Chem*3560
Structure and Function in Biochemistry
Winter 2002
Lecturers:
Dr. A. Mellors, Rm 331 MacNaughton Bldg. West Wing,
Phone (519) 824-4120 Ext. 3792; Fax (519) 766-1499
E-mail amellors@uoguelph.ca
Office hours:
Mon., Wed., Fri. 9:30 - 10:30 a.m.
Other times by appointment, please.
Lectures:
Section 01:
Mon., Wed., Fri, 12:30 PM- 1:20 PM. Room: Chemistry and Microbiology 200.
Section 02:
Mon., Wed., Fri, 3:30PM - 4.20 PM.
Room: MacNaughton 105.
Section:
Sections are assigned by the registrar and students are requested to attend only the
section to which they are assigned.
Course
Synopsis:
This is a systems-oriented course where biochemical structure, function and some
metabolism are presented in an integrated fashion.
Textbooks: Required: "Biochemistry" by Lubert Stryer, Fourth Edition, published by W.H. Freeman,
Sufficient copies are available at the Campus Bookstore. Warning:a completely revised
Fifth Edition by Stryer and other authors is about to be published (Dec. 2001). This Fifth
edition will NOT be used for the Winter 2002 semester and will probably not be used in
future years. Several copies of the 4th and previous editions are on reserve (2 hour loan)
at the Library Reserve Desk. The text Lehninger: Principles of Biochemistry (Lehninger,
Cox and Nelson) is not very suitable for this course as it lacks coverage of certain topics.
Sample midterms and a final exam are also available at the Reserve Desk.
Computer
Simulations For assistance with metabolic pathways, used in the second half of the course, students
are encouraged to try the computer simulations available in the Chemistry-Biochemistry
Computer Room, Chem-Micro Building Room B44. The relevant exercises are :
Gluconeogenesis and the pentose-phosphate pathway: Glycogen synthesis and
degradation: Fatty acid oxidation and synthesis.
Web pages: Pages that worked at the start of the semester:
http://www.chembio.uoguelph.ca/educmat/chm356/chm356.htm
For hemoglobin structure and function, useful Web sites are:
http://globin.cse.psu.edu/globin/html/huisman/variants/contents.html
http://www.cryst.bbk.ac.uk/PPS2/course/section12/index.html
http://www.umass.edu/microbio/chime/hemoglob/2frmcont.htm
http://ntri.tamuk.edu/homepage-ntri/lectures/protein/protein.html
http://grserv.med.jhmi.edu/~raj/javanim.html
You can test your general knowledge of protein structure and function by doing the
multiple choice problems shown at:
http://bob.usuf2.usuhs.mil/biochem/exams/bytopic/proteins-f/node1.html
Sickle cell disease:
http://www-rics.bwh.harvard.edu/sickle/menu_sickle.html
Southern blotting and restriction fragment length polymorphism:
http://www.biology.washington.edu/fingerprint/problems.html
http://vector.cshl.org/shockwave/southern.html
Thalassemia:
http://sickle.bwh.harvard.edu/thalover.html
Allosteric behaviour of aspartate transcarbamoylase:
http://bioinfo.mbb.yale.edu/MolMovDB/cgi-bin/morph.cgi?ID=atcase
Prions and mad cow disease:
http://www.airtime.co.uk/bse/welcome.htm
http://www.diseaseworld.com/
http://www.sciam.com/0195issue/prion.html
Blood clotting and fibrinolysis :
http://www.chembio.uoguelph.ca/educmat/chm356/clot/index.htm
http://brie.medlabscience.med.ualberta.ca/mlsci/235/clotcascade.html
Hemophilias :
http://vector.cshl.org/ygyh/mason/ygyh.html?section=whatisit&syndrome=hemo
Glycolysis and glycogenolysis controls:
http://www.jonmaber.demon.co.uk/
http://web.indstate.edu:80/thcme/mwking/glycogen.html#intro
The sodium pump:
http://www.cbc.med.umn.edu/~mwd/cell_www/chapter2/Na-Kpump.html
http://www.bio.davidson.edu/biology/courses/Molbio/26aa/alphabeta.html
An animated cartoon of the Na+/K+-ATP-ase is shown at:
http://199.17.138.73/berg/ANIMTNS/Na-Kpump.htm
Reference
Material:
Other textbooks are available at the Library Reserve Desk.
Grade Assessment:
Midterm Examination 40%
Final Examination 60%
Both exams are required. If the mid-term is not taken then the final exam will be 100% of
the grade.
