Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Molecular Biology (BYMB1) > Week 4: DNA repair > Flashcards

Week 4: DNA repair Flashcards

You may prefer our related Brainscape-certified flashcards:
AP® Biology flashcards Biology 101 flashcards
1
Q

What percentage of random changes every day accumulate permanent mutations?

A

0.02%

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is depurination?

A

Purine bases lost by cells (18,000 a day)

Because their N-glycosyl linkages to deoxyribose is hydrolysed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Name the random change that occurs to cytosine molecules at the rate of 100 bases per day

A

Deamination of cytosine to uracil

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

How are DNA bases occasionally damaged?

A

Encounters with reactive metabolites produced by the cell including reactive forms of oxygen and the high energy methyl donor S-adenosymethionine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What mutations can ultraviolet mutations cause?

A

Can produce a covalent linkage between two adjacent pyrimidine bases in DNA e.g to form thymine dimers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What would happen if uncorrected DNA is replicated?

A
  1. Deletion of one or more base pairs
    Or
  2. Base pair substitution in the daughter DNA chain

The mutations would then be propagated throughout subsequent cell generation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

How is h DNA helix suited for repair?

A

It carries two separate copies of all genetic information (one in each of its two strands)

If one strand is damaged the complementary strand is generally used to restore the correct nucleotide sequence of the damaged strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Why can organisms with large genomes not afford to encode their genetic information in any molecule other than the DNA double helix?

A

Because once damaged the chance of a permanent nucleotide change occurring in single stranded genomes is very high

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What happens in two of the most common pathways of DNA repair?

A
  1. The damage is excised
  2. Original DNA sequence is restored byDNA polymerase that uses the undamaged strand as its template
  3. A remaining break in the double helix is sealed by DNA ligase
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the function of DNA glycolases?

A

Recognition of a specific type of altered DNA and catalyse its hydrolytic removal from its sugar

Travel along the DNA using base flipping to evaluate the status of each base

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is base excision repair?

A

Involves DNA glycosylases that recognise a specific type of altered DNA and catalyse its hydrolytic removal. This includes removal of :

  • deaminated C’s or A’s
  • different types of alkylated or oxidised bases
  • bases with opened rings
  • bases in which carbon- carbon double bond has been converted to a single bond
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

How is an altered base detected within the context of the double helix?

A

An enzyme mediated ‘flipping out’ of the altered nucleotide from the helix which allows the DNA glycosylase to probe all faces of the base for damage

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the ‘missing tooth’ created by DNA glycosylase action recognised by?

A

AP (apurunic/ apryrimidinic) endonuclease

Signifies that the enzyme cleaves within the polynucleotide chain which cuts the phosphodiester backbone after which the resulting gap is repaired

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Depurinations leave a deoxyribose regardless with a missing base. What are they directly repaired beginning with?

A

AP endonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Explain nucleotide excision repair

A

This mechanism can repair the damage any large change in the structure the the DNA double helix.

  1. A large multienzyme complex scans the DNA for a distortion rather than for a specific base change
  2. Once it finds a lesion, it cleaves the phosphodiester backbone of the abnormal strand on both sides of the distortion
  3. A DNA helicse peels away the single strand oligonucleotide containing the lesion
  4. The large gap produced is repaired by DNA polymerase and DNA ligase
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Give examples of large lesions

A
  • those created by covalent reaction of DNA bases with larger hydrocarbons
  • various pyrimidine diners caused by UV radiation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is the function of AP nuclease?

A

Recognises any site in the DNA helix that contains deoxyribose sugar with a missing base

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is an alternative to base and nucleotide excision repair?

A

Direct chemical reversal of DNA damage

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is direct chemical reversal of DNA damage usually employed?

A

For highly mutagenic or cytotoxic lesions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Give an example of direct chemical reversal of DNA damage

A
  1. The alkylation lesion O6- methylguanine has its methyl group removed by direct transfer to a cysteine residue in the repair protein itself, which is destroyed in the reaction
  2. Methyl groups in the alkylation lesions 1-methyladenine and 3-methyl cytosine are burned off by an iron dependent demethylase, with release of formaldehyde from the methylated DNA and regeneration of a native base
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

How do cells direct DNA repair to the sequences that are most urgently needed?

A

They link RNA polymerase to the nucleotide excision pathway.
RNA polymerase stalls at DNA lesions and through the use of coupling proteins directs the excision repair machinery to these sites

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What happens to the stalled RNA polymerase when it reaches a lesion in bacteria?

A

(where the genes are relatively short)

RNA polymerase can be dissociated from the DNA, the DNA is repaired, the gene is transcribed from the beginning

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What happens to the stalled RNA polymerase when it reaches a lesion in eukaryotes?

A

(Where the genes are relatively long)

A more complex reaction is used to back up the RNA polymerase, repair the damage and then restart the polymerase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What caused by a defect in transcription coupled excision repair?

A

Cockayne syndrome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What do individuals who have Cockayne syndrome suffer from?

A
  • growth retardation
  • skeletal abnormalities
  • progressive neural retardation
  • sever sensitivity to sunlight
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

How is hypoxathine produced?

A

Deamination of A

27
Q

What is the simplest purine base capable of pairing with C?

A

Hypoxathine

28
Q

Why does DNA have T instead of U?

A

The repair system would not be able to distinguish between a deaminated C from a naturally occurring U

29
Q

What is employed when DNA suffers heavy damage and the normal repair mechanisms are insufficient to cope with it?

