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2B - Genetics & Evolution > week 3 > Flashcards

week 3 Flashcards

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Biology 101 flashcards
1
Q

What is DNA damage?

A

formation of DNA lesions that change DNA function

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2
Q

Where is DNA damage coming from?

A
  • internal cellular metabolism (reactive oxygen species)
  • UV light
  • ionising radiation
  • alcohol
  • oxidative damage
  • mechanical stress
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3
Q

What is the biggest source of DNA lesions?

A

replication

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4
Q

How DNA replication increases chances of lesions?

A
  1. when chromatin is unpacked, DNA is exposed to UV and ionising radiation to a higher level (no longer shielded)
  2. DNA polymerase makes mistakes: incorporate additional base or skip a base or mismatch
  3. RNA primers nucleotides needs to be removed, if not can be an error
  4. exposed strands are highly exposed and can react chemically, bases can oxidise
  5. interstrand crosslinks
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5
Q

What happens when DNA lesions are not repaired of repaired incorrectly?

A

mutation

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6
Q

DNA structural integrity is altered when (one of these):

  • DNA free ends signal ___ breaks
  • __accumulates/persists
  • base pairing is ____
  • the bases are not only A, T, G and C, could be their ____ or uracil, and the sugar is not ____.
A
  1. backbone
  2. ssDNA
  3. incorrect
  4. modifications, deoxyribose
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7
Q

What enzyme (light-activated) is used to repair small damage with backbone intact?

A

photolyase - cleaving T-T dimers, reverses reaction leaving the DNA as it was prior to introduction of lesion

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8
Q

The principle of CUT & PATCH is used by many different repair enzymes. how does it work?

A

CUT = created by nucleases to remove excise the wrong bases
PATCH = DNA polymerase fills the gap and ligase seals the nick

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9
Q

What are the 2 most dangerous DNA damage??

A

double strand breaks and interstrand cross links

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10
Q

What is DSBs caused by?

A

broken replication fork
unseparated sister chromatids in mitosis

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11
Q

What is ICLs caused by?

A

acetyaldehyde
chemicals and chemotherapeutic drugs

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11
Q

What are the 2 correct repair methods of DSB?

A

ligation of broken ends or homologous recombination

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12
Q

What is erroneous repair and how does it repair DSB incorrectly?

A

Telomere is added to a break and the break is ligated to a telomere of another chromosome. could lead to incorrect rejoining or processing of broken DNA ends during repair

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13
Q

What is gross chromosomal rearrangements?

A

abnormal chromosomes containing large insertions and translocations originating from erroneous DBS repair

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14
Q

What is aneuploidy/CNVs

A

changes in the number of copies of a particular chromosome segment. These variations can result in parts of the genome being duplicated or deleted, leading to gains (more copies) or losses (fewer copies) of DNA segments

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15
Q

Why is ICLs not dangerous for non-proliferating cells?

A

if the ICL is within a transcribed gene, then transcription becomes impossible so its simply not active and has no effect on function or survival.

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16
Q

How is ICL repaired in proliferating cells?

A

ICL converted to DSB and repaired as DSB

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17
Q

Drugs that causes ICL are used to treat ____

A

cancer

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18
Q

What happens in DNA damage response in bacteria in relation to SOS

A

when excess ssDNA is generated from DNA ends being degrade, SOS response triggered: activation of a whole set of genes required for DNA repair and stop division

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19
Q

What does SOS response lead to? which genes and their results?

A

cell division inhibiter genes activated = filament cell growth stop sdividing
homologous recombination genes = accurate repair
TLS genes turned on = mutagenesis

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20
Q

What is unusual about TLS polymerase?

A

can synthesise DNA using damaged templates but they frequently insert wrong nucleotides.

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21
Q

Elaborate the G2 checkpoint activation in yeast (mec1 kinase and Rad9 and 53 protein)

A

mec1 binds to ssDNA phosphorylated Rad9 at damage site. Rad53 binds to Rad9 and undergoes autophosphoryltion. phosphorylated Rad53 blocks mitosis and stimulates DNA repair

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22
Q

What is the probability of acquiring a mutation?

A

probability of lesion x probability of mutation (mismatch frequency x mismatch repair system efficiency)

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23
Q

How does dark room increase effect of UV increase probability of mutation?

A

decreases probability of correct repair - photolyase repairs and requires light

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24
Q

What is somatic mosaicism?

A

person has genetically distinct cell populations in their body due to mutations occurring after fertilization, leading to variation in genetic makeup across different tissues.

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25
Q

List some examples of somatic mosaicism

A

A – inflammatory nevus, very early mutation

B – skin overgrowth on the foot

C – overgrown brain hemisphere

D – patterned skin pigmentation

E - skin cancer - cancer cells are genetically different than normal cells

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26
Q

What is carcinogenesis?

A

the process by which normal cells transform into cancer cells

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27
Q

How does multiplication lead to rapid growth of cancer cells?

A

mutations build up - If Mutation 1 increases the mutation rate 10 - 100 –fold or even more, then the probability of acquiring the next 3 mutations increases 1,000 – 1,000,000 times.

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28
Q

How is BCRA1/2 commonly mutated in cancers?

A
  • cells use the other chromosome to repair the chromosome with break/mutation on BRCA 1 or 2
  • uses non-mutated chromosomes to patch the other chromosome
  • so might end up with 2 good alleles
  • risk: 2 mutant alleles can not repair by homologous combination
  • predisposition
29
Q

Explain synthetic mRNA -> polypeptide in vitro

A
  • using of synthetic messenger RNA and synthesise polypeptides in vitro
  • differenet ribonucleoside diphosphates were incubated with polynucleotide phosphorylase to produce synthetic RNA chains.
  • combined with e.coli cell free extract containing all components needed for translation
30
Q

how did Nirenberg and Matthaei demonstrated the genetic code

A

by using a cell-free system and synthetic RNA. They showed that polyU RNA directs the incorporation of phenylalanine when incubated with a radioactive amino acid mix, proving that the codon UUU codes for phenylalanine. Similarly, they found that AAA codes for lysine and CCC for proline, revealing how RNA sequences determine amino acids

31
Q

How did Khorana discover ACA CAC AAC CAA

A

producing peptides from repeating copolymer mRNAs
- synthesised mRNA with alternating A and C

32
Q

Explain the Triplet Binding Assay

A

testing RNA triplets with ribosome subunits and aminoacyl-tRNAs. If a triplet matched a tRNA, a ribosome complex formed, binding to a filter and leaving a radioactive signal. By testing all 64 codons with labeled amino acids, they determined which codons correspond to each amino acid. For example, AUG was shown to bind methionine tRNA, confirming it codes for methionine. This revealed the genetic code’s degeneracy, where some amino acids are encoded by multiple codons.

33
Q

What does “degenerate” code mean?

A

an amino acid may be encoded by 1-6 different codons

33
Q

How can we explain this degeneracy?

A
  1. There are different aminoacyl tRNAs which recognise different codons but specify the same amino acid.
  2. ‘Wobble’ of the anticodon 5’ base allows flexibility in base pairing
34
Q

Explain the wobble that allows flexibility in base pairings

A

3rb base in the 5’ end wobbles and can pair with 2 diff bases

35
Q

What is an open reading frame?

A

start to stop codon

36
Q

What are the 4 types of single base substitutions?

A

silent, neutral, missense, nonsense

37
Q

What is a silent mutation

A

no amino acid change

38
Q

What is a neutral mutation?

A

amino acid change but protein functional

39
Q

What is a missense mutation?

A

Amin acid change but protein non-functional

40
Q

what is a non-sense mutation?

A

changes amino acid codon to stop codon

41
Q

Single base insertions or deletions can lead to…

A

Frameshift mutation

42
Q

2 ways in which a second mutation can restore gene function

A
  1. true revertant (original sequence is restored
  2. pseudo-revertant (2nd mutation suppresses the first), these are called suppressor mutations
43
Q

Explain the 2 types of pseudo-revertant

A

(i) Intragenic suppressors e.g. Suppression of frameshift mutations.

(ii) Intergenic suppressors. e.g. Suppression of nonsense mutations.

44
Q

How does suppressor tRNA correct nonsense mutations?

A

Suppressor tRNA: A special tRNA with an altered anticodon is able to recognize the stop codon. This tRNA “suppresses” the effect of the nonsense mutation by pairing with the premature stop codon and inserting an amino acid.
Result: This allows translation to continue, bypassing the premature stop and enabling the synthesis of a full-length protein, potentially restoring its function.

45
Q

What is the problem with supressor tRNA

A

reads through stop codons in other genes results in extended polypeptides

46
Q

How do cells with suppressor tRNA survive?

A

Many tRNA genes are duplicated in the genome. For example, there are multiple copies of the tRNATyr gene, which ensures that normal translation can continue even if one copy mutates to become a suppressor tRNA.

47
Q

Why does RNA have uracil instead of thymine?

A
  • thymine is more stable than uracil (DNA is long term)
  • RNA is considered evolutionary precursor of DNA
  • uracil existed before thymine has higher resistance to photochemical mutation: better at lasting long term
48
Q

What is the diff between synonymous and non-synonymous in mutations

A

synonymous = same amino acids
non-synonymous = missense of nonsense

49
Q

How to classify missense?

A
  • conservative = similar chemical properties, fitness and functions
  • non-conservative = AA is very different (polar vs basic etc that affects bonding)
50
Q

What is the function of condensin?

A

organise loose chromatin into visible and structured individual chromosomes

51
Q

Describe the structure of chromosome regions

A

telomere, centromere, euchromatin heterochromatin

52
Q

Sister chromatids
- produced by?
- attached by?
- separated during?
- what separates them?

A
  • DNA replication
  • kinetochore
  • mitosis
  • cytokinesis
53
Q

What is the function of cohesin and when is it degraded?

A

holds tgt sister chromatids, degraded in metaphase

54
Q

How do organelles split during mitosis?

A

mitochondria and chloroplast split by binary fission

54
Q

Meiosis
- only occurs in ___ cells
- can be ____
- ____ chromosome number

A
  • germ
  • inherited
  • halves
55
Q

What gets separated in meiosis I and II

A

I - homologous chromosomes
II - sister chromatids

56
Q

What is the progression of homologous chromosome pairing and separation?

A

DSB formation, DBS repair, SC disassembly, crossover

57
Q

What are the advantages of crossing over?

A
  • prevent accumulation of deleterious mutations
  • if parents are fit it might be deleterious to induce further recomb
58
Q

what is recombination suppression

A

Over time, chromosomal inversions prevented recombination on sex chromosomes, allowing mutations to accumulate, particularly on the Y chromosome, which is often present alone in males. In contrast, females with XX chromosomes can still recombine, which helps maintain genetic diversity.

59
Q

How do the X and Y chromosomes in male individuals (XY) correctly segregate during meiosis despite suppressed recombination?

A

X and Y chromosomes pair and recombine only in the pseudo-autosomal regions (PARs), located at the ends of their chromosomal arms. This allows proper segregation during meiosis, while the rest of the chromosomes do not recombine. Genes outside of the PARs follow sex-linked inheritance patterns.

60
Q

What are the key differences between spermatogenesis and oogenesis in terms of gamete production, timing, and cell division?

A

Spermatogenesis (male) produces 4 similar, motile sperm cells with flagella, and occurs continuously throughout life after puberty. The sperm germline can undergo mitotic divisions throughout the male’s life.
Oogenesis (female) results in 1 large egg (ova) and 3 smaller polar bodies, with uneven cytoplasmic division. Oogenesis is cyclical, occurring once a month, and the number of oocytes is largely fixed before birth.

Key Differences:
Timing: Spermatogenesis is continuous, while oogenesis is periodic (monthly) in females.
Number of Gametes: Males produce millions of sperm, while females have a fixed number of oocytes that are present before birth.
Cell Division: Sperm are produced continuously, while oocytes complete their meiosis in two stages—before birth and after puberty.

61
Q

What us de novo mutations

A

A de novo mutation is a genetic change that occurs for the first time in a germ cell (egg or sperm) or in the fertilized egg, rather than being inherited from the parents.

62
Q

What are the three main parasexual processes for DNA acquisition in bacteria, and how do they differ?

A

Transduction: DNA transfer via viruses (bacteriophages).
Conjugation: DNA transfer via direct physical contact between bacteria.
Transformation: DNA uptake from the environment.

63
Q

How does one less and one extra chromosome have an effect on expression?

A
  • One less chromosomes = 0.5x normal expression
  • one extra chromosomes = 1.5x normal expression (for genes on that chromosome)
64
Q

How is the expression of genes on the X chromosomes regulated in XX vs XY individuals to ensure equal gene dosage?

A

In XX individuals, one of the X chromosomes is completely inactivated through epigenetic mechanisms, including DNA methylation and repressive histone modification, leading to extreme chromatin packing and no expression. can also involve dampening expression from both X chromosomes or enhancing expression from the under-represented chromosome.

65
Q

When does chromosomal segregation go wrong, leading to conditions like cancer and Down syndrome?

A

cancer - mitosis (doesn’t happen to all the cells of the body)

down syndrome - meiosis I or II

66
Q

What causes aneuploidy in mitosis, and how is it regulated?

A

Aneuploidy in mitosis is caused by miss-segregation of sister chromatids, which can occur due to cohesion defects or issues with spindle attachment. This typically affects only a subset of cells. Mitosis is highly regulated to prevent aneuploidy, and if errors occur, a delay or arrest mechanism is triggered to prevent further damage, often leading to cell death as a safety mechanism.

67
Q

How do plants exhibit aneuploidy, and how do they tolerate gene copy imbalances?

A

where seed pods of aneuploid plants show different shapes depending on which chromosome is trisomic. they have dosage compensation mechanisms that regulate gene expression

68
Q

What is one-sided inheritance, and how does it relate to mt-DNA and the Y chromosome?

A

mt-DNA is inherited solely through the maternal line, while the Y chromosome is passed from father to son. There is no or very limited recombination in these regions, meaning alleles are inherited together in blocks called haplotypes.

69
Q

What is the significance of Mitochondrial Eve and Y-chromosomal Adam in human evolution?

A

Mitochondrial Eve and Y-chromosomal Adam refer to the most recent common ancestors from whom all living humans inherited their mitochondrial DNA (maternal line) and Y-chromosome DNA (paternal line), respectively. They were not necessarily alive at the same time, but they represent the individuals who were the most successful at spreading their genes through successive generations, and their genetic material has persisted in the population today.

2B - Genetics & Evolution (9 decks)

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