Proteins and associated diseases

Question 1

combinatorial complexity of proteins is due to

Answer 1

• 20 different AA R groups

Question 2

at turns in prot structure, there is typically____ b/c it liberates phi and psi:

____ makes disulfide bonds (not freely in cytoplasm b/c they are reduced)

_____ makes kinks, restricts angles of AAs

Answer 2

• glycine (small R)
• cysteine
• proline

Question 3

targets c-Abl oncogenes

Answer 3

Gleevec (inhibits using prot structure)

Question 4

ritonavir

Answer 4

• dirsupts proteases in HIV
• In HIV, prot are created as a single protein that is cut by proteases into individual functional domains

Question 5

alpha helices:

Answer 5

• C-O H-bonds to N-H of amino acid.
• abt 3.6 AAs per turn of helix
• phi, psi are -100,-100 for rt. handed (+60, +90) according to SSN; +90, +90 for left
• rt handed more common
• In coiled coils, every 4/7 AAs is hydrophobic

Question 6

Beta sheets

Anti-parallel beta sheets

parallel beta sheets

Answer 6

• R groups above and below a beta sheet are alternating hydrophilic/hydrophobic
• phi and psi of +180, +180 (synopsis) +120, +120 (SSN)
• H bonds are closest aligned; most stable
• need longer loops to connect segments of aligned beta sheet

Question 7

membrane proteins tend to be of the motif

Answer 7

alpha helix, with hydrophobic R groups pointing out; unless their mitochondrial, then beta sheet

Question 8

This protein is a _______, and it binds______

Answer 8

Rossmann fold; nucleotides

Question 9

Forces holding together a 3-D structure of a protein:

Answer 9

• H-bonds due to partial charges (alpha helices, beta sheets)
• Van der Waals forces (clusters of hydrophobic AAs inside a prot)
• ionic bonds (lysine NH3+ to glutamic COO-)
• disufide (S-S) bonds

Question 10

These motifs are representative of ???

1. 4 helix bundles:
2. anti-parallel beta sheets:
3. symmetrical dimers with 2 central coil-coil
4. beta sheets arranged around a central point

Answer 10

1.

Question 11

Tamiflu and Relenze

Answer 11

target beta propellers in the viral protein neuraminidase, which cuts of sialic acid so the virus can be released from the cell

Question 12

Voltage gated channels have

Answer 12

RRRR (arginine chain) in hydrophilic bilayer and are pulled out during cell depolarization; causes channel to oopen

Question 13

Cystic Fibrosis:

1. mutation
   2.

Answer 13

1. mutation of phe508 in CFTR gene (which codes for Cl- channel. CFTR binds ATP, once hydrolyzed, Cl- admitted)

Question 14

the protein _____ is the constant stem of flu viruses and could potentially be targeted for a universal flu vaccine

Answer 14

hemmaglutin