chapter 11 - Gene mutation, DNA repair, homologous recombination

Question 1

What is the role of transposase?

Answer 1

Transposase is responsible for making staggered cuts of the DNA seq and carrying the transposable element to the target sequence.

Question 2

What is an IS element?

Answer 2

Insertion element… is transposable.

Question 3

What is the difference between an IS element and a composite transposon?

Answer 3

Composite - a type of transposon that carries genes such as antibiotic resistant genes

IS element - transposable elements, carry genes that code transposase/catalyze transposition activity

Question 4

What are the steps of transposable element insertion into target sequences?

Answer 4

1 - transposase makes staggered cuts and leave DNA strands from target seq, leaving single stranded ends in the target seq.

2- transposable element is inserted into target seq, carried by transposase

3- gaps filled by DNA polymerase

Question 5

What are transposable elements, also known as “jumping genes”?

Answer 5

-DNA sequences found in both eukaryotes and prokaryotes that have multiple copies and are able to move within the genome

Question 6

What are point mutations?

Answer 6

Changes in one or a few base pairs… can be somatic (non heritable mutations, not egg/sperm) or germ-line (heritable, egg/sperm)

Question 7

What are the two types of BASE PAIR SUBSTITUIONS?

Answer 7

Transition - Purine to purine… pyrimidine to pyrimidine

Transversion - Purine to pyrimidine, pyrimidine to purine

Question 8

What are the types of base-pair substitutions that occur in the coding sequence?

Answer 8

Synonymous mutation
missense mutation
nonsense mutation
frameshift deletion
frameshift insertion

Question 9

What is a wild type sequence also known as?

Answer 9

Sense codon

Question 10

What is a synonymous mutation?

Answer 10

-mutation in coding seq
-change in DNA, amino acids stay the same… change in a wobble

Question 11

What is a missense mutation?

Answer 11

-mutation in coding seq
-change in DNA that changes the amino acid

Question 12

What is a nonsense mutation?

Answer 12

• mutation in coding seq
  -change from a sense codon to a stop codon : UAG, UAA, and UGA
  -shortens seq of proteins

Question 13

What is a frameshift insertion/deletion?

Answer 13

• mutation in coding seq
  -a single base pair is added or removed, causing all of the amino acids to be off

Question 14

What are the four regulatory mutations?

Answer 14

1- Promotor mutation

2- polyadenylation mutation

3- splice site mutation

4- DNA replication mutation (triple repeat expansion)

Question 15

Describe the process of strand slippage, and what type of mutation is it?

Answer 15

-regulatory, DNA replication mutation

1 - DNA segment contains CAG-triplet repeats
2 - DNA polymerase slips off of strand during synthesis of daughter strand , causing the formation of hairpin loop
3 - in the next replication cycle, CAG repeats number is increased due to the hairpin loop (ex: beginning 6 CAG to end 11 CAG)

Question 16

What could result from a promotor mutation?

Answer 16

Change in timing/amount of transcription

Question 17

What could result from a polyadenylation mutation?

Answer 17

Alter sequence of mRNA

Question 18

what may result from a mutation in the splice site?

Answer 18

Retaining introns/excluding exons

Question 19

What may result from a DNA replication mutation?

Answer 19

increase (sometimes decrease) number of short repeats of DNA

Question 20

What are the three types of reverse mutations?

Answer 20

1- true reversion

2- Intragenic reversion

3- second site/intergenic/silence reversion

Question 21

Describe a true reversion?

Answer 21

There is a second mutation (revertant) in the same codon that causes the mutated codon to encode for the wild-type amino acid

Question 22

Describe an intragenic reversion?

Answer 22

-a mutation that occurs in the same gene, but not the same spot
-two base pairs are deleted, following the insertion of two new base pairs, restoring the reading frame to wild type

Question 23

Describe a second site/intergenic/repressor reversion

Answer 23

-a mutation that occurs not in the same gene, occurs in a second gene
- represses certain genes in order to restore to wild-type or near wild-type

Question 24

What is the difference between a spontaneous and induced mutation?

