Brainscape's Knowledge GenomeTM

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


See full index

Molecular Biology - Jourdan > Lecture 4 > Flashcards

Lecture 4 Flashcards

You may prefer our related Brainscape-certified flashcards:
AP® Biology flashcards Biology 101 flashcards
0
Q

How many accidental base changes result in a permanent mutation?

A

fewer than 1/1000

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

What can cause damage to DNA?

A

Replication errors and accidental lesions that occur in the genome.

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

How is the importance of our ability to repair damage evidenced by?

A

By seeing what the mistakes can lead to (genetic defects) and how there are so many pathways and proteins to repair damaged DNA

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

What is depurination?

A

5000 purine bases lost everyday due to a spontaneous reaction (Hydrolysis of the N-glycosyl linkage)

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

What is spontaneous deamination?

A

On cytosine, the amine group is hydrolyzed and then it turns into a Uracil on DNA. It occurs 100 bases/day

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

What does depurination result in during replication?

A

The lost of the purine causes the DNA template to not have a base so the DNA polymerase doesnt know what base to put in

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

What are pyrimidine dimers? What is the cause?

A

A DNA mutation that can produce a covalent linkage between two adjacent (same chain) pyrimidines (T-T or C-T)

Cause: Exposure of UV radiation from sun, Exposure to reactive forms of oxygen in the cell or chemicals in the environment

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

If the DNA replicated is damaged and unrepaired, what can happen?

A

These changes lead to either a deletion or a base pair substitution in the daughter strand

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

What are DNA glycosylases?

A

An enzyme family of at least 6 different types that recognize a specific type of altered base and catalyzes its removal.

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

What is Base excision repair?

A

When DNA glycosylases probe for damage on DNA by mediating “flipping out” of base from the helix.
If it finds an incorrect base, it cleaves the glycosyl bond connecting base with sugar.
AP endonuclease and phosphodiesterase cut phosphodiester backbone.
Gap is repaired by DNA polymerase and DNA ligase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What are directly repaired beginning with AP endonuclease in Base excision repair?

A

Depurinations

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

What is nucleotide excision repair?

A

A repair mechanism that can repair any bulky lesion like those chemically-induced and thymine dimers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

How does Nucleotide excision repair work?

A

A multienzyme complex scans DNA for distortion in double helix instead of specific base change like in BER.
Cleaves phosphodiester backbone on both sides with excision nuclease.
DNA helicase peels lesion containing strand away
Large gap is repaired by DNA polymerase and ligase

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

What is transcription-coupled repair?

A

When cells can preferentially direct DNA repair to sequences that are being actively transcribed by linking RNA polymerase with DNA repair. Sequences that urgently need repair are those being transcribed

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

What does RNA polymerase do during transcription-coupled repair?

A

It stalls at lesions and directs repair machinery there

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

What does transcription-coupled repair work with?

A

BER, NER, and others to repair genes that are being expressed when the damage occurs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is transcription-coupled repair specific for?

A

For DNA that is being transcribed (linked to the RNA polymerase).
Non-transcribed strand is repaired at the same rate as DNA not being transcribed. Transcribed has first priority.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is Cockayne’s syndrome?

A

It is a defect in transcription-coupled repair
The symptoms are growth retardation, skeletal abnormalities, sensitivity to sunlight.
RNA polymerase is permanently stalled at sites of damage in important genes

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

The structure of DNA is optimal for what?

A

Damage detection and repair

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

How id DNA molecule optimally constructed for repair?

A
  1. There are two strands, so one can act as a backup copy

2. The nature of 4 bases makes distinction between damaged/undamaged obvious.

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

How is damage to bases obvious?

A

Every deamination event forms an unnatural base. Examples: cytosine to uracil; Thymine cannot be deaminated, etc.

21
Q

Why is RNA not the hereditary information?

A

Possible reason could be that the difference between deaminated cytosine and natural uracil could not be distinguished

22
Q

What is problematic with methylated cytosines?

A

In vertebrate DNA, cytosine is methylated at some CpG sequences and in inactive genes. If deamination of methyl-C occur it produces a T mismatched with G. Since T is normal in DNA, it can not be easily detected

23
Q

How are deaminated methyl-C fixed? Is this method effective?

A

A special DNA glycosylase recognizes the T mismatched with G and removes the T.
This method is ineffective because even though only 3% of C nucleotides in human genome are methylated, they account for 1/3 of all point mutations associated with inherited human diseases, so this repair isnt working

24
Q

What are causes of double-strand breaks?

A

ionizing radiation, replication errors, oxidizing, agents and other metabolites

25
Q

What happens if double strand break repair is left unrepaired?

A

The chromosomes would break into smaller fragments and be lost

26
Q

What is non-homologous end joining?