Examination Schedule:
Midterm Examination: The midterm will be written on Tuesday February 26th at 5:30
p.m. to 7:00 p.m.) in class-rooms to be announced. Persons with a scheduled academic
conflict should inform the instructor by e-mail (amellors@uoguelph.ca), stating the
conflicting course, by February 15th , and may be granted an alternative exam which will
be held prior to the regular mid-term on Monday February 25th at 5:30 p.m. to 7:00 p.m.
Final Examination: As scheduled by the registrar on the first day of the final exam period,
Tuesday, April 9th , 11.30 a.m. -1.30 p.m. (No exceptions). The final exam is
cumulative. Students who score a significantly higher grade on the Final Exam,
compared with the Midterm, may receive a higher weighting of the Final Exam, at the
discretion of the instructor. A significantly higher grade is one that is 25 percentage points
higher.
Re-grading: Midterm papers may be returned to the instructor for correction of grading errors, only
within one week of the return of the paper to the student, and only if the paper was written
in ink. No additions in ink must be made after return of the paper, and the instructor will
photocopy some or all of the papers at the time of grading. The instructor may refuse to
re-grade a paper at his discretion.
Exam aids: No materials may be brought to the exam except for three pencils, three pens and an
eraser. No calculator, pencil cases, purses, bags, Kleenex boxes or other containers may
be present. All materials are subject to inspection.
Drop and
Add:
Notification is not needed for dropping the course before the DROP deadline (40th class
day). Program approval is only needed for drops and adds if your category is ASpecial@ or
AProvisional@.
Course
Evaluation: As part of the faculty evaluation process in the Department of Chemistry and
Biochemistry, students are reminded that written comments on the teaching performance
of the lecturer may be sent to the Chair, Department of Chemistry and Biochemistry, at
any time. Such letters must be signed; a copy, will be made available to the instructor
after submission of final grades.
Chem*3560 Schedule of topics.
Note: This schedule is tentative and may be modified during the term.
Chapter references are to Stryer.
Stryer
Lehninger et al.
th
4 Edition
References in italics are to similar coverage where available in Lehninger, Cox and Nelson.
PART A: PROTEIN STRUCTURE AND ENZYME REGULATION:
Chapter 7 Oxygen-transporting proteins
Hemoglobin and myoglobin: structures
147-157
Cooperativity: inter-subunit communication in hemoglobin.
157-168
Hemoglobin S and the consequences of mutation.
168-177
Chapter 8 Introduction to enzymes
Review enzyme kinetics. Allosteric enzymes. Sigmoidal kinetics.
Chapter 10 Control of enzymatic activity
Control by allosteric effectors:
ATCase: a regulatory enzyme
237-244
R and T states: concerted model and the sequential model. 166-168
Control by proteolytic cleavage: Zymogen activation.
Serine proteases of digestion: chymotrypsin.
247-249
Blood clotting: a zymogen amplification cascade
252-255
Fibrinogen and formation of the fibrin clot.
Thrombin and prothrombin. Vitamin K. Hemophilia.
255-260
203-206
210-211
206-219
219-221
278-281
No coverage
216
286-287
No coverage
No coverage
No coverage
PART B: REGULATION AND INTEGRATION OF METABOLISM:
Chapter 18: Pentose phosphate pathway and gluconeogenesis
Pentose phosphate pathway.Sources of NADPH for biosynthesis
559-565
Review gluconeogenesis. Regulation of carbohydrate metabolism.
Control by covalent modification (phosphorylation):
244-247
Phosphofructokinase and fructose-1,6-bisphosphatase.
493-495
Role of fructose-2,6-bisphosphate.
569-576
Substrate cycles. Net direction of glycolysis/gluconeogenesis.
Chapter 19: Glycogen metabolism
Glycogen synthase and phosphorylase;
581-598
protein phosphorylation cascade.
Chapter 20: Fatty acid metabolism
Reaction sequence.
614-622
Fatty acid synthase. Contrast with ß-oxidation.
Chapter references are to Stryer.
Stryer
4th Edition
557-559
281-283
732-733
No coverage
730-731
282-286
770-777
Lehninger et al.
References in italics are to similar coverage where available in Lehninger, Cox and Nelson.
Chapter 26: Integration of metabolism
Integration of metabolic pathways.
Hormones: Insulin, glucagon, epinephrine.
763-773
773-782
485-489
869-884
268-278
267, 280
389-398
311-313
309-317
415-421
291-306
421-430
PART C: MEMBRANES
Chapter 12: Introduction to biological membranes
The fluid mosaic model of membrane structure.
