Genetics Quiz Chapeter 15

Mutations are..

-An alteration in DNA sequence of nucleotides §Single base pair substitution §Deletion or insertion of base pairs §Major alteration in chromosomal structure •May occur in somatic or germ cells •May occur in coding or noncoding regions

Tautomeric shifts

-Can change the bonding structure, allowing noncomplementary base pairing -May lead to permanent base-pair changes and mutations

Base analogs (mutagenic chemicals)

-Can substitute for purines or pyrimidines during nucleic acid biosynthesis -Increase in tautomeric shifts -Increase sensitivity to UV light - mutagenic Example: 5-Bromouracil behaves as thymine analog T = A to C---G Transition

Intercalating Agents

-Chemicals with dimensions and shapes that wedge between DNA base pairs -This causes base-pair distortions and DNA unwinding -Structural changes affects transcription, DNA replication and repair. Insertions & deletions during DNA replication and repair (frame-shift mutations) -Example: Ethidium bromide

UV radiation creates thymine dimers

-Dimer formed with two adjacent thymines distort DNA conformation -Errors can be introduced during DNA replication

Alkylating Agents

-Donate alkyl group (CH3 or CH2CH3) to amino or keto groups in nucleotides -Alter base-pairing affinity -Transition mutations result -Examples: Mustard gas Ethylmethane sulfonate (EMS)

Double-strand break repair (DSB repair)

-Double strand breaks are extremely dangerous -Results in chromosomal rearrangements, cancer, cell death -DSB repair pathway reattaches strands -Two pathways involved in DSB repair §Homologous recombination repair §Nonhomologous end joining

Oxidative Damage to DNA

-Due to by-products of normal cellular processes -Exposure to high-energy radiation §Superoxides (O2- ) §Hydroxyl radicals (OH) §Hydrogen peroxide (H2O2)

Homologous Recombination Repair

-Exonuclease recognizes break, digests 5' end, and leaves 3' overhang -3' end aligns with sequence complementary on sister chromatid -Occurs during late S or early G2 phase of cell cycle

E. coli SOS Repair System

-Last resort to minimize DNA damage -RecA binds to single stranded region in gap. This activates RecA, which then induces the expression of over 20 SOS genes -Products of SOS genes: §inhibit cell division to allow time for repair §cause DNA Polymerase III to insert any nucleotide in the gap in order to preserve the integrity of DNA and survive. -DNA synthesis becomes error-prone; inserts random/incorrect nucleotides in places that normally would stall replication -SOS repair can itself become mutagenic; allows cells to survive with DNA damage (cell would otherwise kill itself)

Base and Nucleotide Excision Repair

-Light-independent DNA repair mechanisms exist in all prokaryotes and eukaryotes and involve excision repair -Endonuclease recognizes and cuts distortion/error -DNA polymerase inserts complementary nucleotides in missing gap -DNA ligase seals final "nick" A) Base Excision Repair (BER) B) Nucleotide Excision Repair (NER)

Depurination

-Loss of nitrogenous bases (usually a purine - guanine or adenine), leading to an apurinic site (without purine)

Polygenic Diseases due to Mutations

-Most human genetic diseases are polygenic, caused by mutations in several genes

Adduct-Forming Agents

-Mutation-causing chemicals -Covalently bind to DNA, altering conformation and interfering with replication and repair -Acetaldehyde: Component of cigarette smoke

Photoreactivation Repair

-Photoreactivation Enzyme (PRE) (E. coli) Recognizes thymine dimers. -Enzyme must absorb photon of light to cleave bonds between thymine dimers, reversing effect of UV radiation on DNA - §Humans and other organisms lack photoreactivation repair L

Tautomers

-Purines and pyrimidines exist in tautomeric forms—alternate chemical forms -Increase chance of mispairing during DNA replication

Xeroderma Pigmentosum

-Rare genetic disorder due to defects in NER pathways -Affected individuals exhibit severe skin abnormalities, skin cancers, developmental and neurological defects -Individuals have 2000-fold higher rate of cancer

Nucleotide excision repair (NER)

-Repairs bulky lesions that alter/distort double helix

Postreplication Repair

-Responds after damaged DNA has escaped repair and has failed complete replication -RecA protein directs homologous recombination exchange with the corresponding region on the undamaged parental strand (donor DNA) -Gap can be filled in by repair synthesis

Frameshift mutations

-Result from insertions or deletions of base pair -Reading Frame of triplet codons is altered during translation. -Often results in loss of function of protein product

Which nucleotide will base‑pair with the enol form of 5‑bromouracil?

