Molecular Biochemistry Week 3

Question 1

Name differnt types of damage that can affect DNA

Answer 1

• Environmental damage:
  Chemical agent and radiation
• spontaneous damage

Question 2

Name the 2 reasons for mutations

Answer 2

• Uncorrected replication errors
• DNA damage from : oxidative deamination, radiation and chemical agents

Question 3

Name the 3 different types of mutations

Answer 3

• point mutation
• Insertion
• Deletion

Question 4

What is point mutation

Answer 4

When one base is substituted with another

Question 5

What is insertion

Answer 5

When one or more nucleotides are added

Question 6

What is deletion

Answer 6

When one or more nucleotides are removed

Question 7

Explain the process for general DNA repair

Answer 7

• Damaged or mismatched DNA is removed
• DNA polymerase then fills in the gaps using the undamaged strand as a template
• DNA ligase then seals the new strand into the DNA

Question 8

Name the key enzymes involved in general DNA repair processe

Answer 8

Endonuleases
Exonucleases
DNA polymerase
DNA ligase

Question 9

Name 4 differnt types of DNA Repair mechanisms

Answer 9

• Nucleotide excision repair (NER)
• Base Excision Repair (BER)
• Mismatch Repair (MMR)
• Transcritpion- Coupled Repair (TCR)

Question 10

Explain the function of the DNA repair mechanism nucleotide Excision Repair (NER) + what it is used for

Answer 10

Removes a group of nucleotides including the damaged ones
- used for bulky lesions like Uv-induced damage

Question 11

Explain the function of the DNA repair mechanism Base excision repair (BER) and what it uses

Answer 11

• Creates and AP site , which is then cut and repaired
• uses glycosylase to remove a damaged base

Question 12

Explain the function of the DNA rapid mechanism - Mismatch repair

Answer 12

• It fixes mismatched base pairs from replication errors

Question 13

Explain the the DNA repair mechanism- Transcription coupled repair (TCR)- when it is triggered + what is recruited and what do they do

Answer 13

• Triggered when transcription machinery detects DNA damage in active genes
• repair enzymes is recruited to fix the damage before transcription resumes

Question 14

Cytosine can be deaminated to form what

Answer 14

Uracil

Question 15

Bases can be lost through what?

Answer 15

• Through hydrolysis of the sugar-phosphate backbone

Question 16

Deaminating agents like nitrous acid converts these to what?
- Cytosine -
-Adenine-
-Guanine

Answer 16

-cytosine- Uracil
-Adenine- Hypoxanthine
-Guanine- Xanthine

Question 17

Name an alkylating agent

Answer 17

• Dimethyl sulfate

Question 18

What is the purpose of Base excision repair(BER)

Answer 18

-Fixes small, non bulky lesions

Question 19

Explain the full process in BER + enzymes starting with Glycosylase

Answer 19

• Steps:

Glycosylases remove abnormal bases → leaves AP sites (apurinic/apyrimidinic).

AP endonucleases cut near the AP site (5’ side).

Lyase removes the sugar-phosphate remnant.

DNA pol I fills the gap.

DNA ligase seals the strand.

Question 20

What doe Uv light cause

Answer 20

• Pyrimidine dimers

Question 21

What is the function of the Uv light

Answer 21

-Block DNA polymerase, stopping replication

Question 22

What is the purpose of Nucleotide Excision Repair (NER)

Answer 22

• Removes bulky lesions like T-T dimers or large chemical adducts

Question 23

Explain all the steps in NER including enzymes starting from (uvrABC)

Answer 23

Steps:

1.UV-specific endonuclease (uvrABC) cuts both sides of the dimer.

Damaged fragment is excised.

DNA pol I fills in the gap.

DNA ligase seals it.

Question 24

Explain the full process of Mismatch repair in DNA

Answer 24

-Mismatch Repair Steps:

Recognition of mismatch.

Endonuclease cuts the strand.

Exonuclease removes the error and nearby nucleotides.

DNA polymerase fills the gap using the sister strand as a template.

DNA ligase seals the strand.

Question 25

What is Mismatch reapir in E coli handled by

Answer 25

- Mut proteins

Question 26

Explain the role of Mut proteins in Mismatch repair in Ecoli

Answer 26

Discriminates correct vs. incorrect strand via methylation (GATC sites methylated on A by DNA adenine methylase). The new (unmethylated) strand is repaired.

Question 27

In humans what does Mismatch repair involve

Answer 27

Homologs like MSH2 and MLH1

Question 28

What do mutations in homologs in human MMR lead to

Answer 28

- Lynch syndrome

Question 29

What causes double strand break repair

Answer 29

- Ionizing radiation, chemotherapy, oxidative stress

Question 30

Name the 2 mechanisms in Doube strand repair

Answer 30

-NHEJ -HR

Question 31

What is the challenge in Double strand break(DSB) repai

Answer 31

Both dna strands are broken so there is no template strand

Question 32

Explain the NHEJ repai mechanism in double strand break repair

Answer 32

- Directly links broken ends

Question 33

What do defects in the NHEJ repair mechanism in double strand repair cause

Answer 33

Cancer and immunodeficiency

Question 34

What does Homologous recombination (HR) repair mechanism in Double strand break repair use + what phases in the cell cycle are they active

Answer 34

A homologous sequence as a template - Active in Late S and G2 phase

Question 35

What does HR repair require

Answer 35

BRCA1/BRCA2

Question 36

When in the cell cycle is NHEJ repair mechanism active

Answer 36

All throught the cell cycle

Question 37

What can cause mismatch bases

Answer 37

DNA replication errors

Question 38

Which repair mechanism is more accurate in Double strand break repair - DSB and why

Answer 38

Homologus Recombination as it uses a Homologus sequence