Study Materials for Final Spring 2014 (Note: this may not represent all possible subjects or
problems.)
The exam will be divided into two parts. You will be allowed to take a short break between the two
parts. Supplemental Information will be provided. No additional material (notes, etc.) permitted.
Show logic and calculations where appropriate. There will be multiple choice questions.
You will be provided with a periodic table, an electronegativity table, a list of polyatomic ions, a table of
pKa for some acids, some English to metric conversions, the Henderson-Hasselbach equation, some
constants, structures for the side chains of amino acids, and a table of the genetic code.
0. Review the previous study guides and exams, lecture notes, and problems from the back of the lab
manual. Although anything is fair game for questioning, the following list of concepts from the first two
exams will have a higher probability of showing up on the final.
Important concepts from the first two exams.
1. About the disease, PKU
2. Unit conversions and proper sig.fig in calculations
Math problems that indicate you understand use of your calculator
Rearranging equations to solve for a variable.
3. Protons, neutrons and electrons in atoms and ions and their electron configuration
4. Writing correct formulas for ionic compounds. Predicting products and balancing chemical equations.
5. Ionic bonds and covalent bonds. Ionic compounds and molecules.
6. Lewis dot structures, electron pair geometry, molecular shape and polarity.
7. Gas laws
8. Inter molecular forces and relationship to the boiling point of molecules
9. Conversion between grams and moles, moles and molecules, and g to mol to mol to g.
10. What is a solution? What affects solubility?
11. Calculation of molarity. Titration problem.
12. Kinetics problems (like the homework I gave you.)
Study Guide for Material Not Yet Tested for Final Spring 2014
001. Shown below is a balanced equation for the decomposition of H2S to form H2 and S2.
2 H2S (g)  2 H2 (g) + S2 (g)
a) Write an equilibrium constant expression for the reaction.
b) Given the equilibrium concentrations: [H2S] = 0.1007 M, [H2] = 0.0219 M, and [S2] = 3.30 × 10-3 M,
calculate the numerical value of Keq.
c) Assume the equilibrium is perturbed. When equilibrium is reestablished, the following concentrations are
observed: [H2] = 0.00287 M and [S2] = 0.171 M. Calculate [H2S] under these new conditions.
d) What can you say about the forward and reverse reaction rates when the system is at equilibrium?
e) How is Keq defined? (I am not asking you to write an equilibrium constant expression using concentrations.)
002. a) Qualitatively, for the reaction shown in the problem above, would the ∆G° value be positive or negative?
Explain your logic.
b) Assuming I told you the reaction above was relatively fast. Draw a reaction coordinate diagram that describes
that system. Then draw another showing how the system would be changed in the presence of a catalyst. Be sure
to clearly label all important quantities.
0.1 What is the definition of a Brønsted-Lowry acid?
0.2. Identify the acid and base on the reactant side of the equation shown below. Predict the products
of the reaction and indicate the conjugate of each reactant.
NH3 + HBr 
0.3.(a) Write a balanced chemical reaction for the dissociation of acetic acid (CH3COOH) in water, and then
(b) write the Ka expression for that rxn. Acetic acid is a relatively weak acid. It is a weaker acid than formic acid.
(c) Would formic acid dissociate to a greater or lesser extent in water compared to acetic acid? (d) Which acid
would have the larger pKa?
0.4.(a) Calculate the [H3O+], [OH-], and pH of a 7.00 x 10-3 M solution of HNO3. (b) Is this solution acidic, basic
or neutral? (c) Would the pH be the same for a 7.00 x 10-3 M solution of acetic acid? Explain.
0.5. How does a buffer function to keep the pH of a solution relatively constant when strong acid or base is
added? Make sure your answer includes equations for chemical reactions.
0.6. What weak acid could be used to make a buffer that was effective around pH 4.25? (See table at end.) You
must explain your answer thoroughly to receive full credit. Write the conjugate base for that weak acid.
0.7. Why (chemically) are you inhaling? Why are you exhaling? Which of these would you expect to have the
most direct affect on acidosis. Explain using equations.
0.8. Identify the functions that must be achieved for living things to stay living. Briefly describe each function
and indicate how it contributes to staying alive.
0.9. Draw a generalized structure for an amino acid (use may use “R” for the side chain”).
0.10. Show how the amino acid glycine and the amino acid alanine would join to form a peptide bond. (Note: you
will be given the structures for the side chains, but you must connect them properly to each of the amino acids.)
