What is Biochemistry?

1. What is Biochemistry? • A science that integrates life with chemistry • A science that attempts to determine how lifeless molecules combine to give the attributes of life • A science that operates by the principle that life’s molecules are selected for the functions they perform. • A science that delves into the world of the unseen for answers to life’s mysteries.

2. What are the Challenges of Biochemistry? To understand the chemical complexity of a cell To determine how cells are able to extract and transform energy from their surroundings To learn how cells are capable of self-replication To determine how cells sense and respond to changes in their environment To understand the structural logic behind the selection of specific molecules for specific tasks

3. How does Biochemistry Differ from Organic Chemistry? See Tutorial “Getting Started” • Organic chemistry is the chemistry of carbon compounds. Biochemistry is the study of carbon compounds that crawl -Mike Adam A Biochemist is a person who can’t tell the difference between a plant or an animal -E Harris

4. What are the Objectives of Biochemistry 410 • To introduce students to the properties of molecules found in living cells. • To compare and contrast the properties of molecules in the different categories. • To demonstrate the structure-function principle of biochemistry. • To threaten, cajole, or otherwise persuade students that a knowledge of biochemistry is essential to understanding the properties of life.

5. Chemical Perspective The Elements and Molecules of Life

6. C H O N S P C H O = Carbohydrates Lipids C H O N S = PROTEINS C H O N S P = Nucleic Acids

7. 21 Inorganic Elements of life Na, K, Ca, Mg, Cl Fe, Zn, Cu, Mn, Co Se, Mo, V, Si, Cr, Sn, I, Br, F, Ni B

8. CHEMICAL BONDING Non-covalent Covalent Peptide bond Ionic bond H-bond Glycosidic bond Hydrophobic bond Phosphodiester bond Disulfide bond Take Home: Weak and strong forces hold biomolecules together.

9. Important Functional Groups in Biomolecules Methyl CH3- Ethyl CH3CH2- CH3C- Acetyl O CH3(CH2)nC- Acyl O Phenyl R-SH Sulfhydryl Disulfide R-S-S-R

10. Important Functional Groups (Continued) R-OH Hydroxyl (alcohol) Amino (amine) R-NH3 NH2 Guanidinium C NH- H2N O Phosphate O-P-O O

11. O CH3(CH2)nCH2 -C-O- CH2 CH3(CH2)nCH2 -C-O- CH2 O O CH2 O-P-O O Carboxyl CH2OH Hydroxyl H Methyl O CH3-C-COO OH NH3 + HO Amino HO OH Phenyl Hydroxyl H H CH2-C-COO CH2-C-COO HO- NH3 + NH3 + Acyl Trimethyl- amine Sulfhydryl H + CH2-C-COO HS- CH2-CH2-N(CH3)3 NH3 + Phospho

14. BIOENERGY Electrical Light CHEMICAL Osmotic Mechanical Sound Heat? Energy Transformations (Sight) Light to electrical Chemical to mechanical (Muscle contraction) Sound to electrical (Hearing)

15. Basic Thermodynamics Q: How do we know when a given reaction or process will occur spontaneously or in a favored direction? A: Berthelot (1860) All spontaneous reactions occur with the liberation of heat. Therefore, spontaneous reactions are exothermic. A: Gibbs (1870). Heat is not the only index of spontaneity. Many spontaneous processes occur without liberating heat. The order or entropy must also be considered. Q: Is it possible for a reaction to actually absorb heat or remain isothermal and still be favored in one direction? A: Yes Q: Can you give an example? A: When ice melts or salt dissolves in water or when a gas confined to one chamber diffuses to occupy two chambers, these are spontaneous reactions that absorb heat.

16. Q: So, knowing the favored direction must account for both energy release and order. Free energy change Entropy change Enthalpy change A: Yes, energy as heat is called enthalpy. Enthalpy change or H measures energy released at constant pressure. In a favored reaction H is less than 0, i.e., H is negative. Entropy is a probability function. The probability that the system will exist in any form other than perfect order. In a favored reaction entropy change or S is positive. The combination gives rise to a state function called the free energy. A reaction will always be favored in the direction that free energy change is negative or less than 0. Q: Can you give me a equation that helps me see this A: G = H - TS Maximal (– G) occurs when H is negative and S is positive

17. Glucose + 6O2 6CO2 + 6H2O Enthalpy: H Energy Change at constant pressure Energy locked in chemical bonds Bomb Calorimeter Final State Initial State H = heat evolved Take Home: Because energy differential is independent of path taken, energy from combustion in a bomb calorimeter is the same as in the body

18. Oxidation of Palmitic Acid (C16H32O2) H2O H2O H2O O2 CO2 H2O Initial State Final State Reaction H = qp H = heat evolved at constant pressure At constant pressure and volume, no work has been done against or by the surroundings.

19. w 1 atm H2O H2O H2O O2 CO2 H2O q 1 atm H2O CO2 CH3(CH2)14COOH + 23O2 16CO2 + 16H2O 1 atm 1 atm q Initial State q=E + w At constant P, if the surroundings can do work on the system… more heat can be evolved w = PV w = nRT Final State

20. ENTROPY S Relates to molecular order Energy unavailable during a chemical transition “A spontaneous reaction is one that favors movement from order to disorder…occurs with a positive change in entropy” “To go from disorder back to order requires input of energy” Take Home: Living system take chemicals from their disordered environment and assemble them into ordered arrays of structural molecules. Hence, living systems live on NEGATIVE entropy.