Transcript BIOL 200 (951): Final Exam Study Guide and Review questions

BIOL 200 (921):
Final Exam Study Guide and Review questions
FINAL EXAM (IN CLASS) FROM 1 PM TO 3:30 PM ON JULY 7, 2006
The final exam will cover material covered up to and including the
Lecture on July 7 and will also include the pre-midterm material. Be
prepared to integrate material covered in these lectures. Emphasis will
be placed on understanding of general concepts, experimental
approaches, and ability to interpret new information and data in light of
what you know. You should supplement your class notes with details and
questions from the textbook and the BIOL 200 web site material.
You are responsible for the reading material listed in the outlines for
each lecture, and the material provided in the lecture notes,
tutorials and powerpoint slides. The Study Questions from the
textbook given in the lecture outlines are a good way to review most of
the topics covered. Reading in the text is designed to expand upon and
support this material. You may be asked to consider information in such
figures, as it relates to material we have covered in lecture.
BIOL 200 (921): Final Exam Study Guide and Review questions
As a guide, here are some specific comments about questions in the
relevant chapters:
• Understand the relationship between structure, cellular composition
and function of cell organelles and macromolecules.
• Understand basic terminology and concepts in cell biology e.g.
membrane transport systems, membrane transport processes,
protein sorting and transport, photophosphorylation, oxidative
phosphorylation, microtubules and associated proteins, cyclins and
CDKs, DNA replication, cell division phases etc.
• Understand how the biochemical and cell biological
approaches/techniques we have discussed can be used to answer
questions in cell biology. Be prepared to propose the use of systems
and tools to approach a specific problem.
• Concentrate on understanding cell biological processes e.g.
membrane transport processes, protein sorting and transport,
photophosphorylation, oxidative phosphorylation, microtubules/actin
filaments and associated proteins, cyclins and CDKs, DNA
replication, cell division, membrane structure and transport etc.
BIOL 200 (921): Final Exam Study Guide and Review questions
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Final exam preparation material:
For the Final exam, one sheet of 8.5 x 11 paper, double-sided, "study sheet" will
be allowed as a memory aid.
Memorizing facts are not the goal of this course, you must be able to use
information to solve problems and defend a point of view.
Specific type of questions to consider:
There will be an essay question on a major cell biology topic in the final exam.
Short answer, Multiple-choice, definitions, true/false, fill in the blanks, small essaytype questions. Test objectives: Familiarity with terms, concepts, and basic
principles covered in lectures. Ability to make connections between different topics
covered.
Problem (e.g. explain experimental results which are presented, explain how to
approach a particular problem, predict results from an experiment, etc). Test
objectives: Ability to use information in new situations and to solve problems,
depth of knowledge concerning basic concepts, understanding of approaches
used to investigate cell biology. Ability to integrate information. Please study the
problems and their solutions given in your textbook.
Structure-function relationships of cell, organelles, macromolecules etc.
Structural and functional differences between different cell types (e.g. animal,
plant, bacterium)
Use of appropriate experimental methods/techniques to support cell biological
hypotheses/theories/results
Ability to analyze a given set of data in the form of a Table or Figure pertaining to
topics covered in lectures.
See the Study Questions from the textbook given in lecture outlines.
Some examples of exam questions are given below.
BIOL 200 (921): Final Exam Study Guide and Review questions
Final Exam Review Questions
Question 1. Briefly explain the structure-function
relationship of the following:
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Myosin-II filament:
trans Golgi network:
1. The Myosin head
tightly locked onto an
actin filament.
17_45_myosin_walks.jpg
2. ATP binds to the myosin
head. The Myosin head
released from actin.
3. The myosin head displaced
by 5 nm. ATP hydrolysis.
4. The myosin head attaches
to a new site on actin filament.
Pi released. Myosin head
regains its original
conformation (power stroke).
ADP released.
5. The myosin head is
again locked tightly to
the actin filament.
one Golgi stack [Fig. 15-24]
Protein modifications
in Golgi [Fig. 12-6
from Becker]
Predict the location of enzymes,
galactosyl transferase and
sialic acid transferase
• Question 2. Short Answer
• Explain in one or 2 sentences why plants
need to have mitochondria in every cell,
even when the sun is shining.
• There are no motor proteins that move on
intermediate filaments. Can you suggest a
reason based on the structure of the
intermediate filaments? What does this tell
you about motor proteins?
Question 3. Fill in the blanks:
• A small GTP-binding
protein called
___________
assembles around
the neck of each
coated vesicle and
helps in pinching off
the vesicle from the
membrane.
• __________ is the
motor protein that
moves along
cytoplasmic
microtubules and
towards the plus end
of the microtubule.
Question 4. Design an experiment using appropriate
experimental technique(s) to study the kinesin-assisted
transport of macromolecules.
1.
Immunofluorescence microscopy: Primary antibodies bind to
cytoskeletal proteins. Secondary antibodies labeled with a
fluorescent tag bind to the primary antibody. Cytoskeletal proteins
glow in the fluorescence microscope.
2.
