Transcript Biochemical Thermodynamics - Research Centers | Center for

Introduction to Biochemistry
Andy Howard
Biochemistry, Fall 2008
IIT
08/21/08
Biochemistry: Introduction
1
What is biochemistry?
By the end of this course you should
be able to construct your own
definition; but for now:
 Biochemistry is the study of
chemical reactions in living tissue.
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Plans
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What is biochemistry?
Cells
Cell components
Organic and
biochemistry
Concepts from organic
chemistry to remember
Small molecules and
macromolecules
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Classes of small
molecules
 Classes of
macromolecules
 Water
 Catalysis
 Energetics
 Regulation
 Molecular biology
 Evolution
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What will we study?

Biochemistry is the study of chemical
reactions in living tissue, both within cells and
in intercellular media.
 As such, it concerns itself with a variety of
specific topics:
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Topics in biochemistry
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What reactions occur;
The equilibrium energetics and kinetics of those
reactions;
How the reactions are controlled, at the chemical and
cellular or organellar levels;
How the reactions are organized to enable biological
function within the cell and in tissues and organisms.
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Organic and biological chemistry

Most molecules in living things
(other than H2O, O2, and CO2)
contain C-C or C-H bonds, so
biochemistry depends heavily on
organic chemistry
 But the range of organic reactions
that occur in biological systems is
fairly limited compared to the full
range of organic reactions:
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Why we use only a subset of
organic chemistry in biochemistry
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Biochemical reactions are
almost always aqueous.
Frederich
They occur within a narrow temperature and
Wöhler
pressure range.
They occur within narrowly buffered pH ranges.
Many of the complex reaction mechanisms
discovered and exploited by organic chemists since
the 1860's have no counterparts in the biochemical
universe.
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Cells
Most biochemical reactions (but not all!)
take place within semi-independent
biological entities known as cells
 Cells in general contain replicative and
protein-synthetic machinery in order to
reproduce and survive
 They often exchange nutrients and
information with other cells
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Cell components
Cells are separated from their
environments via a selectively porous
membrane
 Individual components (often called
organelles) within the cell may also
have membranes separating them from
the bulk cytosol and from one another
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Eukaryotes and prokaryotes
The lowest-level distinction among
organisms is on the basis of whether
their cells have defined nuclei or not
 Cells with nuclei are eukaryotic
 Cells without nuclei are prokaryotic
 Eubacteria and archaea are prokaryotic
 Other organisms (including some
unicellular ones!) are eukaryotic
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Eukaryotic organelles I
Nucleus: contains genetic information;
site for replication and transcription
 Endoplasmic reticulum: site for protein
synthesis and protein processing
 Ribosome: protein-synthetic machine
 Golgi apparatus: site for packaging
proteins for secretion and delivery
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Eukaryotic organelles II
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Mitochondrion: site for most energyproducing reactions
 Lysosome: digests materials during
endocytosis and cellular degradation
 Peroxisome: site for oxidation of some
nutrients and detoxification of the H2O2
created thereby
 Cytoskeleton: network of filaments that
define the shape and mobility of a cell
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Eukaryotic organelles III
Chloroplast: site for most photosynthetic
reactions
 Vacuoles: sacs for water or other
nutrients
 Cell wall: bacterial or plant component
outside cell membrane that provides
rigidity and protection against osmotic
shock
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Concepts from organic chemistry

There are some elements of organic
chemistry that you should have clear in your
minds.
 All of these are concepts with significance
outside of biochemistry, but they do play
important roles in biochemistry.
 If any of these concepts is less than
thoroughly familiar, please review it:
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Organic
concepts I
Image courtesy Michigan State U.
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Covalent bond: A strong attractive interaction
between neighboring atoms in which a pair of
electrons is roughly equally shared between
the two atoms.
– Covalent bonds may be single bonds, in which
one pair of electrons is shared; double bonds,
which involve two pairs of electrons; or triple
bonds, which involve three pairs (see above).
– Single bonds do not restrict the rotation of other
substituents around the bond; double and triple
bonds do.
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Organic concepts II

