene expression and possibly contribute to
progression to
cancer.
UV Damage (sunburn) -
Extremophile -
DNA Repair (Natural Defenses)
-
Regeneration (stem cells)
DNA Double Stranded Break is when both strands in the double helix are
severed and become particularly hazardous to the cell because they can
lead to genome rearrangements.
Single-Strand
Damage is when only one of the two strands of a double helix has a
defect, the other strand can be used as a template to guide the correction
of the damaged strand. In order to repair damage to one of the two paired
molecules of DNA, there exist a number of excision repair mechanisms that
remove the damaged nucleotide and replace it with an undamaged nucleotide
complementary to that found in the undamaged DNA strand.
Key genes linked to DNA damage and human disease uncovered. Scientists
unveil 145 genes vital for genome health, and possible strategies to curb
progression of human genomic disorders. More than one hundred key genes
linked to DNA damage have been uncovered through systematic screening of
nearly 1,000 genetically modified mouse lines, in a new study published
February 14 in Nature. Using CRISPR screening, researchers showed this
effect triggered by DSCC1 loss could be partially reversed through
inhibiting protein SIRT14. This offers a highly promising avenue for the
development of new therapies.
Telomeres
Telomere is a region of repetitive
nucleotide sequences at each end of a
chromosome,
which protects the end of the chromosome from deterioration or from fusion
with neighboring chromosomes. Its name is derived from the Greek nouns
telos (τέλος) "end" and merοs (μέρος, root: μερ-) "part". For vertebrates,
the sequence of nucleotides in telomeres is TTAGGG, with the complementary
DNA strand being AATCCC, with a single-stranded TTAGGG overhang. This
sequence of TTAGGG is repeated approximately 2,500 times in humans. In
humans, average telomere length declines from about 11 kilobases at birth
to less than 4 kilobases in old age, with average rate of decline being
greater in men than in women. During chromosome replication, the enzymes
that duplicate DNA cannot continue their duplication all the way to the
end of a chromosome, so in each duplication the end of the chromosome is
shortened (this is because the synthesis of Okazaki fragments requires RNA
primers attaching ahead on the lagging strand). The telomeres are
disposable buffers at the ends of chromosomes which are truncated during
cell division; their presence protects the genes before them on the
chromosome from being truncated instead. The telomeres themselves are
protected by a complex of shelterin proteins, as well as by the RNA that
telomeric DNA encodes (TERRA). Over time, due to each cell division, the
telomere ends become shorter. They are replenished by an enzyme,
telomerase reverse transcriptase.
Telomerase is a ribonucleoprotein that
adds a species-dependent telomere repeat sequence to the 3' end of
telomeres. A telomere is a region of repetitive sequences at each end of a
eukaryotic chromosomes in most eukaryotes. Telomeres protect the end of
the chromosome from DNA damage or from fusion with neighbouring
chromosomes. The fruit fly Drosophila melanogaster lacks telomerase, but
instead uses retrotransposons to maintain telomeres. Telomerase is a
reverse transcriptase enzyme that carries its own RNA molecule (e.g., with
the sequence "CCCAAUCCC" in vertebrates) which is used as a template when
it elongates telomeres. Telomerase, active in normal stem cells and most
cancer cells, is normally absent from, or at very low levels in, most
somatic cells.
Longevity -
Telomere
Copy-Number Variation is a relatively
new field in genomics and it is defined as a phenomenon in which sections
of the genome are repeated and the number of repeats in the genome varies
between individuals in the human population. Copy number variation is a
type of structural variation, specifically, it is a type of duplication or
deletion event that affects a considerable number of base pairs. However,
note that although modern genomics research is mostly focused on human
genomes, copy number variations also occur in a variety of other organisms
including E. coli. Recent research indicates that approximately two thirds
of the entire human genome is composed of repeats and 4.8-9.5% of the
human genome can be classified as copy number variations. In mammals, copy
number variations play an important role in generating necessary variation
in the population as well as disease phenotype. Copy number variations can
be generally categorized into two main groups: short repeats and long
repeats. However, there are no clear boundaries between the two groups and
the classification depends on the nature of the loci of interest. Short
repeats include mainly bi-nucleotide repeats (two repeating nucleotides
e.g. A-C-A-C-A-C...) and tri-nucleotide repeats. Long repeats include
repeats of entire genes. This classification based on size of the repeat
is the most obvious type of classification as size is an important factor
in examining the types of mechanisms that most likely gave rise to the
repeats, hence the likely effects of these repeats on phenotype.
Mutations in Evolution
-
Genetic Disorders
Haploinsufficiency is a mechanism of
action to explain a phenotype when a diploid organism has lost one copy of
a gene and is left with a single functional copy of that gene.
Haploinsufficiency is often caused by a loss-of-function mutation, in
which having only one copy of the wild-type allele is not sufficient to
produce the wild-type phenotype. It occurs when an organism has a single
functional copy of a gene, and that single copy does not produce enough
product to display the wild type's phenotypic characteristics. The
genotypic state in which one of two copies of a gene is absent is called
hemizygosity. Hemizygosity is not the same as haploinsufficiency;
hemizygosity describes the genotype, and haploinsufficiency is a mechanism
that may have caused the phenotype. The general assumption is that the
single remaining functional copy of the gene cannot provide sufficient
gene product (typically a protein) to preserve the wild-type phenotype
leading to an altered or even diseased state. As such, haploinsuffiency is
typically transmitted with dominant inheritance, either autosomally or
X-linked in female humans. Dominance describes the circumstance in which
both alleles in a diploid organism are present but one allele is
responsible for the phenotype. That genotypic state is one of
heterozygosity (with two different alleles). Co-Dominance is that
situation where the effects of both alleles are apparent in the phenotype.
Atavism is an evolutionary throwback,
such as traits reappearing that had disappeared generations before.
Atavisms can occur in several ways. One way is when genes for previously
existing phenotypical features are preserved in DNA, and these become
expressed through a mutation that either knocks out the overriding genes
for the new traits or makes the old traits override the new one. A number
of traits can vary as a result of shortening of the fetal development of a
trait (neoteny) or by prolongation of the same. In such a case, a shift in
the time a trait is allowed to develop before it is fixed can bring forth
an ancestral phenotype. In the social sciences, atavism can also describe
a cultural tendency of reversion—for example, people in the modern era
reverting to the ways of thinking and acting of a former time. The word
atavism is derived from the Latin atavus. An atavus is a
great-great-great-grandfather or, more generally, an ancestor.
Chromosomes
Chromosome is a
DNA molecule with part
or all of the
genetic material or genome of an
organism. Prokaryotes
usually have one single circular chromosome, whereas most eukaryotes are
diploid, like humans. Chromosomes in
eukaryotes are composed of chromatin
fiber. Chromatin fiber is made of nucleosomes. A nucleosome is a histone octamer with part of a longer DNA strand attached to and wrapped around
it. Chromatin fiber, together with associated proteins is known as
chromatin. Chromatin is present in most cells, with a few exceptions, for
example, red blood cells. Occurring only in the nucleus of eukaryotic
cells, chromatin contains the vast majority of DNA, except for a small
amount inherited maternally, which is found in the mitochondria.
Chromosomes are normally visible under a light microscope only when the
cell is undergoing the metaphase of cell division. Before this happens
every chromosome is copied once (S phase), and the copy is joined to the
original by a centromere resulting in an X-shaped structure. The original
chromosome and the copy are now called sister chromatids. During
metaphase, when a chromosome is in its most condensed state, the X-shape
structure is called a metaphase chromosome. In this highly condensed form
chromosomes are easiest to distinguish and study. In prokaryotic cells,
chromatin occurs free-floating in cytoplasm, as these cells lack
organelles and a defined nucleus. Bacteria also lack histones. The main
information-carrying macromolecule is a single piece of coiled
double-helix DNA, containing many genes, regulatory elements and other
noncoding DNA. The DNA-bound macromolecules are proteins that serve to
package the DNA and control its functions. Chromosomes vary widely between
different organisms. Some species such as certain bacteria also contain
plasmids or other extrachromosomal DNA. These are circular structures in
the cytoplasm that contain cellular DNA and play a role in horizontal gene
transfer. Compaction of the duplicated chromosomes during cell division
(mitosis or meiosis) results either in a four-arm structure if the centromere is located in the middle of the chromosome or a
two-arm structure if the centromere is located near one of the ends.
Chromosomal recombination during meiosis and subsequent sexual
reproduction plays a significant role in genetic diversity. If these
structures are manipulated incorrectly, through processes known as
chromosomal instability and translocation, the cell may undergo mitotic
catastrophe and die, or it may unexpectedly evade apoptosis leading to the
progression of cancer. In prokaryotes and viruses, the DNA
is often densely packed and organized: in the case of archaea, by homologs
to eukaryotic histones, and in the case of bacteria, by histone-like
proteins. Small circular genomes called plasmids are often found in
bacteria and also in mitochondria and chloroplasts, reflecting their
bacterial origins. Some use the term chromosome in a wider sense, to refer
to the individualized portions of chromatin in cells, either visible or
not under light microscopy. However, others use the concept in a narrower
sense, to refer to the individualized portions of chromatin during cell
division, visible under light microscopy due to high condensation.
X
Chromosome is one of the two sex-determining chromosomes (allosomes)
in many organisms, including mammals (the other is the Y chromosome), and
is found in both
males and
females. It is a part of the XY sex-determination system and X0
sex-determination system. The X chromosome was named for its unique
properties by early researchers, which resulted in the naming of its
counterpart Y chromosome, for the next letter in the alphabet, after it
was discovered later.
Y
Chromosome is one of
two sex
chromosomes (allosomes) in mammals, including humans, and many other
animals. The other is the X chromosome. Y is the sex-determining
chromosome in many species, since it is the presence or absence of Y that
determines the male or female sex of offspring produced in sexual
reproduction. In mammals, the Y chromosome contains the gene SRY, which
triggers testis development. The DNA in the human Y chromosome is composed
of about 59 million base pairs. The Y chromosome is passed only from
father to son. With a 30% difference between humans and chimpanzees, the Y
chromosome is one of the fastest-evolving parts of the human genome. To
date, over 200 Y-linked genes have been identified. All Y-linked genes are
expressed and (apart from duplicated genes) hemizygous (present on only
one chromosome) except in the cases of aneuploidy such as XYY syndrome or
XXYY syndrome.
How human cells maintain the correct number of chromosomes. Cell
division is an essential process in humans, animals and plants as dying or
injured cells are replenished throughout life.
Cells divide at least a billion times
in the average person, usually without any problem. However, when cell
division goes wrong, it can lead to a range of diseases, such as cancer,
and problems with fertility and development, including babies born with
the wrong number of chromosomes as in
Down's syndrome.
"During
cell division, a mother cell
divides into two daughter cells, and during this process the DNA in the
mother cell, wrapped up in the form of chromosomes, is divided into two
equal sets. To achieve this, rope-like structures called microtubules
capture the chromosomes at a special site called the kinetochore, and pull
the DNA apart," said Dr Viji Draviam, senior lecturer in structural cell
and molecular biology from QMUL's School of Biological and Chemical
Sciences. We have identified two proteins -- tiny molecular machines --
that enable the correct attachment between the chromosomes and
microtubules. When these proteins don't function properly, the cells can
lose or gain a chromosome. This finding gives us a glimpse of an important
step in the process of cell division.
