Problems dealing with New Material

Study Materials for Final Spring 2015 (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 midterm
exams will have a reasonable probability of showing up on the final.
Important concepts from the first two exams.
1. Unit conversions and proper sig.fig in calculations
Math problems that indicate you understand use of your calculator
2. 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: Writing general rate laws and using initial rates to determine a rate. Understanding the
relationship between rate, the rate constant and activation energy.
13. Be able to explain how/why changes in temperature result in changes in a rate constant, k, including use of
an appropriate graph.
14. Be able to write equilibrium constant expressions for equilibrium equations. Given appropriate data,
be able to calculate the value for Keq. If the equilibrium is perturbed be able to determine the new
equilibrium concentrations. What does it mean if Keq is greater than one or less than one?
15. Be able to draw and label Reaction Progress Diagrams given appropriate kinetic and equilibrium
data.
16. What is the definition of a Brønsted-Lowry acid?
17. Be able to complete an acid-base equation based on the donation and acceptance of one H+ ion to form a
conjugate acid and conjugate base.
18. What is a weak acid? What is a weak base? Be able to write reactions showing the dissociation of an acid in
water. Be able to write a Ka expression for the reaction. Be able to compare the strength of acids.
19. Be able to determine the concentration of OH- given the H3O+ concentration, and vice versa. Be able to tell if
the solution was acidic or basic.
Problems dealing with New Material
0.1 What would the pH be for a 7.00 x 10-3 M solution of acid?
0.2. 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.
0.3. What weak acid could be used to make a buffer that was effective around pH 4.25? You must explain your
answer thoroughly to receive full credit. Write the conjugate base for that weak acid.
0.4. 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.
0.5. 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.
0.6. Draw a generalized structure for an amino acid (use may use “R” for the side chain”).
0.7. Show how the amino acid, tyrosine, could join to form a peptide bond with the amino acid, methionine.
(Note: you will be given the structures for the side chains, but you must connect them properly to each of the
amino acids.)
O
0.8. Why would it be very appropriate for the amino acid, aspartic acid,
to lie on the outer surface of a cytoplasmic protein?
R
CH
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.
O
CH
R
N
H
C
O
N
O
CH
O
N
C
H
C
R
CH
H
C
CH
R
H
O
H
N
C
R
N
C
C
CH
H
R
H
R
0.11. Determine the amino terminal end of each protein strand shown
to the right. What level of protein structure does this represent? What
is the name of this type of structure?
CH
N
O
O
O
O
CH
N
0.10. Given an organic molecule, be able to circle the chiral carbons.
C
CH
R
H
R
H
N
C
0.9 What are the levels of protein structure? What kinds of forces/bonds
maintain this structure?
N
C
CH
R
N
3. Describe the molecular basis of sickle cell anemia and one treatment
that was discussed in lecture.
4. What is the “Central Dogma of Molecular Biology?”
5. 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?
6. What is the quaternary structure of proteins? What kinds of forces/bonds maintain this structure?
7. 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.
8. 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.
9. 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.
10. Draw a cartoon model of DNA indicating how the three major pieces are connected. Indicate the location of
hydrogen bonds.
11. Given the following DNA sequence, what would the complementary DNA sequence be? Indicate the polarity
of the new DNA strand.
5' ATGGACGTGCGTAA 3’
12. 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?
NH
2
N
N
13. Is the nucleic acid strand shown on the left RNA or DNA?
O
How do you know? Draw an arrow that represents the
5’ to 3’ direction.
N
N
5'
HN
1'
H
H
H2N
H
3'
2'
H
N
N
5'
NH2
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'