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Course Description for Basic Biochemistry - Fall 1999 | CHM 305, Study notes of Biochemistry

Material Type: Notes; Class: Basic Biochemistry; Subject: Chemistry; University: Lourdes College; Term: Summer I 1999;

Typology: Study notes

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Course Outline
CHM 305 Basic Biochemistry
May 1999
Department: Chemistry and Physical Sciences
Credit Hours: 3
Prerequisite: CHM/CHL 302 or approval of instructor
General Education: 7.1 Scientific Literacy
College Learning Outcomes: Scientific Literacy 7a-d, Critical Thinking 2a,b
Course Description
Includes the chemistry of living systems, considers carbohydrates, lipids, nucleic acids, and
proteins.
Purpose of the Course
To introduce the student to the basic concepts and language of biochemistry.
College Learning Outcomes and Objectives:
L.O. 7 Scientific Literacy โ€“ Graduates can demonstrate an understanding of natural
and behavioral scientific principles, technology, and methods.
a. They can distinguish between the qualitative and quantitative characteristics of
natural phenomena.
b. They can apply scientific principles and methods to support or disprove hypotheses.
c. They can use theories to explain past observations and to predict answers to new
questions.
d. They can understand the uses of scientific technology and their implications.
L.O. 2 Critical Thinking Ability โ€“ Graduates can analyze issues and theories rationally,
logically, and coherently using both qualitative and quantitative information.
a. They can demonstrate an explicit understanding of principles of critical thought.
b. They can demonstrate the ability to reflect on issues and/or theories systematically
Course Objectives
In order to gain mastery in the field of biochemistry, the student should be able to:
1. Identify the four major classes of biological molecules. (L.O. 7a)
2. Understand protein structure and the role it plays in the function of proteins. (L.O. 7a-
d, 2a, 2b)
3. Explain enzyme kinetics. (L.O. 7a-d, 2a, 2b)
4. Understand metabolism of carbohydrates, fats and proteins. (L.O. 7a-c, 2a, 2b)
5. Explain the electron transport chain, oxidative phosphorylation and Kreb's cycle. (L.O.
7a-c, 2a, 2b)
6. Explain the roles of DNA and RNA in heredity. (L.O. 7a-d, 2a, 2b)
Topical Outline
I. Water, pH and Ionic Equilibria
A. Properties of water
B. pH
1. Dissociation of strong electrolytes
2. Dissociation of weak electrolytes
3. Henderson-Hasselbach equation
4. Titration curves
C. Buffers
II. Amino acids
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Course Outline CHM 305 Basic Biochemistry May 1999

Department: Chemistry and Physical Sciences Credit Hours: 3 Prerequisite: CHM/CHL 302 or approval of instructor General Education: 7.1 Scientific Literacy College Learning Outcomes: Scientific Literacy 7a-d, Critical Thinking 2a,b

Course Description Includes the chemistry of living systems, considers carbohydrates, lipids, nucleic acids, and proteins.

Purpose of the Course To introduce the student to the basic concepts and language of biochemistry.

College Learning Outcomes and Objectives: L.O. 7 Scientific Literacy โ€“ Graduates can demonstrate an understanding of natural and behavioral scientific principles, technology, and methods. a. They can distinguish between the qualitative and quantitative characteristics of natural phenomena. b. They can apply scientific principles and methods to support or disprove hypotheses. c. They can use theories to explain past observations and to predict answers to new questions. d. They can understand the uses of scientific technology and their implications.

L.O. 2 Critical Thinking Ability โ€“ Graduates can analyze issues and theories rationally, logically, and coherently using both qualitative and quantitative information. a. They can demonstrate an explicit understanding of principles of critical thought. b. They can demonstrate the ability to reflect on issues and/or theories systematically

Course Objectives

In order to gain mastery in the field of biochemistry, the student should be able to:

  1. Identify the four major classes of biological molecules. (L.O. 7a)
  2. Understand protein structure and the role it plays in the function of proteins. (L.O. 7a- d, 2a, 2b)
  3. Explain enzyme kinetics. (L.O. 7a-d, 2a, 2b)
  4. Understand metabolism of carbohydrates, fats and proteins. (L.O. 7a-c, 2a, 2b)
  5. Explain the electron transport chain, oxidative phosphorylation and Kreb's cycle. (L.O. 7a-c, 2a, 2b)
  6. Explain the roles of DNA and RNA in heredity. (L.O. 7a-d, 2a, 2b)

