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Text: Concepts in Biochemistry, 2nd Edition (Rodney Boyer)
Supplementary material: Interactive Concepts in Biochemistry CD
Website: http://www.boyerbiochem.com
Chapter
Lecture
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Topic
CD Resources/
Assignment
Part I. Molecules and Life, Chapters 1-4
Course Introduction, Organic Chemistry
Overview
What is biochemistry? Organelles, Cells,
and Organisms
Noncovalent interactions. Brief overview
of biological information, DNA, RNA, and
protein synthesis
Cutting Edge: Hot Careers in
Biochemistry, Visionaries of Science
Interactive Animation: Cell Structure
Structure Tutorial: DNA, tRNA
Interactive Animation: Central Dogma of
Biochemistry, Protein Synthesis, Signal
Transduction; Concept Review:
Noncovalent bonding
Cutting Edge: Molecular Recognition
Concept Review: Logarithms;
Water, pH and noncovalent bonding
Structure of water. Biomolecules in water,
pH, pKa
Henderson-Hasselbalch Equation, Buffers
Properties of amino acids: acid base
Interactive Animation: Amino Acid Game
reactions, classification, reactivity
Structure Tutorial: Antibodies
Polypeptides and proteins. Protein
function, size, composition, properties
Protein structure, sequencing,
chromatography
Examination # 1, Chapters1-4
Background Material
Needed for Lecture
Overview of organic chemistry
principles
Organic Chemistry: functional
groups
Electronegativity. Chemical
bonding: covalent, polarcovalent, and ionic bonds
Acids and bases. Hydrogen
bonding
Stereochemistry: isomerism,
chiral molecules, drawing
chemical structures.
Noncovalent interactions
Part II. Dynamic Function of Biomolecules, Chapters 5-9
5
9
10
Protein design: 10, 20 structure.
Protein design: 30, 40 structure. Biological
function of some proteins
6
11
Enzymes: catalysis, nomenclature,
kinetics (Michaelis-Menten equation)
Enzymes: reactions, mechanism,
inhibition
12
Structure Tutorials: Secondary Structure
Interactive Animation: Protein Folding
Structure Tutorials: Myoglobin,
Hemoglobin, Kinesin, Antibodies.
Cutting Edge: Prions
Concept Review: Elementary Kinetics
Interactive Animation: Catalysis, Enzyme
Specificity, Enzyme Inhibition
Cutting Edge: AIDS Therapies
Noncovalent interactions.
Properties of amino acid side
chains (Chapter 4)
Interpreting graphs. Slope of a
line. Acids and bases.
Noncovalent interactions.
7
13
14
Enzymes: coenzymes
Enzymes: regulation
Structure Tutorial: Antibodies
Cutting Edge: Ribozymes, Catalytic
Antibodies
8
15
16
Carbohydrates: structure, reactions
Carbohydrates: disaccharides,
polysaccharides, glycoproteins
Cutting Edge: Molecular Recognition
9
17
18
Lipids: structure, function
Lipids: biological membranes, membrane
transport
Interactive Animation: Cholesterol,
Cellular Transport
Cutting Edge: Fat blockers
Interpretation of graphs.
Formation and cleavage of
phosphoesters, amides,
disulfides.
Oxidation of aldehydes.
Hemiacetal and acetal
formation. Stereochemistry:
isomerism, chiral molecules,
drawing chemical structures.
Cell structure (Chapter 1).
Nonpolar interactions.
Formation and cleavage of
esters, amides.
Examination # 2, Chapters 5-9
Part III. Storage and Transfer of Biological Information, Chapters 10-13
10
19
20
11
12
21
22
23
13
24
14
25
DNA, RNA: composition, structural
elements
DNA, RNA: nucleases, nucleic acidprotein complexes
Structure Tutorial: DNA, tRNA
Interactive Animation: Central Dogma of
Biochemistry, Nucleotides Game,
Restriction Digestion and Electrophoresis
Cutting Edge: AIDS Therapies
DNA: replication, damage and repair
Interactive Animation: DNA Replication
RNA: synthesis (transcription), processing Cutting Edge: Telomeres, Ribozymes
RNA Translation: genetic code, protein
Structure Tutorial: tRNA, Protein-DNA
synthesis, processing, regulation
Interactions.
