Biology 107, Fall 2022

Midterm #2
Review Question Answers

These questions are designed to provide you some extra opportunities to practice for
our second Midterm, which covers Topics 5 (The Central Dogma, Parts A and B), 6
(The Membrane), and 7 (Internal Cell Structures) and to review the material from these
topics. These questions are for review and do not represent the exact style or
distribution of the questions that will be found on the Midterm.

The most effective way to use these questions is to do them like a practice test, then
check your answers against the answer key posted in Mêskanâs. This strategy will help
you to identify which areas may require more review.

Definitions:

1. Heredity: The transmission of traits from one generation to the next.

2. Chromosome: A structure in cells that is comprised of DNA and protein.

3. Transformation: Change in cell traits due to uptake of external DNA by a cell.

4. Bacteriophage: A virus that infects bacteria.

5. Radioactive Isotope: An unstable form of an element that emits detectable energy.

6. Semi-conservative Replication: Mechanism of DNA replication where the two

strands of DNA are separated, and each parental strand acts as a template to create
a new strand of DNA.

7. DNA Polymerase: Enzyme that incorporates new nucleotides onto the 3’ end of a
growing DNA molecule during DNA replication.

8. Gene Expression: The process by which DNA directs the synthesis of proteins.

9. Transcription: The synthesis of RNA by copying of a DNA template.

10. RNA Polymerase: Enzyme that incorporates new RNA nucleotides onto the 3’ end of
a growing RNA molecule during transcription.

11. Promoter: Specific sequence of DNA where RNA polymerase binds and begins
transcription.

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12. Terminator: Specific sequence of DNA where RNA polymerase falls off template and
ends transcription.

13. Pre-mRNA: The initial RNA transcript before additional modifications have been
made.

14. Mature mRNA: A eukaryotic mRNA that has undergone processing, and is ready for
translation.

15. Introns: Intervening sequences that do not encode proteins.

16. Exons: Expressed sequences that do encode proteins.

17. Spliceosome: Enzyme that cuts out introns from pre-mRNA, and joins together
exons, to form an mRNA transcript that is ready to be used in eukaryotic translation.

18. Translation: The synthesis of a polypeptide using the information encoded in an

mRNA molecule.

19. Codon: A three-letter sequence of DNA or RNA that specifies a particular amino
acid.

20. Reading frame: The way a cell’s translation machinery groups the mRNA
nucleotides into codons during protein synthesis.

21. Start codon: A three-letter codon present at the beginning of all open reading
frames, which signals the initiation site for translation. This codon (AUG) also
encodes the amino acid methionine.

22. Stop codon: One of 3 three-letter codons which does not encode an amino acid, but
instead signals the termination site for translation. All open reading frames end with
a stop codon.

23. Template strand: The DNA strand that acts as the template for RNA synthesis during
transcription.

24. Non-template strand: The DNA strand that has the same sequence as the RNA
molecule produced during transcription.

25. Untranslated region: Any region of an mRNA transcript that is not translated into a
polypeptide sequence. UTRs are found at the 5’ end and 3’ end of mRNA
transcripts.

26. Anticodon: Three ribonucleotides on one end of a tRNA molecule that recognizes a
specific complementary codon on the mRNA molecule.

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27. Amphipathic: A molecule having both hydrophobic and hydrophilic regions.

28. Fluid-mosaic model: The model of plasma membrane structure that says that the
membrane is a mosaic of amphipathic proteins inserted into a fluid bilayer of
phospholipids.

29. Integral membrane protein: Protein that resides within the hydrophobic core of the
lipid bilayer (usually they span the bilayer).

30. Peripheral membrane protein: Protein that is loosely bound to the surface of the
membrane through lipid or protein attachment.

31. Glycoprotein: A membrane carbohydrate attached to an integral membrane protein

on the outside surface of the cell.

32. Glycolipid: A membrane carbohydrate attached to the head group of a phospholipid

on the outside surface of the cell.

33. Selectively permeable: Means a membrane is permeable to only some types of

molecules and prevents the movement of other types of molecules across the
membrane.

34. Passive transport: Movement of a substance down its concentration or

electrochemical gradient; releases energy.

35. Active transport: Movement of a substance against its concentration or

electrochemical gradient; requires energy input.

36. Diffusion: The tendency of molecules to spread out into available space. This is a
passive (energy-releasing) process.

37. Concentration gradient: The range of concentrations of substances across a given

area.

38. Facilitated diffusion: Diffusion of substances that usually are unable to cross the
plasma membrane, aided by transport proteins.

39. Osmosis: Diffusion of water across a selectively permeable membrane.

40. Hypertonic: When comparing two solutions, it is the solution with the higher
concentration of solutes.

41. Hypotonic: When comparing two solutions, it is the solution with the lower
concentration of solutes.

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42. Isotonic: When comparing two solutions, both have the same concentration of
solutes.

43. Electrochemical gradient: A combination of chemical gradient (or concentration

gradient) of a substance and the electrical gradient (or membrane potential) that
exists across biological membranes.

44. Membrane potential: A separation of charges (or voltage) across the membrane.

45. Primary active transport: Active transport in which the transport protein directly
breaks down ATP to provide energy for transport.

46. Electrogenic pump: An active transporter that generates an electrochemical

gradient as it pumps its substrate across the cell membrane.

47. Secondary active transport: Active transport in which the energy is provided by a
facilitated diffusion of an ion gradient.

48. Symport: Type of secondary active transport in which the ion and solute to be
transported move in the same direction.

49. Antiport: Type of secondary active transport in which the ion and solute to be
transported move in opposite directions.

50. Vesicle: A small, membrane-bounded compartment in the cytoplasm.

51. Exocytosis: Process by which cells secrete proteins and other molecules by the
fusion of vesicles with the plasma membrane.

52. Phagocytosis: Endocytosis in which cells engulfs particles using pseudopodia,

forming new vesicles from the plasma membrane.

53. Pinocytosis: Endocytosis in which the cell non-specifically engulfs extracellular fluid,
forming new vesicles from the plasma membrane.

54. Receptor-mediated endocytosis: Endocytosis in which uptake of a specific substrate

is mediated by interaction with a receptor protein in the membrane. This method is
used for uptake of high concentrations of specific substrates.

