W3 Intracellular proteolysis

Question 1

Serine

Answer 1

Cleaves peptide bonds in proteins, in which serine serves as the nucleophilic amino acid at the active site

Question 2

Cysteine

Answer 2

Protein degradation in lysosomes

Question 3

Aspartyl

Answer 3

Use an activated water molecule bound to one or more aspartate residues for catalysis (acidic pH)

Question 4

Metalloproteases

Answer 4

Zinc ion as cofactor, any protease w/metal

Question 5

Protein activation by proteolysis

Answer 5

Trypsinogen into trypsin by enteropeptidase
Trypsin into sigma-chemotrypsin into alpha-chemotrypsin by autolysis

Synthesized in RER (because these are secreted enzymes) + both serine proteases
Trypsin formed in small intestine when it’s proenzyme form (trypsinogen) produced by pancreas is activated

Question 6

Why splice acceptor site required

Answer 6

Required for introns to be removed so shift in reading frame as shift is 2 nucleotides instead of 3 thus translated into completely different AA sequence

Question 7

HIV-1 protease

Answer 7

G + GP (pro proteins) need to be processed by proteolysis, not processed = not infective
Key part of discovery was crystallisation of enzyme so can see 3D image by X-Ray crystallography = thus can design drugs that fit into AS
It needs to be cleaved off a larger precursor protein itself
HIV-1 protease cleaves poly-protein precursors to form functional proteins

Question 8

Ubiquitous pathway

Answer 8

Ubiquitin = small peptide, less than 100 AA can mark them for degradation through proteasome
Carboxyl terminus attached to cysteine through thioester bond

Question 9

Ubiquitin-activating enzyme (E1)

Answer 9

Formation of thioester bond between COOH terminus of ubiquitin and a cysteine in E1
Reaction requires ATP

Question 10

Ubiquitin-conjugating enzyme (E2)

Answer 10

Transfer of ubiquitin to a cysteine on E2

Question 11

Ubiquitin-protein ligase (E3)

Answer 11

Transfer of ubiquitin from E2 to a lysine on the target protein
Many different E3s exist that recognize specific target proteins

Question 12

N-end rule

Answer 12

U3 ubiquitin ligases have poor affinity for stabilizing amino-terminal residues

Question 13

Statins

Answer 13

Block CL synthesis by inhibition of HMG CoA

Question 14

SREBP cycle for cholestrol regulation

Answer 14

If CL levels low taken from outside the cell as otherwise a lot of ATP would be used
SREBP is a TF which activates genes needed for CL supply, anchored in membrane of ER w/SCAP + Insig
SCAP + SREBP form v.tight complex
Proteases in golgi to seperate complex to release (active) N-SREBP - rest gets degraded