A

A double strand break repair mechanism that degrades the uneven ends (nucleotides casualties) brings broken ends together and rejoins by DNA ligation; one or more nucleotides will be lost.

27
Q

Is the double strand break repair mechanism safe?

A

It predominates in humans and is generally ok since so little of genome is protein coding. Typical 70 year old will have 2000 of these DNA scars

28
Q

What is homologous recombination?

A

When there is an accidental double-strand break in one of the sister chromatids. The ends are degraded to be even, and using information from sister chromatid, DNA is repaired accurately with no deletion

29
Q

What are checkpoints?

A

Ensure the completion of one stage in the cell cycle before the next can begin. Gives the cell extra time to repair DNA damage

30
Q

What various checkpoints are triggered by DNA damage in the cell cycle?

A

Checkpoints are at:
G1 that blocks entry into S phase
Slows down progression through S phase
Blocks transition from G2 to M phase

31
Q

What are the functions of homologous recombination?

A
  • Repair of double-strand breaks especially at stalled or broken replication forks
  • Exchange of genetic information to create new combinations of genetic sequences (crossing over and gene conversion in meiosis)
  • Mechanical role in assuring accurate chromosome segregation
32
Q

The process of homologous recombination can be found in what organisms?

A

Fundamental process is common to all organisms

33
Q

How does HR repair stalled or broken replication fork?

A

Process requires base pairing but it doesnt have to be a perfect match.
Replication fork will collapse and break when nick is encountered.
5’ exonuclease chews back parental strand to prepare for “strand invasion”
Strand breaks/dissociate
DNA synthesis continues

34
Q

What is Strand invasion?

A

Pairs single-stranded DNA with complementary strand in different double-stranded helix, and forms a region of heteroduplex DNA

35
Q

Where does homologous recombination take place?

A

Between sequences that are similar.

36
Q

When there are strands of DNA in a test tube and strands are separated(denaturation) the DNA does what?

A

DNA duplexes “sample” each other looking for regions of homology

37
Q

What is hybridization?

A

DNA double helix reforming from its separated single strands

Also called renaturation

38
Q

Once a region of homology is found what happens?

A

The single strands rapidly pair up

39
Q

What is heteroduplex DNA?

A

Creation of a double helix from strands that originate from different molecules

40
Q

What does DNA hybridization require?

A

A single stranded DNA freed from pairing with complement so it can pair with the 2nd strand

41
Q

How does the single stranded DNA stay in single stranded form and not hair pin?

A

The single-stranded invading strand is directed by RecA (Rad51 in eukaryotes) and other proteins.

42
Q

What occurs during the DNA synapsis reaction?

A

RecA Binds cooperatively to single stranded DNA and holds it together with the double helix until homologous sequence is found. At some points there is 3 stranded DNA. The single strand searches via an unknown mechanism

43
Q

Once homologous sequence is identified after DNA synapsis reaction what occurs?

A

Strand invasion occurs and forms a heteroduplex

44
Q

What is the branch point?

A

Where you have the first have the hybridization of the two different strands

45
Q

What is branch migration?

A

movement of the branch point: once strand invasion occurs, the point of exchange can move

46
Q

During branch migration what does an unpaired region of one single strand do to the other paired region?

A

Displaces a paired region on the other

47
Q

When can branch migration occur?

A

Happens spontaneously in both direction or can be catalyzed by special helicase to move in one direction (ATP)

48
Q

Compare and contrast double -strand break repair processes of non-homologous end joining and homologous recombination?

A

Non-homologous:
-no template required
-creates a mutation at the site of repair
-can also create translocations
Homologous:
-Uses daughter DNA duplex as template
-No loss or alteration of DNA at repair site
-Can repair other types of DNA damage (very versatile, mechanism and proteins conserved in all organisms)

49
Q

Describe in detail the repairing of double stranded breaks by HR

A
  • 5’ ends degraded by exonuclease
  • one 3’ end invades homologous template and primes repair DNA synthesis
  • The newly synthesized 3’ end of the invading strand is then able to anneal to the other original 3’ overhand in the damaged chromosome through complementary base pairing
  • Gaps are filled in and ligated
50
Q

What are some problems that still can occur even with accurate repair process?

A

Loss of heterozygosity

  • Use of a non-functioning homolog (bad gene x) to “repair” the other homolog
  • Critical first step in cancer development, rare
51
Q

How are repairs prevented when there is no damage?

A
  • Repair proteins dispersed throughout the cell
  • After damage, repair occurs in “factories” or “foci” at the sites of damage
  • Brca2 maintains Rad51 inactive (mutation in BRAC2 lead to increase risk of breast cancer)

Molecular Biology - Jourdan (8 decks)

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