Biology 204

Principles of Biology I

Assignment 1A

For students with first names starting with the letters A to G.

This assignment is graded out of 110 points, and is worth 10% of

your final mark. Please submit this assignment after you have
completed Chapter 7 and before you write the midterm exam.

A. Definition/Comparison Questions

Instructions: In your own words, define the pairs of terms given

below. Write in complete sentences, stating the differences and
relationships between the two terms, and give specific examples
where appropriate.
A complete answer usually requires four to eight sentences.

Each question is worth four marks, for a total of 40 marks.

1. eye / eyespot
 eyes are sensory organs of multicellular animals

 eyespots are organelles of Euglena and some other protists that allow
unicellular organisms to perceive light intensity and direction

 eyes are multicellular, more complex, to a degree that requires a brain to

process the information from the eyes

 ocelli as the simplest types e.g. in Planaria

 compound eyes, composed of ommatidia in insects

 complex camera eyes with retina and cornea

2. UV radiation / light
 both a narrow section of electromagnetic radiation

 ER nature as waves and particles (photons)

Principles of Biology I 1
  light visible, 400-700nm, used for photosynthesis

 UV shorter waved, more energy-rich, damages DNA

 UV is absorbed by ozone layer, but some reaches surface

3. endergonic / endothermic
 endergonic reactions have a positive free energy Δ G, which means the
products have more free energy than reactants; non spontaneous

 reaction needs energy (from ATP) to proceed

 endothermic reactions have a positive ΔH = enthalpy;

 the products have more enthalpy than reactants; non spontaneous in

most cases

 however they can be spontaneous if there is a strong increase in entropy

 the products have more free energy than reactants; non spontaneous

 ΔG = ΔH –TΔS

4. competitive inhibition / non-competitive inhibition

 in competitive inhibition an inhibitor competes with the substrate for
the active site of the enzyme

 the enzyme is not changed as a result of the inhibition; as more active

sites are occupied the substrate cannot interact with the enzyme

 non-competitive, usually allosteric, the inhibitor affects the enzyme on

a site other than the active site, and as a result changes the conformation
of the enzyme, rendering it temporarily unable to bind to the substrate

 may be feedback inhibition

5. Golgi complex / endoplasmic reticulum (ER)

 Golgi complex: stacked membranous sacks that may receive material like proteins
from the ER and may also release vesicles to other parts of the cell.

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  ER: a system of intermolecular channels.

 Rough ER: surface covered by ribosomes and involved in protein synthesis

 Smooth ER: no ribosomes and involved in lipid synthesis

 Can pinch off vesicles to transport substances

 Both are parts of the endomembrane system in eukaryotic cells and connect together.

6. substrate level phosphorylation / oxidative phosphorylation

 Both are part of the cellular respiration.

 Substrate level phosphorylation: takes place in the cytosol during glycolysis, where
glucose and other fuel molecules pyruvate.

 After transport into the mitochondrion, pyruvate is oxidized (pyruvate oxidation) to an

acetyl group, which is carried to the citric acid cycle by CoA.

 Electrons are then carried by NADH and FADH2

 Oxidative phosphorylation: the mode of ATP synthesis that is linked to the oxidation of
energy rich molecules by an electron transport chain.

 Compared with substrate level phosphorylation that occurs during glycolysis and citric
acid cycle, oxidation phosphorylation relies on the action of a large multiprotein
complex that spans the inner mitochondrion called ATP synthase.

7. CAM pathway / C4 pathway

 both are plant adaptations to avoid photorespiration in dry/hot climates

 biochemically identical

 the Calvin is preceded by fixation of CO2 using the enzyme PEP carboxylase
into C4 acids (malic acid); eventually CO2 is released again and enters the
Calvin cycle

 difference: C4 plants separate Calvin cycle and primary fixation spatially:

malic acid moves to bundle sheath cells where CO2 is released; CAM plants
separate the two processes in time: stomata open during the night, CO2 is fixed

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 by PEP carboxylase; malate releases CO2 during the day when stomata are
closed.