Topical Outline I. Water, pH and Ionic Equilibria A. Properties of water B. pH

  1. Dissociation of strong electrolytes
  2. Dissociation of weak electrolytes
  3. Henderson-Hasselbach equation
  4. Titration curves C. Buffers

II. Amino acids

A. Structure of amino acids B. Acid-base chemistry C. Reactions D. Optical activity and stereochemistry

III. Proteins: Biological Functions and Structure A. Formation of the peptide bond B. Characteristics of the peptide bond C. Biological functions of proteins D. Primary structure E. Forces influencing protein structure

  1. Hydrogen bonds
  2. Hydrophobic interactions
  3. Electrostatic interactions
  4. Van der Waals interactions F. Secondary structure
  5. Alpha-helix
  6. Beta-pleated sheet
  7. Beta-turn
  8. Supersecondary structure G. Protein folding and tertiary structure
  9. Fibrous proteins
  10. Globular proteins
  11. Molecular chaperones
  12. Protein modules H. Quaternary structure
  13. Symmetry of quaternary structure
  14. Forces driving quaternary structure

IV. Lipids and Membranes A. Classes of lipids

  1. Fatty acids
  2. Triacylglycerols
  3. Glycerophospholipids
  4. Sphingolipids
  5. Waxes
  6. Terpenes
  7. Steroids B. Membranes
  8. Spontaneously formed lipid structures
  9. Fluid mosaic model
  10. Asymmetry C. Structure of membrane proteins
  11. Integral membrane proteins
  12. Lipid-anchored membrane proteins

V. Carbohydrates A. Nomenclature B. Monosaccharides

  1. Classification
  2. Stereochemistry
  3. Cyclic structures and anomeric forms
  4. Haworth projections
  5. Derivatives of monosaccharides C. Oligosaccharides
  6. Disaccharides

F. Physical significance of thermodynamic properties G. Effect of pH on standard-state free energies H. Effect of concentration on net free energy changes I. Coupled processes in living things J. Energy-rich compounds

  1. ATP and other phosphoric acid anhydrides
  2. Equilibria involved in ATP hydrolysis

VIII. Overview of metabolism A. Carbon and nitrogen cycles B. Catabolism C. Anabolism D. Role of NAD+, NADP+, and FAD

IX. Glycolysis A. Importance of coupled reactions B. First phase (reactions 1-5) C. Second phase (reactions 6-10) D. Metabolic fates of NADH and pyruvate E. Anaerobic pathways for pyruvate F. Regulation of glycolysis G. Utilization of other substrates in glycolysis

X. The tricarboxylic acid (TCA) cycle A. Overview of the TCA cycle B. Bridging step between glycolysis and the TCA cycle C. Reactions of the TCA cycle D. Regulation of the TCA cycle E. Anaplerotic reactions

XI. Electron transport and oxidative phosphorylation A. Reduction potentials B. Overview of the electron transport chain C. Reactions of the electron transport chain D. Chemiosmotic coupling โ€“ formation of ATP E. Inhibitors of oxidative phosphorylation F. Uncouplers that disrupt the coupling of the electron transport and ATP synthase G. Shuttle systems for cytosolic NADH H. ATP-ADP translocase

XII. Gluconeogenesis, glycogen metabolism and the pentose phosphate pathway A. Gluconeogenesis reactions B. Regulation of gluconeogenesis C. Glycogen catabolism D. Glycogen synthesis E. Control of glycogen metabolism F. Pentose phosphate pathway

XIII. Fatty acid catabolism A. Mobilization of fats from dietary intake and adipose tissue B. Reactions of beta oxidation of fatty acids C. Beta oxidation of odd-carbon fatty acids D. Beta oxidation of unsaturated fatty acids E. Ketone bodies

XIV. Nucleotides and nucleic acids

A. Components of nucleotides

  1. Nitrogenous bases
  2. Pentoses
  3. Phosphate B. Composition of nucleic acids
  4. DNA
  5. RNA C. Primary structure of nucleic acids D. Secondary structure of DNA E. Tertiary structure of DNA F. Denaturation and renaturation of DNA G. Chromosome structure H. Secondary and tertiary structure of RNA

XV. DNA replication General features of DNA replication

  1. Semiconservative
  2. Bidirectional
  3. Semidiscontinuous
  4. RNA primers