Guanine

Why are liver extracts used in the Ames test?

Liver enzymes may activate some innocuous compounds, making them mutagenic.

Systems of DNA Repair

Mismatch repair (if proofreading fails) becomes activated -Mismatches are detected, cut, and removed (endonuclease and exonuclease). Correct nucleotide inserted by DNA polymerase

Mutagens

Natural or artificial agents that induce mutations -All cells are exposed to plethora of mutagens Examples: §Fungal toxins §Cosmic rays §Ultraviolet light §Industrial pollutants §Medical X rays §Chemicals in tobacco smoke

UV Light

Purines and pyrimidines absorb UV at 260 nm

Transversions

Purines and pyrimidines are interchanged (A,C,T,G)

Transitions

Pyrimidine replaces pyrimidine, or purine replaces purine (T<-> C A<-> G)

Which repair system uses the RecA and LexA proteins?

SOS repair

Describe the mutagenic action of the following two mutagens: 5-bromouracil and ultraviolet light.

The mutagen 5-bromouracil is an analog of THYMINE, which anomalously pairs with GUANINE. Ultraviolet light causes THYMINE DIMERS.

What are the consequences of having pyrimidine dimers in DNA?

These dimers distort the DNA structure and result in errors during DNA replication.

In its rare form, 5BU pairs with guanine.

True

Tautomers of nucleotide bases are isomers that differ from each other in the location of one hydrogen atom in the molecule.

True

Thymine dimers can be repaired by Photoreactivation Repair or Nucleotide Excision Repair.

True

Sex-linked mutations

X-linked and Y-linked mutations occur within genes located on X and Y chromosome, respectively

In terms of its involvement in mutagenesis, 5BU is best described as _______.

a base analog that can cause either A-T > G-C or G-C > A-T transitions

Generally speaking, which of the following mutations would most severely affect the protein coded for by a gene?

a frameshift deletion at the beginning of the gene

A class of mutations that results in multiple contiguous amino acid changes in proteins is likely to be which of the following?

frameshift

Which bacteria grow on the agar plate if the Ames test is positive?

his + prototrophs

Somatic Mutations

occur in any cell except germ-line cells; are not heritable

Germ-line mutations

occur in gametes; are inherited

Autosomal mutations

occur within genes located on autosomal chromosomes

Nonhomologous end joining pathway (NHEJ)

-Activated in G1 prior to replication -Repairs double-strand breaks -Complex of proteins is involved in end joining -Proteins bind free ends and ligate ends back together

Expandable Trinucleotide Repeat Sequences

-Short DNA sequences found in mutant genes -Normal individuals may have a low number of repetitions -Individuals with over 20 disorders exhibit over 200 repeats -e.g. Long CAG repeats: • long tracks of glutamine protein aggregation • mRNA with long CAG repeats bind to important regulatory proteins to sequester them and prevent their function •DNA regions with long CAG repeats may become highly methylated leading to silencing of gene transcription. Examples: Huntington disease (HD) Myotonic dystrophy (MD)

Monogenic diseases due to Mutations

-Single base-pair change in one of approximately 20,000 human genes may lead to serious inherited disorders

Which of the following are two mutagens that would be classified as base analogs?

5-bromouracil and 2-aminopurine

What is meant by the term photoreactivation repair?

A process in which UV-induced DNA damage can be partially reversed if cells are briefly exposed to light in the blue range of the visible spectrum.

Deamination

Amino group changed to keto group. •cytosine is converted to uracil •adenine converted to hypoxanthine -Result: Change in base pairing of original bases C---G converted to T=A; A=T converted to G---C

If a segment of DNA were replicated without any errors, the replicated strand would have the following sequence of nucleotides: 5' - ACTACGTGA - 3' Sort the following replicated DNA sequences by the type of point mutation each contains (frameshift, base substitution, or neither), as compared to the correct sequence shown above.

Base Substitution: ACTAAGTGA, ACTACGTGT Frameshift Mutation: ACTCGTGA, ACTTACGTGA

Which of the following events could result in a frameshift mutation?

