Class 4 E1

Question 1

ubiquitination

Answer 1

targets proteins for destruction, original protein cannot be recovered; not reversible.

Question 2

What is the name of this enzyme?

ADP + Pi -> ATP

Answer 2

ATP synthase.

Question 3

Roles of AA’s in biochemistry?

Answer 3

1. nitrogen disposal (urea cycle)
2. lipid metabolism
3. neurotransmitters (GABA, glutamate
4. source of E when sugar fats are low

Question 4

What are the 4 levels of protein structure?

Answer 4

1. Primary
2. Secondary
3. Tertiary
4. Quaternary

Question 5

What does ATP kinase do?

Answer 5

phosphorylates ADP (adds a phosphate).

Question 6

What does ADP phosphorylase do?

Answer 6

Removes a phosphate.

Question 7

primary structure

Answer 7

linear sequence of AA’s made by ribosome, crucial to protein function.

Question 8

What are the 2 ends of a primary structure?

Answer 8

1. Amino / N-terminus

2. Carboxy / C-terminus

Question 9

What does a deletion mutation in the CFTR gene produce?

Answer 9

cystic fibrosis, stops exporting chloride ions.

Question 10

Which would explain the defect in the chloride channel function in humans with CFTR mutations?
A. missing Phe important for stabilizing alpha helices in CFTR protein.
B. missing Phe important for CFTR recognition by protein folding chaperones.
C. missing Phe part of beta sheet - no longer has correct structure w/o it.
D. missing F shifted neighboring amino acids out of frame - no longer contribute to folding.
E. all of the above.

Answer 10

E. all of the above.

Question 11

What do ribosomes do?

Answer 11

translates mRNA into proteins, adds one AA at a time, makes peptide bond btw AA’s.

Question 12

Which way do we read primary structures?

Answer 12

Amino / N-terminus to Carboxy / C-terminus.

Question 13

Cysteine is in its oxidized form when?

Answer 13

its sulfhydryl group loses its Hs and forms a single bond btw 2 sulfurs.

2 sulfhydryl groups are in:
reduced form when they lose e-‘s to H
oxidized form when they share e-‘s w/ H.

Question 14

What do disulfide bonds do?

Answer 14

stabilize protein structures using cysteines.

Question 15

secondary structure

Answer 15

held together by H bonding

Question 16

What are the 2 major structural components of secondary structures?

Answer 16

1. alpha helix

2. beta sheet

Question 17

What are some other structural components of secondary structures?

Answer 17

coiled coil, zinc finger, hairpin loops.

Question 18

alpha helix

Answer 18

predicted from primary AA seq, part of secondary structure, R groups play a role.

Question 19

beta sheets

Answer 19

parallel or antiparallel, form pleated sheets, R groups play a role.

Question 20

What is a parallel beta sheet?

Answer 20

C-terminus and N-terminus on same sides.

Question 21

What is an antiparallel beta sheet?

Answer 21

C-terminus and N-terminus on each side.

Question 22

tertiary structure

Answer 22

gives overall 3-D shape of protein, combines elements of secondary structure, beta sheet and alpha helix.

Question 23

motifs

Answer 23

combinations of secondary structures, determined by appearance not function.

Question 24

domains

Answer 24

portion of protein that retains structure / function in absence of rest of protein, discretely folding 3D structure.

Question 25

helix-turn-helix is an example of a?

Answer 25

motif

Question 26

DNA-binding domain is an example of a?

Answer 26

domain

Question 27

There is a physical and conceptual overlap btw?

Answer 27

motifs and domains.

Question 28

What types of alpha helices are found in motifs?

Answer 28

helix-turn-helix, four-helix bundle, goblin fold (8 helices)

Question 29

beta mofifs

Answer 29

include beta barrel, Greek key motif, and beta propeller.

Question 30

What are the stabilizing forces involved in protein structure?

Answer 30

van der Waals forces, H-bonds, disulfide bridges, salt bridges.

Question 31

Where is a G-protein coupled receptor located?

Answer 31

embedded in plasma membrane (typically).

Question 32

Function of G-protein coupled receptors?

Answer 32

huge family of proteins: changes in receptor lead to activation and recruitment of other proteins on intracellular surface of receptors and transmit signals.

Question 33

What are transmembrane domains?

Answer 33

span membrane, have many hydrophobic residues.

Question 34

Hydrophobic effects help?

Answer 34

proteins bind, fold, embed into membranes.

Question 35

hydrophobic effect

Answer 35

phenomenon where hydrophobic groups cluster together.

Question 36

What are the 3 integral proteins?

Answer 36

1. alpha-helix
2. helical bundle
3. beta-barrel

Question 37

What are peripheral proteins?

Answer 37

enzymes, anchorage, transporters (carriers).

Question 38

alpha helices are used for and by?

Answer 38

recognition, receptors.

Question 39

Helical bundles are used for and by?

Answer 39

enzymes, transporters, receptors.

Question 40

beta-barrels are used for and by?

Answer 40

transporters, channel proteins.

Question 41

quaternary structure

Answer 41

complex structure, incorporates multiple subunits / diff proteins.

Question 42

Multimers are made of?

Answer 42

monomers

Question 43

monomers

Answer 43

single chains of AA’s folded into active protein.

Question 44

multimers

Answer 44

several subunits, each is its own protein monomer (polypeptide chain) and are labeled based on function (catalytic / regulatory / etc.), not usually covalently linked.

Question 45

What are the 3 types of multimers?

Answer 45

1. dimers
2. trimers
3. tetramers

Question 46

DNA helicase

Answer 46

unwinds DNA

Question 47

What is the diff btw integral and peripheral proteins?

Answer 47

integral proteins span the cell membrane while peripheral proteins are on one side of the cell membrane.