Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
33 Cards in this Set
- Front
- Back
|
Place where a protein binds is called ___________? |
ligand or subrstrate |
|
|
Function of a protein depends its ability to ________ with other molecules |
bind |
|
|
Affinity Specificity Both of these are dependent on what? |
affinity is strength of bind Preferentially bind to unique ligand Molecular complementarity |
|
|
Molecular complementarity is dependent on? (3) |
non-covalent interactions between facing surfaces Look at the shapes! Specific amino acids also important (charge) |
|
|
Questions: what does cAMP do? Note that goes with this on the other side |
cAMP is an important regulatory molecule that can modulate protein function The binding pocket in its primary sequence had amino acids very spread out. When it was folded it formed a pocket that cAMP fits into. Also all the amino acids clumped together in this pocket to enhance chemical interaction. Only cAMP fits good here |
|
|
Binding affinity is measured by? |
association constant for binding equilibrium (Keq)
|
|
|
First right the Keq equation then explain it |
L + P -----Keq-----> LP Lingand + protein and the complex (LP) High Keq would be reaction going to the right, this indicated high affinity interaction This would also be a low Kd, disassociation constant |
|
|
equation for calculating Keq |
[LP]/[L][P] Often though, binding reactions are described in terms of the dissociation constant (just reverse your answer) |
|
|
What is a catalysis and what does it do? |
Catalysis is when an enzyme binds to its ligand (substrate) and promotes a chemical reaction Catalysis' lower the activation energy of a reaction. Reaction can follow through with lower energy requirement |
|
|
How much can an enzyme speed up a reaction? |
10^6 - 10^12 times normal speed |
|
|
Active site has two functional regions. What are they and what do they do? |
binding site - determines specificity catalytic site - promotes reaction |
|
|
Vmax Km? what is it and what does it measure? |
Vmax is the maximal velocity of a reaction at saturating substrate concentrations Km (Michaelis constant) = concentration of substrate at which reaction velocity is half maximal Measures affinity of an enzyme for the substrate LOOK AT GRAPH SLIDE 14-17 IF YOU THINK YOU SHOULD |
|
|
Do low affinity and high affinity substrates have the same Vmax? How about Km? Explain |
Yes they have the save Vmax Different Km. Km measure the affinity by looking at the concentration of substrate needed to reach half the Vmax |
|
|
Low Km indicates? |
high affinity |
|
|
What happens to Vmax when concentration of the enzyme has changed (eg. decrease)? What happens to Km |
Decrease in enzyme will decrease Vmax. Vmax is limited by number of available substrate-binding sites. Quarter as much enzyme, quarter the binding sites. Km does not change. This measures the affinity. Affinity does not change. |
|
|
-What does PKA (protein kinase A) do? -How many substrates and what are they? -How many domains and what are they? -Binding pockets? What do they make up? -What is the target peptide recognized by? |
-Adds phosphate group to a target protein -2, target protein and the nucleotide ATP -2 domains, the glycine lid and the large domain -nucleotide binding pocket (ATP specific) and substrate binding pocket (target peptide) which make up the kinase core. TARGET PEPTIDE OBVIOUSLY CAN ALSO BIND -recognized by glutamic acid residues |
|
|
PKA Open and closed conformations What happens when binding (of what) occurs? (beware, long description) |
Open conformation: Substrates bind, ADP and phosphorylated peptide are released Closed conformation: glycine-rich lid traps substrates, phosphorylation When binding of ATP occurs, small domain and large domain move together due to change in shape of the hinge. substrates trapped together, transfer of phosphate from ATP to target peptide. Now ADP in PKA, this has very low affinity and leaves as soon as it goes back to open conformation |
|
|
Allosteric modulators: -What usually happens to the protein? Can have two different affects, describe them |
-small molecules that bind to sites other than the active site of a protein to modify function -A conformational change usually occurs -This means it can increase activity (positive) or decrease activity (negative) |
|
|