55. Cytosol: The semi-fluid portion of the cytoplasm.

56. Nucleoid: Region of the prokaryotic cytoplasm where the chromosome is located.

57. Plasmid: Small circular piece of self-replicating DNA that is found in some bacterial
cells in addition to their chromosome.

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58. Cytoplasm: All the cellular contents (organelles and cytosol) between the nuclear
and plasma membranes.

59. Organelle: Membrane-bound structure inside the cell; has a different internal
environment and unique function when compared to the surrounding cytosol.

60. Nuclear envelope: Double membrane system that encloses the eukaryotic nucleus.

61. rRNA: RNA molecules that are combined with ribosomal proteins to form ribosomal
subunits.

62. Hydrolytic enzyme: An enzyme that catalyzes a hydrolysis reaction to break down
complex molecules.

Review Tables:
1. Eukaryotic Organelles: You should be able to fill in this table, and label each of
these structures on a diagram of a eukaryotic cell.)
Organelle General Structure General Function

Double membrane Directs activities of the cell.

separated by perinuclear Contains the DNA.
space.
Contains pores lined with
protein complex.
Nucleus Nuclear lamina inside
envelope maintains nuclear
shape.
Contains chromosomes,
condensed by histone
proteins.

Two subunits, both Protein synthesis

composed of rRNA and
Ribosome
ribosomal proteins.
May be free or bound.

Smooth ER Network of membrane Lipid synthesis,

tubules and sacs detoxification of poisons.
(cisternae). ER membrane
continuous with nuclear

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 envelope.

Same as for, and Protein synthesis and

continuous with, the smooth modification.
Rough ER
ER; studded with bound
ribosomes.

Flattened sacs (cisternae) Modification and sorting of

of membrane stacked proteins.
Golgi Apparatus together.
Has two faces (cis and
trans).

Membrane-bound sac Digestion of

Lysosome containing hydrolytic macromolecules (food or
(animal cells only) enzymes. damaged organelles).
Low pH.

Large sac of membrane. Storage (energy, metabolic

wastes, pigments,
Central Vacuole defensive compounds,
(plant cells only) water).
May have similar function to
lysosomes for plant cells.

Double membrane, Site of cellular respiration:

separated by generates ATP using
intermembrane space. energy from sugars, in a
Inner membrane has process requiring O2.
Mitochondria infoldings called cristae,
and contains enzymes for
(all eukaryotic cells) respiration and ATP
synthesis.
Inside is matrix, which
contains enzymes,
ribosomes, and DNA.

Chloroplast Double membrane, Site of photosynthesis:

separated by using the suns’ energy to
(photosynthetic eukaryotes intermembrane space. produce sugar and O2 from
only – plants and algae) Inside is stroma, which CO2 and H2O.
contains enzymes,
ribosomes, DNA, and

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 thylakoids.
Thylakoids are surrounded
by the thylakoid membrane,
and are stacked together.

Multiple Choice Questions:

1. If radioactive sulfur (35S) is used in a culture medium of bacteria that contains

bacteriophage viruses, it will later appear in the
a) viral DNA
b) bacterial RNA
c) viral protein coat
d) viral RNA
e) bacterial cell wall

2. In an analysis of the nucleotide composition of DNA, which of the following is true?

a) A=C
b) A=G and C=T
c) A+C = G+T
d) A+T = G+C
e) Both B and C are true

3. DNA replication is called semiconservative because _______________ of the

original duplex appears in the duplex formed in replication.
a) none
b) most
c) half
d) hardly any
e) all
4. What is the percentage of adenines in a piece of double stranded DNA if the
percentage of cytosine is 30%?
a) 30%
b) 20%
c) 60%
d) 40%
e) Unable to calculate with the information provided.

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5. An actively dividing bacterial culture is grown in a medium containing radioactive
adenine (A*). After all the adenine is labeled, the bacteria are transferred to a
medium containing nonradioactive adenine (A). Following one round of DNA
replication in the nonradioactive medium, the DNA is analyzed. Which of the
following sequences could represent this DNA?
a) 5’-A* A* T T G A* T C -3’
3’-T T A A C T A G -5’
b) 5’-A* A T T G A* T C -3’
3’-T T A* A* C T A G -5’
c) 5’-A A T T G A T C -3’
3’-T T A A C T A G -5’
d) 5’-A* A* T T G A* T C -3’
3’-T T A* A* C T A* G -5’
e) E) None of the above

6. RNA differs from DNA in that RNA:

a) contains ribose as its sugar
b) is found only in the cytoplasm
c) contains uracil instead of cytosine
d) A and C are correct
e) A, B, and C are correct

7. In nucleic acids, the phosphate group is attached to the _______________ carbon

of the sugar.
a) 5'
b) 4'
c) 3'
d) 2'
e) 1'

8. Which of the following statements is FALSE about the central dogma?

a) Transcription uses a DNA template to make RNA
b) Transcription can synthesize DNA from an RNA template
c) Transcription occurs in the cytoplasm in all organisms
d) More than one, but not all, of these statements is false
e) All of these statements are false

9. The sequence of one strand of a DNA fragment is:

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 5'-ATGCGTGACTAATTCG-3'
Which of the following is the CORRECT double-stranded sequence?

a) 5'-ATGCGTGACTAATTCG-3'
3'-TACGCACTGATTAAGC-5'

b) 5'-ATGCGTGACTAATTCG-3'
5'-TACGCACTGATTAAGC-3'

c) 5'-ATGCGTGACTAATTCG-3'
3'-TUCGCUCTGUTTUUGC-5'

d) 5'-ATGCGTGACTAATTCG-3'
3'-ATGGCACTGATTAAGC-5'

e) 5'-ATGCGTGACTAATTCG-3'
3'-UACGCACUGAUUAAGC-5'

10. Which of the following is NOT CORRECT?

a) In prokaryotic cells, translation of an mRNA into protein can begin even while the
3' end is still being transcribed from DNA
b) In eukaryotes the 5' end cap contains a modified G nucleotide
c) In eukaryotic mRNA, there is a poly-U sequence at the 3’ end
d) The initial steps in the processing of all eukaryotic pre-mRNA transcripts occur at
the two ends, and the modifications are retained in mRNAs.
e) All of the above are correct

