BIO 311 - Genetics Exam 2

mutation

any permanent change in the nucleotide sequence of a strand of DNA —> increases diversity

*can be in coding and noncoding regions

benefits of mutations

• allows development of new genes

• new species

• adaptation to new environments

point mutations

mutations that only are only caused by one base pairing

silent point mutation

change in DNA result in NO CHANGE in amino acids

missense point mutation

change in DNA results in change in ONE amino acid

neutral mutation

missense mutation that does not affect phenotype

nonsense point mutation

change in DNA results in an early “stop” codon causing a shortened polypeptide/protein lacking proper function

Frameshift mutation

a mutation that changes the reading frame of the DNA sequence —> IDELS

insertion frameshift mutation

an extra nucleotide is added

deletion frameshift mutation

a nucleotide is missing

somatic mutation

mutations that affect non-sex cells (*only in sexually reproducing multicellular organisms)

generally not heritable unless organism reproduces through mitosis (asexually)

germline mutation

mutations that affect gametes —> heritable

(*only in sexually reproducing multicellular organisms)

germline cells

• spermatogonia and oogonia

• primary spermatocytes and oocytes

• secondary spermatocytes and oocytes

• spermatids

• ova and sperm

effects of somatic mutations

*very common —> ~1 mutation per day

• cell phenotype is unchanged

• non-functioning

• targeted for apoptosis

somatic mutations and cancer

• somatic mutations tend to lead to cancer under the right conditions

• in some cases, like hemimegaloencephaly, this enlargement is non-cancerous

  • but can still cause changes in behavior or nutrient intake to brain

chromosome mutations

large scale mutations that affect the structure of an entire chromosome

gene mutations

small-scale mutations affecting individual genes

duplication (chromosomal mutations)

when a region of a chromosome is copied twice over into a chromosome

inversion (chromosomal mutations)

when a region of a chromosome is flipped upside down and reinserted into the chromosome

deletion

when a portion from chromosome is missing

insertion

when a portion of one chromosome is inserted into another chromosome

translocation

when two pieces of two different chromosome switch places

base substitution

another term for point mutation; can be classified based on their effect on the protein (silent, missense, nonsense) or mechanism

transition (base substitution mechanism)

substituting a purine (A-G) for another purine or pyrimidine (C-T) for another pyrimidine (*more common)

*because A-G and C-T are a similar structure, mistakes are more common

transversion (base substitution mechanism)

substituting a purine for a pyrimidine and vise verse (*less common)

reading frames

6 total, 3 for each strand of DNA

• can start at any of the 3 sports in the first codon

• the correct reading frame is the one that results in the longest uninterrupted reading frame

closed reading frames

reading frames that are not used for gene expression — usually marked by interspersed stop codons

open reading frames (orfs)

the correct reading frame that has the promoter region in front of it

expanded nucleotide repeats

mutations that result from duplicated repeat regions, often within genes (typically in non-coding regions but can cause mutations in coding regions)

• ex: CAG (micro-satellite sequences) repeated mistakenly

• can affect phenotype if found within a gene or even outside the gene —> can also be caused by toxic RNA transcript

genetic diseases caused by expanding nucleotide repeats

• spinal and bulbar muscular atrophy (CAG)

• fragile X syndrome (CGG)

• Huntington disease (CAG)

Fragile-X syndrome

results from tandem repeats (CGG) in the X-chromosome

• more common in males (heritable)

• symptoms are mostly cognitive (impairment, delayed development, learning disability)

• CGG repeats create CpG islands that are more prone to DNA methylation —> silencing of the gene —> lose level of development

strand slippage

misalignment of the sequences; occurs during DNA synthesis

• slips back and recopies DNA again

forward mutation

mutation that affect a wild-type (normal) phenotype is called

reverse mutation

reversal of a forward mutation back to wild type (normal)

loss of function

mutations result from missing or nonfunctioning protein product

GW2 gene (growth width) - loss of function

normal function: stops growth of the plant

• loss of function: allow plant to continue growing

gain of function

results in a function that is not normally present - due to entirely new protein or protein produced in inappropriate tissue or time during development

Craniosynostosis - gain of function

results from improper timing of fusion of cranial plates in infants — due to improper timing of protein production

• gains function earlier than expected

• can cause significant cognitive repair

mutation rates

refers to the frequency in which wild-type alleles are permanently changed

• rate reference can be within the cells of an individual or within populations or within taxa

• smaller genome = higher mutation rate (increased reproductive rate)

• large genome = lower mutation rate (DNA repair mechanisms and more accurate DNA replication)

factors of mutation rate

• frequency at which changes in DNA take place

• probability of DNA repair

• detectability (need to be able to see/measure it)

• *mutations are more common in non-coding regions and in wobble position

adaptive mutation

in stressful environments, bacteria may accumulate mutations at a faster rate (induced) which may help them survive

• ex: antibiotic resistance

spontaneous mutation

mutations that arise under normal conditions, spontaneously without external influence or mutagens

