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Biochem FINAL > Chapter 35: DNA Repair and Recombination > Flashcards

Chapter 35: DNA Repair and Recombination Flashcards

0
Q

DNA is the only cellular macromolecule that can be _____. _____ can have a very high cost.

A

Repaired; Mutations

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1
Q

A _____ is a physical or chemical agent that changes the genetic material.

A

Mutagen - causes mutations

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2
Q

What is the purpose of the Ames’ test?

A

To test if a chemical is a mutagen

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3
Q

What repairs DNA?

A

1.) DNA Polymerase II does a great job, but not good enough

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4
Q

DNA Polymerase II introduces errors in about _____ nucleotides added, which it _____.

A

1 in 10^7 nucleotides added which it does NOT correct

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5
Q

Most mistakes and damages to DNA are corrected ( _____ - leaving just a few - only _____ are left

A

99% - leaving just a few - only 1 in 10^9 errors are left

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6
Q

When exposed to oxygen metabolism, what error occurs and how is it fixed?

A

8oxoG, AP site error fixed by base excision repair

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7
Q

When exposed to replication infidelity, what error occurs and how is it fixed?

A

Mismatch error fixed by mismatch repair

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8
Q

When exposed to UV light, what error occurs and how is it fixed?

A

CPD error (Cyclobutane pyrimidine dimers) fixed by nucleotide excision repair

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9
Q

When exposed to X-rays, what error occurs and how is it fixed?

A

Double-strand break error fixed by recombinational repair

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10
Q

First type of repair is called DIRECT repair:

A

Damaged bases can be directly repaired.
In a few cases, the covalent modifications of nucleotides can be reversed by specific enzymes
Simple

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12
Q

Example 1 of direct repair: UV exposure

What happens? What repairs it directly?

A

When exposed to UV light, 2 thymines will form a dimer and create a kink in the DNA. When T-T occurs, a part of the DNA is skipped (Frameshift mutation - protein would not be made).
DNA photolyase takes away the bond between 2 thymines

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13
Q

Example 2 of direct repair: Alkylating Agents causing base damage
What happens? What repairs it directly?

A

Aflatoxin (a fungus found in maize, nuts) is converted into a highly reactive epoxide that reacts with G, forming a compound that, during replication, converts a G-C to A-T bp.
Repaired by Alkyltransferase which recognizes that guanine is methylated and normal structure of G restored

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14
Q

_____ in cigarette smoke and automobile exhaust can also be converted into _____.

A

Benza(pyrene) converted into reactive epoxides

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15
Q

Second type of repair is called: Base Excision Repair (BER)

A

Involves a category of enzymes known as DNA-N-glycosylases

Depending on the species, this repair system can eliminate abnormal bases

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16
Q

DNA-N-glycosylases can recognized a _____ and cleave the bond between it and the sugar in the DNA.

A

Single damaged base

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17
Q

DNA-N-glycosylases removes _____ and replaces _____ using Pol adding 3’ ends then ligase attaching to 3’ end.

A

Removes one base, excises several around it

Replaces with several new bases

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18
Q

Some examples of abnormal bases that BER can repair are…

A

Uracil, thymine dimers, 3-methyladenine, and 7-methylguanine

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19
Q

Oxygen radicals in the cell can convert…

A

Guanine to Oxoguanine

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20
Q

Without OGG1, guanine can…

A

Only base pair with adenine

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21
Q

Oxoguanine base pairs with?

A

C (Normal)

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22
Q

With a few generations of replication, there will be a _____ BP where there was a _____ base pair.

A

A-T where there was a C-G

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23
Q

Deamination of nitrogenous bases occurs by…

A

Nitrous acid

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24
Q

When C–>U is deaminated, a C-G BP can convert to a…

A

A-T BP

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25
Q

When A–>Inosine is deaminated, an A-T BP converts to a…

A

G-C BP

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26
Q

When G–>Xanthine is deaminated, a G-C BP is converted to a…

A

A-T BP

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27
Q

When G–>Oxanine is deaminated, a G-C BP is converted to a…

A

A-T BP

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28
Q

It is important to note that there are several places where _____ base can be repaired, as there are several places where it can be damaged by _____, _____ and _____.

A

Where guanine base can be repaired.

Damaged by alkylation, oxidation and radiation

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29
Q

When N-glycosylase recognizes an abnormal base and cleaves the bond between the P and sugar, _____ is created.

A

A nucleotide that is either apyrimidinic or apurinic

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30
Q

When a nucleotide is apurinic or apyrimidinic, _____ recognizes the missing base and cleaves the _____.

A

AP endonuclelease

backbone on the 5’ side of the missing base

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31
Q

_____ uses 5’ to 3’ exonuclease activity to remove the damaged region and fill in with normal DNA. _____ seals the region.

A

DNA polymerase; DNA ligase

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32
Q

Modified base U (deamination of C). What glycosylases recognize them?

