1-8 Protein Homeostasis

Question 1

Formation of acmino-acyl-tRNA

Answer 1

1. tRNA with an anticodon loop/ anticodon properly folded
2. linkage of amino acid to tRNA via tRNA SYNTHETASE (each AA has own specific syntehtase): expends 1 ATP->AMP +PPi, creates high energy bond
3. anticodon on the tRNA binds to the codon from the mRNA (antiparralell)

Question 2

Ribosome structure

Answer 2

Large subunit: exit, peptidase, amino actyl transferase (EPA) sites

small subunit: mRNA binding site

Question 3

Eukaryotic translation steps: initiation

Answer 3

1. Initiation:
   (happen simultaenously)
   Event 1: GTP binding protein is bound by GTP which then binds initation tRNA (special methyl trna), complex formed enters small subunit

Event2: Cap binding complex binds methyl guanine cap and polyAAA tail (ATP expended)

small subunit with loaded met-trna binds activated mRNA, helicase in the complex unsips and small subunit scans until finds start codon- hydrolysis and release of GTPbound protein frees methyl tRNA, cap binding complex also dissociates, large subunit now recruited

2. Elongation: tRNAs randomly diffuse into A site, if associate for long enough time tRNA elongation factor will hydolyze GTP->GDP + Pi (proof reading step), PEPTIDYL TRANFERASE will make the new peptide bond and ribosome scoots over, P to E exit requires GTP, mRNA tail weaves out a channel in the large subunit whilst extending

Energy requirements: 2ATP to charge each tRNA, 2GTP for each AA added

3. Termination: once reach stop codon no tRNA will fit and a “binding release factor” enters site, hydolysis and carboxyterminus added to peptide chain, ribosome dissociates
   * polyribosomes happen*

Question 4

Cap dependent

Cap independent

Answer 4

mRNA translation
dependent: majority

independent: IRES sequences can recruit necessary factors without the cap involved,

Question 5

mRNA regulation at 5’ and 3’ UTRs

Answer 5

ex: iron response elements ferritin and transferrin regulated by binding of cytosolic aconitase at either 5 or 3 UTRs during iron starved/rich states

Question 6

Stabilization of mRNA

Answer 6

1. 5’ guanine cap put on backwards so nucelases cannot recognize and degrade
2. polyA tail is gradually shortening once in cytoplasm but protects for long enough to be translated

Question 7

Micro RNAs

Answer 7

involved in controlling translation

Can repress different parts of RNA to affect elongation efforts, can decap, can deadenylate

Question 8

mTOR

Answer 8

“master regulator” of cell growth via,

1. ribosome synthesis
2. S6 small subunit synthesis
3. ribosome associated factor synthesis

Fed signals from PI3K and Amino acid levels

Question 9

Oligomer

Aggregates

Answer 9

small aggregation of proteins, can happen if all deformed

large group

Question 10

Protein degradation

Answer 10

by Uniquitin Proteasome System

Overview: proteins get polyubiquinated at lysine by expending ATP and attaching Ub, protein enters active sites of proteosome, degrades protein, recycles Ub

Question 11

Lysosome degradation types

Answer 11

degrades protein from multiple sources

1. endocytosis
2. phagocytosis
3. autophagy “self eating”

Question 12

ERAD

Answer 12

ER associated degradation: misfolded proteins in the ER and exported to the cytosol for proteosome mediated degredation

ERAD triggers the unfolded protein response with lumen side receptors sensing misfolded proteins and activating signal cascade in cytosol which activates genes to help increase folding capacity of the ER

Question 13

Macroautophagy

Answer 13

Phagophore (double membrane sheet derived from ER) associates with LC3 circle proteins on edges, grows and engulfs cargo to degrade, autophagosome formed, fuses with lysosome, LC3 recycled and contents broken down into smaller parts to be released and reused by cells as new materials

Question 14

Microauthophagy

Answer 14

by lysosomes, smaller amounts of material at a time

Question 15

Types of autophagy

Answer 15

1. macro
2. micro
3. chaperone mediated

Question 16

Chaperone mediated autophagy

Answer 16

Protein with a specific motif tag recgonized by chaperone and directed towards receptor on lysosome to enter lysosome and degrade

very regulated

Question 17

Amyloid

Answer 17

normally very many alphahelix, if misfolded forms goofy betasheets which aggregate to oligomer->protofibrils->fibrils

bad clump do a disrupt

Prions: infectious amyloid

Question 18

Protein aggregates affect on cell fxn

Answer 18

loss of function
gain of toxic
inflammation

Question 19

Prions

Answer 19

misfolded proteins with the ability to transmit their misfolded shape onto normal variants of the same protein

ex. infectious amyloid