Gene Function, Phenotype, and Mutation

Question 1

Affect a diploid phenotype when present in two copies

Answer 1

recessive

Question 2

Most loss of function alleles

Answer 2

recessive

Question 3

affect a diploid as a single copy

Answer 3

dominant

Question 4

most gain of function alleles

Answer 4

dominant

Question 5

occurs when one functional copy of a gene is not enough to carry out function (example of loss of function dominant allele)

Answer 5

haploinsufficiency

Question 6

the nonfunctional copy interferes with the functional copy (example of loss of function dominant allele)

Answer 6

dominant negative

Question 7

change of single nucleotide: silent, missense, or nonsense

Answer 7

substitutions

Question 8

insertions and deletions can result in

Answer 8

frameshifts

Question 9

reverse the effects of a mutation in another gene

in tRNAs can prevent DNA changes from altering protein sequence

Answer 9

suppressor mutations

Question 10

Occur through cellular error or biochemical variation
- tautomeric shift
- replication error or slippage
- reactions in cellular environment
- transposons

Answer 10

spontaneous mutations

Question 11

Occur due to extracellular influence from toxin, chemical, radiation, etc
- Base analogs
-alkylating agents and intercalating agents
- UV radiation
Ionizing radiation

Answer 11

Induced mutations

Question 12

Change from one purine/pyrimidine pair to the other purine/pyrimidine pair

A/T <–> G/C
T/A <–> C/G

Answer 12

Transition

Question 13

Change between a purine/pyrimidine pair and a pyrimidine/purine pair

A/T <–> T/A
G/C <–> C/G
A/T <–> C/G
G/C <–> T/A

Answer 13

Transversion

Question 14

• can lead to incorporation of the wrong complementary base during DNA replication
• Bases exist in one of two forms and a small minority of bases exist as alternate tautomers
• mismatches due to tautomeric shifts can be corrected by DNA polymerase proofreading

Answer 14

Spontaneous Mutation: tautomeric shift

Question 15

• repetitive sequences can confuse DNA polymerase III and it can “lose its place”
• spontaneous deletions/insertions may arise in repetitive DNA during replication

Answer 15

Spontaneous Mutation: DNA Replication Slippage

Question 16

• Ex: Bromodeoxyuridine (BrdU)
• increases rate of tautomeric shift and thus adding BrdU to cells increases the chance of mismatch mutations during replication

Answer 16

Induced Mutation: Chemical mutagens- Base Analogs

Question 17

Chemical agent that can directly alter chemical structure of nitrogenous bases within DNA, causing them to mispair during replication (i.e. ethyl methanesulfonate (EMS) alkylates guanines GC -> AT)

Answer 17

Induced Mutation: Chemical Mutagens - Base Modifiers

Question 18

Distort DNA double-helix, causing DNA polymerase slippage and insertion/ deletion mutations

ex: ethidium bromide (agarose gels), acridine, Proflavin

Answer 18

Induced Mutation: Chemical Mutagens- Intercalating Agents

Question 19

Causes thymine-thymine dimers - bulge in DNA helix

Deletion in opposite strand during DNA replication

may stall DNA replication and cause cell death

Answer 19

Induced Mutation: UV irradiation

Question 20

Strong enough to break phosphodiester bonds –> double-strand breaks in DNA

Answer 20

Stronger Ionizing Radiation (X-rays, Gamma rays, cosmic rays)

Question 21

Determines if agent is mutagenic and if so, what type of mutations it can cause

Answer 21

Ames Test

Question 22

1. auxotrophic mutation (his- cannot grow in absence of histidine)
2. Different strains carry different mutations in the his gene that can be used to assay for reversion of substitutions and frameshifts
3. Uniformly cover plate that lacks histidine with bacteria
4. Incubate to promote colony growth
5. Control: spontaneous his+ revertant colony
6. Experiment: Potential mutagenic compound added, induced his+ revertant colonies

Answer 22

Steps of Ames Test

Question 23

Create a mutant phenotype and identify the causative mutation

Answer 23

Forward Genetics

Question 24

Target a sequence for mutation and observe phenotype

Answer 24

Reverse genetics

Question 25

1. What genes are required for a particular biology process? 2. Treat organism/ cells with a mutagen to induce random mutations 3. Screen organisms/cells for defects in process of interest (phenotype) 4. Map/clone the mutation to identify a gene required for the process of interest 5. Study the gene/protein to determine how it works in the process of interest

Answer 25

Forward genetic screens

Question 26

Corrects replication errors missed by DNA Polymerase III proofreading 1) recognition of mismatch 2) recruitment of proteins 3) excision of DNA strand containing wrong nucleotide 4) resynthesis of excision gap by DNA pol using remaining DNA strand as template 5) ligation

Answer 26

Mismatch Repair (MMR)

Question 27

Bacteria: methylation Eukaryotes: interaction of repair proteins with DNA replication machinery

Answer 27

How a strand with errors is identified with a mismatch (MMR)

Question 28

Pathways that remove damaged base(s) and DNA polymerase and ligase replace the excised bases and seal the nick Damage can be detected by proteins that survey the genome, or damage can be detected during transcription when RNA polymerase stalls at a lesion or adduct

Answer 28

Base Excision Repair (BER) and Nucleotide Excision Repair (NER)

Question 29

Can be induced by high ionizing radiation (gamma rays, cosmic rays) or through oxidative stress in the cell

Answer 29

Double-Strand Breaks (DSBs)

Question 30

DSBs can be repaired through...

Answer 30

Homologous Recombination (HR) or Non-Homologous End Joining (NHEJ)

Question 31

no template is used for repair repair may not be accurate- can lead to genome rearrangements

Answer 31

NHEJ

Question 32

homologous chromosome is used as a template for extending the broken chromosome beyond the break point strands can separate and DNA is filled-in and ligated by DNA pol I and ligase can result in exchange of DNA between homologous chromosomes (DSB repair) or copying DNA from one chromosome to another (synthesis-dependent strand annealing) Can cause a crossover

Answer 32

HR

Question 33

Introduce DNA to a cell that contains a selectable marker flanked by sequences homologous to a target

Answer 33

Target Gene Inactivation (Knockout)