Polyploid cells and
organisms are those containing more than two paired (homologous) sets of
chromosomes. Most species whose cells have nuclei (
Eukaryotes)
are diploid, meaning they have two sets of chromosomes—one set inherited
from each parent. However, polyploidy is found in some organisms and is
especially common in
plants. In
addition, polyploidy occurs in some tissues of animals that are otherwise
diploid, such as human muscle tissues. This is known as endopolyploidy.
Species whose cells do not have nuclei, that is, Prokaryotes, may be
polyploid organisms, as seen in the large bacterium Epulopiscium
fishelsoni . Hence ploidy is defined with respect to a cell. Most
eukaryotes have diploid somatic cells, but produce haploid gametes (eggs
and sperm) by meiosis. A monoploid has only one set of chromosomes, and
the term is usually only applied to cells or organisms that are normally
diploid. Male bees and other Hymenoptera, for example, are monoploid.
Unlike animals, plants and multicellular algae have life cycles with two
alternating multicellular generations. The gametophyte generation is
haploid, and produces gametes by mitosis, the sporophyte generation is
diploid and produces spores by meiosis.
Aneuploidy is the presence of an abnormal number of chromosomes in a
cell, for example a human cell having 45 or 47 chromosomes instead of the
usual 46. It does not include a difference of one or more complete sets of
chromosomes, which is called euploidy. An extra or missing chromosome is a
common cause of
genetic disorders, including
some human birth defects. Some cancer cells also have abnormal numbers of
chromosomes. Aneuploidy originates during cell division when the
chromosomes do not separate properly between the two cells.
Centromere is the specialized DNA sequence of a chromosome that links
a pair of sister chromatids (a dyad). During mitosis, spindle fibers
attach to the centromere via the kinetochore. Centromeres were first
thought to be genetic loci that direct the behavior of chromosomes. The
physical role of the centromere is to act as the site of assembly of the
kinetochores – a highly complex multiprotein structure that is responsible
for the actual events of chromosome segregation – i.e. binding
microtubules and signalling to the cell cycle machinery when all
chromosomes have adopted correct attachments to the spindle, so that it is
safe for cell division to proceed to completion and for cells to enter
anaphase.
Chromosomal
Inversion is a chromosome rearrangement in which a segment of a
chromosome is reversed end to end. An inversion occurs when a single
chromosome undergoes breakage and rearrangement within itself. Inversions
are of two types: paracentric and pericentric. Paracentric inversions do
not include the centromere and both breaks occur in one arm of the
chromosome. Pericentric inversions include the centromere and there is a
break point in each arm. nversions usually do not cause any abnormalities
in carriers as long as the rearrangement is balanced with no extra or
missing DNA. However, in individuals which are heterozygous for an
inversion, there is an increased production of abnormal chromatids (this
occurs when crossing-over occurs within the span of the inversion). This
leads to lowered fertility due to production of unbalanced gametes. The
most common inversion seen in humans is on chromosome 9, at inv(9)(p12q13).
This inversion is generally considered to have no harmful effects, but
there is some suspicion it could lead to an increased risk for miscarriage
or infertility for some affected individuals. An inversion does not
involve a loss of genetic information, but simply rearranges the linear
gene sequence. Families that may be carriers of inversions may be offered
genetic counseling and genetic testing.
Transcription
Transcription
in genetics
is the
first step of gene expression, in which a particular segment of DNA
is
copied into RNA (especially mRNA) by the enzyme RNA polymerase. Both
DNA and RNA are nucleic acids, which use base pairs of nucleotides as a
complementary language. During transcription, a DNA sequence is read by an
RNA polymerase, which produces a complementary, antiparallel RNA strand
called a primary transcript.
Transcription proceeds in the following
general steps: RNA polymerase, together with one or more general
transcription factors, binds to promoter DNA. RNA polymerase creates a
transcription bubble, which separates the two strands of the DNA helix.
This is done by breaking the hydrogen bonds between complementary DNA
nucleotides. RNA polymerase adds RNA nucleotides (which are
complementary to the nucleotides of one DNA strand). RNA
sugar-phosphate backbone forms with assistance from RNA polymerase to form
an RNA strand. Hydrogen bonds of the RNA–DNA helix break, freeing the
newly synthesized RNA strand. If the cell has a nucleus, the RNA may be
further processed. This may include polyadenylation, capping, and
splicing. The RNA may remain in the nucleus or exit to the cytoplasm
through the nuclear pore complex.
*
The stretch of DNA transcribed
into an RNA molecule is called a transcription unit and encodes at least
one gene. If the gene encodes a protein, the transcription produces
messenger RNA (mRNA); the mRNA, in turn, serves as a template for the
protein's synthesis through translation. Alternatively, the transcribed
gene may encode for either non-coding RNA (such as microRNA), ribosomal
RNA (rRNA), transfer RNA (tRNA), or other enzymatic RNA molecules called
ribozymes. Overall, RNA helps synthesize, regulate, and process proteins;
it therefore plays a fundamental role in performing functions within a
cell. In virology, the term may also be used when referring to mRNA
synthesis from an RNA molecule (i.e., RNA replication). For instance, the
genome of a negative-sense single-stranded RNA (ssRNA -) virus may be
template for a positive-sense single-stranded RNA (ssRNA +). This is
because the positive-sense strand contains the information needed to
translate the viral proteins for viral replication afterwards. This
process is catalyzed by a viral RNA replicase.
Promoter in genetics is a region of DNA
that initiates
transcription of a particular gene. Promoters are located
near the transcription start sites of genes, on the same strand and
upstream on the DNA (towards the 5' region of the sense strand). Promoters
can be about 100–1000 base pairs long.
Long time Storage of Information in DNA (Knowledge Preservation)
Gene Regulatory Networks is a
collection of molecular regulators that interact with each other and with
other substances in the cell to govern the gene expression levels of mRNA
and proteins. These play a central role in morphogenesis, the creation of
body structures, which in turn is central to evolutionary developmental
biology (evo-devo). The regulator can be DNA, RNA, protein and complexes
of these. The interaction can be direct or indirect (through transcribed
RNA or translated protein). In general, each mRNA molecule goes on to make
a specific protein (or set of proteins). In some cases this protein will
be structural, and will accumulate at the cell membrane or within the cell
to give it particular structural properties. In other cases the protein
will be an enzyme, i.e., a micro-machine that catalyses a certain
reaction, such as the breakdown of a food source or toxin. Some proteins
though serve only to activate other genes, and these are the transcription
factors that are the main players in regulatory networks or cascades. By
binding to the promoter region at the start of other genes they turn them
on, initiating the production of another protein, and so on. Some
transcription factors are inhibitory. In single-celled organisms,
regulatory networks respond to the external environment, optimising the
cell at a given time for survival in this environment. Thus a yeast cell,
finding itself in a sugar solution, will turn on genes to make enzymes
that process the sugar to alcohol. This process, which we associate with
wine-making, is how the yeast cell makes its living, gaining energy to
multiply, which under normal circumstances would enhance its survival
prospects. In multicellular animals the same principle has been put in the
service of gene cascades that control body-shape. Each time a cell
divides, two cells result which, although they contain the same genome in
full, can differ in which genes are turned on and making proteins.
Sometimes a 'self-sustaining feedback loop' ensures that a cell maintains
its identity and passes it on. Less understood is the mechanism of
epigenetics by which chromatin modification may provide cellular memory by
blocking or allowing transcription. A major feature of multicellular
animals is the use of morphogen gradients, which in effect provide a
positioning system that tells a cell where in the body it is, and hence
what sort of cell to become. A gene that is turned on in one cell may make
a product that leaves the cell and diffuses through adjacent cells,
entering them and turning on genes only when it is present above a certain
threshold level. These cells are thus induced into a new fate, and may
even generate other morphogens that signal back to the original cell. Over
longer distances morphogens may use the active process of signal
transduction. Such signalling controls embryogenesis, the building of a
body plan from scratch through a series of sequential steps. They also
control and maintain adult bodies through feedback processes, and the loss
of such feedback because of a mutation can be responsible for the cell
proliferation that is seen in cancer. In parallel with this process of
building structure, the gene cascade turns on genes that make structural
proteins that give each cell the physical properties it needs.
Scientists map networks regulating gene function in the human brain.
Research details the brain's cellular and molecular regulatory elements
and their impact on brain function. Approximately 2% of the human genome
is composed of genes that code for proteins. The remaining 98% includes
DNA segments that help regulate the activity of those genes.
Profiling
DNA Profiling is a
forensic technique
used to identify individuals by
characteristics of their DNA. A DNA
profile is a small set of DNA variations that is very likely to be
different in all unrelated individuals, thereby being as unique to
individuals as are fingerprints (hence the alternate name for the
technique). DNA profiling should not be confused with full genome
sequencing. First developed and used in 1984, DNA profiling is used in,
for example, parentage testing and criminal investigation, to identify a
person or to place a person at a crime scene, techniques which are now
employed globally in forensic science to facilitate police detective work
and help clarify paternity and immigration disputes. DNA fingerprinting
has also been widely used in the study of animal and floral populations
and has revolutionized the fields of zoology, botany, and agriculture.
Although 99.9% of human DNA sequences are the same in every person, enough
of the DNA is different that it is possible to distinguish one individual
from another, unless they are monozygotic ("identical") twins. DNA
profiling uses repetitive ("repeat") sequences that are highly variable,
called variable number tandem repeats (VNTRs), in particular short tandem
repeats (STRs), also known as microsatellites, and minisatellites. VNTR
loci are very similar between closely related individuals, but are so
variable that unrelated individuals are extremely unlikely to have the
same VNTRs.
Profiling Dangers.
DNA Phenotyping is the process of
predicting an organism’s
phenotype using only genetic information
collected from genotyping or DNA sequencing. This term, also known as
molecular photofitting, is primarily used to refer to the prediction of a
person’s physical appearance and/or biogeographic ancestry for forensic
purposes. DNA phenotyping uses many of the same scientific methods as
those being used for genetically-informed personalized medicine, in which
drug responsiveness (pharmacogenomics) and medical outcomes are predicted
from a patient’s genetic information. Significant genetic variants
associated with a particular trait are discovered using a genome-wide
association study (GWAS) approach, in which hundreds of thousands or
millions of single-nucleotide polymorphisms (SNPs) are tested for their
association with each trait of interest. Predictive modeling is then used
to build a mathematical model for making trait predictions about new
subjects.
Gene Editing
Restriction Fragment is a DNA fragment
resulting from the cutting of a DNA strand by a restriction enzyme
(restriction endonucleases), a process called restriction. Each
restriction enzyme is highly specific, recognising a particular short DNA
sequence, or restriction site, and cutting both DNA strands at specific
points within this site. Most restriction sites are palindromic, (the
sequence of nucleotides is the same on both strands when read in the 5' to
3' direction), and are four to eight nucleotides long. Many cuts are made
by one restriction enzyme because of the chance repetition of these
sequences in a long DNA molecule, yielding a set of restriction fragments.
A particular DNA molecule will always yield the same set of restriction
fragments when exposed to the same restriction enzyme. Restriction
fragments can be analyzed using techniques such as gel electrophoresis or
used in recombinant DNA technology.
Dysgenics is the study of factors
producing the accumulation and perpetuation of defective or
disadvantageous genes and traits in offspring of a particular population
or species. The adjective "dysgenic" is the antonym of "eugenic". It was
first used c. 1915 by David Starr Jordan, describing the supposed dysgenic
effects of World War I. Jordan believed that healthy men were as likely to
die in modern warfare as anyone else, and that war killed only the
physically healthy men of the populace whilst preserving the disabled at
home.
