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BIOCHEMISTRY > EXAM2_L18_L19_Control_Gene_Expression > Flashcards

EXAM2_L18_L19_Control_Gene_Expression Flashcards

1
Q

PROKARYOTES:
if no glucose available, what is used for energy?
What happens if it is the only carbon source?

A

Lactose (glucose + galactose)

Three genes from LAC OPERON:
1. B-galactosidase (cleaves lactose)

  1. Lactose Permease (transports lactose cyto membrane)
  2. B-Galactoside Transacetylase (tx acetyl from AcetylCoa to B-galactoside)
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2
Q

Lac Operon Structure

A

Promoter(PI)/Repressor(I)/CAP/pLac/Operator||| Z/Y/A genes
Z- b-galactosidase
Y- Permease
A- Transacetylase

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3
Q

Positive control of lac operon:

When does it happen?
What are the 5 steps?

CAP: “catabolite activator protein”

A

No glucose-> lactose metabolism via CAP-cAMP

  1. adenylyl cyclase activated (low glucose)
  2. [cAMP] increases
  3. cAMP binds CAP
  4. CAP-cAMP binds DNA @ CAP SITE
  5. RNApol binds promoter & makes 3 genes of lactose metabolism
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4
Q 
When is cAMP high? Low?
What is CAP?
Why is cAMP so important?
 What happens if there is high cAMP? 
Sequence of 4 events?
A

LOW glucose= HIGH cAMP
HIGH glucose = LOW cAMP

CAP: “catabolite activator protein”

CAP can only bind to DNA if cAMP present

  1. if there is high cAMP that means no glucose & lac operon activation needed.
  2. cAMP binds CAP, CAP binds DNA,
  3. RNApol recruited & makes 3 lac genes,
  4. lac operon/metabolism ACTIVE
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5
Q

Negative Control of “lac I gene” & “lac repressor”

When is the lac operator inhibited?
What inhibits?
Why?
What makes repressor?

A

Lac OPERATOR inhibited– if NO LACTOSE
-REPRESSOR binds/inhibits OPERATOR (if no lactose)

*The only reason to TURN ON lac operator is if there is lactose to be metabolized

“lac I” gene encodes “lac repressor”
lac I- always present in cells (constitutively expressed)

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6
Q

lac I gene and lac repressor activity:

What happens if cell has LACTOSE?
What needed for RNApol to bind and transcribe?

A

Lactose» allolactose “inducer”

allolactose binds/inhibits repressor.
–>OPERATOR now active

If cAMP–CAP binds DNA–DNApol binds–>Transcription

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7
Q

What two ways is the lac operon negatively controlled?

A
  1. Lac repressor binding operator when no lactose
    - repressor constitutively available
    - binds regardless of glucose or CAP
  2. No CAP-cAMP binding to CAPsite
    - CAP only binds if cAMP available (no glucose)
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8
Q

When will lac operon be active?

A

ONLY ACTIVE IF:

  1. no glucose (cAMP binds CAP-> binds DNA)
  2. has lactose (repressor disabled/releases from operator)

RNApol can bind and transcribe at START site

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9
Q

Differences in Eukaryote Transcriptional regulation:

What are two levels of control of gene expression?

A
  1. no Operons
  2. complex (has nucleus thus separate areas of transcription/translation)
  3. Short Term Control (daily needs on/off quickly)
  4. Long Term Control (gene reg in development/differentiation)
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10
Q

What are 6 ways to regulate Eukaryotic gene expression?

A

1. transcription (activate/repress)
2. RNA processing (alternative splicing)
3. mRNA transport (stuck in nucleus=degraded)
4. mRNA Translation (rate & re-initiation: 5’cap/polyA tail)
5. mRNA degradation (Long polyA tail= longer life)
6. Protein activity/degredation (post translat modification)

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11
Q 
CIS (cis-acting elements)
TRANS Elements (trans-acting elements)
A

CIS– ENHANCER SEQUENCE ON DNA (regulatory)

TRANS- An ACTIVATOR PROTEIN BINDS CIS SEQUENCE

CIS Elements= Regulatory DNA seq. where TF’s bind
— ie:(promoters/enhancers)

TRANS- gene regulatory proteins that recognize cis elements.
—-ie: (TFIID, Activators)

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12
Q

Eukaryotic Gene Transcription Regulation:

GTF’s

A

General transcription factors- REQUIRED FOR INITIATION

- bind to promoter region of a gene

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13
Q

What are activators, enhancers, transcription factors?
What do they do?
How do they work?

