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BIOLOGY AP, December, 2006
Practice Final Exam
NAME ___________________________
PER
1 2 3 4 5 6 7
"I understand the Monta Vista Academic Code and will not give or receive any improper aid for this examination."
signed __________________________________
QUESTION 1
You have recently begun your new job as a research assistant at Genencor in the Protein Engineering Department. Your
first project is to attempt to make Proteinase K (an enzyme) more stable at lower pH's (such as pH 4). You will be
changing the amino acid sequence of the enzyme to try to make the enzyme stable AND still functional at lower pH's.
1a) Briefly, describe the four levels of protein structure that could be used to characterize Proteinase K.
Primary ______________________________________________________________________________
_____________________________________________________________________________________
Secondary ____________________________________________________________________________
_____________________________________________________________________________________
Tertiary ______________________________________________________________________________
_____________________________________________________________________________________
Quaternary __________________________________________________________________________
_____________________________________________________________________________________
The breakdown of proteins in an exothermic reaction
1b) Draw an example of this exothermic reaction to the right
(without enzyme). Be sure to label the reactants and products and
the axes of the reaction diagram (energy and time). For your
purposes, list the reactant as a "protein". The products would be
considered "amino acids".
1c) Using a dotted line on top of your previous drawing, draw
what the reaction would look like with Proteinase K.
1d) Molecularly, explain how a "lower than ideal" pH can cause an enzyme to no longer function. _____________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
1e) Choose one other condition (other than low pH) that can affect an enzyme's function. State the condition and then
describe how it molecularly affects an enzyme. _______________________________________________________
______________________________________________________________________________________________
______________________________________________________________________________________________
You decide to look at inhibitors that might prevent Proteinase K from working. You find a chemical named Prozblok.
Using x-ray crystallography, you find that Prozblok seems to bind to Proteinase K in a region that is on the opposite side
of the enzyme as the active site.
1f) Would you describe Prozblok as: (circle one)
A) a competitive inhibitor
B) a non-competitive inhibitor?
1g) Explain your anwer to (1f) ____________________________________________________________________
______________________________________________________________________________________________
1h) Besides inhibitors, enzymes can be controlled by other mechanisms. Which of the following is LEAST likely to
be a mechanism for enzyme control within a cell. (circle one)
A) allosteric regulation
B) negative feedback
C) phosphorylation
D) denaturation
You design an experiment to determine how well the Proteinase K will work under different conditions.
1i) Which of the following strategies will be the best to determine the activity of Proteinase K? (circle one)
A) Rate of disappearance of protein (substrate)
C) Rate of decrease of free energy of the reaction
B) Rate of disappearance of Proteinase K
D) Rate of disappearance of amino acids (product)
QUESTION 2
Having just graduated from UC San Diego with a degree in virology, you begin work at the National Institutes of Health
(NIH) in Bethesda, Maryland in the HIV lab. Part of your job is looking at new mutations in the HIV virus. The samples
come to you from blood samples of infected individuals. A blood sample (Sample X) arrives that possibly contains a new
mutation of the HIV virus. You believe that the mutation in this virus may be in the Gag protein. You do a few tests on
the new sample and determine that part of the genetic sequence of the gag gene in the virus sample is the following:
5' CCTCAAATCA CTCTTTGGCA ACGACCCTTA GTCACAGTAA GAATAGGGGG ACAGATAATA GAAGCCCTAT 3' GGAGTTTAGT GAGAAACCGT TGCTGGGAAT CAGTGTCATT CTTATCCCCC TGTCTATTAT CTTCGGGATA - TAGACACAGG AGCAGATGAT ACAGTATTAG AAGACATAAG TTTACCAGGA AAATGGAAGC CAAAAATGAT - ATCTGTGTCC TCGTCTACTA TGTCATAATC TTCTGTATTC AAATGGTCCT TTTACCTTCG GTTTTTACTA - AGGGGGAATT GGAGGTTTTA TCAAAGTAAG ACAATATGAC CAGATACTTA TAGAAATTTG - 3'
- TCCCCCTTAA CCTCCAAAAT AGTTTCATTC TGTTATACTG GTCTATGAAT ATCTTTAAAC - 5'
2a) You decide to use PCR to determine if this Gag protein matches that of 3 different, already identified
mutations. The first thing you will need to do is design primers for your PCR reaction. Suppose you want to amplify
the entire sequence shown above. Design primers that are 9 nucleotides long. Be sure you label the 5' and 3' ends.
