BCH 4053 (section 2)
Fall 2003

Dr. Michael Blaber

Lecture: MWF 12:20 - 1:10 p.m.
303 MCH

Course URL:
http://wine1.sb.fsu.edu/bch4053/

 

Syllabus

 

Description/Objectives

General Biochemistry I. Lecture 3 hours per week.

The first biochemistry course recommended for chemistry and biology majors and for students who intend to study medicine. Proteins, carbohydrates, lipids and nucleic acids; Thermodynamics, kinetics and enzymology; Metabolism, glycolysis, TCA cycle and oxidative phosphorylation.

Text: Biochemistry. Garrett and Grisham. Second Edition. Harcourt Brace College Publishers.
ISBN: 0-03-022318-0

Web resource: http://wine1.sb.fsu.edu/bch4053/bch4053.htm
Online syllabus: http://wine1.sb.fsu.edu/bch4053/syllabus/syllabus.htm

This is a very difficult course that covers a large amount of material. IT IS EASY TO FALL BEHIND, and once behind, it is difficult to catch up. The best thing you can do to pass this course is to set up a study schedule that will enable you to adequately read and study the required material. It is recommended that you read the relevant text material before coming to lecture.

Requirements

Prerequisites: 1 year organic chemistry (e.g. CHM 2210 and 2211) or equivalent. Note that this is a prerequisite and NOT a co-requisite (i.e. it must have already been completed and cannot be taken concurrently).

Grading/Evaluation

Exam

Material

Date

EXAM 1

Part I.

Molecular components of cells

Chapters 1-7

Chemistry is the logic of biological phenomena
Water, pH and ionic equilibria
Thermodynamics of biological systems
Amino acids
Proteins: their biological functions and primary structure
Proteins: secondary, tertiary and quaternary structure
Carbohydrates

Monday Sep 29

Exam 2

Part I.

Molecular components of cells

cont.

Chapters 8-13

Lipids
Membranes and cell surfaces
Membrane transport
Nucleotides and nucleic acids
Structure of nucleic acids
Recombinant DNA: cloning and creation of chimeric genes

Wednesday Oct 29

Exam 3

Part II.

Protein dynamics

Chapters 14-17

Enzyme kinetics
Enzyme specificity and regulation
Mechanisms of enzyme action
Molecular motors

Monday Nov 17

Final Exam

Part III.

Metabolism and its regulation

Chapters 18-21

Metabolism: an overview
Glycolysis
The tricarboxylic acid cycle
Electron transport and oxidative phosphorylation

Tuesday Dec 9

10:00 a.m. - 12:00 noon
Location: 303 MCH

 

Click here for the regrade form

³ 93%

A

³ 90%

A-

³ 87%

B+

³ 83%

B

³ 80%

B-

³ 77%

C+

³ 73%

C

³ 70%

C-

³ 60%

D

<60%

F

Contact with Instructor

Dr. Michael Blaber
406 Kasha Institute of Molecular Biophysics
(850) 644-1863
blaber@sb.fsu.edu

Office Hours

Monday and Wednesday, 10:00-10:50 a.m., Room 406 Kasha Institute of Molecular Biophysics

Honor Code

Students are expected to uphold the Academic Honor Code. The Academic Honor System of The Florida State University is based on the premise that each student has the responsibility to:

1. Uphold the highest standards of academic integrity in the student's own work,
2. Refuse to tolerate violations of academic integrity in the University community, and
3. Foster a high sense of integrity and social responsibility on the part of the University community.

Click on Academic Honor Code for a full statement of the FSU Code.

While you may work with other students on the homework assignments, exams are an exercise in individuality. Any cheating on an exam will result in an automatic score of 0 points for that exam and may result in a grade of 'F' for the course.

ADA Requirements

This syllabus and other class materials are available in alternative format upon request.

Students with disabilities needing academic accommodations should:
1. Register with and provide documentation to the Student Disability Resource Center (SDRC).
2. Bring a letter to the instructor form the SDRC indicating you need academic accommodations. This should be done within the first week of class.


