BC351 Principles of Biochemistry Study Guide for Exam 3 Lecture 07 1 The structure of every integral membrane protein have yet to be solved and yet it is predicted that every one of these proteins will have well defined secondary structure in their membrane spanning regions Why is this the case 2 Do all membrane spanning helices have to be close to 100 hydrophobic residues How about membrane spanning strand What do I mean when I say a hydrophilic core and how does this compare to globular water soluble proteins that we have talked about 3 Membrane spanning strand will not form a sheet but rather a barrel why 4 What is the thermodynamic basis for membrane transport In other words what determines the direction a solute will move spontaneously How is it illustrated by this equation a Gt RT ln C2 C1 ZF 5 Why is it necessary in biology to facilitate membrane transport even when a large electrochemical gradient has been set up How does the membrane protein catalyze the rate of the transport How is this similar to enzymes 6 How can you determine the specificity of a membrane protein for a particular solute 7 Make sure you understand the Na glucose symporter from a thermodynamic perspective and a qualitative perspective In this system what ensures the existence of a Na gradient If there is so much energy available from this gradient Na do you suspect that it takes energy to create it Where does this energy come from 8 What is primary active transport and how does it relate to secondary active transport Where is the energy derived from in primary active transport 9 What is a channel What is the purpose of the K channel that we talked about in the small intestine How do channels compare to carriers 10 Problems from the Textbook pg 416 19 pg 417 22 Lecture 08 1 Catabolic vs anabolic a How does each relate to acetyl CoA 2 Thermodynamics a What is equilibrium again 1 How does this relate to Gibb s free energy standard and actual b G vs G 1 How is G affected by G 2 Can you have a rxn in a cell with a highly positive G that will still favor product formation If so how In other words how can the driving force favor products even if the standard free energy suggests that at equilibrium reactants will out weigh products 3 How is G affected by the equilibrium constant If this constant is large what does that mean if it is small what does it mean 4 How is G affected by the mass action ratio Q If this is large what does it mean How about small 5 What does it mean that free energies are additive 6 You need to be able to interpret these concepts graphically as well c The 1st law 1 How is it exhibited in metabolism 2 What are the types of transfers we will see 3 Redox a What is reduction and oxidation b How can you tell if a particular carbon has been oxidized or reduced c What is a dehydrogenation reaction What does alcohol dehydrogenase do In this reaction alcohol dehydrogenase what is oxidized what is reduced If it were thermodynamically favorable to go in the direction that we talked about in class in other words standard free energy change is negative what does this tell us about the respective reduction potentials of each molecule c E and E 1 What is a reduction potential What is the change in reduction potential What if these are high or low 2 Where do electrons flow From a high reduction potential to a low or vice versa 3 If E is positive is the redox going to be spontaneous What does a positive E mean in terms of G Why is this important in terms of metabolism 4 Phosphorylation energy a What is ATP What bonds are being hydrolyzed What are the products Why is this reaction important in biology b ATP energy conservation 1 In a group transfer reaction how is energy conserved 2 What happens to the free energy of the reactant when a phosphate group is attached to it 3 How might ATP be used to make thermodynamically unfavorable reactions go 5 Problems from the Textbook pg 523 4 6 8 pg 525 23 pg 526 27 Lecture 09 1 Which enzymes are irreversible what does this mean why are they irreversible why is this important 2 How can it be that the G 16 kJ mol for hexokinase and yet the G 34kJ mol Why is this coupled to ATP hydrolysis 3 How does reversibility work In other words how can a reversible reactions direction change 4 How can the G 23 for aldolase and yet the G 0 with no thermodynamically favorable direction This reaction isn t coupled to ATP hydrolysis so what is happening What does this tell us about Q smaller or larger than 1 5 Which is the committed step in glycolysis 6 Compare and contrast the prep phase vs the payoff phase 7 Where does the energy come from to make hexokinase and PFK 1 go How do these reactions exhibit the 1st law of thermodynamics 8 For GAPDH answer the following a In this reaction what is oxidized and what is reduced b Be able to identify which carbon is oxidized c How is the energy of the redox reaction harnessed to allow the addition of the phosphate 9 How can ATP be made in the payoff phase Where does this energy come from 10 What are the fates of pyruvate Why do anaerobic cells need to make lactate 11 Why do gluconeogenesis GNG Why can it NOT be the reverse of the glycolysis pathway 12 How does this GNG compare to glycolysis What are the enzymes that differ Are these enzymes at equilibrium or G close to zero 13 What do each of the GNG enzymes do or what rxn do they catalyze 14 What is the malate shuffle Why is the malate shuffle necessary What purpose does it serve 15 What is the end result of the GNG pathway does it require energy 16 Problems from the Textbook pg 565 5 pg 566 10 11 pg 567 22