Practice Final Exam PER 1 2 3 4 5 6 7

BIOLOGY AP, December, 2006NAME ______

Practice Final Exam 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 regulationB) negative feedbackC) phosphorylationD) 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) helicaseB) gyraseC) ligaseD) exonuclease E) primer

2d) The primer you will use fits into which of the following biomolecule groups? (circle one)

A) carbohydrateB) lipidC) nucleic acidD)amino acid / proteinE) 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) ironB) aluminumC) silverD) magnesiumE) 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.

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 transformedE. 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).

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 + BamHISample 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 bpSample 4 = band at 1100 bp

Sample 2 = bands at 300, 800 bpSample 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-DOMINANCEB) INCOMPLETE DOMINANCEC) 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 GCGGACGTGC-

3'-ATATACCTGT TAGAAGATGC CGGTCATGAC ACTATCGCTA GCATCGCAAT CTATATTATA CGCCTGCACG-

-AGTGCCCGTC GGAGTGCGCG ACCatggagg agccgcagtc agatcctagc gtcgagccccctctgagtca-

-TCACGGGCAG CCTCACGCGC TGGTACCTCC TCGGCGTCAG TCTAGGATCG CAGCTCGGGG GAGACTCAGT-

-ggAaacattt tcagacctat ggaaactact tcctgaaaac aacgttctgt cccccttgcc gtcccaagTT-

-CCTTTGTAAA AGTCTGGATA CCTTTGATGA AGGACTTTTG TTGCAAGACA GGGGGAACGG CAGGGTTCAA-

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 regionSecond 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 wallb. lysosomec. plasma membraned. 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. primaryb. secondaryc. tertiaryd. quanternary

6) During PCR, the 95C heating step replaces the action of which enzyme?

a. DNA Polymerase IIIb. Gyrasec. RNA Polymerased. 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 bpd. 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 bondsc. polar covalent bonds

b. ionic bondsd. hydrogen bonds

The following diagram refers to questions 12-17.

12) DNA Replication occurs in what phase of the cell cycle? (circle one)

a. G1b. Sc. G2d. M

13) What kind of bonds does "E" break?

a. Covalentb. Van der waalsc. Ionic d. Hydrogen

14) What molecule does “H” represent?

a. DNA Polymerase IIIb. DNA Ligasec. Gyrased. RNA Primase

15) What molecule does "B" represent?

a. DNA Polymerase IIIb. DNA Ligasec. RNA Primased. 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 bondsb. 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. Monerab. Protistac. Fungid. Plantaee. 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 coAb. fatsc. amino acidsd. 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 mitosisd. 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!