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Biochem Test Prac
|Define T State
|Tense state usually less active
|Define R State
|Relaxed state usually more active
|Concerted Model of Allosteric Behavior
|Only 2 States; Equilibrium in absence of ligand/Ligand Binds tightly to R state
|Molecular Change that results in coopertivity in hemogloblin binding
|BPG binds to the 4 subunit interface. Salt bridge formation favors a shift to T state/ facilitating O2 release
|Why is reversible binding of O2 critical for hemogloblin to function?
|O2 must be taken up in the lungs and released in the tissues. If O2 was bound more tightly then oxygen will not be delivered to tissues and if less tightly Hb would not get saturated in the lungs
|What is the role of ATP and ATP hydrolysis in the cycle of actin-myosin association and disassociation that leads to muscle contraction?
|ATP binds to myosin/ releasing it from actin/ ATP hydrolysis to ADP + Pi leads to conformational change and power stroke
|For a reaction that can take place with or without catalysis by an enzyme/ what would be the effect of the en zyme on the: Free energy change/ Ea/ Vo/ EQ of reaction
|energy = none/ Ea = Decrease/ Velocity = Increase/ Eq = none
|Explain Terms of Michalis-Menton Eq
|Vo = Initial Veloctiy/ Vmax = when enzyme is saturated/ [s] substrate concentration/ Km = michalis constant/ Km = [s] when Vo = 1/2vmax
|Serine-195/ Aspartate 102/ Histidine - 57
|Catalytic Triad of Chymotrypsin
|Role of Serine-195
|Nucleophile and covalently attacks O=C-NH
|Role of Histidine-57
|General acid/base - pulls proton off Ser-OH and protonates leaving group
|Role of Aspartate-102
|Ion Pair/H bonding - Stabalizes the charge on His-57
|General Acid/Base Catalysis Example
|Group other than water that donates/accepts proton
|Covalent Catalysis Example
|Transient enzyme-substrate covalent bond in mechanism
|Metal-Ion Assisted Catalysis Example
|Metal stabalizes transition state like Mg2+
|General Acid/Base Catalysis Example in enzyme
|His-57 in chymotrypsin pulls of proton off ser-195
|Covalent Catalysis Example in enzyme
|Ser-195 covalanetly bonds to substrate
|Metal-Ion Assisted Catalysis Example in enzyme
|Mg2+ in enolase bonds to the substrate/ making the C-H bond more accurate
|How does the kinetic curve for an allosteric enzyme differ from the kinetic curve for an enzyme that follows Michaelis-Menten kinetics?
|Allosteric curve is below and MM is above. Allosteric is sigmoid
|What effect will an allosteric activator have on the kinetic curve of the allosteric enzyme?
|Shifts to the left
|No BPG = Higher than normal curve; mutant below no bpg/ higher than regular; bohr = way below curve
|Give an example of one type of irreversible covalent modification that is used to regulate enzyme behavior.
|Carbohydrates are much more information rich than proteins or DNA.
|Why is carbs more information rich than DNA/RNA?
|More branching than DNA/RNA/ more modifications avaiable and not linear
|Roles of Carbohydrates and use
|Energy (Glycogen/ Starch/ Sugar)/ Structure (Chitin/ Cellulose)
|Describe the molecular changes that happen when oxygen (O2) binds to hemoglobin.
|1. The iron atom shrinks slightly and moves back into the heme ring/ making it more planar. ; 2.The proximal his is then pulled out of position slightly by the iron l 3. This then pulls the helix that contains the proximal his residue ; Other shifts resul
|Why is cooperativity essential for hemoglobin to function as an effective oxygen carrier in our systems?
|It enables Hb to bind more oxygen in the lungs and release more at the extremities
|The sequential model of cooperative binding
|Ligand binding induces the shift from T to R/ Tetramer can contain both T and R subunits
|The concerted model of cooperative binding
|T and R are in equilibrium all the time; Tetramer is either all T or all R
|What is the chemical basis for the specificity of binding of an immunoglobin antibody to a particular antigen?
|A series of non-covalent bonds between the antigen and the antigen binding site at the variable region of the antibody.
|What is the impact of 2/3-bisphosphoglycerate (BPG) binding to hemoglobin?
|It decreases the affinity of Hb for oxygen so that it can release more oxygen to the peripheral tissues
|7) Sometimes the difference in (standard) free-energy content/ ?G'°/ between a substrate S and a product P is very large/ yet the rate of chemical conversion/ S ? P/ is quite slow. Why?
|Rate depends on energy of activation/ not free energy content
|8) What is the relationship between the free energy G' and the equilibrium constant (Keq’)?
|DG’Ñ = -RNln Keq’
|Units of Vmax
|10) What is transition state theory and how does it help us to understand the working of enzymes?
|Transition state theory is the idea that enzymes accelerate reactions by stabilizing the transition state So when we study enzymes/ we consider any features that might lead to stabilization of the transition state
|Role of Aspartate in serine proteases
|Positions the histidine / Balances any charge that forms on it during the reaction
|Role of histidine in serine proteases
|Pulls the proton from the serine/ Then donates it back to either the leaving group or the serine
|12) The activity of chymotrypsin drops dramatically when the pH increases above pH 8. What causes this?
|The histidine side chain becomes deprotonated and loses its positive charge
|14) How can you tell the difference between an allosteric enzyme and an enzyme that follows Michaelis-Menten kinetics? A drawing is suggested but not required
|Allosteric curve is sigmoidal
|15) Why are some enzymes (such as proteases involved in blood clotting) synthesized and released as inactive precursors
|To prevent unwanted or premature activation of metabolic processes
|Beta glucose oh positoin
|Describe the similarities and differences between proteoglycans and glycoproteins.
|Both are made up of proteins and polysaccharides.; In proteoglycans/ the carbohydrate moiety dominates/ . In glycoproteins/ the protein constitutes a larger fraction
|Another shape for a protiens; and how protiens can convert from a T state to the R state
|One molecular change that occurs in Hb when O2 is bound to it
|Fe2+ in the heme ring becomes smaller
|What is a catalyst
|Accelerates reaction/ but is not changed in the process
|What unique feature of the mechanism of hexokinase contributes to the selective reaction of ATP with glucose/ rather than water?
|Beta Glucose Structure
|O-UDUDU(CH2OH) UD= refers to OH
|What is the energetic basis for the tightness of the interaction? for antibody
|Groups on the antibody for hydrogen bond/ salt bridge and hydrophobic interactions with the antigen Each of these non-covalent contacts reduces the energy of the interaction/ leading to increased in binding affinity.
|allosteric control and application
|A regulatory molecule binds at a regulatory site on the enzyme to increase or decrease the activity of the enzyme.
|reversible covalent modification and application
|A group such as phosphate can be added to or removed from an enzyme to control activity
|irreversible covalent modification and application
|An enzyme such as chymotrypsinogen is covalently converted from an inactive (zymogen) form to an active form.This frequently occurs in extracellular locations and can be used to start cascades such as digestion or blood clotting.