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Flashcards in Mutagenesis and repair Deck (75):
1

What does the word "cytogenetics" mean?

The study of structure properties and behaviour of chromosomes

2

What is the difference between cytogenetics and molecular genetics?

Molecular genetics looks at structure and function at the molecular level.

*The line between cytogenetics and molecular genetics is blurring. This is because molecular methods can detect cytogenetic abnormalities.

3

What kind of tests are usually involved in molecular genetics?

Tests are usually DNA or RNA based.

4

What are epigenetics?

The study of which genes are expressed and which genes are not in different cells and at different times.

5

What is a gene?

An inherited factor (region of DNA) that helps determine a characteristic

6

What is an allele?

1 or 2 or more alternative forms of a gene

7

What is a locus?

Specific place on a chromosome occupied by an allele

8

What is a genotype?

Set of alleles possessed by an individual organism

9

What is a phenotype?

A trait. The appearance or manifestation of a characteristic

10

What is a characteristic/character?

An attribute or feature possessed by an organism

11

How are somatic cells different to gametes?

Somatic cells are diploid (46 chromosomes; 22 pairs of autosomes, 1 pair of sex chromosomes)

Gametes are haploid (1 set of chromosomes)

12

What is a germline cell?

Cell line which gametes are derived from. Germ cells are deliberately set aside in embryo, migrate to the developing gonads where they undergo cell division and differentiation into sperm and ova.

13

How can germline mutations be detected?

Any tissue can be sampled for genetic testing if the mutation is in the germline (eg BRCA1 and BRCA2)

14

What kind of diseases result from accumulation of somatic mutations?

Cancer

15

What is independent assortment and how many different combinations can arise from it?

Independent assortment is the idea that chromosomes are randomly distributed prior to meiosis and there are 2 ways each chromosome can be arranged meaning the daughter cells can have 2^23 different combinations of chromosomes. This is important for maintaining diversity in a population.

16

What is a monogenic disease?

A disease that is caused by change/s in one gene.

17

Where do genetic errors typically occur?

They can occur at many levels:

Translation (protein affected)

Transcription (mRNA and protein affected)

Self-replication (DNA, RNA, and protein affected)

Mutations can be passed to other cells and cause permanent changes in population of cells.

18

What changes can arise from mutations?

Mutations can be beneficial

Mutations can be deleterious (loss of function mutations)

Gain of function mutations (can be beneficial or deleterious)

Lethal mutation causes premature death

19

What is a base substitution mutation?

Changes in a single base of DNA

20

What is the difference between a transition and transversion mutation?

Base substitution in which a purine replaces a purine or a pyrimidine replaces a pyrimidine. (Opposite of a transversion which is purine -> pyrimidine and vice versa)

21

What is an insertion mutation?

Addition of one or more nucleotides

22

What is a deletion mutation?

Deletion of one or more nucleotides

23

What is a frameshift mutation?

insertion or deletion that alters the reading frame. If 3 or a multiple of 3 nucleotides are added then it is an in-frame deletion or insertion mutation.

24

What are forward and reverse mutations?

Forward mutation is mutation from wild type to mutant. Reverse mutation is mutation back to wild type.

25

What is the difference between a misense and nonsense mutation/

Missense mutation results in different amino acid to be added to the chain.

Nonsense mutation results in STOP codon resulting in termination of transcription prematurely.

26

What is a silent mutation?

Mutation that does not change the amino acid by using an analagous codon.

27

What is a neutral mutation?

Changes the amino acid sequence of protein without altering its ability to function

28

What is a loss-of-function mutation?

Causes a complete or partial loss of function

29

What is a gain-of-function mutation?

Causes the appearance of a new trait or function can be in an inappropriate tissue and time.

30

What is a lethal mutation?

Mutation that results in death

31

What is a suppressor mutation?

Mutation that causes suppression of the effect of another gene.

Can be inter or intragenic.(within or without the gene)

32

What is the use of mutations?

Mutations produce a change in the genome which results in genetic variation (polymorphism)

33

What are polymorphisms?

Natural variations in a gene, DNA sequence, or chromosome that occur with fairly high frequency in the general population

34

How common is DNA damage?

DNA damage due to environmental factors and normal metabolic processes inside the cell occurs at a rate of 1000 to 1000000 molecular lesions per cell per day.

*DNA is under constant stream of attack from both endogenous and exogenous damage.

35

What is the consequence of unrepaired molecular lesions in DNA?

It impedes a cell's ability to carry out normal function and increases the likelihood of tumour formation.

36

Is DNA damage the same as a mutation?

No, damage is merely a physical change in DNA structure whereas a mutation is a change in the nucleotide sequence. Damage can lead to mutations.

37

What is DNA replication and repair errors important for?

For genetic variation

38

Do all loci have the same rate of mutations?

No, new mutation rates vary across different loci

39

How do mutagens affect DNA?

Mutagens can either directly or indirectly damage DNA. Mutagenic agents 'prefer' to damage specific nucleotides which can produce recognisable patterns of mutagenesis.

40

How do cells respond to DNA damage?

4 common ways:

- Cell cycle arrest until DNA damage is repaired
- DNA repair without stopping cell cycle
- Apoptosis in cases of irretrievable cell damage
- Transcription (induction of proteins and ncRNA involved in the cell cycle, signalling and DNA repair)

ncRNA = non-coding RNA

41

What are the types of mutations (as defined by cause)?