Ionic bond: a strong
attractive interaction
between atoms in
which one atom or
group is positively
charged, and another
is negatively charged.
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Organic concepts III
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Hydrogen bond: A weak attractive
interaction between neighboring atoms in
which a hydrogen atom carrying a slight,
partial positive charge shares that positive
charge with a neighboring electronegative
atom.
Cartoon
courtesy
CUNY
Brooklyn
– The non-hydrogen atom to which the hydrogen
is covalently bonded is called the hydrogenbond donor;
– the neighboring atom that takes on a bit of the
charge is called the hydrogen-bond acceptor
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Organic
concepts IV
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Van der Waals
interaction:
A weak attractive
interaction between
nonpolar atoms,
arising from
transient induced
dipoles in the two
atoms.
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Image courtesy
Columbia U. Biology Dept.
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Organic
Concepts V
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Chirality: The property of
a molecule under which it
cannot be superimposed
upon its mirror image.
Image courtesy DRECAM, France
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Organic
Concepts VI

acetone
propen-2-ol
Tautomerization: The interconversion of two
covalently different forms of a molecule via a
unimolecular reaction that proceeds with a low
activation energy. The two forms of the molecule
are known as tautomers: because of the low
activation barrier between the two forms, we will
typically find both species present.
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Organic Concepts
VII
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Nucleophilic substitution: a
reaction in which an electron-rich
(nucleophilic) molecule attacks an
electron-poor (electrophilic)
molecule and replaces group or
atom within the attacked species.
– The displaced group is known as a
leaving group.
– This is one of several types of
substitution reactions, and it occurs
constantly in biological systems.
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Organic Concepts VIII
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Polymerization: creation of large
molecules by sequential addition of simple
building blocks
– often by dehydration, i.e., the elimination of
water from two species to form a larger one:
R1-O-H + HO-R2-X-H  R1-X-R2-OH + H2O
– The product here can then react with
HO-R3-X-H to form
R1-X-R2-X-R3-OH with elimination of another
water molecule, and so on.
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Organic Concepts IX
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Equilibrium: in the context of a chemical
reaction, the state in which the concentrations
of reactants and products are no longer
changing with time because the rate of
reaction in one direction is equal to the rate in
the opposite direction.
Kinetics: the study of the rates at which
reactions proceed.
Conventionally, we use the term
thermodynamics to describe our
understanding of the energetics of equilibrium
systems
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Organic Concepts X
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Catalysis: the lowering of the energetic barrier
between substrates and products in a reaction by the
participation of a substance that ultimately is
unchanged by the reaction
– It is crucial to recognize that catalysts (chemical agents that
perform catalysis) do not change the equilibrium position of
the reactions in which they participate:
– they only change the rates (the kinetics) of the reactions they
catalyze.
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Zwitterion: a compound containing both a positive
and a negative charge
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Classes of small molecules
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Small molecules other than
water make up a small
percentage of a cell's mass, but
small molecules have significant
roles in the cell, both on their
own and as building blocks of
macromolecules. The classes of
small molecules that play
significant roles in biology are
listed below. In this list, "soluble"
means "water-soluble".
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iClicker quiz (for attendance)
How many midterms will we have?
 (a) 1
 (b) 2
 (c ) 3
 (d) 4
 (e) I don’t care.
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Biological small molecules I
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Water: Hydrogen hydroxide. In liquid form in
biological systems. See below.
 Lipids: Hydrophobic molecules, containing
either alkyl chains or fused-ring structures. A
biological lipid usually contains at least one
highly hydrophobic moeity.
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Biological small molecules II
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Carbohydrates: Polyhydroxylated
compounds for which the building
blocks are highly soluble.
– The typical molecular formula for the
monomeric forms of these compounds is
(CH2O)n, where 3 < n < 9,
– but usually n = 5 or 6.
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Biological small molecules III
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Amino acids: Compounds containing an
amine (NH3+) group and a carboxyl (COO-)
group.
The most important biological amino acids
are a-amino acids, in which the amine
group and the carboxyl group are separated
by one carbon, and that intervening carbon
has a hydrogen attached to it. Thus the
general formula for an a-amino acid is
H3N+ - CHR - COO-
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Biological small
molecules IV
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Nucleic acids: Soluble compounds that
include a nitrogen-containing ring system.
– The ring systems are derived either from purine or
pyrimidine.
– The most important biological nucleic acids are
those in which the ring system is covalently
attached to a five-carbon sugar, ribose, usually
with a phosphate group attached to the same
ribose ring.
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Small molecules V
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Inorganic ions: Ionic species containing no
carbon but containing one or more atoms and
at least one net charge.
– Ions of biological significance include
Cl-, Na+, K+, Mg+2, Mn+2, I-, Ca+2, PO4-3, SO4-2,
NO3-, NO2-, and NH4+.
– Phosphate (PO4-3) is often found in partially
protonated forms HPO4-2 and H2PO4– Ammonium ions occasionally appear as neutral
ammonia (NH3), particularly at higher pH values
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Biological Small Molecules VI
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Cofactors: This is a catchall category for organic
small molecules that serve in some functional role in
biological organisms. Many are vitamins or are
derived from vitamins; a vitamin is defined as an
organic molecule that is necessary for metabolism
but cannot be synthesized by the organism. Thus the
same compound may be a vitamin for one organism
and not for another.
Ascorbate (vitamin C) is a vitamin for humans and
guinea pigs but not for most other mammals.
Cofactors often end up as prosthetic groups,
covalently or noncovalently attached to proteins and
involved in those proteins' functions.
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Biological
macromolecules
Most big biological
molecules are polymers, i.e.
molecules made up of large
numbers of relatively simple
building blocks.
 Cobalamin is the biggest
nonpolymeric biomolecule I
can think of (MW 1356 Da)
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Structure
courtesy
Wikimedia
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Categories of biological polymers
Proteins
 Nucleic acids
 Polysaccharides
 Lipids (sort of):
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– 2-3 chains of aliphatics attached to a
polar head group, often built on glycerol
– Aliphatic chains are usually 11-23 C’s
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Polymers and oligomers
These are distinguished only by the
number of building-blocks contained
within the multimer
 Oligomers: typically < 50 building
blocks
 Polymers  50 building blocks.
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Categories of biopolymers
Category
Protein
# monomers
20
<mol wt/
# mono- Branchmonomer> mers
ing?
110
65-5000 no
RNA
4-10
220-400
50-15K
no
DNA
4
200-400
50-106
no
Polysaccharide
~10
180
2-105
Sometimes
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Water: a complex substance
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Oxygen atom is covalently bonded to 2
hydrogens
Single bond character of these bonds means
the H-O-H bond angle is close to 109.5º =
acos(-1/3): actually more like 104.5º
This contrasts with O=C=O (angle=180º) or
urea ((NH2)2-C=O) (angles=120º)
Two lone pairs available per oxygen:
these are available as H-bond acceptors
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Water is polar