Glycolipids and glycoproteins.
Chapter 37: Membrane Transport
Na+-K+ ATPase
Chapter 39: Excitable membranes and sensory systems
Channels and the action potential
The instructor reserves the right to change any of the above, in accordance with University of Guelph
regulations.
Chem*3560
LECTURE SUMMARY:
Lecture 1:
Structure and function of the oxygen binding proteins, myoglobin and hemoglobin.
Heme; protoporphyrin IX; Myoglobin; Hemoglobin, the O2 carrier in blood
Lecture 2:
The Globins. Myoglobin; Hemoglobin; The 3-dimensional structures; What determines
folding?; Comparing amino acid sequences of globins; Helical segments; Connecting
loops; Hemoglobin-A, Adult; Hemoglobin F; Fetal; Embryonic hemoglobin
Lecture 3 and review , assignment 1: O2 Binding by Myoglobin and Hemoglobin.Absorbance;
oxyhemoglobin; O2 affinity of myoglobin versus hemoglobins
Lecture 4:
Cooperative oxygen binding by hemoglobin.
Hyperbolic binding; sigmoidal binding; Hill Equation; The cooperative binding model;
The sequential model of; The concerted or symmetry model
Lecture 5:
Monod,
Allosteric cooperative binding of O2 and the structure of hemoglobin.
Wyman and Changeux model (MWC); X-ray crystallography studies of hemoglobin
Lecture 6 and review assignment 2: Oxygen binding proteins.
Lecture 7:
Other factors controlling O2 binding by hemoglobin.
Effect of pH and CO2; 2,3-bisphosphoglycerate
Lecture 8:
Hemoglobin genetics and Molecular diseases.
Sickle cell anemia; molecular disease; malarial parasite; sequence of the mutant DNA;
Thalassemias; The globin genes in humans
Lecture 9 and review assignment 3: Allosteric control of enzymes. Aspartate transcarbamoylase.
Lecture 10:
Structural studies of ATCase.
Lecture 11:
The allosteric mechanism of ATCase: more experimental evidence.
Lecture 12 and review assignment 4: Allosteric Cooperativity. Regulation by covalent modification
of enzymes by phosphorylation and dephosphorylation
Lecture 13:
Regulation by proteolysis; Proteolytic activation; Digestive enzymes; Zymogens;
Chymotrypsin, Proteases; Blood clotting; Prothrombin; Thrombin.
Lecture 14:
Blood clotting.Fibrin; fibrinogen; Intrinsic pathway; Extrinsic pathway; activation
cascade; Factor VIIIa; Factor Va; Hemophilia; Vitamin K; γ-carboxyglutamate
Lecture 15 and review assignment 5: Blood clotting. Fibrinolysis, plasminogen; tissue plasminogen
activator
Lecture 16:
Regulation of protein function and metabolic control.
Lecture 17:
Review of glucose metabolism, glycolysis and pentose phosphate pathway.
Lecture 18 and review assignment 6: Pentose phosphate pathway balance sheet and experimental
tests.
Lecture 19:
Midterm review.
Lecture 20:
Control of glycolysis and gluconeogenesis at the phosphofructokinase-1 step.
Lecture 21 and midterm post-mortem: Final steps of gluconeogenesis; fructose-1,6-bisphosphatase;
Fructose-2,6-bisphosphate.
Lecture 22:
Glycogen synthesis and glycogenolysis. Glycogen phosphorylase; glycogen synthase;
UDP-glucose pyrophosphorylase
Lecture 23:
Fatty acid synthesis. Fat metabolism; Fatty acid synthesis, Acetyl CoA carboxylase.
Lecture 24 and review assignment 7: Fatty acid biosynthesis (continued). Fatty acid biosynthesis
cycle; phosphopantotheine; Coenzyme A; ACP.
Lecture 25:
Products of Lipid metabolism: Triacylglycerols; Phosphatidate; phospholipids; Micelle;
Bilayers; Adipose cells; hormone sensitive lipase; Insulin
Lecture 26:
Integration of metabolism - Who does what. Liver, Brain; Muscle; Kidney; Adipose
Tissue.
Lecture 27 and review assignment 8: Metabolic crossroads.
Lecture 28:
Lecture 29:
Membranes and Transport:
Integral membrane proteins; Peripheral membrane
proteins; receptors; structural components; proteins responsible for transporting
substrates
Glycoproteins and glycolipids, Blood groups, antigens and antibodies
Lecture 30 and review assignment 9: Membranes and transport: Basis of protein mediated transport;
uniport; antiport; symport; simple diffusion; facilitated diffusion; active transport;
electrogenic transport; ion-pumping ATPase
Lecture 31:
Membranes and Transport: Ion-pumping ATPases; Na+/K+ ATPase; ion gradients;
membrane potentials; Nernst equation.
