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biochem > Module 10 > Flashcards

Module 10 Flashcards

1
Q

When do supercoils form?

A

when DNA is underwound or overwound

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2
Q

Relaxed vs strained DNA example

A

relaxed = 8 turns
strained = 7 turns

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3
Q

Tension leads to . . .

A

supercoiling

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4
Q

How does supercoiling affect the structure of DNA?

A

it makes it more compact

the more supercoiled the DNA, the FASTER it will migrate through an agarose gel towards a cathode

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5
Q

What is the role of topoisomerase?

A

it can relax supercoiled DNA and decatenate interlocked DNA

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6
Q

What does Type I topoisomerase do?

A

relaxes supercoiled DNA and alleviates the DNA helical constraints

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7
Q

What does Type II topoisomerase do?

A

unknots & untangles DNA by passing an intact helix through a transient double-stranded break that it generates in a separate helix

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8
Q

Along with Type II topoisomerase, what other protein is involved in the unknotting and untangling of DNA?

A

DNA gyrase

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9
Q

Briefly describe the structure of topoisomerase (Type II).

A
  • ATPase domain
  • cleavage domains
  • scaffolding
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10
Q

Describe the structure of a nucleosome.

A
  • 2 loops of DNA wrapped around 8 histones
  • when DNA is wrapped around histones it is at its loosest
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11
Q

How is DNA protected within the cell?

A

by always being bound by proteins

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12
Q

Together, the DNA + proteins are called. . .

A

chromatin

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13
Q

What are some features of histones?

A
  • small, basic proteins
  • 5 major classes
  • highly conserved over species
  • have amino tails which are highly disordered (protrude from nucleosome)
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14
Q

What do histone modifications affect?

A

1) the structure + packing of chromatin

2) the access to the DNA of DNA binding proteins

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15
Q

Histones can be. . .

A

covalently modified

these are proposed to be part of a ‘histone code’ which marks the DNA for specific biological processes

some of the amino acid tails can interact w. the tails of the neighboring nucleosome

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16
Q

Histone acetylation regulates. . .

A

chromatin condensation (the availability of the DNA for protein binding)

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17
Q

HDAC (histone deacetylase) vs HAT (histone acetyl transferase)

A
  • both are involved in regulation of chromatin structure and gene expression
  • HDAC –> condenses chromatin
  • HAT –> decondenses chromatin
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18
Q

1st level of DNA compaction

A
  • nucleosomes
  • beads on string
  • 7 fold compaction
  • active DNA ~ 200 nm fiber
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19
Q

2nd level of DNA compaction

A
  • nucleosome + one histone H1 wrapped into another coil
  • 100 fold compaction
  • inaccessible DNA ~ 30 nm fiber
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20
Q

Where is H1 found?

A

Histone H1 is located in the interior of the chromatin 30-nm filament

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21
Q

What is a chromosome scaffold?

A
  • can be transcribed
  • areas of gene activity are NOT as tightly packed
  • high level expression of genes in loop
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22
Q

How does DNA methylation change chromatin structure?

A
  • NO effect on base-pairing
  • occurs on CG dinucleotides
  • extended regions of CG nucleotides = CpG islands
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23
Q

Where are CpG island found?

A

usually in PROMOTERS & regulate transcription levels

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24
Q

DNA methylation ______ expression of a gene

A

REPRESSES

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25
Q

What are de novo DNA methyltransferases (DNMT)?

A
  • enzymes that can methylate CpG islands
  • are directed to specific areas of the DNA by DNA-specific binding proteins
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26
Q

How can the methylation of CpG dinucleotides be inherited?

A

because half-methylated sequences (hemi-methylated) are recognized by maintenance DNA methyltransferases (DNMT genes in mammals)

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27
Q

Describe epigenetic changes

A

epigenetic changes are reversible and do not change your DNA sequence, but they can change how your body reads a DNA sequence

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28
Q

Are epigenetic changes inherited from cell to cell?

A

Yes

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29
Q

Examples of epigenetic changes

A

methylation of cytosines

acetylation of histones in nucleosomes

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30
Q

Epigenetic changes are maintained in the cell but. . .

A

can be altered by signals (to turn genes on and off)

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31
Q

Why is tight regulation of gene expression important for prokaryotes?

A

it ensures that a cell’s resources are not WASTED making proteins that the cell does not need at the time

conserves energy + space

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32
Q

What is an operon?

A

a cluster of genes that are transcribed tog to give a single messenger (mRNA) molecule, which therefore encodes multiple proteins

33
Q

Describe the Trp operon.

A
  • 5 genes in operon
  • each gene in the mRNA has its START & STOP codon
  • the promoter is converted into mRNA which is then converted into an inactive protein
34
Q

What does the Trp operon produce?

A

produces tryptophan when there is none in the environment the E coli is growing in

35
Q

Tryptophan absent –>

A

repressor INACTIVE

operon ON

36
Q

Tryptophan present –>

A

repressor ACTIVE

operon OFF

37
Q

As tryptophan accumulates, . . .

A

it inhibits its own production by activation the repressor protein, which binds to the operator, blocking transcription

38
Q

TrpR produces what?

A

it produces a repressor protein that is initially inactive

it only becomes activated (to repress) once tryptophan binds to it

this allows it to bind to the operator and block transcription

39
Q

Lactose absent –>

A

repressor active

operon off

40
Q

lactose present –>

A

repressor inactive

operon ON

41
Q

How does the lac repressor work?