_____________________________
_____________________________
2b) One of your coworkers tells you, "You don't need primers that are that long! Why don't you just make the
primers 3 nucleotides long? It will be much cheaper." Explain why this is not a good idea to your coworker by
giving specific reasons related to the PCR procedure. __________________________________________________
______________________________________________________________________________________________
2c) Which of the following are important for DNA Replication, but NOT PCR? (circle all that apply)
A) helicase
B) gyrase
C) ligase
D) exonuclease
E) primer
2d) The primer you will use fits into which of the following biomolecule groups? (circle one)
A) carbohydrate B) lipid
C) nucleic acid
D)amino acid / protein
E) porphyrin
2e) Chelex will remove metal ions from the cellular solution before PCR. After the Chelex beads have been removed
when preparing any DNA sample, what metal ion must be added back into the solution for the PCR reaction? (circle
one)
A) iron
B) aluminum
C) silver
D) magnesium
E) gold
You do one PCR reaction on the sequence above. After your first set of experiments, you run the PCR product on a gel
with a size standard. Much to your dismay, when you look at your gel under UV light the only bands you see are your
size standard bands.
2e) Of the following choices, which are possible errors that could cause this result? (check all possible reasons)
___ The buffer was not added to the PCR reaction
___ Nucleases contaminated the PCR reaction
___ You forgot to add ethidium bromide to the gel
___ You punctured the wells when loading your PCR sample.
Having fixed your error, you do one PCR reaction and run another gel.
2f) Draw what these results would look like on the gel to the right. You use
a size standard that is 400 bp, 300 bp, 200 bp, 100 bp, 50 bp. The top of the gel is
the negative electrode while the bottom of the gel is where the positive electrode is.
*The size standard should go in Lane 1 (left lane). Label the sizes of each standard.
*Your PCR product (from using the primers in 2c) should go in Lane 2 (right lane).
2g) Is it possible for you to use the primers above on a different allele of the
gag gene (has a different sequence) in another HIV mutated strain and still get
a band with your PCR reaction? (circle one) YES or NO
2h) Explain your answer to (2g). ________________________________________
____________________________________________________________________
QUESTION 3
Impassioned by his experiences with the feral cats on campus, Mr. Krieger decides to put his biology expertise to use in
looking at a possible genetic basis for feral cat behavior. Specifically, he would like to study the MOW protein. The
MOW protein is thought to have effects on regions of the brain that deal with aggressive behavior. In order to study this
protein more closely, Mr. Krieger must make many copies of the protein using genetic engineering principles.
In order to make these copies of the protein, he will need to use E. coli and plasmids.
3a) Specific enzymes are needed to insert the MOW gene into the plasmid. Fill in the table below to show what
each of the enzymes does in the process of creating this recombinant DNA.
Enzyme
Restriction Enzyme (endonuclease)
Ligase
Function in creating recombinant DNA
The plasmid you decide to use in your experiments is the pFLX plasmid. This plasmid already has the following genes on
it:
penR gene-- This codes for a protein that breaks apart the antibiotic penicillin. This causes the penicillin to no
longer function as an antibiotic.
HLN gene-- This codes for the HLN protein which glows a fluorescent yellow color when it is exposed to UV light.
stp90 gene-- This codes for the stp90 protein what binds to the operator region in front of the HLN gene to prevent
transcription (when activated). The stp90 protein becomes activated(to bind to operator) when there is mannose (a
sugar) present.
You can assume that the E. coli you use do not have any antibiotic resistance genes or any of the genes found on the
pFLX plasmid on its chromosome.
You successfully engineer the pFLX plasmid by inserting the MOW gene into it. You do a transformation procedure with
the newly engineered pFLX plasmid and E. coli, then plate your results on a variety of media and incubate at 37C for 24
hours.
3b) What are 2 different ways that you could identify successfully transformed E. coli cells using culturing
techniques?
#1) ______________________________________________________________________________________
__________________________________________________________________________________________
#2) ______________________________________________________________________________________
__________________________________________________________________________________________
3c) Based on the bacteria you would expect to see alive after 24 hours of growth at 37C, fill in the table below. For
each of the conditions, indicate if the statement will be true for ALL cells, SOME cells, or NONE of the cells. If
there are no colonies, you should not fill out the remaining columns for that row. LB is the standard media for all E.
coli growth. It contains no mannose or antibiotics in it (unless otherwise stated).
Condition
LB- plain
LB- with ampicillin
LB- with mannose +
penicillin
LB with penicillin
LB with mannose
Any
colonies?
Yes or
No
Cells contain the
pFLX plasmid?
All, Some, None
Cells produce
HLN mRNA?
All, Some,
None
Cells contain the
PenR protein?
All, Some, None
Cells produce
Stp90 protein?
All, Some,
None
Cells glow yellow
under UV light?
