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D1 Fall - Biochem > 10/19: DNA Repair and How Mutations Occur? > Flashcards

10/19: DNA Repair and How Mutations Occur? Flashcards

1
Q

What are types of genetic disorders?

A

Single gene disorders
Chromosome disorders
Multifactorial or complex disorders

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2
Q

What are chromosome disorders?

A

Rearragnements/translocaitons, deletions, insertions, duplications, anomalies in chromosome number: trisomies, monosomies

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3
Q

What are specific examples of genetic chromosome disorders?

A
  • Autosomal, sex linked, and mitochondrial
  • Germline (heritable) or somatic (non-heritable)
  • Dominant, recessive, co-dominant
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4
Q

What are multifactorial or complex disorders?

A

Multiple gene variants, gene variant x environment interactions

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5
Q

What is a mutation

A

Inherent association with disease, pathology, or mutant
**negative connotations for patients

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6
Q

Most phenotypes are on a _________

A

spectrum (bell curve)

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7
Q

What is a variant?

A

Implies nothing about a disease state, just a different form

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8
Q

Variants still arise by

A

mutation process

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9
Q

What can a variant be described as?

A
  • novel, rare, common
  • having low or high impact
  • benign, likely pathogenic, or pathogenic
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10
Q

What are multigenic or multifactorial diseases typically caused by

A

combined effect of numerous common, low impact variants that individually would not cause the disease

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11
Q

What can risk be influenced more by?

A

New genetic variants and environmental factors

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12
Q

What are two causes of mutations?

A

Spontaneous mutation
Induced mutation

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13
Q

What are spontaneous mutations

A

Arise naturally during DNA replication (mitosis or meiosis)

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14
Q

What are examples of enduced mutations

A

Radiation
Chemicals

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15
Q

Where can mutations occur?

A

Anywhere in the nuclear (or mitochondrial) DNA

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16
Q

Where else can mutations cause a disease?

A

Outside the exons of a gene

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17
Q

Where can SNVs or point mutations be present?

A

Coding and non-coding DNA

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18
Q

What does non-coding DNA include?

A

Gene regulatory elements, introns, repetitive elements (viral DNA, transposons)

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19
Q

What are the 3 types of coding SNVs?

A

SIlent (synonymous)
Nonsense
Missense (non-synonymous)

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20
Q

What are silent mutations?

A

have no effect on the amino acid produced by a codon

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21
Q

What are nonsense mutations?

A

No amino acid is produced; causes a stop codon to occur

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22
Q

What are missense mutations?

A

still code for an amino acid, but not the correct amino acid

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23
Q

What are the ways that SNVs can be described?

A
  • in terms of significance of the resulting change in the amino acid side chain
  • by the chemical nature of the nucleotide change
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24
Q

What can deletions/insertions involve?

A

A single amino acids (3bp) or many base pairs, removing or disrupting exons and/or regulatory sequences

25
Q

What do rearrangements involve?

A

Large segments of DNA

26
Q

What do framshift variants involve?

A

Deletion or insertion of <3bp (i.e. 1 or 2bp) within the coding sequence, disrupting the codon reading frame and thus the amino acid sequence

27
Q

What can a reading frameshift also arise from?

A

A larger deletion
ex: a deletion that removes one or more exons

28
Q

What are other types of mutations?

A

Promoter/enhancer/silencer
Splice acceptor/donor site
splice enhancer/silencer element
Repeat expansion
Transposons

29
Q

The nomenclature of variants can be represented as:

A

Genomic coordinate
mRNA (cDNA) coordinate
Protein (amino acid) coordinate

30
Q

What is genomic coordinate?

A

Citing the version of the genome sequence used

31
Q

What is mRNA coordinate?

A

Citing the reference cDNA sequence used

32
Q

What is protein (amino acid) coordinate?

A

Citing the reference protein sequence used

33
Q

What is more commony used when referring to variants that are very common in a population, hence “polymorphism”

A

SNP

34
Q

SNP = ________

A

SNV

35
Q

What are usually benign?

A

SNPs

36
Q

What is an allele?

A

One of the two copies of a gene
- you inherit one allele of each autosomal gene from your mother and one from your father

37
Q

If each member of a chromosome carries the same allele, the individual is called __________ for that allele

A

homozygous

38
Q

If each member of a chromosome carries the different allele, the individual is called __________ for that allele

A

heterozygous

39
Q

The phenotype of a dominant allele can be observed in a ____________ individual

A

heterozygous

40
Q

The phenotype of a recessive allele can be observed in a ____________ individual

A

homozygous

41
Q

How do mutations occur?

A
  1. oxidative damage by reactive oxygen species
  2. uncontrolled methylation (CH3-)
  3. hydrolytic attack
  • deamination and depurination, most frequent reactions
42
Q

How can DNA bases be damaged?

A
  1. reactive metabolites
  2. exposure to chemicals
  3. UV radiation
43
Q

What happens when methylated cytosines are accidentally deaminated?

A

They form the natural nucleotide thymidine, so NOT removed by base excission repair

44
Q

Mismatched bases are corrected through a process called_____________

A

Nucleotide excision repair

45
Q

What is base excision repair?

A

Specific glycosylases remove damaged bases

46
Q

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

A

AP site (apurinic/apyrimidinic site)

47
Q

How do modifications of nucleotides produce mutations?

A

In case of deamination:

DNA substitution

In case of deputination:

DNA deletion

48
Q

What is the “quick and dirty” mechanism

A

non-homologous end joining

49
Q

When does homologous recombination occur?

A

During meiosis

50
Q

What does homologous recombination involve?

A

Base pairing between DNA strands

51
Q

What is homologous recombination used to facilitate?

A

Genetic exchange between homologous chromosomes

52
Q

What does DNA base pairing guide?

A

Homologous recombination
*highly accurate repair mechanism

53
Q

When is homologous recombination deployed?

A

To repair double strand DNA breaks as well as single strand breaks that arise during DNA replication

54
Q

What does repair involve?

A

Number of enzymes and accessory proteins
- any loss of these repair proteins is lethal
- loss or mutation of accessory proteins leads to cancer

55
Q

Most spontaneous changes to nucleotides are repaired when?

A

Before they become a stable part of the DNA

56
Q

When mutations occur in somatic tissues, can they be inherited?

A

No, but can give rise to diseases such as cancer

57
Q

When mutations arise in the DNA of the gametes, where are the passed on to?

A

Offspring

58
Q
A

D1 Fall - Biochem (29 decks)

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