BILD 1 FINAL EXAM – Chemistry of Life and Macromolecules

14 Jun BILD 1 FINAL EXAM – Chemistry of Life and Macromolecules

Question
BILD1 / Spring 2007 / FINAL EXAM
Kiger

NAME: _________________________________
Student ID#:____________________________

BILD 1 – FINAL EXAM
PRINT YOUR NAME LEGIBLY ON EVERY PAGE!!
ALL STUDENTS READ THE FOLLOWING:
Exams may be picked up in Room 6109 of the Natural Sciences Building on or after 6/19/07. Exams not
picked up by the end of Summer Session I will be discarded.

NAMES OF STUDENTS SITTING ON EITHER SIDE OF YOU:
________________________________

__________________________________

PROBLEM:

POINTS:

1.

Macromolecules

________ (30 total)

2.

Cell Structure

________ (30 total)

3.

Respiration & Photosynthesis

________ (30 total)

4.

Cell Signaling & Cell Cycle

________ (30 total)

5.

Genetics

________ (30 total)

6

DNA Heredity & Replication

________ (30 total)

7.

Transcription & Translation

________ (30 total)

8.

Viruses & Bacteria

________ (30 total)

9.

Gene Regulation & DNA Technology

________ (30 total)

10.

True/False

________ (30 total)

Extra Credit

________ (15 possible)

TOTAL

________ (300 points total)

BILD1 / Spring 2007 / FINAL EXAM
Kiger

NAME: _________________________________

PROBLEM 1. Chemistry of Life and Macromolecules (30 POINTS)
1.

(5 POINTS) An element has 6 protons in its nucleus.
How many electrons does it have? _____
How many bonds can this element form with itself? ______ With hydrogen? ______
What is its valence? _____ What is the name of this element? _________________

2.

(1 POINT) Scientists propose that life elsewhere in the universe might be based on the element silicon,
rather than on carbon, as on Earth. What properties does silicon share with carbon that would make
silicon-based life more likely than, say, neon-based life?

3.

(6 POINTS) For each of the following macromolecules, list below: (a) the name for the specific bond
that forms for that class of polymers, and (b) the name of the specific functional groups on the
monomers involved in the bond formation.
Carbohydrates
Polypeptides
Nucleic Acids
(a) Bond?

_______________

_______________

_______________

(b) Groups?

_______________

_______________

_______________

4.

(3 POINTS) List three biologically important and distinct molecules that contain phosphorus.

5.

(2 POINTS) (a) A solution that has pH 4 is considered acidic, neutral or basic? _________________
(b) Specifically, what property does pH measure? ________________________________________

6.

(2 POINTS)

Hydrocarbons are fairly insoluble in water. Why?

7.

(2 POINTS) Write the formula for a monosaccharide that has four carbons. ____________________

8.

(4 POINTS) How do saturated fats differ from unsaturated fats, both in structure and behavior?

9.

(2 POINTS) Differentiate between secondary and tertiary structure of a protein by describing the parts
(of amino acids) that participate in the bonds that hold together each level of structure.

10.

(3 POINTS) Name the three main parts that make up a nucleotide:
1.
2.
3.

Page 1

BILD1 / Spring 2007 / FINAL EXAM
Kiger

NAME: _________________________________

PROBLEM 2. Cell Structure (30 POINTS)
1.

(6 POINTS) The plasma membrane is a type of phospholipid bilayer.
Draw a small segment of a phospholipid bilayer to the right.
Clearly label the hydrophobic and hydrophilic regions.

2.

(9 POINTS) Match the letter of ONE best answer for each of the blanks below:
(A)
(B)
(C)
(D)
(E)
(F)
(G)
(H)
(I)
(J)
(K)
(L)
(M)

Nucleus
Endoplasmic Reticulum
Lysosome
Microfilament
Vacuole
Flagella
Pilus
Chloroplast
Peroxisome
Golgi Apparatus
Mitochondria
Microtubule
Cytoplasm

_______ vesicular cargo exits its trans side
_______ RNA synthesis occurs here
_______ considered “the powerhouse” of the cell
_______ bacterial structure for conjugation
_______ glycolysis occurs here
_______ synthesis of secreted proteins occurs here
_______ acidic compartment for protein hydrolysis
_______ the Light Reactions occur here in eukaryotes
_______ kinetochores are attached to these polymers

3.

(4 POINTS) Describe the structural and functional distinctions between the rough and smooth ER.

