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Biosci 202 > Midsem test - topic 2 > Flashcards

Midsem test - topic 2 Flashcards

1
Q

Polymorphism

A

Mutation carried by more than 1% of the population

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2
Q

Fluctuation test

A
  • Luria and Delbruck
  • Innoculated E.coli with bacteriophage to study mutations
  • no poisson distribution so concluded that mutations are spontaneous and resistant mutants are pre-existing
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3
Q

Gene regulation

A

cellular transcription machinery controls whether or not genes are expressed and to what level

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4
Q

Structural mutations

A

alter protein/RNA structure or activity

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5
Q

Regulatory mutations

A

alter gene expression

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6
Q

Control at transcription

A
  • gene copy number
  • transcription efficiency = action of RNA pol
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7
Q

Control at translation

A
  • post transcription control (mRNA modifications)
  • mRNA stability (half life)
  • mRNA translation - rate of initiation and translation
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8
Q

Control at folding

A
  • protein stability
  • post translation effects - modifications which repress or activate
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9
Q

What does transcriptional gene regulation involve

A
  • whether or not gene is expressed
  • level of gene expression
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10
Q

Promoter

A

specific sequence to aid gene recognition and start transcription, RNA pol binds here

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11
Q

Strong promoters

A

initiate transcription faster which has sequences that bind well

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12
Q

Weak promoters

A

bind RNA less well

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13
Q

Key sites for activator/repressor function

A
  • DNA binding site = recognises specific DNA sequence
  • allosteric site = effector binds here causing conformational change which sets binding site to functional or non-functional
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14
Q

Lac operon - NO LACTOSE

A

repressor binds to operator - no transcription

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15
Q

Lac operon - LACTOSE PRESENT

A

lactose binds to repressor so it cannot bind to operator, transcription occurs

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16
Q

Oc mutations

A
  • constitutive mutation in operator
  • repressor cannot bind to operator
  • operon always on
  • cis acting
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17
Q

cis acting

A

effect restricted to only the chromosome where the mutation is located

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18
Q

I mutation

A

defective repressor protein which cant bind to operon
operon always on
trans acting

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19
Q

Trans acting

A

effects multiple genes

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20
Q

cAMP in lac operon

A
  • in high presence when low glucose
  • cAMP forms complex with CAP which activates transcription of lac operon
  • complex bends DNA to improve RNA polymerase recognition of binding site
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21
Q

high glucose, no lactose, no cAMP

A

no transcription

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22
Q

high glucose, high lactose, no cAMP

A

little transcription

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23
Q

low glucose, high lactose, high cAMP

A

high transcription

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24
Q

Negative control

A

inactivates repressor

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25
Q

Positive control

A

activator required for expression

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26
Q

Arabinose operon

A
  • both negative and positive control
  • positive control = AraC binds to araI to initiate when arabinose is present, CAP-cAMP complex
  • negative control = AraC binds to AraO and AraI, creates a DNA loop so transcription cannot occur, arabinose is absent
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27
Q

Sigma factor

A
  • RNA polymerase subunit
  • when associated with RNA polymerase it allows RNA polymerase to bind to DNA sequence
  • when transcription starts its released
  • sigma 70 = recognises -35/-10
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28
Q

Consensus sequence

A

comprises the most commonly encountered nucleotides found at a specific location in DNA or RNA, made by comparing sequences via sequence alignments

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29
Q

Multicellular organisms

A

start as pluripotent stem cells and differentiate into all cell types in body

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30
Q

Pluripotent

A

cells that can differentiate into any cell type

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31
Q

Similarities between eukaryote and prokaryote gene expression

A
  • promoter sequences vary to specific level of transcription initation
  • use activator or repressor proteins
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32
Q

Differences of eukaryotes to prokaryotes

A
  • have intron RNA that needs to be removed before translation
  • in eukaryotes transcription and translation occur separately due to nucleus
  • default state of eukaryote DNA is off due to the nucleosome position blocking promoter
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33
Q

