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Name: ________________________________________ Date: ___10/6/11______
AP Biology EXAM 4
Directions: Answer each question below. Read ALL the choices first.
1. The R group or side chain of the amino acid serine is –CH2-OH. The R group of
side chain of the amino acid alanine is –CH3. Where would you predict to find
these amino acids in a protein in solution?
a. Both serine and alanine would be in the interior of the protein.
b. Both serine and alanine would be on the exterior of the protein.
c. Serine would be in the interior, and alanine would be on the exterior of
the protein.
d. Alanine would be in the interior, and serine would be on the exterior of
the globular protein.
e. Both serine and alanine would b in the interior and on the exterior of
the protein.
2. Draw an organic molecule. This molecule must be either (A) an aldehyde or a
ketone and (B) include at least four unique functional groups. (C) Two groups
must act as acids and one as a base. (D) Circle and label all four groups and
indicate if they acts as acids/bases. (E) If there is an asymmetric carbon, label this
carbon(s) with a star. (F) Label whether it’s an aldehyde or ketone. This molecule
need not be in three dimensions.
3. Using dash-wedge draw (A) ammonia - NH3, and (B) Methylamine – CH3NH2,
(C) formaldehyde – COH2 and (D) dimethyl ketone (aka acetone) – CH3COCH3.
Indicate the overall shape of each molecule below it. Show all lone pairs.
Molecule
(dash-wedge)
Shape
(A)
(B)
(C)
(D)
Not Needed
4. The _________________ structure of a protein is held together ONLY by main
chain hydrogen bonds.
5. The _________________ structure of a protein is the unique three-dimensional
shape of the fully folded single polypeptide.
6. A polypeptide can best be described as a
a. Monomer of a protein polymer
b. Polymer containing only 20 amino acid molecules
c. Polymer containing 19 peptide bonds
d. Polymer of amino acids
e. Polymer containing 20 peptide bonds
7. A new organism is discovered in the forest of Costa Rica. Scientists determine
that the polypeptide sequence of hemoglobin from the new organism has 72
amino acid differences from humans, 65 differences from a gibbon, 49 differences
from a rat, and 5 differences from a frog. These data suggest that the new
organism
a. Is more closely related to humans than to frogs
b. Is more closely related to frogs than to humans
c. May have evolved from gibbons but not rats
d. Is more closely related to humans than to rats
e. May have evolved from rats but not from humans and gibbons
8. Proteins like hemoglobin and insulin have different structures because they have
different ______________________, which is also known as the protein’s
_____________________ structure.
9. Amino acid molecules are to proteins as ______________ are to polysaccharides.
a. oils
b. amino acids
c. fatty acids
d. phospholipids
e. monosaccharides
10. Draw all possible structural isomers for C3H9N.
11. Enzymes ____________________________ chemical reactions and bring them
to _______________________ without themselves being __________________.
The region of the enzyme where the reaction occurs is known as the
_________________________. The _______________________ enters this
region and is/are converted to ______________________.
12. Describe, using only what we have learned in class thus far, how a mutation in a
single gene leads to sickle cell anemia starting at the level of the gene.
13. Draw a schematic diagram showing the steps and players of The Central Dogma.
The following terms must be present (you’re welcome): mRNA, polypeptide,
tRNA, DNA, gene, ribosome, RNA polymerase, translation, transcription
____________
____________
____________
14. A. Circle and label the two types of secondary structure elements shown in the
image below.
B. What class of macromolecule is this and what level of structure are you
observing as a whole?
C. What part of the protein are you looking at when viewing a ribbon diagram
(basically, what has been omitted).
D. Draw an amino acid side chain (cysteine) on the above diagram to scale.
15. (A) Draw a 5’-AU-3’ dinucleotide. (B) Label the 5’ and 3’ ends. (C) Circle the
connection between the two nucleotides. This connection is known as the
(D)____________________ _____________________. (E) Label the bases with
an A or U *AND with the name of the base group to which it belongs. (F) Make
sure all charges are indicated.
16. In the great library analogy, the ____________________ is the nucleus, the
_______________________ are the books of (humans have ________ books), the
________________________________ is/are the paper and the
_________________________ is/are the ink. The “literate protein” is
___________________________.
17. Draw a dipeptide consisting of two DIFFERENT amino acids. One must be
cysteine and the other must be from one of the other groups of amino acids.
a. Use an arrow to point to the peptide bond.
b. Put squares around the side chains.
c. Circle the backbone/main chain.
d. Label the alpha carbons with the alpha symbol ().
e. Indicate the N-terminus and C-terminus.
f. Indicate for each amino acid the amino acid group to which it belongs.
g. Identify the asymmetric carbons with stars
18. The approximate age of earth is __________________________, while the oldest
known fossils date back to around____________________________. The first
eukaryotes appeared around _________________________ years ago, while the
animal kingdom appeared on Earth approximately _________________________
years ago according to the fossil record. All of the elements on the periodic table
greater in mass than lithium came from ___________________________.
19. Identify six unique general functions of proteins and give the name of a
representative protein for of each.
Enzyme Function
Representative
1.
2.
3.
4.
5.
6.
20. All _________________ helices found in proteins are ________________
handed. This means if you look down the axis it will turn
_____clockwise/counter-clockwise (circle one) ____ This is due to the fact that
the amino acids that make them up are all ___________-amino acids. There are
________________ amino acids per turn in such helices and assuming the helix is
seventeen amino acids in length, the 10th amino acid would hydrogen bond to the
__________________(number)___ amino acid. All h-bonds in a helix is made by
the ____________________________ of the polypeptide.
21. (A) Explain in detail why lowering the pH below the optimum value for a given
protein could cause it to denature. (B) Compare the optimum pH for enzymes
found in the stomach vs. enzymes found in a hepatocyte.
22. (A) Draw the reaction of a monomer being added to a trimer to form a tetramer.
Use simple circles as monomers and show any additional molecules as molecular
formulae. (B) What do we call this type of chemical reaction?
23. A strong covalent bond between amino acids that functions in maintaining a
polypeptideʹs specific three-dimensional shape is a (an)
A) ionic bond.
B) hydrophobic interaction.
C) van der Waals interaction.
D) disulfide bond.
E) hydrogen bond.
24. What would be an unexpected consequence of changing one amino acid in a
protein consisting of 325 amino acids?
A) The primary structure of the protein would be changed.
B) The tertiary structure of the protein might be changed.
C) The biological activity or function of the protein might be altered.
D) Only A and C are correct.
E) A, B, and C are correct.
25. What method did DrT use to elucidate the structure of XDH?
A) X-ray crystallography
B) bioinformatics
C) analysis of amino acid sequence of small fragments
D) NMR spectroscopy
E) DrT is Superman…he has X-ray Vision Baby!
BONUS
26. How many different kinds of polypeptides, each composed of 12 amino acids,
could be synthesized using the 20 common amino acids?
27. Conversion: How many Planck Lengths in a yoctometer? Ummm…
28. Draw any L-amino acid