4.

(2 POINTS) How are different organelles of the endomembrane system integrated with one another?

5.

(2 POINTS) Describe two common characteristics of mitochondria and chloroplasts that make them
different from other cytoplasmic organelles.

6.

(4 POINTS) A concentration gradient exists with more sodium ions outside the cell than inside the cell.
(a) What process will move more sodium ions inside the cell?

_______________________

(b) What process is needed to move more sodium ions outside the cell? _______________________
7.

(3 POINTS) Explain the theory of endosymbiosis and provide one piece of evidence.

Page 2

BILD1 / Spring 2007 / FINAL EXAM
Kiger

NAME: _________________________________

PROBLEM 3. Respiration & Photosynthesis (30 POINTS)
1.

2.

(9 POINTS) Answer the following questions True (T) or False (F).
(a)

____

Reduction is defined as a net gain of electrons.

(b)

____

An anabolic reaction has a ∆G < 0 and therefore occurs spontaneously.

(c)

____

Glycolysis is a catabolic reaction.

(d)

____

Substrate-level phosphorylation transfers a free Pi group to an organic product.

(e)

____

The citric acid cycle liberates carbon from complex molecules in the form of CO.

(f)

____

The three inputs into photosynthesis are light, CO2 and H2O.

(g)

____

Only photosystem I is involved in cyclic electron flow.

(h)

____

Activation energy determines whether a reaction is spontaneous.

(i)

____

Chlorophyll is a green pigment, therefore most plants are green.

(8 POINTS) Electrons travel energetically “downhill” in electron transport chains in both respiration and
photosynthesis. In each process, the electron flow coincides with the generation of a proton gradient to
drive chemiosmosis. Answer the related questions for each process below.
Respiration
Photosynthesis
(a) What is the major electron shuttle?

____________

____________

(b) What is the final electron acceptor?

____________

____________

(c) Where in the cell (be specific) are protons
pumped to generate a proton gradient?

____________

____________

(d) Where in the cell (be specific) is
ATP generated by chemiosmosis?

____________

____________

3.

(3 POINTS) Name the three major end-products of glucose break-down.

4.

(2 POINTS) What factor determines whether fermentation will occur, instead of the citric acid cycle?

5.

(4 POINTS) Define carbon fixation, and name during what step of photosynthesis it occurs.

6.

(4 POINTS) Both electron flow and the Calvin cycle cease when a plant is placed in the dark. Which of
the two reactions will stop first? Why?

Page 3

BILD1 / Spring 2007 / FINAL EXAM
Kiger

NAME: _________________________________

PROBLEM 4. Cell Signaling & Cell Cycle (30 POINTS)
1.

(2 POINTS) (a) What critical feature of all molecular “switches” (for example, kinase or GTPase
activity) is important in order for cell signal transduction pathways to function normally?
(b) How are molecular switches implicated in cancer?

2.

(8 POINTS) Place the letter of ONE correct term for each statement below. Terms may be used once,
more than once, or not at all.
(A) telophase

3.

(B) anaphase

(C) prometaphase

(D) metaphase

(E) prophase

Cytokinesis immediately follows from this.

____________

Centrioles begin to move apart in animal cells.

____________

This is the longest of the mitotic stages.

____________

Sister chromatids are separated and move towards opposite poles.

____________

(12 POINTS) To the right is a diagram of a cell at a particular stage of the cell cycle. Use this diagram
to answer the following questions:
(a) Is this cell in meiosis or mitosis? ________________________________
(b) What stage of meiosis or mitosis is it in? __________________________
(c) Is the cell haploid, diploid, or triploid? _____________________________
(d) How many chromosomes are in a gamete from this organism? __________
(e) How many daughter cells will result when this process is completely finished? ___________
(f) What are the likely relative protein levels of the MPF Cyclin? _________________________

4.

5.

(6 POINTS) While working at Sea World, you prepare a karyotype to predict the gender of a fetal
porpoise being carried by a pregnant star performer. You know that porpoises are diploid mammals that
have a haploid chromosome number of 44 (n = 44). Answer each question for the karyotypes below:
(a) How many chromosomes do you expect to find from a fetal cell in G1?

_______________

(b) How many chromatids do you expect to find from a fetal cell in G1?

_______________

(c) How many chromosomes do you expect to find from a cell in metaphase?

_______________

(d) How many chromatids do you expect to find from a cell in metaphase?

