7 minute read
Genes
Recombination allows chromosomes to exchange their genetic information, producing new combinations of genes, which is efficient for the natural selection process. It allows for new proteins to evolve, some of which will be evolutionarily advantageous, while some will not. The most common type of crossover is called a homologous crossover, where two very similar chromosomal segments exchange information. In general, non-homologous recombination is not evolutionarily advantageous and usually damages the cell or causes genetic abnormalities.
The enzymes that do the recombination process are called recombinases, of which there are several types. They break a double strand by using an endonuclease and join the broken strand to another strand of DNA. Only strands that have similar polarity will exchange during the recombination process. There are two types of cleavage reactions, one that cleaves both strands of DNA, while another that cleaves just one strand of the DNA. Either will allow for genetic diversity that can be advantageous to the offspring.
Advertisement
The DNA genome contains all of the genetic information that allows the cell and the organism to survive and reproduce. It is believed that the earliest forms of life just used RNA and didn’t involve DNA. Eventually, organisms were based on DNA and the RNA was responsible for making the proteins in the ribosomes. No one knows how or where the original base pairs came from or how they were created to make complex forms of life. All of this happened billions of years ago and DNA fragments don’t last very long so they can’t be isolated from fossils.
A gene is a segment or region of DNA that is made of up nucleotides that together have the potential to create a protein used by the cell. Genes make up the genotype of the cell and are ultimately responsible for the physical features or “phenotype” of the organism. Genes represent the molecular units of heredity. Most biological features are the result of multiple genes acting together but there are some genes that act alone to create a certain protein or feature in an organism. Some genetic traits are easily seen, like hair and eye color, the number of limbs, and the color of the skin. Other genes code for things that aren’t recognizable, like those for intracellular enzymes and those for a person’s blood type.
Genes can become mutated leading to different alleles or variations of the gene. In the population, these different alleles account for a genetic variation, natural selection, and, in many cases, the survival of the fittest—which are those organisms that have the very best alleles that allow for some improvement in the way the organism functions.
Genes are usually closely connected to their regulatory regions but this just doesn’t have to be the case, as was relatively recently discovered. Coding regions related to a specific gene can be separated into several exons that are spliced together in the coding process. Some viruses will store their entire genome in a segment or several segments of RNA instead of DNA and some
products of the genetic code will encode for RNA that is regulatory in nature and doesn’t go to any type of protein.
The vast majority of genes in nature come from strands of polynucleotides that make up DNA. As mentioned, DNA is a long-chained molecule made from many connected subunits of four different nucleotide bases—adenine, thymine, guanine, and cytosine. The molecule is a double helix with a phosphate-sugar backbone that spirals around the outside with the bases pointing inward, pairing in a specific way with one another using hydrogen bonding.
The two strands of DNA are always complementary to one another so they are a perfect match, with adenine and thymine pairing using two hydrogen bonds, and guanine and cytosine pairing with three hydrogen bonds. There is directionality to both the DNA strands and the genes that they make. The transcription of a gene always goes in just one direction. Transcription always occurs in the 5’-3’ direction because new nucleotides are always added by a dehydrating reaction that uses the hydroxyl end at the 3’ end attracting a new nucleotide.
The gene first gets expressed so it is available for the transcription by RNA. The RNA is attracted to a promotor region and RNA polymerase is attached, allowing the RNA to be built base-by-base into a whole RNA molecule that may need to be further modified before using. The gene is read in three-base increments called codons that code for a specific protein or code for a specific thing to happen to the transcription process—as is true of a stop codon. The genetic code is specific to an organism but, surprisingly, it is very similar among all known organisms despite marked differences in phenotype.
While the total complement of all of the genes in an organism is its genome, it can be stored in more than one chromosome. Humans have 46 chromosomes that contain the entire genome. There are hundreds of active genes on each chromosome and each is located at a specific locus on the gene. Every person has his or her own allele of a specific gene that makes them a unique phenotypical organism.
Histones are proteins that allow long chromosomes to be compacted into the nucleus without difficulty. The histone plus its DNA is called chromatin. The manner in which a gene is connected to a histone protein determines how accessible it is to become transcribed. There are separate sections in a given chromosome, such as its centromere (important in replication and cell division), its telomere (which caps its end so that it doesn’t have degradation at the end of the chromosome), and replication regions (which help in the replication process). Replication regions are where the DNA separates in initially to begin the process of making two daughter chromosomes. Each time a chromosome is copied, the length of its telomere shortens and, when it is too short, the cell does not survive—which is important in cellular senescence.
Prokaryotes do not have chromosomes or a nucleus but just have one large, circular chromosome. Some eukaryotic organelles have circular genetic material. Plasmids are small circles of DNA made by viruses that can get transferred from cell to cell or from species to species by means of horizontal gene transfer. Prokaryotes have most of their genetic material coded for into proteins but eukaryotes do not. Most of eukaryotic DNA has no known function and is just junk DNA. This DNA may have a function that we just don’t know about yet.
The structure of a gene consists of many different elements of which the part that codes for the actual protein is often a very small aspect of the gene. These include untranscribed regions and regions that get transcribed but don’t go into the making of a protein. All genes have a regulatory sequence that controls its expression. A promoter sequence is necessary to bind transcription factors and RNA polymerase to start the process of gene transcription. Some genes have strong promoter regions that tightly bind RNA polymerase, while others have weak promoter regions.
Regulator regions can be far or near to the gene they regulate. They act by binding to transcription factors that cause the DNA to loop so that the bound transcription factor, RNA polymerase, and the coded region come close together. Then there are enhancers that increase the transcription rate by binding to an activator protein that helps to recruit the RNA polymerase to the promoter site. There are silencer proteins and repressor proteins that make the DNA less accessible to the RNA polymerase.
The pre-mRNA that gets transcribed from the gene contains regions that are untranslated at both ends. They contain a ribosome binding site, a terminator codon, a start codon, and a stop codon. There are also open reading frames that contain untranslated introns that get removed before the exons are spliced together to make exons, which are translated into proteins. There are certain reading sequences on the RNA that tell where to remove an intron and splice back together the exons to make the mature mRNA molecule.
Deciding which section of the DNA constitutes the “gene” is not easy. There are regulatory regions that may be far from the transcription region but that are technically part of the gene. The introns in a gene may be far larger than the exons in a gene. Regulatory regions can operate from different chromosomes, which make it even more difficult to identify what constitutes the “gene”. In addition, there is no such thing as a one gene-one protein situation. A given gene can code for different proteins depending on how things get spliced into and out of either the RNA or the protein.
Each gene has a start codon and three stop codons that define when to start and stop the protein coding process. Because there are more codons than amino acids, an amino acid can be created