What does PKA contain as an inactive tetramer? What activates this inactive PKA? how? At low concentration of cAMP, PKA is ___________ |
-Has two regulatory subunits and two catalytic subunits. The two catalytic subunits are pseudosubstrates and block binding site, therefore inactive -cAMP is an allosteric activator. Binds to regulatory subunits, produces a conformational change and releases the catalytic subunits -Inactive |
|
|
Structure of ATCase Regulation in aspartate transcarbomoylase (ATCase), what type it it? What is the protein that does this? Describe briefly what happens? |
-6 catalytic and 6 regulatory subunits -Allosteric inactivation -CTP -When CTP binds to the ATCase conformational changes cause this to become inactive. Therefore, high concentration of CTP = inactivity. Low concentrations.... |
|
|
Allosteric Inhibition is a good way of providing Negative Feedback in a metabolic pathways, describe this? Give an example of this. What are the advantages? |
Basically this means that there is a series of reaction. And the overall product of this series of reactions actually inhibits the first or second step of this series of reactions. eg. pathway that produces CTP for the cell. ATCase enzyme used as the second step in this pathway. CTP is a negative modulator for this enzyme. It is the presence of CTP that prevents production of too much CTP. advantages: saves energy |
|
|
ATCase has an allosteric inhibtor and activator Which is which? Which has higher Km/Vmax/affinity what is ATCase's substrate/ |
Inhibitor: CTP, higher km, same Vmax, low affinit Activator: ATP, lower km, same Vmax, high affin substrate: aspartate This affinity etc. is all for aspartate |
|
|
Co-operative allostery Whats the shape of the curve? Talk about ligand concentration and Vmax? |
Binding of one ligand molecule affects binding of subsequent ligand molecules S shape. Put S on its side. Slide 29 also go to 31 At the beginning has low affinity, after has high affinity. Takes very little increase in ligand concentration to get to Vmax |
|
|
What type of regulation does hemoglobin show? Why? Has two states. |
-Cooperative allostery, affinity of oxygen needs to be high in lungs but low in the tissues -Oxygen is the substrate and the allosteric activator -T state (tight) inactive low O affinity, R state (relaxed) is active with high O affinity |
|
|
Hemoglobin vs Myoglobin |
Hemoglobin has cooperative allostery, shows larger difference in amount of oxygen when you compare tissue to lungs. S shaped curve/sigmoidal curve Myglobin shows smaller difference. Shows typical kinetics curve |
|
|
Hemoglobins allosteric activator? Inhibitor? |
activator is Oxygen Inhibitor is 2,3-BPG |
|
|
Where is the binding site for 2,3-BPG? What happens when 2,3-BPG is bound? Where might you expect to find 2,3-BPG in your body? |
middle of hemoglobin Affinity for Oxygen decreases in hemoglobin Target tissues |
|
|
Two types of hemoglobin? Difference? |
Fetal and Adult. The fetal hemoglobin has higher affinity for oxygen (used in fetus from women) Fetal hemoglobin also has lower affinity for 2,3-BPG |
|
|
Phosphorylation What does it do in CDK |
Addition of 2 negative charges CDK cannot bind to substrate cuz substrate-binding pocket is blocked by red domain. After phosphorylation red domain moves opening substrate binding pocket. This activates the protein. Increase in negative charges allows red domain to form new ionic charges |
|
|
Proteolytic cleavage Few eg in humans |
Allows a cell to make a lot of a protein in an inactive conformation. Then rapidly cleave polypeptide at specific points to activate it. eg. enzymes, clotting factors, hormones, collagen...... |
|
|
What is chymotrypsin What happens with chemotrypsin? Reversible? |
Digestive enzym At first it can be safely transported without digesting the bodies own cells. (cuz it usues proteolytic cleavage) Cleavage creates an amino-terminal group at IIe 16 that can fold inward and form an ionic bond with Asp 194 Not reversible |
|
|
Ways to increases speed of a metabolic pathway? (2) |
multimeric complex: addition of protein-protein interaction domains allows the three proteins to bind to one another creating a multimeric complex
assembly on a scaffold: addition of a scaffold protein to which the three enzymes can bind In both intermediates can move quickly from one enzyme to the next |
|
|
asdlf; |
as;dkf j |
