Exam 2: Chapter 5-11.1 Flashcards
What does the dissociation constant mean?
Indicates how tightly bound a molecule is. A smaller Kd value shows higher affinity
What is myoglobin?
Favors oxygen moving from the blood to the muscle cell
What is the oxygen carrier in blood?
Hemoglobin
What does it mean when a ligand is cooperative?
The binding of one molecule will influence the binding of other molecules.
Why is hemoglobin a cooperative ligand?
Oxygen binding at one subunit increases the affinity for O2 at the remaining subunits.
What are the 2 conformational states that hemoglobin can exist in?
The T state has low affinity for O2 while the R state has high affinity for O2.
Why is the T-state favored in the absence of O2?
Due to the formation of salt bridges involving the C-term residues of the a and b subunits.
What is a salt bridge?
Connecting 2 regions using ions.
Why does oxygenated hemoglobin favor the R-state?
Formation of the Fe-O2 bond is favorable and pulls the Fe2+ into the plane of the porphyrin ring, which shortens the Fe-N bond giving a lower free energy.
Why are intermediate conformations between R-state and T-state disfavored?
Due to steric clashes
What is the Bohr Effect?
Hemoglobin binding H+ favors unloading O2 to the tissue that needs O2 the most.
Why does muscle metabolism favor the T-state of hemoglobin?
Muscle metabolism causes a pH drop in surrounding tissues, the increase [H+] protonates the hemoglobin which favors salt-bridge formation that stabilizes the T-state.
How does the presence of BPG affect oxygen binding to hemoglobin?
BPG binds in the central cavity of T-state hemoglobin and contributes to further salt-bridge formation.
What would happen to oxygenation of tissues without BPG?
Without BPG, hemoglobin would bind O2 too tightly to unload a significant fraction to the tissues.
How does BPG affect oxygenation at higher altitudes?
An incr. in BPG decr. the affinity for O2 helps in lower O2 environments because it means hemoglobin doesn’t hold onto O2 as tight in the blood so more oxygen is releases and reach body tissue.
What is special about fetal hemoglobin?
Fetal hemoglobin doesn’t have beta subunits so it binds BPG poorly and therefore has a stronger affinity for O2 and favors movement of O2 across the placental membrane.
What is sickle cell anemia?
Sickle cell anemia is a mutation arising from a Glu6Val mutation on hemoglobin b. Sickled cells may block small blood vessels, limiting O2 delivery.
What is sickling triggered by?
Factors that promote T-state hemoglobin. (eg. high altitude & dehydration)
What is the biochemical basis for sickle cell anemia?
A hydrophobic pocket is exposed on the b-subunit when hemoglobin is in the T-state. This pocket bind the exposed Val on a neighboring hemoglobin and aggregation produces long, rigid strands of hemoglobin which deform the cell into a sickle shape.
What are the classes of cytoskeletal fiber?
Actin microfilaments, Intermediate filaments, Microtubules
What is the structure of hemoglobin?
Hemoglobin is composed of 2 alpha chains and 2 beta chains.
How do actin monomers form microfilaments?
Actin monomers (G-actin) polymerize to form ‘F-actin’ microfilaments because the negative charges on the cleft are attracted to the positive charges of other actin monomers.
What is the role of actin microfilaments?
Microfilaments help determine cell shape, allow some cells to move, and are part of the contractile apparatus in muscles.
What are the steps of the contraction cycle?
- Myosin head bound to an actin subunit of the thin filament. ATP binds and myosin releases actin.
- Hydrolysis of ATP to ADP + Pi rotates the myosin lever and increases the affinity of myosin for actin.
- Myosin binds to an actin subunit farther along.
- Binding to actin causes Pi + ADP to be released. The myosin lever returns to its original position. The thin filament moves (power stroke).
What is the structure of keratin?
Two long helices forming a coiled-coil. Each helix has a repeating 7 amino acid sequence where the 1st and 4th residues of each repeat are hydrophobic.