Fluorescence techniques: Fluorescent versions of cytoskeletal
proteins are made and introduced into living cells. Fluorescence
microscopy and video cameras are used to view the proteins as
they function in the cell.
3.
Computer-enhanced digital videomicroscopy: High resolution
images from a video camera attached to a microscope are
computer processed to increase contrast and remove background
features that obscure the image.
4.
In vitro and in vivo studies [Figs. 17-19 to 17-22, pp 585-88]
GFP=green fluorescent protein
GFP
protein of interest
1. GFP gene fused to gene coding for protein
of interest
2. Transform cell with GFP-protein gene fusion.
3.Gene is expressed, targeted, protein functions.
4. Localize Green fluorescence with fluorescent.
light microscopy (or confocal)
Control-cytoplasmic GFP, i.e. no protein of interest
fused onto GFP.
Question 5. Three phospholipids X, Y and Z are distributed in the
plasma membrane as shown. For which of these phospholipids does a
flippase probably exist?
a. X only
b. Z only
c. X and Y
d. Y and Z
e. X and Z
Explain your answer
briefly.
ANSWER:
Three phospholipids X, Y and Z are distributed in
the plasma membrane as shown. For which of
these phospholipids does a flippase probably
exist?
C = X and Y
Explain your answer briefly.
Lipids are inserted into the membrane on the
lumen face of the SER (which corresponds
to cytosolic side of the plasma membrane).
Therefore both X and Y would need
flippases to move to the external leaflet.
Must know that flipping can’t occur
spontaneously and that all lipids are
inserted into the same leaflet. Must mention
SER.
Question 6. Based on your understanding of cell structure and
function, please state if the following statements are TRUE or
FALSE and provide an explanation for your choice.
• a) Membrane-bound and free ribosomes, are
structurally and functionally identical and differ
only in the proteins that they happen to be
making at a particular time.
• b) All of the glycoproteins in the intracellular
membranes have their oligosaccharide chains
facing the lumen, whereas those in the plasma
membrane have their oligosaccharide chains
facing the outside of the cell
• c) The pH of the chloroplast thylakoid space (or
lumen) increases in the light.
a) Membrane-bound and free ribosomes, are structurally
and functionally identical and differ only in the proteins
that they happen to be making at a particular time.
TRUE. Cytosolic ribosomes are translating proteins with no
sorting signals/ proteins destined to remain in the
cytoplasm. Ribosomes of the RER are translating
proteins with ER signal sequence, i.e. the subsequent
events leading to attachment of ribosomes to the ER
membrane are a result of the interaction of the signal
peptide amino acid sequence with the signal recognition
particle (SRP) and the SRP receptor in the ER
membrane.
b) All of the glycoproteins in the intracellular membranes
have their oligosaccharide chains facing the lumen,
whereas those in the plasma membrane have their
oligosaccharide chains facing the outside of the cell
TRUE. For glycoproteins as the oligosaccharide
chains are transferred onto the protein in the ER
lumen, then further modified in the Golgi. When
those proteins are secreted via exocytosis, the
oligosaccharide chains are facing the
extracellular space or comment on extracellular
space being topologically equivalent to
endomembrane lumen.
c) The pH of the chloroplast thylakoid
space (or lumen) increases in the light.
FALSE. The pH of the thylakoid space
decreases due to accumulation of protons
driven into the space by the flow of
electrons along the photosynthetic
electron transport chain.
QUESTION 7:
Tubulin polymerization
A typical time course for polymerization of
purified tubulin to form microtubules is
shown below.
Explain the different
parts of the curve
labeled A, B and C.
How would the curve change if centrosomes
were added at the onset?
ANSWER:
Tubulin polymerization
A typical time course for polymerization of purified
tubulin to form microtubules is shown below.
A – lag phase. Nucleation of MTs
B – rapid polymerization
C - equilibrium
How would the curve change if centrosomes were
added at the onset?
Lag phase eliminated
Question 8. Circle the correct answer on the exam.
A. What are the molecular components of ATP?
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adenine, thymine, and phosphates
adenine plus three phosphates
adenine, ribose and three phosphates
alanine, ribose and three phosphates
alanine, threonine and phosphate
B. A yeast strain that has a mutation that prevents vesicle fusion with
the plasma membrane may have a mutation in the gene that
codes for:
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–
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Clathrin
COP protein
Dynamin
Adaptin
V SNARE
C. What keeps the Golgi apparatus in the middle of the cell, and away
from the periphery?
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–
–
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Intermediate filaments
Kinesin
Dynein
Myosin
Actin
Question 9. Essay Question.
Sorting of proteins to the correct intracellular
compartment is essential to cells. I-cell disease is
a rare human disorder in which enzymes normally
found in lysosomes are actually secreted from the
cell. Describe the process of synthesis of
lysosomal enzymes in normal individuals in
comparison with individuals affected by I-cell
disease. Your description should begin with the
mature mRNA in the cytoplasm that encodes a
lysosomal enzyme and describe how the protein
produced by translation of this mRNA is sorted
through each successive organelle. Do not
describe the details of the translation process.
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Normal cotranslational insertion steps up to the occurrence of the defect.
Protein synthesis begins on a free ribosome in the cytosol
The first part of the protein synthesized (N terminus) contains a signal sequence.
