Genetic and Cellular Mechanisms and Variation

I am proposing this thread to focus on basic genetic and cellular mechanisms and how they produce variation. The emphasis will be on molecular processes rather than population systems and as such will not, for the most part, deal with common evolutionary subjects such as genetic drift, natural selection and the fossil record. Furthermore, unless otherwise specified, discussion will center on eukaryotic cell biology rather than prokaryotic, since I suspect more people are interested in the evolutionary processes of metazoans than they are of bacteria.This is a substantial subject and I don’t expect to get through this material quickly. My goal will be to make at least one significant post every week unless there is significant discussion regarding a previous post. As I thought about how to begin this series, I decided I would start with the assumption that most people have an elementary knowledge of genetics, such as the structure of DNA, so I am going to skip the most rudimentary topics.As for my credentials, I am not a professional as such yet. I have a B.A. in Environmental Biology and am anxiously awaiting my acceptance letter from MSU into their Plant Pathology program. I did very well in both my undergrad Genetics and Cell Biology courses (both taught by the most difficult professor in the NS department). I am currently teaching a Microbiology lab and a Human Physiology lab as an adjunct instructor.My primary reference source will be Lodish, et. al. (2013). Molecular Cell Biology 7th edition, W.H. Freeman and Co. Any material that should be referenced will be considered to have come from this source. Material from other sources will be referenced appropriately. Credits for images can be found by using the peek button unless otherwise noted.While questions, comments and even discussions about the topics being covered are certainly welcome, I would like this thread to be primarily informational (I am reluctant to call it a course though) and would ask that debates, especially regarding EvC issues be addressed in separate threads.Biological Evolution, please.HBD

Chromosome refers to the basic organizational structure which eukaryotic cells package their DNA. Although how the chromosome is arranged does have an effect on gene expression and regulation, there is nothing particularly special about how the DNA is packaged that relates to organismal complexity or size.More specifically, the term chromosome refers to the highly condensed structures that are visible with a light microscope during cell division. In non-dividing cells, the DNA is more diffuse and spread throughout the nucleus. If the DNA strands in a human cell were stretched out end to end, they would be about 1.2 meters long! Obviously, the cell needs a way to package these long strands in order to fit them within the confines of a cell. It also needs to package it in such a way as to be readily accessible for transcription, replication, and repair, to prevent tangling and knotting, and to preserve integrity during cell division. The first step is to form nucleosomes in which the DNA strand is wrapped around a complex of histone proteins. This structure has the appearance of beads on a string with nucleosomes separated by free DNA called linker DNA. Nucleosomes consist of about 150 bp of DNA wrapped around the histone complex about one and two-thirds times. The length of the linker DNA varies from 10 to 90 bp depending on the organism and cell type. This complex of histones and DNA is referred to as chromatin and is the primary organizational structure of genes undergoing active transcription.Remarkably, the general structure of chromatin is highly similar in the cells of all eukaryotes, including plants, animals and fungi. The amino acid sequences of the histone proteins are highly conserved, even between distantly related species. For example, the histone H3 varies by only one amino acid between the sea urchin and calf thymus and the H3 histone from the garden pea differs from calf thymus by only four amino acids.The chromatin in regions that are not undergoing active transcription or replication form a structure know as a 30nm fiber. In this structure, another histone protein (H1) associates with the nucleosomes and wraps the strands of nucleosomes into a tight, left-handed double helix with the nucleosomes stacking on top of each other. The folding of eukaryotic chromatin during cell division is not well understood, but generally the 30nm fiber loops into a 300nm loop domain and again loops into the 700nm fiber of the metaphase chromatid.
Source: DNA Learning Center
Only about 1.5% of human DNA encodes functional proteins or RNA molecules. The remainder is mostly spacer DNA between genes and introns within genes. Below is a brief description of the major type of DNA sequences.
Major types of DNA sequences
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Single-copy genes
Gene families
Tandemly repeated genes
Introns
Simple-sequence DNA
Transposable DNA elements
Spacer DNA(Lodish, p. 224)
Genes are the primary unit of inheritance. It is common to think of a gene as a segment of DNA that encodes a protein, but genes actually include much more than simple protein coding sequences. A gene is the entire nucleic acid sequence that is necessary for the synthesis of a functional gene product, which could be a polypeptide or an RNA molecule. Therefore, a gene includes all of the DNA sequences of the introns, exons, promoters, enhancers, and transcription-control factors associated with that gene product. Single-copy genes appear only once within the genome. Gene families are a set of genes that appear to have arisen by duplication and have subsequently diverged due to small changes in nucleotide sequences. Tandemly repeated genes are multiple copies of identical or nearly identical genes most often occurring one after the other in a head-to-tail fashion. These multiple copies are needed to meet the high demand of some gene products. Introns are part of the primary transcription unit but are spliced out during mRNA processing and not included in the mature mRNA product. Most introns are broken down and recycled but some are known to form usable RNA products. Simple-sequence DNA, also called satellite DNA, is short, tandemly repeated sequences that are found at centromeres and telomeres as well as at other locations that are not transcribed. Transposable DNA element is a DNA sequence that is not present in the same chromosome position of all members of a species, but can move to a new position by a cut-n-paste method. Also called a mobile DNA element or interspersed repeat. You may have heard this referred to as a "jumping gene." Spacer DNA is unclassified DNA sequences that lie between transcription units. It also is found in transcription-control regions and helps regulate transcription from distant promoters or enhancers. Some spacer sequences are highly conserved indicating they may have a significant function, such as contributing to the structural organization of chromosomes. Roughly 25% of human DNA is in this category of unclassified spacers.This post provides a basic overview of how eukaryotic chromosomes are organized. We will discuss these various types of DNA sequences, how mutations can accumulate in them and how we can use those mutations for identification as this thread progresses.HBD

Thread copied to the Genetic and Cellular Mechanisms and Variation thread in the Biological Evolution forum, this copy of the thread has been closed.