Chemistry 3510

BIOCHEMISTRY I
Lecture 1

The Meaning of Life

Prof. John Bellizzi

August 24, 2015

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Course Information (Full Syllabus on Blackboard)

Blackboard: Syllabus/Schedule, Lecture Slides, Handouts, Discussion Board, Grades
Textbook: 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 points
Cumulative nal examination






150
Homework + Clickers Combined*





150
Total










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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Biochemistry I Prof. Bellizzi

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 agempt

Assigned 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.



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Biochemistry I Prof. Bellizzi

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 Diversity

All life forms share striking similarities:

Same fundamental morphological unit

Same molecular constituents

Similar/identical metabolic pathways

Same mechanisms for storage/transfer of biological information

There 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 organisms
Prokaryotes (without nuclei) unicellular
Bacteria
Archea

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Cells

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
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Prokaryotic Cells

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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 diameter
More complicated internal structures.

Organelles
Membrane-enclosed
compartments within cytoplasm
Specialized functions
Cytoskeleton
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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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.
102 Chapter 4 Centrifugation Techniques in Biochemistry
Sucrose-density centrifugation ner
separation of particles based on dierent
ratios of lipid to protein.
FIGURE 4.5
Each fraction can then be studied to
Rotors for a highspeed centrifuge.
characterize its biochemical contents.
A Fixed-angle;
B Swinging-bucket;

C Vertical.
Courtesy of

Beckman Coulter.
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centrifugations of temperature-sensitive biological samples. Rotor chambers in

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most instruments are maintained at or near 4C.
Three types of rotors are available for high-speed centrifugation: the fixedangle, the swinging-bucket, and the vertical rotor (Figure 4.5AC). Fixed-angle
rotors are especially useful for differential pelleting of particles (Figure 4.6A). In