_______________

(e) You observe non-homologous sex chromosomes that have dissimilar sizes
and banding patterns. What do you predict will be the gender?

_______________

(f) What are the identities of the fetal sex chromosomes?

_______________

(2 POINTS) List two events during meiosis that give rise to genetic variation that drives evolution.

Page 4

BILD1 / Spring 2007 / FINAL EXAM
Kiger

NAME: _________________________________

PROBLEM 5. Genetics (30 POINTS)
1.

(3 POINTS) (a) In a diploid individual, how many different alleles of a single gene can occur? ________
(b) How many different alleles of a gene can be found in a population of individuals? _______________
(c) If there are 5 possible alleles for a certain gene, how many different genotypes are possible? _____

2.

(9 POINTS) A woman suffering from a genetically-based skin disease had a son and a daughter with a
man who had normal skin. Both children also developed the skin disease. From this information,
suggest possible explanations for recessive and dominant inheritance of this disease.
Indicate ALL the possible combination(s) of parental genotypes and for each, give the expected
genotypes of their diseased children. Use the letters D and d.
If Recessive:

If Dominant:

Possible parental genotypes:

_____________________

_____________________

Genotype of diseased offspring:

_____________________

_____________________

(b) The afflicted son, above, had 8 healthy children (4 normal boys, 4 normal girls) by a woman who did
not have the disease. Altogether, what is the most likely explanation (recessive or dominant) for
inheritance of this disease?
3.

(10 POINTS) Tallness (T) is dominant to dwarfness (t), while red (R) flower color is dominant to white
(r). The heterozygous condition results in pink (Rr) flower color. (a) For the following crosses, indicate
how many phenotypically different progeny can be produced.
Cross A:
Cross B:
Cross C:
Tt Rr x tt rr
TT rr x tt RR
Tt RR x tt rr
Number of phenotypes:

___________

___________

___________

(b) Which cross(es) above (A, B, C) result in progeny that are dwarf with pink flowers?
(c) Determine the probability of progeny that would be dwarf with pink flowers from TtRr x Ttrr.

4.

(4 POINTS) (a) Briefly, what does it mean when it is stated that two genes are linked?
(b) The crossing-over frequency between two genes is 49.6%. Are the genes linked or unlinked? Why?

5.

(4 POINTS) Four babies were born in the hospital on the same night, and the nurse mixes them up!
Given the co-dominance of blood group alleles, use the blood groups of the babies and the possible
parents to help the nurse reassign the babies. Write the blood group of the baby on the line next to to
their correct parents.
Babies: O, A, B, AB
Parents:
O and O_________
AB and O_________
A and B_________
B and B _________

Page 5

BILD1 / Spring 2007 / FINAL EXAM
Kiger

NAME: _________________________________

PROBLEM 6. DNA Heredity and Replication (30 POINTS)
1.

(7 POINTS) Match the letter of the scientific reagents or methods with the most appropriate statement
below. Letters may be used more than once or not at all. Give only one best answer per question.
A.
B.
C.

Mixture of live and dead bacteria
X-Ray diffraction
15
N and 14N
i.
ii.
iii.
iv.
v.
vi.
vii.

2.

D.
E.
F.

32

P and 35S
adenine, thymine, cytosine, guanine
pea plants

______Used to demonstrate that DNA replicates semi-conservatively
______Hershey & Chase used these radioisotopes to label different viral components
______Precisely quantified in different organisms to establish Chargaff’s rule
______Meselson & Stahl used these to label mass of dividing bacterial DNA
______Griffith did this and showed transformation of inheritable material between cells
__ ___Franklin used this to help determine the structure of DNA
______Used to prove that DNA rather than protein contains inheritable information

(12 POINTS) Shown below is a DNA replication fork. On this structure, draw the following items:
(a)
(b)
(c)
(d)
(e)

An arrow below that denotes the overall direction of DNA synthesis.
Indicate the leading strand. Draw in 5’ and 3’ ends.
Indicate the lagging strand. Draw in 5’ and 3’ ends.
Several Okazaki fragments and label them.
Draw a single primase molecule where it would most likely be localized at this stage.

5’

5’
3.

(3 POINTS) Briefly explain this statement: DNA replication is semi-conservative.

4.

(4 POINTS) (a) What is Chargaff’s Rule? (b) How did the Watson-Crick structure of DNA explain the
basis for this rule? Be specific.

5.

(4 POINTS) Explain what happens, and why, when DNA Polymerase utilizes di-deoxy-NTPs (ddNTP).

