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Final Exam Review for BCHM470

Chapter 10 (Overall Concepts)


1) Passive Vs. Active Transport
2) The Thermodynamics of Transport (Knowing how to use G equation)
3) Function of Ion channels
4) Difference between Uniport, Antiport and Symport
5) Classes of ATPases (specifically, P-type and ABC)
6) Active Vs. Secondary Active

Chapter 11
1) Classes of Enzymes
2) How active sites function and the role of cofactors
3) Activation energy and productive collisions as they function in catalytic (enzymatic)
kinetics
4) Transition State role in catalysis
5) Know the specific active sites covered in class

Chapter 12
1) Michaelis-Menten Kinetics and the definitions of Km, kcat and Vmax
2) Lineweaver Burke plots
3) Competitive, Uncompetitive and Noncompetitive Inhibition

Since we didnt have an Assignment for end of chapter 11 and chapter 12, Here are some practice
problems:
Chapter 11: 10, 12, 14, 18 (4th Edition, 12, 14, 17, 24)
Chapter 12: 7, 10, 13, 14, 18, 19 (4th Edition 7, 10, 19, 20, 24, 27)

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Math for New material: Know new equations, just know how to use the G equation and how
to calculate Km and Vmax

Exam 1 Material
1) Formic Acid is a weak acid with a pKa = 3.75 at 25oC, what is the equilibrium constant for the
dissociation of Formic acid to it conjugate base Formate?

b) At standard state, is the dissociation of Formic Acid spontaneous?

c) What is G0 for the dissociation of Formic Acid?

d) What is the pH of a solution containing 0.1 M Formic Acid and 0.05 M Formate at 37oC?

2) Not really a question, but be sure you know the 20 amino acid structures, 1 letter codes and 3
letter codes.

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3) What is the structure of Tyrosine at pH = 5, pH=7 and pH=9?

4) (5 pts) What is the pI of Tyrosine?

5) In the following amino acid pairs, identify which amino acid is the most soluble in water.
a) Asp, Ala

b) Glu, Ile

6) Draw the structure of the dipeptide given by the primary sequence; AD.

7) What two structural features define the secondary structure of a protein?

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8) What is the covalent bond that appears in the primary structure of a protein?

9) What is the covalent bond that appears in the tertiary structure of a protein?

10) (Use the chart below to answer the following questions.


Size (kDa)
pI
protein X
65
7.2
protein Y
69
7.9
Albumin
66
4.8
a) If the proteins in the chart above are in a pH = 6.5 buffer, Which chromatography techniques
discussed in class is the best technique to separate the protein Albumin from the other proteins?

b) Which media is the best column media to use to separate the protein Albumin at a pH = 6.5
from the other proteins: Sepharose, Sepharose-CM or Sepharose-DEAE?

11) Hemocyanin is the oxygen transport protein found in many water dwelling invertebrate such as the
horseshoe crab. Is the P50 for hemocyanin greater than or less than the P50 for hemoglobin?

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12) Hemocyanin has a hill coefficient of about 2.0 compared to a hill coefficient of about 3 for
Hemoglobin. Is Hemocyanin a multisubunit protein like Hemoglobin?

Exam 2 Material
13) Describe the interaction between Myosin and Actin that causes muscle contraction.

14) Draw the alpha and beta conformation Glucofuranose, Glucopyranose, Fructofuranose and
Fructopyranose.

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15) Draw and name the sugar alcohol, aldonic acid and the uronic acid of Glucose and the sugar
alcohol and the uronic acid of Fructose.

16) Why was the aldonic acid of Fructose not on the list in question 15?

17) What is the defining bond of a glycosidic compound?

18) Draw the nitrogenous base, nucleoside and nucleotide for Adenine.

19) Draw the backbone for DNA and RNA and label the 3 and 5 end.
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20) Show the hydrogen bonding between the bases Adenine/Thymine and Cyotsine/Guanine.

21) Name and identify the fatty acids highlighted in class.

22) Show the basic structure of a phospholipids and a shingolipid.

23) Name three chemical changes to the lipids in a membrane that could affect permeability.

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24) Draw the defining structure of a steroid?

New Material
25) Cells in the thyroid gland have a Na+/I- transporter in there membranes that transporter 2 Na+
and 1 I- ions in to the cell. Is this active or passive transport?

b) Is this transporter an antiporter or a symporter?

c) Given what you know about the relative Na+ concentration inside and outside of the cell, is
there a gradient in the I- concentration inside and outside of Thyroid cells?

d) Given the conditions below calculate the free energy for the transport of 2 Na+ into the cell
and 1 I- into the cell at 37oC.
[Na+]in = 5mM [Na+]out = 145 mM [I-]in= 1.4 mM [I-]out=0.085 mM =-0.07 V
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26) Describe the activity of the Na+/K+ transporter and how it maintains the electrochemical
gradient.

27) Describe the two types of ion channels that play a role in the firing of a neuron.

28) Describe the difference between an ABC transporter and an ATPase

29) What is the term for a Hemoglobin subunit without the Heme cofactor bound?

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30) The enzyme triose phosphate catalyzes the following reaction:


dihyrodoxyacetone phosphate glyceraldhyde 3 phosphate

Go=7.66 kJ/mol

Which of the following are true and why?


a) The reaction would proceed spontaneously as written under standard conditions

b) Go is different for the catalyzed and the uncatalyzed reaction.

c) The reaction rate forward is greater than the reverse reaction rate at equilibrium.

d) The equilibrium constant for the reaction can be calculated with the given information.

e) Whether or not this reaction is spontaneous depends on the presence of enzyme.

31) An enzyme decreases the activation energy of a reaction by 10 kJ/mol, what affect would it
have on the activation energy of the reverse reaction?

32) Describe the catalytic activity of the catalytic triad.

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33) Describe the catalytic activity of carbonic anhydrase.

34) How specifically does a serine protease stabilize the transition state of the catalyzed
reaction?

35) Contrast the lock and key method with that of the induced fit method.

36) Define the terms KM, kcat and Vmax.

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37) What is the difference between a substrate and a transition state analog?

38) Know how to calculate KM and Vmax from a Lineweaver Burk Plot

39) Know the affect of competitive inhibition, uncompetitive inhibition and noncompetitive
inhibition (mixed and pure) on a Lineweaver-Burk Plot.

40) Using the typical model for Michealis- Menten Kinetics (E +S ES E + P) to illustrate
of competitive inhibition, uncompetitive inhibition and noncompetitive inhibition

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