Proteins

Question 1

Influenza Virus Proteins

Answer 1

Neuraminidase- on surface

Hemagglutinin- on surface, conformational change at pH 6 found in endosomes, has cyclic C-3 symmetry

Question 2

Myoglobin Structure and Properties

Answer 2

8 alpha helices w/ heme group with 4 N binding Fe II
F8His—Fe II—-O2—-HisE7
Held in pocket with ValE11 and PheCD1
After denaturing and dialysis it needs help/heme needs moiety to reform SS bridges

Question 3

Carboxypeptidase A

Answer 3

Center of mixed Beta sheets (strands twist right) with left twist, surrounded by alpha helices

Question 4

Bacteriorhodopsin

Answer 4

All alpha helices in lipid bilayer

Question 5

Rhodopsin

Answer 5

Helices, vision protein

Question 6

OmpF Porin

Answer 6

All beta strands form barrel in membrane

Question 7

GAPDH

Glyceraldehyde-3-phosphate dehydrogenase

Answer 7

Enzyme
4 subunits, 2 domains in each of mixed alpha/beta
C-term- Substrate binding
N-term- Cofactor binding

Question 8

D-Glucose

Answer 8

6 membered ring w/ 1 O in it and OH’s, Alpha when C-1 OH is down.
1-4 linking cellulose, Glycogen branches with a 1-6 bond every 8-14 units

Question 9

Amino Acid Derivatives

Answer 9

Aspartame- a dipeptide of L-Aspartic Acid and L Phe binds to taste receptors TAS1R1 and 1R2 a sweetener.
Glutathion GSH- Maintains reducing environment in cell, Glu links to Cys by the carboxyl group on side chain vs normal spot, Cys link normally to Gly
Glu —> GABA y-Aminobutyric Acid
His—->Histamine, Tyr—>Dopamine, Tyr—> Thyroxine

Question 10

Amino Acid Side Chain Modifications

Answer 10

Phosphorylation (PO3) of Ser, Tyr, and Thr OH group
Oxidation forms disulfide bridges
OH –> Proline in Collagen
CO2—> Glu
CH3—> His in muscles COCH3 in histones in DNA compaction
Glycosylation for Secretion of bilayer use- A core of pentasaccharide plus other mods that act as antenna

Question 11

Cytochrome B

Answer 11

4 alpha helixes

Question 12

Immunoglobulin Structure

Answer 12

7 beta strands alternating, 1 plus 6 in greek key

Question 13

Lactate Dehydrogenase Structure

Answer 13

A and B mixed alternating, 12 total secondary structure form 1 domain

Question 14

TIM- TriosePhosphate Isomerase Structure

a common domain found in many proteins

Answer 14

A and B alternating 8X to form a ring with helices on the outside and strands in center to form a barrel

Question 15

Beta Sheet Structure Details

Answer 15

Parallel strand H bonds are angled and less strong, Antiparallel H bonds are straight shorter thus stronger, can alternate side chains making a hydrophobic and hydrophilic side, both makes pleats of 7 A long

Question 16

Alpha Helix Details

Answer 16

1.5 A rise per residue, phi is -57, psi is -47, 3.6 residues per rotations, 100 degree right hand turns H bonds made from C==O to H—N 4 residues up the chain

Question 17

To Denature Proteins

Answer 17

Ave 40 kJ/M (10 kCals) to to destabilize 100 units,
Heat, Guanidinium 6M, Urea 8M, BME B-Mercaptoethanol breaks SS bridges
PDI breaks and reforms improper SS bridges
Examples- Muslce Aldolase reassembles easy, Ribonuclease A needs help re oxidation to reform SS bonds, Myoglobin needs help too

Question 18

Proteases

Answer 18

Break peptide bonds
Trypsin- breaks after positive, Arg/Lys except is Pro come next
Chymotrypsin- breaks after bulky aromatic, Phe, Trp, Tyr, Leu except if Pro comes next

Question 19

Keratin

Answer 19

2 strands with globular ends with right hand helix twisted together to the left, aprrox 310 residues, 450 A long, 7 sequence long abcdefg with a and d non-polar hydrophobic residues that make the strands stick together, a –> d, d—>a , 2 rows of dimers —> protofilament, 2 protofilaments —-> protofibril, 4 protofibrils —-> microfibril, bundle of microfibril–> macrofibril

Question 20

Collagen

Answer 20

Most Common is Type I, two Alpha 1 and one alpha 2 strands, Chain has a right twist is 1000 residues longs, 14 A wide, 3000 A long, 30% Gly with 15-30% 4-hydroxyPro, Gly X Y common Gly Pro Hyp, So much Gly allows the chains to be close together Gly-NH to Pro O

Question 21

Calmodulin

Answer 21

4 domains bind 4 Ca2+, then bind CaM Kinase going through a big conformational change wrapping itself around the CaM kinase

Question 22

Symmetry

Answer 22

Tetra, 3,3,2 12 subunits
Octa, 4,3,2 24 subunits
Icosa, 5,3,2 60 subunits

Question 23

GroES

Answer 23

Cap to “protein folding machine”

Cyclic- C7 like a donut, 140 A wide 10 A hole

Question 24

GroEL

Answer 24

“Folding machine body” it plus cap is 184 tall

D7 dihedral, binds 7 ATP at a time, flips back and forth one side in use at a time

Question 25

Pyruvate Dehydrogenase

Answer 25

Octahedral 24 subunits 4 3 2

Forms a hollow cube

Question 26

Actin Structure

Answer 26

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.

Question 27

Tobacco Mosaic Virus TMV

Answer 27

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

Question 28

A/B holotoxin from Cholera toxin and Enterotoxin

Answer 28

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

Question 29

Histones

Answer 29

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

Question 30

PDI Protein Disulfide Isomerase

Answer 30

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

Question 31

HSP70

Answer 31

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

Question 32

Hemoglobin

Answer 32

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

Question 33

BPG 2-3 Bisphosphoglycerate

Answer 33

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

Question 34

Hemocyanins

Answer 34

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

Question 35

Sickle Cell Anemia

Answer 35

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

Question 36

Ribonuclease A / RNase A

Answer 36

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

Question 37

Metal Ion Catalyst

Carbonic anhydrase

Answer 37

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.

Question 38

Proximity Catalysis

Answer 38

Can increase by 10^8

Ribosome peptide formation is example of this

Question 39

Covalent Catalyst

Answer 39

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

Question 40

Nucleophile and electrophile examples

Answer 40

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

Question 41

Serine Proteases

Scissel Bond to be broken in peptide N beta C

Answer 41

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

Question 42

Neuraminidases

Answer 42

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

Question 43

Trypsin Cleaves?

Answer 43

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

Question 44

Zymogens and their Cascade?

Answer 44

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.

Question 45

ATCase how does it work?

Answer 45

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

Question 46

Positive Amino Acids

Answer 46

Lys K 10
Arg R 12.5
His H 6.0

Question 47

Negative Amino Acids

Answer 47

Asp D 3.9

Glu E 4.2

Question 48

Other pK to know of Cysteine and Tyrosine

Answer 48

8. 3 C

10. 1 Y