 both pathways are costly, but worth the investment in hot and dry climate

8. glycolysis / fermentation
 glycolysis is the first phase of aerobic respiration as well as fermentation

 glucose is transformed in several reactions into 2 pyruvate

 has energy investment and energy gain phase

 does not require O2

 produces 2 ATP (net ) and 2 NADH

 location in cytosol

 fermentation: starts with glycolysis, pyuruvate is reduced, absence of O2

 low net energy gain

 alcoholic: pyruvate decarboxylated, acetaldehyde reduced

 lactic acid fe.: pyruvate reduced to lactic acid

 fermentation in lactic acid bacteria, yeasts, human muscle cells

9. NADH / ATP
 nicotinamid adenine dinucleotide is a coenzyme

 is used as the common reduction molecule in the cell (and NAD for oxidation)

 is created in several reaction in the first three phases of aerobic respiration and
used in the ETC for synthesis of ATP (oxidative phosphorylation)

 adenosine triphosphate

 common energy currency of the cell, used in most reactions that require
energy, produced from ADP + P

 bond between the last phosphate group and ADP contains the energy

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  formulas not required, but names

 universal in all organisms

 created by oxidative p. and by substrate level p., in the latter a phosphate is

directly transferred from another substrate

 often part of a coupled reaction when phosphate is directly transferred

10. photosystem I / photosystem II

 Both part of the photosynthetic apparatus in the thylakoid membrane

 P700/P680 respectively, based on absorption max.

 consist of antenna complexes with many pigments and protein and the reaction
center

 photosystem I involved in cyclic and non-cyclic electron transport

 photosystem is the site of photolysis, starting point of non-cyclic electron

transport, not involved in cyclic ET

 flow of electrons from photosystem II, down the ETC to photosystem I where
more photons excite photosystem I, continuing the ETC and ending with the
formation of NADPH

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 B. Short Answer/Short Essay Questions

Instructions: Answer each of the questions given below in your own

words. Write in complete sentences where appropriate. A complete
answer usually requires one to two sentences per mark, so a three-
mark question would be answered in three to six sentences. This
section is worth a total of 40 marks.

(4 marks) 1. Explain how rhodopsin functions as a light receptor.

 The pigment molecule retinal is embedded in the protein opsin and the latter is a
transmembrane protein embedded in a plasma membrane.

 Light reception changes the shape of retinal triggering changes in the conformation of
opsin leading to electrical signals that allow to process the reception.

(6 marks) 2. Explain the Miller-Urey experiment. What are the implications of

this experiment?

 The miller-urey experiment is considered as the basis experiment for origin of life. It
explains the chemical evolution of life on earth.

 Miller used water, methane, ammonia and hydrogen

 All chemicals were sealed inside a sterile array of glass tubes and flasks connected
together in a loop, with one flask half-full of liquid water and another flask containing
a pair of electrodes.

 The glass containing liquid water was heated to induce evaporation.

 Sparks were fried between the electrodes in other flask containing all chemicals to
simulate lightning and then atmosphere was allowed to cool so that the water could
condense and come back into the first flask in a continuous cycle.

 Operation for 1 week converted 15% of the carbon in the atmosphere inside the
apparatus into a variety of organic compounds.

(4 marks) 3. Explain the term RNA world.

 The term originated when it was discovered that occasionally RNA molecules can
act as catalysts (ribozymes)

 This opened the RNA world hypothesis because RNA could credibly be the first
macromolecule of life as it has both properties of information storage and
potentially catalytical properties

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  Previously it was assumed that life started with DNA, but it was never explained
how catalytic functional requirements are met. Likewise proteins who do have
catalytical properties require nucleic acids to be synthesized.

(4 marks) 4. What is the relationship between the surface area and volume of
a cell? Explain how the two major groups of organisms differ in
this respect, and why.
 The larger the cell, the more volume and surface, but volume grows by the factor
3

 Therefore large cells have a small surface/volume ratio, small cells have a large
ratio.

 Prokaryote cells are on average around 1 µm, eukaryote cells at least 10µm

 Therefore bacteria with their large surface volume ratio have no problems
exchanging matter with their environment; this could be however a problem for
eukaryote cells;

 eukaryotes have overcome this problem by having a large specialized

endomembrane system and many organelles, this allows them to have much larger
cells

(6 marks) 5. Draw and label a simple line diagram of a cell membrane.