Lecture 32:
Electrical activity in membranes:
selectivity.
Nerve action; voltage gates; ion selective; ion
Lecture 33 and review assignment 10: Na+ channel; K+ channels; Tetrodotoxin; Digitoxin
Lecture 34 and review: Review of Membrane Function.
Lecture 35: Semester review.
Check-list of Chemical Formulae and Required Structures:
Nature of covalent bond; non-covalent bond; salt linkages (electrostatic bonds); hydrogen bond.
Oxygen, carbon dioxide, carbon monoxide, cyanide anion.
Pyrrole, tetrapyrrole, methene bridge.
Histidine, lysine, glutamate, glutamine, apartate, asparagine, serine, cysteine.
2,3 bisphosphoglycerate, carbamate.
Carbamoylphosphate, N-carbamoylaspartate, N-phosphonoacetyl-L-aspartate (PALA) and transition
state for ATCase.
Reagents: p-hydroxymercuribenzoate (p-HMB) and di-isopropylfluorophosphate (DIFP).
Oxidative phase of the pentose phosphate pathway (to ribulose 5 phosphate).
Glucose (Glc), and its phosphates;
UDP-Glc; Fructose (Fru) and its phosphates.
Cyclic 3'-5' adenosine monophosphate (cAMP).
Fatty acid synthase pathway, triacylglycerol, phosphatidylcholine.
N-acetylglucosamine (GlcNAc); N-acetylgalactosamine (GalNAc); ceramide (N-acyl-sphingosine).
Check-list of Metabolic Controls and Mechanisms:
Myoglobin and hemoglobin, functions in oxygen binding.
Effects of BPG, H+, CO2 on oxygen binding.
Bohr effect and its causes.
Sickle cell anemia, thalassemia, Southern blotting method for determining defects.
Control of enzyme activity, ATCase, allosteric regulation by Asp, CTP, ATP.
ATCase structural studies, use of PALA.
Michaelis-Menten binding (hyperbolic) versus non-hyperbolic (allosteric, co-operative, sigmoidal).
Concerted versus symmetric mechanisms of allosteric behaviour.
Zymogens and blood clotting; serine proteases in clotting.
Seven serine proteases: thrombin, VIIa, IXa, Xa, XIa, XIIa and kallikrein.
Thrombin action on fibrinogen; also on factors V, VII, VIII, and XIII.
Fibrinogen -> soft clot -> hard clot, transamidation.
Extrinsic (tissue factor) cascade and intrinsic (surface contact) cascade.
Hemophilias A and B; anticoagulants, antithrombin III.
Fibrinolysis, plasminogen and tPA.
Calcium ion and phospholipid roles in clotting.
Pentose phosphate pathway, its location, controls, and regulation by NADP+.
Tests for P.P.P. and a balanced equation for glucose oxidation.
Glycolysis and glycogenolysis. (Glycogen to 3-phosphoglyceraldehyde).
Phosphofructokinase-1 and its control; Fru-1,6 bisphosphate 1-phosphatase.
Allosteric regulation by Fru 2,6 bisphosphate and the bifunctional enzyme.
Covalent regulation of the bifunctional enzyme.
Cyclic AMP dependent protein kinases; protein phosphorylation cascades;
Glucagon, epinephrine, insulin, modes of action. Protein phosphatases.
Glycogen breakdown and synthesis; controls of glycogen phosphorylase and glycogen synthase.
Liver versus muscle, differences in glycogen and glucose metabolism.
Fat synthesis, acetyl CoA carboxylase; fatty acid synthase in mammals.
Integration of metabolism, cross-road compounds, tissue specialization.
Fasting and starvation, mobilization of glycogen and fats.
Membrane structure and function.
Ionic gradients and membrane potentials; Nernst equation.
Glycolipids and sphinglipids.
Glycoproteins, antigens, ABO (ABH) blood groups.
Na+/K+ ATPase and the sodium pump.
Na+ channel, K+ channel, and voltage gating. The action potential.
Acetylcholine receptor and ligand gating.
Chem*3560
Assignment 1
1
How many Angstrom units (D) are there in a metre?
2
Why is heme (Fe II-protoporphyrin IX) not used to transport or store oxygen?
3
Which molecules probably evolved first: respiratory cytochromes; chlorophylls; hemoglobins?