Interactive Animation: Central Dogma of
Biochemistry, Protein Synthesis
Recombinant DNA: cloning vectors,
Interactive Animation: Cloning,
applications
Polymerase Chain Reaction
Cutting Edge: DNA Fingerprinting
Examination # 3, Chapters 10-13
Hydrophobic interactions,
hydrogen bonds. Formation of
phosphoesters, N-glycosidic
bonds. Structure of aromatic
heterocyclic compounds.
Nucleotide structure. DNA,
RNA structure. Enzymes.
Cell structure, Ribosomes, ER
(Chapter 1). Protein structure
(Chapter 5).
Bacterial cell. Bacterial, and
eukaryotic DNA.
Part IV. Metabolism and Energy, Chapters 14-20
Introduction to metabolism, Bioenergetics
Concept Review: Thermodynamics,
Redox Reactions, Logarithms
Interactive Animation: Introduction to
Metabolism
Bond energy, Hess’s Law.
Standard Free Energy change
for reactions, Go.
Phosphoester, thioester and
amide formation and hydrolysis.
15
16
17
18
26
Metabolism of Carbohydrate: Glycolysis.
Dietary carbohydrates, glycogen and
starch.
27
28
Metabolism of Carbohydrates: Lactate,
ethanol fermentation. Gluconeogenesis,
regulation of carbohydrate metabolism.
Pyruvate Dehydrogenase Complex
29
The Citric acid cycle, regulation and roles
Structure Tutorial: Hexokinase,
Phosphofructokinase
Interactive Animation: Glycolysis,
Gluconeogenesis
Interactive Animation: Gluconeogenesis
Cutting Edge: Alcohol Abuse; Methanol
as fuel
Interactive Animation: Pyruvate Dehydrogenase Complex, Citric Acid Cycle
Interactive Animation: Citric Acid Cycle
30
Electron transport
Concept Review: Redox Reactions
31
Oxidative phosphorylation
Interactive Animation: Oxidative
Phosphorylation
32
Photosynthesis
Interactive Animation: Photosynthesis
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34
19
35
36
20
37
38
Examination # 4, Chapters 14-17
Metabolism of Lipids: triacylglycerols, beta Interactive Animation: Fatty Acid
oxidation of fatty acids
Metabolism
Cutting Edge Article: Fat Blockers
Metabolism of Lipids: biosynthesis of fatty Interactive Animation: Cholesterol
acids, cholesterol, transport of lipids
Metabolism of Amino Acids and other
Cutting Edge Article: Homocysteine
Nitrogen Compounds: Nitrogen cycle, biosynthesis and catabolism of amino acids.
Metabolism of Amino Acids and other
Cutting Edge Article: Nitric Oxide and
Nitrogen Compounds: Amino acid
Viagra
metabolism, Urea cycle, purine and
pyrimidine metabolism.
Integration of metabolism: Strategies of
Interactive Animation: Cori Cycle
metabolism, specialization and integration Interactive Animation: Metabolic Process
Location
Integration of metabolism: Metabolic
Cutting Edge Article: Fat Blockers
control, response to stress, obesity
Cumulative Final Examination
Carbohydrate structure
(Chapter 8).
Regulation of Allosteric
Enzymes (Chapter 7). Signal
transduction (Chapter 2).
Cell structure; organelles,
(Chapter 1). Coenzymes
(Chapter 7)
Metabolic reaction types
(Chapter 14). Gluconeogensis
(Chapter 15)
Cell structure; organelles
(Chapter1). Cell membranes
(Chapter 9). Oxidationreduction principles.
Bioenergetics (Chapter 14).
Structure of ATP (Chapter 14).
Structure of plant cells (Chapter
1). Cell membranes (Chapter 9)
Structure of fatty acids,
triglycerides (Chapter 9)
Metabolic reaction types
(Chapter 14)
Amino acid structures (Chapter
4). Citric acid cycle (Chapter 16)
Overview of carbohydrate, lipid,
and nitrogen metabolism.
Signal transduction (Chapter 2).