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Applied Biochemistry > DNA Repair and How do Mutations Occur? > Flashcards

DNA Repair and How do Mutations Occur? Flashcards

1
Q

types of genetic diseases (4)

A

chromosome disorders
single gene disorders
multifactorial or complex
sex linked and mitochondrial

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2
Q

Chromosome Disorders

4

A

Rearrangements/Translocations, Deletions, Insertions, Duplications

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3
Q

Single Gene Disorders

3

A

Dominant, Recessive, Codominant

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4
Q

Multifactorial or Complex

2

A

Multiple genes, gene-environment

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5
Q

general categories of mutations (2)

A

somatic

germline

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6
Q

Somatic mutation

A

non-inheritable

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7
Q

somatic mutation example

A

cigarette smoking and lung cancer, p53 mutations

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8
Q

germline mutation

A

inherited

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9
Q

— entries in OMIM currently

A

12,000+

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10
Q

causes of mutations (2)

A

spontaneous

induced

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11
Q

Spontaneous Mutations

A

arise naturally during DNA replication (mitosis) or during meiosis

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12
Q

Induced Mutations (2)

A

every day exposure

radiation
chemicals

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13
Q

silent mutation

A

no change

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14
Q

missense mutation

A

single amino acid change

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15
Q

nonsense mutation

A

stop codon produced truncated protein

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16
Q

transition

A

Pur/Pur or Pyr/Pyr

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17
Q

transversion

A

Purine / Pyrimidine

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18
Q

deletion or insertion

A

Extra or Missing amino acids

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19
Q

frameshift mutation

A

Altered protein

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20
Q

other types of mutations (4)

A
  • Promoter/Enhancer - Nuclear Receptors
  • Splice Site
  • Expanded Repeat
  • Transposons
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21
Q

nomenclature of mutations

A

• Amino acid designations
• genomic (gDNA) vs. mRNA (cDNA) vs. protein
• coordinates
• substitution(s)
• example:
• A1215T alanine at postion 1215 in the protein is
changed to a threonine

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22
Q

Alleles are

A

sequence variants of a gene

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23
Q

You inherit one

allele of each autosomal gene from

A

your mother and one

from your father

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24
Q

Single nucleotide polymorphisms (SNPs) are

A

single base

differences at a specific position in the genome

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25
Q

SNPs

occurring within a gene (can) give rise to an

A

allele

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26
Q

There are

— of SNPs in the genome

A

hundreds of thousands (millions)

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27
Q

Maintaining the genetic stability that an organism needs for its survival requires (2)

A

an extremely accurate mechanism for replicating DNA

mechanisms for repairing the many accidental lesions that occur continually in DNA

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28
Q

Most such spontaneous changes in DNA are — because they are immediately
corrected by a set of process that are collectively called — —

A

temporary

DNA repair

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29
Q

Of the thousands of random changes created every day in the DNA of a human cell by
(4), only a few accumulate as mutations in the DNA sequence

A

heat, metabolic accidents, radiation of various sorts, and exposure to substances in the environment

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30
Q

For example, we now know that fewer than one in 1000 accidental base changes in DNA
results in a — —

A

permanent mutation

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31
Q

the rest are eliminated with remarkable efficiency by

A

DNA repair

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32
Q

The importance of DNA repair is evident from the large investment that cells make in

A

DNA enzymes

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33
Q

For example, analysis of the genomes of the bacteria and yeasts has
revealed that several percent of the coding capacity of these organisms is devoted solely
to

A

DNA repair functions

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34
Q

he importance of DNA repair is also demonstrated by the increased rate of mutation
that follows the

A

inactivation of a DNA repair gene

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35
Q

Many DNA repair

A

proteins and the genes that encode them

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36
Q

Many DNA repair proteins and the genes that encode them- which we now know operate
in a wide range of organisms, including humans- were originally identified in bacteria by
the isolation and characterization of mutants that displayed an increased mutation rate
or an increased sensitivity to

A

DNA-damage agents

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37
Q

DNA is a highly stable material (compared to RNA), but it is a complex organic molecule
that is susceptible to

A

spontaneous changes that would lead to mutations if left

unrepaired even under normal cell conditions

38
Q

DNA of each human cell loses about — purine bases (adenine/guanine) everyday
due to their deoxyribose hydrolyzation of N-glycosyl linkages, a spontaneous reaction
called —

A

5000

depurination

39
Q

A spontaneous deamination of cytosine to uracil in DNA occurs at a rate of about —
bases per cell per day

A

100

40
Q

DNA bases are also occasionally damaged by

3

A

• an encounter with reactive metabolites produced in the cell (including reactive forms of
oxygen, H2O2, -OH, and -O2)
• exposure to chemicals in the environment.
• ultraviolet radiation from sun can produce a covalent linkage between two adjacent
pyrimidine bases in DNA to form thymine dimers (presented later in this lecture)

41
Q

Oxidative damage by

A

reactive oxygen species

42
Q

Uncontrolled methylation (CH3-) by

A

the methyl group donor S-adenosyl-methionine

43
Q

Hydrolytic attack

A

deamination and depurination

44
Q

most frequent spontaneous chemical reactions

A

hydrolytic attack

45
Q

Without DNA repair, spontaneous DNA damage would rapidly

change

A

DNA sequences

46
Q

About 3% of the C nucleotides in vertebrate DNAs

are methylated to help in

A

controlling gene

expression

47
Q

When these 5-methyl C nucleotides are
accidentally deaminated, they form the natural
nucleotide