4
What is a pyrrole?
5
Why are the amino acids of myoglobins and hemoglobins labelled after the regions (domains,
helices) and not numbered in sequence as for other proteins?
6
What is the function of the E7 His of myoglobins and hemoglobins?
7
What is a methene bridge?
8
What chemical differences does the ferrous iron show when it is in myoglobin or hemoglobin as
Fe(II)-heme, compared to FeSO4.
9
Answer Yes or No to the questions in the following table:
Fe(II)
heme
Myoglobin
Hemoglobin
Contains protein?
Water-soluble?
Binds O2 reversibly?
Reduced CO binding?
Co-operative or allosteric O2
binding?
10 What would be the physiological effect of replacing Hb4 within erythrocytes (R.B.C.) with
myoglobin?
11. If carbon monoxide binds to the Fe(II) of hemoglobin 200 times better than oxygen binds, what
percentage of carbon monoxide in air is equal in binding power to that of 20% oxygen in air?
Chem*3560 #2
1
What are the structural differences between myoglobin (Mb) and hemoglobin (Hb)?
2
What are structural similarities between Mb and Hb?
3
What are the functional differences between Mb and Hb?
4
Which of the following does not describe the binding of O2 by Hb:
(a) Sigmoidal
(b) Cooperative
(c) Hyperbolic
(d) Allosteric.
5
Why is n in the Hill equation never larger than the number of oxygen binding sites for
hemoglobin?
6
Oxygen concentration in the lung is much lower than in the air. Why?
7
Define P50 as used in the Hill equation.
8
Why is P50 similar to the Km for an enzyme reaction?
9
Why is blood bank blood thrown out after a few weeks of storage?
10 "R" state Hb is identical to:
(a) Oxyhemoglobin
(b) Deoxyhemoglobin
(c) the Hb conformation with high O2 affinity
(d) the Hb conformation with low O2 affinity
(e) the Hb conformation that binds BPG
11 Decreased affinity of Hb for O2 is given: (a) at higher pH
(c) at higher [H+]
(d) at lower [BPG]
(b) at lower [CO2]
12 Fetal Hb, Hb F, has a reduced capacity to bind BPG. What effect will this have on the affinity of Hb
F for oxygen, and what physiological advantage will this achieve?
13 What structural differences does high resolution X ray diffraction reveal for oxyHb compared to
deoxyHb?
Chem*3560 #3
1
What is the easiest way to determine if a solution of hemoglobin is oxygenated or not?
2
Why is cyanide CN- poisonous, and why is nitrite NO2 - which forms methemoglobin, used to treat
victims of cyanide poisoning?
3
Why is sickle cell anemia more commonly found in West Africans than in the U.S. black population
whose ancestors came from West Africa?
4
What makes thalassemias different from the anemias caused by genetic variants of Hb structure?
5
Where might you expect to find the highest proportion of thalassemias among the population?(A)
Guelph, Ontario
(B) Anchorage, Alaska
(C) Moscow, Russia
(D) Edinburgh, Scotland
(E) Beijing, China
6
DNA analysis is preferred as a method of testing fetuses for the sickle cell condition. Why not test
for HbS directly?
7
In "Southern blotting", the specific radioactive probe used is:
(A) a small DNA fragment
(B) an antibody
(C) messenger RNA
(D) a small peptide
(E) transfer RNA
8
Why is DNA in the region of the sickle cell gene (βs) cleaved only twice by the restriction
endonuclease enzyme that cleaves the normal β-globin gene region three times?
9
Butyrate CH3.CH2.CH2.COO promotes transcription of the γ globin gene. Why does this help to
-
alleviate sickle cell anemia?
10 Would butyrate therapy help all thalassemia patients?
Chem*3560 #4
1
Draw the activation energy barrier curve for an endergonic reaction. Which point corresponds to
the "transition state" and what is the effect of a catalyst on the shape of the curve?
2
What methods reveal that aspartate transcarbamoylase has quaternary structure?
3
What is the effect of p-hydroxymercuribenzoate on the enzyme activity of ATCase?
4
β-Mercaptoethanol (2-thioethanol) is used in biochemistry as :
(A) positive allosteric modulator
(B) negative allosteric modulator
(C) oxidizing agent
(D) reducing agent
(E) denaturing agent
5
Why is PALA (N-phosphoacetyl-L-aspartate) used to study binding to the active site of aspartate
transcarbamoylase (ATCase), instead of N-carbamoyl phosphate and L-aspartate?