All, Some, None
QUESTION 4
As a Cadet working in the Criminology Lab at the San Jose FBI labs, it is your job to correctly perform PCR, restriction
analysis, and gel electrophoresis on human samples obtained from a crime scene. You perform PCR on your sample, then
use restriction enzymes to divide the DNA into fragments. Your sample is linear DNA.
Sample 1 = DNA + EcoRI
Sample 4 = _________ (see below)
Sample 2 = DNA + BamHI
Sample 5 = _________ (see below)
Sample 3 = DNA + BamHI + EcoRI
In your wells on your gel, you will place each of your samples. Sample 4 and 5 are controls.
4a) Sample 4 is used to ensure that the DNA you are using isn’t already in different fragments, and so you can
determine what the maximum fragment length can be. What is sample 4? __________________________________
4b) Sample 5 will give you a way to determine the approximate length of each fragment. What is sample 5? ______
______________________________________________________________________________________________
4c) You add loading dye to each sample, then load them into their appropriate wells. What is the significance of the
loading dye. The dye will: (check each statement that applies).
___ weigh down the sample in the well
___ color the sample so it is easy to see if the well was properly loaded
___ cut the DNA into fragments
___ make the bands of DNA visible under UV light
You run your gel and come up with the following results.
Sample 1 = bands at 200, 900 bp
Sample 4 = band at 1100 bp
Sample 2 = bands at 300, 800 bp
Sample 5 = bands at 200, 300, 500, 600, 800, 900, 1100, 1200 bp
Sample 3 = bands at 200, 300, 600 bp
4d) What is the total size of the DNA? _________
4e) How many EcoRI Restriction Enzyme sites are on the DNA? _______ BamHI sites? _______
4f) Sketch a picture of the original DNA fragment and its restriction enzyme sites. (A) Label the beginning of the
sequence with 0 (zero). (B) Label each site with a base pair location and a restriction enzyme type.
QUESTION 5
Your backyard has become infested with ants. While your brothers and sisters are spooked by the creatures, you have a
special interest in them. You trap and count 300 ants and categorize them according to their exoskeleton color. 186 of
them have a gray exoskeleton. 93 of them have a black exoskeleton. 21 have a white exoskeleton. You hunt in ant
genetics literature online and find that having a white exoskeleton is a recessive trait. The gray coloring is the
heterozygous phenotype. All exoskeleton coloration is assumed to be controlled by only two alleles (a single gene).
5a) The ant exoskeleton color is an example of: (circle one)
A) CO-DOMINANCE
B) INCOMPLETE DOMINANCE
C) GENETIC DRIFT
You find a male and female ant “courting” as you explore your yard further, and encase them in a little box. They
produce 8 ant eggs. Several days later the eggs hatch and you count two white ants, two black ants, and four gray ants.
5h) What were the genotypes of the parents (assume h represents “white”)? ________ and _________
QUESTION 6
You are studying the p53 gene This gene is found on Chromosome #17 in humans. It is important in ensuring that the
nuclear DNA is correct before replication begins. Mutations in this gene have been implicated in many cancers. The
sequence of the gene is below. The upstream region of this gene and the entire transcribed region is: (both strands are
shown)
5' -TATATGGACA ATCTTCTACG GCCAGTACTG TGATAGCGAT CGTAGCGTTA GATATAATAT GCGGACGTGC3' -ATATACCTGT TAGAAGATGC CGGTCATGAC ACTATCGCTA GCATCGCAAT CTATATTATA CGCCTGCACG-AGTGCCCGTC GGAGTGCGCG ACCATGGAGG AGCCGCAGTC AGATCCTAGC GTCGAGCCCC CTCTGAGTCA-TCACGGGCAG CCTCACGCGC TGGTACCTCC TCGGCGTCAG TCTAGGATCG CAGCTCGGGG GAGACTCAGT-GGAAACATTT TCAGACCTAT GGAAACTACT TCCTGAAAAC AACGTTCTGT CCCCCTTGCC GTCCCAAGTT-
-CCTTTGTAAA AGTCTGGATA CCTTTGATGA AGGACTTTTG TTGCAAGACA GGGGGAACGG CAGGGTTCAA-
EUKARYOTIC PROMOTER SITES
-75 (5'-GGACAATCT-3')
-25 (5-TATAAT-3')
6a) For the above sequence, underline the promoter sites and label them.
6b) Circle the approximate +1 position in the above gene.
6c) How (molecularly) does the RNA polymerase recognize where to begin transcription? _______________
______________________________________________________________________________________________
6d) Using the genetic code table, what are the first four amino acids of the p53 protein? ______________________
6e) Describe how the p53 protein will stop being translated in your cells. __________________________________
______________________________________________________________________________________________
Patient #1 is found that has the underlined sequence above deleted
6f) Explain what effect this mutation might have on the production of p53. _________________________________
______________________________________________________________________________________________
Patient #2 is found to have two different mutations. They are both italicized and bold above.
