1. Biochemistry 1 CHEM 271

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4. What is Biochemistry? BIOLOGY CHEMISTRY BIOCHEMISTRY
- The study of the structure, organization and interactions of cells, tissues and organisms.
CHEMISTRY
- The study of the structure, organization and interactions of atoms and molecules.
BIOCHEMISTRY
- The study of the structure, organization and functioning of living matter in molecular terms.
- « the chemistry of life »
Source: Dr. Steven Kawai

5. “Molecules of life” Proteins Carbohydrates Lipids Nucleic acids
structure, catalysis, motion, signaling
Carbohydrates
Energy, storage of energy
Lipids
Energy, cell membranes
Nucleic acids
Genetic information

7. Applications of Biochemistry
medicine
dentistry
agriculture
forensics
anthropology
environmental sciences
many other fields

8. “Central Dogma” of Biology
DNA
RNA
Protein
[1(+) per gene]
Information as coded sequences of chemical ‘letters’
structural building blocks
receptors
transporters
enzymes
* Chapter 1 of the textbook explains the structure and function of DNA in chemical terms: similar chemical principles underlie the structure and function of proteins

9. Chemical bonds, a summary
Covalent (C-H, C-O)
Noncovalent
Electrostatic interaction
Hydrogen bonds
van der Waals interaction
Hydrophobic effect

10. What will we be studying?
Part 1: Structure and properties of proteins
Quaternary
structure
- Hemoglobin
(structure & function)
Tertiary (3D) structure
- Characterizing proteins
Enzymes
(structure & function)
- Serine proteases
Secondary structure
Enzyme kinetics
- Amino acids (20)
Enzyme inhibitors
- Acids/bases
- Primary structure / non-covalent
interactions
Source: Dr. Steven Kawai

11. What will we be studying?
Part 2: Central metabolism (Glucose → ATP): enzymes, regulation, strategy, thermodynamics
Citric acid cycle
Energy capture and biosynthetic intermediates
Metabolism
- Glycolysis
- Gluconeogenesis
Oxidative phosphorylation
(Electron-transport chain)
- Glycogen metabolism
- Cofactors
Carbohydrates
(structure & function)
Oxidative phosphorylation
(ATP synthesis)
ATP is the major storage form of energy in the cell
Enzyme regulation strategies

12. A possible time line for biochemical evolution
NH4 + CH4 + H2O + H2 + electricity
(Miller-Urey experiment on abiogenesis)
>20 amino acids

13. A tree of life; 3 related domains

14. Biological diversity and similarity

15. Protein Structure

16. Building blocks of proteins
Amino acids
Building blocks of proteins

17. 20 amino acids are the building blocks of proteinsCa
Amino acids (with a non-hydrogen R group) are chiral:

18. AMINO ACIDS (hydrophobic)

19. AMINO ACIDS (hydrophobic)

20. AMINO ACIDS (Polar)

21. AMINO ACIDS (Positively charged)
pKa!!!

22. AMINO ACIDS (Negatively charged)

23. Histidine, a special case

24. Amino acid abbreviations

25. CHEM 271 Fall 2015 Learning outcomes 1
Proteins: Amino acids
You should know the properties of
Chemical bonds: Covalent bonds and the different non covalent interactions (you may have to read this on your own, if you don’t remember it from previous courses)
What characterizes an α-amino acid
You should know the structures, names, three letter abbreviations, and one letter abbreviations of all 20 amino acids found in proteins.
You should know the properties of the different amino acids, for example if it is hydrophobic or polar