11. If proteins were composed of only 12 different amino acids, what would be the
smallest possible codon size in a genetic system with four different nucleotides?
a) 1
b) 2
c) 3
d) 4
e) 12

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12. A possible sequence of nucleotides in the template strand of DNA that would code
for the polypeptide sequence phe-leu-ile-val would be (note that on the quiz, the
genetic code table will be provided for you):
a) 5’-TTG-CTA-CAG-TAG-3’
b) 3’-AAC-GAC-GUC-AUA-5’
c) 5’-AUG-CTG-CAG-TAT-3’
d) 3’-AAA-AAT-ATA-ACA-5’
e) 3’-AAA-GAA-TAA-CAA-5’

13. A DNA sequence (3’-AGA GAG AGA GAG AGA GAG-5’) was mutated to
3’-AGA AGA GAG ATC GAG AGA-5’ (in the template strand). What amino acid
sequence will be generated based on the mutated DNA?
a) arg glu arg glu arg glu
b) glu arg glu leu leu leu
c) ser leu ser leu ser leu
d) ser ser leu
e) leu phe arg glu glu glu

14. A particular eukaryotic protein is 300 amino acids long. How many nucleotides are
needed in the corresponding DNA sequence to encode the sequence of amino acids
in this protein?
a) 3
b) 100
c) 300
d) 900
e) 1,800

15. All of the following could be found in the prokaryotic messenger RNA except:
a) the AUG codon
b) the UGA codon
c) introns
d) uracil
e) cytosine

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16. Ribosomes contain which of the following?
a) tRNA
b) rRNA
c) Protein
d) Both A and C
e) Both B and C

17. Which of the following will cause an increase in the fluidity of a bacterial membrane
at colder temperatures?
A. saturated fatty acids
B. cholesterol
C. unsaturated fatty acids
D. triglycerides
E. carbohydrate side chains

18. Biological membranes form because phospholipids:

A. are hydrophilic
B. contain saturated fatty acids
C. have bends in their fatty acid tails
D. are amphipathic
E. contain hydrocarbons

19. The sucrose-H+ cotransporter protein provides an example of:

A. a pumping protein
B. passive transport
C. facilitated diffusion
D. osmosis
E. secondary active transport

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20. All of the following statements about membrane structure and function are true
EXCEPT:
A. diffusion, osmosis, and facilitated diffusion do not require any energy input
from the cell
B. voltage across the membrane depends on an unequal distribution of ions
across the plasma membrane
C. special membrane proteins can transport two solutes by coupling facilitated
diffusion with active transport
D. diffusion of gases is faster in air than across membranes
E. both sides of a membrane are identical in structure and function

21. All of the following membrane activities require ATP energy EXCEPT:
A. active transport
B. Na+ ions moving out of the cell
C. proton pumps
D. facilitated diffusion
E. endocytosis

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22. A patient had a serious accident and lost a lot of blood. In an attempt to replenish
body fluids, a large amount of water was transferred directly into one of his veins.
What will be the most probable result of this transfusion?
A. it will have no unfavorable effect as long as the water is free of bacteria
B. it will have serious consequences, because there will be too much fluid for the
heart to pump.
C. it will have serious consequences because the red blood cells will be
hypertonic relative to the body fluids and will burst.
D. it will have serious consequences because the red blood cells will be
hypotonic relative to the body fluids and will burst.
E. it will have serious consequences because the red blood cells will be
hypertonic relative to the body fluids and will shrivel.

23. Which of the following characterizes the sodium-potassium pump?

A. sodium ions are pumped out of the cell against their gradient
B. potassium ions are pumped into a cell against their gradient
C. the pump protein undergoes a conformational change
D. only A and C are correct
E. A, B, and C are all correct

24. Membrane proteins are involved in all of the following functions EXCEPT:
A. cell-cell recognition
B. intracellular joining
C. attachment to the cytoskeleton
D. storage of amino acids
E. transport

25. Which of the following statements IS CORRECT in describing all the different
classes of transport proteins?
A. all transport proteins are transmembrane proteins.
B. energy is required by all transport proteins to move molecules across the cell
membrane.
C. all transport proteins use ATP to move molecules across the cell membrane.
D. transport proteins always move molecules against their concentration
gradients.
E. molecules always move down their concentration gradients through transport
proteins.

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26. Which of the following statements concerning the movement of molecules across the
membrane via simple diffusion is correct?
1) The rate of movement depends on the hydrophobicity of the molecule.
2) The rate of movement is faster in comparison to facilitated diffusion.
3) Molecules can move against their concentration gradient.
4) A specific protein is required for the movement of a specific molecule via
simple diffusion.
5) The rate of movement depends on the concentration gradient.

A. 1, 2, 3
B. 1, 5
C. 1, 4, 5
D. 2, 3, 4, 5
E. 2, 4

27. When placed in a hypotonic solution:

A. an animal cell would be unaffected, but a plant cell would be flaccid
B. an animal cell would burst but a plant cell would not
C. an animal cell would shrivel, and a plant cell would be plasmolyzed
D. both an animal cell and a plant cell would burst
E. both an animal cell and a plant cell would be unaffected

28. Chloramphenicol is a drug that inhibits protein synthesis on prokaryotic ribosomes.

Which of the following cells or cell parts would have protein synthesis inhibited if
they were grown in the presence of chloramphenicol?
A. bacteria only
B. mitochondria only
C. chloroplasts only
D. b and c are correct
E. a, b, and c are correct

29. Which of the following would not be found in a prokaryotic cell?

A. nucleoid region
B. cell wall
C. transport vesicle
D. ribosome
E. rRNA

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30. Which of the following is not enclosed by a double membrane?
A. the eukaryotic nucleus
B. mitochondria
C. chloroplast
D. lysosome
E. both A and D

31. Which of the following is a property not shared by mitochondria and chloroplasts?
A. they both contain thylakoids
B. they both arose from an endosymbiotic event
C. they both contain their own DNA
D. they are both bound by a double membrane
E. they both can divide autonomously within the cell

32. The nuclear lamina is an array of filaments on the inner side of the nuclear
membrane. If a method were found that could cause the lamina to fall into disarray,
what would you expect to be the most likely consequence?
A. the loss of all nuclear function
B. the inability of the cell to withstand enzymatic digestion
C. a change in the shape of the nucleus
D. failure of chromosomes to carry genetic information
E. inability of the nucleus to keep out destructive chemicals