Eugenics is a set of beliefs and
practices that aims at improving the genetic quality of the human
population.
Computational
Genomics refers to the use of
computational and statistical analysis to decipher biology from genome
sequences and related data, including both DNA and RNA sequence as well as
other "post-genomic" data (i.e., experimental data obtained with
technologies that require the genome sequence, such as genomic DNA
microarrays). These, in combination with computational and statistical
approaches to understanding the function of the genes and statistical
association analysis, this field is also often referred to as
Computational and Statistical Genetics/genomics. As such, computational
genomics may be regarded as a subset of bioinformatics and computational
biology, but with a focus on using whole genomes (rather than individual
genes) to understand the principles of how the DNA of a species controls
its biology at the molecular level and beyond. With the current abundance
of massive biological datasets, computational studies have become one of
the most important means to biological discovery
Gene Deletion is a
mutation (a genetic aberration) in
which a part of a chromosome or a sequence of DNA is lost during DNA
replication. Any number of nucleotides can be deleted, from a single base
to an entire piece of chromosome. The smallest single base deletion
mutations are believed to occur by a single base flipping in the template
DNA, followed by template DNA strand slippage, within the DNA polymerase
active site. Deletions can be caused by errors in chromosomal crossover
during meiosis, which causes several serious genetic diseases. Deletions
that do not occur in multiples of three bases can cause a frameshift by
changing the 3-nucleotide protein reading frame of the genetic sequence.
The examples given below of types and effects of deletions are
representative of eukaryotic organisms, particularly humans, but are not
relevant to prokaryotic organisms such as bacteria.
Transformation is the
genetic alteration
of a cell resulting from the direct uptake and incorporation of exogenous
genetic material from its surroundings through the cell membrane(s). For
transformation to take place, the recipient bacteria must be in a state of
competence, which might occur in nature as a time-limited response to
environmental conditions such as starvation and cell density, and may also
be induced in a laboratory. Transformation is one of three processes for''
horizontal gene transfer'', in which exogenous genetic material passes
from bacterium to another, the other two being conjugation (transfer of
genetic material between two bacterial cells in direct contact) and
transduction (injection of foreign DNA by a bacteriophage virus into the
host bacterium). In transformation, the genetic material passes through
the intervening medium, and uptake is completely dependent on the
recipient bacterium. As of 2014 about 80 species of bacteria were known to
be capable of transformation, about evenly divided between Gram-positive
and Gram-negative bacteria; the number might be an overestimate since
several of the reports are supported by single papers.
"Transformation" may also be used to describe the insertion of new genetic
material into nonbacterial cells, including animal and plant cells;
however, because "transformation" has a special meaning in relation to
animal cells, indicating progression to a cancerous state, the process is
usually called "transfection".
Mutations.
Reprogramming
refers to erasure and remodeling of
epigenetic marks, such as DNA methylation, during mammalian development or
in cell culture. DNA Methylation patterns are largely erased and then
re-established between generations in mammals. Almost all of the
methylations from the parents are erased, first during gametogenesis, and
again in early embryogenesis, with demethylation and remethylation
occurring each time. Demethylation of early embryogenesis occurs in the
preimplantation period in two stages – initially in the zygote, then the
first few embryonic replication cycles of morula and blastula. A wave of
methylation then takes place during the implantation stage of the embryo,
with CpG islands protected from methylation. This results in global
repression and allows housekeeping genes to be expressed in all cells. In
the post-implantation stage, methylation patterns are stage- and
tissue-specific with changes that would define each individual cell type
lasting stably over a long time.
Gene Editing (Crispr) -
Genetic Modification.
Transdifferentiation also known as
lineage reprogramming, is a process in which one mature somatic cell
transforms into another mature somatic cell without undergoing an
intermediate pluripotent state or progenitor cell type. It is a type of
metaplasia, which includes all cell fate switches, including the interconversion of stem cells. Current uses of transdifferentiation
include disease modeling and drug discovery and in the future may include
gene therapy and regenerative medicine. The term 'transdifferentiation'
was originally coined by Selman and Kafatos in 1974 to describe a change
in cell properties as cuticle producing cells became salt-secreting cells
in silk moths undergoing metamorphosis.
Transgenesis is the process of
introducing an exogenous gene—called a transgene—into a living organism so
that the organism will exhibit a new property and transmit that property
to its offspring. Transgenesis can be facilitated by liposomes, enzymes,
plasmid vectors, viral vectors, pronuclear injection, protoplast fusion,
and ballistic DNA injection. Transgenesis can occur in nature. Transgenic
organisms are able to express foreign genes because the genetic code is
similar for all organisms. This means that a specific DNA sequence will
code for the same protein in all organisms. Due to this similarity in
protein sequence, scientists can cut DNA at these common protein points
and add other genes. An example of this is the "super mice" of the 1980s.
These mice were able to produce the human protein tPA to treat blood
clots.
Parahuman are humans who have undergone
a traumatic experience (known as a "trigger event") and awakened
superpowers.
Optogenetics is a biological technique which involves the
use of
light to control cells in living tissue, typically
neurons, that have been genetically modified to express
light-sensitive ion channels.
Biology -
Science
Size Variations
(nano) So how does each tiny cell pack a two-meter length of DNA
into its nucleus, which is just one-thousandth of a millimeter across?
Polygenes
or multiple
factor,
multiple gene inheritance, or quantitative gene is a group of non-epistatic
genes that together influence a phenotypic trait. Traits with polygenic
determinism correspond to the classical quantitative characters, as
opposed to the qualitative characters with monogenic or oligogenic
determinism. In essence instead of two options, such as freckles or no
freckles, there are many variations. Like the color of skin, hair, or even
eyes.
Diversity.
Polygenic
Risk Score
is a sum of trait-associated alleles across many genetic loci, typically
weighted by effect sizes estimated from a genome-wide association study.
Genome-Wide Association Study in genetic epidemiology, a genome-wide
association study (GWA study, or GWAS), also known as whole genome
association study (WGA study, or WGAS), is an examination of many common
genetic variants in different individuals to see if any variant is
associated with a trait. GWASs typically focus on associations between
single-nucleotide polymorphisms (SNPs) and traits like major diseases.
Genetic
Epidemiology is the study of the role of genetic factors in
determining health and disease in families and in populations, and the
interplay of such genetic factors with environmental factors. Genetic
epidemiology seeks to derive a statistical and quantitive analysis of how
genetics work in large groups.
Epigenetics
Complex Segregation Analysis is a technique within genetic
epidemiology to determine whether there is evidence that a major gene
underlies the distribution of a given
phenotypic trait,
which is an obvious, observable, and measurable trait. CSA also provides evidence to whether the implicated
trait is inherited in a Mendelian dominant, recessive, or codominant manner.
Single-Nucleotide Polymorphism often abbreviated to SNP (pronounced
snip; plural snips), is a variation in a single nucleotide that occurs at
a specific position in the genome, where each variation is present to some
appreciable degree within a population.
DNA Methylation is a process by which methyl groups are added to DNA
segments.
Methylation changes the activity of a DNA segment without
changing the sequence. This is known as an epigenetic modification. When
located in a gene promoter, DNA methylation
typically acts to repress gene
transcription. DNA methylation is essential for normal development and is
associated with a number of key processes including
genomic imprinting,
X-chromosome inactivation, repression of repetitive elements,
aging and
carcinogenesis.
Two of DNA's four bases, cytosine and adenine, can be methylated. Cytosine
methylation is widespread in both eukaryotes and prokaryotes, even though
the rate of cytosine DNA methylation can differ greatly between species:
14% of cytosines are methylated in Arabidopsis thaliana, 8% in Physarum,
4% in Mus musculus, 2.3% in Escherichia coli, 0.03% in Drosophila, 0.006%
in Dictyostelium and virtually none (< 0.0002%) in Caenorhabditis or yeast
species such as Saccharomyces cerevisiae and S. pombe (but not N. crassa).
Adenine methylation has been observed in bacterial, plant, and recently in
mammalian DNA, but has received considerably less attention. Methylation
of cytosine to form 5-methylcytosine occurs at the same 5 position on the
pyrimidine ring where the DNA base thymine's methyl group is located; the
same position distinguishes thymine from the analogous RNA base uracil,
which has no methyl group. Spontaneous deamination of 5-methylcytosine
converts it to thymine. This results in a T:G mismatch. Repair mechanisms
then correct it back to the original C:G pair; alternatively, they may
substitute G for A, turning the original C:G pair into an T:A pair,
effectively changing a base and introducing a mutation. This
misincorporated base will not be corrected during DNA replication as
thymine is a DNA base. If the mismatch is not repaired and the cell enters
the cell cycle the strand carrying the T will be complemented by an A in
one of the daughter cells, such that the mutation becomes permanent. The
near-universal replacement of uracil by thymine in DNA, but not RNA, may
have evolved as an error-control mechanism, to facilitate the removal of
uracils generated by the spontaneous deamination of cytosine. DNA
methylation as well as many of its contemporary DNA methyltransferases has
been thought to evolve from early world primitive RNA methylation activity
and is supported by several lines of evidence. In plants and other
organisms, DNA methylation is found in three different sequence contexts:
CG (or CpG), CHG or CHH (where H correspond to A, T or C). In mammals
however, DNA methylation is almost exclusively found in CpG dinucleotides,
with the cytosines on both strands being usually methylated. Non-CpG
methylation can however be observed in embryonic stem cells,[10] and has
also been indicated in neural development. Furthermore, non-CpG
methylation has also been observed in hematopoietic progenitor cells, and
it occurred mainly in a CpApC sequence context.
Gene Silencing -
Silent Mutation.
Twins
Twin are two
offspring
produced by the same
pregnancy. Twins can be either monozygotic ("
identical"), meaning that
they develop from one zygote, which splits and forms two embryos, or
dizygotic ("
fraternal"), meaning that each twin develops from a separate
egg and each egg is fertilized by its own sperm cell. In contrast, a foetus that develops alone in the womb is called a singleton, and the
general term for one offspring of a multiple birth is multiple.
Non-related look-alikes whose resemblance parallels that of twins are
referred to as
doppelgangers.
Monoamniotic Twins are
identical
twins that
share the same amniotic sac within their mother’s uterus. Monoamniotic twins are always identical, always monochorionic and are
usually termed Monoamniotic-Monochorionic ("MoMo" or "Mono Mono") twins.
They also share the placenta, but have two separate umbilical cords.
Monoamniotic twins develop when an embryo does not split until after
formation of the amniotic sac, at about 9-13 days after fertilization.
Monoamniotic triplets or other monoamniotic multiples are possible, but
extremely rare. Other obscure possibilities include multiples sets where
monoamniotic twins are part of a larger gestation such as triplets,
quadruplets, or more.
Reproduction (Birth).
Chimera is an ordinary person or animal except that some of their
parts actually came from their twin or from the mother. A chimera may
arise either from monozygotic twin fetuses (where it would be impossible
to detect), or from dizygotic fetuses, which can be identified by
chromosomal comparisons from various parts of the body. The number of
cells derived from each fetus can vary from one part of the body to
another, and often leads to characteristic mosaicism skin coloration in
human chimeras. A chimera may be intersex,
composed of cells from a
male twin and a female twin. In one case DNA tests determined that a
woman, mystifyingly, was not the mother of two of her three children; she
was found to be a chimera, and the two children were conceived from eggs
derived from cells of their mother's twin.
