chapter 19 genetics

silent mutation

do not alter amino acid sequence even though the base sequence changed

missense mutation

base substitutions that cause one amino acid change

sometimes cause inhibitory effects sometimes dont

nonsense mutations

base substitutions that involve a change from a codon that specifies an amino acid to a stop codon

affects many amino acids because many are lost due to truncation

likely inhibitory effect

frameshift mutation

involve the addition or deletion of nucleotides that is not divisible by 3

changes the reading frame

results in a completely diffreent amino acid sequence downstream from the mutation

likely to cause negative effects

mutations outside of the coding sequence

promotor mutations: may increase or decrease the rate of transcription

enhancer/operator site mutations: may disrupt the ability of the gene to be properly regulated

5’-UTR/3’-UTR: may alter the ability of mRNA to be translated; may alter mRNA stability

splice recognition site mutation: may alter the ability of pre-mRNA to be properly spliced

position effect

when a gene’s expression is altered when it is moved to a new chromosomal location

a gene may be moved next to a regulatory sequence for a different gene such as an enhancer

gene may be moved to a heterochromatic region where its expression may be turned off

germ-line vs somatic mutation

A germ-line mutation can occur directly in a sperm or egg cell, or it can occur in a precursor cell that produces gametes. If a mutant gamete participates in fertilization, all cells of the resulting offspring will contain the mutation. The mutation may be passed along to future generations of offspring.

A somatic mutation can occur in a single embryonic cell and cause a portion of the adult body to contatin the mutation. The size of the affected region depends on the timing of the mutation. The earlier the mutation occurs during development, the larger the region. A somatic mutation cannot be passed from parent to offspring via sperm or egg cells.

spontaneous vs induced mutations

spontaneous mutations are changed in DNA structure that result from natural biological or chemical process: abnormal recombination or segregation, errors in DNA replication, ROS, transposable elements, depurinations, deamination, tautomeric shifts

Induced mutations are caused by environmental agents: chemical agents, physical agenrs (x rays, UV light)

depurination

involves the removal of a purine (adenine or guanine)

deamination

removes the amino group from the cytosine base, producing uracil

5-methyl cytosines are spontaneuous mutation hotspots because when they are deaminated it gets recognized as thymine 

Oxidation

reactive oxygen species are products of oxygen metabolism and can cause oxidative DNA damage if they accumulate. DNA bases are very susceptible to oxidation, especially guanine

mechanism for trinucleotide repeat expansion

1. DNA replication proceeds just past the TNRE

2. the hairpin forms in the triplet repeat and causes DNA polymerase to slip off the template strand

3. DNA polymerase essentially backs up and hops back onto the DNA strand and resumes DNA replication from the end of the hairpin. When this occurs, DNA polymerase is synthesizing most of the hairpin region twine

4. Hairpins within DNA are short lived so they can spread out, which leaves a gap in the opposite strand

5. The gap is later filled in by DNA polymerase and ligase. The end result is that the TNRE has become longer

Mutagen

Mutagens are agents known to alter the structure of DNA and thereby cause mutations

Chemical mutagens: nitrous acid, nitrogen mustard, ethyl methanesulfonate, proflavin, 5-bromouracil, and 2-aminopurine

Physical mutagens include X rays and UV light and beta particles

Base modifiers

Base modifiers are mutagens that act by covalently modifying the structure of the bases. When the altered DNA replicated, mutations can occur because these modified bases pair differently than the original bases.

Intercalating agents

Intercalating agents are mutagens that exert their effects by directly interfering with the DNA replication process. These mutagens may insert themself between base pairs and distort the helical structure, When DNA containing these mutagens is replicated, single-nucleotide additions and/or deletions can occur in the newly made daughter strands, causing frameshift mutations

Base analogs

Base analogs are mutagens that become incorporated into daughter strands during DNA replication. These mutagens act as other bases that can change base pairing in the DNA and lead to mutations from this change.

