topic 04 protein function

Question 1

what do conformation changes drive?

Answer 1

motor proteins, sensory function of receptors, control of enzyme activity, etc

Question 2

how do proteins bind to molecules with great specificity?

Answer 2

using multiple weak bonds between side chains and tertiary structures that bring residues together in space

Question 3

define active site

Answer 3

aka substrate-binding site

small area of protein complimentary to the structure of another molecule (ligand)

Question 4

what constant characterizes ligand binding?

Answer 4

dissociation constant K
= (protein - ligand)/(protein ligand complex)

on a graph: y = (L)/(K+L)
on the graph, K = ligand concentration at which binding sites on proteins are 50% saturated

small K: high affinity - low disocciation
larger K: low affinity - high disocciation

Question 5

what are some post-translation modifications and what do they do?

Answer 5

phosphorylation, acetylation, & hydroxylation involve modifying a functional group: alters stability and signaling

ubiquitination & sumoylation involve adding whole proteins to side chains: also alters stability and signaling

glycosylation involves adding sugars to side chains: affects protein folding, binding, solubility, and secretion

myristoylation & farnesylation involve adding lipids to side chains: alters location

Question 6

which amino acids can be phosphorylated?

Answer 6

serine, threonine, tyrosine

all have hydroxyl group

phosphorylated by kinases and can be removed by phosphatases

Question 7

what does the dissociation constant indicate about the ligand binding?

Answer 7

smaller Ka = higher affinity = tighter binding

larger Ka = lower affinity = looser binding

Question 8

describe myoglobin: where its found? its structure? its purpose? the steps in its process?

Answer 8

found in muscles

consists of 8 alpha-helices and 1 heme-prosthetic group (helices are labeled A to H)

myoglobin is saturated with oxygen, it allows oxygen, which isn’t that soluble in water, to efficiently diffuse through muscle tissue.

1. oxygen binds reversibly to HistidineF8 (Histidine bonded to the 8th residue of helix F) to complete iron coordination. it binds to the non-protein prosthetic group: heme. the iron in heme is coordinated by its 4 nitrogens and side chains, Histidine.
2. another Histidine, HistidineE7 (Histidine bonded to the 7th residue of helix E), forms a hydrogen bone with the oxygen to stabilize bonding

Question 9

which amino acid is found in myoglobin?

Answer 9

Histidine

Question 10

ligand binding to a protein is represented graphically by a binding isotherm, what does the graph reveals when K is equal to the ligand concentration?

Answer 10

the binding sites on the protein are 50% saturated

half of the binding sites are occupied

Question 11

how could you reformulate the dissociation constant equation to find concentrations more easily?

Answer 11

Y = [C] / (K + [C])

reminderr C could be concentration or partial pressure

Question 12

what are some similarities between myoglobin and hemoglobin?

Answer 12

the ligand is oxygen, which in both case, bind to the prosthetic group on the protein: heme

have similar folds, but their primary structures greatly differ (less than 50% of conservation)

Question 13

describe hemoglobin: where its found? its structure? its purpose?

Answer 13

found in red blood cells

consist of 4 polypeptides and 4 heme groups. the 4 polypeptides are 2 alpha-globin subunits and 2 beta-globin subunits

hemoglobin binds to oxygen, transports it through the blood stream, and delivers it to the tissues

it also facilitates CO2 removal from tissue and expiration in lungs

Question 14

how many oxygens can hemoglobin bind up to?

Answer 14

4

Question 15

what are the states of hemoglobin? when do they occur? what do they result in?

Answer 15

T-state
- no oxygen bonded and it has a low affinity for oxygen
- promoting T state promotes oxygen release

R-state
- at least one oxygen bonded, the remaining oxygen will bind with high affinity
- promoting R state promotes oxygen binding

Question 16

what happens when oxygen binds to the hemoglobin?

Answer 16

R-state (promotes oxygen bonding)

heme flattens out from from its tense, puckered up state. Histidine 58 is pulled up. this conformation change is transmitted to the rest of the hemoglobin to snap it into the R state, a new interlocking arrangement with new hydrogen bonds

Question 17

describe the bohr effect

Answer 17

in the lungs, hemoglobin is originally protonated but when it binds to oxygen, protons are released

when oxygen is delivered to the tissue, the hemoglobin picks up oxygen

Question 18

what happens when hemoglobin picks up protons? when does hemoglobin pick up protons? why is this so?

Answer 18

protons are picked up before? the hemoglobin releases oxygens in the tissue

when protons are picked up, they promote the T state and decrease the affinity for oxygen, facilitating oxygen release

the pH in the tissue is lower than in the lungs, meaning it has a high proton concentration. this encourages proton binding for hemoglobin, which weakens the affinity for oxygen and promotes oxygen release

Question 19

what is 2,3, Bisphosphoglycerate (BPG)? give an example of it being used

Answer 19

it stabilizes hemoglobin’s T-state by binding to the hemoglobin’s central cavity, decreasing the affinity for oxygen and stimulating larger oxygen release in the tissue

BPG can only bind when hemoglobin is in the T-state

more BPG is produced when one experiences thinner air to compensate for lack of oxygen and allows greater volumes to be released in the tissue

Question 20

when graphing out hemoglobin’s activity with oxygen, what does shifting the curve to the right mean?