How is keratin assembled to form hair?
Disulfide bonds between dimers help strengthen keratin microfibrils.
How can the crosslinks between keratin fibers be manipulated in hair?
Heat can temporarily unfold proteins and allow the hair to be shaped.
What is activation energy?
The energy to go from the ground state to the transition state.
How do catalysts increase the rate of a reaction?
Catalysts increase the rate of reaction by lowering the activation energy for both the forward and reverse reaction.
How do enzymes bind substrates specifically?
Substrate binding occurs in a pocket or cleft on the surface of the enzyme.
What type of reaction is catalyzed using an Oxidoreductase enzyme?
Oxidation-reduction reactions
What type of reaction is catalyzed using an Transferase enzyme?
Transferases swap a functional group between substrates.
What type of reaction is catalyzed using an Hydrolase enzyme?
Hydrolases use water to break a bond or condense to eliminate water.
What type of reaction is catalyzed using an Lysase enzyme?
Lyases break bonds without the use of redox activity or water and produce an extra double bond (or ring) in the products.
What type of reaction is catalyzed using an Isomerase enzyme?
Isomerases rearrange functional groups within a substrate, but keep the chemical formula the same.
What type of reaction is catalyzed using an Ligase enzyme?
Ligases use ATP energy to connect 2 other substrates.
What is a coenzyme?
Coenzymes are organic cofactors.
What is prosthetic group?
Prosthetic groups are coenzymes that are tightly associated with the enzyme.
What are cosubstrates?
Cosubstrates are coenzymes that transiently associate with the enzyme.
What is a holoenzyme?
An active enzyme with its required cofactors.
What is an apoenzyme?
An inactive enzyme without its required cofactors.
What is a cofactor?
A cofactor is a small organic molecule or metal ion that is required for enzymatic activity.
What is acid-base catalysis?
In acid-base catalysis, a H+ is transferred between an enzyme and the substrate.
What is ionization?
Ionization requires picking up a proton or losing a proton.
What amino acids may participate in acid-base catalysis?
Charged amino acids, Cys, His, Ser, Tyr
How does RNase A hydrolyze RNA?
RNase A is an example of acid-base catalysis with histidine residues transferring H+ with the RNA substrate.
What is enzyme covalent catalysis?
A stable intermediate is formed when the enzyme covalently binds to the substrate.
What are the ways a metal ion aids catalysis?
- Stabilize negative charges that form in the transition state
- Shield charges that might repel the attacking group
- Promote nucleophilic attacks through the ionization of water
- Participate in redox reactions
How does the proximity and orientation of substrates affect catalysis?
An enzyme can speed up a reaction by positioning the reactants properly.
What is chymotrypsin?
An intestinal protease that helps you digest proteins by breaking peptide bonds.
How does the chymotrypsin recognize which peptide bond to break?
The specificity pocket only binds amino acids that it is complementary too, which position the peptide bond for cleavage.
What are zymogens?
Inactive precursors of proteases.
What is a protease?
An enzyme which breaks down proteins and peptides.
Why don’t proteases destroy the small intestine where they are made?
Zymogens are secreted into the small intestine and cleaved by other proteases so that they acquire a conformation where the specificity pocket and oxyanion hole are available for catalysis. However, inhibitors in the blood stream and pancreas bind the protease to inhibit any proteases that are active outside the small intestine.
How do you know if an enzyme is more optimized for substrate or transition state binding?
The more tightly an enzyme binds to the transition state form, relative to the substrate, the greater the rate of the catalyzed reaction.
What is the hyperbolic shape of the rate dependence curve due to?
The formation of an enzyme-substrate complex.
What are the criteria for the Michaelias-Menten kinetics being valid?
- Measurements are made before much product has formed.
- There is only one substrate.
- The reaction occurs in a single step.
- Binding is non-cooperative.