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BIO230 > BIO230 Lecture 2 > Flashcards

BIO230 Lecture 2 Flashcards

0
Q

Genomes are made out of ______, but _____ for viruses.

A
  1. DNA

2. RNA

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1
Q

Define: Genome

A

Information to make and maintain an organism

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2
Q

Genome expression

A

Release of biological info stored in genome

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3
Q

First product of genome expression

A

Transcriptome

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4
Q

Transcriptome

A

RNA molecules present present in a cell at a particular time

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5
Q

DNA microarray

A

Gives snapshot of transcriptome

Shows differences in mRNA expression in different cells

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6
Q

How is the transcriptome maintained?

A

Transcription

DNA -> RNA synthesis

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7
Q

What is the second product of genome expression?

A

Proteome

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8
Q

Define: Proteome

A
  • Collection of proteins in a cell

- Define biochemical functions of the cell

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9
Q

What does 2D GEL ELECTROPHORESIS do?

A
  • Gives snapshot of the proteome
  • Allows us to visualize differences b/t two protein samples
  • Separates based on size (y-axis) and charge (x-axis)
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10
Q

What do the red and blue spots in 2D gel electrophoresis readings mean?

A

Red = same proteins are in both samples

Blue = different proteins are the samples

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11
Q

Define: isoelectric point

A

The PH where a protein has no charge

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12
Q

Describe the method of DNA microarray (simple)

A

mRNA islation followed by hybridization to DNA microarrays

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13
Q

How is the proteome maintained?

A

Translation

RNA -> protein

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14
Q

What is the “central dogma” of molecular biology?

A

Genome (DNA) -> transcriptome (RNA) -> proteome (protein)

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15
Q

Do different cells of the same multicellular organism contain the same or different genome?

A

Same

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16
Q

How are different cell types produced? (e.g. liver cell, brain cell)

A

Differences in genome expression

Same DNA, but choose to express certain aspects resulting in different behaviour.

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17
Q

What percentage of the human genome is expressed at any one time?

A

30~60%

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18
Q

The bacterial toxin cyclohexamide inhibits eukaryotic translation. Which of the following would you expect to be most affected in human cells treated with cyclohexamide?

A) Genome
B) Transcriptome
C) Proteome

A

C) Proteome

translation = RNA to proteins -> proteome would be affected because none would be made

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19
Q

Where can eukaryotic gene expression be controlled?

A
  1. Transcriptional control
  2. RNA processing control
  3. RNA transport & localization control
  4. Translation control
  5. mRNA degradation control
  6. Protein activity control
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20
Q

Regulation of gene expression is crucial because…

A
  1. Response properly to extracellular stimuli (for both multicellular & unicellular organisms)
  2. A cell’s individuality; defining cell types (only multicellular organisms)
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21
Q

What enzyme is responsible for transcribing DNA -> RNA?

A

RNA Polymerase

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22
Q

In what direction does transcription occur?

A

3’ -> 5’

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23
Q

What direction does the newly formed RNA come out of the RNA polymerase during transcription?

A

5’ comes out of the RNA channel first

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24
Q

What is used to form mRNA during DNA transcription?

A

Ribonucleoside triphosphates

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25
Q

Where does the ribonucleoside triphosphate go into the RNA polymerase during transcription?

A

Ribonucleoside triphosphate uptake channel

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26
Q

What is the RNA polymerase holoenzyme composed of?

A

sigma factor + RNA polymerase

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27
Q

Outline prokaryotic transcription

A
  1. DNA has promotor section (that may not be the transcription start site) that positions the start site
  2. Sigma factor binds to promotor, then RNA polymerase binds -> forms holoenzyme
  3. Holoenzyme unwinds DNA
  4. Transcription begins
  5. Sigma factor released after ~10 nucleotides synthesized
  6. Transcription elongation
  7. Transcription termination (stem loop/hairpin structure usually forms from the RNA) -> RNA released
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28
Q

Can genes be transcribed at different speeds?

A

Yes, some are faster than others.

