Proteins Flashcards

Question

Pyruvate Dehydrogenase

Answer 1

Octahedral 24 subunits 4 3 2 | Forms a hollow cube

Answer 2

4 Globular mixed A and B domain subunits C4 that bind ATP and Ca2+ or Mg2+of 375 amino acids that connect in a chain with 2 chains twisting together in a helix with a gentle right hand twist. 750 A long for each turn, 13 units per turn. Also called F-Actin.

Answer 3

Single strand of RNA wrapped by 150 amino acid capsid proteins, 18 nm wide * 300 nm long, 2.3 nm rise per turn

Answer 4

1- A subunit- enzyme activity, modifies human protein inside the cell 5 B subunits with C5 symmetry that form ring each with an active receptor site to bind to surface of human cell

Answer 5

8 2x4 proteins D4, ~146 base pairs wrap around, ~100 A wide

Answer 6

In reduced form disconnects improperly formed SS bridges and reforms them, in oxidized form it makes proper SS bridges

Answer 7

A chaperon protein in cytosol, uses ATP to keep proteins from folding prematurely

Answer 8

4 Myoglobin like subunits 2 alpha are same and 2 beta are same kitty corner clockwise a2, b1, a1, b2, 57% dif between a and b, changes conformation from T deox to R ox state, closes center and breaks salt bridges and edges, heme group binds like myo His F8--FeII--O2--E7 which pulls heme group flat, Deox UV at 560, Oxy increased 580 UV absorbance, pH affects binding low stabilizes T state, high will shift binding curve to left, Hill coefficient can define binding curve, steeper = bigger hill coefficient

Answer 9

Decreases O binding in O High altitude blood levels go from 4 mM to 8 mM, binds one mole to mole in center f hemoglobin tetramer when in deoxy state decreasing hemo's affinity for O

Answer 10

500-10000 kDa vs 80 in hemoglobin Molusks 10-20 subunits Arthropods- Hexamers D3, 75 kDa each unit, binds 2 Cu and 1 O in the middle of 6 His

Answer 11

Beta Glu 6----> to Val 6 mutation | B2 Val 6 hydrophobic fits into hydrophobic pocket on B1 w/Phe 85 Leu 88 making tetramers form long fibers

Answer 12

Endonuclease cleave P—O next to Base B next to O- Cleave RNA’s His 12-N lone pair Deprotonates Base A C2 OH O- then attacks P which breaks P—-O bond O—CH2—-C4 of Base B at the same time as His 119 donates proton to O so Base B leaves with OH group. Next enter water which reprotonates His 119 N and the OH- attacks the P causeing the original new OP bond to break and those electrons steals the H off of the original N on His 12. Concerted! Acid Base

Answer 13

His 96, His 94, His 119 hold Zn2+ in place which grabs OH from water leaving a H+ to float away... Lone pair on OH attack C from CO2 and forms leaving group. New water molecule comes in and it does it again.

Answer 14

Can increase by 10^8 | Ribosome peptide formation is example of this

Answer 15

Nucleophile on enzyme attack electrophile on substrate and slopes reaction to occur, stabilizes transition state

Answer 16

``` Nucleophiles ROH deprotonated RO RSH deprotonated RS RNH3+ deprotonated RNH2 IMID+ deprotonated N in ring has lone pair ``` ``` Electrophiles Protons + Metal Ions + Ketone or Carbonyl Groups RR—C double bond NH+ imines ```

Answer 17

Use covalent catalyst Concerted Acid Base Transitions state stabilization Asp 102 orients His 57 with a H bond Allowing His 57 to take Ser 195’s H making it O- so it attacks the C with the O double bond on the peptide back bone making the electrons the bond the C to the N grand the H from His 57 where RNH2 leaves(1 part of the peptide. Other side is still attached to Ser 195. Water comes in and His 57 N grabs H and OH- attacks C from Nucleotide cause the C—-O Ser 195 to grab the elections to grab a H back from His making Ser HO leaving other side of nucleotide free as a carboxyl group Gly 193 and Ser 195 create an oxyanion hole to stabilize the intermediate Names same in each but numbers are different because of convergent evolution... they are all in different places on the chain

Answer 18

4 active sites C4 geometry,6 4 beta strand blades which bond sialic acid in center which when bound C2 becomes planer. DANA looks almost like Sialic Acid and does competitive inhibition doesn’t bond super tight.... changed to 4 Guanidino Dana with Argine like side chain on and increased flu virus binding 10000 and decreased human neura binding by 100 which selectivity is improved ~1 million

Answer 19

Chymotrypsinogen to pi chymotrypsin between 15 and 16, then Chymo breaks it self between 146 and 149 and the 3 chains fold activating it...

Answer 20

Precursor to digestive enzymes made in pancreas and secreted in inactive form Trypsinogen activated by enteropeptidase the. Trypsin activates more of itself and others But it is held in check by pancreatic trypsin inhibitor by interaction between Lys 15 and Asp 189 until it is in the duodenum Ki 10^-13 Ribonuclease is even stronger Ki 10^-14 Horseshoe shaped mixed Alpha Beta strands. Surrounds RNase.

Answer 21

Carbomoyl and Aspartate activated by ATCase —-> go through 6 more steps and make CTP Presence of CTP inhibits ATCase by binding in a non active site R subunits changing it conformationally to T inactive state CTP moves graph to right ATP though can increase reaction by binding in allosteric not active site R and conformationally changing it into R state which favors substrate binding ATP moves graph to left Sigmoidal the result of cooperitivity ATCase is D3 with 12 subunits PALA- competitive inhibitor of ATPCase binds In active site so switch’s from T to R active state but since is in active substrate can’t bind

Answer 22

Lys K 10 Arg R 12.5 His H 6.0

Answer 23

Asp D 3.9 | Glu E 4.2

Answer 24

8. 3 C | 10. 1 Y