-For the first italicized region, the patient's sequence is GCAA (rather than GCAG)
-For the second italicized region, the patient's sequence is AGCC (rather than ATCC)
Your professor asks you to determine which region (or both) is most likely the cause of the lung cancer.
6g) Your answer is (circle one) First italicized region
Second italicized region
BOTH regions
6h) Explain your answer to (7g) ___________________________________________________________________
______________________________________________________________________________________________
AP-LIKE MULTIPLE CHOICE (circle the best answer)
2) Which of the following is NOT a characteristic of bacteria?
a. cell wall
b. lysosome
c. plasma membrane
d. ribosome
3) If a cell contains 20% thymine, what % of the DNA will contain guanine?
a. 20%
b. 30%
c. 40%
d. 80%
4) You are looking at the amount of unsaturated fatty acid tails in the phospholipids of Atlantic Salmon. More
unsaturated fatty acids would mean:
a. a high melting temperature for the membrane
b. a more fluid cell membrane
c. less H+ ions that could cross the membrane
d. higher amount of van der waals forces between fatty acid tails
5) When a protein is denatured due to extreme temperatures, which level of protein structure is NOT affected?
a. primary
b. secondary
c. tertiary
d. quanternary
6) During PCR, the 95C heating step replaces the action of which enzyme?
a. DNA Polymerase III
b. Gyrase
c. RNA Polymerase
d. DNA Helicase
7) The pNCK89 plasmid has a total length of 3200 base pairs and 2 restriction sites for the enzyme PstI at the 1500
position and 2100 position. When the plasmid DNA is digested with PstI, how large will the resulting fragments be?
a. 1500 bp and 2100 bp
c. 600 bp & 2100 bp
b. 2100 bp and 3600 bp
d. 600 bp & 2600bp
10) Hemophilia is considered an X-linked recessive trait. If a male with hemophilia marries a female carrier of the
disease (she is heterozygous), which of the following predictions about their potential children would be true?
a. All of their sons would inherit the disease.
b. 50% of the their sons and 50% of their daughters would inherit the disease.
c. All of their daughters would inherit the disease.
d. All of their children would be carriers of the disease.
11) Steroids have a large amount of:
a. nonpolar covalent bonds
c. polar covalent bonds
b. ionic bonds
d. hydrogen bonds
The following diagram refers to questions 12-17.
12) DNA Replication occurs in what phase of the cell cycle? (circle one)
a. G1
b. S
c. G2
d. M
13) What kind of bonds does "E" break?
a. Covalent
b. Van der waals
c. Ionic
d. Hydrogen
14) What molecule does “H” represent?
a. DNA Polymerase III
b. DNA Ligase
c. Gyrase
15) What molecule does "B" represent?
a. DNA Polymerase III
b. DNA Ligase
c. RNA Primase
d. RNA Primase
d. Single Stranded Binding Proteins
16) What end of the nucleic acid does "F" represent?
a. 5'
b. 3'
17) Which DNA strand is considered the Leading Strand?
a. "C"
b. "G"
18) A substrate molecule is least likely to be bound to the active site of an enzyme by
a. hydrogen bonds
b. van der waals forces
c. covalent bonds
d. ionic bonds
19) An organism that is eukaryotic, multicellular, heterotrophic, and lacks cell walls belongs to which of the following?
a. Monera
b. Protista
c. Fungi
d. Plantae
e. Animalia
20) Which of the following is a correct statement about the relationship between pH and the hydrogen-ion concentration
of a solution?.
a. There are no hydrogen ions present in a solution with a neutral pH of 7.0.
b. The concentration of hydrogen ions in a solution with a pH of 7.0 is 20 times as great as that in a solution with a
pH of 9.0.
c. The concentration of hydrogen ions in a solution with a pH of 3.0 is 100 times that in a solution with a pH of 5.0.
d. The concentration of hydrogen ions in a solution with a pH of 3.0 is 2 times that in a solution with a pH of 5.0.
21) All of the following can be used to produce cellular energy EXCEPT
a. acetyl coA
b. fats
c. amino acids
d. carbon dioxide
22) One of the most pronounced differences between animal and plant cells is that
a. animal cells alone have one or more large vacuoles.
c. animal cells will undergo cellular respiration.
b. animal cells alone undergo mitosis
d. plant cells alone have thick cell walls
Reminders:
Lab concepts from the entire semester will also be on the final exam
Do not rely on this practice final entirely—it is just meant to give you practice with the types of questions you
might see.
Ask questions early!