BTW: Turn on the recorder

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• BTW Turn on the recorder

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http//www.columbia.edu/cu/biology/courses/c2005/i
ndex.html
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Note to myself for Lec. 1 Web site is required
reading (at least twice a week) Problem book Web
lectures Email questions, QA database, office
hours Evening vs. morning lectures Recitation
sign-up Note exam dates and times (drop an exam)
note final date Transparency Exam topics,
nature
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What is expected of you as a student
If you can
then you will
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What is expected of you as a student
If you can
then you will
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Physics
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Chemical Physics
Hydrogen atom
Schrodinger equation
Probability of finding an electron at a given
position
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Chemistry
http//www.wou.edu/las/physci/ch336/lecture/lect10
.htm
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Biology
Predicting the amount of energy released in a
chemical reaction
products
Q
reactants
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Chemistry and Math for this course

• basic atomic structure and bonding
• ions
• salts
• moles
• molecular weight
• stoichiometry
• chemical equilibria, equilibrium constants
• pH
• etc.?
• and
• 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 one1.
complexity
Artificial polypropylene polyester 5 dye
molecules_____ 7 different
distinguishable molecules
Real 20,000 different distinguishable molecules
And each one is doing a job.
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2. Chemical interaction with the environment
CO2
O2
NO3-
H2O
Real
Artificial
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3. Reproduction
Cannot reproduce itself
Can reproduce itself
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Consider 2 approaches to studying biology
1. Focusing on differences to learn about nature
Darwins finches
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2. Focusing on similarities to learn about nature
Reductionism
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Chemistry analogy basic building block is the
molecule
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Alive?
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Cell theory end
(i.e., not alive)
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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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membonly


Outside
Inside
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Memnuc
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Memnucorg
Organelles mitochondria
lysosomes
ribosomes
etc.
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A cell
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Sizes

• 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
• Smallest cells 1 micron in diameter (so volume
  1/1000 of skin cell)

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bactcell0
A bacterial cell
A bacterium
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bactcell1
No nucleus (DNA is in the cytoplasm) No
membrane-bound organelles
No. of cells in the whole organism 1
(unicellular)
Prokaryote, prokaryotic
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Unicellular
Multicellular

• Prokaryotes
• (mostly bacteria)
• Pneumococcus (pathogen)
• Rhizobium (nitrogen fixation)
• Escherichia coli (lab)
• Eukaryotes
• Amoeba (pond)
• Paramecium (pond)
• Plasmodium (malaria)
• Yeast (beer, wine, bread, lab)

• Prokaryotes
• Very few examples
• Eukaryotes
• Human being
• Worm (C. elegans)
• Fruit fly (Drosophila)
• Zebra fish
• Mustard plant (Arabidopsis)
• Mouse
• (these are all popular research organisms)

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binfission
Escherichia coli
E. coli
?-------------------------------------------------
--- One hour -----------------------------------
---------?
2
1
One net bacterial cell in 1 hour (in minimal
medium)
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20,000,000 molecules in 2 cells
10,000,000 molecules in 1 E. coli cell 5000
types of molecules
types of molecules
5000
Net increase 10,000,000 organic molecules,
synthesized in one hour
What are these molecules and whence do they come?
The newly synthesized stuff must come from the
stuff thats in the medium . . .
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A minimal medium for E. coli
C6H12O6 glucose, a sugar KH2PO4 MgSO4  NH4Cl
ammonium chloride H2O water trace
elements (e.g., Zn, Fe, Cu, Se, )
potassium phosphate
magnesium sulfate
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MM with glucose
A minimal medium for E. coli
C6H12O6 glucose, a sugar KH2PO4 MgSO4  NH4Cl
ammonium choride H2O
water trace elements (e.g., Zn, Fe, Cu, Se, )
potassium phosphate
magnesium sulfate
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Net synthesis of an E. coli cell
20,000,000 molecules in 2 cells
10,000,000 molecules in 1 cell 5000 types of
molecules
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 (OK, and
salts) in one hour
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Preview

• 1. What is an E. coli cell?
• Polysaccharides,
• Lipids,
• Nucleic Acids,
• Proteins,
• Small molecules
• 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.

Organic chemicals
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1cell
Exponential growth
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1cellbigger
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2cells
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2cellsbigger
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4cells
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1 generation
1 generation
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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.
• Looks like 2 is a key number 212, 22 4,
  23 8, and so in general, N 1 x 2g
• And if we start with 100 cells, then have 200,
  400, 800, etc, so N 100 x 2g
• Or in general N No x 2g And to
  express growth in terms of real time
• g t/tD where tD the doubling time, or
  generation time.
• So the number of cells as a function of time is
  N No2t/tD
• Or if we let k 1/tD, then N No2kt
• But 2 is not a common base, so we can also write
• N No10kt , but here k log(2)/tD rather than
  1/tD (log log base 10)
• Or we can use the natural log, e N Noekt
  where k ln(2)/tD
• And if we take the log of both sides, we get
  (base 10 case)
• log(N/No) kt (k log(2)/tD
  0.3/tD)
• and

See exponential growth handout
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Growth linear
N No10kt
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Growth semilog
A semi-log plot
N
logN 8 7 6 5 4 3 2 1 0
log(N/No) kt
NNo10kt N/No 10kt log(N/No)
kt Note just used k here not k, k defined in
context in general
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Growth phases
Real life
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Use calculus if you know it, its more
natural 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 No has exactly doubled
in that case N/No 2 and t tD, so N Noekt ?
2 ektD To solve for k, take the natural
logarithm of both sides ln2ktD, or kln2/tD,
so the constant comes out exactly as before as
well. See exponential growth
handout
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E. coli molecule 1
water
H2O
HOH
105o
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Waterdeltas
d partial charge, not quantified Not
, a full unit charge, as in the formation of ions
by NaCl in solution NaCl ? Na Cl- Water
is a POLAR molecule (partial charge separation)
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• Got this far

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waterHbonds
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waterHbonds
Hydrogen bond H-bond (strength 3 kcal/mole)
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Ethanol and Water
3
2
2
3
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amide3
O is more electronegative than C
R any group of atoms
R-CONH2 is an amide, -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 chemical structures of the functional groups
used in this course must be memorized. See the
Functional Groups handout. This is one of very
few memorizations required.