Include the major types of membrane proteins. On your diagram, also
indicate how the following pass through the cell membrane:
 oxygen gas
 ions
 large volumes of water

Principles of Biology I 7
  O2 transported through passive diffusion
 Na+ diffusion through aqueous channel
 Na+ - K+ diffusion through active transport against concentration gradient with input
of energy
 Glucose through facilitated diffusion with a carrier protein

(3 marks) 6. What is a proton-motive force, and how is it achieved in cellular

respiration?
 Refers to chemiosmosis

 gradient in charge and in concentration of protons between matrix and

intermembrane space

 provides the energy to drive ATP synthesis as protons move to matrix along their
gradient; move through channel proteins with ATP synthase

 Electrons moving along the ETC in the last stage of aerobic respiration provide
the energy to pump protons into the intermembrane space which creates the
gradient in the first place

(4 marks) 7. Most organisms are aerobic. What is the major advantage of

having an aerobic metabolism? What is a major problem associated
with an aerobic metabolism?

 Aerobic respiration is more advantageous than anaerobic respiration. It is more

energy efficient.

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  It can produce 38 ATP molecules from a single glucose molecule. So more
energy from less food

 the major problem associated with aerobic respiration is that, the electron
transport chain is not 100% efficient and reactive oxygen species are released;
which damage the macromolecules by oxidation damage. The energy is not
released immediately

(5 marks) 8. Explain in detail what happens after an electron absorbs light.

 When hit by a photon, an electron jumps from its ground state to a more energy
rich excited state

 it may move back to its ground state releasing heat or light of a longer
wavelength than the light it received (fluorescence)

 it may move back to its ground state and the energy is passed on to a
neighboring pigment molecule (inductive resonance)

 the pigment molecule may lose its electron completely if there is an acceptor
(as in the reaction center chlorophyll)

(4 marks) 9. Explain the second law of thermodynamics and entropy.

 Second law: whenever energy is transformed from one state to another, there
us a loss of energy that cannot be used to do work; this results in an increase in
disorder called entropy; organisms use energy all the time to minimize entropy.

Principles of Biology I 9
 Multiple Choice Questions

Instructions: Select the single best answer to each of the questions

given below. Each question is worth one mark, for a total of 30
marks.

1. Which of the following is true for photons?

a. They have a tiny mass but no energy.
b. They have no mass but a tiny amount of energy.
c. They have both a tiny mass and a tiny amount of energy.
d. They cannot interact with matter.
e. They are always reflected when they collide with matter.

2. Bioluminescence
a. is important for photosynthesis.
b. produces a large amount of heat.
c. usually involves chloroplasts.
d. occurs in some plants living in the deep seas.
e. occurs when an excited electron returns to its ground state.

3. Pigment molecules absorb light because

a. they have a conjugated system of single and double carbon
bonds.
b. they have a highly complex chemical structure.
c. they have several ring systems.
d. they are able to reflect photons back and forth.
e. their molecules have a characteristic size and shape.

4. The 9+2 structure refers to

a. the arrangement of microfilaments in prokaryotes.
b. the arrangement of microfilaments in eukaryotes.
c. the arrangement of microtubules in the flagella of eukaryotes.
d. microfilaments in a cross-section of prokaryote flagella.
e. the intermediate filaments in eukaryotes.

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 5. Which of the following processes would be considered most
recent in evolutionary terms?
a. photosynthesis
b. oxygenic photosynthesis
c. fermentation
d. aerobic respiration
e. anaerobic respiration

6. Which of the following structures is NOT found in both

prokaryotes and eukaryotes?
a. flagella
b. cytoplasm
c. DNA
d. nucleoid
e. ATP

7. Which of the following terms refers to the idea of an RNA world?

a. ribozymes
b. ribosomes
c. ATP
d. virus
e. bacterium

8. Trade winds are

a. winds near the poles.
b. ocean currents.
c. winds in temperate zones.
d. winds in the tropics.
e. westerly winds.

9. A bacterial population that becomes resistant to antibiotics is an

example of
a. adaptive radiation.
b. selection.
c. chemoautotrophy.
d. transmission.

Principles of Biology I 11
 e. biodiversity.

10. The sun shines directly over the equator

a. during summer solstice.
b. during winter solstice.
c. during March equinox.
d. during both summer and winter solstices.
e. throughout the year.

11. Chemoheterotrophs
a. use light as an energy source and organic matter as a carbon
source.
b. use light as an energy source and CO2 as a carbon source.
c. oxidize substances to gain energy, and use CO2 as a carbon
source.
d. oxidize substances to gain energy, and use organic matter as a
carbon source.
e. none of the above

12. All of the following are functions of the cell membrane EXCEPT
a. transmitting signals.
b. participating in energy transfer.
c. being freely permeable to all substances.
d. regulating the passage of materials.
e. participating in chemical reactions.