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29
Q

What regulates gene expression in both prokaryotes and eukaryotes?

A

Gene Regulatory Proteins (transcription factors)

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30
Q

Where do Gene Regulatory Proteins bind to?

A

Regulatory regions of DNA (cis elements)

Can be found in/before/after promotor, or in coding sequence, or anywhere.

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31
Q

What are activators?

A

Gene regulatory proteins that can turn genes on; positive regulators

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32
Q

What are repressors?

A

Gene regulatory proteins that can turn genes off; negative regulators

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33
Q

Give one example of a repressor.

A

Tryptophan (Trp) operon

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34
Q

How were gene regulatory proteins discovered?

A

Bacterial genetics

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35
Q

Who was responsible for discovering gene regulating proteins?

A

Francois Jacob
Andre Lwoff
Jacques Monod

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36
Q

What conditions do e.coli follow in terms of transcription regulation?

A

Food availability.

Change regulation by food availability.

37
Q

List some traits of E. coli.

A
  • unicellular prokaryote
  • one chromosome of circular DNA
  • encodes ~4300 proteins
38
Q

Define: operon

A

Multiple genes can be transcribed into a single mRNA.

Allow gene expression to be coordinately controlled.

39
Q

Are operons in eukaryotes or prokaryotes, or both?

A

Only prokaryotes

40
Q

How many genes does the tryptophan operon have?

A

5

41
Q

Is the Trp operon an activator or repressor?

A

Repressor

42
Q

What does the Trp operon do?

A

encode enzymes for tryptophan biosynthesis

43
Q

How is the Trp operon regulated?

A

Transcriptionally regulated by a single promotor

44
Q

In a diagram of the promoter region, where does the sigma factor bind to?

A

The “yellow” areas (two blocks near each end of the promoter area)

-35 and -10

45
Q

How many protein-bound states does the Trp operon promoter have?

*protein-bound = how many types proteins can bind to the promoter?

A

2

46
Q

What are the protein-bound states of the Trp operon promoter?

A
  1. Bound by RNA polymerase

2. Bound by tryptophan repressor protein

47
Q

When the Trp operon promotor is bound by RNA polymerase, what is the gene expression like?

A

Tryptophan gene expression ON -> make 5 genes and tryptophan

48
Q

When the Trp operon promotor is bound by a tryptophan repressor protein, what is the gene expression like?

A

Tryptophan gene expression OFF -> tryptophan repressor protein bind to operator (specific area of promotor sequence that prevents RNA polymerase from binding)

49
Q

What happens when Trp levels is high in a cell?

A

The tryptophan repressor protein binds to the operator section of the promotor area and prevents more tryptophan from being made.

50
Q

What happens when Trp levels are low in a cell?

A

RNA polymerase binds to -35 and -10 of the promotor area and makes more tryptophan.

51
Q

How is tryptophan repressor regulated?

A

2 molecules of tryptophan is needed to activate the repressor (proving that there is an excess)

52
Q

What happens when Trp levels drop while Trp repressor protein is bound?

A

Trp repressor protein releases the 2 Trp required to activate it -> becomes inactive -> allow RNA poly to bind

53
Q

What type of DNA binding motif does Tryptophan repressor contain?

A

Helix-Turn-Helix

54
Q

What is the most common DNA-binding motif?

A

Helix-Turn-Helix

55
Q

Where does the Helix-Turn-Helix bind to?

A

Major groove of DNA double helix.

Contacts the edges of base pairs.

56
Q

Define: recognition helix

A

C-terminal alpha helix of the Helix-Turn-Helix structure.

57
Q

What is the recognition sequence responsible for?

A

Sequence specific recognition of DNA.

58
Q

What is the N-terminal of the Helix-Turn-Helix structure responsible for?

A

Structural component.

Positions recognition sequence.

59
Q

When tryptophan binds to the Trp repressor, what happens?

A

Conformation change of Trp repressor occurs -> bind the DNA sequence (Helix-Turn-Helix) -> block transcription of genes that encode enzyme to make Trp operon -> genes turned off

60
Q

Where does the Trp repressor fit on the DNA?

