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Note to myself for Lec. 1:
Web site is required reading (at least twice a week)
Problem book
Web lectures
Exam topics, nature
Email questions, Q&A database
Recitation sign-up
Evening vs. morning lectures
Note exam dates and times (drop an exam); note final date
Transparency
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Chemical Physics
Hydrogen atom
Schrodinger equation:
Probability of finding an electron at a given position
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Chemistry
Predicting the effect of temperature on reaction rates (Arrhenius equation).
k=A*e(-Ea/R*T)
Biology
Predicting the amount of energy released in a chemical reaction
Δ G = Δ Go + RTln(Q)
Δ Go = - RTln(Keq)
Chemistry and Math for this course
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basic atomic structure and bonding
ions
salts
moles
molecular weight
molarity
stoichiometry
chemical equilibria
pH
etc.?
and:
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exponents
logarithms
algebra
no calculus
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Characteristics of living things
1) Structure = complex
2) Metabolism = chemical interaction with the environment
3) Reproduction = duplication of the complex, metabolizing
structure
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Artificial rubber plant vs. a real one:
complexity
Artificial:
Real:
polypropylene
polyester
5 dyes_____
7 different
distinguishable molecules
20,000 different
distinguishable molecules
And each one is doing a job.
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Chemical interaction with the environment
CO2
dust
O2
H 2O
Artificial
Real
NO3-
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Reproduction
Cannot reproduce itself
Can reproduce itself
Focusing on differences to learn about nature
Darwin’s finches
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Focusing on similarities to learn about nature
}
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}
Common
denominator?
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Chemistry analogy: basic building block is the molecule
Corn syrup
+
Take smaller bits
a molecule
sweet
sweet
Not glucose
2 different molecules
not sweet
(lost it)
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Alive
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Cut
Alive
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Cut
Alive
Alive?
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Cut
Growth
medium
Alive
Alive?
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Cut
Growth
medium
Alive
Alive?
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Klaus Becker
Cut
Growth
medium
Alive
Alive?
Alive
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Cut
Growth
medium
Alive
Alive
Shake
apa rt
Alive
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Klaus Becker
Cut
Growth
medium
Alive
Alive
Sha ke
a pa rt
Alive
Alive?
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Take
one
cell
Cut
Growth
medium
Alive
Alive
Sha ke
a pa rt
Alive
Alive?
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Take
one
cell
Cut
Growth
medium
Sha ke
a pa rt
Growth
medium
Alive
Alive
Alive
Alive?
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Take
one
cell
Cut
Growth
medium
Shake
apa rt
Growth
medium
Alive
Alive
Alive
Alive
Alive
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Take
one
cell
Cut
Growth
medium
Shake
harder
(blender)
Shake
apa rt
Growth
medium
Alive
Alive
Alive
Alive
Alive
Alive?
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Take
one
cell
Cut
Growth
medium
Shake
harder
(blender)
Shake
apa rt
Growth
medium
Alive
Alive
Alive
Alive
Alive
X
Cell theory end
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Take
one
cell
Cut
Growth
medium
Shake
harder
(blender)
Shake
apa rt
X
Growth
medium
Alive
Alive
Alive
Alive
Alive
Dead
Cell Theory
All living things are made up of cells (or their by-products), and all cells
come from other cells by growth and development.
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Outside
Inside
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Mem+nuc
Organelles without membranes
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Organelles without membranes
Organelles with membranes
Organelles
“mitochondria”
“lysosomes”
“ribosomes”
etc.
A cell
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10 microns
Sizes
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Skin cell ~ 10 micrometers (microns, um) in diameter
– Millimeter (mm) = 1/1000 of a meter: e.g., head of a pin
– Micron = 10-6 meters (1 millionth of a meter, 1/1000 of a millimeter): e.g., cells
– Nanometer (nm) = 10-9 meters (1 billionth of a meter, 1/1000 of a micron): e.g.,
diameter of molecules
– Angstrom (A) = 1/10 of a nanometer: e.g, distance between 2 atoms in a
molecule
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Smallest cells ~ 1 micron in diameter (so volume = ~1/1000 of skin cell)
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bactcell0
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A bacterial cell
A bacterium
bactcell1
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No nucleus
No membrane-bound organelles
No. of cells in the whole organism = ~ 1 (unicellular)
Prokaryote, prokaryotic
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Unicellular
Multicellular
Prokaryotes:
Prokaryotes:
(mostly bacteria)
Very few examples
Pneumococcus (pathogen)
Rhizobium (nitrogen fixation)
Escherichia coli (lab)
Eukaryotes:
Amoeba (pond)
Paramecium (pond)
Plasmodium (malaria)
Yeast (beer, bread, lab)
Eukaryotes:
Human being
Worm (C. elegans)
Fruit fly (Drosophila)
Zebra fish
Mustard plant (Arabidopsis)
Mouse
(these are all popular research organisms)
binfission
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Escherichia coli
E. coli
---------------------------------------------------- One hour --------------------------------------------
1
One net bacterial cell in 1 hour
(in minimal medium)
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~10,000,000 molecules in 1 cell
~5000 types of molecules
~20,000,000 molecules in 2 cells
~5000 types of molecules
Net increase = 10,000,000 organic molecules,
synthesized in one hour
What are they and from whence do they come?