Answer 24

Spontaneous - no external reason for mutation outside of cell

induced - can detect a reason outside of the cell for mutation

Question 25

Describe chemical mutagen: Hydroxylating agent

Answer 25

• addition of hydroxyl (OH) group to a recipient compound by a donor known as hydroxylating agent
• hydroxylamine is a hydroxylating agent that adds a hydroxyl group to cytosine by displacing an H2, creating hydroxylaminocytosine.
  -Hydroxylaminocytosine pairs with guanine but frequently mispairs with adenine, leading to transition mutations

Question 26

What is the purpose of the Ames test?

Answer 26

• Uses bacteria to detect carcinogens
• determine if chemicals can cause mutations in the cell
• chemicals that have mutagenic effect on cells is considered carcinogenic
• detects a reversion from his- to his+

Question 27

Why add s9 activation enzymes from rat liver in the Ames test?

Answer 27

The S9 extract allows you to see if a mutagenic substance can be created by digestive reactions.

Question 28

How does his- strains differ with base-pair substitutions and frameshift mutations?

Answer 28

Base pair sub - there is consistent growth in revertant colonies as medium increases

frameshift - there is no growth at all ]

conclusion: his- strains only revert under base-pair substitution

Question 29

What are UV photoproducts?

Answer 29

formation of photoproducts cause by UV irradiation

formed from adjacent pyrimidines (TT)

distorts double helix, blocks replication

Question 30

How does UV radiation damage DNA?

Answer 30

• mutagenic properties of UV radiation derives from legions it creates in DNA
• alters DNA nucleotides by inciting formation of additional bonds known as photoproducts (TT bonds)

Question 31

Describe photoreactive repair?

Answer 31

1- UV light causes a thymine dimer to form (TT)

2- photolyase binds to the dimer

3- visible light (300-500 nm) energized photolyase

4- photolyase released, DNA repaired

Question 32

Describe Nucleotide excision repair (NER)?

Answer 32

1- UVR A binds to UVR B and helps it get to the damage site, binding opposite of the thymine dimer

2- UVR A leaves, and UVR C binds to UVR B, catalyzing 3’ and 5’ cuts.

3 - UVR D (helicase) releases damaged strand, DNA poly + ligase fill gaps, restoring DNA

Question 33

What is Xeroderma Pigmentosum?

Answer 33

a skin condition caused by a mutation in the NER system, individuals are homozyous recessive and cannot go into the sun

• freckles
  -photophobia
• skin cancer
  -tumor in eye
  -premature skin aging
• neurological problems

Question 34

Describe Mismatch repair?

Answer 34

1 - mutH binds to hemi-methylated CTAG recognition site

2 - MutS binds to the mismatch site

3- MutL is attracted by MutS, forms the bed which contacts MutH

4 - MutH cleabes from pre mismatch to site of methylation, causing single strand gap

5 - gap filled in by ligase and polymerase

Question 35

What are the three types of DNA repair systems?

Answer 35

1 - photoreactive repair

2 - nucleotide excision repair (NER)

3 - Mismatch repair

Question 36

Describe Meiotic recombination?

Answer 36

Crossing over occurs during meiosis between two homologous non sister chromatids….

1 - protein binds to one of the strands, causing a double strand break, making the strands offset

2 - Enzymes bind to the strands, digesting them 5-3 creating single strand segments

3 - proteins bind to exposed single strands, top strand falls between the two bottom strands (strand invasion), causing bottom strand to form a D Loop/holliday junction/heteroduplex region

4 - strands are extended by polymerase, displaced D loop, pairs with complementary single strand dna to form second heteroduplex region

5 - dna poly extension fills gaps in strand paired with d loop, forming a second d loop in top strands

6 - double hollidays junctions form

Question 37

What are the two possible outcomes of meiotic recombination?

Answer 37

Opposite sense resolution:
- EW and NS cuts : common, results in recombination of flanking genes, creates offset heteroduplex regions.

Same sense resolution:
- EW and EW cuts : not common, no recombination of flanking genes, creates offset heteroduplex region