33. Which type of organelle is primarily involved in the synthesis of oils, phospholipids,
and steroids?
A. ribosome
B. lysosome
C. smooth endoplasmic reticulum
D. mitochondrion
E. contractile vacuole

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34. The Golgi apparatus has a polarity or sidedness to its structure and function. Which
of the following statements correctly describes this polarity?
A. Transport vesicles enter one side of the Golgi and leave from the opposite
side.
B. Proteins in the membrane of the Golgi may be sorted and modified as they
move from one side of the Golgi to the other.
C. Lipids in the membrane of the Golgi may be sorted and modified as they
move from one side of the Golgi to the other.
D. Soluble proteins in the cisternae (interior) of the Golgi may be sorted and
modified as they move from one side of the Golgi to the other.
E. All of the above correctly describe polar characteristics of the Golgi
function.

35. Which of the following is a compartment that often takes up much of the volume of a
plant cell?
A. lysosome
B. vacuole
C. mitochondrion
D. Golgi apparatus
E. chloroplast

36. Which of the following modifies polysaccharides that will be secreted from the cell?
A. lysosome
B. vacuole
C. mitochondrion
D. Golgi apparatus
E. peroxisome

37. Which of the following contains its own DNA and ribosomes?
A. lysosome
B. vacuole
C. mitochondrion
D. Golgi apparatus
E. endoplasmic reticulum

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38. Which statement is CORRECT?
A. prokaryotic cells have cell walls, but eukaryotic cells do not.
B. prokaryotic cells have a very small nucleus.
C. prokaryotic cells have internal membranes.
D. all prokaryotic and eukaryotic cells have a plasma membrane that
controls which organic molecules and ions can enter the cell.
E. Gram-positive bacteria have an inner membrane that functions as the plasma
membrane and an outer membrane outside of the cell wall.

39. Which of the following organelles is not part of the endomembrane system?
A. nuclear envelope
B. Golgi apparatus
C. ER
D. plasma membrane
E. chloroplast

40. Which of the following statements describe similarities between plant and animal
cells? Both types of cells have….
1) a cytoskeleton.
2) a cell wall.
3) mitochondria.
4) a central vacuole.
5) a plasma membrane.
A. 2, 3
B. 3, 5
C. 2, 4
D. 1, 3, 5
E. 2, 4, 5

41. The rough endoplasmic reticulum is required for the synthesis of which of the
following?
A. phospholipids
B. DNA
C. cytosolic proteins
D. RNA
E. lysosomal enzymes

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Short Answer Questions:

1. For each of the following scientists, use 3-4 sentences to explain their experiment(s)
and the conclusion(s) they reached involving DNA. (4 marks each)

A. Griffith: He studied the ability of different strains of S. pneumoniae bacteria to

infect and kill mice. Control experiments showed that the S (smooth) strain was able
to kill mice, while the R (rough) strain and the heat-killed S strain were unable to kill
mice. However, when heat-killed S bacteria were mixed with live R bacteria, the R
cells were transformed into S cells and were able to kill the mice. He concluded that
the S bacteria contain a heat-stable component that was able to be transferred to
the R bacteria, and conferred the ability to kill mice.

B. Avery, MacLeod, and McCarty: They repeated Griffith’s experiment by taking

heat-killed S cells and treating samples to remove protein, RNA, or DNA. These
samples were then mixed with live R cells, and properties of the treated R cells were
tested. He found that in samples that contained DNA (but lacked either RNA or
protein) R cells were transformed into S cells, but samples that lacked DNA were
unable to transform R cells into S cells. He concluded that the transforming material
that carries the information needed to covert nonvirulent R cells into virulent S cells
is DNA.

C. Hershey and Chase: They prepared radioactively-labeled bacteriophage

(bacterial viruses) in which either the DNA was labeled with 32P or the protein was
labeled with 35S. The labeled bacteriophage were used to infect bacteria, the
unincorporated viral components were removed from the bacterial cells with a
blender, and the bacteria were separated from the viral components using
centrifugation. They found that the 32P-labeled viral DNA was found in the bacterial
pellet, indicating that it had been inserted into the bacterial cells, while the 35S-
labeled viral protein was found only in the supernatant, indicating that it did not enter
the bacterial cells. They concluded that the viral DNA was the component that
entered the bacterial cells and provided the instructions to reprogram the bacteria,
and therefore DNA is the hereditary material.

2. Explain why a mixture of heat-killed smooth cells and living rough cells of S.
pneumoniae is able to kill mice. (2 marks)

The DNA released during the heat killing of the smooth cells encodes the
information needed to direct the killing of the mice (the ability to cause an infection).
This DNA is taken up by the living rough cells, and gives them the genetic ability to

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 cause an infection in mice. This in effect converts the rough cells into smooth cells,
and allows them to cause a lethal infection in the mice.

3. In a bacteriophage, what does 35S label? What does 32P label? Explain why.
(3 marks)

The 32P labels only the DNA component of the bacteriophage, because only DNA
and not protein contains phosphorous. The 35S labels only the protein coat of the
bacteriophage, because only protein and not DNA contains sulfur.

4. Name the 2 purines and the 2 pyrimidines in DNA. How many rings does each type
of nitrogenous base have? (3 marks)

The two purines are adenine and guanine, and they each contain two rings. The two
pyrimidines in DNA are cytosine and thymine, and they each contain one ring. [Note
that uracil is also a pyrimidine and contains 1 ring, but it is found only in RNA, not in
DNA.]

5. What is Chargaff’s rule? If the DNA of an organism is 16% adenine, what

percentage guanine would it be? (2 marks)

Chargaff’s rule is that in DNA the amount of adenine always equals the amount of
thymine, and the amount of guanine always equals the amount of cytosine.

If an organism contains 16% adenine, then it must also contain 16% thymine, 34%
guanine, and 34% cytosine.