A minimal medium for E. coli
C6H12O6 glucose, a sugar
KH2PO4 potassium phosphate
MgSO4
magnesium sulfate
NH4Cl
ammonium chloride
H2O
water
+trace elements (e.g., Zn, Fe, Cu, Se, … )
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MM with glucose
A minimal medium for E. coli
C6H12O6 glucose, a sugar
KH2PO4 potassium phosphate
MgSO4
magnesium sulfate
NH4Cl
ammonium choride
H2O
water
+trace elements (e.g., Zn, Fe, Cu, Se, … )
Net synthesis of an E. coli cell
~10,000,000 molecules in 1 cell
~5000 types of molecules
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~20,000,000 molecules in 2 cells
~5000 types of molecules
Net increase = 10,000,000 organic molecules,
synthesized in one hour
What are they and from whence do they come?
“You can make an E. coli cell from glucose in one hour”
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Preview
• 1. What is an E. coli cell?
– Polysaccharides,
– Lipids,
– Nucleic Acids,
– Proteins,
– Small molecules
Organic chemicals
• 2. How do we get those chemicals (in minimal medium)?
-- From glucose,
-- via biosynthetic chemical reactions (= metabolism).
• 3. Where does the energy for this process come from?
-- From glucose, via energy metabolism.
• 4. Where does E. coli get the information for doing all this?
-- it's hard-wired in its DNA.
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gu
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Exponential growth
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4cells
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1 generation
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1 generation
2 generation
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So, starting with one cell, after 1 generation , get 2 cells, after 2 gens., 4 cells, after 3 gens, 8 cells, etc.
And so in general, N = 1 x 2g
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And if we start with 100 cells, then have 200, 400, 800, etc, so N = 100 x 2g :
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Or in general:
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And to express growth in terms of real time:
N = No x 2g
• g = t/tD where tD = the doubling time, or generation time.
N = No2t/tD
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So the number of cells as a function of time is :
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Or: if we let
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But 2 is not a common base, so we can also write:
k= 1/tD,
then
N = No2kt
• N = No10k’t , but here k’ = log(2)/tD rather than 1/tD
N = Noek”t
k” = ln(2)/tD
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Or we can use the natural log, e:
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And if we take the log of both sides, we get (base 10 case):
log(N/No) = k’t
and ln(N/No) = k”t
where
(log = log base 10)
(k’ = log(2)/tD = 0.3/tD)
(k” = ln(2)/tD = 0.69/tD)
See exponential growth handout
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A semi-log plot
N
logN
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5
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3
2
1
0
N=No10kt
N/No = 10kt
log(N/No) = kt
Note: just k used here not k’, k defined in context
Growth phases
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Real life
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dN/dt = kN
Separating variables:
dN/N = kdt
Integrating between time zero when N = No and time t, when N = N,
dN/N = kdt,
we get:
lnN - ln No = kt - 0,
or ln(N/No) = kt,
or N = Noekt,
which is exactly what we derived above.
But is this k the same k as before?
We can now calculate this constant k by considering the case of the time interval over which N o
has exactly doubled; in that case N/No = 2 and t = tD, so:
2 = ektD.
Taking the natural logarithm of both sides:
ln2=ktD, or k=ln2/tD,
so the constant comes out exactly as before as well.
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E. Coli molecule #1
water
H2O
HOH
H O
105o
H
Our first “functional group”:
hydroxyl, -OH
Waterdeltas
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δ+ = partial charge, not quantified
Not “ + ” , a full unit charge,
as in the formation of ions by NaCl in solution:
NaCl  Na+ + ClWater is a POLAR molecule (partial charge separation)
Negative pole
Positive pole
waterHbonds
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waterHbonds
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Hydrogen bond
Ethanol and Water
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R= any group of atoms
R-CONH2 is an “amide”,
O is more electronegative than C
-CONH2 is an amide group
(another functional group - the whole –CONH2 together)
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ethanol, an alcohol
an amide
Hydrogen bonds between 2 organic molecules
Water often out-competes this interaction (but not always)
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The functional groups used in this
course must be memorized.
See the Functional Groups handout.
This is one of very few memorizations required.