Page 6

BILD1 / Spring 2007 / FINAL EXAM
Kiger

NAME: _________________________________

PROBLEM 7. Transcription & Translation (30 POINTS)
(Use the genetic code provided on the last page of the exam to help with the following questions.)
1.

(4 POINTS) Both DNA replication and RNA transcription utilize polymerases to form polymers. Provide
two distinct differences between DNA and RNA Polymerase initiation of strand synthesis.

2.

(15 POINTS) You isolate an mRNA highly expressed in brains of stressed rats subjected to maze tests.
(a) Clearly circle the start codon and cross out the stop codon in the mRNA below.

5’-GGUAUGGCAGAGACGUUGGAGUUACAGUGAUUUGCACAA-3’
(b) Write out the polypeptide made by this mRNA. Indicate the N and C termini. Indicate the direction
of translation with an arrow.
(c) Which end of the mRNA would you expect to find a stretch of polyA sequences? _______________
(d) You isolated the gene for the protein described above and found that the DNA coding sequence is
150 base pairs in length. Offer a likely explanation for why the gene is much longer than the mRNA?
(d) How many total activated tRNA molecules are required to make your polypeptide? _____________
(e) You isolate a variant sequence with a single nucleotide change in the first codon. You try but fail to
recover a polypeptide expressed from this variant cDNA in bacteria. What is the most likely type of
mutation that occurred (missense, nonsense, silent, frameshift)? Speifically, why are you unable to
express a polypeptide from this particular variant sequence?

3.

(11 POINTS) A protein needs to be synthesized and delivered to the lysosome. Number the steps in
the synthesis of this protein in the order of their occurrence. READ ALL steps before writing!
Ribosome docks on the Endoplasmic Reticulum.
The small ribosomal subunit binds mRNA at the 5’CAP.
The Signal Recognition Particle binds the newly synthesized peptide.
The next activated tRNA is brought to the A site to form peptide bond with MET.
The initiator tRNAMET binds at the start codon, then translocates to the P site.
The mRNA exits the nucleus.
Protein is sorted for destination.
Protein signal sequence is cleaved off.
Protein is inserted in a vesicle for export to the Golgi Apparatus.
Vesicle fuses with the lysosome!!!
The mRNA is spliced.

Page 7

BILD1 / Spring 2007 / FINAL EXAM
Kiger

NAME: _________________________________

PROBLEM 8. Viruses & Bacteria (30 POINTS)
1.

(2 POINTS) As an infectious disease specialist, you encounter a new virus and would like to analyze
its features. You first determine the viral genome contains 24% G and 31% C. From this information
alone, can you determine whether the viral genome is single or double stranded? How do you know?

2.

(4 POINTS) Bacteriophage can reproduce by two different mechanisms. (a) Name each viral life cycle.
(b) State which cycle involves a “prophage” stage. (c) Explain what the term prophage means.

3.

(4 POINTS) (a) What specific protein does a retrovirus like HIV need, as compared to a DNA virus like
herpesvirus, in order to reproduce in human cells? (b) Is this protein encoded in viral or host cell
genomes?

4.

(2 POINTS) A cell is infected with experimentally constructed viral particles composed from HIV capsid
and membrane proteins and an influenza viral RNA genome, in order to target entry of influenza into
specific cell types. The newly infected cells will produce new particles with what combination of parts?
____(a) HIV protein and influenza RNA
____(b) HIV protein and HIV RNA
____(c) a mixture of both HIV and influenza protein and RNA
____(d) influenza protein and influenza RNA

5.

(12 POINTS) The bacterial lac operon is an inducible operon negatively controlled by the lacI gene
product (the repressor). Consider the following 4 different E. coli bacterial strains:
Strain 1:
Strain 2:
Strain 3:
Strain 4:

Normal wild-type strain
Carries a mutation in the lacI gene such that repressor cannot bind allolactose
Carries a mutation in operator sequence such that repressor cannot bind
Combines both mutations of Strains 2 and 3

Indicate ON (for expression of lac operon) and OFF (for no expression of the operon) regarding the
ability of each strain to express the lac operon when grown in media containing only lactose or glucose.
Strain
1
2
3
4
6.