6
What effect does PALA have on ATCase activity?
7
Complete the table:
ATCase subunit(s)
c6r6
c3
r2
c
r
Catalytic activity? + or Heterotropic allosteric behaviour?
Binding to CTP or ATP?
Binds substrates fully?
8
Large particles usually sediment in the ultracentrifuge faster than small particles. Why does
ATCase plus PALA sediment more slowly than ATCase alone?
9
Classify the following pairs of proteins and their ligands as (a) positive or negative;
(b) homotropic or heterotropic:
(1) Hemoglobin A:O2
(2) Hemoglobin A:BPG
(3) Hemoglobin A:CO2
(4) ATCase:ATP
(5) ATCase: carbamoylphosphate and L-aspartate
10 The concerted or symmetric model (M-W-C model) for allosteric effects only explains positive
homotropic effects and not negative homotropic effects. Why?
11 For the normal binding of Hb A tetramer to 4 O2, is the concerted (symmetric) model or the
sequential model the best explanation of allosteric behaviour?
12 Protein structures in texts are often represented as below. What secondary or tertiary structural
features can you deduce from the diagram?
13 Two proposed conformations for a single protein are shown below. In conformation I, this protein
is a harmless normal component of cells. In conformation 2, it is an infectious lethal agent of
disease, called a prion. How could a single protein be a cause of infectious disease transmitted
from one individual to another? How could a protein reproduce itself? Clue: think of co-operativity
between protein subunits, as in hemoglobin or ATCase. A full answer is found in AScientific
American@ January 1995, pages 48 - 57, and on the web pages
http://www.airtime.co.uk/bse/welcome.htm
http://www.diseaseworld.com/
http://www.sciam.com/0195issue/prion.html
Chem*3560 #5
1
How could you tell if a patient with a blood clotting deficiency has a defect in the "extrinsic pathway"
or in the "intrinsic pathway".
2
Aspirin reduces the clotting rate and increases the "bleeding time" of a patient, by reducing the
number and activity of platelets. Why should this slow the rate of clotting? ( Give 3 reasons ).
3
What kind of chemical bonding occurs when fibrin clots?
4
Why is a blood clot red in colour?
5
What laundry advice would you offer to a mass-murderer who wishes to get blood stains out of her
sheets?
6
Why does fibrinogen not polymerize whereas fibrin does?
7
Prothrombin binds to cell surfaces through Ca2+, but thrombin does not. Why?
8
Why does dicoumarol in "sweet clover" cause hemorrhagic disease in cattle?
9
In hemorrhagic disease in cattle, transcription and translation of the prothrombin gene is the same
as in normal cattle, yet prothrombin does not bind to calcium as does the normal prothrombin.
Why?
10 In what ways does thrombin resemble trypsin or chymotrypsin?
11 Why is the tissue-type plasminogen activator (tPA) often injected into patients immediately after
they have suffered a coronary artery blockage of the heart or a "stroke" (clot in the brain)?
12 Classic hemophilia (type A) is a deficiency of factor________ and hemophilia type B is a deficiency
of factor ___________.
13 What are the common biochemical features in proteolysis by the seven serine proteases of the
blood clotting cascade?
Chem*3560 #6
1.
Define the terms glycolysis; glycogenolysis; gluconeogenesis.
2.
You have isolated an animal tissue of unknown metabolism, which use
glucose as its energy source. How do you test the route of glucose breakdown in this tissue?
Give three tests.
4.
Why should mammalian liver, which carries out 90% of glucose
breakdown by the aerobic glycolytic route, at the same time carry out the pentose phosphate
pathway for glucose oxidation?
5.
Why should mammalian liver, at the same time as carrying out glycolytic and pentose phosphate
path breakdown of glucose, also be capable of the synthesis of glucose?
6.
Which of the following sugar phosphates would you expect to show mutarotation,
that
interconversion in water between α and β anomers?
Fru-2,6-bisphosphate; Fru-1,6-bisphosphate; Fru-6-phosphate; Ribulose-5-phosphate.
is,
7. The phosphofructokinase enzyme and the fructose 1,6 bisphosphate-1
phosphatase catalyze the same reaction in opposite directions.
(A) What are the essential differences in the two reactions?
(B) What would be the result of both reactions acting simultaneously?
(C) What physiological benefit could be derived from (B)?
(D) What physiological harm (pathology) could arise from (B)?
8.
When fructose 6 phosphate accumulates in glycolytic tissues such as
liver, a small amount is converted to fructose 2,6 bisphosphate. What effect will this synthesis have
on the breakdown and synthesis of Fru-6-phosphate?
