Proteins Flashcards
Influenza Virus Proteins
Neuraminidase- on surface
Hemagglutinin- on surface, conformational change at pH 6 found in endosomes, has cyclic C-3 symmetry
Myoglobin Structure and Properties
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
Carboxypeptidase A
Center of mixed Beta sheets (strands twist right) with left twist, surrounded by alpha helices
Bacteriorhodopsin
All alpha helices in lipid bilayer
Rhodopsin
Helices, vision protein
OmpF Porin
All beta strands form barrel in membrane
GAPDH
Glyceraldehyde-3-phosphate dehydrogenase
Enzyme
4 subunits, 2 domains in each of mixed alpha/beta
C-term- Substrate binding
N-term- Cofactor binding
D-Glucose
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
Amino Acid Derivatives
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
Amino Acid Side Chain Modifications
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
Cytochrome B
4 alpha helixes
Immunoglobulin Structure
7 beta strands alternating, 1 plus 6 in greek key
Lactate Dehydrogenase Structure
A and B mixed alternating, 12 total secondary structure form 1 domain
TIM- TriosePhosphate Isomerase Structure
a common domain found in many proteins
A and B alternating 8X to form a ring with helices on the outside and strands in center to form a barrel
Beta Sheet Structure Details
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
Alpha Helix Details
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
To Denature Proteins
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
Proteases
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
Keratin
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
Collagen
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
Calmodulin
4 domains bind 4 Ca2+, then bind CaM Kinase going through a big conformational change wrapping itself around the CaM kinase
Symmetry
Tetra, 3,3,2 12 subunits
Octa, 4,3,2 24 subunits
Icosa, 5,3,2 60 subunits
GroES
Cap to “protein folding machine”
Cyclic- C7 like a donut, 140 A wide 10 A hole
GroEL
“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
Pyruvate Dehydrogenase
Octahedral 24 subunits 4 3 2
Forms a hollow cube
Actin Structure
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.
Tobacco Mosaic Virus TMV
Single strand of RNA wrapped by 150 amino acid capsid proteins, 18 nm wide * 300 nm long, 2.3 nm rise per turn
A/B holotoxin from Cholera toxin and Enterotoxin
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
Histones
8 2x4 proteins D4, ~146 base pairs wrap around, ~100 A wide
PDI Protein Disulfide Isomerase
In reduced form disconnects improperly formed SS bridges and reforms them, in oxidized form it makes proper SS bridges
HSP70
A chaperon protein in cytosol, uses ATP to keep proteins from folding prematurely
Hemoglobin
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
BPG 2-3 Bisphosphoglycerate
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
Hemocyanins
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
Sickle Cell Anemia
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
Ribonuclease A / RNase A
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
Metal Ion Catalyst
Carbonic anhydrase
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.
Proximity Catalysis
Can increase by 10^8
Ribosome peptide formation is example of this
Covalent Catalyst
Nucleophile on enzyme attack electrophile on substrate and slopes reaction to occur, stabilizes transition state
Nucleophile and electrophile examples
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
Serine Proteases
Scissel Bond to be broken in peptide N beta C
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
Neuraminidases
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
Trypsin Cleaves?
Chymotrypsinogen to pi chymotrypsin between 15 and 16, then Chymo breaks it self between 146 and 149 and the 3 chains fold activating it…
Zymogens and their Cascade?
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.
ATCase how does it work?
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
Positive Amino Acids
Lys K 10
Arg R 12.5
His H 6.0
Negative Amino Acids
Asp D 3.9
Glu E 4.2
Other pK to know of Cysteine and Tyrosine
- 3 C
10. 1 Y