Answer 20

larger oxygen release and lower affinity for oxygen

Question 21

describe heme’s resistance to oxidation

Answer 21

normally, heme is resistant to oxidation! it is in protected environment where it can bind to oxygen but resist oxidation. the oxygen reversibly binds without reacting with the iron.

however, as blood dries, the hemoglobin protein breaks down, exposing the heme to oxidation

Question 22

what is methemoglobin? what causes it?

Answer 22

the methemoglobin doesn’t bind to oxygen properly, compromising oxygen delivery – brown blood

caused by mutations: Boston, Iwate, Milwaukee (a mutated Histidine E7/F8 to Tyrosine OR a mutated Valine to Glutamate)

Question 23

there are two mutations that disrupt hydrogen bonds stabilizing one of hemoglobin’s states. which one disrupts the T state? which one disrupts the R state?

Answer 23

Yakima disrupts T state
- promotes less delivery of oxygen to tissues

Kansas disrupts R state
- promotes less binding of oxygen in lungs

Question 24

what hemoglobin variant/mutation leads to sickle cell anemia? describe sickle cell anemia

Answer 24

mutation of E6V in beta-chains result in a decrease of 2 charges

sickle cell is when red blood cells are elongated and can not properly pass through capillaries, damaging the tissue as it builds up, and is unable to carry oxygen well

the mutation of E6V is accommodated by a hydrophobic pocket in one of hemoglobin’s subunits. hemoglobin can form long polymers which cause sickle cell

Question 25

describe collagen

Answer 25

extra cellular, it forms strong fibers/sheets

each molecule has 3 polypeptides, forming triple helix

Question 26

what is the most common protein in animals

Answer 26

collagen

Question 27

describe collagen’s triple helix

Answer 27

each of collagen’s peptides have a poly-proline type II helix. the presence of so much proline prevents the formation of an alpha helix. it also contains hydroxyl proline.

more stretched out than an alpha helix. it has no hydrogen bonds holding it together as the amide nitrogen and oxygen atoms are too far apart. hydroxyl groups of hydroxyl proline form hydrogen bonds, keeping the chain together

stabilized by the steric repulsion of the proline side chains.

every 3 residues must by glycine, which is small enough to fit in between polyprotein helices. glycine chain allows overall chain to come closer together

hydrophobic due to its glycine and proline composition

Question 28

what is the importance of hydroxylation in collagen?

Answer 28

hydroxylation of proline stabilizes the triple helix structure

hydroxylation of lysine serves as a site of sugar addition

Question 29

what is the role of lysine in collagen?

Answer 29

lysine is involved in cross-linking reaction that creates covalent bonds between collagen fibrils

hydroxyl lysine serves as a site of sugar addition

Question 30

describe the collagen synthesis process

Answer 30

each collagen molecule is synthesized with amino and carboxyl terminal pro-peptides (pro-collagens) that are hydrophilic. these allow molecules to remain soluble and prevents premature fiber formation

1. pro-collagen secreted from cell (contains pro-peptides which don’t form triple helical structures)
2. outside cell, enzyme pro-peptidase cleaves off pro-peptides. then, collagen assembled into fibrils
3. collagen molecules covalently cross-linked in the fibril due to enzyme lysyl-oxidase (cross link increases strength of fiber)
4. glycosylation facilitates extracellular solubility & water absorption

Question 31

describe the lysyl cross linking process in collagen

Answer 31

1. lysyl-oxidase removes amino group from end of lysine, leaving carbonyl group behind. this results in allysine
2. two groups, if near, spontaneously react with each other in a condensation reaction to release water and form covalent bonds

Question 32

what are some collagen related diseases? describe them

Answer 32

SCURVY
caused by lack of vitamin C (ascorbic acid) which is needed for the enzyme that hydroxylates proline. non hydroxylated proline = unstable collagen = degradation of skin

OSTEOGENESIS
caused by glycine mutations = lack of collagen needed for bone formation = malformed/absent bone.. glycine is essential

ENLERS-DANLOS SNYDROME (EDS)
caused by mutation in collagen genes or in processing enzyme (procollagen N proteinase or lysyl oxidase). leads to defects in collagen synthesis and group of inherited connective tissue disorders

Question 33

which amino acids are present in collagen?

Answer 33

all 20!

but rich in proline and glycine

Question 34

what does prolyl hydroxylase require to function?

Answer 34

vitamin C (ascorbic acid)