7 Protein Structure

Question 1

in a water soluble protein, where would you find hydrophobic interactions?

Answer 1

on the inside of the protein

Question 2

what do destabilizing amino acid mutations do to the protein?

Answer 2

cause it to fold incorrectly

Question 3

what happens if a protein is not folded?

Answer 3

they aggregate and are improperly trafficked

Question 4

what is the specific activity of a protein?

Answer 4

amount of activity per amount of protein

Question 5

what amino acid is strongly disfavored in alpha ehlices?

Answer 5

proline

Question 6

what charge of amino acids are disfavored for alpha helices?

Answer 6

same charges next to each other

Question 7

T/F alpha helices can be amphipathic? what is amphipathic?

Answer 7

• True

- a molecule that has both hydrophobic and hydrophilic parts

Question 8

T/F prolines can be incorporated into beta sheats?

Answer 8

Tru

Question 9

what orientation are adjacent side chains in in beta sheets

Answer 9

-opposite (C and N terminus are flipped with every chain)

Question 10

what connects strands of beta sheets?

Answer 10

hydrogen bonds

Question 11

what is a primary characteristic of glycine?

Answer 11

it is small

Question 12

what is a key feature of tyrosine and tryptophan that allows us to measure proteins?

Answer 12

they both absorb UV light

Question 13

how many domains does the CFTR have and what are their characteristics?

Answer 13

• 5 domains
• 2 transmembrane
• 2 nucleotide binding
• 1 R domain

Question 14

how is the CFTR protein activated and what does this allow for?

Answer 14

1. phosphorylation of the R domain
2. ATP binding and hydrolysis by NBD domains
   - allows passage of chloride ions through the plasma membrane

Question 15

what is kalydeco used for?

Answer 15

to treat patients with the rare G551D mutation that causes CF (mutation in a codon that typically codes for a glycine)

Question 16

what does a glycine residue allow for in protein structure?

Answer 16

allows for sharp bends in the protein so that other amino acids can interact with each other

Question 17

in what situation is a desmosine cross link important and what amino acid allows for this to happen?

Answer 17

• important in elastin in order to give tissues an elastic property
• formed between two lysine residues

Question 18

keratin contains what protein structure in order to induce strength and shape?

Answer 18

alpha helices

Question 19

fibrous proteins are soluble in water, T/F

Answer 19

false

Question 20

elastin contains what type of cross linking?

Answer 20

desmosine, facilitated by lysine residues

Question 21

what is the protein of hair, nails , and skin , and what is the shape of the protein?

Answer 21

keratin

-it is very helical

Question 22

conceptually what is the pka?

Answer 22

the ph at which you have 50% of the conjugate acid and 50% in conjugate base form: this is when it can best absorb changes in pH

Question 23

what is a major buffer inside the blood?

Answer 23

phosphate and bicarbonate

Question 24

what is the carbonic acid equillibrium in the blood

Answer 24

CO2 + H2O - H2CO3 - H + HCO3

Question 25

if the pH is off, what might happen to some of the side chains?

Answer 25

the charge on them might be wrong, leading to dysfunction

Question 26

hows is pH important to aspirin?

Answer 26

The pH will dictate if aspirin is a charge molecule or not. If aspirin is charged, then it will not be able to diffuse through cell membranes and have its effect.

Question 27

what is the isoelectric point?

Answer 27

the pH at which a molecule is electrically neutral

Question 28

when does maximum buffering occur?

Answer 28

when there is an equal amount of conjugate acid and base

Question 29

three major buffers in the body

Answer 29

• phosphate
• bicarbonate
• proteins