Charge is somewhat unequally shared
 Small positive charge on H’s (d+); small
negative charge on O (2d-) (Why?)
 A water molecule will orient itself to align
partial negative charge on one molecule
close to partial positive charges on
another.
 Hydrogen bonds are involved in this.
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Liquid water is mobile
The hydrogen-bond networks
created among water molecules
change constantly on a subpicosecond time scale
 At any moment the H-bonds look like
those in crystalline ice
 Solutes disrupt the H-bond networks

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Water in reactions

Water is a medium within which reactions
occur;
 But it also participates in reactions
 Enzymes often function by making water
oxygen atoms better nucleophiles or water
H’s better electrophiles
 Therefore water is a direct participant in
reactions that wouldn’t work in a
nonenzymatic lab setting!
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Water’s physical properties
High heat capacity:
stabilizes temperature in living
things
 High surface tension
 Nearly incompressible (density
almost independent of pressure)
 Density max at 3.98ºC

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Catalysis
Catalysis is the lowering of the
activation energy barrier between
reactants and products
 How?
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– Physical surface on which reactants
can be exposed to one another
– Providing moieties that can temporarily
participate in the reaction and be
restored to their original state at the end
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Biological catalysts
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1890’s: Fischer realized that there had
to be catalysts in biological systems
1920’s: Sumner said they were
proteins
It took another 10 years for
the whole community to accept that
It’s now known that RNA can be
catalytic too:
– Can catalyze modifications in itself
– Catalyzes the key step in protein
synthesis in the ribosome
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Energy in biological systems
We distinguish between
thermodynamics and kinetics:
 Thermodynamics characterizes the
energy associated with equilibrium
conditions in reactions
 Kinetics describes the rate at which a
reaction moves toward equilibrium
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Thermodynamics
Equilibrium constant is a measure of
the ratio of product concentrations to
reactant concentrations at
equilibrium
 Free energy is a measure of the
available energy in the products and
reactants
 They’re related by DGo = -RT ln Keq

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Kinetics
Rate of reaction is dependent
on Kelvin temperature T and
on activation barrier DG‡
preventing conversion from
one site to the other
 Rate = Qexp(-DG‡/RT)
 Job of an enzyme is to reduce
DG‡

