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Biology 311 > Lectures II-ii > Flashcards

Lectures II-ii Flashcards

1
Q

+1 start site

A

transcription start site (present in prokaryotes and eukaryotes)

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2
Q

promoter sequence

A

(-35 TTGACAT and -10 TATAAT) in prokaryotes, (-30 TATA) in eukaryotes

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3
Q

Shine-Dalgarno sequence

A

helps ribosome find the correct start codon-present in prokaryotes

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4
Q

PPE (promoter-proximal elements) + enhancers

A

present in eukaryotes

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5
Q

polyadenylation termination sequence

A

tells transcription when to stop - present in eukaryotes

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6
Q

intrinsic termination and rho-dependent terminator

A

tells transcription when to stop - present in prokaryotes

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7
Q

SNPs and SSLPs can become mutations if they occur in:

A
  1. regulatory sequences important for transcription (promoter, terminator, promoter and PPE/enhancer)
  2. coding regions (anything between start and stop codon)
  3. intron boundaries (applies only to eukaryotes, found within the coding region)
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8
Q

what effect does SNPs and SSLPs in regulatory regions have?

A
  • prevents transcription machinery from recognizing promoter and starting transcription
  • allows transcription machinery to bind more strongly to promoter, enhancing transcriptional rates
  • destroys termination site, preventing proper transcription termination
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9
Q

how do you detect effect of a mutation on transcription?

A

use Northern Blot (isolate RNA and run agarose gel, transfer RNA to filter and incubate with a radioactive probe)

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10
Q

DNA code is degenerate, meaning:

A

there are multiple codons that code for the same amino acid

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11
Q

the last nucleotide position in a codon is known as:

A

the wobble position, SNP’s at the location may or may not cause mutation

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12
Q

what effect does SNPs have in coding regions

A

synonymous/silent mutation, conservative missense mutation (chemically similar amino acid produced), nonconservative missense mutation (chemically dissimilar amino acid produced), nonsense mutation (early chain termination)

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13
Q

how can you detect effect of SNP on protein expression?

A

use Western Blot (isolate proteins and run on a POLYACRYLAMIDE gel, transfer proteins to a filter and incubate with a radioactive probe-antibody)

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14
Q

what effect does SSLPs have in coding regions

A

frameshift mutation (base insertion or base deletion) - this can be detected by Western Blots)

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15
Q

eukaryotes genes are made up of two regions:

A

introns (non-coding junk DNA) and exons (coding region)

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16
Q

post-transcriptional modification removes:

A

all introns before proceeding to translation (done by splicing/spliceosome)

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17
Q

how do spliceosome recognize introns?

A

5’ GU-AG 3’ rule

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18
Q

what effect does SNPs in introns have?

A

can cause frameshift by removing or creating GU/AG sites, results in improper removal of introns which can change phenotype of protein produced

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19
Q

what effect does SSLPs in introns have?

A

could result in changes to splice sites by destroying site, creating new sites, or moving the original site

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20
Q

how can you detect SNPs and SSLPs in introns?

A

Nothern Blot (mRNA changes) and Western blot (detect protein expression)

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21
Q

what mechanisms do cells need for gene regulation?

A

1) able to recognize environmental conditions in which they should activate or repress the transcription of relevant genes
2) able to turn on or off the transcription of each specific gene or group of genes

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22
Q

promoter

A

DNA segment that interacts with RNA polymerase to determine where transcription begins

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23
Q

activator/repressor

A

DNA segments near the promoter that serve as binding sites for sequence-specific regulatory proteins by controlling accessibility to RNA polymerase

24
Q

operator

A

binding site for repressors

25
Q

positive regulation

A

presence of bound protein is required for transcription

26
Q

negative regulation

A

absence of bound repressor allows transcription to begin

27
Q

DNA binding is effected through the interaction of two different sites in the protein:

A
  1. DNA binding domain (can be functional or nonfunctional) and is determined by….
  2. allosteric site which interacts with allosteric effects that bind to the allosteric site of the regulatory protein in such a way as to change its activity
28
Q

metabolism of lactose requires two enzymes:

A

structural genes:

  1. permease (Z) - transports lactose into the cell
  2. B-galactosidase (Y) - cleaves molecule to yield glucose and galactose
29
Q

coordinately controlled

A

genes whose transcription is controlled by a common means

30
Q

what are the regulatory components for the lac regulatory circuit?

A

1) gene for Lac repressor (I) - blocks expression of Z Y A
2) lac promoter site (P) - site where RNA polymerase binds to initiate transcription of structural genes
3) lac operator site (O) - site on DNA to which the Lac repressor binds

31
Q

the lac operon consists of

A

P O Z Y A

32
Q

operon

A

a segment of DNA that encodes a multigenic RNA as well as the adjacent common promoter and regulatory region

33
Q

characteristics of Lac repressor

A
  • is not part of operon
  • has a DNA binding site that recognizes operator sequence
  • allosteric site binds to either allolactose or analogs
  • binds tightly only on O site of DNA on genes it controls
34
Q

allosteric transition

A

change in shape of repressor protein when allolactose or its analogs bind to it (no longer has binding affinity)

35
Q

induction

A

the relief of repression for system

36
Q

inducers

A

allosterically inactivate the repressor

37
Q

enzyme induction

A

the appearance of a specific enzyme only in the presence of its substrates

38
Q

constitutive mutations

A

cause the lac operon structural genes to be expressed regardless of whether inducers were present

39
Q

Oc mutations

A

repressor cannot bind to operator, always “on,” only affects the chromosome it is on “cis-acting”

40
Q

operator only influences:

A

expression of structural genes linked to it, cis-acting

41
Q

I- mutations

A

dominant to I+, I+ are trans-acting-can regulate all structural lac operon genes (on same or different DNA molecules, constitutive mutation

42
Q

supperrepressor Is mutations cause:

A

repression to persiste even in the presence of an inducer (dominant over I+)
-alters the allosteric site so that it can no longer bind to an inducer

43
Q

promoter mutations are:

A

cis-acting, affects transcription of all adjacent structural genes in the operon

44
Q

what are the conditions that must be met for lactose metabolic enzymes to be expressed?

A

1) Lactose must be present in the environment

2) glucose cannot be present in the cell’s environment

45
Q

catabolite repression

A

presence of a breakdown product (glucose/catabolite) that represses the system by activator proteins

46
Q

in the presence of high concentrations of glucose…

A

low concentrations of cAMP

47
Q

in the presence of low concentrations of glucose…

A

high concentrations of cAMP

48
Q

cAMP

A

cyclic adenosine monophosphate

49
Q

for activation of lac operon, high concentrations of ……

A

cAMP are necessary

50
Q

CAP

A

catabolite activator protein

51
Q

how does CAP-cAMP system work?

A

cAMP is an allosteric effector that binds to CAP and activates the lac operon, the system binds to DNA promoter and interacts with RNA polymerase to increase enzyme affinity for the lac promoter

52
Q

what do repressor and activator binding sites have in common?

A

the sequences display rotational symmetry

53
Q

negative control

A

signal that results in blockage of normal expression

ex. inducer-repressor control of the lac operon

54
Q

positive control

A

signal that activates the system

ex. CAP-cAMP system

55
Q

the lac operon is:

A

a cluster of structural genes that specify enzymes taking part in lactose metabolism

56
Q

lac operon genes are controlled by:

A

the coordinated actions of cis-acting promoter and operator regions

57
Q

the activity of promoter and operator regions is determined by:

A

repressor and activator molecules specified by separate regulator genes

Biology 311 (6 decks)

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