GCD 3022 - Final

Which mutation would cause the most deleterious (harmful) phenotypic consequence?

nonsense

A mutation within the 5'-UTR of an mRNA may result in what? Explain

no translation of the mRNA, as ribosomes may not bind to it; the 5'-UTR contains specific sequences that are required for the initiation of translation.

A down promoter mutation causes the promoter of a gene to be (                    ) like the consensus sequence and (                         ) transcription.

less, inhibits

A (                         ) mutation changes a mutant allele back to a wild-type allele.

reverse

Which of the following mutations appropriately describes an example of a position effect?

• Chromosomal translocation decreases gene expression. 

• A point mutation in an enhancer decreases the rate of transcription

• A mutation in a gene's promoter decreases gene transcription.

• A mutation at 3’ splice site of an intron generates an altered mature RNA.

Chromosomal translocation decreases gene expression. 

What is a position effect?

when a gene is left intact but its expression may be altered because of its new location

Which mutation(s) affect base substitutions?

missense, silent, nonsense

Which mutation(s) affect base additions/deletion?

frameshift

What would happen if a mutation affects the promoter/enhancer?

gene transcription may increase/decrease

What would happen if a mutation affects the 5’-UTR?

it may influence the ability of mRNA translation

What would happen if a mutation affects the 3’-UTR?

mRNA stability may be altered

What would happen if a mutation affects splice sites?

some exons may not be included, or introns may be included in mRNA

What is a forward mutation?

changes the wild-type genotype into some new variation

What is a wild-type genotype?

the relatively prevelant genotype

True or false: genes with multiple alleles may have no more than two wild-types

false

What is a reverse mutation?

changes a mutant allele back to the wild-type

What is a point mutation?

base substitution where there is a change in a single base pair

What is transition?

a change of a pyrimidine (C/T) to another pyrimidine or a purine (A/G) into another purine

What is transversion?

a change of a pyrimidine to a purine + vice versa

True or false; transitions are less common than transversions

false

What are silent mutations?

base substitutions that do not alter the amino acid sequence of the polypeptide (the last base is changed)

What likely effect would a silent mutation have on protein function?

none (neutral)

What are missense mutations?

base substitutions in which an amino acid change occurs (1st or 2nd base pair is changed)

How many amino acids are altered with missense mutations?

1

What likely effect would a missense mutation have on protein function?

Depends (can be neutral or inhibitory)

What are framshift mutations?

base additions/deletions of a number of nucleotides that is not divisible by 3

How many amino acids are altered with frameshift mutations?

Many

What likely effect would a frameshift mutation have on protein function?

negative

What are nonsense mutations?

base substitutions that change a normal codon to a stop codon

What likely effect would a nonsense mutation have on protein function?

negative

How many amino acids are altered with nonsense mutations?

many

What are germ line cells?

cells that give rise to gametes (sperm/egg)

What are germ line mutations?

mutations that occur directly in a sperm/egg

What do spontaneous mutations result in?

abnormalities in cellular/bio processes; underlying causes originate within the cell (e.g., errors in DNA replication)

What are the 3 causes of spontaneous mutations?

depurination, deamination, oxidative damage

What is depurination?

the removal of a purine (A/G) from the DNA to form an AP site

Can AP sites be repaired? How?

yes, base excision repair

What is deamination of cytosine?

removal of an amino acid group from the cytosine base; C becomes U

Why can DNA repair enzymes easily recognize and remove U but not T after deamination of C?

U is not an appropriate base in DNA whereas T naturally exists in DNA

What is deamination of 5mC?

removal of an amino acid group of methylated cytosine; 5mC becomes T

What is oxidative stress?

an imbalance between the production of ROS and an organism’s ability to break them down

What is ROS?

reactive oxygen species (molecules incuding free radicals) produced by aerobic organisms

What happens if there is oxidation of G?

G can be converted to 8-oxoG to pair with A during replication

What are induced mutations?

chemical or physical mutations caused by environmental agents

What are mutagens?

agents known to alter DNA structure

True or false: mutagens can be chemical or physical

true

What are the 3 types of chemical mutagens?

base modifiers, intercalating agents, base analogues

What do base modifiers do?

covalently modify base structure/disrupt pairing by alkylating bases

What do intercalating agents do?

directly interfere with replication process

What do base analgoues do?

incorporate flat planar structures into double helix DNA and disrupt structure

What type of mutation might occur if intercalating agents are replicated?

frameshift

What effect does EMS have?

alkylate G to pair it with T instead of C as a result of base modifying agents; changes just one base pair

What effect does proflavin have?

causes frameshift mutation; changes multiple base pairs

What effect does 5BU have?

incorporates into DNA to replace T; it can pair with purines (A/G)

What are 2 main types of physical agents?