13. Active membrane transport involves

a. NADH.
b. diffusion.
c. movement against a concentration gradient.
d. exocytosis.
e. all of the above.

14. Which of the following terms relates to phagocytosis?

a. endocytosis
b. exocytosis

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 c. pinocytosis
d. cell drinking
e. all of the above

15. Aquaporins are

a. peripheral proteins.
b. phospholipids.
c. glycolipids.
d. carbohydrate groups.
e. integral proteins.

16. Which of the following terms does NOT refer to allosteric

regulation?
a. feedback inhibition
b. competitive inhibition
c. allosteric activation
d. reversible inhibition
e. enzyme shape

17. The substance on which an enzyme acts is called the

a. free energy.
b. cofactor.
c. substrate.
d. product.
e. ATP.

18. Which of the following statements concerning activation energy

is FALSE?
a. Catalysts raise a reaction’s activation energy.
b. Activation energy is the energy required to break existing
bonds.
c. Endergonic reactions have an energy of activation.
d. Exergonic reactions have an energy of activation.
e. Enzymes lower a reaction’s activation energy.

19. With increasing temperatures, the rate of an enzyme-catalyzed

reaction

Principles of Biology I 13
 a. does not change.
b. increases and then levels off.
c. increases and then decreases rapidly.
d. decreases and then increases rapidly.
e. decreases and then levels off.

Use this figure to answer the next question

20. In the figure above, A represents

a. activation energy without an enzyme.
b. activation energy with an enzyme.
c. the change in enthalpy.
d. the change in entropy.
e. the free energy of the reactants.

21. During chemiosmosis in the mitochondria, ATP is produced as

a. protons are pumped by ATP synthase into the mitochondrial
matrix.
b. cytochrome is reduced.
c. oxygen―the final electron acceptor―is reduced.
d. NADH is oxidized to NAD+.
e. none of the above

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 22. What is the immediate fate of the electrons in NADH during
fermentation?
a. They are used to make CO2.
b. They are used to form H2O.
c. They are transferred to an organic molecule.
d. They are transferred to O2.
e. They are transferred to the electron transport chain.

23. Which of the following statements about lactic acid fermentation

is NOT correct?
a. It produces two ATP molecules for every glucose molecule.
b. It is inefficient compared to aerobic respiration.
c. Oxygen is the final electron acceptor of this pathway.
d. It uses glucose as a substrate.
e. Glycolysis is the only energy-yielding step of this pathway.

24. Which of the following steps in the citric acid cycle directly
produces a molecule of GTP?
a. citrate → isocitrate
b. isocitrate → α-ketoglutarate
c. succinyl CoA → succinate
d. malate → oxaloacetate
e. succinate → fumarate

25. In glycolysis, the activity of ________ is controlled through

feedback inhibition by ________.
a. phosphofructokinase; ATP
b. phosphoglucoisomerase; AMP
c. pyruvate dehydrogenase; oxaloacetate
d. phosphofructokinase; AMP
e. phosphoglucoisomerase; glucose-6-phosphate

26. Red and blue light support the highest rates of photosynthesis
because
a. these wavelengths activate the ATP synthase enzyme.

Principles of Biology I 15
 b. these are the only wavelengths that carotenoids cannot
absorb.
c. these wavelengths have the highest energy in the visible
spectrum.
d. chlorophyll absorbs these wavelengths more than other
wavelengths.
e. these are the only wavelengths reaching Earth from the Sun.

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 27. Which of the following applies to cyclic electron transport but
does NOT to apply to acyclic electron transport?
a. Protons are moved into the thylakoid lumen.
b. production of ATP, but not NADPH
c. production of both ATP and NADPH
d. photolysis
e. P680

28. Which of the following may happen AFTER an electron is

induced by a photon?
a. The electron may accept another photon.
b. A neighbouring pigment molecule donates energy to the
electron.
c. The electron returns to ground level while keeping its high
energy.
d. The electron releases energy as heat as it moves back to
ground level.
e. all of the above

29. Which of the following is common to both photosynthesis and

aerobic respiration?
a. the Calvin cycle
b. glycolysis
c. CO2 and O2 as end products
d. thylakoids
e. chemiosmosis

30. Chlorophyll absorbs primarily ________ and ________ regions

of the visible spectrum.
a. red; yellow
b. red; green
c. blue; yellow
d. green; yellow
e. blue; red

— End of Assignment 1A —

Principles of Biology I 17