A

U/G repaired by U/G glycosylase

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33
Q

Modified 8-oxoG paired with C (oxidation of G) repaired by…

A

8-oxoguanine glycosylase

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34
Q

When adenine is across from 8-oxoG, this is considered a…

A

Misincorporation

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35
Q

Deamination of 5-meC results in…

A

T/G repaired by thymine glycosylase

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36
Q

Alkyl-adenine (3-meA, 7-meG, hypoxanthine) is repaired by…

A

Alkylated adenine glycosylase

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37
Q

A disease caused by failure in repair: Sickle Cell Anemia?

A
  • RBCs have the protein called Hb
  • *A single base change - substitution causes the disease (Mutation in the gene of Hb)
  • Less O2, block blood vessels and short life expectancy
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38
Q

Third type of repair is called: Nucleotide Excision Repair (NER)

A
  • Signal for NER is structural distortion.
  • Ultraviolet repair enzyme A (UvrA) recognizes bulky regions and recruits UvrB (5’) and UvrC (3’) to make cuts in backbone around the distortion.
  • UvrD kills off the whole bulky lesion from where cuts are made
  • DNA pol removes the gap and DNA ligase seals the nick
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39
Q

Nucleotide excision repairs takes ALL _____ together, unlike _____.

A

ALL nucleotides together, unline BER which takes them separately

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40
Q

What happens when excision repair does not function?

A

Mutations in any of at lease 7 genes in NER cause an inherited sensitivity to UV-induced skin cancer called Xeroderma pigmentosum. The XP proteins are among >30 required for nucleotide excision repair.

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41
Q

Patients with XP have 3 things…

A

Sensitivity to the sun, much greater risk of skin cancer, and about 20% have neurological disorders

42
Q

Errors during replication are exceedingly rare, less than _____ BPs

A

once in 10^9 BPs

43
Q

Fourth type of repair: Mismatch Excision Repair: Proofreading enzymes correct errors made during replication:

A

-The 3’->5’ exonuclease activity of DNA pol recognizes mismatched bases and excises them

44
Q

If errors slip through proofreading in bacteria:

A

Methyl-directed mismatch repair finds these errors on newly synthesized strands and corrects them

45
Q

If errors slip through proofreading in eukaryotes:

A

Mismatch repair finds these errors on newly synthesized strands and corrects them

46
Q

When DNA pol is reading through and puts in a wrong base, what repair is needed?

A

Mismatch Repair System

47
Q

If proofreading fails, the _____ systems comes to the rescue.

A

Methyl-directed mismatch repair system

48
Q

Mismatch repair system is…

A

Found in all species

49
Q

In humans, mutations in the mismatch repair system are associated with particular types of _____.

A

Cancer

50
Q

Methyl-directed mismatch repair recognizes _____, excises the _____, and then carries out _____.

A

Recognizes mismatched BPs
Excises the incorrect bases
Carries out repair synthesis.

51
Q

The combined action of _____, _____ and one of many different exonucleases removes a segment of the new strand between the _____ cleavage site and a point just beyond the mismatch.

A

DNA helicase II, SSB

Between the MutH

52
Q

The resulting gap in mismatch repair is filled in by _____ and the nick is sealed by _____.

A

Filled in by DNA pol III

Sealed by DNA ligase

53
Q

Hereditary Non-polyposis Colon Cancer (HNPCC)?

A

Results from mutations in genes involved in DNA mismatch repair, including:

  • several dif MutS homologs
  • Mut L homolog
  • Other proteins: perhaps they play the role of MutH, but not by recognizing hemi-methylated DNA
54
Q

The fifth type of repair is called: Double-strand break repair and recombination, What is recombination?

A

Exchange or transfer of pieces of DNA from one chromosome to another or within a chromosome

55
Q 
What is homologous recombination?
Homologous recombination (HR) - repair of broken DNA using the intact homologue, very similar to meiotic recombination. Very accurate.
A

-Repair of broken DNA using the intact homologue, very similar to meiotic recombination - VERY accurate
-Occurs between pieces of DNA that have closely related sequences
Ex: Genetic recombination

56
Q

Nonhomologous recombination occurs between…

A

Unrelated sequences (ex: transposons)

57
Q

Site-specific recombination is…

A

Recombination at a specific location

58
Q

Expansion of a CAG (glutamine) triplet repeat within the…

A

Huntingtin gene

59
Q

Normal people have _____ CAG repeats

Disease state?

A

Normal - 10-29 times CAG repeats

Disease - 40-80 times CAG repeats

60
Q

If the CAG repeats are less than or = to 28,

A

HD will not develop

61
Q

If the CAG repeats are between 29-34,

A

Individual will not develop HD but the next generation is at risk

62
Q

If the CAG repeats are between 35-39,

A

Some, but not all, individuals in this range will develop HD, next generation is also at risk

63
Q

If the CAG repeats are greater than or = to 40,

A

Individual WILL develop HD

64
Q

Cancers are caused by mutations in the genes that _____.

A

Control growth

65
Q

DNA repair enzymes act as…

A

Tumor suppressors

66
Q

If both copies of a DNA repair enzyme are mutated…

A

Cancer is more likely to develop

67
Q

Because tumors lack DNA repair systems, damaging the DNA with chemicals such as _____ and _____ is a strategy to prevent cancer growth.