A

The major groove of the operator section.

61
Q

Define: dual regulation

A

Both positive and negative control

62
Q

What organism is the Lac operon found in?

A

E. coli

63
Q

What is the Lac operon code?

A

3 genes that transport lactose into cell for catabolism (breakdown into simpler materials)

64
Q

The Lac operon can ______ regulate.

A

Dual

65
Q

What does the Lac operon allow the cell to do when there is a lack of glucose?

A

Use lactose for energy

66
Q

What conditions MUST be met in order for a cell to use lactose as an energy source?

A

Glucose low AND lactose high.

Lac operon will be on -> E. coli use lactose for energy

67
Q

What acts as the ACTIVATOR for the Lac operon?

A

Catabolite Activator Protein (CAP)

Promotes Lac expression (low glucose & high lactose)

68
Q

What acts as the REPRESSOR for the Lac operon?

A

Lac Repressor Protein

Inhibits Lac expression (low lactose and/or high glucose)

69
Q

What is the first gene of the Lac operon?

A

LacZ

70
Q

What is LacZ responsible for?

A

Codes for beta galactosidase

71
Q

What is beta galactosidase responsible for?

A

Break down lactose -> glucose & galactose

72
Q

Where does the catabolite activator protein (CAP) bind?

A

CAP-binding site

blue section before the promotor

73
Q

Where does the RNA polymerase bind?

A

RNA-polymerase binding site (promotor)

74
Q

Where does the Lac repressor bind?

A

Operator (to the right of where the sigma factor binds, but still inside the promotor)

75
Q

When is the Lac repressor bound to the operator?

A

Lactose levels are low.

76
Q

Does Lac operon gene expression turn off?

A

No, but very very low.

77
Q

What are 2 conditions that have to be met in order for the Lac operon to be on?

A
  1. Lac repressor not bounded

2. CAP bounded.

78
Q

What happens when there is high glucose and high lactose?

A

CAP is not bound.

Lac repressor not bound.

79
Q

What happens when there is high glucose and low lactose?

A

CAP not bound.

Lac repressor bound.

80
Q

What type of relationship does lactose and allolactose have?

A

Positively correlated relationship:
More lactose = more allolactose
Less lactose = less allolactose

81
Q

Define: allolactose

A

Isomer of lactose

82
Q

What is required in order for lactose -> allolactose?

A

Beta galactosidase

83
Q

How does increased lactose remove Lac repressor from the operator?

A
  • When allolactose is high, it binds to Lac repressor
  • Lac repressor undergoes conformational change
  • Conformational change decreases DNA-binding activity of Lac repressor
  • Lac repressor releases from the operator
84
Q

Why is an activator needed in order to transcribe the Lac operon?

A
  • RNA pol inefficiently binds to Lac promotor

- CAP needs to be bound (RNA pol likes CAP, therefore will bind efficiently)

85
Q

What structural feature does CAP contain?

A

Helix-turn-Helix DNA binding domain

86
Q

How is CAP DNA binding activated?

A

Low glucose

87
Q

What is the relationship between glucose and cyclic AMP (cAMP)?

A

Negative relationship:
More glucose = less cAMP
Less glucose = more cAMP

88
Q

What does cAMP do to the CAP protein?

A
  • Conformational change
  • CAP increase DNA binding activity -> bind to DNA
  • RNA pol bind to CAP binding site
89
Q

Under conditions where both glucose and lactose levels are low, you would expect the expression of the Lac operon to be…

A

Off (very low)

90
Q

Why is important that expression of the Lac operon is always slightly on?

A) E. coli needs B-galactosidase encoded by Lac operon to use glucose
B) E. coli needs B-galactosidase encoded by Lac operon to respond to lactose
C) RNA polymerase requires B-galactosidease ended by Lac operon to bind DNA
D) Lac can be completely shut down without consequence

A

B

B-galactosidase break down lactose -> allolactose -> bind to repressor -> repressor does not bind to RNA

BIO230 (3 decks)

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