The ONLY Safety Trainings that will be held this quarter will be:

NEW STUDENTS: Monday, Sept. 29th, 5:30PM -7:30PM in CB270 REFRESHING STUDENTS: Wed., Oct. 1st, 5:30 PM - 6:30PM in CB270 Please reply NOW if you have a time conflict. Refreshments will be served. You must sign up in advance. Sign up sheets are in the main office.

ALL students working in the research and teaching labs in the Chemistry Department must complete safety training ANNUALLY (includes student employees, those in research credit courses, and volunteers). On-line and organic safety quizzes do not count.

Read pp. 19-29

Fall Quarter 2003 Chem/Biol 471 BioChemistry

• Instructor: Gerry Prody

• Office CB444– Office hrs: M 12-1:30 pm and W 2-3:30 pm– You can also find me TR 11-2 in CB 210.

• prody@chem.wwu.edu

• Course web site: http://lightning.chem.wwu.edu/dept/facstaff/ prody/prody-471.htm

What is Biochemistry?

• the systematic torture of students with copious incomprehensible jargon, cryptic fomulae, and impossible insoluble problems.

“Biochemistry is the study of Life as a process that can be understood.”

Primary Objective: understand the molecular mechanisms that constitute the living state (“Molecular Logic”)

Apply Biochemical Understanding to:

• advances in medicine and healthcare (gene therapy,

biopharmaceuticals, diagnostics)

• agricultural practices

• biological responses to environmental signals(chemical toxicity, hormone action)

(crop protection, animal husbandry)

How Does Science Describe the Living State?

• Organisms must extract energy from their environment

• Ability to adapt to change

• Possess ability to self-replicate and self-assemble

Lehninger: “Molecular Logic”“A living cell is a self-assembling, self-regulating, self-replicating isothermal open system of organic molecules operating on a principle of maximum economy of parts and processes; it promotes many consecutive, linked organic reactions for the transfer of energy and for the synthesis of its own components by means of organic catalysts that it produces itself.”

Biol/Chem 471; Biol/Chem 472 ; Biol/Chem 473

smaller organicmolecules

How does science describethe living state?

Biopolymers/Macromolecules

atoms, subatomicparticles…the undiscovered

Table 1-3 Elemental Composition of the Human

Body.

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Figure 1-14 Example of the hierarchical organization ofbiological structures.

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Figure 1-2 Schematic drawing of a prokaryotic cell.

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Table 1-1 Molecular Composition of E. Coli.

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Figure 1-13 Simulated cross section of an E. coli cellmagnified around one millionfold.

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Figure 1-4 Phylogenetic tree.

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Figure 1-10 Drawings of some human cells.

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Figure 1-5 Schematic diagram of an animal cellaccompanied by electron micrographs of its organelles.

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Figure 1-6

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Figure 1-9 Drawing of a plant cell accompanied byelectron micrographs of its organelles.

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Phosphatidyl choline

Polar headgroup

Hydrophobic tail

Blue turbulence: chaos and order:

Net dipole moment for water

Lone pair electrons

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Figure 1-15 Polymeric organization of proteins, nucleicacids, and polysaccarides.

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ATP

Adenosine 5’triphosphate

Figure 1

Figure 1-36 The three stages of the evolution of life.

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Figure 1-37 Apparatus for emulating the synthesis of organic compounds on the

prebiotic Earth.

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Table 1-4 Yields from Sparking a Mixture of CH4, NH3,

H20, and H2.

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Acids, Bases and Buffers!!!

• pH = pKa + log [A]» [HA]

Examples: Calculate the pH for a solution of 0.2 M HCl.

Add 10 mL of this solution to 50 mL of 0.2 M NaAc (pK=4.7). Now what is the pH?

How could you prepare 2 L of a solution of sodium acetatepH=5.

In what pH range is acetate a “good” buffer?

Figure 2-1 Structure of the water molecule.

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Figure 2-2 Hydrogen bond between two water molecules.

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Figure 2-3 Structure of ice.

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Figure 2-4 Theoretically predicted and spectroscopically

confirmed structures of the water trimer, tetramer, and pentamer.

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Figure 2-5 Solvation of ions by oriented water molecules.

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Figure 2-6 Hydrogen bonding by functional groups.

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Figure 2-7 Examples of fatty acid anions.

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Figure 2-8 Associations of amphipathic molecules in

aqueous solutions.

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Figure 2-9 Mechanism of hydronium ion migration in aqueous solution via proton

jumps.

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Figure 2-10 Acid-base titration curves of 1-L solutions of 1M acetic acid, H2PO4

–, and NH4

+ by a strong base.

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Figure 2-11 Distribution curves for acetic acid and acetate

ion.

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Figure 2-12 Titration curve of a 1-L solution of 1M H3PO4.

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Figure 2-13 Ionization of an acid that has two nonequivalent

protonation sites.

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Table 2-1 Dielectric Constants and Permanent Molecular Dipole

Moments of Some Common Solvents.

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Table 2-2 Ionic Mobilitiesa in H2O at 25°C.

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Table 2-3 (top) Dissociation Constants and pK’s at 25°C of

Some Acids in Common Laboratory Use as Biochemical

Buffers.

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Table 2-3 (bottom) Dissociation Constants and pK’s at 25°C of

Some Acids in Common Laboratory Use as Biochemical

Buffers.

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