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CMCB Fall > #26 Gene Expression > Flashcards

#26 Gene Expression Flashcards

1
Q

Sites for Gene Expression Control

A

transcription, pre-mRNA processing, nuclear export, translation, and in some case prtoein activation (phosphorylation)

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2
Q

How do you idetinfy protein expressio levels with 2D polyacrylamide gel electrophoresis?

A

spearates proteins based on size and charge

vertical axis by weight (heavy on top) and charge on horizonal axis (acidic on left, baisc on right)

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3
Q

What shape is the starte site on the humanenome?

A

target adopts a very regulat shape B-form DNA

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4
Q

What is the B-form DNA grooves?

A

Major groove is board and accessible to protein recognition

Minor groove is shallow but still accessible

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5
Q

What is the most distinctive accessible hydrophoic contact?

A

5’ methyl group of thymine

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6
Q

Why is site-specific recognition challenign in the minor groove?

A

b/c the accessible features in teh this groove do not differentiate btween A, C, U, and G

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7
Q

The only distinctive H bond acceptor is the distinctive feature of 2’exocylci amine of Guanosine

A

yep

IT is easy to districminate a bp containing a G form those withotu a G

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8
Q

what is a method to identify protein expressino levels?

A

perform 2D polyarcrylamide gel electrophoresis that separtes proteins on teh basis of size and charge

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9
Q

How do proteins reach and contact expsed exocyslic functional gorups in major and minot groove of B-form DNA?

A

they can’t, they use secondary strucutral elemtsn that dock into these grooves

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10
Q

What kind of of secondary structural elemtns dock inot the major groove of DNA?

A

alpha helix is mst common

Beta hairpins and protein loops are also observed

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11
Q

What do side chains of Asn or Gln recognize?

A

N6 and N7 of adenosine bases and si

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12
Q

What do side chains of arg reognize?

A

O6 and N7 of guanin bases

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13
Q

What are helix-turn-helix motifs?

A

common preotin-DNA recognition motif found in prokaryotes and bacteriophage

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14
Q

Are helix-turn helix motifs homodimers or heterodimers?

A

homodimers

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15
Q

What is the 1st and 2nd helix

A

1st helix lies outside of DNA moand turn oritents the second helix in the oppsite direction

Second helix is calle the RECOGNITION HELIX b/c it docks inot he major groove of a B-form helix

PALINDROME

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16
Q

What do eukaryotic TFs emply to dock into major groove of DNA

A

alpha helices

17
Q

What are examples of of alha helices used to dock inot major grove of DNA

A
  1. Homeodomains
  2. Zinc Fingers
  3. Leucine Zippers
18
Q

What are homeodomains

A

consist of 3 consecutive alpha helices, with the 3rd one docking into the major groove

19
Q

What are zinc fingers?

A

DNA bidnng proteins that contain one or more zinkc atoms

most common DNA bindin domains in euk, 3% of hman gnome

chas beta hairpin and recognition alpha helix that is held together by a covalently bound zinc atom

20
Q

What are leucine zippers

A

chopsticks

21
Q

What are operons?

A

bacterial genes orgnized into operons that contain a group of genes that carry out a related funciton

22
Q

what is trp operon?

A

negative feedback

5 genes in trop operon that cod for 5 enzymes needed to syntehsize amino acid tryptophan

23
Q

What are the 5 genes needed for trp operon?

A

Tryp A, B ,C, D, E

24
Q

what happens when trp concentration is high?

A

trp binds to trp repressor protein –> recognition helices on trp repressor allows complex to bind to operator site –> bidning of trp repressor complex prevents RNA polymease binding and transcription

25
Q

at low concnetration of tryp

A

trp dissociats from repressor to trigger conformatino change that prevents recogntion helices from simultatnusly dockign to major groove of target DNA

26
Q

does repressor binding turns gene on or off?

A

OFF

27
Q

What is positive vs negative feedback repressor bindign

A

positive feedback- high ligant concentrion drives ligan bnidng to repressor –> repressor dissociates from operator? –> turns genes ON

negative feedback–> high ligant concentraiton drives ligant bindign to repressor –>repressor binds to operator site to sterically blcok RNA polymerase and transcrition_–> turns genes OFF

28
Q

Activator binding turns genes

A

ON

activtors are DNA binding roteins that bind to DNA oeprator sites to recrut DNA polymerase

29
Q

positive feedback vs negative feedback with activator

A

negative feedback–> high ligand concentraiton drives ligant bidnign to activator –> activator does not bid to operator site –> RNA polymerase is not recruited –> gene is OFF

positive feedback –> high ligan concentration dries liggand binding to actioro –> binds to operator site to recruit RNA polymears and tuen genes ON

30
Q

lac operon

A

regulated by both activator and repressor

lac operon codes for protein required to transprot lactose into cell and metbolize disaccharide

31
Q

What is the catabolic activator protein (CAP) on lac operon

A

enables bacteria to use non-glucose energy source like lactose

32
Q

lac repressor is activated when …is scarce and ….is abundant

A

glucose is scarce….lactose is abundant

33
Q

lac operon: high glucose, high lactose

A

operon OFF

presence of glucose leads to low cAMP concentration –> free CAP , doesnt bind to DNA, not active

lactose increases concentration of isomer of lactose allolactose –> binds to lac repressor –> cuases repressor to dissociate from its operator binding site –> RNA poly is not stericlaly locked

but CAP activator off =–> no RNA poly recruited

34
Q

high glucose, low lactose

A

CAP off –> no RNA poly recruit

allolactose low –> repressor blocks poly site

35
Q

low glucose, low lactose

A

CAP off

repreossr blocks

36
Q

low glucose, high lactose

A

CAP binds to DNA

lac repressor dissociated form operator binding site
ONNNN

37
Q

how can activation occur at a disntance?

A

enhancer

CMCB Fall (17 decks)

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