Conjoined Twins are identical twins joined in uterus. A very rare
phenomenon, the occurrence is estimated to range from 1 in 49,000 births
to 1 in 189,000 births, with a somewhat higher incidence in Southwest Asia
and Africa. Approximately half are stillborn, and an additional one-third
die within 24 hours. Most live births are female, with a ratio of 3:1. Siamese twins.
Twins Early Development Study or TEDS is an ongoing longitudinal twin
study headed by principal investigator psychologist Robert Plomin and
based at King's College London. The main goal of TEDS is to use
behavioural genetic methods to find out how nature (genes) and nurture
(environments) can explain why people differ with respect to their
cognitive abilities, learning abilities and behaviours.
Over 15,000 pairs
of twins originally signed up for the study and more than 13,000 pairs
remain involved to the present day. This demonstrates the continued
support of all twins and their families for more than a decade.
In the Womb - Identical Twins (youtube)
A sister and brother in Australia are the second-ever Semi-Identical Twins
to be identified. The pair share identical DNA from their mother, but
didn’t get identical DNA from their father. But occasionally a single egg
gets fertilised by two sperm. Normally, the resulting embryo dies because
it has three sets of chromosomes instead of the usual two. This means on
average 75 per cent of semi-identical twins’ DNA will be identical. The
technical term for semi-identical twins is sesquizygotic. In the case of
the Brisbane twins, the embryo split in two with each half somehow ending
up with the correct number of chromosomes. They received exactly the same
set of chromosomes from their mother, but one twin got their second set of
chromosomes from one sperm and one got it from another. Identical twins
come about when a single fertilised egg splits in two, meaning they have
exactly the same DNA – they are clones. Fraternal twins form when two
separate eggs are fertilised by two separate sperm. Because each egg and
sperm has a different mix of parental DNA, only 50 per cent of their DNA
is identical on average – just like siblings who aren’t twins.
Twins Days.
Cloning is the process
of producing individuals with identical or virtually identical DNA, either
naturally or artificially. In nature, many organisms produce clones
through asexual reproduction. Cloning in biotechnology refers to the
process of creating clones of organisms or copies of cells or DNA
fragments (molecular cloning).
Plant Cloning.
CRISPR - Gene Editing
CRISPR allows researchers to
edit genes
very precisely, easily and quickly. It does this by harnessing a mechanism
that already existed in bacteria. Basically, there's a protein that acts
like a scissors and cuts the DNA, and there's an RNA molecule that directs
the scissors to any point on the genome you want. The result is basically
a word processor for genes. You can take an entire gene out, put one in,
or even edit just a single letter within a gene. And you can do it in
nearly any species. CRISPR is short for
Clustered
Regularly
Interspaced
Short
Palindromic
Repeats.
Playing God -
DNA Repair -
Mutations
Cas9 or CRISPR associated
protein 9 is an
RNA-guided DNA endonuclease associated with the CRISPR (Clustered
Regularly Interspaced Short Palindromic Repeats) type II adaptive immunity
system in Streptococcus pyogenes, among other bacteria. S. pyogenes
utilizes Cas9 to interrogate and cleave foreign DNA, such as invading
bacteriophage DNA or plasmid DNA. Cas9 performs this interrogation by
unwinding foreign DNA and checking whether it is complementary to the 20
basepair spacer region of the guide RNA. If the DNA substrate is
complementary to the guide RNA, Cas9 cleaves the invading DNA. In this
sense, the CRISPR-Cas9 mechanism has a number of parallels with the RNA
interference (RNAi) mechanism in eukaryotes. Native Cas9 assists in all
three CRISPR steps: it participates in adaptation, participates in crRNA
processing and it cleaves the target DNA assisted by crRNA and an
additional RNA called tracrRNA. Native Cas9 requires a guide RNA composed
of two disparate RNAs that associate to make the guide - the CRISPR RNA (crRNA),
and the trans-activating RNA (tracrRNA).
CRISPR-Cas9 technique targeting Epigenetics Reverses Disease in mice.
A modified CRISPR-Cas9 technique that alters the activity, rather than the
underlying sequence, of disease-associated genes.
CRISPR-based Diagnostic Tool advanced, miniature paper test developed.
A
strip of paper can
now indicate presence of pathogens, tumor DNA, or any genetic signature of
interest. 100-fold greater sensitivity, the ability to detect multiple
targets at once, and other new features further enhance SHERLOCK's power
for detecting genetic signatures.
Genome Editing is a type of
genetic engineering
in which DNA is inserted, deleted, modified or replaced in the genome of a
living organism. In 2018, the common methods for such editing use
engineered nucleases, or "
molecular scissors".
These nucleases create site-specific double-strand breaks (DSBs) at
desired locations in the genome. The induced double-strand breaks are
repaired through nonhomologous end-joining (NHEJ) or homologous
recombination (HR), resulting in targeted mutations ('edits'). As of 2015
four families of engineered nucleases were used: meganucleases, zinc
finger nucleases (ZFNs), transcription activator-like effector-based
nucleases (TALEN), and the clustered regularly interspaced short
palindromic repeats (CRISPR/Cas9) system. Nine genome editors were
available as of 2017. Genome editing with engineered nucleases, ie all
three major classes of these enzymes—zinc finger nucleases (ZFNs),
transcription activator-like effector nucleases (TALENs) and engineered
meganucleases—were selected by Nature Methods as the 2011 Method of the
Year. The CRISPR-Cas system was selected by Science as 2015 Breakthrough
of the Year.
Epigenetics.
Gene-editing offers hope for people with hereditary disorder. A group
of New Zealand patients with a serious
genetic
condition have come off their medications after a single gene-editing
treatment. The investigational therapy, called NTLA-2002, utilizes in vivo
CRISPR/Cas9 technology to target the KLKB1 gene, which is responsible for
producing plasma prekallikrein.
New AI tool makes speedy gene-editing possible. An artificial
intelligence program may enable the first simple production of
customizable proteins called
zinc
fingers to treat diseases by turning genes on and off. The researchers
who designed the tool say it promises to accelerate the development of
gene therapies on a large scale.
Zinc-finger
editing offers a potentially safer alternative to CRISPR, a key
gene-editing technology with applications that range from finding new ways
to kill cancer cells to designing more nourishing crops. Unlike the
entirely human-derived zinc fingers. Zinc finger nucleases are a class of
engineered DNA-binding proteins that facilitate targeted editing of the
genome by creating double-strand breaks in DNA at user-specified
locations.
CRISPR-Cas9 can generate unexpected, heritable mutations. CRISPR-Cas9,
the 'genetic scissors', creates new potential for curing diseases; but
treatments must be reliable. In a new study, researchers have discovered
that the method can give rise to unforeseen changes in DNA that can be
inherited by the next generation. These scientists therefore urge caution
and meticulous validation before using CRISPR-Cas9 for medical purposes.
New genetic analysis tool tracks risks tied to CRISPR edits.
Classification system uses genetic fingerprints to identify unintentional
'
bystander'
edits linked with new disease therapies. While CRISPR has shown
immense promise as a next-generation therapeutic tool, the gene editing
technology's edits are still imperfect. Researchers have developed a new
system to test and analyze CRISPR-based DNA repair and related risks from
unintended but harmful 'bystander' edits.
Even good gene edits can go bad. Finding large deletions, other
anomalies in 'on-target' CRISPR-Cas9 editing. Researchers are working to
reveal potential threats to the efficacy of CRISPR/Cas9 gene editing, even
when it appears to be working as planned.
Gene Editing can now change an entire species — forever (video and
Interactive text)
CRISPR or
Clustered Regularly
Interspaced Short Palindromic Repeats, are segments of prokaryotic DNA
containing short, repetitive base sequences. In a palindromic repeat, the
sequence of nucleotides is the same in both directions. Each repetition is
followed by short segments of spacer DNA from previous exposures to
foreign DNA (e.g., a virus or plasmid). Small clusters of cas (CRISPR-associated
system) genes are located next to CRISPR sequences. The CRISPR/Cas system
is a prokaryotic immune system that confers resistance to foreign genetic
elements such as those present within plasmids and phages that provides a
form of acquired immunity. RNA harboring the spacer sequence helps Cas
proteins recognize and cut exogenous DNA. Other RNA-guided Cas proteins
cut foreign RNA. CRISPRs are found in approximately 40% of sequenced
bacterial genomes and 90% of sequenced archaea. A simple version of the
CRISPR/Cas system, CRISPR/Cas9, has been modified to edit genomes. By
delivering the Cas9 nuclease complexed with a synthetic guide RNA (gRNA)
into a cell, the cell's genome can be cut at a desired location, allowing
existing genes to be removed and/or new ones added. The Cas9-gRNA complex
corresponds with the CAS III crRNA complex in the above diagram. CRISPR/Cas
genome editing techniques have many potential applications, including
medicine and crop seed enhancement. The use of CRISPR/Cas9-gRNA complex
for genome editing was the AAAS's choice for breakthrough of the year in
2015. Bioethical concerns have been raised about the prospect of using
CRISPR for germline editing.
Scientists unveil CRISPR-based diagnostic platform that targets RNA
(rather than DNA) as a rapid, inexpensive, highly sensitive diagnostic
tool with the potential for a transformative effect on research and global
public health. Detecting the presence of Zika virus in patient blood or
urine samples within hours; Distinguishing between the genetic sequences
of African and American strains of Zika virus; Discriminating specific
types of bacteria, such as E. coli; Detecting antibiotic resistance genes;
Identifying cancerous mutations in simulated cell-free DNA fragments; and
Rapidly reading human genetic information, such as risk of heart disease,
from a saliva sample.
Teaching CRISPR and antibiotic resistance to high school students.
BioBits Health
brings hands-on, low-cost, high-tech synthetic biology into the classroom.
CRISPR/Cas9 used to Control Genetic Inheritance in Mice.
-
Heredity.
Enzymes can't tell artificial DNA from the real thing. The genetic
alphabet contains just four letters, referring to the four nucleotides,
the biochemical building blocks that comprise all DNA. Scientists have
long wondered whether it's possible to add more letters to this alphabet
by creating brand-new nucleotides in the lab, but the utility of this
innovation depends on whether or not cells can actually recognize and use
artificial nucleotides to make proteins.
Genome Damage from CRISPR/Cas9 gene editing higher than thought.
Caution required for using CRISPR/Cas9 in potential gene therapies.
New tool facilitates clinical interpretation of genetic information.
Despite the increasing use of genomic sequencing in clinical practice,
interpreting rare genetic mutations, even among well-studied disease
genes, remains difficult. Current predictive models are useful for
interpreting those mutations, but they are prone to misclassify those that
do not cause diseases, contributing to false positives. Researchers from
the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
in Dresden, the Center for Systems Biology Dresden (CSBD) in Germany, and
the Harvard Medical School in Boston, USA, have developed a tool called
Deciphering Mutations in Actionable Genes (DeMAG) published in the journal
Nature Communications. DeMAG is an open-source web server (demag.org) that
offers an interpretation of the effects of all potential single amino acid
mutations could occur in 316 clinically relevant genes that cause diseases
for which preventive diagnostics and treatments are already available.
DeMAG provides medical professionals with a tool that allows them to more
accurately assess the effect of mutations in those genes by reducing the
false positive rate, which means that less benign mutations are predicted
as pathogenic. As a result, the tool can support clinical decision-making.