6. Describe the three major pieces of existing knowledge or evidence used by Watson
and Crick to solve the structure of DNA. (3 marks)

a) Chargaff’s rules: A=T and G=C, but A+T not equal to G+C

b) Knew the chemical composition of DNA (nucleotides containing nitrogenous

bases, ATGC)

c) X-ray diffraction data suggested a helical molecule gave some information about
distances between atoms

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7. Identify the components that make up the backbone of each DNA strand, and
describe how are they attached together. (2 marks)

The DNA backbone is composed of the pentose sugar (deoxyribose) and the
phosphate group of the nucleotides. They are attached together by covalent bonds
that form between the 3’ hydroxyl group of one deoxyribose and the 5’ phosphate
group attached to the next deoxyribose. This linkage is known as a phosphodiester
bond.

8. Describe the hydrogen bonding that occurs in the DNA double helix. (2 marks)

Hydrogen bonding in DNA occurs between the paired nitrogenous bases on the
interior of the DNA double helix. These hydrogen bonds therefore hold the two
strands of DNA together. There are two H-bonds in the A-T base pair, and there are
three H-bonds in the C-G base pair.

9. Explain what is meant by the terms 3’ and 5’ with respect to a nucleic acid strand.
(2 marks)

A nucleic acid strand (DNA or RNA) has two distinct ends. At the 5’ end, a free
phosphate group is attached to the 5’ carbon of the pentose sugar. At the 3’ end,
there is a free hydroxyl group attached to the 3’ carbon of the pentose sugar.

10. Describe the source of the energy used to form phosphodiester bonds during DNA
replication. (1 mark)

Energy comes from the hydrolysis of the triphosphate group of the incoming
nucleotide, which releases a pyrophosphate group that is further broken down into
two inorganic phosphate molecules.

11. State the central dogma of molecular biology. (2 marks)

The central dogma states that the transfer of information in the cell from DNA to
protein occurs in two steps: first information is transferred from DNA to RNA by
transcription, and then that information is transferred from RNA to protein by
translation.

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12. Name the different types of RNA molecules found in the cell. Describe the
similarities and differences between them. (3 marks)

Types: messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA)

All are similar in that they all have the same chemical composition (made of the four
ribonucleotides A, U, G, and C) are produced by transcription from the DNA.

The main difference is in the function of the different types of RNA. Only mRNA
encodes proteins; the other types of RNA play structural and/or enzymatic roles.

13. Describe the role of the promoter in the process of transcription. (2 marks)

The promoter is a specific sequence of the DNA that indicates where the RNA
polymerase should bind, where the process of transcription should start.

14. If you changed the DNA sequence of a promoter, how would this affect the ability of
the cell to transcribe the corresponding gene? Explain your answer. (2 marks)

It could prevent the gene from being transcribed. The promoter sequence tells the
RNA polymerase where to bind. If this sequence is changed, the RNA polymerase
may be unable to bind anymore, preventing transcription from occurring.

15. Briefly describe the events that occur during the process of transcription. (3 marks)

First, RNA polymerase binds to the DNA at the promoter and separates the DNA
helix, exposing the single-stranded template strand.

Next, RNA polymerase moves down the DNA template and elongates the RNA
transcript adding new ribonucleotides (G, C, A, or U) to the 3’ end of the transcript
based on complementary base-pairing to the DNA template.

Last, the RNA polymerase reaches a terminator sequence in the DNA, which causes
the completed RNA transcript to be released and the RNA polymerase to detach
from the DNA.

16. Describe the source of the energy used to form phosphodiester bonds during
transcription. (1 mark)

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 The energy that powers RNA synthesis comes from the hydrolysis of the
triphosphate group of the incoming ribonucleoside triphosphate (NTP), first to
pyrophosphate and then to two molecules of inorganic phosphate. This is very
similar to the way that DNA synthesis is powered during replication.

17. Describe the differences in the process of gene expression between prokaryotes
and eukaryotes. Explain the reasons that these differences exist. (4 marks)

In prokaryotic cells, both transcription (mRNA synthesis) and translation (mRNA use)
occur in the cytoplasm. In addition, nothing must be done to the mRNA before it can
be used in translation (no processing). This means that in prokaryotes, transcription
and translation are coupled; in other words, translation of the 5’ end of an mRNA
molecule can begin while the 3’ end of the same mRNA molecule is still being
transcribed from the DNA.

In eukaryotic cells, transcription occurs in the nucleus while translation occurs in the
cytoplasm. Before the mRNA can be used in translation, it must be modified
(processed) and then transported out of the nucleus into the cytoplasm. This
requirement means that transcription and translation are separated in both time
(before vs. after processing) and location (nucleus vs. cytoplasm), and are not
coupled as seen in prokaryotes.

18. Describe the modifications that are made to the ends of eukaryotic mRNAs, and
explain the function of each of these modifications. (4 marks)

5’ cap: A modified guanine nucleotide is added to the 5’ end of the transcript. This
cap functions to protect the RNA from degradation, and aids in attachment to the
ribosome.

3’ Poly-A tail: 50-250 adenine nucleotides are added to the 3’ end of the transcript.
This tail functions to protect the RNA from degradation, and aids in export of the
transcript from the nucleus to the cytoplasm.

19. Briefly describe the process of mRNA splicing. (3 marks)

The process of mRNA splicing is the removal of introns from the pre-mRNA and the
joining together of the remaining exon sequences to form a mature mRNA transcript
with a continuous coding sequence. This process is catalyzed by an enzyme
complex called the spliceosome.

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20. Briefly describe the roles of the tRNA and the ribosome in translation. (3 marks)

The role of the tRNA is to carry the correct amino acid to the ribosome. The role of
the ribosome is to accept the amino acids from the tRNA and attach them into a
polypeptide by forming peptide bonds, with the order of the amino acids determined
by the sequence of the mRNA.

21. Describe the composition of a ribosome. (2 marks)

A ribosome is made of two subunits, a small subunit and a large subunit. Each
subunit is a complex of proteins and rRNA molecules.

22. Given the mRNA sequence 5’-AUG-GAU-GGA-CUU-ACA-CCG-UAG-3’, predict the

amino acid sequence.