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Svante Arrhenius
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Regulation
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Biological reactions are regulated in the
sense that they’re catalyzed by enzymes, so
the presence or absence of the enzyme
determines whether the reaction will proceed
 The enzymes themselves are subject to
extensive regulation so that the right
reactions occur in the right places and times
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Typical enzymatic regulation
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Suppose enzymes are involved in converting A to
B, B to C, C to D, and D to F. E is the enzyme that
converts A to B:
(E)
ABCDF
In many instance F will inhibit (interfere) with the
reaction that converts A to B by binding to a site
on enzyme E so that it can’t bind A.
This feedback inhibition helps to prevent
overproduction of F—homeostasis.
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Molecular biology

This phrase means something much more
specific than biochemistry:
 It’s the chemistry of replication, transcription,
and translation, i.e., the ways that genes are
reproduced and expressed.
 Most of you have taken biology 214 or its
equivalent; we’ll review some of the contents
of that course here, mostly near the end of the
semester.
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The molecules of
molecular biology

Deoxyribonucleic acid: polymer; backbone is
deoxyribose-phosphate; side chains are
nitrogenous ring compounds
 RNA: polymer; backbone is ribosephosphate; side chains as above
 Protein: polymer: backbone is
NH-(CHR)-CO; side chains are 20
ribosomally encoded styles
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Steps in molecular biology:
the Central Dogma

DNA replication (makes accurate copy of
existing double-stranded DNA prior to
mitosis)
 Transcription (RNA version of DNA message
is created)
 Translation (mRNA copy of gene serves as
template for making protein: 3 bases of RNA
per amino acid of synthesized protein)
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Evolution and Taxonomy

Traditional studies of interrelatedness of
organisms focused on functional similarities
 This enables production of phylogenetic trees
 Molecular biology provides an alternative,
possibly more quantitative, approach to
phylogenetic tree-building
 More rigorous hypothesis-testing possible
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Quantitation
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Biochemistry is a quantitative science.
Results in biochemistry are rarely significant unless
they can be couched in quantifiable terms.
Thermodynamic & kinetic behavior of biochemical
systems must be described quantitatively.
Even the descriptive aspects of biochemistry, e.g. the
compartmentalization of reactions and metabolites
into cells and into particular parts of cells, must be
characterized numerically.
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Mathematics in biochemistry
Ooo: I went into biology rather than
physics because I don’t like math
 Too bad. You need some here:
but not much.
 Biggest problem in past years:
exponentials and logarithms

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Exponentials

Many important biochemical equations are
expressed in the form
Y = ef(x)
 … which can also be written
Y = exp(f(x))
 The number e is the base of the natural
logarithm system and is, very roughly,
2.718281828459045
 I.e., it’s 2.7 1828 1828 45 90 45
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Logarithms
First developed as computational tools
because they convert multiplication
problems into addition problems
 They have a fundamental connection
with raising a value to a power:
 Y = xa  logx(Y) = a
 In particular, Y = exp(a) = ea
lnY = loge(Y) = a

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Algebra of logarithms
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logv(A) = logu(A) / logu(v)
logu(A/B) = logu(A) - logu(B)
logu(AB) = Blogu(A)
log10(A) = ln(A) / ln(10)
= ln(A) / 2.30258509299
= 0.4342944819 * ln(A)
ln(A) = log10(A) / log10e
= log10(A) / 0.4342944819
= 2.30258509299 * log10(A)
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Course structure
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Two midterms plus a final
All exams will be closed-book, closed-notes
exams. Calculators are not allowed.
Each exam will be accompanied by a helpsheet with many helpful facts
Gauge your memorization with the help-sheet
before you: what’s on the help sheet doesn’t
need to be memorized
My exams tend to be long but easy:
budget your time carefully!
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Grading
I’m a moderately tough grader, but I do curve
this course
 The cutoff for an A is likely to be around an
82, but it’s uncertain
 Homework, literature assignments, iClicker
quizzes, and discussion-board participation
count
 Internet students will get a substitute
assignment to replace iClicker quizzes

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Textbook and Lecture Notes
Garrett & Grisham is a detail-rich and
well-written text: read it!
 Many of my lectures are derived from
Horton et al rather than from Garrett &
Grisham, particularly in the version that
I’ve already posted to the Internet
 Be prepared for the lecture notes
themselves to evolve during the course

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Office Hours
I should be available 3:30-5pm
Tuesdays and Thursdays in most cases
 If that doesn’t work, make an
appointment
 The discussion board is another good
way to reach me and the rest of the
class as well!

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Assignments
Regular homeworks will be due weekly,
probably on Fridays
 But no assignment due tomorrow
 Literature assignments are due weekly,
probably on Tuesdays
 Specific readings already posted will be
augmented but not deleted

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