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BIO230 > Lecture 7 and 8 > Flashcards

Lecture 7 and 8 Flashcards

1
Q

Shine Dalgarno sequence

A

mRNAs have a 6-nucleotide Shine-Dalgarno sequence upstream of the AUG start codon.
it correctly positions AUG in the ribosomes and provides translational control mechanisms.

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2
Q

Translational control mechanisms

A
  1. A specific RNA-binding protein blocks access to the Shine Dalgarno sequence.
  2. Temperature-regulated RNA structures - stem-loop of RNA structure blocks access to shine Dalgarno at lower temperatures.
  3. Riboswitch (S-adenosyl methionine) - small molecules cause a conformational change to RNA blocking Shine Dalgarno sequence
  4. Antisense RNA -it base pairs with mRNA and blocks SD
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3
Q

Antisense RNA mechanism example

A

Iron Storage proteins

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4
Q

Riboswitch mechanism example

A

S-adenosyl methionine

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5
Q

Temperature regulation mechanism example

A

virulence genes of human pathogen Listeria monocytogenes

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6
Q

eIF2

A
  1. plays a crucial role in translation initiation
  2. eIF2 forms a complex with GTP and recruits initiator tRNA (methionyl) to the small ribosomal subunit
  3. The small ribosomal subunit binds the 5’ end of mRNA and scans for the first AUG
  4. when AUG is recognized, eiF2, hydrolyzes GTP to GDP
  5. GTP hydrolysis causes a conformational change in eiF2
  6. eIF2 bound to GDP is released and inactive
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7
Q

Reactivation of eIF2

A

it requires eIF2B which is a guanine nucleotide exchange factor (GEF) - it causes the exchange of GDP for GTP

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8
Q

How is eIF2 reactivation regulated

A

phosphorylation
1. phosphorylated eIF2 sequesters eIF2B as an inactive complex
2. since there is more eIF2 than eIF2B in cells, all eIF2B is sequestered and translation is dramatically reduced.

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9
Q

What happens when eIf2 is phosphorylated?

A

There is no exchange of GDP and GTP

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10
Q

What steps do proteins undergo to become functional?

A
  1. they must fold properly to adopt their 3D structure
  2. they are covalently modified with chemical groups (eg. sugars, phosphate)
  3. They interact with other proteins and small molecules (cofactors)
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11
Q

Protein folding

A

Hydrophobic amino acids are buried in the interior core.

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12
Q

When does the folding of proteins begin?

A

For some proteins, folding begins as they emerge from ribosomes, some are completely folded after synthesis

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12
Q

hsp60 nd hsp70

A
  1. they both interact with exposed hydrophobic residues of misfolded proteins.
  2. they use energy from ATP hydrolysis to promote proper folding.
    hsp70 works before hsp60
    hsp70 binds to protein as it emerges from the ribosome - help fold it. there can be correctly and incorrectly folded proteins.
    hsp 60 - double barrel shape
    incorrectly folded protein will bind to the sites in the barrel. it will use ATP. Groes cap will come on, and it will give protein more time to fold.
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13
Q

Chaperones for protein folding

A

many chaperones are called heat shock proteins since they are synthesized to high amounts by cells at elevated temperatures - as proteins begin to get denatured at higher temps

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14
Q

Proteasome

A

Protein degrading apparatus

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15
Q

What do exposed hydrophobic residues do?

A

they mark protein for degradation by the proteasome, competes with chaperones for misfolded proteins

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16
Q

Where is the proteasome found?

A

cytosol and nucleus

17
Q

Describe the structure of the proteasome

A

It is a hollow cylinder with a cap at each end and an active site in the core, the cap protects cellular proteins from degradation

18
Q

What proteins does proteasome act on?

A

The proteasome acts on proteins that have been marked for destruction by the addition of a small protein tag named ubiquitin

19
Q

Ubiquitin-conjugating system

A

it is made up of three enzymes and it adds ubiquitin to proteins

20
Q

Three enzymes in the ubiquitin conjugating system

A

E1, E2 and E3

21
Q

E1

A

an ATP-dependent ubiquitin-activating enzyme creates an activated E1-bound ubiquitin

22
Q

E2 and E3

A

E2 is a ubiquitin-conjugating enzyme that accepts ubiquitin from E1 and exists as a complex with E3, a ubiquitin ligase that selects substrates

23
Q

process of addition of ubiquitin

A
  1. ubiquitin gets added to E1, ATP gets converted to AMP
  2. E2 binds to E1
  3. E2 accepts ubiquitin from E1
  4. E3 nd E2 will form a complex
  5. E3 binds to specific degradation sequences in substrates
  6. Ubiquitin is added to a lysin residue on the target protein
  7. this process is repeated until a polyubiquitin chain is formed

Ubiquiting does NOT go on E3

24
Q

function of monoubiquitylation

A

histone regulation

25
Q

multiubiquitylation

A

endocytosis

26
Q

polyubiquitylation

A

proteasomal degradation + DNA repair

27
Q

How can E2 - E3 complex get activated

A

Phosphorylation by protein kinase, allosteric transition caused by ligand binding, allosteric transition caused by protein subunit addition

28
Q

how can a degradation signal get activated?

A

Phosphorylation by protein kinase, unmasking by protein dissociation, creation of destabilizing N terminus

29
Q

Protein Kinase A mediated gene exoression

A

Numerous extracellular stimuli result in increased levels of small
molecule cyclic AMP (cAMP)
- Activates protein kinase A (PKA)

30
Q

what does inactive PKA have?

A

2 regulatory subunits and 2 catalytic subunits

31
Q

What happens when cAMP binds to regulatory subunits?

A

Binding of cAMP to the regulatory subunits causes a conformational
change and release of the active catalytic subunits

32
Q

What does PKA substrate include

A

PKA substrates include enzymes involved in glycogen metabolism in skeletal muscle and liver

33
Q

glycogen metabolism - pka

A

Ligand = adrenaline (epinephrine)
* Response = to promote glucose release
* Activated PKA has 2 effects:
1. promote breakdown of glycogen
2. inhibit glycogen synthesis
* Glycogen is broken down into glucose-1-
phosphate

34
Q

where is the inactivated PKA located?

A

cytosol

35
Q

what do PKA catalytic subunits
phosphorylate

A

specific substrate
proteins
 activation of target genes with
cAMP Responsive Elements
(CRE)

35
Q

where does activated pka units translocate

A

nucleus

36
Q

how do protein interactions provide insight into function

A

guilt by association
eg. DNA damage response network

36
Q

Activation of target genes with cAMP
Responsive Elements (CRE):

A
  • Activated PKA phosphorylates
    CREB (CRE Binding protein)
  • CREB recruits CBP coactivator
    (CREB Binding Protein)
  • Target genes are transcribed
37
Q

Ferritin RNA release mechanism when iron starvation

A

Cytosolic aconitase will bind to ferritin RNA near the start site and block translation

38
Q

Ferritin RNA release mechanism when excess RNA

A

Cytisikic aconitase will bind to iron, there will be a conformational change and the ferritin RNA is released.

BIO230 (6 decks)

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