Induced (mutagen present) - greater dose means more mutations

Spontaneous (Mutagen absent) - ultimate source of genetic variation but rate is low - one cell in 10^5 - 10^8

42

With regards to mutagenesis what is the shape of the dose/response curve?

It is linear

43


Are DNA changes predictable?

In some cases, changes are understood and predicted. Particularly recurring mutations with lots of existing evidence supporting the link with the disease such as trisomy 21 and phe del mutation in CFTR gene causing cystic fibrosis

In other cases, they aren't making understanding their consequences trickier. In this case it is necessary to go back to first principles to assess likelihood that the change will cause detectable impairment in cell function and then result in disease.

44

What errors can occur at the splicing level that lead to disease?

A whole exon can be deleted as a result of mutations in splice signals. (exon skipping)

Part of exon can be deleted as a result of mutations in normal splice signals. Cryptic splice site selection.

45

What is a common example of diseases caused by errors in splicing?

Beta thalassaemia, (Can be caused by exon skipping, cryptic splice-site selection, and new splice site creation)

46

What kind of effect do mutagens instigate in cells?

Mutagens are specific for both type and site of mutation.

47

What are the mechanisms of mutagen activity?

Can replace a base in DNA

Can alter a base causing it to pair incorrectly

Can damage a base making it unable to pair.

48

What are mutagen "hot spots"?

Sites in genes where mutations occur more frequently than other sites in the gene.

49

How can spontaneous lesions generate mutations?

Deamination

Depurination

Oxidative damage

Replication errors

Base mispairing

50

What kind of pairing changes happen in non-watson-and-crick base pairing?

The purine - pyrimidine base pairing is maintained but there is a swap in type of purine/pyrimidine on either side of the pairing.

51

How does wobble base pairing result in different DNA strands?

DNA strand separates during DNA replication; one of the strands contains wild type and the other strand contains the mutant. This is because one of the base pairs is the correct nucleotide whereas the other isn't.

52

What kind of mutations does wobble base pairing result in?

Due to the purine not becoming a pyrimidine this is known as a transition mutation.

53

Are wobble base pairing mutations common?

No, due to being energetically unfavourable and presence of lots of protective mechanisms in the cell to prevent these mutations.

54

Why does deamination cause mutations?

Deamination of cytosine results in uracil. This uracil is removed by uracil glycosylases resulting in apyramidinic sites that can cause mutation.

55

What happens if 5-methylcytosine is deaminated?

It is converted into thymine

56

What is a more common mutation; mutation of a cytosine site or 5-methylcytosine?

5-methylcytosine is more common due to lack of uracil glycosylase action.

57

What is the mutagen that causes deamination commonly from smoked meat?

Nitrous acid

58

What is depurination?

Loss of purine base from a nucleotide. This results when covalent bond connecting purine to 1'-carbon atom of deoxyribose sugar breaks producing apurinic site.

Mutation results because it cannot act as a template for a complementary base.

59

What mutagen causes depurination and how?

Aflatoxin B1, a toxin derived from fungus that grows on peanuts. This carcinogen attaches to N-7 guanine and breaks the bond between the base and the sugar and so it often leads to an insertion of A.

60

How does depurination lead to permanent mutation?

In replication apurinic site cannot provide template for complementary base.

Nucleotide with incorrect base is incorporated into new strand

Next round of replication has incorrect base being used as a template

Leading to permanent transversion mutation.

61

What kind of mutation does depurination result in?

Transversion

62

How many purines are lost from DNA in 20h cell-generation period at 37degrees in vitro?

10000

63

What causes oxidative damage?

Reactive oxygen species produced as by-products of normal aerobic metabolism.

64

What kind of errors can occur in DNA replication?

Base substitutions (illegitimate base pairing due to reaction not being 100% efficient)

Base insertion/deletion

65

Where are base insertions/substitutions common?

In repeat sequences

66

How does replication slippage cause insertions?

Newly synthesized strand loops out

Resulting in addition of one nucleotide on new strand (due to complementary base looping out and being paired again by DNA polymerase)

67

How does replication slippage cause deletions?

Template strand loops out

One less nucleotide is added by DNA polymerase during replication.

68

What are trinucleotide repeat diseases?

Diseases caused by repeated trinucleotides. eg huntington's and fragile X syndrome.

69

What is huntington's disease caused by?

Trinucleotide CAG repeats. Severity of disease correlates with number of repeats. Normal person has +/- 10 - 35 repeats, Huntington's patients have 40 - 120.

CAG can cause lots of Gln amino acids in the protein forming a poly glutamine expansion that is toxic to cells.

70

What is Huntington's disease characterized?

Autosomal dominant neural degeneration that is late onset.

71

What is fragile X syndrome?

Most common form of inherited mental retardation. Seen cytologically by a fragile site on X-chromosome causing breaks in-vitro.

72

What causes fragile X syndrome?

Change in number of CGG repeats in region of FMR-1 gene that is transcribed but not translated.

73

Why does the mutation cause the symptoms of fragile X syndrome?

Mutation results in no transcription near that region containing genes important for neural development and so that results in mental retardation.

74

Does everyone with the CGG expansion have fragile X syndrome?

No, there is a variation between people with CGG repeats in the FMR-1 gene. Unaffected parents and grandparents have the premutation and they can have offspring with fragile X syndrome.

75

Why is DNA the molecule that has been "chosen" by evolution to store genetic information?

It is highly stable but not inert.