+ Lactose
_________
_________
_________
_________

+ Glucose
_________
_________
_________
_________

(6 POINTS) We discussed three methods for introducing genes into bacteria. Briefly describe how each
DNA delivery method works.
A. Conjugation:
B. Transduction:
C. Transformation:

Page 8

BILD1 / Spring 2007 / FINAL EXAM
Kiger

NAME: _________________________________

PROBLEM 9. Gene Regulation and DNA Technology (30 POINTS)
1.

(4 POINTS) (a) What is the basic unit of DNA packaging called? ____________________________
(b) What class of proteins are part of this structure?

____________________________

(c) Name two ways that these proteins are reversibly modified, and their affects on chromatin structure.

2.

(2 POINTS) During which phase of the cell cycle does the greatest degree of DNA folding occur?

3.

(8 POINTS) List FOUR general ways that a cell can regulate the amount of a particular enzyme
(besides direct regulation of enzyme activity)?

100 bp
4.

(8 POINTS) You are given the above DNA fragment to cut with restriction
enzymes. You first digest it with the enzyme HindIII, then you separate the
fragments based on size using gel electrophoresis. Draw a picture, using
the gel lane on the right, of what your fragments would look like on the gel.
Label the approximate sizes of the fragments. Add in the + and – poles of
the gel.

5.

(2 POINTS) Let’s say you wanted to amplify the AvaII-SmaI restriction fragment above using PCR.
Draw on the picture above to show where you would have your PCR primers placed to specifically
amplify this region. Use ARROWS ( ) to represent your primers and their required 5’ 3’ orientation.

6.

(2 POINTS) Why is denaturation the first step during PCR?

7.

(2 POINTS) You want to genetically engineer bacteria to express the human insulin gene. Name TWO
types of enzymes you would need to clone the insulin gene into a bacterial plasmid and briefly indicate
their function.

Page 9

BILD1 / Spring 2007 / FINAL EXAM
Kiger

NAME: _________________________________

PROBLEM 10. TRUE/FALSE (30 POINTS)
Circle either TRUE or FALSE for each statement.
TRUE / FALSE

1.

Sister chromatids are attached at the centrosome.

TRUE / FALSE

2.

Meiosis and Mitosis both use the same cytoskeletal structure to separate DNA.

TRUE / FALSE

3.

There is no DNA replication step between Meiosis I and Meiosis II.

TRUE / FALSE

4.

Independent assortment of chromosomes occurs during Meiosis.

TRUE / FALSE

5.

Homologous chromosomes are completely identical.

TRUE / FALSE

6.

In anaphase of mitosis, 1 chromosome is 1 chromatid.

TRUE / FALSE

7.

DNA is replicated with high fidelity only in eukaryotes.

TRUE / FALSE

8.

If two genes are tightly linked, crossing over between the genes is unlikely.

TRUE / FALSE

9.

Activated tRNAs enter at the E site on ribosomes.

TRUE / FALSE

10.

Translation starts at the codon AUG.

TRUE / FALSE

11.

The ribosome and spliceosome use non-coding RNAs

TRUE / FALSE

12.

GTP is needed for translation.

TRUE / FALSE

13.

The ribosome synthesizes proteins in the direction from the N to C terminus.

TRUE / FALSE

14.

Operons are found in both prokaryotes and eukaryotes.

TRUE / FALSE

15.

Operons often contain genes involved in related synthesis pathways.

Extra Credit. (15 POINTS)
1.

(5 POINTS) A single-stranded viral genome is 18,000 bases in length. If we assume the average size of
a protein is 300 amino acids, calculate the greatest number of proteins specified by this genome? (No
calculators allowed, nor necessary!)

2.

(5 POINTS) Cystic fibrosis (CF) is inherited as a simple autosomal recessive in humans at the
occurrence of 1/2000 live births in the United States. Down’s Syndrome (DS) is inherited as a result of
non-disjunction, at an occurrence of 1/600 live births in the United States. A couple (both normal) gave
birth to one normal child, and then later, to another child that suffered from the rare and unfortunate
occurrence of both CF and DS.
(a) What is the probability that any additional child from this couple will be born with CF? Why?
(b) What is the probability that any additional child will be born with DS (think about it!)? Why?

3.

(5 POINTS) (a) On what form of DNA did Rosalind Franklin initially focus her careful structural studies?
(b) What experimental (‘wet lab’) work did Watson & Crick do to help solve the structure of DNA?

Page 10

BILD1 / Spring 2007 / FINAL EXAM
Kiger

NAME: _________________________________

The Genetic Code

THE END!!
Have a great Summer!
You can pick up your exam after June 19th
outside of NSB 6109.