CH112: Chemistry of Organic and
Biological Molecules

Day/Date

Web Links

Chapter Readings

Activities

Organic Chemistry

1, 1/13 Tu2

Introduction to Organic Chem

syllabus review;

representing molecular structure;

structure/properties of molecules:

glucose vs hexane

2, 1/15 Th4

Functional Groups

Computer Lab: Functional Groups

Chapt 23

pg 984-1000 (to alkene and reactions);

Functional Group "dry lab".

3: 1/19 M6

Introduction to Organic Chem (con't)

Reaction Mechanisms;Drawing Reaction Mechanisms

Nucleophiles, electrophiles

Intro. to carbonyl chemistry

Chapt 23

Qz: Identify Functional Groups;

isomers: structural/configurational

Breaking bonds to carbon: carbanions, carbocations, free radicals

4, 1/21 W2

Chemistry: of Carbonyls : nucleophile addition and substition

1. Aldehydes, Ketones

2. Carboxylic Acid Derivatives

3. Protonation/Deprotonation of Intermediates

4. hydrolysis of carboxylic acid derivatives

1. Acids and Bases - A review

2. Animation:  Reaction of HCl and water.
3. Formation of Molecular Ions from Acids
4. HCl + H20: Space fill model, electron density model, and reaction mechanism.
5. Strengths of Acids: Stability of negatively charged product (base)

Relative reactivity of carboxylic acid anhydrides to hydrolysis

Chapt 4.6; 15.1-15)

5, 1/23 F4

Ordering Strong and Weak Acids

Organic Molecules as Acids: pKa's

4 Rules of Chemical Reactivity

Review of Bases - Amines as weak bases

Lab Day 5 (Monday  1/26):  functional group identification

Quiz:  Mechanism - carboxylic acid derivative;

Review web links to left;

Book:  .

6, 1/27 Tu6

Redox Reactions

1. Review Oxidation/Reduction

2. Counting Electrons:  Oxidation Numbers

3. Oxidation Organic Molecules: Problem Set

4. Oxidation of Alcohols - Oxidizing Agents and Identification

7, 1/29 Th 2

Oxidation of Alkenes and Aldehydes - Oxidizing Agents and Identification

Chemistry of Alkenes, Aromatics, Alcohols

Quiz:  rx mechanisms 2

8, 2/2/04, M 4

Phosphoesters, Phosphoanhydrides, and ATP

The Meaning of ΔG, ΔG^o_stab, and ΔG_conc

Lab Day 5 (2/3):  Alcohols

Chapt. 12.1, 12.10, 12.12;

Chapt 13.1-13.2, 13.5-13.10;

Example: ΔG and the reactions of hydrochloric acid and acetic acid

Reaction Rates and Equilibrium

Chapt. 12.1, 12.10, 12.12;

Chapt 13.1-13.2, 13.5-13.10;
Chapt 8.7, 8.13-14; 17.1-17.3;

Homework: Do in Groups of no more than 3:  Reaction Review |KEY

10, 2/6

F 2

Driving Unfavorable Reactions

pH and buffers

Read pH and buffer web site

11, 2/10

Tu 4

pH and buffers

Read pH and buffer web site

Th 6

pH and buffers

Read pH and buffer web site

12, 2/16

M 2

Biological Molecules and the Central Dogma of Biology

13, 14

2/18 W4

2/20 F6

Carbohydrates

1. straight chain and cyclic sugars

2. 5 and 6 C sugars to know

3. hemiacetals, acetals, and dissacharides

4. polysaccharides: starch, glycogen, and cellulose

5. amylose, amylopectin

Chapt 24.7-24.10

15,

2/24 Tu 2

Lipids

1. Fatty Acids

2. Phospholiids

3. Micelles and Bilayers

4. single chain amphiphile | micelle
5. micelle
6. double chain amphiphile | bilayer membranes
7. bilayer

    

Chapt 24.11)

16,

2/26 Th 4

Proteins

1. 20 naturally occurring amino acids

2. Primary structure of proteins

3. Secondary Structure - alpha helix and beta sheets

4. Tertiary Structure - 3D structure of proteins

5. Membrane Protein

Lab 2/27 F: CHO  amylose, amylopectin

Chapt 24.1-24.6

17,18, 19

3/8, 3/10, 3/12

M 6, W 2

F 4

DNA

1. The Structure of DNA

2. Central Dogma of Biology

3. Sickle Cell Hemoglobin

Chapt 24.12-24.14

Carbohydrate Metabolism

20

3/16

Tu 6

1. Glycolysis

   • Glycolysis - detailed highlights

.

21

3/18

Th 2

1. Cori Cycle

2. Gluconeogenesis

   • Gluconeogeneis - detailed highlghts

.

22

3/22

M 4

1. Gluconeogeneis - detailed highlghts

2. Regulation of enzyme activity: allosteric enzymes; kinases/phosphatases

.

23

3/24

W6

1. Glycogen Breakdown - Glycogenolysis

   • Regulation of glycogen phosphorylase

2. Glycogen Synthesis

   • Glycogen Synthesis - detailed highlights

3. ATP as Substrate, Allosteric Activator/Inhibitor, and Covalent Regulator of Enzyme Activity

.

24

3/26

F 2

1. Glycogen Breakdown - Glycogenolysis

   • Regulation of glycogen phosphorylase

2. Glycogen Synthesis

   • Glycogen Synthesis - detailed highlights

3. ATP as Substrate, Allosteric Activator/Inhibitor, and Covalent Regulator of Enzyme Activity

4. Allosteric and Phosphorylation Control of Glycogen Phosphorylase

.

Lipid Metabolism

25, 3/30

Tu 4

Krebs Cycle, Oxidative Phosphorylation, ATP synthesis

1. Pyruvate Dehydrogenase

2. Kreb's Cycle - TCA CYCLE

   • Krebs Cycle - detailed highlights

26, 4/1

Th 6

Test 2

Study Guide 2

27, 4/5

M 2

1. Electron transport and proton gradient formation in the mitochondria
2. Lipophilic electron carrier, ubiquinone, UQ

3. mitochondria ATP synthesis

4. substrate-level ox-phos in glycolysis

28, 4/7

W 4

1. Fatty Acid Oxidation

2. Fatty Acid Synthesis

.

Integration of Metabolism/Misc.

29, 4/14

W 6

1. Triacylglyceride Metabolism

2. Ketone Body Synthesis - Ketogenesis

3. Ketone Body Utilization

.

30, 4/16

F 2

Horror Film

31, 4/20

Tu 4

Discussion Horror Film: Influenza

32, 4/22

Th 6

Organ Specialization and Hormone Signaling

• Integration of Metabolism I

• Integration of Metabolism II

• Organ Specialization

33, 4/26

M 2

• Integration of Metabolism I

• Integration of Metabolism II

• Organ Specialization

• The Liver

34, 4/26

W 4

35, 4/26

F 6

PPARs, Leptin, Adiponectin, Review

.