• ex: error in DNA repair, transcription, polymerization, replication

induced mutation

mutations that arise from outside environmental factors

• ex: toxins or UV damage

tautomers

different versions of a nucleotide in which hydrogen atoms shift position, causing them to form bonds with incorrect base pair

• ex: instead of G-C —> G-T

• primary cause of spontaneous mutations

wobble base-pairing

incorrect nucleotide base-pairing with only two congruent pairings instead of three

• ex: T-G and C-A

incorporated error

base substitution causes a mispaired base to be incorporated; can be fixed

replicated error

a mistake made during DNA replication where incorrect nucleotides are incorporated into the new DNA strand, which can lead to permanent mutations if not corrected.

strand slippage in insertions and deletions

occurs when the DNA polymerase slips during replication, leading to insertions or deletions in the new DNA strand; forms a hump in the new strand

misalignment in crossing over in insertions and deletions

misalignments in crossing over can lead to unequal exchange of DNA segments, resulting in insertions or deletions in the chromosomes; typically chromosomal mutations

• results in a shortened chromosome and an elongated chromosome

depurination in spontaneous mutations

chemical change in DNA that causes a loss of a purine (A & G) base from a nucleotide

• usually replaced with an A from ATP (incorporated error), which can cause improper replication in both strands (replicated error)

steric hindrance

causes the loss of purines in DNA; loss of pyrimidines is much less common

deamination

a chemical reaction that leads to a loss of an amino group (NH2) from the nitrogenous base, which causes inappropriate base-pairing

• ex: cytosine —> uracil & 5-methylcytosine —> thymine

mutagens

chemicals in the environment that may damage DNA or alter its structure

• ex: processed foods, cigarettes, UV rays, mustard gas

base analogs

chemicals with structures similar, or analogous, to natural nitrogenous bases

• these chemicals are identical to nitrogenous bases in the perspective of DNA polymerase so it incorporates them into a growing DNA strand during replication

• ex: 5-bromouracil is a thymine analog that normally pairs with adenine but can also incorrectly pair with guanine

alkylating agents

chemically modify nucleotide bases by adding alkyl groups, causing incorrect base pairing

• ex: methyl groups (CH3) or ethyl groups (CH3-CH2)

• ex: guanine + ethyl group = G-T pairing

oxidative radicals

reactive forms of oxygen that can cause chemical changes in DNA

• ex: hydrogen peroxide is a reactive oxygen species

• guanine + hydrogen peroxide = G-A

interculating agents

insert themselves in between adjacent bases, which causes indels

• ex: acridine orange

radiation

is a form of energy release

particle radiation

subatomic particles such as neutrino or protons are released from a material

acoustic radiation

energy is released as gravitational waves

electromagnetic radiation

release of energy in the form of photons which act as a particle and a wave

• the shorter the wavelength the higher the energy and higher frequency

• the longer the wavelength the lower the energy and lower frequency

ionizing radiation

when radiation is high enough, it can dislodge electrons from atoms, which causes the formation of a free radical or ion

• this can cause DNA breaks and damage

pyrimidine dimers

non-ionizing radiation mutation caused by UV radiation, which can halt DNA replication by forming a kink in the DNA

Ames test

used to test for carcinogens (causes cancer) in a substance

• first bacteria is modified to prevent them from producing histidine (amino acid necessary for growth), then the substance is put in

• if mutations occur, we expect reverse mutation, so that the bacteria regain the ability to produce histidine —> carcinogen

• *some chemicals are not carcinogenic until they are metabolized, so rat liver extract is added to the test

transposable elements (transposons)

mobile DNA that can move around in the genome and can cause mutations by inserting into a gene or promoting chromosomal rearrangements (deletions, duplications, inversions)

• *highly variable in sequence but often have flanking repeats (caused by staggered cuts)

• *similar to viruses —> make staggered cuts and insert themselves into target DNA

• often contain code for a transposase enzyme — this cuts DNA open to allow the transposon to insert itself

terminal inverted repeat

sequences 9-40 bp long that are inverted complements of each other that are found at the ends of many transposable elements and play a crucial role in their mobility

• *DIFFERENT than flanking direct repeat

DNA transposons

a class of transposable elements that move within the genome through a "cut-and-paste" mechanism, allowing them to insert into new locations (target DNA) and potentially alter gene function.

retrotransposon

use reverse transcription

1. uses transcription to make an RNA intermediate

2. uses reverse transcription to make a DNA intermediate

3. which is then able to insert itself into target DNA

defenses against transposons

• methylating DNA regions where transposons are common —> silence and prevent reverse transcription

• use piwi-interacting RNA (piRNA) —> combines with argonaut protien to identify transposons and recruit methylating machinery

process of transposition

1. staggered cuts in target DNA (by transposase)

2. transposon is joined to single-stranded ends

3. DNA is replicated to fill in the gaps

replicative transposition

a copy is mad so original transposon may remain in original location (class 2)

nonreplicative transposition

transposon is cut out of original site and locates elsewhere

transposable elements in deletion

pairing by looping and crossing over between two transposable elements oriented in the same direction leads to deletion

transposable elements in inversion

pairing by bending and crossing over between two transposable elements oriented in opposite directions

mismatch repair

1. mismatch recognition (accessory proteins)

