Gene


The word "gene" is shared by many disciplines, including whole
organism-based or "classical" genetics, molecular genetics, evolutionary
biology and population genetics. It has multiple uses within each of these
contexts. But in the primary sense "genes" are material things that parents
pass to offspring during reproduction and through which they propagate their
biological traits or characteristics. This sense, which is common to all of
the above disciplines, is also the original historical meaning of "gene."

Following the discovery of DNA, and in parallel more recently with the
ascent of biotechnology and projects to sequence the human genome, common
usage of the word in ever more instances has echoed uses in molecular
biology. In the primary, molecular sense, genes are segments of DNA within
chromosomes. In particular, they are the subset of such DNA which cells
transcribe into RNAs and translate, at least in part, into proteins.

Encoders of Proteins

A gene, in this primary sense, specifies a protein by way of its chemical
structure. Any of four types of sequentially linked nucleotides make a DNA
molecule or "strand" (more at DNA). These four represent the genetic
alphabet, while the various possible sequences of three, called codons,
represent the genetic vocabulary. The sequence in which different codons
appear in a gene specifies the amino-acid sequence of a protein, and the
genetic code describes which amino acids relate to which codon. This code is
more or less the same from bacteria to humans; in other words, common to all
cellular life.

Through the proteins they "encode," genes govern the cells in which they
reside. In multicellular organisms they control development of the
individual from the fertilized egg and the day-to-day functions of the cells
that make up tissues and organs. The instrumental roles of their protein
products range from mechanical support of the cell structure to the
transportation and manufacture of other molecules and to the regulation of
other proteins' activities.

Gene Activity and Regulation

Because it is through proteins that genes exert their effects, and because
gene transcripts (which are a prerequisite for protein synthesis) degrade
rapidly, genes are in a sense inactive when they are not actively being
transcribed. Cells appear to regulate the activity of genes primarily by
increasing or decreasing their rate of transcription. Over the short term,
this regulation occurs through the binding or unbinding of proteins known as
transcription factors, which attach to specific "non-coding" DNA sequences
called regulatory elements. Over longer periods of time, genes may be
"silenced" through DNA methylation or changes in the DNA packing of the
chromosomes.

Organization of Genes

In many species of organism, very little of the DNA in the chromosomes
encodes proteins. Rather, the genes are separated by often vast sequences of
so-called junk DNA, and they are sometimes fragmented internally by
"non-coding" sequences called introns, which may be many times longer than
the genes themselves. Introns are removed on the heels of transcription by
splicing. In the primary molecular sense they represent parts of a gene, however

All the genes and intervening DNA together make up the genome of an
organism, which in many species is divided among several chromosomes and
typically present in two or more copies. The location or locus of a gene and
the chromosome on which it is situated is in a sense arbitrary. Genes that
appear together on the chromosomes of one species, such as humans, may
appear on separate chromosomes in another species, such as mice. Two genes
sited close together on a chromosome may encode proteins that figure either
in the same cellular process or in completely unrelated processes. As an
example of the former, many of the genes responsible for human sexual
characteristics reside together on the Y chromosome.

Genetic Variation

Due to rare, spontaneous errors in DNA replication, for example, mutations
and hence variations in the sequence of a gene arise within a species
population. Variants of a single gene are known as alleles, and differences
in alleles may give rise to differences in traits, for example eye color.

In the many species that carry more than one copy of their genome within
each of their somatic cells, these copies are in effect never identical.
With respect to each gene, the copies that an individual possesses are
liable to be distinct alleles, which may act either synergistically or
antagonistically to generate a trait or phenotype (more at genetics, allele).

Genetic Complexity of Traits and Pitfalls in Common Usage

In common speech, "gene" is often used to refer to the hereditary cause of a
trait, disease or condition--as in "the gene for obesity." A biologist, in
contrast, might refer to an allele or a mutation that had been implicated in
or correlated with obesity. Based on the incidence of obesity across parents
and offspring, not to mention common sense, biologists know that not only
genes but factors such as upbringing, culture and the availability of food
decide whether or not a person is obese. To continue with the same example,
it also appears unlikely that variations within a single gene--or single
genetic locus--determine one's genetic predisposition for obesity. These
aspects of inheritance--the interplay between genes and environment, the
influence of many genes--appear to be the norm with regard to many and
perhaps most traits. The term phenotype refers to the characteristics that
result from this interplay, along with the effects of chance in the
migration and division of cells during development.