Enhancers

A

where activators/repressors bind in eukaryotes, distant from gene

34
Q

Transcription factors

A
  • bind specific DNA sequences
  • help RNA polymerase bind the promoter
  • interact with mediator protein complex to promote transcription to determine whether RNA polymerase binds
35
Q

TAD

A

chromosomes organised into 3D territories into loops

36
Q

GAL system - NO GALACTOSE

A
  • repressor Gal80 binds to Gal4
  • Gal4 cannot activate transcription
37
Q

GAL system - GALACTOSE

A
  • Gal 3 binds galactose
  • conformational change allows increased binding of gal 3 to gal 80
  • gal 3 binds to gal 80
  • gal 4 can bind to mediator and activate gene expression
  • TFIID can bind
  • DNA loops
38
Q

Chromatin

A

complex of proteins, RNA and DNA that forms chromosomes within nuclei

39
Q

Euchromatin

A

open and accessible

40
Q

Heterochromatin

A

highly condensed and inaccessible

41
Q

Constitutive heterochromatin

A

part of gene is permanently heterchromatin as its gene poor

42
Q

Facultative heterochromatin

A

heterochromatin can change to euchromatin

43
Q

Histone acetylation

A

associated with active transcription

44
Q

4 major chromatin states

A
  • active euchromatin
  • inactive euchromatin
  • facultative heterochromatin
  • constitutive heterochromatin
45
Q

Position effect variegation

A
  • when a gene normally in euchromatin is juxtaposed with heterochromatin by rearrangement or transposition
  • if gene is integrated beside heterochromatin it can spread to gene and silence it
  • in drosophila white colour gene is inverted which allows heterochromatin to spread giving patches of red and white
46
Q

DNA methylation

A
  • cytosine methylated to methylated cytosine
  • represses gene expression
  • can be inherited - CG bases
  • long term repression method
47
Q

small RNA regulation

A
  • DICER cuts long DSRNA into short dsRNAS
  • RISC binds small RNA and denatures it
  • incorporates one strand
  • IF siRNA = RISC finds complementary mRNA and degrades it
  • IF mIRNA = RISC pairs imperfectly with mRNA which leads to inhibition of translation
48
Q

Advantages of small RNA regulation

A
  • easy to use - only have to make small RNA antisense to target gene
  • transient - allows reduced expression of essential genes
  • powerful and flexible - can introduce many small RNAs at once to decrease expression
49
Q

Alternative splicing

A
  • introns have to be spliced via spliceosome
  • 5’ and 3’ splice sites are very short so spliceosome doesnt know which one is correct so leads to alternative splicing
  • produces different proteins
50
Q

Point mutations

A
  • single nucleotide changes in sequence = substitution
  • transitions = type of base is conserved
  • transversions = type of base changes
51
Q

INDELS

A
  • insertions/deletions
52
Q

Large scale mutations

A
  • large duplications/deletions
  • translocations = breakage and movement of DNA
  • inversions = piece of DNA breaks out and rejoins in inverse orientation
  • transposition = DNA moves via a transposon
53
Q

Chromosome mutations

A

change in number of individual chromosomes due to non-disjunction = ANUEPLOIDY

54
Q

Mechanisms of mutation

A
  • errors during DNA replication and repair
  • spontaneous chemical changes of bases that change their pairing
  • induced chemical changes of bases from external mutagens
55
Q

repair DNA polymerase vs normal DNA polymerase

A

repair DNA polymerase has lower accuracy so higher error rate

56
Q

Spontaneous base chemical changes

A
  • cytosine deamination to uracil, TRANSITION
  • methylcytosine deamination to thymine, more prone to deamination than cytosine
57
Q