A

ACTIVATORS (TF’s)- Bind to a DNA enhancer sequence to increase transcription. VIA signals

Activators bind enhancer and then they can regulate RNApol II- - Increases efficiency/rate regardless of distance or position

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14
Q

If Enhancer is over 1000bp’s away how can they activate transcription at the START SITE?

A

DNA Looping (brings the two regions close together)

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15
Q

Two domains of Trans-acting factors

What are the roles of each?

A
  1. DNA binding domain- (binds dna) at motif
  2. Activation domain:
    - binds GTF’s and co-activators
    - Modifies chromatin structure
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16
Q

What are 4 structural motifs commonly found in the DNA-binding domains of regulatory transcription factors?

A
  1. Zinc-finger
  2. Leucine Zipper
  3. Helix-loop-Helix
  4. Helix-turn-helix
17
Q

Zinc Finger

binding domain example?
Cis-Element?

A

Protein bind Zn ions & form loops/fingers

IE: Steroid hormone receptor (estrogen)

-Cis-element: HRE (hormone response element)

18
Q

Leucine Zipper Motif

binding domain example?
Cis-Element?

A

2 alpha helix w/ leucines facing each other along length of helix

-Dimerization allows protein to bind on both sides of double helix

Ex: CREB (cAMP response element binding protein)
cis-element: CRE

19
Q

Helix-loop-Helix motif

binding domain example?
Cis-Element?

A

DNA-binding domains formed by dimerization of two polypeptide chains

Ex: transcription factor MYC
cis-element: E-BOX

20
Q

Helix-Turn-Helix Motif
binding domain example?
Cis-Element?

A

2 helix separated by turn (a turn is longer than a loop)
- one helix binds, 2nd helix stabilizes by lying across it

Ex: Homeodomain (HOX) proteins
- embryonic development (CNS, axial skeleton, etc)

cis-element: HOMEOBOX

21
Q 
PIT-1 TF
What does it encode?
What genes does it transcribe?
What happens if misregulated?
What happens if pit1 is low?
How do you treat children?
A

Pituitary gland makes–>Growth Hormone

PIT-1 gene encodes PIT-1 TF
PIT-1 TF required for transcribing GH & PROLACTIN genes (and important for pituitary development)

  • Misregulated PIT-1 results in GH deficiency
  • Low PIT-1 –> DWARFISM
  • Children can be treated effectively w/ GH injections
22
Q

Functions of the activating domain of regulatory proteins

HAT= histone acetyltransferase

A

Allows TF’s to

  1. bind other TF’s
  2. Help RNApol II form initiation complex
  3. Recruits multisubunit complexes (HATS)
23
Q

HATs HDACs

What is acetylated histone?

A

HAT- histone aminoactyltransferase
HDAC- histone deacetylases

HATs- Acetylation Cut Histones into smaller pieces and make DNA more accessible for Transcription

HDAC- puts them back together

ACETYLATED HISTONES= ACTIVE CHROMATIN

24
Q

Transcriptional Repressors

4 modes of transcriptional repression:

A

inhibit tissue genes in inappropriate cell types

  • binding motifs sames as activators (Znfinger, HtH,Leuzipper, HLH)
    1. Competition (activator/repressor compete for same site)
    2. Inhibition (repressor binds/inhibits by protein interaction)
    3. Direct repression (repressor binds to repressor binding site and prevent TF’s/RNApol function)
    4. Indirect repression (recruits HDACs)
25
Q

RNA interference (RNAi) or Post-transcriptional Gene Silencing (PTGS)

What is it? how big? What is its function in humans?

A

SHORT DOUBLE STRANDED RNA!!!
(21-23ntds)dsRNA

RNAi regulates gene expression in embryonic development to control the timing of development of various tissues

26
Q

RNAi mechanism
4 steps:
siRNA = small interfering RNA

A
  1. dsRNA cut into siRNA by DICER
  2. siRNAs bind RISC (only one strand binds)
  3. ssRNA hybridizes w/ mRNA target
  4. mRNA cut or translation blocked
27
Q

WET AMD
What is it characterized by?
How is it treated?
Outcome?

A

Wet Age-related macular degeneration
1. BV hyperplasia- leaks blood/fluid into eye (PAINFUL)

Treat w/ siRNA against VEGF (vasc endothel gf)

  • inject into eye
  • Inhibits bv growth, improved vision, extend time between injections
28
Q

Reticulocytes inhibiting translation of Hb using eIF2

How does it work?

A

If no heme available, kinase phosphorylates eIF2
Blocks exchange of GTP for GDP (can’t bind ribosome)
Hb Synthesis inhibited

eIF2 transfers initiator met-tRNA to Small ribosome
kinase activity blocks exchange of GDP to GTP
inhibited

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