UV and x-ray

What does UV induce?

T (pyrimidine) dimers; causes base subs

What does x-ray induce?

DNA double strand breaks; causes chromosome aberrations

What is mutation rate?

the likelihood that a gene will be altered by a new mutation

What is the mutation frequency?

# mutant genes / total genes

What is a key difference between mutation rate vs frequency?

rate = new mutations, frequency = all mutations

What are the 2 types of direct repair?

photolyase and alkyltransferase

What does photolyase do?

fix thymine dimer in bacteria

What does alkylktransferase do?

fix O6-alkylguanine (caused by EMS/other agents)

What does base excision repair do?

removes U (or other damaged bases - limited) and fix AP sites due to depurination

What does nucleotide excision repair do?

fix T dimer and bulky lesions + other DNA damage (broad range)

What type of cancer is caused by defects in NER?

skin cancer

What does mismatch repair do?

fix base mismatches after DNA replication

What type of cancer can defects in mismatch repair cause?

colon cancer

How can DNA double strand breaks be fixed in bacteria?

homologous recombination repair (HRR)

When is direct repair used?

fix O6-alkylguanine from EMS or T dimers from UV

What enzymes are involved in base excision repair?

DNA N-glycosylases

What do DNA N-glycosylases do?

recognize an abnormal base and cleave the bond between it and the sugar in the DNA

Which abnormal bases can DNA N-glycosylases eliminate?

U, 3mA, 7mG

How do you fix DNA double stranded breaks humans?

NHEJ or HRR

What is NHEJ?

error-prone repair system that recognizes double strand breaks by end-binding proteins to form a crossbridge

Which phase(s) of the cell cycle does NHEJ function in?

G1

Which phase(s) of the cell cycle does HRR function in for eukaryotes?

S and G2

What is HRR?

error-free repair system that uses sister chromatids as a template to synthesize DNA and close the gap in double stranded breaks

Do HRR and NHEJ occur in both eukaryotes and prokaryotes?

no; NHEJ is only eukaryotes

What are DNA double-strand breaks?

the breakage of chromosomes into pieces caused by ionizing radiation/chemical mutagens or ROS; they cause chromosomal rearrangements and deficiencies

What is TLS?

translesion synthesis polymerases that are enzymes which can bypass/replicate through DNA lesions to repair damaged DNA

What is a negative effect of TLS?

low fidelity (error prone)

What are mutations?

heritable changes in genetic material

What is cancer?

uncontrollable cell division

What are oncogenes?

a dominant/over expressed mutant gene that contributes to cancerous growth

What are proto-oncogenes?

normal celluar genes that can be mutated into an oncogene; its expression becomes abnormally active

True or false: oncogenes are an example of loss-of-function mutations

false

How do oncogenes occur?

• increased amount of coded protein

• overly active coded protein

• abnormally expressed coded protein

What do growth factors do?

bind to cell surface receptors and initiate a cascade of cellular events to ultimately lead to cell division

What do ras proto-oncogenes do?

example of missense mutations that increase cell signaling to cause cancer

What are the main 3 ways cancer-causing mutations occur?

missense mutations, gene amplification, chromosomal translocations

What is N-myc?

example of gene amplification that increase cell copy number and therefore the amount of protein to cause cancer

What is CML?

chronic myelogenous leukemia which is example of chromosomal translocation; codes an abnormal fusion protein and causes cancer

What are tumor-suppressor genes?

genes that prevent cancer

What would a loss-of-function mutation in tumor-suppressor genes do?

allows cancerous growth to occur

What are examples of tumor-suppressor genes?

Rb, p53, BRCA1/BRCA2

How can tumor-suppressor genes be silenced?

• mutation in tumor-suppressor gene itself

• aneuploidy (abnormal number of chromosomes)

How do mutations in tumor-suppressor genes themselves occur?

• inactivation of promoter (transcription cannot be initiated)

• early stop codon (nonsense mutation)

When does aneuploidy contribute to the progression of cancer?

if the lost chromosome carries one or more tumor-suppressor genes

What do proteins that maintains genome integrity do in regards to tumor-suppressor genes?

• prevent damaged cells from dividing

• perform DNA repair