Lecture 1 The Meaning of Life

Prof. John BellizziAugust 24, 2015

Chemistry 3510BIOCHEMISTRY I

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Course Information (Full Syllabus on Blackboard)Blackboard: Syllabus/Schedule, Lecture Slides, Handouts, Discussion Board, GradesTextbook: Nelson and Cox, Lehninger Principles of Biochemistry (6th Ed)Homework: Sapling Learning (www.saplinglearning.com) Clickers: TurningPoint RF ResponseCard

Starting Wed 9/2/15(Register on Blackboard by Mon 8/31/15)Oce Hours:WO 3205B Mon 23:45, Wed 11:0011:45, Wed 3-4, Thu 3-4 and by appointment

Grading Four mid-term examinations (100 points each - lowest exam dropped)300 pointsCumulative nal examination 150Homework + Clickers Combined* 150Total 600 points*13 homework assignments @ 10 points each, ~50 clicker questions @ 1 point each.

Exam Dates: Friday 9/18/15, Friday 10/16/15, Friday 11/6/15, and Friday 12/4/15. Final Exam: Wed 12/16/15.

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Course Information (Full Syllabus on Blackboard)Sapling Homework One assignment due (almost) every week, generally due Wednesdays Each assignment is worth 10 points Variable number of questions Late assignments accepted; will lose 2 points per day Unlimited agempts at each questions; will lose 5% of credit for each incorrect agemptAssigned textbook readings should be completed before class for the week they are listed.Practice exams and solutions will be handed out before each exam.There will be no makeups for missed homework assignments and clicker points.There will be no makeup exams. Students with legitimate reasons for absence from an exam must take the exam early. Students who have a legal absence with an exam without advance notice and provide adequate documentation will be excused from the exam.Lecture 1 8/24/15 Biochemistry I Prof. Bellizzi 3

What You (SHOULD) Already Know

Important concepts from General and Organic Chemistry that you are expected to know. Lewis structures, formal charges, and resonance Hybridization, molecular geometry Conformations open chains and rings Stereochemistry

cis/trans Chiral centers (enantiomers, diastereomers)

Intermolecular forces (electrostatic, polar, van der Waals, H-bonds) Thermodynamics (G, H, S), equilibrium (Keq), kinetics (rates) Structures, properties and characteristic reactions of functional groups (e.g. carbonyl

groups, alcohols, aromatic rings) Reactions

Proton-transfer reactions (acid-base chemistry, pKa values) Nucleophilic Substitution and -elimination Carbonyl Chemistry (additions, eliminations, acyl substitutions)

How to use curved arrows to draw reaction mechanisms

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Biochemistry:The study of the chemistry of living things

Chemistry:

Life:

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Biochemistry Operational Denition

A system of chemical reactions orchestrated in a controlled fashion (by proteins, for the most part) within and among cells. Increasing complexity storage and expression of information Requires a constant ux of energy and mager

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Life Requires Energy

Living organisms require a constant input of energy to remain living Synthesis of molecules (growth, repair) Active transport of molecules against a concentration

gradient Mechanical work Generation and maintenance of complexity and order

(decreases entropy locally!)Energy transduction: Cells couple energy derived from sunlight (phototrophs) or oxidation of organic molecules (chemotrophs) to the energy consuming processes.

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Classication of organisms by energy and carbon source

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Biochemical Unity Underlies Biological DiversityAll life forms share striking similarities: Same fundamental morphological unit

Same molecular constituents

Similar/identical metabolic pathways

Same mechanisms for storage/transfer of biological informationThere is an inherent molecular logic to all living things.This is consistent with all living cells being descended from a common ancestor.

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The Tree of Life

Phylogenetic tree determining how closely related organisms are on the basis of similarities/dierences.

Originally done on the basis of comparative anatomy. Now done on the basis of DNA or protein sequence similarity

Eukaryotes (with nuclei) includes unicellular and multicellular organismsProkaryotes (without nuclei) unicellular Bacteria Archea

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Cells

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Common features of all cells: Plasma membrane

Hydrophobic barrier Maintains integrity

Cytoplasm Cytosol

Aqueous solution Very concentrated Proteins, RNA, small molecules and ions (soluble)

Larger insoluble particles suspended in cytosol (e.g. ribosomes; organelles in eukaryotes)

Chromosome(s) Genetic material (storage of biological information) In the form of one or more massive DNA molecules

Prokaryotic Cells E. coli the prototypical bacterium 2 m long, 1 m diameter Cell membrane and cell wall (peptidoglycan

layer provides mechanical strength) Single circular DNA molecule Ribosomes nucleoprotein particles that

synthesize proteins

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Eukaryotic Cells

5-100 m diameterMore complicated internal structures.Organelles Membrane-enclosed

compartments within cytoplasm Specialized functionsCytoskeleton Networks of protein laments Provide structure, organization to

cytoplasm Cell shape, motility Smaller protein subunits which

assemble/disassemble to make dynamic laments

Multicellular eukaryotes have dierent cell types with dierent properties and functions.

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Hierarchical Nature of Living Ma\er

a

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102 Chapter 4 Centrifugation Techniques in Biochemistry

FIGURE 4.5Rotors for a high-speed centrifuge. A Fixed-angle;B Swinging-bucket;C Vertical.Courtesy ofBeckman Coulter.

Centrifugal force

A

B

C D

FIGURE 4.6Operation of afixed-angle rotor. A Loading ofsample. B Sampleat start ofcentrifugation.C Bands form asmolecules sediment.D Rotor at restshowing separationof two components.

centrifugations of temperature-sensitive biological samples. Rotor chambers inmost instruments are maintained at or near

Three types of rotors are available for high-speed centrifugation: the fixed-angle, the swinging-bucket, and the vertical rotor (Figure 4.5AC). Fixed-anglerotors are especially useful for differential pelleting of particles (Figure 4.6A). Inswinging-bucket rotors (Figure 4.5B), the sample tubes move to a position per-pendicular to the axis of rotation during centrifugation, as shown in Figure 4.7.These are used most often for density gradient centrifugation (see below). In thevertical rotor (Figure 4.5C), the sample tubes remain in an upright position(Figure 4.8). These rotors are used often for gradient centrifugation. Prior to the

4C.

Subcellular Fractionation

Dierent compartments in the cell (cytosol, organelles) contain dierent molecules.

Organelles (and the proteins and other molecules they contain) can be separated from one another by dierential centrifugation.

Cells are resuspended in an aqueous solution and homogenized to rupture the plasma membrane.

The crude homogenate is centrifuged. Dierent organelles have dierent sizes

and will sediment at dierent rates. Sucrose-density centrifugation ner

separation of particles based on dierent ratios of lipid to protein.

Each fraction can then be studied to characterize its biochemical contents.

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