For more information about services available to FSU students with disabilities, contact the Assistant Dean of Students:
sdrc@admin.fsu.edu, Disabled Student Services, 08 Kellum Hall, Florida State University, Tallahassee, FL 32306-4066, (850) 644-9566.
 

Course Calendar

Date

Chapter

Subject

Section

Text

pp

Mon
Aug 25

Part I. MOLECULAR COMPONENTS OF CELLS

Chapter 1:
Chemistry is the logic of biological phenomena

Distinctive properties of living systems
Biomolecules: the molecules of life
A biomolecular hierarchy

1.1
1.2
1.3

3-6
6-9
9-12

10

Wed
Aug 27

Properties of biomolecules reflect their fitness to the living condition
Organization and structure of cells
Viruses

1.4
1.5
1.6

12-23
23-30
30-31

20

Fri
Aug 29

Chapter 2:
Water, pH, and ionic equilibria

Properties of water
pH
Buffers
Water's unique role

2.1
2.2
2.3
2.4

35-43
43-49
50-53
53

19

Mon
Sep 1

Labor Day
no class

Wed
Sep 3

Chapter 3:
Thermodynamics of biological systems

Basic thermodynamic concepts
The physical significance of thermodynamic properties
The effect of pH on standard-state free energies

3.1
3.2
3.3

57-63
63-64
64-65

9

Fri
Sep 5

Effect of concentration on net free energy changes
Coupled processes in living things The high-energy biomolecules
Complex equilibria involved in ATP hydrolysis
Daily human ATP requirement

3.4
3.5
3.6
3.7
3.8

65
65-66
66-76
77-78
78-79

15

Mon
Sep 8

Chapter 4:
Amino Acids

Amino acids: building blocks of proteins
Acid-base chemistry of amino acids
Reactions of amino acids

4.1
4.2
4.3

82-87
88-93
93-96

15

Wed
Sep 10

Optical activity and stereochemistry of amino acids
Spectroscopic properties of amino acids
Separation and analysis of amino acid mixtures

4.4
4.5
4.6

96-99
99-101
101-105

10

Fri
Sep 12

Chapter 5:
Proteins: their biological functions and primary structure

Proteins are linear polymers of amino acids
Architecture of protein molecules
The many biological functions of proteins

5.1
5.2
5.3

108-115
115-120
120-126

19

Mon
Sep 15

Some proteins have chemical groups other than amino acids
Reactions of peptides and proteins
Purification of protein mixtures
The primary structure of a protein
Nature of amino acid sequences
Synthesis of polypeptides

5.4
5.5
5.6
5.7
5.8
5.9

126-128
128
128-130
130-142
142-149
149-150

25

Wed
Sep 17

Chapter 6:
Proteins: secondary, tertiary and quaternary structure

Forces influencing protein structure
Role of the amino acid sequence in protein structure
Secondary structure in proteins

6.1
6.2
6.3

159-160
160-161
161-171

13

Fri
Sep 19

Protein folding and tertiary structure
Subunit interactions and quaternary structure

6.4
6.5

171-200
200-206

36

Mon
Sep 22

Chapter 7:
Carbohydrates

Carbohydrate nomenclature
Monosaccharides

7.1
7.2

210
210-220

11

Wed
Sep 24

Oligosaccharides
Polysaccharides

7.3
7.4

221-226
227-235

15

Fri
Sep 26

Chapter 8:
Lipids

Fatty acids
Triacylglycerols
Glycerophospholipids
Sphingolipids
Waxes
Terpenes
Steroids

8.1
8.2
8.3
8.4
8.5
8.6
8.7

239-242
242-243
243-249
249-251
251
251-254
254-256

18

Mon
Sep 29

Exam 1:
Chapters 1-7

Wed
Oct 1

Chapter 9:
Membranes and cell surfaces

Membranes
Structure of membrane proteins

9.1
9.2

260-270
270-278

19

Fri
Oct 3

Membranes and cell-surface polysaccharides
Glycoproteins
Proteoglycans

9.3
9.4
9.5

279-284
284-289
289-293

15

Mon
Oct 6

Chapter 10:
Membrane transport

Passive diffusion
Facilitated diffusion
Active transport systems
Transport processes driven by ATP