Cracking the code of life: new AI model learns DNA's hidden language.
With GROVER, a new
large language model trained on human DNA, researchers could now
attempt to decode the complex information hidden in our genome. GROVER
treats human DNA as a text, learning its rules and context to draw
functional information about the DNA sequences. Since the discovery of the
double helix, scientists have sought to understand the information encoded
in DNA. 70 years later, it is clear that the information hidden in the DNA
is multilayered. Only 1-2 % of the genome consists of genes, the sequences
that code for proteins. DNA has many functions beyond coding for proteins.
Some sequences regulate genes, others serve structural purposes, most
sequences serve multiple functions at once. Currently, we don't understand
the meaning of most of the DNA. When it comes to understanding the
non-coding regions of the DNA, it seems that we have only started to
scratch the surface. This is where AI and large language models can help.
However, unlike a language, DNA has no defined words that we know of. DNA
consists of four letters (A, T, G, and C) and genes, but there are no
predefined sequences of different lengths that combine to build genes or
other meaningful sequences.
Multiomics is a
biological analysis approach in which the data sets are multiple "omes",
such as the genome, proteome, transcriptome, epigenome, metabolome, and
microbiome (i.e., a meta-genome and/or meta-transcriptome, depending upon
how it is sequenced); in other words, the use of multiple omics
technologies to study life in a concerted way. By combining these "omes",
scientists can analyze complex biological big data to find novel
associations between biological entities, pinpoint relevant biomarkers and
build elaborate markers of disease and physiology. In doing so, multiomics
integrates diverse omics data to find a coherently matching
geno-pheno-envirotype relationship or association. The OmicTools service
lists more than 99 softwares related to multiomic data analysis, as well
as more than 99 databases on the topic.
In-Vitro
-
Synthetic Biology -
Biomimicry -
Crispr -
Sequencing
Artificial Gene Synthesis refers to a group of methods that are used
in synthetic biology to construct and assemble genes from nucleotides de
novo. Unlike DNA synthesis in living cells, artificial gene synthesis does
not require template DNA, allowing virtually any DNA sequence to be
synthesized in the laboratory. It comprises two main steps, the first of
which is solid-phase DNA synthesis, sometimes known as
DNA printing. This produces
oligonucleotide fragments that are generally under 200 base pairs. The
second step then involves connecting these oligonucleotide fragments using
various DNA assembly methods. Because artificial gene synthesis does not
require template DNA, it is theoretically possible to make a completely
synthetic DNA molecule with no limits on the nucleotide sequence or size.
Breakthrough in molecular control: New bioinspired double helix with
switchable chirality. Scientists developed an artificial double-helical
complexes that exhibits controllable chirality-switching properties. The
control of
artificial double-helical structures,
which are essential for the development of high-order molecular systems,
remains difficult. In a new study, researchers have developed novel
double-helical monometallofoldamers that exhibit controllable helicity
inversion and chiral information transfer, in response to external
stimuli. These monometallofoldamers can lead to novel artificial
supramolecular systems for molecular information transmission,
amplification, replication, and other exciting applications in various
fields of technology. The deoxyribonucleic acid or DNA, the molecular
system that carries the genetic information of living organisms, can
transcribe and amplify information using its two helical strands. Creating
such artificial molecular systems that match or surpass DNA in
functionality is of great interest to scientists. Double-helical foldamers
are one such molecular system. Helical foldamers are a class of artificial
molecules that fold into well-defined helical structures like helices
found in proteins and nucleic acids. They have garnered considerable
attention as stimuli-responsive switchable molecules, tuneable chiral
materials, and cooperative supramolecular systems due to their chiral and
conformational switching properties. Double-helical foldamers exhibit not
only even stronger chiral properties but also unique properties, such as
the transcription of chiral information from one chiral strand to another
without chiral properties, enabling potential applications in higher-order
structural control related to replication, like nucleic acids. However,
the artificial control of the chiral switching properties of such
artificial molecules remains challenging due to the difficulty in
balancing the dynamic properties required for switching and stability.
Although various helical molecules have been developed in the past,
reversal of twist direction in double-helix molecules and supramolecules
has rarely been reported.
DNA Enhancements - Playing God
This fear and fascination about
designing babies is ridiculous because it's
already been happening since the beginning, it's called
reproduction and
eugenics. And our DNA is being modified by
toxins and
pollution
and by
bad food already. So some of the biggest threats
humans have comes from
institutional education
and
media propaganda. Even if
you could change physical attributes of a baby, you still have a software
problem. If you change a behavior, what are you replacing that behavior
with? And do you understand the differences between those two behaviors?
It's a good idea to
remove defects in the DNA that cause disease, but not
a good idea to pre-program physical traits that ignorant people would
consider a good
body image. The focus should
be more on
modification for
adaptation and not for alterations
based on perceived superior traits.
Biodiversity is what life
uses to protect itself. Saying that someone is
Playing God is a ridicules statement. You have no idea who God is. And
you should never assume that
God
was playing when God was creating the universe or when God was creating
life and human life. God created humans to have a
manual option to protect life. So
we are not playing god, we are just using the gifts that God gave us, just
as
long as we
use our gifts wisely
that is. We should
enhance education and
modify our mental selves so that
people are more educated so they can logically decide whether modifying the body is even
worth the risk.
Asexual
Reproduction.
"If we're going to act like God's, we should at
least be Gods who are good, loving and fair."
Gattaca
is a 1997 American
dystopian science fiction thriller film that presents a biopunk vision
of a future society driven by eugenics where potential children are
conceived through genetic selection to ensure they possess the best
hereditary traits of their parents. The film draws on concerns over
reproductive technologies that facilitate eugenics, and the possible
consequences of such technological developments for society. It also
explores the idea of destiny and the ways in which it can and does govern
lives. Characters in Gattaca continually battle both with society and with
themselves to find their place in the world and who they are destined to
be according to their genes.
Bio-Hacking -
DIY Biology -
GMO'sGene Drive
is a
natural process and technology of
genetic engineering that propagates a particular suite of genes throughout
a population by altering the probability that a specific allele will be
transmitted to offspring (instead of the
Mendelian 50% probability). Gene drives can arise through a variety of
mechanisms. They have been proposed to provide an effective means of
genetically modifying specific populations and entire species. The
technique can employ adding, deleting, disrupting, or modifying genes.
Proposed applications include exterminating insects that carry pathogens
(notably mosquitoes that transmit malaria, dengue, and zika pathogens),
controlling invasive species, or eliminating herbicide or pesticide
resistance. Gene drive
is a technique that promotes the
inheritance of a particular gene to
increase its prevalence in a population. Gene drives can arise through a
variety of mechanisms. They have been proposed to provide an effective
means of genetically modifying specific populations and entire species.
The technique can employ adding, deleting, disrupting, or modifying genes.
Gene drives affect only sexually reproducing species, excluding viruses or
bacteria. Applications include exterminating insects that carry pathogens
(notably mosquitoes that transmit malaria, dengue and zika pathogens),
controlling invasive species or eliminating herbicide or pesticide
resistance. As with any potentially powerful technique, gene drives can be
misused in a variety of ways or induce unintended consequences. For
example, a gene drive intended to affect only a local population might
spread across an entire species. Many non-native species have a high
likelihood of returning to their original habitats, through natural
migration, environmental disruption (storms, floods, etc.), accidental
human transportation, or purposeful relocation. Specimens whose
reproduction/survival is compromised that somehow return to their native
habitat, could unintentionally drive their species to extinction. Several
molecular mechanisms can mediate a gene drive. Naturally occurring
mechanisms arise when alleles evolve molecular mechanisms that give them a
transmission chance greater than (the normal) 50%.
Selfish
Genetic Element are genetic segments that can enhance their own
transmission at the expense of other genes in the genome, even if this has
no positive or a net negative effect on organismal fitness.
Gene Expression
(hereditary traits) -
Gene Therapy -
Stem Cells
Genetic Engineering without unwanted side effects helps fight parasites.
Modified CRISPR-Cas9 gene editing scissors are enabling researchers to
make alterations to the genetic material of single-cell organisms that are
indistinguishable from natural mutations. This method is making it
possible to develop a (harmless) experimental live vaccine for the
widespread parasite Toxoplasma gondii.
RNA-Programmed Genome Editing in Human Cells.
Easily 'Re-Programmable Cells' could be key in creation of new life forms.
New study addresses a long-standing diversity bias in human genetics.
Data includes groups traditionally neglected in research. Scientists have
generated a new catalog of human gene expression data from around the
world to address how most research in human genetics has historically
focused on people of European ancestries -- a bias that may limit the
accuracy of scientific predictions for people from other populations.
A
step towards Biological Warfare with Insects? The programme called '
Insect
Allies' intends for insects to be used for dispersing genetically
modified viruses to agricultural plants in fields. These viruses would be
engineered so they can alter the chromosomes of plants through 'genome
editing'. This would allow for genetic modifications to be implemented
quickly and at a large scale on crops that are already growing in fields,
such as corn.
Genetically Modified Mosquitoes. Male Anopheles gambiae mosquitoes
engineered with the mutation can mate with normal female mosquitoes,
passing along the changed gene. Anopheles gambiae mosquitoes are the
primary vector responsible for spreading malaria in sub-Saharan Africa.
The ethics of wiping out a Mosquito Species.
A cell could be programmed, for example, with a so-called
NOT logic
gate. This is one of the simplest logic instructions: Do NOT do something
whenever you receive the trigger. Cells are basically tiny computers: They
send and receive inputs and output accordingly your blood sugar spikes,
and your pancreatic cells get the message. Output: more insulin.
RapidHIT™ Human DNA Identification System
Retron Library Recombineering is a new gene editing technique that
enables millions of genetic experiments to be performed simultaneously and
can generate up to millions of mutations simultaneously, and 'barcodes'
mutant bacterial cells so that the entire pool can be screened at once. It
can be used in contexts where CRISPR is toxic or not feasible, and results
in better editing rates.
Scientists Use Revolutionary Gene-Editing Tool To Edit Inside A Patient.
For the first time, scientists have used the gene-editing technique CRISPR
to try to
edit a gene while the DNA is still
inside a person's body. The groundbreaking procedure involved
injecting the microscopic gene-editing tool into the eye of a patient
blinded by a rare genetic disorder, in hopes of enabling the volunteer to
see. They hope to know within weeks whether the approach is working and,
if so, to know within two or three months how much vision will be
restored. In this new experiment, doctors at the Casey Eye Institute in
Portland, Ore., injected (into the eye of a patient who is nearly blind
from a condition called
Leber congenital amaurosis) microscopic droplets carrying a harmless
virus that had been engineered to deliver the instructions to manufacture
the CRISPR gene-editing machinery. Beginning in infancy, the rare genetic
condition progressively destroys light-sensing cells in the retina that
are necessary for vision.
Vision impairment with LCA varies widely, but most patients are
legally blind and are only able to differentiate between light and dark or
perhaps to detect movement.
PCR Analyzer or Polymerase Chain Reaction
is a technique used in medical and biological research labs for a variety
of applications including qualitative and quantitative nucleic acid
analysis; DNA cloning for sequencing, DNA-based phylogeny, or functional
analysis of genes; the diagnosis of hereditary.
Somatic Gene
Editing doesn't change reproductive cells so it does not get passed on. Germline gene editing modifies reproductive cells so it gets passed down
to future generations.