A

Translesion polymerase

Human cells have 7*

30
Q

Why are translesion polymerases not as accurate?

A
  • They lack exonucleic proofreading activity
  • Many are less selective than replicative polymerase in choosing which nucleotide to incorporate initially

Each translesion polymerase is give the chance to add only one or a few nucleotides before the highly accurate replication polymerase resumes DNA synthesis

31
Q

What causes DNA change?

A
  • spontaneous
  • endogenous factors
  • exogenous factors
32
Q

What are the two main types of spontaneous DNA damage?

A
  • hydrologic depurination

- hydrolytic deamination of bases

33
Q

What is formed when adenine is deaminated?

A

Forms hypoxanthine

34
Q

What is formed by the deamination of guanine?

A

Xanthine

35
Q

What are some endogenous factors?

A

Endogenous factors are produced by the metabolism of the cell

  • superoxide O2-
  • Hydrogen peroxide H202
  • Hydroxyl radicals OH
36
Q

What are some exogenous factors?

A
  • high energy radiation (UV,X-Ray and gamma radiation)

- organic compounds

37
Q

What is the relationship between wavelength and energy?

A 
Shorter wavelength= highest energy 
In order of longest wavelength 
UV-A
UV-B
UV-C
38
Q

What part of the DNA absorbs UV radiation

A

Aromatic rings

39
Q

X-ray wavelengths (0.01-10 nm), energy >

A

124eV

40
Q

Gamma radiation (<0.01nm) energy >

A

1,000,000 eV

41
Q

What does energy transfer lead to?

A

Ionisation and radical formation.

42
Q

What are the host harmful species arising from water and oxygen

A

OH- and O2 radicals

43
Q

What do alkylating agents do?

A

Transfer alkyl groups (methyl, ethyl etc) on electron rich atoms

44
Q

What are electron rich atoms found in DNA?

A

Nitrogen

Oxygen

45
Q

What is cis platin?

What does it do?

A

A cancer drug
It blocks transcription and DNA replication
Forms cross-links

46
Q

What are the consequences of DNA modification?

A
  • Modifications of bases can change base pairing
  • changed base pairing can result in a mutation
  • double strand breaks can lead to gene rearrangement and loss of numerous genes
  • mutations are inherited
  • crosslinking of DNA strands inhibits transcription, translation and can kill a cell
47
Q

What are the main types of mutations?

A
  • point mutation= change of a bp
  • deletion= one or several bp are lost
  • insertion= one or several by are inserted
48
Q

What is a silent mutation?

A

No consequences for the protein sequence

49
Q

What is a nonsense mutation?

A

Protein sequence changed

Stop codon prematurely added

50
Q

What can mutations in promoter/activator regions do?

A

Can modify gene expression and regulation

51
Q

What can mutations in exons/ introns Boundaries do?

A

Disrupt the reading frame of a protein

52
Q

How do translesion polymerases pose risks to the cell?

A
  • responsible for most of the base substitution and single nucleotide deletion mutations that accumulate in genomes
  • they generally produce mutations when copying damaged DNA
  • they create mutations create mutations, at a low level, on undamaged DNA
53
Q

What would happen if major lesions (sites where both strands of the double helix are broken) were left unrepaired?

A

They would quickly lead to the breakdown of chromosomes into smaller fragments and loss of genes when the cell divides

54
Q

What is non-homologous end joining?

A

A fairly inaccurate method of double stranded break repair that predominates in humans
Broken ends are simply brought together and rejoined by DNA ligation, generally with the loss of nucleotides at the site of joining
Usually takes place when cells have not yet duplicated their DNA

55
Q

Where is nonhomologous end joining a common mechanism for repair?

A

In mammalian somatic cells

56
Q

What danger is presented by nonhomologous cell joining as a mechanism for repair?

A

There seems to be no mechanism to ensure that the two ends being joined together were originally next to each other in the genome this can cause unfavourable rearrangements:
One broken chromosome becomes covalently attached to each other which can result in chromosomes with two centromeres and chromosomes lacking centromeres altogether

57
Q

What is the function of telomeres?

A

Specialised structures that prevent the natural ends of chromosomes from being mistaken from broken DNA and “repaired”

58
Q

What is homologous recombination?

A

A more accurate method of double stranded break repair used only during and shortly after DNA replication (in S and G2 phase)
The DNA is repaired using the sister chromosome as a template

59
Q

Which method of double stranded DNA repair restores the original DNA

A

Homologous recombination

In non-homologous end joining the initial degradation of the broken DNA ends is important because the nucleotides at the site of the initial break are often damaged and cannot be ligated thus altering the original DNA sequence when repairing a broken chromosome

60
Q

What protein plays a central role in homologous end joining?

A

Ku protein

A heterodimer that recognised then grasps the broken chromosome ends

61
Q

What could cause a delay in the cell cycle?

A

The detection of DNA damage which can block entry from G1 to S phase, it can slow S phase once it has begun and it can block the transition from G to M phase. These delays facilitate repairs by providing the time for the repair to reach completion

62
Q

What is the function of the ATM protein?

A

It is a large kinase needed to generate the intracellular signals that sound the alarm in response to many different types of spontaneous DNA damage

63
Q

What is the disease caused by the absence of the ATM protein?

A 
Ataxia telangiectasia (AT)
Symptoms:
- neurodegeneration 
- predisposition for cancer 
- genome instability
64
Q

What is formed when cytosine is deaminated?

A

Uracil

Molecular Biology (BYMB1) (14 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions