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BIOL2202 > Module 1: Genes and Mutations > Flashcards

Module 1: Genes and Mutations Flashcards

1
Q

What are the two levels of specificity required by tRNAs?

A
  1. aminoacyl-tRNA synthase activity:
    - Identify elements in the acceptor step
  2. Codon specificity
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2
Q

What are the deviations from the standard genetic code?

A
  1. Prokaryotes alternative start codons:
    - GUG and UUG instead of AUG
  2. Candida species:
    - CUG encodes serine instead of leucine
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3
Q

Start and stop codons

A

Start: AUG
Stop: UAA, UAG, UGA

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4
Q

Wobble table

A 
C --> G
A --> U
U --> A, G
G --> U, C
 I  --> U, C, A
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5
Q

Forwards mutation

A

mutation from WT –> mutant

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6
Q

Types of reverse mutations

A

overall: a second mutations that restores the original phenotype
1. Back mutation: a second mutation at the same site
2. Suppressor mutation: a second mutation at a different location

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7
Q

Conditional lethal mutations

A
  • lethal in the restrictive condition

- viable in the permissive condition

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8
Q

What are the types of point mutations and their effects?

A
  1. synonymous mutation:
    - new codon, no amino acid change
  2. non-synonymous, conservative:
    - new amino acid but with similar physical properties to original
  3. non-synonymous, non-conservative:
    - new amino acid with different physical properties
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9
Q

Nonpolar, alipathic amino acids

A
  1. valine (Val)
  2. proline (Pro)
  3. glycine (Gly)
  4. leucine (Leu)
  5. alanine (Ala)
  6. methionine (Met)
  7. isoleucine (Ile)
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10
Q

Aromatic amino acids

A
  1. Phenylalanine (Phe)
  2. Tyrosine (Tyr)
  3. Tryptophan (Trp)
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11
Q

Polar, uncharged amino acids

A
  1. Glutamine (Gln)
  2. Serine (Ser)
  3. Cysteine (Cys)
  4. Asparagine (Asn)
  5. Threonine (Thr)
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12
Q

Positive amino acids

A
  1. Arginine
  2. Lysine
  3. Histidine
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13
Q

Negatively charged amino acids

A
  1. Aspartate (Asp)

2. Glutamate (Glu)

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14
Q

Missense mutations

A
  • amino acid substitution leads to protein being defective
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15
Q

Nonsense mutation

A
  • creates a stop codon, prematurely ending the codon –> loss of function mutation
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16
Q

Tautomeric Shifts

A

Isomerisation caused by a reversible change in the location of a hydrogen atom in a base
Can cause substitution mutations by modifying base pairing

17
Q

Types of base substitutions

A

Transitions: pyrimidine -> pyrimidine; puring -> purine
Transversions: pyrimidine -> purine; purine -> pyrimidine

18
Q

Mutagenic effects of 5-bromouracil

A
  1. C:G –> T:A substitution and visa versa

cytosine –> 5BU
need to finish this

19
Q

Mutagenic affects of nitrous acid

A

Causes oxidative deamination of bases

  1. Cytosine –> uracil (pairs with A instead of G)
  2. adenine –> hypoxanthine (pairs with C instead of T)
20
Q

Mutagenesis by UV radiation

A
  1. hydrolysis of cytosine causes mispairing during replication
  2. Cross liking of adjacent thymines –> thymine dimers block DNA replaication and activate error-prone DNA repair
21
Q

Mutagenesis by acridine dye

A

Intercalation of acridine dye causes frameshift mutations

  • IN/DEL of base pairs not divisible by three alters reading frame
  • usually positive and inserts into DNA
22
Q

How do IN/DELs affect phenotype

A
  • in ORF: cause frameshift mutations
  • usually result in frameshift mutations (premature stop)
  • usually encode nonsense proteins
23
Q

How were suppressor mutations discovered?

A
  1. mutate bacteria, select and auxotroph (e.g. leu-)
  2. grow up leu- mutant on medium containing leucine
  3. mutate the leu- cells
  4. select second mutant that is now prototrophic
  5. sequence the gene encoding leu biosynthesis enzyme in:
    - WT
    - first mutant (Leu-)
    - second mutant (revertant to Leu+)
  6. compare sequences
24
Q

Intragenic vs Intergenic suppressor mutations

A
  1. Intragenic:
    - second mutation within the same gene, but different codon
  2. Intergenic:
    - second mutation in a different gene
25
Q

Amber mutations and their suppression

A

Amber: TAG stop codon

26
Q

Describe photreactivation in E.coli

A
  • thymine dimers are caused by UV radiation
  • fixed using light dependent repair
  • photolyase absorbs blue light for energy
  • cleaves thymine dimers, restoring original state
27
Q

Base excision repair

A
  • deamination of cytosine to uracil
  • excision of uracil
  • sugar-phosphate removed by AP endonuclease and phosphodiesterase
  • DNA polymerase adds cytosine base back -> uses the undamaged complementary strand and the template
  • DNA ligase seals the break left by polmerase
28
Q

Nucleotide excision repair

A
  • Thymine dimer in DNA strand
  • Polypeptide trimer (containing 2 x UvrA and 1 x UvrB) recognises and binds to damaged DNA
  • Energy from ATP is used to bend DNA and change conformation of UvrB –> UvrA released
  • UvrC binds to UvrB and DNA and cleaves DNA around UvrB protein
  • UvrD helicase releases excised oligodimer
  • DNA pol1 replaces UvrB and fills in gaps using complementary strand as template
  • DNA ligase seals the nick
29
Q

The Ames Test

A

??

30
Q

Mismatch Repair in E.coli

A
  1. MutS recognises mismatches and binds to them to initiate the repair process
  2. MutH and MutL join the complex
  3. MutH (endonuclease) cleaves the unmethylated strand at hemimethylated GATC sequences on eitther side of the mismatch
  4. Excision requires MutS, MutL, MutU and an exonuclease
  5. DNA pol III fills in the gap and ligase seals the nick
31
Q

How are thymine dimers dealt with post replication?

A
  1. a thymine dimer in the template strand blocks replication
  2. DNA pol III restarts DNA synthesis past the dimer, leaving a gap in the nascent strand
  3. RecA binds to the single strand of DNA at the gap and mediates base pairing with the homologous segment of the sister double helix to fill the gap
  4. DNA pol fills the gap using information from the other strand
  5. ligase seals the nick
32
Q

What happens in the SOS response in E.coli

A
  1. if DNA is heavily damaged by mutagens, the SOS response is activated
  2. DNA pol V replicates the damaged regions, but damaged sequences are not replicated accurately
  3. When extensive DNA damage occurs, RecA binds to single-stranded regions of DNA in damaged regions
  4. This activates RecA, which stimulates LexA to inactivate itself, turing on SOS
  5. LexA usually represses that regulate SOS response
33
Q

Describe the Holliday Model of recombination and crossing over

A
  1. Pairing of homologous chromosomes
  2. Formation of single-strand breaks –> endonucleases nick chromsomes
  3. Helicase and DNA single stranded binding proteins unwinds DNA
  4. Strand exchange occurs by RecA type protein
  5. Formation of a covalent, single-stranded bridge

BIOL2202 (3 decks)

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