9.
If a major function of the pentose phosphate pathway is to supply
reducing power for biosynthetic reductions, what molecule would you expect to be the major
controlling factor in this pathway? (A) NADP+; (B) NAD+ ; (C) ATP ; (D) NADH
10. Which of the following ratios is maintained HIGH in a tissue which
breaks down glucose?
(A) NADH/NAD+ ;
(B) NADPH/NADP+ ;
(C) AMP/ADP ;
(D) ADP/ATP
11. How does a tissue like liver, which produces both NADH and NADPH,
manage to maintain a low ratio ( reduced / oxidized) for one and a high ratio for the other?
1.
Chem*3560 #7
If you assume that caffeine acts only by affecting cyclic AMP levels, what effect would you predict
for caffeine on the level in liver of:
(A) Glycolysis
(B) Glycogenolysis
(C) Gluconeogenesis
(D) Fru 2,6 bisphosphate
2.
The enzyme Glc 6-phosphatase, which hydrolyzes Glc 6-phosphate to yield free Glc and Pi is found
in liver but not in muscle. Why?
3.
Protein kinases are enzymes that transfer phosphate groups from ATP to side chains on protein
amino acid residues:
(A) Thr (threonine)
(B) Ser (serine) (C) Tyr (tyrosine) (D) Cys (cysteine)
4.
In bacteria, cyclic AMP is made in response to
(A) excess glucose in medium (B) low glucose in medium (C) glucagon in medium
5.
In intestinal (gut) tissue, a toxin made by the cholera bacterium binds to a G protein associated with
hormone receptor and adenylate cyclase, and results in the massive secretion of salts and water
into the gut (diarrhea). What does this suggest about the control of water secretion?
6.
Cystic fibrosis is the most common genetic defect in Caucasians. It causes dry mucus to
accumulate in the lungs, due to the lack of water and chloride ion secretion across mucus
membranes. It is due to a defect in chloride ion transport from the cell to the exterior, and so less
chloride ion and water enter the gut and lungs. What benefit could this defect confer on
heterozygotes, which would lead to the conservation of this deadly genetic disease?
7.
The pancreatic hormone insulin has the opposite effect on blood glucose to that of glucagon.
Would you expect insulin to be secreted mainly
(A) before a meal (B) after a meal (C) during fasting or starvation?
8.
Why is a branched glucose polymer (glycogen) a much better storage form of glucose than a
linear glucose polymer such as amylopectin which is part of starch?
9.
There are numerous genetic diseases that result in the lack of muscle enzymes for glycogen
breakdown, including defective phosphorylase, branching enzyme, debranching enzyme etc. What
symptoms might you predict for these diseases?
10 The bifunctional or tandem enzyme ( phosphofructokinase 2/ FBP-2-phosphatase);
and glycogen phosphorylase; and glycogen synthase, are all
(A) activated by serine phosphorylation (B) inactivated by serine phosphorylation
(C) directly regulated by the same protein kinase
(D) controlled through cAMP-dependent serine kinase cascades.
11. What processes lead to the lowering of phosphorylase activity in liver or muscle cells? What
conscious actions can you take to lower this activity in muscle and liver?
Chem*3560 #8
1.
Muscle glycogen phosphorylase has sites on the enzyme for the binding of:
(A) ATP (B) AMP (C) Pyridoxal phosphate (D) Glycogen (E) Glucagon
2.
Protein phosphatase 1, an enzyme that dephosphorylates glycogen phosphorylase, hydrolyzes the
serine phosphate residue on:
(A) phosphorylase b T-form
(B) phosphorylase a T-form
(C) phosphorylase b R-form
(D) phosphorylase a R-form.
3.
Phosphorylase kinase in muscle is activated by (A) phosphatase action (B) calcium ion (C) cAMPdependent protein kinase (D) glucose.
4.
Fill in the following table for the effects of high and low blood glucose on the levels of enzymes and
metabolites ( High or Low) in liver:
Blood
Glucose
Cyclic
AMP
Glycogen
phosphorylase
Glycogen
Synthase
Protein phosphatase I
Low
High
5.
Fill in the following table to show how fatty acid synthesis contrasts with β-oxidation of fatty acids, in
mammals:
β-Oxidn.
Cell
location
Electron
carrier
Thioester
involved
Units
+/-
Mitochondria
NAD+ 6
NADH
Acyl-CoA
Acetyl
removed
Fatty Acid
Synthase
6.
