Basic Genetics

The first place we should start for understanding basic genetics is with the word "gene" itself. This page is just meant to be a short review of some fundamental concepts for those who have not had the background, or it has been a long time and you're a little rusty.

What is a gene?

A gene is a segment of DNA (deoxyribonucleic acid) that codes for a protein or ribonucleic acid (RNA). Early geneticist (e.g. Gregor Mendel) identified many traits, such as wrinkled vs smooth peas, eye color in fruit flies, that were determined by various genes. Later with the advent of biochemical and finally molecular techniques, we came to understand that many genes code for protein while others code for RNA. It is the proteins that determine the traits studied my early geneticist. In the ensuing decades, we have come to understand that genes can be very complicated.

Based on the Human Genome Project which has sequenced the DNA of humans, we now know that the genome contains some 30,000 or so genes. DNA sequences of many other complex organism from fruitflies to mammals has lead to similar numbers of genes.

Interestingly, we have enough DNA to code for a million or more genes. What is all this extra DNA doing? (below)

Gene versus locus

As our understanding of genetics and genes grew, the word "gene" has come to mean a number of different concepts and can be very confusing. It is used interchangeably to indicate a particular gene or for its variants, called alleles (discussed below). Therefore, we use the word locus for what most of us normally think of as a gene. Locus is derived from the idea that a given gene has a specific location on a specific chromosome.

Chromosomes

Genes or loci (plural for locus) "live" (are located at, reside) on a specific chromosome. Humans, for example, have 23 different chromosomes. For each or these 23 chromosomes, we get one from each of our parents, that is, one from our dad and one from our mom, for a total of 2 x 23=46 chromosomes.

For example, let us take hemoglobin? We all actually have three hemoglobin (Hb) genes: alpha-Hb, Beta-Hb, and fetal-Hb. The first two are active, meaning expressed, after we are born. The last, in utero (while we are developing in the uterus) and phases out after birth. The sickle cell anemia gene is an allele of the alph-Hb gene.

Any given individual then could have up to six different "genes" for hemoglobin, i.e., two alleles for each of the three genes (2 x 3=6). But wait, it gets more complicated... (Did I hear a sigh?)

Genes in Populations

In any given population, there can be several different alleles for any particular gene (locus). A population is a group of local individuals of the same species. The town you live in would be an example of a population. The tribe used to be a population. Not many tribes around these days, however.

In a population, let us say at the alpha-Hb locus, there might be two, three, or more different alleles for that locus. We then talk of the relative frequency of the alleles. The sum of the relative frequencies will always equal to one. Lets go back to our alpha-Hb locus and designate three different alleles as 1, 2, and 3. In our hypothetical population, let us say the frequency of the alpha-Hb-1 allele is .80, that of the alpha-Hb-2 allele is .15, and of the alpha-Hb-3 allele is .05. Note that the relative frequencies add up to 1.

Genes in individuals

Now let us look at genes in individuals again...

Homozygous and heterozygous

If an individual contains the same allele at a locus, s/he is referred to as being homozygous. If he has two different alleles at a specific locus, he is referred to as being heterozygous.

Phenotype versus genotype

An individual's phenotype, to paraphrase an old Flip Wilson phrase, is what you see. It's genotype is what you get. "Genotype" refers to the alleles the individual carries. In more lay lingo, the phenotype may be a "carrier" for a given allele.

Dominance and recessiveness

Some alleles are said to be dominant or recessive to other allele(s) at a specific locus. For example, in fruitflies, the red eye color allele (+) is dominant to the white eye color allele (w). What this means is that in heterozygotes that carry both the wild type and white alleles (i.e. +/w), the phenotype of the individual will be red eye. While he is a carrier for the white eye allele, you cannot see the white eye phenotype. Consequently, both the +/+ and +/w phenotypes will have the red eye color. Only the w/w individuals will show the white eye phenotype.

At the biochemical and molecular level you do not see dominance and recessiveness. Proteins from both alleles are equally expressed or produced. Thus, at the protein/RNA level, the alleles are said to be "co-dominate", that is both traits (proteins/RNA's) are observed.

OK, lets talk a little more about what genes do...

What genes do

Genes carry our genetic information. As said above, genes code for proteins or RNA. All genes code for RNA, but not all genes code for proteins. First, let us look at a basic human cell (highly simplyfied):Cell

Surrounding the cell is the cell membrane. Inside this is the cytoplasm, a complexly organized matrix containing different cell organelles (e.g. mitochondria, ribosomes, Golgi complexes, lysosomes, endoplasmic reticulum, etc). Then comes the nucleus, which is delineated from the cytoplasm by the nuclear membrane (not labeled). Inside the nucleus we find the chromosomes on which are located the genes.

Transcription

A RNA copy of the gene is first made from one of the DNA strands. This process is called transcription and is diagrammed below. It takes place in the cell's nucleus.

transcription

The DNA double helix is first opened: the two DNA strands that make of the double helix temporarily separate in the region of the gene.

A RNA copy is then made of one of the strands. This is a specific strand, called the "sense" strand. (The other strand is called? You guessed it, the "non-sense" strand.)

After the RNA copy is made, it may require additional processing. Eventually, if it is a gene coding for a protein, the RNA is moved out of the nucleus and into the cell's cytoplasm. If it is a RNA that carries the code for a protein, it is referred to messenger RNA, abbreviated, mRNA.

If the gene codes only for RNA, i.e. RNA that is does not code for a protein, it may stay in the nucleus or move out into the cytoplasm. Some processing is still required to make it into its final RNA product. Examples of this type of RNA are ribosomal RNA that make up part of the ribosomes (below) and transfer RNA (tRNA). Both of these play roles in protein syntheis in terms of translation...

Translation

The protein coding mRNA is moved out of the nucleus into the cytoplasm (cell plasm). There in the cytoplasm the mRNA joins up with ribosomes, which are the translation machines of the cell. The ribosomes/mRNA complex then call forth specific amino acids encoded for by the mRNA and join these together to form the specific protein. This process is illustrated below:

translation

Often the proteins that are produced will require further processing before the end up in their final form and job. This in itself is a very complex process.

Other important concepts...

Other relevant areas for a modern understanding of genes discussed on additional pages are:

Genes on Chromosomes

Chromosomes are not just a bunch of genes linked together on a chromosome. This page describes a little of what we know about how genes are organized on the chromosome.

Repetitive DNA and Extrasensory Perception

One of the important findings from the Human Genome Project is that there is much more DNA in our cells than needed to code for the 30,000 or so genes we have. What is all this extra DNA doing? Much of it is called repetitive DNA. Repetitive DNA is short sequences of DNA that are repeated over and over again from a few thousands to millions of time. Again, what is this DNA doing. It is too metabolically expensive to maintain all this "junk" DNA if it is not doing something. Natural selection would have weeded it out long ago.

Gene Regulation

Genes are not just sitting there being transcribed and translated (a.k.a expressed). They are highly regulated. Think of a water facet as analogy, with the facet being the gene and the water coming out, the protein (or RNA). The facet can be turned all the way off, all the way on, or somewhere in between. Genes operate more like this facet analogy.

Split Genes and RNA Processing

Most, if not all of genes, are actually split into pieces. There will be a segment of the gene that contains sequences that code for the protein or RNA flanked by non-coding sequences. These non-coding, intervening sequences have to be spliced out or removed before an actual protein or functional RNA can be made from them.

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