ionizing radiation (X rays)

short wavelength and high energy

can penetrate deeply into biological tissue

produces chemically reactive molecules known as free radicals that can cause base deletions, single strnad and double strand breaks in the DNA backbone, crosslinking, and the oxidation of abses

non-iodizing radiation (UV light)

less energy

penetrates only the surface of an organism, such as the skin

energy in UV light causes the formation of thymine dimers- adjacent thymine bases that have become covalently linked. Thymine dimers do not base pair properly during DNA replication and therefore can produce a mutation when the DNA strand is replicated

the ames test

1. the suspected mutagen is mixed with a rat liver extract and a strain of S typhimurium that cannot synthesize histidine. A mutagen may require activation by cellular enzymes, which are provided by the rat liver enzymes which are provided by the rat liver extrace. This step improves the ability of the test ot identify agents that may cause mutation in mammals

2. after the incubation period, a large number of bacteria are then plated on a growth medium that does not contain histidine

3. the bacterial cells of this salmonella strain are not expected the grow on these plates. however, if a mutation has occured that allows a bacterial cell to synthesize histidine, such a cell can divide many times and form a visible bacterial colony composed of millions of cells

4. researchers compare the mutation rate in the presence and absence of the suspected mutagen

general features of DNA repair systems

generally, first, one or more proteins in the DAN repair system detect an irregularity in DNA structure, Next, the abnormality is removed by the action of DNA repair enzymes. Finally, normal DNA is synthesize via DNA replication enzymes.

base excision repair and nucleotide excision repair: an abnormal base or nucleotide is first recognized and removed from the DNA, and a segment of DNA in this region is excied. Then the complemntary DNA strand is used as a tempalte to synthesize a normal DNA strand

Nucleotide excision repair (NER)

can repair many different type of DNA damage, including thymine dimers, chemically modified bases, missing bases, and certain types of crosslinks

several nucleotides in the damaged strand are removed from the DAN and the intact strand is used as a template for resynthesis of a normal complementary strand

four key proteins UvrA, UvrB, UvrC, UvrD, plus DNA polymerase and ligase.

1. a protein complex containing two UvrA and one UvrB molecule tracks along the DNA in search of damaged DNA, Such DNA has a distorted double helix which is detected

2. When a damaged segment is identified, the two UvrA proteins are released and UvrC binds to the site

3. The UvrC protein makes cuts in the damaged strand on both stides of the damaged site. Typically the damaged strand is cut 8 nucleotides from the 5’ end of the damaged site and 4-5 nucleotides away from the 3’ end.

4. After this process, UvrD, which is a helicase, recognizes the region and spearates the two strands of DNA. This releases a short DNA segment that contains the damaged region and UvrB and UvrC are also released

5. Following the excision of the damaged DNA, DNA polymerase fills in the gap, using the undamaged strand as a template. Finally, DNA ligase makes the covalent connection between the newly made DNAand the orignal DNA strand

Homologous recombination repair

occurs when homologous DNA strands, usually from a sister chromatid are used to repair a double stranded break in the other sister chromatid.

only available during S and G2 phases of the cell cycle.

1. A double stranded break occurs in the DNA

2. This DSB is processed by the digesting of short segments of the DNA strand at the break site

3. This processing event is followed by the exchange of DNA strands between the broken and unbroken sister chromatids

4. the unbroken strands are then used as templates to synthesize DAN in the region where the break occurred

5. finally, the crisscrossed strands are resolved, which means they are broken and then rejoined in a way that produces separate chromatids

Nonhomologous end joining

the brokwn ends of DNA are simply pieced back together

can occur at any stage of the cell cycle but causes a deletion

1. a double stranded break occurs

2. the DSB is recognized by end-binding proteins. These proteins are then recognized by additional proteins that form a crossbridge that prevent the two ends from drifting apart

3. additional proteins are recruited to the region and may process the ends of the broken chromosome by digesting particular DNA strnads. This processing mayy result in the deletion of a small amount of genetic material from the region

4. finally any gaps are filled in by DNA polymerase and the DNA ends are ligated together

sister chromatid exchange and homologous recombination

when recombination occurs between sister chromatids, tjis is called sister chromatid exchange. Because sister chromatids are genetically identical, SCE does not produce a new combination of alleles.

crossing over may occur between homologous chromosomes during meiosis in which it produces new combinations of alleles in the resulting chromosomes.

Holliday model vs double-stranded break model

holliday model says that two homologous chromatids are aligned with each other and a break or nick occurs at identical sites in one strand of each of the two homologus chromatids

the double-strand break model suggests that a double-strand break in one chromatid initiates the recombination process.