A Glossary of Useful Terms
(With many thanks to
the sites from which I stole them)
In molecular biology, the 5' end and the 3' end
(pronounced 5-prime and 3-prime) are respectively the leading and tail ends of
a strand of nucleic acid. These strands are unidirectional,
i.e. they may only be read in one direction (for purposes of transcription, translation, replication
and other processes). The sugar (ribose or deoxyribose) molecules in the nucleic acid are all
oriented in the same direction. Their carbon atoms are
numbered: the 5' carbon atom is always on the side of the sugar molecule
that faces the leading end, while the 3' carbon atom always faces the
tail end (see figure).
ATGC:
● adenine,
thymine, guanine, cytosine
● Each
gene's code combines the four chemicals in various ways to spell out 3-letter
"words"
that specify which amino acid is needed at every step in making a protein.
● In
DNA, adenine always binds with thymine and guanine always binds with
cytosine. In RNA,
thymine is replaced by uracil.
Adenosine
triphosphate (ATP), the energy currency
or coin of the cell, transfers energy from chemical bonds to endergonic
(energy absorbing) reactions within the cell. Structurally, ATP consists of the
adenine
nucleotide
(ribose
sugar, adenine base, and phosphate group, PO4-2) plus two
other phosphate groups.
bp = base pair
 |
| Fig.6. Molecular modeling of DNA repair (Photo credit: Wikipedia) |
In genetic studies the chi-squared
test is used to evaluate a genetic theory or hypothesis by comparing actual
breeding results to theoretically expected results. The test is designed to
convert the differences (or deviations) between the two into the probability of
their occurring by chance, taking into account both the size of the sample and
the number of variables (degrees of freedom).
It is used to
determine whether two variables are independent of one another. In Chi-squared
testing we compare a set of observed values (O)
against a set of expected values (E) --- values that would be expected if
there were no association between the variables. We calculate a value, chi2,
using the identity:
chi2= sum of ((0-E)^2/E)
A chromosome,
from the Greek χρώμα (color) and σώμα (body) is, minimally, a
very long, continuous piece of DNA (a single DNA molecule), which contains many
genes, regulatory elements and other intervening nucleotide
sequences. In the chromosomes of eukaryotes,
the uncondensed DNA exists in a quasi-ordered structure inside the nucleus,
where it wraps around histones
(structural proteins,
Fig. 1), and where this composite material is called chromatin.
In shotgun DNA
sequencing projects, a contig (from contiguous) is a set of
overlapping DNA
segments derived from a single genetic source. A contig in this sense can be
used to deduce the original DNA sequence of the source.
CpG effect: an excess of substitutions where C and G
are neighbours.
Deamination: To
remove an amino group, NH2,
from (an organic compound).
In early development (fertilisation
to 8-cell
stage), the eukaryotic genome is demethylated.
From the 8-cell stage to the morula, de novo
methylation of the genome occurs, modifying and adding epigenetic
information to the genome.
Dinucleotide: see
nucleotide
Epigenesis: The
theory that an individual is developed by successive differentiation of an
unstructured egg rather than by a simple enlarging of a preformed entity.
Exon: The region of a gene that contains the code
for producing the gene's protein. Each exon codes for a specific portion of the
complete protein. In some species (including humans), a gene's exons are
separated by long regions of DNA (called introns
or sometimes "junk DNA") that have no apparent function.
The DNA that makes
up the human genome can be
subdivided into information bytes called genes. Each gene encodes a unique protein that performs a specialized
function in the cell. The human
genome contains more than 25,000 genes.
Gene Expression:
The process by which proteins are made from the instructions encoded in DNA.
The term gene
silencing is generally used to describe the "switching off" of a
gene by a mechanism other than genetic mutation. That is, a gene which would be expressed
(turned on) under normal circumstances, is switched off by machinery in the
cell.
