proteins

Question 1

amino acid form in cells

Answer 1

represented as the ionized form found in most cells

act as both an acid and a base

Question 2

non polar amino acid side chains

Answer 2

makes them hydrophobic

Question 3

polar amino acid side chains

Answer 3

makes them hydrophilic , at physiological pH of 7.4

none are charges

Question 4

histidine

Answer 4

can act as a buffer at cellular pH

Question 5

protein structure

Answer 5

primary, secondary, tertiary, quarterly structure

Question 6

peptide orientation

Answer 6

amino terminal

carboxylate terminal end

Question 7

secondary structure

Answer 7

refers to the 3D structure of local segments of a polypeptide

defined by the hydrogen bonding pattern between carboxyl and amino groups

generally arrange themselves such that hydrogen bonding is maximized

Question 8

alpha helix

Answer 8

right handed spiral
made of a polypeptide backbone core with the side chains extending outwards
Carboxy1 - 4th amino group

Question 9

beta plated sheet

Answer 9

proteins chains are extended with the side groups alternating above and below the plane of the peptide bond

H bonds occur between parallel (same direction) or anti-parallel (opposite direction) strands

Question 10

Beta turns

Answer 10

found where a polypeptide chain abruptly reverses directions such as at the ends of 2 anti-parallel beta pelted sheets

Question 11

random coils

Answer 11

sections of polypeptides have little regularity

Question 12

tertiary sturcuture

Answer 12

defined as the configuration that the protein takes in space and is determined by the interactions between the various secondary structure domains

• described as fibrous or globular

Question 13

stabilizing forces of the tertiary structure

Answer 13

electrostatic interactions

hydrogen bonds

hydrophobic interactions

disulfide bonds [covalent bond between 2 cysteine residues]

Question 14

globular proteins

Answer 14

usually ellipsoidal and water soluble

ex. myoglobin

inside of the protein contains non polar amino acids that attract each other weakly and repel water

Question 15

fibrous proteins

Answer 15

elongated, water insoluble

structural function

ex. collagen

have a high concentration of hydrophobic amino acids

Question 16

what determines the tertiary structure

Answer 16

primary sequence
- folding prices involved the peptide chain collapsing into a conformation in which the stabilizing offices combine to yield the more stable conformation

Question 17

chaperones

Answer 17

assist the filing process

Question 18

denaturation

Answer 18

change in structure which leads to a change in function

ie. high temp, high pH, detergents disrupts H bonds

Question 19

performic acid

Answer 19

disrupts disulfide bonds

Question 20

renaturation

Answer 20

re-folding of the protein to make it functional again

- if no covalent bonds were broken, restoring the original conditions can usually do this

Question 21

quaternary structure

Answer 21

arrangement assumed by 2 or more distinct polypeptides and/ or cofactors when the are bound together

• note: same forces that stabilize the quaternary structure as the tertiary structure

Question 22

hemoglobin

Answer 22

transports O2 from lungs

buffers CO2 movement from the tissues to the lungs

Question 23

hemoglobin structute

Answer 23

• 125-175 residues - 1 string
• 8 alpha helical regions connected by random coils
• globular - water soluble
• 4 subunits working together

Question 24

in the lungs

Answer 24

exhaling CO2 requires elimination of hemoglobin- bound protons and plasma - dissolved bicarbonate

CO2 + H20 -> H2CO3 _> H+ +HCO3-
- both reaction is catalyzed by canonic anhydrase

H+ + HCO3- [bicarb] -> H2CO3 [carbonic acid}

then carbonic acid decomposed to water and CO2
- CO2 is exhaled

Histidine residues now have a neutral charge

Question 25

oxygen affinity for hemoglobin

Answer 25

improves when there is no proteins associated with the histidine residues
- oxygen readily binds to hemoglobin because the proteins have been used up during exhalation, causing the heme group to adopt a planar conformation

Question 26

in the tissues

Answer 26

CO2 is creased as a byproduct

CA catalyzes conversion of water and CO2 into carbonic acid , which dissociates into protons [ protons bind to Sistine residues] and bicarb[ dissolved in the plasma]

pH is acidic , so more protons bind to hemoglobin

oxygen affinity of hemoglobin decreases because the histidine residues now have a positive charge when it has more bound protons

structure of heme becomes more domed when O2 dissociates

decreases affinity of hemoglobin and causes oxygen to dissociate and deposit in the tissues

Question 27

rhodopsin

Answer 27

has a quaternary structure because the protein needs 11-cis retinal to be active

Question 28

rhodopsin primary estruture

Answer 28

350 residues

Question 29

post trans- national modifications of rhodopsin

Answer 29

N terminus has 2 short chain carbohydrates that anchor the molecule in correct membrane orientation

c terminus contains several hydroxy amino acids which are phosphorylated to fine tune light sensitivity

Question 30

rhodopsin secondary structure

Answer 30

7 Alpha helical regions connected by random coils

Question 31

rhodopsin tertiary structure

Answer 31

globular, membrane spanning region = hydrophobic = strong anchor into membrane

N- terminus is always in the instradiscal space or extracellular space to maintain functional role

Question 32

opsin

Answer 32

apoprotein

Question 33

rhodopsin quaternary structure

Answer 33

prosthetic group is a metabolite of vitamin A which is bound to protein

Rhodopsin = holoprotein