Base deletion

Strand Discrimination

Based on DNA methylation (-CH3) Adenine methylase (enzyme in bacteria) recognizes 5'-GATC-3 DNA sequences and adds methyl group to adenine residues -Newly synthesized strand of replication remains unmethylated -Mismatch repair proteins recognize unmethylated daughter strand and repairs it using the methylated parent strand as template.

Which of the following statements regarding Nucleotide Excision Repair (NER) and Base Excision Repair (BER) is true?

Both NER and BER involve the removal of one or more damaged bases by a nuclease.

Point mutation or base substitution:

Change from one base pair to another. Classified by effects on Codon specificity.

Silent mutation

Change in codon sequence that still codes for the same amino acid. (e.g. UAU--> UAC tyr--> tyr)

Nonsense mutation

Change in codon sequence to create a stop codon (translation terminated prematurely). (e.g. UAU--> UAA tyr--> stop)

Missense mutation

Change in codon sequence to specify a different amino acid (e.g. UUC-->CUC phe -->leu)

Which enzyme is responsible for proofreading during replication?

DNA polymerase

For 5BU to cause a transition mutation, which of the following must occur?

DNA with incorporated 5BU must replicate.

Which of the following statements about deamination is true?

Deamination is induced by nitrous acid.

DNA Base Damage

Depurination and deamination §Common causes of spontaneous mutations §Lead to new base pairing and mutations

All compounds that have been found to be mutagenic in the Ames test are also carcinogenic.

False

Bacteria can distinguish between a newly replicated DNA strand and the original template strand because the newly replicated strand is methylated, whereas the original template strand is not.

False

When a base substitution mutation occurs, one nucleotide in a replicating DNA sequence is substituted for another, which results in the production of a mutant strand of DNA. The result of the mutation depends on how the substituted nucleotide base alters the string of amino acids coded by the mutant DNA. The three types of base substitution mutations are nonsense mutations, missense mutations, and silent mutations. Each type is defined by how it affects protein synthesis.

a) silent b) nonsense c) missense d) frameshift

Base substitutions

are classified according to the type of base change.

Which repair mechanism is most likely affected if the enzyme DNA glycosylase is not functioning properly?

base excision repair

Mutations that arise in nature, from no particular artificial agent, are called ________.

spontaneous mutations

Thymine dimers form when ________.

two thymines on the same strand and adjacent to each other bind together

Ultraviolet light causes pyrimidine dimers to form in DNA. Some individuals are genetically incapable of repairing some dimers at "normal" rates. Such individuals are likely to suffer from ________.

xeroderma pigmentosum

Spontaneous mutation

§Changes in nucleotide sequence that occur naturally §Arise from normal biological or chemical processes that alter nitrogenous bases §Spontaneous mutation rates vary, but are exceedingly low for all organisms

Induced mutations

§Result from influence of extraneous factors, either natural or artificial •Radiation •UV light •Natural and synthetic chemicals

Single Base-Pair Mutations and b-Thalassemia (monogenic disease)

§b-Thalassemia -Inherited autosomal-recessive blood disorder -Most common single-gene disease -Results from reduction or absence of hemoglobin. Less oxygen carried by red blood cells. -Over 250 mutations in the b-globin gene §Single nucleotide change or insertions/deletions

Proofreading and mismatch repair

• DNA polymerase "proofreads," removes and replaces incorrectly inserted nucleotides

Heterocyclic amines (HCAs)

•Cancer-causing chemicals created during cooking of meats (e.g., beef, chicken, and fish) •17 different HCAs are linked to cancers of stomach, colon, and breast

Transposable Elements

•DNA elements that move within or between genomes •Present in all organisms •Can act as naturally occurring mutagens •Can disrupt important DNA coding sequences or important cis-acting elements that regulate transcription. •Can also bring along new coding sequences •Can create chromosomal damage: DNA inversions, translocations, double-stranded breaks

Ionizing Radiation

•X rays, gamma rays, cosmic rays have very high energy of radiation -Penetrate deeply into tissues -Causes ionization of molecules to form free radicals (chemical species containing one or more unpaired electrons). Highly reactive. -Free radicals directly or indirectly affect DNA §Alter purines and pyrimidines §Break phosphodiester bonds. Single and double strand DNA breaks §Produce deletions, translocations, and fragmentation