Biochemistry 330

Fall 2008

Current schedule:

Concepts for Week 15
1. Why is the proton gradient generated by the electron transport chain important.
2. How does ATP synthase work? What are the components of the F₀ and F₁ subunits?
3. How is ATP synthase a molecular machine? What is the experimental evidence?
4. Other than ATP synthesis, what is the proton gradient used for?

Concepts for Week 14
1. How do transport proteins work? How are they different from ion channels?
2. Describe the difference between passive transport, primary active transport and secondary active transport.
3. Review oxidation reduction chemistry.
4. Know the components of the electron transport chain; understand how the order of the components was discovered.

Concepts for Week 13
1. What are lipids? Describe 5 uses of lipids.
2. What is the difference between triacylglycerides and phospholipids? What is the difference between phospholipids and sphingolipids?
3. Describe the function of difference vitamin that are lipids.
4. Describe the composition of a membrane.
5. What affects membrane fluidity? How does cholesterol affect fluidity?
6. How can a transmembrane protein be identified from its sequence?

Concepts for Week 12
1. Understand how the genetic code works
2. Know the following tools of molecular biology and what they can do
          Restriction enzymes
          PCR
          Plasmids
          Site-directed mutagenesis
          Northern and Southern blotting
          Variable nucleotide tandem repeat analysis
          Restriction Fragment Length Polymorphism

Concepts for Week 11

1. Know the difference between a nucleotide, a nucleoside, and a base. Know how to name them.
2. Be able to describe the structure of DNA. Know the information that was used to determine the structure.
3. The difference between the A, B and Z forms of DNA.
4. Know what a phosphodiester bond is. Know how it is broken.
5. Know why palindromic sequences are important in DNA.
6. What is meant by DNA melting? How is observed? What changes the Tm?
7. Be able to describe the chemical changes that cause mutations in DNA.
8. Be able to interpret and describe DNA sequencing.

Concepts for Week 10

1. Know the structures of ribose, glucose, fructose, mannose, and galactose.
2. What is meant by an anomer?
3. What are oxidizing sugars? How can they be identified?
4. What is a glycosidic bond? How can it be broken? How is it made?
5. Know the components of common disacchrides: lactose, sucrose.
6. Know the structure of glycogen, starch and cellulose.

Concepts for Week 9

1. Be able to use initial rates or integrated rate law to determine order of a reaction.
2. Be able to describe the ways in which enzymes are regulated. (Allosterically, covalent modification, zymogens)

Concepts for Week 8
1. What are the different types of catalyzed binary reactions?
2. What is the difference between competitive, uncompetitive, and mixed (non-competitive) inhibitors.
3. What is a nucleophile? What is an electrophile?
4. What does the active site of chymotrypsin look like?
5. What is the catalytic triad?
6. What is the difference between Sn1 and Sn2? E1 and E2?

Concepts for Week 7
1. What is the cause of sickle cell anemia?
2. What is an enzyme and what does it do?
3. What is the transition state? What is binding energy?
4. What is Michaelis-Menton kinetics? What assumptions are made?
5. What is Km? What is Vmax? What it kcat?
6. What is a Lineweaver-Burk plot?

Concepts for week 6 (topics will be on exam 2, not exam 1)

1. How can protein structures be determined at the atomic level? What is meant be resolution?
2. What is a cofactor? Describe the cofactor in myoglobin (and hemoglobin). How is it attached to the protein?
3. What is meant by cooperativity?
4. What regulates oxygen binding in hemoglobin? Name at least 3 substances.
5. What is Kd? How is it related to ligand affinity?

Concepts for week 5

1. Know the different secondary structures and why these structurre are common. Know the secondary structures that are found in fibrous proteins. Know the different levels of fibrous protein structure and what holds them together.
2. Know the forces that cause proteins to fold.
3. Know what is meant by "denature" and how to cause and detect denaturation of a protein.
4. Know what molecular chaperones are.

Concepts for the fourth week of class

1. Know what nucleophiles, leaving groups and protecting groups are.
2. Understand the different ways to purify protein (centrifugation, ion exchange chromotagraphy, affinity chromatography, etc.)
3. Understand how to characterize protein (gel electrophoresis, isolelectric focusing)
4. Know the different types of secondary stuctures and why these structure are common.

Concepts for the third week of class
1. Know characteristics of a peptide bond.
2. Know how to find the pI of a protein. Know how this relates to column chromatography (a purification method).
3. Know steps of peptide systhesis and peptide sequencing.