This sequence binds to a signal recognition particle (SRP) which binds to the
ribosome. It causes translation to pause
The SRP binds to a SRP receptor in the ER membrane. This leads to the
formation of a translocation channel that is connected to the ribosome. The SRP
is released.
Translation resumes. The hydrophobic signal sequence binds to the hydrophobic
core of the membrane that is exposed in the interior of the translocation channel.
The rest of the protein proceeds into the lumen of the ER.
The signal sequence is cleaved off of the protein by the signal peptidase
enzyme that is in the ER membrane, and is degraded. The protein is now free in
the lumen of the ER.
Glycosylation. In the ER an enzyme transfers an oligosaccharide tree containing
the sugar mannose from a membane glycolipid/dolichol to the lysosomal protein.
Vesicle transport from ER to Golgi, through Golgi
The protein is then transferred to the cis Golgi via COP-coated transport
vesicles.
In the cis golgi an enzyme normally phosphorylates mannose residues in the
oligosaccharide attached to the lysosome- destined protein. This enzyme is
missing or defective in individuals with I cell disease.
• Normal processing of lysosomal proteins:
– The lysosome destined proteins proceed through the Golgi stack,
presumably through a vesicle transport process.
– In the trans Golgi network normal lysosome-destined proteins are bound
to mannose-6-phosphate receptors in the membrane, and are
incorporated into clathrin- coated vesicles that are targeted to late
endosomes.
– In the late endosome the acidic environment causes the lysosomedestined protein to separate from the mannose-6-phosphate receptor.
– The receptors are recycled to the trans Golgi network by vesicle
transport.
– The lysosome-destined proteins proceed to lysosomes
• Alternate processing of proteins normally destined to lysosomes in
individuals with I cell disease.
- Since the normal targeting signal for lysomal proteins (mannose-6phosphate) is not present, the proteins will enter the constitutive
secretory pathway and be delivered to the cell surface.
- As the vesicles fuse with the plasma membrane the proteins
normally destined for lysosomes will be deposited in the
extracellular space.
Question 10. Essay question. Beginning with the electron donor molecule,
describe in detail, using essay format (NO DIAGRAMS) the cellular
events that result in electron transport, proton pumping and ATP synthesis
during oxidative phosphorylation or photophosphorylation
• Discuss the initial electron donor, multiprotein
complexes, mobile electron carriers/proteins, final
electron acceptor in ETC in mitochondria and chloroplast
• Mention the site(s) and direction of proton pumping in
mitochondria and chloroplast
• Discuss the subcellular site, structure, function and
mechanism of ATP synthesis in mitochondria and
chloroplast
• Discuss the chemiosmotic theory
• Role of light energy in electron flow in chloroplast
• Energy transformation in oxidative- and photophosphorylation
Electron transport and H+ pumping in mitochondria
14_10_resp_enzy_comp.jpg
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Electrons flow from –ve to +ve redox potential carriers
14_21_Redox_potential .jpg
Electron transport and H+ pumping in chloroplast
14_36_thylakoid_memb.jpg
Photophosphorylation and NADP reduction [Fig. 14-37]
FO-F1 ATP synthase complex: Uses proton
electrochemical gradient to make ATP [Fig. 14-14]
Binding-change mechanism of ATP synthesis
Lehninger Principles of Biochemistry
An overview of cytoskeleton
• Three major cytoskeletal systems and their general properties
• a) Intermediate Filaments - a system of elastic fibers - used to
strengthen cells and to transmit mechanical strain across cells in a
tissue. These filaments are purely skeletal in nature.
• b) Microtubules - rigid protein tubules. These are involved in
generation of cell shape and provide substrate for two different types
of motor systems, dyneins and kinesins. The mitotic spindle is a
variant form of the microtubular cytoskeleton.
• c) Microfilaments (actin filaments) - this is the most complex
system. Occurs in many forms, bundles of fibers or networks.
Interacts with many types of molecules including its own class of
motor proteins, the myosins. Its most elaborate form occurs in
striated muscle. Microfilaments are responsible for cytoplasmic
streaming and amoeboid motion.
Cyclin-CDK complex [Fig. 18-5]
Cyclin-dependent
kinase (Cdk)
Cyclinamount
varies during
cell cycle
Factors affecting the activity of
Cdks
1.
2.
3.
4.
Cyclin degradation by ubiquitination
Phosphorylation and dephosphorylation
Positive feedback
Cdk inhibitor proteins
Selective phosphorylation and dephosphorylation
18_11_M_Cdk_active.jpg
activate M-Cdk [Fig. 18-11]
Thr 14,
Tyr 15
Thr 161
II. DNA Replication
• DNA synthesis starts at replication origins
• New DNA is synthesized by DNA
polymerase at replication forks (Y-shaped
junctions in DNA)
• The DNA replication forks are asymmetric
in nature
• DNA polymerase has self-correcting
(proofreading) activity
DNA replication forks are asymmetrical [Fig. 6-12]
06_12_asymmetrical.jpg
06_17_group proteins.jpg
A group of proteins
act together at a
replication fork