Readings

Readings are from Berg, Tymockzko, Gatto, and Stryer Biochemistry (8th Edition) OR from Miesfeld & McEvoy Biochemistry. Read one or the other. There is no need to read both.

[BTGS] = Berg, Jeremy M., John L. Tymoczko, Gregory J. Gatto, and Lubert Stryer. Biochemistry. 8th ed. W. H. Freeman & Co., 2015. ISBN: 9781464126109.

[MM] = Miesfeld, Roger L., and Megan M. McEvoy. Biochemistry. W. W. Norton & Company, 2017. ISBN: 9780393614022.

lec #	topic	readings
Part I: Biomolecules, Methods, and Mechanisms (Lectures by Prof. Michael B. Yaffe)
1	Introduction; Classes of Biomolecules; pH, Buffers, and Titration Curves	[BTGS] pp. 1–4, 13–17, 22–23 (Appendix 1) or [MM] pp. 3–17, 56–60, 71–78
2	Amino Acids and Proteins	[BTGS] pp. 27–39, 57–59 or [MM] pp. 11–12, 147–168
3	Protein Purification I	[BTGS] pp. 65–84, 92–95 or [MM] pp. 210–226
4	Protein Purification II, Protein Structure II	[BTGS] pp. 35–49, 59–62, 85–92 or [MM] pp. 162–193, 227–230
5	Protein Structure II, Protein Folding	[BTGS] pp. 6–9, 44–60, 169–182 or [MM] pp. 56–67, 193–204, 232–237
6	Hemoglobin and Allostery	[BTGS] pp. 191–212, 286–292, 356–358 or [MM] pp. 259–276
7	Hemoglobin and the Bohr Effect	[BTGS] pp. 191–212 or [MM] pp. 259–276
8	Enzyme Chemistry	[BTGS] pp. 215–218, 237–238, 251–264 or [MM] pp. 309–319, 332–336
9	Enzymes as Catalysts	[BTGS] pp. 219–225, 240–241, 299–303 or [MM] pp. 3319–332, 362–363
10	Enzyme Mechanisms	[BTGS] pp. 264–268 (Carbonic Anhydrase), 455–456 (TPI) or [MM] pp. 326–327 (Carbonic Znhydrase), 455–457 (TPI)
11	Enzyme Kinetics	[BTGS] pp. 225–236 or [MM] pp. 341–356
12	Carbohydrates/Introduction to Membranes (Lecture by Prof. Matthew Vander Heiden)	[BTGS] pp. 313–337 or [MM] pp. 632–672
13	Channels, Transporters and Pumps, Protein Modules	[BTGS] pp. 367–393 or [MM] pp. 276–295
14	Hormones and Signal Transduction I	[BTGS] pp. 293–298, 397–419 or [MM] pp. 359–360, 371–397
15	Receptors, Small G-proteins, and Signal Transduction II	[BTGS] pp. 367–393, 397–419 or [MM] pp. 255–256, 276–295, 383–385, 397–415
16	Nucleic Acids	[BTGS] pp. 4–6, 105–118 or [MM] pp. 23–27, 91–101, 107–115
17	tRNAs and Protein Translation	[BTGS] pp. 827–844, 941–944, 119–123, 859–880, 925–931, 945–947 or [MM] pp. 999–1009, 1010–1021, 1065–1071, 1077–1098
18	Translation and the Ribosome	[BTGS] pp. 876–890 or [MM] pp. 1055–1061, 1074–1086
Part II: Metabolism (Lectures by Prof. Matthew Vander Heiden)
19	Introduction to Metabolism/Polysaccharides/Bioenergetics/Intro Pathways	[BTGS] Ch. 11.1-11.2, 15, 16.1-16.3, 21 or [MM] Ch. 9, 14.2-14.3
20	Bioenergetics/Intro Pathways/Glycolysis I	[BTGS] Ch. 17 or [MM] Ch. 10
21	Glycolysis II/Regulation	[BTGS] Ch. 17 or [MM] Ch. 10
22	Glucogenesis/Carbohydrate Storage/TCA Cycle I	[BTGS] Ch. 11.1-11.2, 15, 17, 16.1-16.3, 21 or [MM] Ch. 9, 10, 14.2-14.3
23	TCA Cycle II	[BTGS] Ch. 17 or [MM] Ch. 10
24	Lipids and Fatty Acid Oxidation	[BTGS] Ch. 12.1–12.5, 18, 19, 22 or [MM] Ch. 11, 12, 15.1–15.3, 16.1
25	Oxidative Phosphorylation	[BTGS] Ch.12.1–12.5, 18, 19, 22 or [MM] Ch. 11, 12, 15.1–15.3, 16.1
26	Oxidative Phosphorylation/Photosynthesis I	[BTGS] Ch. 12.1–12.5, 18, 19, 22 or [MM] Ch. 11, 12, 15.1–15.3, 16.1
27	Photosynthesis II/CO₂ Assimilation	[BTGS] Ch. 12.1–12.5, 18, 19, 20.1–20.2, 22 or [MM] Ch. 11, 12, 15.1–15.3, 16.1
28	Pentose Phosphate Pathway	[BTGS] Ch. 19, 20 or [MM] Ch. 14.1
29	Lipid Synthesis	[BTGS] Ch. 20.3–20.5, 22.4–22.6 or [MM] Ch. 16.2
30	Nitrogen/Amino Acid Metabolism I	[BTGS] Ch. 23.3–23.5, 24 or [MM] Ch. 17
31	Amino Acid Metabolism II	[BTGS] Ch. 23.3–23.5, 24 or [MM] Ch. 17
32	Nucleotide Metabolism	[BTGS] Ch. 25 or [MM] Ch. 18

Additional textbooks that may be helpful for specific topics:

Campbell, Iain D. Biophysical Techniques. Oxford: Oxford University Press, 2012. ISBN: 9780199642144

This book has an excellent discussion of many currently used techniques to characterize macromolecules. It is a very useful text for those of you who are doing (or plan to do) biochemical research.

Branden, Carl, and John Tooze. Introduction to Protein Structure, 2nd ed. New York: Garland Publishing, 2009. ISBN: 9780815323051

Provides an elegant description of a variety of protein structures, including many of the proteins we discuss in class such as G-proteins, proteases, and nucleic acid-binding proteins. Use this book if you want to get a different, somewhat better understanding of the structural basis for how these proteins work than that provided in the Stryer textbook. Carl Branden is the inventor of the so-called “Branden Rules” that allow ligand binding sites to be predicted in α/β proteins by looking at the α-helix cross-over positions on the β-sheet, and places in the sheet where the order of β-strands reverses itself.

Rhodes, Gale. Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models, 3rd ed. Academic Press, 2006. ISBN: 9780125870733

This is an outstanding introduction to how protein structures are solved using crystallography. If the handwaving explanation of the phase problem that I provide in class is not satisfying enough for you, and you really want to understand how Fourier transforms are used to solve X-ray structures, this is the book for you.

Tanford, Charles, and Jacqueline A. Reynolds. Nature’s Robots: A History of Proteins. Oxford University Press, 2004. ISBN: 9780198606949

This is a classic book on the history of protein discovery and characterization, written by a pioneer in the field of biophysical chemistry. Prof. Tanford is also the author of two classic textbooks in chemistry and biochemistry, and he has a very unique and deep knowledge of the field. If you are a fan of the history of science, this is the kind of book you take on vacation to read for fun.

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General Biochemistry