Concepts for the second week of class

1. Understand ester and amide formation and hydrolysis.
2. Know the difference between stong and weak acids; strong and weak bases; know how to calculate the pH of these solutions.
3. Know how to calculate the pH of a buffer. (Hendersen-Hasselbach)
4. Know how to calculate the pH of a buffer/weak acid/weak base after a strong acid or strong base has been added to the solution.
5. Learn the amino acids. Know general pKa's of amino acids.

Study questions for the first week of class.

    1. Draw the following functional groups and describe their importance in biochemistry:
                         Amides (how are these made)
                         Phosphoanhydride
                         Thioester
                         Sulfhydryl (Thiol)
                         Disulfide
    2. What chemical process converts between alcohols to carboxylic acids?
    3. Why is stereochemistry important in biochemistry?

    4. What is meant by non-covalent interactions? Describe non-covalent interactions that are important for biological molecules. Which ones are most important for protein structure?

Current schedule

Date	Topics/Slides	Reading in Lehninger text	Extra Recommended Problems	Other assignments
8/27	Chemistry what you should remember	Skim section 1.2	None	Review notes from previous chem. classes. Chemistry review Assignment 1
8/29	Molecular forces in biology	Chapter 2	None
9/01	Water and buffers	Chapter 2	1-3,5,6,7 Chapter 2	Buffer handout
9/03	Buffers (cont.)			Buffer problem handout and Case study: Blood buffering systems. Chemistry review Assignment 2
9/05 9/08	Amino acids	Chapter 3 pp. 75-88	1-4 Chapter 3
9/10	Peptides and primary sequence Slides	Chapter 3 pp. 96-110	7, 8, 13, 17 Chapter 3
9/12	Working with proteins Slides	Chapter 3 pp. 89-96	5, 9, 12,18 Chapter 3
9/15 9/17	Working with proteins cont. Amino acid quiz			Organic mechanisms Ester hydrolysis mechanism
9/19, 9/22	Protein secondary structure Fibrous proteins Slides	Chapter 4 pp. 116-132	1,2,4,6,9 Chapter 4	Assignment 3
9/24, 9/26	Protein tertiary structures Slides	Chapter 4 pp. 132-152 (Skim section on motifs)
9/29 10/3	Protein Function (Myoglobin and Hemoglobin) Slides	Chapter 5 pp. 157-174	Chapter 5 1-6	Handout
10/1	Exam 1
10/6	Enzymatic Principles Slides Enzyme Kinetics Slides	Chapter 6 pp. 190-213	Chapter 6 1,3,4,6-13	Handout on thermodynamics and kinetics
10/17	Enzyme inhibitors
10/22	Enzyme mechanism Slides	Chapter 6 pp. 213-225	Chapter 6 14,18
10/24 10/27	Enzyme regulation Slides	Chapter 6 pp. 225-233
10/29, 10/31	Carbohydrates Slides	Chapter 7 pp.239-253	Chapter 7 1,2,4,9,10
11/3	Exam II	Chapter 5 and 6
11/5	Carbohydrates continued	Chapter 7 pp. 239-253
11/7	Nucleic acids Slides	Chapter 8 pp. 273-291	Chapter 8 1,2
11/10	Nucleic Acid Chemistry Slides	Chapter 8 pp. 291-301	Chapter 8 7,8,9,11
11/12 11/14 11/17	Working with nucleic acids Slides	Chapter 9 pp. 306-330	Chapter 9 1,3,4,8,10
11/19 11/21	Lipids Slides	Chapter 10 pp. 343-366	Chapter 10 1,4,5,6,15,18
11/23	Membranes Slides	Chapter 11 pp. 369-388	Chapter 11 1,4,5,6,15,18
12/1	Transport proteins Slides	Chapter 11 pp. 388-410	Chapter 11 7-10, 19, 20	Transport handout
12/3	Exam III
12/5	Electron transport chain Slides	Chapter 19 pp. 690-704	Chapter 19 1-5	Redox handout
12/8	ATP synthesis Slides	Chapter 19 pp. 704-716	Chapter 19 6,8,12

Example exams*

Exam I 2005
Exam I 2005 key
Exam II 2005
Exam II 2005 key
Exam III 2005
Exam III 2005 partial key
Final Exam 2005
Final Exam key 2005

*Since the topics in class are a little different each year, the content of this years' exams may be different. However you may expect a similar format of questions.