Regulatory Elements and Heredity

Natural variations within regulatory sequences appear also to underlie many
of the heritable characteristics seen in organisms. The influence of such
variations on the trajectory of evolution through natural selection may be
as large as or larger than variation in sequences that encode proteins.
Thus, though regulatory elements are often distinguished from genes in
molecular biology, in effect they satisfy the shared and historical sense of
the word. Indeed, a breeder or geneticist, in following the inheritance
pattern of a trait, has no immediate way to know whether this pattern arises
from coding sequences or regulatory sequences. Typically, he or she will
simply attribute it to variations within a "gene."

RNA Genes

RNA is always the intermediary between genes and proteins, but for some gene
sequences RNA molecules are actually the end products. These molecules may
be capable of enzymatic function, such the RNAs known as ribozymes,or they
may engage in regulatory base pairing, as in the case of "small interfering
RNAs".

The DNA sequences from which such RNAs are transcribed are known as RNA genes.

More on Molecular Nomenclature and Usage

For various reasons, the relationship between genes and proteins is not so
simple as "one nucleotide sequence-->one amino-acid sequence." For example,
cells may splice the transcripts of a gene in alternate ways to produce not
one but a variety of proteins (alternative splicing). On the chromosome
meanwhile, a single DNA sequence may contain overlapping genes. In addition,
accidents over the course of evolution may lead to the duplication of a gene
to a second locus, where it may fall under different regulation. Though the
two sequences may remain the same or be only slightly altered, they are
typically regarded as separate genes (i.e. not as alleles of the same gene).
The same is true when duplicate sequences appear in different species. Yet,
though the alleles of a gene differ in sequence, nevertheless they are seen
to represent one gene.

Finally, a molecular biologists will often use "gene" to refer to just a
nucleotide sequence of a gene; and at times the sequence of only its coding
regions without the introns. This more abstract sense of gene underlies the
sense of genes as information. It also means that, by way of its sequence,
not only DNA but RNA may be said either to be to carry a gene (see below).

RNAs are Genes in Some Viruses

Although all cell-based organisms carry their genes and transmit them to
offspring as DNA, many of the viruses that parasitize and reproduce in them
carry only RNA. Because they use RNA, their cellular hosts may synthesize
their proteins as soon as they are infected and without the delay in waiting
for transcription. RNA "retroviruses", on the other hand, require
"retrotranscription" of their genome from RNA into DNA.

"Selfish" Gene

The genes that exist today are those that have reproduced successfully in
the past. This is the basis of the selfish gene view, publicised by Richard
Dawkins. He points out in his book, The Selfish Gene, that all DNA exists
with no other purpose than to propagate itself, even at the expense of the
host organism's welfare. The possibly disappointing answer to the question
"what is the meaning of life?" may be "the survival and perpetuation of
ribonucleic acids and their associated proteins".

History

The existence of genes was first suggested by Gregor Mendel, who studied
inheritance in pea plants and hypothesized a factor that conveys traits from
parent to offspring. Although he did not use the term "gene", he explained
his results in terms of inherited characteristics. Mendel was also the first
to hypothesize independent assortment, the distinction between dominant and
recessive traits, the distinction between a heterozygote and homozygote, and
the difference between what would later be described as genotype and
phenotype.

Wilhelm Johannsen coined "gene" in 1909, based on the work of Gregor Mendel.

Typical numbers of genes in an organism:

The following table gives typical numbers of genes and genome size for some
organisms. Estimates of the number of genes in an organism are somewhat
controversial, because it is only possible to discover a gene, and no
techniques currently exist to prove that a DNA sequence contains no gene.
Nonetheless, estimates are made based on current knowledge.

       organism        # of genes  base pairs

 Plants                <50000     <1011

 Humans                35000      3x109

 Flies                 12000      1.6x108

 Fungi                 6000       1.3x107

 Bacteria              500-6000   5*105-107

 Mycoplasma genitalium 500        580.000
 DNA viruses           10-300     5000-200.000
 RNA viruses           1-25       1000-23.000
 Viroids               0-1        ~500
 Prions                0          ;0

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