Genomic Imprinting
is the phenomenon whereby a small subset of all the genes in the genome are
expressed according to their parent of origin. Some imprinted genes are
expressed from a maternally inherited chromosome and silenced on the paternal
chromosome; while other imprinted genes show the opposite expression pattern
and are only expressed from a paternally inherited chromosome. Contrary to
expectation, 'imprints' can act as a silencer or an activator for imprinted
genes.
Housekeeping gene: A gene involved in basic functions
needed for the sustenance of the cell. Housekeeping genes are constitutively
expressed (they are always turned ON).
Intron: see exon
Mb = megabase
In biological systems, methylation
is catalyzed
by enzymes; such
methylation can be involved in modification of heavy
metals, regulation of gene expression, regulation of protein
function, and RNA metabolism.
(CH3 =
methyl)
Mitotic: having
to do with mitosis (cell division)
mRNA: Template
for protein synthesis. Each set of three bases, called codons, specifies a
certain protein in the sequence of amino acids that comprise the protein. The
sequence of a strand of mRNA is based on the sequence of a complementary strand
of DNA.
Murine: of or
relating to rats/mice
nt = nucleotide
A nucleotide
consists of a base (one of four chemicals: adenine, thymine, guanine, and
cytosine) plus a molecule of sugar and one of phosphoric acid. Dinucleotide: A sequence of 2 base
pairs.
Oligonucleotides are short sequences of nucleotides
(RNA or DNA), typically with
twenty or fewer bases. Automated synthesizers allow the synthesis of oligonucleotides
up to 160 to 200 bases. Oligonucleotides are often used as probes for detecting
complementary DNA or RNA because they bind readily to their complements. Examples of
procedures that use oligonucleotides are DNA
microarrays, Southern blots, and fluorescent in situ hybridization
(FISH). Oligonucleotides can also be used for the synthesis of artificial genes.
Two genes are to be orthologous
if they diverged after a speciation event
P-value: For
example, say an experiment is performed to determine if a coin flip is fair
(50% chance of landing heads or tails), or unfairly biased toward heads
(> 50% chance of landing heads). The null hypothesis is that the coin
is fair, and that any deviations from the 50% rate can be ascribed to chance
alone. Suppose that the experimental results show the coin turning up heads 14
times out of 20 total flips. The p-value of this result would be the chance of
a fair coin landing on heads at least 14 times out of 20 flips (as
larger values in this case are also less favorable to the null hypothesis of a
fair coin). The calculated p-value for this is 0.058.
Generally, the smaller the P value, the more people there
are who would be willing to say that the results came from a biased coin.
Polymerase: Any
of various enzymes, such as DNA polymerase, RNA polymerase, or reverse
transcriptase, that catalyze the formation of polynucleotides of DNA or RNA
using an existing strand of DNA or RNA as a template.
Promoter: The
region of an operon that acts as the initial binding site for RNA
polymerase. Operon: A unit of genetic
material that functions in a coordinated manner by means of an operator, a
promoter, and one or more structural genes that are transcribed together.
Promoter: In molecular biology, a site on DNA to
which the enzyme RNA polymerase can bind and initiate the transcription of DNA
into RNA.
Traditionally, sensitivity
of a predictive method is measured in terms of fraction of the positive data
points correctly predicted by the method and specificity is measured in terms of fraction of the predictions
that are correct.
A Single Nucleotide Polymorphism or SNP
(pronounced snip) is a DNA
sequence variation occurring when a single nucleotide
- A, T, C, or G - in the genome differs
between members of the species. For example, two sequenced DNA fragments from
different individuals, AAGCCTA to AAGCTTA, contain a difference
in a single nucleotide. In this case we say that there are two alleles :
C and T.
Totipotent:
embryonic cells are totipotent; they can turn into anything
Cells use the two-step process of transcription
and translation to read each
gene and produce the string of amino
acids that makes up a protein. (check out the awesome illustration I stole.)
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