A

Cyclophosphamide and cisplatin

68
Q

Why is recombination needed?

A
  • Mutation gives new genetic variation

- Recombination within a genome - parent chromosomes are NOT the same as progeny chromosomes of DNA

69
Q

_____ probably evolved to help DNA repair (confers a selective advangtage)

A

Recombination enzymes

70
Q

Severe lesions in DNA can be repaired by…

A

Strand exchange from intact daughter chromosome to defective daughter

71
Q

Very important process - More than _____ genes from E. coli are involved in…

A

100 genes

Recombination and repair

72
Q

What happens when double-strand break repair doesn’t function?

A

BRCA1 and BRCA2 - required for normal recombination repair of DS breaks in DNA
Approx. 12,000 cases caused by mutations in these two genes
Breast cancer risk

73
Q

DSBs probably most severe form of DNA damage, can cause _____.

A

Loss of genes or even cell death (apoptosis)

74
Q

DSBs caused by 4 things:

A
  1. ionizing radiation
  2. certain chemicals
  3. some enzymes (topoisomerases, endonucleases)
  4. torsional stress
75
Q

Non-homologous end joining (NHEJ)

A
  • Ligating non-homologous ends.

- Prone to errors, ends can be damaged before re-ligation (genetic material lost) or get translocations.

76
Q

Which is more often used in plants and animals? HR or NHEJ?

A

NHEJ&raquo_space; HR in plants and animals

77
Q

3 Types of Recombination

A

Homologous
Site-specific
Transposition

78
Q

Homologous recombination occurs between sequences that are…

A

Nearly identical (ie. during meiosis)

79
Q

Site-Specific recombination occurs between sequences with a limited _____; involves specific sites (occurs during recombination in yeast gene knock-in/knock-out)

A

Limited stretch of similarity

80
Q

Transposition – DNA element moves _____, usually _____ sequence similarity involved

A

From one site to another; little similarity

81
Q

Failure of proper recombination and chromosomal segregation - Clinical Significance: _____

A

Aneuploidy

82
Q

The point at which two sister chromatids crossover is called a _____.

A

Chiasma (chi)

83
Q

What are two practical uses of recombination?

A
  1. Used to map genes on chromosomes - recombination frequency proportional to distance between genes
  2. Making transgenic cells and organisms
84
Q

Crossing over accounts for the various _____.

A

Recombinant phenotypes

85
Q

Slipped mispairing causes _____.

A

Repeat expansion

86
Q

. BRCA mutations account for _____ inherited breast cancer

A

70-80%

87
Q

BRCA1 gene is responsible for _____.

A

Repairing of DNA damage. Tumor suppressor

88
Q

If the BRCA1 gene is mutated,

A

There is no more DNA repair.

89
Q

If there is a change to a cell check point gene and that gene can no longer be repaired, _____.

A

Cells grow out of control.

90
Q

Many cancers are caused by defective DNA repair. Treat cells with _____ and because of lack of DNA repair, _____.

A

Treat with cisplatin

The cells die

91
Q

“Transposons” =

A

“Jumping Genes”

92
Q

Transposons are DNA segments spontaneously _____.

A

Entering or exiting chromosomes

93
Q

Transposition into a gene constitutes a _____.

A

Large insertion (Gene normally inactivated)

94
Q

Transposition out of a gene may…

A

Restore gene function

95
Q

_____ varied as DNA sequences jumped in and jumped out, messing with the pigment genes.

A

Kernel color

  • no pigment
  • partial pigment
  • normal pigment
96
Q

How does the Ames’ test work?

A

Colonies (bacterial growth) are added to a Petri dish that is missing a nutrient required for growth to occur further (on histidine). If the colonies added are not growing more colonies, then they are not mutagenic. If they are growing colonies, they are mutagenic.

97
Q

A mutation which inactivates telomerase would result in:

  • An increased rate of replication
  • A progressive shortening of the linear ends of the chromosome
  • A high number of errors located near the chromosome end
  • A rapid lengthening of the linear ends of the chromosome
  • The formation of branched structures in the center of the chromosome
A

A progressive shortening of the linear ends of the chromosome

98
Q

Hydrolytic deamination of cytosine produces:

  • uracil
  • cytosine
  • guanine
  • adenine
  • thymine
A

Uracil

99
Q

Exposure to UV radiation can result in formation of:

  • reactive epoxide species
  • methylated cytosines
  • T-T dimers
  • triplet repeats
  • telomeres
A

T-T dimers

100
Q

Huntingtons disease is caused by:

  • suppressor mutants
  • cytosine deamination
  • trinucleotide expansion
  • double strand break repair defects
  • replication origin defects
A

Trinucleotide expansion

101
Q

Which of the following is used in both excision repair and DNA replication in E. coli?

  • Primase
  • Endonuclease
  • DNA polymerase III
  • Origin binding protein
  • DNA polymerase I
A

DNA polymerase I

102
Q

BRCA1 and BRCA2 are involved in:

  • DNA replication
  • repair of T-T dimers
  • mismatch repair
  • double strand break repair
  • All of the above
A

Double strand break repair

Biochem FINAL (6 decks)

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