Somatic Cell is any biological cell forming the body of an organism;
that is, in a multicellular organism, any cell other than a gamete, germ
cell, gametocyte or undifferentiated stem cell. In contrast, gametes are
cells that fuse during sexual reproduction, germ cells are cells that give
rise to gametes, and
stem cells are
cells that can divide through mitosis
and differentiate into diverse specialized cell types. For example, in
mammals, somatic cells make up all the internal organs, skin, bones, blood
and connective tissue, while mammalian germ cells give rise to spermatozoa
and ova which fuse during fertilization to produce a cell called a
zygote, which divides and differentiates into the cells of an embryo.
There are approximately 220 types of somatic cells in the human
body. Theoretically, these cells are not germ cells (the source of
gametes); they never transmit to their descendants the mutations they have
undergone. However, in sponges, non-differentiated somatic cells form the
germ line and, in Cnidaria, differentiated somatic cells are the source of
the
germline. (somatic cells die with you).
Germ
Cell is any biological cell that gives rise to the gametes of an
organism that reproduces sexually. In many animals, the germ cells
originate in the primitive streak and migrate via the gut of an embryo to
the developing gonads. There, they undergo meiosis, followed by
cellular differentiation into mature gametes, either eggs or sperm. Unlike
animals, plants do not have germ cells designated in early development.
Instead, germ cells can arise from somatic cells in the adult (such as the
floral meristem of flowering plants).
T-Cells.
Human genome editing to make
edits in somatic cells for purposes of
treating genetically inherited diseases. Genome editing changes the
DNA sequence so that the cells can make the right proteins again. Advances
in genome editing hold promise for enabling the treatment of thousands of
genetic diseases. Somatic gene therapy is the transfer of genes into the
somatic cells of the patient, such as cells of the bone marrow, and hence
the new DNA does not enter the eggs or sperm.
Somatic mutation is a genetic alteration
acquired by a cell that can be passed to the progeny of the mutated cell
in the course of
cell division.
Somatic mutations differ from germ line
mutations, which are inherited genetic alterations that occur in the
germ cells (i.e., sperm and eggs).
Germline
in a multicellular organism is the population of its bodily cells that are
so differentiated or segregated that in the usual processes of
reproduction they may
pass on their genetic material to the progeny.
As a rule this passing-on happens via a process of sexual reproduction;
typically it is a process that includes systematic changes to the genetic
material, changes that arise during recombination, meiosis and
fertilization for example. However, there are many exceptions, including
processes and concepts such as various forms of apomixis, autogamy,
automixis, cloning, or parthenogenesis. The cells of the germline commonly
are called
Germ
Cells, which is any biological cell that gives rise to the gametes of
an organism that reproduces sexually.
Germline Mutation or germinal mutation, is any detectable variation
within germ cells (cells that, when fully developed, become sperm and
ovum).
Mutations in these cells are
the only mutations that can be passed on to offspring, when either a
mutated sperm or oocyte come together to form a zygote. After this
fertilization event occurs, germ cells divide rapidly to produce all of
the cells in the body, causing this mutation to be present in every
somatic and germline cell in the offspring; this is also known as a
constitutional mutation. Germline mutation is distinct from somatic
mutation.
Homozygous vs. Heterozygous
Gene Delivery is the process of introducing foreign genetic material,
such as DNA or RNA, into host
cells.
Genetic material must reach the nucleus of the host cell to induce gene
expression. Successful gene delivery requires the foreign genetic material
to remain stable within the host cell and can either integrate into the
genome or replicate independently of it. This requires foreign DNA to be
synthesized as part of a vector, which is designed to enter the desired
host cell and deliver the transgene to that cell's genome. Vectors
utilized as the method for gene delivery can be divided into two
categories, recombinant viruses and synthetic vectors (viral and
non-viral). In complex multicellular eukaryotes (more specifically
Weissmanists), if the transgene is incorporated into the host's germline
cells, the resulting host cell can pass the transgene to its progeny. If
the transgene is incorporated into
somatic cells, the transgene will stay with the somatic cell line, and
thus its host organism. Gene delivery is a necessary step in gene therapy
for the introduction or silencing of a gene to promote a therapeutic
outcome in patients and also has applications in the genetic modification
of crops. There are many different methods of gene delivery for various
types of cells and tissues.
Viral
Vector are tools commonly used by molecular biologists to deliver
genetic material into cells. This process can be performed inside a living
organism (in vivo) or in cell culture (in vitro). Viruses have evolved
specialized molecular mechanisms to efficiently transport their genomes
inside the cells they infect. Delivery of genes, or other genetic
material, by a vector is termed transduction and the infected cells are
described as transduced. Molecular biologists first harnessed this
machinery in the 1970s. Paul Berg used a modified SV40 virus containing
DNA from the bacteriophage ? to infect monkey kidney cells maintained in
culture. In addition to their use in molecular biology research, viral
vectors are used for gene therapy and the development of vaccines.
Horizontal Gene Transfer is the movement of genetic material between
unicellular and/or multicellular
organisms other than by the ("vertical") transmission of DNA from
parent to offspring. HGT is an important factor in the evolution of many
organisms. Horizontal gene transfer is the primary mechanism for the
spread of
antibiotic resistance in
bacteria, and plays an important role in the evolution of bacteria
that can degrade novel compounds such as human-created pesticides and in
the evolution, maintenance, and transmission of virulence. It often
involves temperate bacteriophages and plasmids. Genes responsible for
antibiotic resistance in one species of bacteria can be transferred to
another species of bacteria through various mechanisms such as F-pilus,
subsequently arming the antibiotic resistant genes' recipient against
antibiotics, which is becoming medically challenging to deal with. It is
also postulated that HGT promotes the maintenance of a universal life
biochemistry and, subsequently, the universality of the genetic code. Most
thinking in genetics has focused upon vertical transfer, but the
importance of horizontal gene transfer among single-cell organisms is
beginning to be acknowledged. Gene delivery can be seen as an artificial
horizontal gene transfer, and is a form of genetic engineering.
Palindromic
Sequence is a nucleic acid sequence on double-stranded DNA or RNA
wherein reading 5' (five-prime) to 3' (three prime) forward on one strand
matches the sequence reading 5' to 3' on the complementary strand with
which it forms a double helix. This definition of palindrome thus depends
on complementary strands being palindromic of each other.
Analog DNA Circuit Does Math in a Test Tube DNA computers could one
day be programmed to diagnose and treat disease.
Computer program can translate a free-form 2-D drawing into a DNA
structure. Researchers at MIT and Arizona State University have
designed a computer program that allows users to translate any free-form
drawing into a two-dimensional,
nanoscale structure made of DNA.
Recording analog memories in human cells. Engineers program human
cells to store complex histories in their DNA.
The era of Personal DNA Testing is here: Sebastian Kraves (video and
interactive text) - Portable DNA analyzers can help us quickly detect
viruses, so that we can stop a
pandemics
and the spreading of disease. With a portable DNA analyzer we can quickly
assess whether our food is safe to eat. A farmer can take fluid samples
from livestock and then take a drop of that genetic material and put it
into a little analyzer smaller than a shoebox, program it to detect DNA or
RNA from the swine flu virus. These machines used in a court law can
decide whether someone is innocent or guilty based on DNA evidence. These
machines can also help verify the identification of a substance by knowing
key factors about its DNA. Personal DNA machines are now aboard the
International Space Station, where they can help monitor living conditions
and protect the lives of astronauts.
Transduction in genetics is the process by which
foreign DNA is
introduced into a cell by a virus or viral vector. An example is the viral
transfer of DNA from one bacterium to another. Transduction does not
require physical contact between the cell donating the DNA and the cell
receiving the DNA (which occurs in conjugation), and it is DNase resistant
(transformation is susceptible to DNase). Transduction is a common tool
used by molecular biologists to stably introduce a foreign gene into a
host cell's genome (both bacterial and mammalian cells).When viruses,
including bacteriophages (viruses that infect bacteria), infect bacterial
cells, their normal mode of reproduction is to harness the replicational,
transcriptional, and translation machinery of the host bacterial cell to
make numerous virions, or complete viral particles, including the viral
DNA or RNA and the protein coat.
Genetically Modified - GMO
Genetic Engineering is the direct
manipulation of an organism's genome
using
Biotechnology. It is a set of
technologies used to change the genetic makeup of
cells, including the
transfer of genes within and across species boundaries to produce improved
or novel organisms. New DNA may be inserted in the host genome by first
isolating and copying the genetic material of interest using molecular
cloning methods to generate a DNA sequence, or by synthesizing the DNA,
and then inserting this construct into the host organism. Genes may be
removed, or "knocked out", using a nuclease. Gene targeting is a different
technique that uses homologous recombination to change an endogenous gene,
and can be used to delete a gene, remove exons, add a gene, or introduce
point
mutations.
CRISPR.
Genetically Modified Organism or
GMO,
is any
organism whose genetic
material has been altered using genetic engineering techniques. The exact
definition of a genetically modified organism and what constitutes genetic
engineering varies, with the most common being an organism altered in a
way that "does not occur naturally by mating and/or natural
recombination". A wide variety of organisms have been genetically modified
(GM), from animals to plants and microorganisms. Genes have been
transferred within the same species, across species (creating transgenic
organisms) and even across kingdoms. New genes can be introduced, or
endogenous genes can be enhanced, altered or knocked out. Creating a
genetically modified organism is a multi-step process. Genetic engineers
must isolate the gene they wish to insert into the host organism and
combine it with other genetic elements, including a promoter and
terminator region and often a selectable marker. A number of techniques
are available for inserting the isolated gene into the host genome. Recent
advancements using genome editing techniques, notably CRISPR, have made
the production of GMO's much simpler.
Life from non-living matter.
Ginkgo Bioworks specializes in using genetic engineering to produce
bacteria with industrial applications. Ginkgo Bioworks is an analytics
company that designs organisms for customers in a range of industries. It
is the self-proclaimed "Organism Company". Ginkgo Bioworks designs
microbes in analytical labs it calls synthetic biology foundries, which
comprise software and hardware tools that allow for rapid prototyping and
high-throughput screening. Several publicly-stated products include
chemical intermediates, flavors, and fragrances; as well as microbes that
provide health benefits to the human gut microbiome and agricultural crop
root microbiomes.
Transgene is a gene or genetic material that has been transferred
naturally, or by any of a number of genetic engineering techniques from
one organism to another. The introduction of a transgene (called "transgenesis")
has the potential to change the phenotype of an organism.
Transgenesis is
the process of
introducing an exogenous gene—called a transgene—into a
living organism so that the organism will exhibit a new property and
transmit that property to its offspring. Transgenesis can be facilitated
by liposomes, enzymes, plasmid vectors, viral vectors, pronuclear
injection, protoplast fusion, and ballistic DNA injection. Transgenesis
can occur in nature. Transgenic organisms are able to express foreign
genes because the genetic code is similar for all organisms. This means
that a specific DNA sequence will code for the same protein in all
organisms. Due to this similarity in protein sequence, scientists can cut
DNA at these common protein points and add other genes. An example of this
is the "super mice" of the 1980s. These mice were able to produce the
human protein tPA to treat blood clots.
Transduction.