10.1
10.2
10.3
10.4

297-298
298-301
301
301-309

13

Wed
Oct 8

Transport processes driven by light
Transport processes driven by ion gradients
Group translocation
Specialized membrane pores
Ionophore antibiotics

10.5
10.6
10.7
10.8
10.9

309-311
311-312
312-313
313-321
321-324

16

Fri
Oct 10

Chapter 11:
Nucleotides and nucleic acids

Nitrogenous bases
The pentoses of nucleotides and nucleic acids
Nucleosides are formed by joining a nitrogenous base to a sugar
Nucleotides are nucleoside phosphates
Nucleic acids are polynucleotides

11.1
11.2
11.3
11.4
11.5

328-330
330-331
331-333
333-336
336-338

11

Mon
Oct 13

Classes of nucleic acids
Hydrolysis of nucleic acids

11.6
11.7

338-347
347-353

16

Wed
Oct 15

WEB LECTURE

Chapter 12:
Structure of nucleic acids

The primary structure of nucleic acids
The ABZ's of DNA secondary structure
Denaturation and renaturation of DNA

12.1
12.2
12.3

357-363
363-371
371-375

19

Fri
Oct 17

WEB LECTURE

Supercoils and cruciforms: tertiary structure in DNA
Chromosome structure
Chemical synthesis of nucleic acids
Secondary and tertiary structure of RNA

12.4
12.5
12.6
12.7

375-378
378-382
382-386
386-390

16

Mon
Oct 20

Chapter 13:
Recombinant DNA: cloning and creation of chimeric genes

Cloning
DNA libraries

13.1
13.2

396-405
405-417

22

Wed
Oct 22

Polymerase chain reaction
Recombinant DNA technology

13.3
13.4

417-419
419-422

6

Fri
Oct 24

Part II. PROTEIN DYNAMICS

Chapter 14:
Enzyme kinetics

Enzymes - catalytic power, specificity and regulation
Introduction to enzyme kinetics
Kinetics of enzyme-catalyzed reactions

14.1
14.2
14.3

427-431
431-434
434-443

17

Mon
Oct 27

Enzyme inhibition
Kinetics of enzyme-catalyzed reactions involving two or more substrates
RNA and antibody molecules as enzymes: ribozymes and abzymes

14.4
14.5
14.6

443-448
448-454
454-458

16

Wed
Oct 29

Exam 2:
Chapters 8-13

Fri
Oct 31

Chapter 15:
Enzyme specificity and regulation

Specificity is the result of molecular recognition
Controls over enzymatic activity
The allosteric regulation of enzyme activity
Model for the allosteric behavior of proteins

15.1
15.2
15.3
15.4

461-462
462-468
468-469
469-473

13

Mon
Nov 3

Glycogen phosphorylase: allosteric regulation and covalent modification
Hemoglobin and myoglobin

15.5

473-480
480-493

21

Wed
Nov 5

Chapter 16:
Mechanisms of enzyme action

The basic principle - stabilization of the transition state
Enzymes provide enormous rate accelerations
The binding energy of ES is crucial to catalysis
Entropy loss and destabilization of the ES complex
Transition-state analogs bind very tightly to the active site
Covalent catalysis
General acid-base catalysis
Metal ion catalysis
Proximity

16.1
16.2
16.3
16.4
16.5
16.6
16.7
16.8
16.9

501-503
503-504
504-505
505-507
507-508
508-511
511
511-512
512-513

13

Fri
Nov 7

Typical enzyme mechanisms
Serine proteases
The aspartic proteases
Lysozyme

16.10
16.11
16.12
16.13

513-514
514-519
519-526
526-530

18

Mon
Nov 10

Chapter 17:
Molecular motors

Molecular motors
Microtubules and their motors

17.1
17.2

533-534
534-540

8

Wed
Nov 12

Skeletal muscle myosin and muscle contraction
A proton gradient drives the rotation of bacterial flagella

17.3
17.4

540-561
561-563

24

Fri
Nov 14

Part III. METABOLISM AND ITS REGULATION
Homecoming
CLASS WILL BE HELD!