Induced chemical changes of bases

A
  • substitution of natural bases for base analogs which can act as mutagens if they have unusual base-pairing
  • EMS acetylates bases which alters base pairing, Guanine will bind to thymine
  • BP converted to a mutagen via CYP450 which binds irreversibly to guanine
  • 5-bromouracil can pair with either adenine or guanine
  • ionising radiation = induces breaks
58
Q

effects of point mutations

A
  • silent/synonymous mutation = change in AA sequence that doesnt change codon
  • missense/nonsynonymous = change in AA causing a codon change
  • conservative = nonsynonymous mutation which changes to a similar AA
  • nonconservative = nonsynonymous which changes to dissimilar AA
  • nonsense = premature stop codon
59
Q

effects of INDELS

A
  • can cause frameshift mutations if it occurs in coding region
60
Q

effects of regulatory mutations

A
  • affect level of gene expression so can alter transcription rate
  • if in a trans regulatory gene it will affect gene expression of multiple genes
61
Q

neutral mutation

A

has no effect on function

62
Q

deleterious mutation

A

compromise function

63
Q

beneficial mutation

A

improve function

64
Q

Suppressor mutations

A
  • suppress phenotype of another mutation
  • tRNA mutations are example
  • mutating tRNA anticodon to recognise mutated codon
65
Q

Transposons in maize

A
  • mutant causing a lack of colour gene but revered to WT colour at high frequency
  • produced via transposition
  • Ds jumped into c gene causing a frame shift
  • movement of Ds relies on Ac
  • when Ds moves out of C gene it restores function so purple reappears in patches
66
Q

Inverted repeats

A

same sequence on opposite strands

67
Q

direct repeats

A
  • duplication of target site
  • same sequence on same strand
  • made by all transposons
68
Q

2 classes of transposons in bacteria

A
  • simple = single transposons with short inverted repeats at termini
  • composite = a gene sandwiched between simple transposons and move as a block
69
Q

transposases

A
  • enzymes that catalyse movement of transposons
  • bind transposon inverted repeats at termini
  • causes cleavage and insertion into target DNA
70
Q

class 2 transposons

A
  • move via DNA intermediate
  • DNA is copied/excised and moves to a new site
71
Q

class 1 transposons

A
  • retrotransposons
  • move via RNA intermediate
  • transposon transcribed then reverse transcribed back to DNA
  • integrates into genome
  • replicative = move by copy and paste
72
Q

conservative transposon

A

move via cut and paste

73
Q

autonomous transposon

A

encode transposase genes and catalyse their own transposition

74
Q

non-autonomous transposon

A

rely on transposases from autonomous - Ds rely on Ac

75
Q

effects of insertion of transposon

A
  • cause mutations when inserted into genes or regulatory sequences
  • white grapes = insertion into promoter, loss of colour
76
Q

effects of transposon rearrangement

A
  • recombo between transposons at different sites can cause duplications and deletions
  • most occur in repair
  • transposons on different chromosomes can cause translocations
  • can cause problems with pairing in meiosis
77
Q

LTR

A
  • long terminal repeat retrotransposons
  • retrovirus like
  • no autonomous
  • have promoter to allow for transcription
  • have reverse transcriptase
  • makes short target site duplications
78
Q

LINES

A
  • long interspersed nuclear elements
  • have 5’ promoter and reverse transcriptase
  • both autonomous and non autonomous
79
Q

SINES

A
  • small interspersed nuclear elements
  • small, nonautonomous retrotransposons
  • most abundance
  • believed to use LINE transposases machinery so have a similar target side duplication
  • almost all derived from tRNA genes that have mutated to transposons - EXCEPT Alu
  • Alu = most abundant SINE, derived from small RNA
80
Q

Transposon silence mechanisms

A
  • heterochromatic chromatin with repressive histone modifications
  • DNA methylation
  • small RNAs with silencing mechanisms
  • fungi target G/C to A/T mutations
81
Q

conflict against transposon theory

A

transposon transcription is turned on in mammalian stem cells and early development

82
Q

role of transposons

A
  • help regulate global gene expression = LINES and SINES mediate different chromatin structures so different expression patterns
  • regulating gene expression = placental development

Biosci 202 (4 decks)

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