topic 04 protein function Flashcards
what do conformation changes drive?
motor proteins, sensory function of receptors, control of enzyme activity, etc
how do proteins bind to molecules with great specificity?
using multiple weak bonds between side chains and tertiary structures that bring residues together in space
define active site
aka substrate-binding site
small area of protein complimentary to the structure of another molecule (ligand)
what constant characterizes ligand binding?
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
what are some post-translation modifications and what do they do?
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
which amino acids can be phosphorylated?
serine, threonine, tyrosine
all have hydroxyl group
phosphorylated by kinases and can be removed by phosphatases
what does the dissociation constant indicate about the ligand binding?
smaller Ka = higher affinity = tighter binding
larger Ka = lower affinity = looser binding
describe myoglobin: where its found? its structure? its purpose? the steps in its process?
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.
- 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.
- another Histidine, HistidineE7 (Histidine bonded to the 7th residue of helix E), forms a hydrogen bone with the oxygen to stabilize bonding
which amino acid is found in myoglobin?
Histidine
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?
the binding sites on the protein are 50% saturated
half of the binding sites are occupied
how could you reformulate the dissociation constant equation to find concentrations more easily?
Y = [C] / (K + [C])
reminderr C could be concentration or partial pressure
what are some similarities between myoglobin and hemoglobin?
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)
describe hemoglobin: where its found? its structure? its purpose?
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
how many oxygens can hemoglobin bind up to?
4
what are the states of hemoglobin? when do they occur? what do they result in?
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
what happens when oxygen binds to the hemoglobin?
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
describe the bohr effect
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
what happens when hemoglobin picks up protons? when does hemoglobin pick up protons? why is this so?
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
what is 2,3, Bisphosphoglycerate (BPG)? give an example of it being used
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
when graphing out hemoglobin’s activity with oxygen, what does shifting the curve to the right mean?
larger oxygen release and lower affinity for oxygen
describe heme’s resistance to oxidation
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
what is methemoglobin? what causes it?
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)
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?
Yakima disrupts T state
- promotes less delivery of oxygen to tissues
Kansas disrupts R state
- promotes less binding of oxygen in lungs
what hemoglobin variant/mutation leads to sickle cell anemia? describe sickle cell anemia
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
describe collagen
extra cellular, it forms strong fibers/sheets
each molecule has 3 polypeptides, forming triple helix
what is the most common protein in animals
collagen
describe collagen’s triple helix
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
what is the importance of hydroxylation in collagen?
hydroxylation of proline stabilizes the triple helix structure
hydroxylation of lysine serves as a site of sugar addition
what is the role of lysine in collagen?
lysine is involved in cross-linking reaction that creates covalent bonds between collagen fibrils
hydroxyl lysine serves as a site of sugar addition
describe the collagen synthesis process
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
- pro-collagen secreted from cell (contains pro-peptides which don’t form triple helical structures)
- outside cell, enzyme pro-peptidase cleaves off pro-peptides. then, collagen assembled into fibrils
- collagen molecules covalently cross-linked in the fibril due to enzyme lysyl-oxidase (cross link increases strength of fiber)
- glycosylation facilitates extracellular solubility & water absorption
describe the lysyl cross linking process in collagen
- lysyl-oxidase removes amino group from end of lysine, leaving carbonyl group behind. this results in allysine
- two groups, if near, spontaneously react with each other in a condensation reaction to release water and form covalent bonds
what are some collagen related diseases? describe them
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
which amino acids are present in collagen?
all 20!
but rich in proline and glycine
what does prolyl hydroxylase require to function?
vitamin C (ascorbic acid)
