Chapter 10: 10.1 Repair and Recombination

Question 1

Mutations in DNA occur when…

Answer 1

There is a change in the normal DNA sequence

Question 2

What are spontaneous mutations known as?

Answer 2

Point mutations

Question 3

What can point mutations be caused by?

Answer 3

• Errors in DNA replication
• Environmental exposure to damaging agents (UV light, radiation etc.)
• Harmful chemicals/toxins
• Byproducts of normal cell metabolism (e.g. lipid oxidation)

Question 4

What are the types of point mutations?

Answer 4

1. Nonsense mutations
2. Missense mutations
3. Silent mutations

Question 5

Nonsense mutations

Answer 5

A premature stop codon is introduced into a sequence

Question 6

Missense mutation

Answer 6

A change to the amino acid sequence

Question 7

Silent mutation

Answer 7

No change to the amino acid sequence

Question 8

Can mutations be beneficial?

Answer 8

Mutations can be:
* Beneficial
* Benign
* Harmful

Question 9

Beneficial mutations

Answer 9

Improves the fitness of an organism

Examples
* Resistance to a virus
* Lactose tolerance

Question 10

Benign mutations

Answer 10

Does not change the overall fitness of an organism

Examples
* Change in eye color or silent mutations

Question 11

Harmful mutations

Answer 11

Negatively impacts the fitness of an organism

Examples
* Development of diseases (cancer, birth defects)

Question 12

DNA polymerases make a mistake approximately every…

Answer 12

1 in 10,000 bases

Question 13

What is the actual number of mistakes that researchers found in DNA?

Answer 13

1 in 1,000,000,000 bases

Question 14

Processes:

DNA Replication Proofreading

Answer 14

1. The DNA polymerase(s) pause
2. 3’-5’ exonuclease removes the incorrect base pair
3. DNA polymerase(s) adds the correct one

Question 15

What is Base Excision Repair used to repair?

Answer 15

• Spontaneous natural deamination (C becomes U, resulting in a G-U mismatch)
• Depurination (loss of A or G) lesions

Question 16

Processes:

Base Excision Repair (BER)

Answer 16

1. DNA glycosylase identifies + removes U from sugar-phosphate backbone
2. APE1 endonuclease removes deoxyribose phosphate that is abasic
3. Specialized DNA polymerase adds a C

Question 17

How does DNA glycosylase remove the base?

Answer 17

Flips the base out of the helix and removes it

Question 18

When are Base Excision Repairs done?

Answer 18

BEFORE replication to prevent the mutation becoming permanent

Question 19

What does Mismatch Excision Repair do?

Answer 19

Fixes mutations that include:
* Base pair mismatches
* Small insertions/deletions of a few nucleotides

Question 20

When does Mismatch Excision Repair occur?

Answer 20

Made AFTER replication

Question 21

What is thought to be the mechanism behind Mismatch Excision Repair?

Answer 21

1. Specialized proteins determine which strand is the template and which is the mutated daughter strand
2. An endonuclease removes the mismatch/insertion/deletion
3. The daughter strand is repaired to produce an exact copy of the template strand

Question 22

What does Nucleotide Excision Repair fix?

Answer 22

A mutation that causes a distortion in the double helix structure of DNA
* E.x. Thymine dimers

Question 23

What is the process of Nucleotide Excision Repair?

Answer 23

1. Distortion is identified by a complex of XP-C and 23B proteins
2. TFIIH helicase, RPA, and XP-Gunwinds the DNA at this site
3. XP-G and XP-F work as endonucleases to cut out the distorted segment of DNA
4. DNA polymerase fills in the gap

Question 24

What are the two main systems for repairing double stranded DNA breaks?

Answer 24

• Non-homolgous end joining
• Homologous recombination

Question 25

How does NHEJ work?

Answer 25

Joins 2 non-homologous ends of DNA together * The two strands are usually still close enough together that they will be ligated back together

Question 26

What are some issues with NHEJ?

Answer 26

* Causes minor deletions * N-terminus of one gene can fuse to the C-terminus of a different gene

Question 27

# True or False: Small deletions from either ends in NHEJ is a major issue

Answer 27

Not necessarily * Majority of DNA is noncoding/intronic DNA

Question 28

Why is the fusing of the N-terminus of one end and the C-terminus of the other end problematic?

Answer 28

Results in chimeric genes * Can result in changes to cell function * Can result in cancer

Question 29

How does Homologous Recombination?

Answer 29

Damaged DNA sequence is copied from an undamaged or highly similar (homologous) copy of DNA * Repaired by an exchange of two different DNA strands (recombination)

Question 30

# True or False: Homologous Recombination is error-free

Answer 30

True