(N-terminus) – Met – Asp – Gly – Leu – Thr – Pro – (C-terminus)

23. Given the template DNA sequence 3’-TAC-GCA-TTG-GTA-CAC-CCT-ATT-5’,

predict the mRNA sequence and the subsequent amino acid sequence.

mRNA: 5’-AUG-CGU-AAC-CUA-GUG-GGA-UAA-3’

Protein: (N-terminus) – Met – Arg – Asn – Leu – Val – Gly – (C-terminus)

24. Draw the structure of a processed eukaryotic mRNA and label all of its parts.

start codon
G 5’ UTR ORF 3’ UTR AAAAAA
stop codon

G = 5’ cap
5’ UTR = the 5’ untranslated region
ORF = open reading frame
3’ UTR = the 3’ untranslated region
AAAAA = the 3’ poly-A tail

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25. A eukaryotic gene is approximately 8000 nucleotides long. It encodes a protein that
consists of 400 amino acids. Explain the discrepancy between the size of the gene
and the size of the protein.

This gene is made up of both introns (intervening sequences) and exons (expressed
sequences). During mRNA processing in eukaryotes, the introns are removed from
the transcript by the spliceosome and the exons are joined together. The resulting
mRNA transcript, composed only of exons, would contain an open reading frame
(ORF) of 1200 nucleotides, which would encode a 400 amino acid protein.

26. The following questions deal with the directionality of transcription and translation:

a. In which direction is mRNA generated (i.e. 3’ → 5’ or 5’ → 3’)?

5’ → 3’

b. In which direction does RNA polymerase move along the TEMPLATE DNA
strand?
3’ → 5’

c. In which direction does the ribosome travel along the mRNA?

5’ → 3’

d. In which direction is a codon read?

5’ → 3’

e. In which direction is a polypeptide synthesized?

N-terminus → C-terminus

f. What end of the protein is coded by the 5’ region of the mRNA?

The N-terminal end

27. a) Describe the phospholipid composition of the membrane of an organism that

lives in extremely cold temperatures. (2 marks)
The bilayer would contain phospholipids with unsaturated hydrocarbon tails. This
would decrease the packing of the phospholipids and would maintain the fluidity
at low temperatures. There might also be sterols (such as cholesterol) to hinder
solidification.

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 b) Imagine that this organism does not have the ability to adjust the phospholipid
composition of the membrane in response to temperature. Describe what you
would expect to occur if this organism was suddenly moved to a much higher
temperature environment. Explain why. (2 marks)

At higher temperatures, this organism’s cell membrane would increase in fluidity

until it became disrupted and the cell contents began to leak across the
membrane. This is because the unsaturated hydrocarbon tails of the
phospholipids are much more fluid at lower temperatures, and are more prone to
be disrupted as temperatures increase.

28. In class, we discussed the role of cholesterol in animal cell membranes. Plant cells
contain a variety of sterols, including the two shown here:
Campesterol Castasterone
INCLUDEPICTURE "https://upload.wikimedia.org/wikipedia/commons/thumb/4/47/Campesterol.png/

1200px-Campesterol.png" \* MERGEFORMATINET
INCLUDEPICTURE "http://img.bocsci.com/structure/80736-41-0.gif" \* MERGEFORMATINET

a) Which of these two plant sterols would you expect to find in the plant cell
membrane? Explain why. (2 marks)

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 Campesterol is found in plant cell membranes. It is mainly non-polar and
hydrophobic (the fused rings and carbon tail), allowing it to interact with the
hydrophobic tails of the membrane phospholipids. The single hydroxyl (-OH)
group would interact with the polar heads of the phospholipids and the aqueous
environment at the surface of the membrane.

b) Describe the role you would predict sterols to play in the plant cell’s membrane,
based on your understanding of animal cells. (2 marks)

At low temperatures, this sterol would insert between the phospholipids in the
membrane, preventing packing and reducing solidification of the membrane. At
high temperatures, this sterol would interact with the tails of the phospholipids,
reducing their movement and limiting membrane fluidity to prevent membrane
disruption.

29. The following is the chemical structure of the amino acid lysine:
INCLUDEPICTURE "https://media.cheggcdn.com/study/7cc/7cc2f2c2-924e-4ab3-bf29-

fad21e91a51e/7077-19-6QP-i5.png" \* MERGEFORMATINET

a) Explain why this molecule would be unlikely to enter the cell via simple diffusion.
(2 marks)

This molecule contains several polar groups as well as three charged groups in
its structure. These groups are unable to interact with the hydrophobic tails of
phospholipids in the middle of the phospholipid bilayer, and would be excluded
from entering the center of the membrane. This prevents the molecule from

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 passing through the phospholipid bilayer portion of the membrane (which is what
occurs in simple diffusion).

b) The concentration of lysine in a cell’s environment is higher than the

concentration in the cell’s cytoplasm. Describe the mechanism by which you
would expect lysine to enter this cell, and explain why it would use this
mechanism. Include as much detail as possible. (5 marks)

The lysine molecule would enter the cell by facilitated diffusion. The following
factors would need to be identified in a complete description of how this process
works and why:
 Passive transport, where the lysine moves down its concentration gradient
without the input of cellular energy. This is possible because the lysine is
in a higher concentration outside of the cell.
 Carrier protein would need to be used. This is because lysine cannot
cross the phospholipid bilayer by simple diffusion (as described above in
(a)), and it is too large to use a channel protein (only used by very small
molecules and ions because it creates an open channel through the
membrane).
 The lysine would bind to the carrier protein specifically (no other
molecules can bind), causing a shape change in the protein that would
allow the lysine to be moved across the membrane into the cytoplasm.
This shape change would not occur for any other molecule (specific) and
does not require energy input from the cell.

30. The following diagram shows the internal structure of an aquaporin protein.
INCLUDEPICTURE "https://askabiologist.asu.edu/sites/default/files/resources/activities/
body_depot/venom/aquaporin_cartoon_large.jpg" \* MERGEFORMATINET

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 a) What types of amino acids would be found in the areas indicated by the blue and
red arrows? Explain why this type of amino acids would be located in each
position. (3 marks)

The red arrow indicates the presence of non-polar amino acids. The non-polar R
groups would interact with the non-polar tails of the phospholipids, helping this
protein to stably pass through the hydrophobic core of the membrane.