A

the lac repressor is innately ACTIVE, & in the absence of lactose is switches OFF the operon by binding to the operator

42
Q

What is the function of allolactose?

A

allolactose is an isomer of lactose that depresses the operon by inactivating the repressor

bind to the active repressor and forms an inactive repressor

  • the lac operon can now be transcribed
43
Q

trp =

allolactose =

A

trp = corepressor

allolactose = inducer

both however are NEGATIVE regulators

44
Q

What are the 3 proteins produced from the lac operon?

A

lac Z = B-galactosidase

lac Y = permease

lac A = transacetylase

45
Q

What are some features of the lac operon?

A
  • 3 operators
  • all operators are palindromes
  • a tetramer binds to the 2 operators (one dimer per operator)
  • forms a loop in the DNA b/w it
46
Q

What is meant by synergistic?

A

multiple activators cooperate to produce a greater effect

47
Q

Explain the combinatorial control of the lac operon in response to lactose + glucose

A
  • the ability of the polymerase will depend on the interactions that occur in the promoter region of the DNA
  • there are usually several important regulators of a single gene

messages are integrated for a single response

48
Q

When glucose is LOW –

A

ATP is LOW, cAMP is HIGH

CAP is activated

transcription

49
Q

When glucose is HIGH –

A

cAMP is LOW

CAP remains inactive

no transcription

50
Q

If lactose is present and CAP is inactive (no cAMP). . .

A

we will have only very low levels of gene expression

51
Q

What is CAP?

A

activator
(positive regulation)

52
Q

cAMP is a signal for. . .

A

LOW GLUCOSE

it is a modification of ATP that accumulate in LOW glucose

53
Q

To be as efficient as possible, E coli should express the lac operon when 2 conditions are met

A

1) lactose IS available

AND

2) glucose is NOT available

54
Q

Where does CAP bind?

A

binds to a region of DNA just before the lac operon promoter and helps RNA polymerase attach to the promoter, driving HIGH levels of transcription

55
Q

Why is this combinatorial control of the lac operon useful?

A

it ensures that bacteria only turn on the lac operon and start using lactose AFTER they have used up all of the preferred energy source (glucose)

56
Q

Glucose high, cAMP low, lactose absent

A

NO GENE EXPRESSION

57
Q

Glucose low, cAMP high, lactose absent

A

NO GENE EXPRESSION

58
Q

Glucose high, cAMP low, lactose present

A

LOW GENE EXPRESSION

59
Q

Glucose low, cAMP low, lactose present

A

HIGH GENE EXPRESSION

60
Q

How does methylation of DNA and histones affect the organization of nucleosomes?

A

causes nucleosomes to pack tightly together

transcription factors cannot bind the DNA & genes are NOT expressed

61
Q

How does histone acetylation affect the organization of nucleosomes?

A

results in loose packing of nucleosomes

transcription factors can bind the DNA & genes are expressed

62
Q

What are some differences in regulation of transcription off prokaryotes vs eukaryotes

A
  • separation of transcription + translation
  • separation can BLOCK RNA pol access
  • basal transcription is LOW
  • majority of regulation is POSITIVE not negative
  • more transcriptional regulation + combinatorial control
63
Q

What is a regulatory element?

A

the DNA sequence that transcription factors bind to

64
Q

Where do repressors bind?

A

bind to silencers

65
Q

Where do activators bind?

A

bind to enhancers or enhancer elements

66
Q

What do mediators do?

A
  • they ‘mediate’ between the activators and general transcription factors
  • coactivator
  • facilitates binding of the TBP
67
Q

Where are regulatory sequences found?

A
  • upstream of gene
  • downstream of gene
  • introns
68
Q

How does a DNA binding protein recognize specific DNA sequences?

A
  • the major groove gives the necessary info for transcription factors
  • major groove gives more info about bases

dif combinations of H bond acceptor, H bond donor, other H, methyl group (code)

69
Q

Example of DNA binding domain

A

Helix-loop-helix

70
Q

What is a DNA binding domain?

A
  • transcription factors are usually made up of several domains
  • there is only a small number of possible DNA binding domains
  • most transcription factors exist in large gene families
71
Q

Features of helix-loop-helix

A
  • operates as a dimer
  • has 2 components: recognition helix & dimer-forming helix
72
Q

What is Max?

A

the human transcription factor which has a HLH structure
- involved in regulating the genes for cell growth and division

73
Q

What are some features of transcription factors?

A

1) modular
2) most are in large gene families
3) members of the transcription factor families can homo-dimerise OR sometimes hetero-dimerse
4) combinatorial control

74
Q

Myc-max

A
  • common in cancer cells
  • when it binds to DNA, it interacts with a specific set of proteins and causes ACETYLATION
    –> ACTIVATION
75
Q

Mad-max

A
  • when it binds to DNA, it interacts w a specific set of proteins and causes DEACETYLATION
  • REPRESSION
  • can no longer divide / grow, but only differentiates
76
Q

Why is alternative splicing important?

A
  • it allows several proteins to be produced from each gene
  • some exons can be spliced OUT along w introns, which increases variety
77
Q

How does alternative splicing occur?

A
  • splicing REPRESSOR binds to RNA and makes a particular intron-exon boundary harder for the spliceosome machinery to recognize
  • won’t recognize that exon - will skip it completely
78
Q

What are splicing activators?

A

the splice boundaries b/w the exons and introns may not be v efficient
however, there may be splicing ENHANCERS that bind to RNA and make it more likely that the spliceosome will splice these boundaries

biochem (9 decks)

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