1. Mutation and Miscellany
Updated Summer by J. D. Hendrix

2. Mutations: Definitions
Lethal mutation: results in death of the cell, and therefore cannot be propagated or studied
Conditional mutation: One that is expressed only under certain environmental conditions; for example, a temperature-sensitive mutation
Biochemical mutations: result in change in a biochemical pathway of the cell; for example, an auxotrophic mutation
Spontaneous mutation: one that arises spontaneously due to error during DNA replication
Induced mutation: one that has been caused by damage resulting from chemical or radiation treatment (mutagen)

3. Mutations: Definitions
Point mutations exchange a single nucleotide for another
These changes are classified as transitions or transversions. Most common is the transition that exchanges a purine for a purine (A ↔ G) or a pyrimidine for a pyrimidine, (C ↔ T). Less common is a transversion, which exchanges a purine for a pyrimidine or a pyrimidine for a purine (C/T ↔ A/G). An example of a transversion is the conversion of adenine (A) into a cytosine (C).
Silent mutations, which code for the same amino acid.
Missense mutations, which code for a different amino acid.
Nonsense mutations, which code for a stop and can truncate the protein.

4. Mutations: Definitions
A frameshift mutation is a mutation caused by insertion or deletion of a number of nucleotides that is not evenly divisible by three from a DNA sequence. Due to the triplet nature of gene expression by codons, the insertion or deletion can disrupt the reading frame, or the grouping of the codons, resulting in a completely different translation from the original
An in-frame mutation is any insertion or deletion that is evenly divisible by three
A nonsense mutation is a point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA, and possibly a truncated, and often nonfunctional protein product.
Missense mutations or nonsynonymous mutations are types of point mutations where a single nucleotide is changed to cause substitution of a different amino acid
A neutral mutation is a mutation that occurs in an amino acid codon that results in the use of a different, but chemically similar, amino acid. The similarity between the two is enough that little or no change is often rendered in the protein. For example, a change from AAA to AGA will encode arginine, a chemically similar molecule to the intended lysine.
Silent mutations are mutations that do not result in a change to the amino acid sequence of a protein

5. Mutations: Mechanisms
Mechanisms of Induced Mutation
Base analogs
A chemical similar in structure to one of the bases and can substitute for it but doesn’t base pair normally
For example, 5-bromouracil substitutes for thymine, but it frequently pairs with a G instead of A
Specific Mispairing
When a mutagen changes a base’s structure and thereby alters its base pairing
For example: nitrosoguanidine adds a methyl group to guanine, causing it to pair with T instead of C.

6. Mutations: Mechanisms
Mechanisms of Induced Mutation (cont.)
Intercalating agents
Examples include acridine orange and ethidium bromide
Flat, planar, aromatic molecules that can fit between the stacked bases (intercalate) in the center of a DNA double helix and distort its geometry
The distortion somehow induces single nucleotide insertions or deletions

7. Mutations: Mechanisms
Mechanisms of Induced Mutation (cont.)
Bypass of replication
Chemical change or damage to bases is so severe that the bases can no longer base pair at all, and cannot serve as a template
Example: formation of thymine dimers by UV irradiation; these cannot hydrogen bond at all
Normally this would be lethal, but there are repair mechanisms that can bypass the damaged template, although many of these repair mechanisms are error-prone so generate a high frequency of mutations

8. Cis- and Trans-acting regulatory elements
Not to be confused with cis and trans linkage
Cis-regulatory elements (CREs) are regions of non-coding DNA which regulate the transcription of nearby genes. The Latin prefix cis translates to “on this side”. CREs are found in the vicinity of the gene, or genes, they regulate. CREs typically regulate gene transcription by functioning as binding sites for transcription factors. Example: the lac o gene (lac operator)
A trans-acting element is usually a DNA sequence that contains a gene. This gene codes for a protein (or microRNA or other diffusible molecule) that will be used in the regulation of another target gene.[1] The trans-acting gene may be on the same chromosome as the target gene, but the activity is via the intermediary protein or RNA that it encodes. Cis-acting elements, on the other hand, do not code for protein or RNA. Both the trans-acting gene, and the protein/RNA that it encodes are said to "act in trans" on the target gene. Example: lac i gene (lac repressor gene)

9. The Histone Code
The histone code is a hypothesis that the transcription of genetic information encoded in DNA is in part regulated by chemical modifications to histone proteins, primarily on their unstructured ends.
Together with similar modifications such as DNA methylation it is part of the epigenetic code.
Histones associate with DNA to form nucleosomes, which themselves bundle to form chromatin fibers, which in turn make up the more familiar chromosome.
Histones are globular proteins with a flexible N-terminus (taken to be the tail) that protrudes from the nucleosome. Many of the histone tail modifications correlate very well to chromatin structure and both histone modification state and chromatin structure correlate well to gene expression levels.
The critical concept of the histone code hypothesis is that the histone modifications serve to recruit other proteins by specific recognition of the modified histone via protein domains specialized for such purposes, rather than through simply stabilizing or destabilizing the interaction between histone and the underlying DNA.
These recruited proteins then act to alter chromatin structure actively or to promote transcription.
Modifications to histones include methylation, acetylation, phosphorylation, and ubiquination