The blue arrow indicates the presence of polar amino acids. The polar R groups
would create a hydrophilic channel that would allow polar water molecules to
pass through the non-polar core of the membrane.

b) Explain how this aquaporin protein is different from a carrier protein. (2 marks)

The aquaporin has an open hydrophilic channel which small molecules can pass
through. In theory, any small molecule (the size of water or smaller) and without
a positive charge could diffuse through this channel. It is therefore selective, but
not specific. In contrast, a carrier protein is a closed channel where the molecule
to be transported must bind to a site in the channel to open it up. This binding
site is very specific, meaning only one specific molecule can move through this
protein.

31. Explain why, in passive transport, charged molecules move down their
electrochemical gradient rather than simply their concentration gradient. (2 marks)
Their movement is affected by the membrane potential as well as their concentration
gradients. The outside of a living cell is positively charged and the inside is
negatively charged, so ions will prefer to move to the side of membrane exhibiting
the opposite charge properties (i.e. a positively-charged ion will want to move to the
negatively-charged interior of the cell based on the membrane potential).

32. Active transport requires an input of energy from the cell. Describe the two sources
of energy that can be used in active transport. (4 marks)
ATP is used to power protein pumps in primary active transport. The hydrolysis of
ATP and temporary addition of the released phosphate group to these membrane
proteins causes a change in the protein shape, which allows ions to be transported
across the membrane against their concentration gradients.

Concentration gradients of ions contain large amounts of potential energy, which can
be used to power secondary active transport. The passive diffusion of ions down
their concentration or electrochemical gradient through the transporter protein
releases this energy. The energy can then be used by the transporter protein to

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actively transport another substance against its electrochemical or concentration
gradient. The energy coupling of these processes results in cotransport of
substances.

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33. The following is an image of a transport protein called a sodium-calcium exchanger.
This transporter is used to remove calcium from cells.

Outside Cell:
High [Ca2+]
High [Na+]

Inside Cytoplasm:
Low [Ca2+]
Low [Na+]

Based on the information shown in this diagram, answer the following questions.
a) Identify the type of transport used remove calcium from cells by this transporter
protein. (1 mark)

This is secondary active transport, using an antiport mechanism.

b) Describe the process for how calcium would be exported from the cell using this
transporter, and explain how the energy would be obtained to power this
transport. (4 marks)

The concentration gradient of Na+ ions would act as the energy source. As the
three Na+ ions diffuse into the cell through the transport protein, potential energy
is released. This energy is used by the transport protein to power a shape
change that allows a Ca2+ ion to be taken from the cytoplasm and moved to the
outside of the cell.

The Na+ gradient that powers this process would need to be created by the
action of a primary active transporter (such as the Na+/K+ pump) which uses
energy from the hydrolysis of ATP to pump Na+ out of the cell to create the
concentration gradient.

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34. You are looking at an unknown cell using an electron microscope.Describe how
would you be able to tell if this cell was prokaryotic or eukaryotic. (2 marks)
You would look at the organization of the cellular contents. If the inside of the cell
shows little organization, other than the DNA being clustered into one region of the
cell (i.e. the nucleoid), then the cell is a prokaryote. If the inside of the cell is highly
organized, with the DNA and other cytoplasmic components partitioned into
membrane-bound compartments (i.e. organelles), then the cell is a eukaryote.

35. Do all cells have the same number of each organelle? Explain why or why not.
(2 marks)
No. Cells will adjust the numbers of each organelle depending on individual needs.
For example, cells requiring lots of energy, like muscle cells, will have more
mitochondria; secretory cells will have more bound ribosomes; liver cells will have
more smooth ER for detoxification of poisons; etc.

36. Several antibiotics, such as the antibiotic erythromycin, inhibit the function of the
ribosomes of bacterial ribosomes.
a) Explain why these antibiotics cause the death of bacterial cells. (2 marks)

Ribosomes are the enzymes responsible for protein synthesis. If the ribosomes
are inhibited, the cell can’t make proteins. Without proteins (including
enzymes, transport proteins, and other essential proteins) the cell would be
unable to carry out essential functions (like producing ATP) and would die.

b) Based on your understanding of the endosymbiotic hypothesis, explain why

these antibiotics might cause negative side effects in animal cells. (3 marks)

The endosymbiotic hypothesis states that mitochondria are evolved from

bacteria that were engulfed by larger cells. The ribosomes in the mitochondria
are therefore more closely related to (and more similar to) bacterial ribosomes
than the ribosomes in the eukaryotic cytoplasm. This means that antibiotics
that target bacterial ribosomes may also negatively affect the function of
mitochondrial ribosomes. If the mitochondria are unable to produce proteins
(including enzymes for cellular respiration) properly, the cells will be unable to
produce ATP efficiently. This may negatively affect the function of the animal
cells.

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37. Imagine that the cell is like a factory. What would be the function of each of the
following organelles or structures in the factory? Make and explain an analogy for
each structure listed below:
Nucleus, ribosome, endoplasmic reticulum, Golgi apparatus, lysosome,
mitochondria, chloroplast, vesicle, central vacuole, cell wall, plasma membrane

Example: The nucleus is like the boss of the factory because it directs all the
activities of the cell (factory). (15 marks)

The ribosomes are like the machinery that assembles the product of the factory,
because they are responsible for the physical assembly (synthesis) of proteins.
The ER is like the factory floor or assembly line, because it is the location where the
synthesis of proteins and lipids occurs (the synthesis is actually carried out by the
machinery – the ribosomes and other enzymes).
The Golgi apparatus is like the shipping and receiving centre, because it accepts
transport vesicles from the ER at its cis face, modifies the proteins as they pass
through the Golgi, and then sorts the final proteins and delivers them to their final
destination (such as the plasma membrane or lysosomes) using new transport
vesicles.
The lysosome is like the surplus or recycling depot where old and broken machinery
is taken apart and the components are then able to be recycled and used at other
locations in the factory. In autophagy, the lysosome helps to break down old
organelles and cellular components so that the monomers can be reused to make
new macromolecules.
The mitochondria are like the power plant that provides the power to run the factory.
They take chemical energy (sugars) and convert it into other forms of energy that
can be used to carry out work in the cell.
The chloroplast is like a solar panel on the roof of the factory, which converts light
energy into another form of energy (chemical) that can be used as a power source in
the cell.
The transport vesicles are like the forklifts that carry the contents of the factory from
one location to another (i.e. from the ER to the Golgi).
The central vacuole is like a warehouse that stores a variety of things needed for the
function of the factory, including new components for manufacturing and waste or
byproducts from the manufacturing process. In plant cells, the central vacuole
stores a wide variety of things, including energy reserves, metabolic wastes,
pigments, defensive compounds, and water.

