Protein Structure

Question 1

amino acid backbone at physiological pH

Answer 1

amine has a positive charge, carboxyl has a negative charge

Question 2

hydrophobic vs hydrophilic R chains

Answer 2

hydrophobic side chains are rich in hydrocarbons whereas hydrophilic side chains have oxygens and nitrogens and charged groups

Question 3

sequence of protein with regards to its family

Answer 3

proteins within the same family have similar sequences for example the CFTR protein is in the is in the ABC ATPase family

Question 4

one example of a therapeutic protein

Answer 4

insulin

Question 5

specific activity

Answer 5

amount of protein activity divided by the amount of protein

Question 6

technique to measure the amount of purified protein

Answer 6

measure the absorbance of a samples since tryptophan and tyrosine absorb UV light

Question 7

alpha hellix

• primary structure formed via what
• disfavored aa and order of aa’s
• orientation of aa’s
• polarity

Answer 7

• primary structure is formed via hydrogen bonding
• proline is strongly disfavored and is known as a helix breaker
• adjacent amino acids that have like charges is also disfavored due to repulsive forces
• side chains are pointing outward of the center of the helix
• can be amphipathic (for instance a transmembrane channel)

Question 8

amphipathic

Answer 8

a molecule having both hydrophobis and hydrophilic parts

Question 9

beta sheet

• primary structure facilitated by
• what it looks like
• amino acids that are ok

Answer 9

• primary structure also formed via hydrogen bonding
• connects long stretches of amino acids
• prolines are ok
• side chains point in opposite direction and the chains themselves are oriented in an anti-parallel fashion

Question 10

the CFTR protein

• domains
• what the domains do in terms of opening and closing the channel

Answer 10

• 5 domains: 2 transmembrane, 2 nucleotide binding (NBD1 and NBD2) and an R domain (RD)
• activation via phosphorylation allows passage of chloride ions through the plasma
• membrane by 2 methods
• specifically, RD gets phosphorylated, then NBD1 facilitates ATP hydrolysis which opens the channel then ATP hydrolysis by NBD2 closes the channel

Question 11

mutations in CFTR

• which domain the mutations occur in
• the two primary mutations
• therapy for one of the mutations

Answer 11

• Many map to the NBD1 domain
• 75% have the more severe form that is the deltaF508 mutation leading to little CFTR present on the cell
• 4-5% of the CFTR patients have the G551D mutation (glycine to another AA) for which Kalydeco was an approved pharmaceutical

Question 12

glycine

Answer 12

• fits into tight spaces, is a very small amino acid, just a hydrogen R chain
• allows proteins to form sharp bends and for polypeptide chains to come in close contact with one another

Question 13

interior of water soluble proteins

Answer 13

• exterior has hydrophilic AA’s

- interior has hydrophobic AA’s

Question 14

mutations may disrupt what in proteins

Answer 14

-structure and contact points

Question 15

elastin

• where its found and function
• secondary structure
• solubility
• desmosine
• rich in what

Answer 15

• predominant protein in elastic tissue such as the lungs
• no regular secondary structure
• relatively water insoluble and elongated
• modified lysine residues form tetrad structures known as desmosine which acts as the cross link between singular elastin proteins
• rich in ala, gly, and val

Question 16

keratin

• contains what shapes
• where found

Answer 16

• contains alpha helices that are wound up so tightly that it can not be digested
• makes up hair, nails and skin

Question 17

fibrous proteins

• solubility
• shape

Answer 17

insoluble

elongated

Question 18

pKa

-relationship to buffers

Answer 18

• the pH at which you have equal amounts of conj A and conj B
• buffers perform the best at pH around their pKa

Question 19

buffer in cells and in blood

Answer 19

blood is bicarbonate

cells is phosphates

Question 20

bicarbonate equilibrium

• what it does in the blood
• taking deep breath

Answer 20

• CO2 and H20 go to carbonic acid which goes to H+ and bicarbonate
• bicarbonate can absord H+ to form CO2 and H2O in the blood
• taking deep breaths causes the blood pH to rise as you are pushing equilibrium to the left

Question 21

charges of amino acid side chains and pH

• function
• certain amino acids that work well as buffers, why

Answer 21

• if not at the right pH, a protein will not have the proper charges
• cysteins and hystideins are good buffers as their pKa’s are right around neutral
• proteins have an optimal pH range that they operate in

Question 22

pharmaceuticals with regard to pH

Answer 22

• some drugs work better at different pH’s and therefor are absorbed in different regions of the body
• aspirin is neutral in the stomach (low pH), and deprotonated in the intestine (higher pH) therefor aspirin is more readily absorbed through the lining of the stomach than in the intestines

Question 23

isoelectric point

Answer 23

• the pH at which the compound is electrically neutral
• utilized in isoelectric focusing assays to sort compounds based upon their pI
• differnt amino acids have different isoelectric points

Question 24

maximum buffering occurs when

Answer 24

conc of base equals conc of acis

Question 25

major buffers in the body

Answer 25

bicarbonate, phosphate, and proteins

Question 26

charged molecules pass through membranes…

Answer 26

poorly