0.11. Why would it be very appropriate for the amino acid, aspartic acid,
to lie on the outer surface of a cytoplasmic protein?
O
R
CH
0.12 What are the levels of protein structure? What kinds of forces/bonds
maintain the structure of each of these levels?
H
H
1. Describe the two conformations of hemoglobin and describe how they
aid in transport of oxygen to your tissues.
2. Draw a reaction coordinate diagram for the hydrolysis of a dipeptide
(like Gly-Ala). Then draw another line on the same diagram to describe
the reaction when catalyzed by an efficient catalyst.
H
C
O
CH
R
N
H
C
O
CH
R
N
H
C
N
O
CH
O
N
C
H
C
R
CH
H
N
C
H
R
O
R
C
CH
R
CH
N
O
O
H
O
CH
N
O
C
CH
R
0.13. Given an organic molecule, be able to circle the chiral carbons.
0.14. Determine the amino terminal end of each protein strand shown
to the right. Would this represent parallel or anti-parallel β-sheet structure?
H
N
C
R
N
C
N
CH
R
3. (From lab) What happens to the rate of an enzyme catalyzed reaction at low substrate concentrations when you
double the substrate concentration? Does the same apply when you are looking at high levels of substrate
concentration? Explain.
4. Describe the molecular basis of sickle cell anemia, one treatment, and indicate why the trait is found at
relatively high levels in some populations.
5 & 6. No question!
7. What is the “Central Dogma of Molecular Biology?”
8. Why is it important that DNA be able to replicate itself millions of times without error? What feature of DNA
structure is particularly important with regard to avoiding errors?
9 & 10. No question!
11. Describe where DNA is located and where proteins are synthesized. What molecules and processes exist that
allow the transfer of this information from one location to the other? Draw a picture to aid in your description.
12. Draw a DNA molecule being replicated. Include the direction the DNA is unwinding, the polarity of the
parent and daughter strands and the direction the daughter strands are being synthesized.
13. (partially from lab) You are attending a family reunion, and the subject of mitochondrial DNA comes up (as
it often will at such gatherings). How likely is it that you have the same mtDNA sequence as your cousin Luke?
Luke is your mother’s sister’s son. Briefly explain your logic.
14. Draw a cartoon model of DNA indicating how the three major pieces are connected. Indicate the location of
hydrogen bonds.
15. Given the following DNA sequence, what would the complementary RNA sequence be? Indicate the polarity
of the RNA.
5' ATGGACGTGCGTAA 3’
NH2
16. No question 16.
N
N
17. If a researcher determined that DNA from a new organism
was 28.3% G, what would be the percentages of A, T and C in the
DNA of this creature?
O
N
N
5'
HN
1'
H
H
H2N
3'
2'
5'
NH2
18. Is the nucleic acid strand shown on the right RNA or DNA?
How do you know? Draw an arrow that represents the
5’ to 3’ direction.
H
H
N
N
H
H
H
O
H
N
5'
O
H
H
H
3'
H
O
O
P
P
O-
N
H
4'
H
O
O
O
O
O
O
N
O
OH
3'
O
5'
Supplemental information
Periodic Table, electronegativity chart, the structures of the side chains of the 20 common amino acids, and a copy of the
genetic code.
-14
K = °C + 273.15
Kw = 1.0 x 10
pH = pKa + log ( )
∆Go = -RT ln Keq
R = 0.0820578 (L·atm/(K·mol)
R = 8.3145 J/(K·mol)
Acid Dissociation Constants as pKas From Chemistry by McMurray & Fay, 4th ed.
Acid
Formula
pka1
pKa2
pKa3
CH3COOH
acetic
4.74
C8H7O2COOH
acetylsalicyclic
3.52
ascorbic
C6H8O6
4.10
C6H5COOH
benzoic
4.19
H3BO3
boric
9.24
H2CO3
carbonic
6.37
10.25
CH2ClCOOH
chloroacetic
2.85
citric
C6H8O7
3.15
HCOOH
formic
3.74
HCN
hydrocyanic
9.31
hydrogen peroxide H2O2
11.62
H2S
hydrosulfuric
7.00
~19
HOBr
hypobromous
8.70
HOCl
hypochlorous
7.46
HOI
hypoiodous
10.64
HIO3
iodic
0.77
C2O4H2
oxalix
1.23
4.19
C6H5OH
phenol
9.89
H3PO4
phosphoric
2.12
6.21
12.32
H3PO3
phosphorous
2.00
6.58
saccharin
C7H5NO3S
11.68