2. strand discrimination (correct sequence strand)

3. mismatched DNA cut out & replaced by DNA polymerase, sealed by ligase

• in prokaryotes, special sequences of GATC nucleotides are methylated on OLD strand

direct repair (DR)

corrects chemically altered nucleotides by restoring their normal structure —> easy fixes

• photolyase in some bacteria can fix thymine dimers caused by UV radiation —> cuts covalent bonds

• does not replace altered nucleotides, restores them

base-excision repair (BER)

repair mechanism where the altered based is cut out and replaces

1. endonuclease cuts phosphodiester bond

2. DNA glycosylase cuts out base

3. other enzymes remove deoxyribose sugar

4. DNA polymerase beta adds new nucleotide

• *base analogs can be repaired via BER

Nucleotide-excision repair (NER)

entire nucleotides are cleaved out and replaced

• any irregularities n the 3D shape of DNA can lead to nucleotide
  excision repair —> intercalating agents (chemical mutagens)

1. Enzymes scan DNA for “bumps”

2. Additional enzymes (helicase) separate the strands and SSBPs stabilize them

3. sugar-phosphate backbone is cleaved on both sides of damage

4. gap is filled by DNA polymerase and sealed by DNA ligase

   • ex: can be used to fixe thymine dimers (along with direct repair)

double strand break repair (DSBR)

a critical cellular process that repairs breaks in both strands of the DNA helix, restoring genomic integrity. It typically involves mechanisms such as homologous recombination and non-homologous end joining.

• can be extremely dangerous — lead to DNA replication stalling and chromosomal rearrangements

Homologous directed repair in DSBR

a process of DNA repair that uses non-damaged sister chromatid as a template strand to fix the damaged DNA

1. nucleotides are removed from broken ends of DNA strands

2. homologous chromosome strand invades

3. DNA polymerase replicates homologous strand to complete broken strand

4. ligase closes broken strands

• ex: BRCA 1 and BRCA 2 are frequently mutated breast cancer cells that are involved in HDR

nonhomologous end joining in DSBR

DNA repair mechanism where the broken strands are simply reattached

• uses Ku protein binding

• more error prone; could have loss of DNA

• occurs in G1 phase of cell cycle

p53 protein

a tumor suppressor protein that prevents cell cycle from going unregulated

cancer

the unregulated growth and division of cells, usually due to a disruption in cell cycle

tumors

large masses of cancerous tissue growth

most common form of cancer

breast cancer

most deadly form of cancer

lung cancer; due to a lack of early, cheap screening tests and environmental factors

how is the type of cancer determined

cancer type is determined by the initial site of development

benign tumor

a tumor that remains in the same location

malignant tumor

a tumor whose cells have moved to another part of the body and formed new tumors in those sites

metastasis

the spread of cancer cells from the original site to other parts of the body

cancer as a genetic disease

1. many mutagens cause cancer - thus many mutagens are carcinogens

2. some cancers are associated with chromosomal abnormalities

3. some cancers run in families

Note: *other cancers that are not genetically passed on are typically caused by environmental factors

retinoblastoma in adults

usually only effects one eye as the cancer is only caused by environmental mutagens

• adults need two mutated alleles in order to develop cancer, which is why the effects only occur in one eye

retinoblastoma in children

usually effects both eyes as the cancer is often caused by inherited genetic mutations, leading to a higher risk in family members

• children already inherit one mutated allele and only need one more in order to develop cancer

Knudson’s 2 hit hypothesis

A model suggesting that two genetic hits or mutations are necessary for the development of certain cancers, such as retinoblastoma. This hypothesis explains how inherited mutations combined with environmental factors can lead to cancer.

Knudson’s multistep hypothesis

proposed thar cancer requires multiple mutations to develop

• most cancers require more then mutations — often at different loci

• *HOWEVER, most tumors develop from spontaneous mutations or mutagens

Clonal evolution

when tumors develop, the cells have mutations that promote proliferation allowing the tumor to grow rapidly

1. bypass checkpoints in cell cycle unnoticed

2. higher number of cells

3. can lead to cells that grow at a faster rate, making them more likely to mutate

aneuploidy

cells that have an uneven amount of chromosomes; these chromosomal mutations can contribute to clonal evolution

• duplicating copies of genes that promote cancer

• deleting copies of genes that prevent cancer

environmental factors in cancer

include various elements such as chemicals, radiation, and lifestyle choices that can increase the risk of mutations leading to cancer

• individuals that migrate from one country to another take on cancer rates of that country

• age can also effect cancer rates due to increased exposure to toxins and the aging of DNA repair mechanisms

allele affinity and cancer

some alleles that are linked to lung cancer are associated with higher rates of addiction due to their influence of dopamine receptors, which can increase likelihood of addiction

oncogenes

behave like dominant alleles - 1 mutated version is enough to promote cancer

• molecules that promote division