A

T

48
Q

However, this T will be paired with G on the

opposite strand, forming a

A

mismatched base pair

49
Q

About one-third of inherited human disorders are

A

single base mutations

50
Q

The spontaneous deamination products of A and G
are recognized as — when they occur in DNA
and thus are readily (2)

A

unnatural

recognized and repaired

51
Q

base excision repair

A

unnatural bases are recognized and removed by a specific DNA glycosylase

52
Q

(2) are the two most frequent

spontaneous chemical reactions known to create serious DNA damage in cells

A

Deamination and depurination, hydrolytic reactions

53
Q

Deamination

A

cytosine to uracil in DNA is estimated to occur at a rate of 100
bases per genome per day

54
Q

Depurination

A

lose 5000 purine bases (A or G) per day in each cell due to thermal
disruption of their N-glycosyl linkages to deoxyribose

55
Q

Pyrimidine (C or T) dimer formation

A

covalent linkage of two adjacent pyrimidines by UV light from the sun

56
Q

These premutagenic lesions alter the structure

of DNA and consequently (2)

A

inhibit polymerases

and arrest replication

57
Q

Dimers may be repaired by (2), but unrepaired

dimers are mutagenic

A

photoreactivation

or nucleotide excision repair

58
Q

AP site (apurinic/apyrimidinic site)

A

a location in DNA that has neither a purine nor a pyrimidine base

59
Q

what does a bread in DS DNA cause

A 
delays 
progression of 
G1 to S phase 
and from S to M 
phase (through 
G2) in the Cell 
Cycle
60
Q

little of the mammalian genome codes for

A

proteins (1.5% of exons) and has function (3.5% of highly
conserved sequences such as 5’ and 3’ UTR, functional RNAs and conserved protein binding site of the
DNA ) that this mechanism is apparently an acceptable solution to the problem of rejoining broken
chromosomes (deletion)

61
Q

If each member of a chromosome pair carries the
same allele, then the individual is called
— for that gene

A

homozygous

62
Q

If each member of a chromosome pair carries a
different allele, then the individual is called
— for that gene

A

heterozygous

63
Q

The phenotype of a — gene will be

observed in the homozygous or heterozygous state

A

dominant

64
Q

The phenotype of a — gene will be observed

only in the homozygous state

A

recessive

65
Q

mendels laws (2)

A

principle of segregation

principle of independent assortment

66
Q

Principle of Segregation

A

Sexually reproducing organisms possess genes that
occur in pairs and that only one member of this pair is
transmitted to the offspring

67
Q

Principle of Independent Assortment

A

Genes at differ loci are transmitted independently

68
Q

homologous recombination

A

Genetic exchange between a pair of homologous

DNA sequences

69
Q

DNA breaks often occur from (2)

A

radiation damage or

reactive chemicals

70
Q 
DNA breaks also arise from DNA replication forks 
that become (2)
A

stalled or broken

71
Q

Homologous recombination is a mechanism to (3)

A
  • Accurately repair double strand DNA breaks
  • Exchange bits of genetic information
  • Assures accurate chromosome segregation during meiosis
72
Q

Homologous recombination has common features in

all

A

cells

73
Q

what guides homologous recombination?

A

DNA base pairing

74
Q

In the test tube base pairing of single stranded DNA

drives

A

DNA renaturation or hybridization

75
Q

DNA renaturation or hybridization is a

(2) driven process

A

temperature and salt

76
Q

High temperature

drives

A

double stranded DNA into single stranded DNA

77
Q

In cells that cannot survive at high temperatures, — are used that bind tightly
to the DNA and hold it an open configuration to serve as a
template for DNA synthesis

A

single

stranded DNA binding proteins

78
Q

Double-strand DNA breaks can be repaired by (3)

A

• Non-homologous end joining without a template which
creates a mutation at the site where the DNA duplexes
are joined.
• Inadvertent joining of two segments from different
chromosomes that results in chromosomal
translocations, which often give rise to disease
• Homologous recombination repairs DNA double strand
breaks accurately without loss or alteration of the DNA
sequence

79
Q

Cells carefully regulate the use of homologous

recombination in

A

DNA repair

80
Q

Repair involves a number of

A

proteins

81
Q

The enzymes catalyzing repair are present at —

concentrations in the —

A

high

nucleus

82
Q

A number of accessory proteins are involved in

A

control of repair

83
Q

Loss of essential proteins needed for repair are generally

— events

A

lethal

84
Q

Loss or alterations (mutations) of accessary proteins

often leads to

A

cancer

85
Q

steps of homologous recombination (2)

A

1) Repair double-stranded breaks accurately

2) Generate crossover in meiosis

86
Q

— — are often formed during homologous recombination

A

Holliday junctions

87
Q

Holliday junction

A

(cross-strand exchange)
two DNA strands switch partners between
two double helices

88
Q

DNA is under constant pressure to

A

acquire changes in its

DNA sequence

89
Q

Most changes are repaired before they

become a

A

stable part of the DNA that is subsequently

passed on to daughter cells

90
Q

Various types of mutations occur in DNA, some of which

will give rise to

A

altered protein variants of any given

gene

91
Q

When mutations occur in somatic tissues, they cannot

be —, but can give rise to diseases such as —

A

inherited

cancer

92
Q

When mutations arise in the DNA of the gametes, they

will be

A

passed on to the offspring

Applied Biochemistry (52 decks)

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