Xenotransplantation is the transplantation of living cells, tissues or
organs from one species to another. Such cells, tissues or organs are
called xenografts or xenotransplants. It is contrasted with
allotransplantation (from other individual of same species), Syngeneic
transplantation (Grafts transplanted between two genetically identical
individuals of the same species) and Autotransplantation (from one part of
the body to another in the same person).
Recombinant DNA molecules are DNA molecules formed by laboratory
methods of genetic recombination (such as molecular cloning) to bring
together genetic material from multiple sources, creating sequences that
would not otherwise be found in the genome.
GMO Plants -
Genetically Modified Food
GMO Mosquitos
Released In High-Security Lab | Science | NPR (youtube) - The
mosquitoes are an entirely new kind of genetically modified organism. The
insects, members of the species that transmits malaria, were modified
using the powerful gene-editing technique CRISPR to carry a sequence of
DNA known as a "gene drive," which is designed to drive the genetic
modification rapidly through entire populations of the species. The
mutation is designed to sterilize populations of malaria-transmitting
mosquitoes in the wild, causing them to crash. And that would, hopefully,
help stop the spread of the malaria parasite. But the experiment is
controversial because of fears that the genetically modified insects could
cause unintended consequences on the environment if they were ever
released in the wild. So the mosquitoes are being tested first in a
specially designed, high-security lab in Terni, Italy. The lab is designed
to mimic the natural environment in sub-Saharan Africa — and to make sure
none of the insects escapes. If they do escape, they will not survive Italy's climate.
Epigenetics
Epigenetics are
stable
heritable traits or
phenotypes
that cannot be explained by changes in DNA sequence. Epigenetics often
refers to changes in a
chromosome that
affect
gene activity and
expression, but can also be used to describe any
heritable phenotypic change that
does not
derive from a modification of the genome, such as prions. Such effects on
cellular and physiological phenotypic traits may result from external or
environmental factors, or be part of normal developmental program. The
standard definition of epigenetics requires these
alterations to be
heritable, either in the progeny of cells or of organisms.
Epigenetics
studies genetic effects not encoded in the DNA sequence of an organism,
Such effects on cellular and physiological phenotypic traits may result
from external or environmental factors that
switch genes on and off and
affect how cells express genes. These alterations may or may not be
heritable, although the use of the term epigenetic to describe processes
that are heritable is controversial. Epigenetics is the study of heritable
changes in gene. Activities that do not involve alterations to the genetic
code.
Eugenics -
Playing God -
CRISPR -
DNA
Repair
Personalized Food -
Personalized Medicine
Epigenome consists of
a record of the chemical changes to the DNA and
histone proteins of an organism; these changes can be passed down to an
organism's offspring via transgenerational epigenetic inheritance. Changes
to the epigenome can result in changes to the structure of chromatin and
changes to the function of the genome. The epigenome is involved in
regulating gene expression, development, tissue differentiation, and
suppression of transposable elements. Unlike the underlying genome which
is largely static within an individual, the epigenome can be dynamically
altered by environmental conditions.
Epigenetic Mechanisms modulated by environmental cues such as diet,
disease or our lifestyle take a major role in regulating the DNA by
switching genes
on
and off. -
Max-Planck-Gesellschaft,
München.
Epigenetic Markers tell
your genes to switch on or off. There are two types of marks: chemical
(e.g., methylation) or. protein (e.g., histones).
Polygene -
Methylation.
Epigenomics is the study of the complete set
of
epigenetic modifications on the genetic material of a cell,
known as the epigenome. The field is analogous to genomics and proteomics,
which are the study of the genome and proteome of a cell. Epigenetic
modifications are reversible modifications on a cell's DNA or histones
that affect gene expression without altering the DNA sequence. Epigenomic
maintenance is a continuous process and plays an important role in
stability of eukaryotic genomes by taking part in crucial biological
mechanisms like DNA repair. Plant flavones are said to be inhibiting
epigenomic marks that cause cancers. Two of the most characterized
epigenetic modifications are DNA methylation and histone modification.
Epigenetic
modifications play an important role in gene expression and
regulation, and are involved in numerous cellular processes such as in
differentiation/development and tumorigenesis. The study of epigenetics on
a global level has been made possible only recently through the adaptation
of genomic high-throughput assays.
Rhonda Patrick on
Diet-Gene Interactions, Epigenetics, the Vitamin D-Serotonin Link and DNA
Damage.(youtube)
Epigenetic enzymes affect 160 genes.
Enzymes regulate the behavior of genes.
Rpd3.
Transgenerational Epigenetic Inheritance
is the
transmittance of information from one generation of an organism to
the next (e.g., parent–child transmittance) that affects the
traits of
offspring without alteration of the primary structure of DNA (i.e., the
sequence of nucleotides)—in other words, epigenetically. The less precise
term "epigenetic inheritance" may be used to describe both cell–cell and
organism–organism information transfer. Although these two levels of
epigenetic inheritance are equivalent in unicellular organisms, they may
have distinct mechanisms and evolutionary distinctions in multicellular
organisms. For some epigenetically influenced traits, the epigenetic marks
can be induced by the environment and
some marks are heritable, leading
some to view epigenetics as a relaxation of the rejection of soft
inheritance of acquired characteristics.
Not all in the genes: Are we inheriting more than we think?
Epigenetics is a rapidly growing field of science that investigates how
our genes are switched on and off to allow one set of genetic instructions
to create hundreds of different cell types in our body. The new research
suggests that epigenetic information, which sits on top of DNA and is
normally reset between generations, is more frequently
carried from mother to offspring than
previously thought. Epigenetic changes can be influenced by environmental
variations such as our diet, but these changes do not alter DNA and are
normally not passed from parent to offspring. While a tiny group of
'imprinted' genes can carry epigenetic information across generations,
until now, very few other genes have been shown to be influenced by the
mother's epigenetic state. The new research reveals that the supply of a
specific protein in the mother's egg can affect the genes that drive
skeletal patterning of offspring. Hox genes control the identity of each
vertebra during embryonic development in mammals, while the epigenetic
regulator prevents these genes from being activated too soon. In this
study, the researchers discovered that the amount of SMCHD1 in the
mother's egg affects the activity of Hox genes and influences the
patterning of the embryo. Without maternal SMCHD1 in the egg, offspring
were born with altered skeletal structures. While we have more than 20,000
genes in our genome, only that rare subset of about 150 imprinted genes
and very few others have been shown to carry epigenetic information from
one generation to another. Variants in SMCHD1 are linked to developmental
disorder Bosma arhinia microphthalmia syndrome (BAMS) and
facioscapulohumeral muscular dystrophy (FSHD), a form of muscular
dystrophy. The researchers say their findings could have implications for
women with SMCHD1 variants and their children in the future.
Methyl Group is an alkyl derived from methane, containing one carbon
atom bonded to three hydrogen atoms — CH3. In formulas, the group is often
abbreviated Me. Such hydrocarbon groups occur in many organic compounds.
It is a very stable group in most molecules. While the methyl group is
usually part of a larger molecule, it can be found on its own in any of
three forms: anion, cation or radical. The anion has eight valence
electrons, the radical seven and the cation six. All three forms are
highly reactive and rarely observed.
Anion (−) is an ion with more electrons than protons, giving it a net
negative charge (since electrons are negatively charged and protons are
positively charged).
Cation (+) is an ion with fewer electrons than protons, giving it a
positive charge.
Radical is an atom, molecule, or ion that has an unpaired valence
electron. With some exceptions, these unpaired electrons make radicals
highly chemically reactive. Many radicals spontaneously dimerize. Most
organic radicals have short lifetimes.
Animal Pharm: Food
For Thought - Real Stories (youtube, 51:17) - Explore how science is
changing the food that we eat. From double-muscled bulls to featherless
chickens, this is breeding on a whole new level. Stepping into the world
of transgenics, we encounter rabbits with a jellyfish gene in their DNA
(they glow in the dark), and salmon engineered to grow four times faster
than normal.
Animal Pharm: From
Mouse To Man - Real Stories (youtube, 51:07) - Explore the spooky
prospect of regeneration, with mice that show powers no mammal was
previously thought to have; and witness how, with tissue engineering,
scientists can now manipulate cartilage and skin cells so they can grow
them into any shape.
Tissue Engineering is the use of a combination of cells, engineering
and materials methods, and suitable biochemical and physicochemical
factors to improve or replace biological tissues. Tissue engineering
involves the use of a scaffold for the formation of new viable tissue for
a medical purpose. While it was once categorized as a sub-field of
biomaterials, having grown in scope and importance it can be considered as
a field in its own.
Bioreactor is a manufactured or engineered device or system that supports a
biologically active environment. In one case, a bioreactor is a vessel in
which a chemical process is carried out which involves organisms or
biochemically active substances derived from such organisms. This process
can either be aerobic or anaerobic. These bioreactors are commonly
cylindrical, ranging in size from litres to cubic metres, and are often
made of stainless steel. A bioreactor may also refer to a device or system
meant to grow cells or tissues in the context of cell culture. These
devices are being developed for use in tissue engineering or biochemical
engineering.
Low Gravity
Environment.
Zygosity
is the degree of similarity of the alleles for a trait in an organism.
Most eukaryotes have two matching sets of chromosomes; that is, they are
diploid. Diploid organisms have the same loci on each of their two sets of
homologous chromosomes, except that the sequences at these loci may differ
between the two chromosomes in a matching pair and that a few chromosomes
may be mismatched as part of a chromosomal sex-determination system. If
both alleles of a diploid organism are the same, the organism is
homozygous at that locus. If they are different, the organism is
heterozygous at that locus. If one allele is missing, it is hemizygous,
and, if both alleles are missing, it is nullizygous.
Eugenics -
Lobotomies -
GMO's (Food and Pesticides)
-
Mutations
Epigenetic drug discovery. Scientists create a machine-learning
algorithm that automates high-throughput screens of epigenetic medicines
and gleans information from microscope images -- allowing for
high-throughput epigenetic drug screens that could unlock new treatments
for cancer, heart disease, mental illness and more.
DNA Printed Out on Paper - Visualizing Scale
If you printed out DNA codes on paper, it would take 175 books with 262,000 pages of information,
which is about 10,000 ATCG code sequences on each page that is 8.5×11 with
an
8pt font size, minus the size of the margins, header and footer.
We know around only two percent of those 175 books. 500 pages, or 5 million ATCG
code sequences, gives each person their
own unique qualities, like facial
and
body characteristics.
99.9% of the DNA code is absolutely identical in every human
being. We all share the same DNA, except,
we don't always
share the same opinion. So everyone is almost
exactly the same or
equal, except for a few
small variations in 3
billion
lines of code, and, in the
variations in what we have learned
as
individuals.
The windows
operating system has
roughly
50 million lines of code. Even though Humans are 97% to 99%
genetically similar to chimpanzee's on average, humans have
39 million base DNA differences from
chimps and 3 million base DNA differences between each other.
Humans are also 90% genetically similar to cats, 85% genetically similar
to mice, 80% genetically similar to cows and 60% genetically similar to
bananas. But don't worry,
everyone is still
unique. Even though we are all very similar, we are all slightly
different in our own way. Since humans have 23 pairs of
chromosomes,
meiosis may result in 8,388,608 possible combinations of chromosomes or
genetic recombination's. There is 2
²³ or 8,388,608 combinations of
chromosomes in every male sperm, and
8,388,608 combinations of
chromosomes in every
female egg, that makes 70,368,744,177,664 possible variations that can
happen when a sperm fertilizes an egg. There are also more combinations in
the way that
proteins fold
then there are atoms in the universe.