What would you consider to be the major differences between the organization of β-oxidation
enzymes, and fatty acid synthase in the mammalian liver?
7.
What B vitamins (or cofactors, or prosthetic groups) would you expect to be vital for the synthesis
of fat in mammals?
8.
What factors regulate acetyl-CoA carboxylase activity in mammals?
Chem*3560 #9
1.
The build-up of the TCA cycle intermediate, citrate, will:
(A) Inhibit acetyl-CoA carboxylase (B) Stimulate glycolysis
(C) Inhibit glycolysis
(D) Stimulate synthesis of malonyl CoA.
2.
In the liver, the compound at the junction of glycolysis, gluconeogenesis, pentose phosphate
pathway, glycogen synthesis and glucose uptake/secretion is:
(A) Glucose 1-phosphate (B) Glucose-6-phosphate
(C) UDP-glucose (D) Fructose-6-phosphate (E) 6-phosphogluconate.
3.
A common starting point for the synthesis of fatty acids, sterols, ketone bodies and citrate is:
(A) Malonyl CoA (B) 3 hydroxy 3 methyl glutaryl CoA (C) Acetoacetyl CoA
(D) Acetyl CoA (E) Malonate.
4.
In prolonged starvation, the principal fuel for the brain is provided by:
(A) Ketone bodies (B) Amino acids (C) Glucose (D) Glycogen
(E) Triacylglycerols.
5.
In early starvation, a major source of energy for the synthesis of glucose in the liver is: (A) Protein
(B) Fat (C) Glycogen (D) Ketone bodies.
6.
When glucagon is released into the blood, what effect might you expect on blood levels of the
following: (A) Blood glucose (B) Blood fatty acid (C) Blood glycerol.
7.
What chemical composition would you expect for a typical plasma membrane? (A) High lipid
(B) High protein (C) No carbohydrate (D) No nucleic acid .
8.
Compared with extracellular fluids, the cytosol has: (A) Low K+ (B) Low protein (C) Low Ca++ (D)
Low Mg++ (E) Low phosphate.
9.
Compared with intracellular fluid (cytosol), the extracellular fluids have:
(A) High K+ (B) High chloride (C) High Mg++ (D) High phosphate (E) High Na+.
10. Predict which of the following lipids are amphipathic and will therefore form ordered structures in
water:
(A) Fatty acid, Na salt
(B) Fatty acid methyl ester
(C) Fatty acyl CoA
(D) Fatty acid, protonated form.
11. Which of the following would you expect to pass easily across the plasma membrane lipid bilayer?
(A) NaCl
(B) H2O
(C) Glycerol
(D) 2,3 bis-phosphoglycerate
(E) Glucose-6-phosphate.
Chem*3560 #10
1.
N-Acetyl-D-glucosamine residues are found in glycoproteins often linked to the side chains of
(A) Asparagine (B) Aspartate
(C) Alanine
(D) Serine
(E) Threonine.
2.
Cerebrosides are glycolipids which contain
(B) Ceramide
(C) N-Acyl groups
3.
Cell surface antigens of the human ABO blood groups are found
(A) In human plasma
(B) In human serum (C) On human lymphocytes
(D) On human erythrocytes (R.B.C.)
(E) Only on human glycoproteins.
4.
The Rhesus antigen on the surface of Rhesus-positive fetal RBC can cause antibody production in
the maternal serum of Rhesus-negative mothers, which leads to hemagglutination in the blood of
new born infants (blue babies). Why are such mothers given intra-venous anti-Rhesus antibodies
at all births?
(A) To titrate antigen
(B) To agglutinate the baby's RBC
(C) To make anti-antibody antibodies
5.
The digitalis (foxglove) component, digitonin, will stop the heart by irreversibly binding to the
Na+/K+ ATPase. However, a smaller amount of digitonin will strengthen the heart muscle
contraction, by increasing the Ca++ content of heart muscle cells. What does this tell you about the
mechanism for controlling Ca++ inside these cells?
(A) There is a Na+/Ca++ symport
(B) There is a Na+/Ca++ antiport
(C) A Ca++-ATP-ase is needed for Ca++ export.
6.
A clumsy murderer might make use of digitalis to poison her victim. A clever murderer would
achieve the same deadly effect by intravenously injecting:
(A) CaCl2 (B) NaCl
(C) KCl.
7.
Arsenate As043- and vanadate V043- both are poisons and useful inhibitors in biochemistry. They
both act through their chemical similarity to (A) ATP (B) ADP (C) AMP (D) Phosphate
(A) Sphingomyelin
(D) Choline (E) Phosphate.