Chapter 18:
Metabolism: an overview

Virtually all organisms have the same basic set of metabolic pathways
Metabolism consists of catabolic and anabolic pathways
Experimental methods to reveal metabolic pathways

18.1
18.2
18.3

569-571
571-579
579-584

16

Mon
Nov 17

Exam 3:
Chapters 14-17

Wed
Nov 19

Nutrition and vitamins

18.4

584-608

25

Fri
Nov 21

Chapter 19:
Glycolysis

Overview of glycolysis
The importance of coupled reactions in glycolysis
The first phase of glycolysis

19.1
19.2
19.3

610
610-613
613-622

13

Mon
Nov 24

The second phase of glycolysis
The metabolic fates of NADH and pyruvate - the products of glycolysis
Anaerobic pathways for pyruvate
The energetic elegance of glycolysis
Utilization of other substrates in glycolysis

19.4
19.5
19.6
19.7
19.8

622-631
631
631-632
632-633
633-637

16

Wed
Nov 26

Chapter 20:
The tricarboxylic acid cycle

Hans Krebs and the discovery of the TCA cycle
The TCA cycle - a brief summary
The bridging step: oxidative decarboxylation of pyruvate
Entry into the cycle: the citrate synthase reaction
The isomerization of citrate by aconitase
Isocitrate dehydrogenase - the first oxidation in the cycle
a-ketoglutarate dehydrogenase - a second decarboxylation
Succinyl-coA synthetase - a substrate-level phosphorylation
Succinyl dehydrogenase - an oxidation involving FAD
Fumarase catalyzes trans-hydration of fumarate
Malate dehydrogenase - completing the cycle

20.1
20.2
20.3
20.4
20.5
20.6
20.7
20.8
20.9
20.10
20.11

641-642
642-644
644
644-648
648-651
651-652
652
652-654
654
654-655
655-659

19

Fri
Nov 28

Thanksgiving
no class

Mon
Dec 1

SUSSAI evaluation of instructor

A summary of the cycle
The TCA cycle provides intermediates for biosynthetic pathways
The anaplerotic, or "filling up" reactions
Regulation of the TCA cycle
The glyoxylate cycle of plants and bacteria

20.12
20.13
20.14
20.15
20.16

659-661
661-663
663-665
665-668
668-671

13

Wed
Dec 3

Chapter 21:
Electron transport and oxidative phosphorylation

Electron transport and oxidative phosphorylation are membrane-associated processes
Reduction potentials - an accounting device for free energy changes in redox reactions
The electron transport chain - an overview
Complex I: NADH-coenzyme Q reductase
Complex II: Succinate-coenzyme Q reductase
Complex III: Coenzyme Q-cytochrome c reductase

21.1
21.2
21.3
21.4
21.5
21.6

674-675
675-679
679-681
681-683
683-685
685-688

15

Fri
Dec 5

Complex IV: Cytochrome c oxidase
The thermodynamic view of chemiosmotic coupling
ATP synthase
Inhibitors of oxidative phosphorylation
Uncouplers disrupt the coupling of electron transport and ATP synthase
ATP exits the mitochondria via an ATP-ADP translocase
What is the P/O ratio for electron transport and oxidative phosphorylation?
Shuttle systems feed the electrons of cytosolic NADH into electron transport

21.7
21.8
21.9
21.10
21.11
21.12
21.13
21.14

688-692
692-694
694-698
698-700
700-701
701-702
702
702-705

18

Tue
Dec 9

Final exam:
Chapters 18-21

10:00a.m. -12:00 noon
Location: 303 MCH

Last Updated on 8/29/03
By Dr. Michael Blaber

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