Diversity -
Twins -
Brain Memory Capacity
How to read the genome and build a human being (video and interactive
text) -
Non-Coding.
How many possible
Alpha Numeric Combinations are there using all letters for 4
characters? With a Latin alphabet of
26 letters and
the 10 digits 0...9, and allowing for repeats, you get: 36^4 = 36 × 36 ×
36 × 36 = 1,679,616 combinations. If you were to include both lower and
upper case characters, the number of possible combinations goes up (due to
26 lower case letters + 26 upper case letters + 10 digits = 62 characters
to choose from): 62^4 = 14,776,336.
Some
where in the DNA code is information from the creator that explains who we are. And that is
what
we are starting to do now. Kind of brings a whole new meaning to the
phrase, "The answers lie within you". Look deep into your heart, or your
DNA.
But not all the information that humans need is in our DNA.
The rest of the information that we need, we need to learn from the
environment so that we can adapt quickly enough so that we don't
go extinct, like 99.9% of
all other life forms have done on this planet. You can say that life has
solved that problem of extinction by creating humans, but life forgot to
inform humans of our abilities and our responsibilities, thus we are
actually contributing to our own extinction instead of assuring our
survival.
Molecular biologists at UC San Diego have unlocked the code that initiates
transcription and regulates the activity of more than half of all human
genes, an achievement that should provide scientists with a better
understanding of how human genes are turned on and off.
Million Veteran Program: A mega-biobank to study genetic influences on health and disease.
Regeneron Genetics Center (RGC) has built one of the world’s most
comprehensive genetics databases, pairing the sequenced exomes and
de-identified electronic health records of more than 100,000 people so
far.
Humans and baker's yeast are more alike than different when it comes
to DNA replication. The findings visualize for the first time a molecular
complex -- called
CTF18-RFC in humans and Ctf18-RFC in yeast -- that loads a 'clamp'
onto DNA to keep parts of the replication machinery from falling off the
DNA strand.
How Does DNA Know What to Do?
How does DNA know when to Communicate and know when not to Communicate?
DNA is essentially a storage molecule. It contains all of the
instructions a cell needs to sustain itself. These instructions are found
within genes, which are sections of DNA made up of specific sequences of
nucleotides. In order to be implemented, the instructions contained within
genes must be expressed, or copied into a form that can be used by cells
to produce the proteins needed to support life. The instructions stored
within DNA are read and processed by a cell in two steps:
Transcription and
Translation. Each
of these steps is a separate biochemical process involving multiple
molecules. During transcription, a portion of the cell's DNA serves as a
template for creation of an RNA molecule. (RNA, or ribonucleic acid, is
chemically similar to DNA, except for three main differences
described later on in this concept page.) In some cases, the newly
created RNA molecule is itself a finished product, and it serves an
important function within the cell. In other cases, the RNA molecule
carries messages from the DNA to other parts of the cell for processing.
Most often, this information is used to manufacture proteins. The specific
type of RNA that carries the information stored in DNA to other areas of
the cell is called messenger RNA, or mRNA. How does transcription proceed?
Transcription begins when an enzyme called
RNA polymerase attaches to the DNA template strand and begins assembling a
new chain of nucleotides to produce a complementary RNA strand. There are
multiple types of types of RNA. In eukaryotes, there are multiple types of
RNA polymerase which make the various types of RNA. In prokaryotes, a
single RNA polymerase makes all types of RNA. Generally speaking,
polymerases are large enzymes that work together with a number of other
specialized cell proteins. These cell proteins, called transcription
factors, help determine which DNA sequences should be transcribed and
precisely when the transcription process should occur.
Initiation. A
schematic shows two horizontal strands of DNA against a white
background, one in the lower half of the image and one arcing in the upper
half. A transparent green globular structure, representing the enzyme RNA
polymerase, is bound to a several-nucleotide-long region along the lower
DNA strand on the right side. The sugar-phosphate backbone is depicted as
a segmented grey cylinder half as long and twice as wide as the
nitrogenous bases. Nitrogenous bases are represented as blue, orange, red,
or green vertical rectangles attached to each segment of the
sugar-phosphate backbone. About three dozen individual nucleotides float
in the background. Two individual nucleotides are visible inside the
transparent enzyme at a higher magnification.
Transcription begins when RNA polymerase binds to the DNA template strand.
Initiation. The first step in transcription is initiation. During
this step, RNA polymerase and its associated transcription factors bind to
the DNA strand at a specific area that facilitates transcription (
Figure
1). This area, known as a promoter region, often includes a
specialized nucleotide sequence, TATAAA, which is also called the TATA box
(not shown in Figure 1).
Strand Elongation.
A
schematic shows two horizontal strands of DNA against a white
background, one in the lower half of the image and one arcing in the upper
half. A transparent green globular structure, representing the enzyme RNA
polymerase, is bound to a several-nucleotide-long region along the lower
DNA strand about 60% of the way from the left side. The sugar-phosphate
backbone of the DNA strand is depicted as a segmented grey cylinder,
whereas the sugar-phosphate backbone of the RNA strand is depicted as a
segmented white cylinder. DNA nitrogenous bases are represented as blue,
orange, red, or green vertical rectangles attached to each segment of the
sugar-phosphate backbone; RNA nitrogenous bases are represented by blue,
green, orange, and yellow vertical rectangles attached to each segment of
the sugar-phosphate backbone. RNA polymerase synthesizes a complementary
RNA strand, forming DNA-RNA pairs of orange-blue, red-green, blue-orange,
or green-yellow, consistent with a thymine to uracil substitution in the
RNA strand. About three dozen individual nucleotides float in the
background. One individual nucleotide is visible inside the transparent
enzyme at a higher magnification. Figure 2: RNA polymerase (green)
synthesizes a strand of RNA that is complementary to the DNA template
strand below it. Once RNA polymerase and its related transcription factors
are in place, the single-stranded DNA is exposed and ready for
transcription. At this point, RNA polymerase begins moving down the DNA
template strand in the 3' to 5' direction, and as it does so, it strings
together complementary nucleotides. By virtue of complementary base-
pairing, this action creates a new strand of mRNA that is organized in the
5' to 3' direction. As the RNA polymerase continues down the strand of
DNA, more nucleotides are added to the mRNA, thereby forming a
progressively longer chain of nucleotides (Figure 2). This process is
called elongation. A schematic compares a single-stranded DNA molecule
with a single-stranded RNA molecule with a similar sequence. Both RNA and
DNA contain nitrogenous bases, represented by vertical colored rectangles,
attached to a sugar-phosphate backbone, represented as a segmented
cylinder. There are two major differences between the composition of RNA
and DNA strands. The sugar in the DNA strand is deoxyribose, represented
by a grey cylinder, whereas the sugar in the RNA strand is ribose,
represented by a white cylinder. In addition, the nitrogenous base thymine
(red) in the DNA strand is replaced by uracil (yellow) in the RNA strand.
Figure 3: DNA (top) includes thymine (red); in RNA (bottom), thymine is
replaced with uracil (yellow). Three of the four nitrogenous bases that
make up RNA — adenine (A), cytosine (C), and guanine (G) — are also found
in DNA. In RNA, however, a base called uracil (U) replaces thymine (T) as
the complementary nucleotide to adenine (Figure 3). This means that during
elongation, the presence of adenine in the DNA template strand tells RNA
polymerase to attach a uracil in the corresponding area of the growing RNA
strand (Figure 4). A schematic shows two rows of nucleotides. Each
individual nucleotide is represented as an elongated, vertical, colored
rectangle (a nitrogenous base) bound at one end to a grey horizontal
cylinder (a sugar molecule). The top row of nucleotides is from RNA, with
an A-C-U-G base sequence. The bottom row of nucleotides is from DNA, with
a T-G-A-C base sequence. Figure 4: A sample section of RNA bases (upper
row) paired with DNA bases (lower row). When this base-pairing happens,
RNA uses uracil (yellow) instead of thymine to pair with adenine (green)
in the DNA template below. Interestingly, this base substitution is not
the only difference between DNA and RNA. A second major difference between
the two substances is that RNA is made in a single-stranded, nonhelical
form. (Remember, DNA is almost always in a double-stranded helical form.)
Furthermore, RNA contains ribose sugar molecules, which are slightly
different than the deoxyribosemolecules found in DNA. As its name
suggests, ribose has more oxygen atoms than deoxyribose. Thus, the
elongation period of transcription creates a new mRNA molecule from a
single template strand of DNA. As the mRNA elongates, it peels away from
the template as it grows (Figure 5). This mRNA molecule carries DNA's
message from the nucleus to ribosomes in the cytoplasm, where proteins are
assembled. However, before it can do this, the mRNA strand must separate
itself from the DNA template and, in some cases, it must also undergo an
editing process of sort.
Termination and editing.
A schematic shows a single-stranded region of RNA on a white surface that
has had a loop, or intron, removed. Figure 6: In eukaryotes, noncoding
regions called introns are often removed from newly synthesized mRNA.
Figure Detail. As previously mentioned, mRNA cannot perform its assigned
function within a cell until elongation ends and the new mRNA separates
from the DNA template. This process is referred to as termination. In
eukaryotes, the process of termination can occur in several different
ways, depending on the exact type of polymerase used during transcription.
In some cases, termination occurs as soon as the polymerase reaches a
specific series of nucleotides along the DNA template, known as the
termination sequence. In other cases, the presence of a special protein
known as a termination factor is also required for termination to occur.
Once termination is complete, the mRNA
molecule falls off the DNA template. At this point, at least in
eukaryotes, the newly synthesized mRNA undergoes a process in which
noncoding nucleotide sequences, called introns, are clipped out of the
mRNA strand. This process "tidies up" the molecule and removes nucleotides
that are not involved in protein production (Figure 6). Then, a sequence
of adenine nucleotides called a poly-A tail is added to the 3' end of the
mRNA molecule (Figure 7). This sequence signals to the cell that the mRNA
molecule is ready to leave the nucleus and enter the cytoplasm.
Once an mRNA molecule is complete, that
molecule can go on to play a key role in the process known as
translation. During translation, the
information that is contained within the mRNA is used to direct the
creation of a protein molecule. In order for this to occur, however, the
mRNA itself must be read by a special, protein-synthesizing structure
within the cell known as a ribosome.
Replication.
Over and Out, meaning "transmission
is over and has ended at that time". This lets the receiver know that the
message has ended and there will be no more
communication at this time,
so the person is not sitting there
waiting for a response.
The receiver must understand the language of the transmitter, and know
when to send a message in return, and also know the length of time between
each transmission. Like
Morse code,
there has to be pauses or breaks, and the receiver must understand what
those pauses mean. How does the DNA know when to implement the code and
when to stop it? The human body is the
interface to
our environment. we have an internal system (mind) interacting with a
external system (environment), these two systems are separate yet
connected
in many different ways. Humans are a living system, and people are the
cells of this system. This is where
that process of
information
transfer becomes into being. Information has to be written, and the
information must know the receiver. You can say that the process doesn't
have to know the reciever, only do what is
programed. But where did this information originate from? Is it God?
Who is creating your dreams when you're sleeping? Is it God? This is like
trying to decipher encrypted messages. You have to analyze the patterns
and line them up with possible causes that they may have ben effected by
these messages that happened before the event. You have to look at
everything that is happening and understand that there was a
cause
and a
reason.
D.N.A. - A Flock of Seagulls (youtube)