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 The cell wall is like the exterior walls of the factory, which provides a rigid casing that
protects the cell (or factory) from physical stresses of the outside environment (i.e.
osmotic and mechanical stresses).
The plasma membrane is like the security guard that protects the entrances to the
factory and controls who can enter and who cannot. The plasma membrane is a
selective barrier that allows certain types of molecules to enter the cells, and
prevents other types of molecules from accessing the cytoplasm.

38. The lysosomes are an important organelle in the cell, involved in the processes of
autophagy and digestion of food particles brought into the cell by phagocytosis.
a) Explain how the acidic pH would be established in these cells. (2 marks)

There are proton pumps in the membrane of the lysosome. This proton pump
will, using energy from the hydrolysis of ATP, pump protons from the cytosol into
the inside of the lysosome. This will produce the low pH needed for the function
of the lysosome enzymes

b) If the lysosome membrane ruptured and the enzymes found inside were
released into the cytoplasm, describe what would happen to the cell. (2 marks)

Nothing would happen to the cell. The hydrolytic enzymes in the lysosome only
function at an acidic pH. In the neutral pH conditions of the cytosol, these
enzymes will not function, and the contents of the cytosol would not be digested.

c) When humans fast (do not consume food for extended periods of time), the
enzymes in the lysosome that are involved in autophagy become more active.
Explain why this might be an effective response to fasting by our cells.
(2 marks)

During fasting, the nutrients needed for the cell to produce energy and the
macromolecules that make up cell structures are not readily available (because
nutrients are not being taken in from food). By increasing autophagy, old and
defective cell organelles and macromolecules will be broken down more rapidly.
The monomers released from breaking down these cell structures can provide a
nutrient source for the cell’s metabolism.

d) Lysosomal storage diseases, in which one of the lysosome’s hydrolytic enzymes

does not function to degrade a specific macromolecule, are usually fatal to the
cell (and to the organism that has the disease). Explain why this type of disease
would have such a harmful effect to the cell. (2 marks)

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 If the lysosome is lacking an enzyme, the cell will not be able to break down the
macromolecule that corresponds to that specific enzyme. This macromolecule
will accumulate in the cell until the entire cell is full of this molecule. This will
start to interfere with the cell’s ability to function normally, and will eventually
result in cell death.

39. The enzymes used by the Golgi apparatus for modification of proteins travel from the
cis face to the trans face in the Golgi compartments as they are modifying proteins.
Once these enzymes reach the trans face, describe what happens to them to allow
them to be reused by the Golgi apparatus. (3 marks)
In the trans compartment of the Golgi, the Golgi modification enzymes would all be
grouped together during sorting and placed in a transport vesicle. This vesicle
would then be sent backwards from the trans face of the Golgi to the cis face of the
Golgi. At the cis face, this vesicle would fuse with other vesicles coming from the
ER, allowing these Golgi enzymes to be re-used to modify the new proteins coming
from the ER.

40. Beginning at the ribosome, describe the pathway of a secreted protein in a cell.
(5 marks)
The protein is made by bound ribosomes that are attached to the rough endoplasmic
reticulum. As it is produced, the protein enters the ER lumen and may be modified
by enzymes within the ER. Once synthesis is complete, the protein is encapsulated
in a transport vesicle that moves from the ER to the cis face of the Golgi apparatus.
The vesicle fuses with other vesicles to form a Golgi compartment, and modifications
to the protein begin. The protein moves through the Golgi from the cis to the trans
face inside a Golgi compartment. Once all the modifications have been made, the
protein is again encapsulated in a transport vesicle that fuses with the plasma
membrane and the protein is released from the cell by exocytosis.

41. You inject a lipid-soluble compound (i.e. can move through membranes) into the
nucleus of a cell. How many lipid bilayers must it pass through to enter:
A. The thylakoid compartment of a chloroplast? 5
B. The most interior part of a lysosome? 3
C. The inside (lumen) of the endoplasmic reticulum? 1
D. The cytoplasm of the cell? 2
E. The outside of the cell? 3

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42. The endosymbiotic theory explains, in part, the evolution of eukaryotic cells.
a) Explain how the endosymbiotic theory explains the origin of mitochondria and
chloroplasts. (4 marks)

The theory describes an event where two prokaryotic cells began to cohabitate,
with one cell living inside the other, due to an advantage for each in the
relationship. The relationship may have begun in a non-symbiotic way.
Perhaps a smaller prokaryotic cell was a parasite in a larger prokaryote. Or,
perhaps, a larger prokaryote intended to ingest a smaller prokaryote and was
unable to do so. At some point, each prokaryote had attributes which benefited
the other (protection, ability to deal with changing atmospheric conditions,
ability to photosynthesize, etc.). Both cells would reproduce during successive
generations. After many years of co-evolution, the two prokaryotes would
become dependent on one another, with the smaller prokaryote “becoming” a
cellular organelle (mitochondria or chloroplast) inside of a eukaryotic cell
derived from the larger prokaryote.

b) Describe any 2 pieces of evidence that support the endosymbiotic theory.

(2 marks)

A correct response would describe any two of the following pieces of evidence:

1. Mitochondria and chloroplasts reproduce like prokaryotes by binary fission.

2. Mitochondria and chloroplasts have double membranes, and the inner

membranes resemble the composition of the plasma membrane of modern
prokaryotes.

3. Mitochondria and chloroplasts contain a single circular chromosome without

histones, just like prokaryotes.

4. Mitochondria and chloroplasts have their own ribosomes, which are similar in
composition to prokaryotic ribosomes not to cytoplasmic eukaryotic ribosomes.

c) Does this theory explain the origin of the nuclear envelope, which also has a
double membrane structure? Explain your answer. (2 marks)

No, it does not. The nuclear envelope is not thought to have been created by
engulfing a smaller bacterial cell. Instead, the nuclear envelope (and the other
organelles of the endomembrane system, like the ER and Golgi) are thought to
have been formed by the folding in of the plasma membrane of the cell to
create internal membrane structures.

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