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Note to myself for Lec. 1:
Web site is required reading (at least twice a week) Problem bookWeb lecturesExam topics, natureEmail questions, Q&A databaseRecitation sign-upEvening vs. morning lecturesNote exam dates and times (drop an exam); note final dateTransparency
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Hydrogen atom
Schrodinger equation:
Probability of finding an electron at a given position
Chemical Physics
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Predicting the effect of temperature on reaction rates (Arrhenius equation).
k=A*e(-Ea/R*T)
Δ Go = - RTln(Keq)Δ G = Δ Go + RTln(Q)
Predicting the amount of energy released in a chemical reaction
Chemistry
Biology
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6Chemistry and Math for this course
• basic atomic structure and bonding• ions• salts• moles• molecular weight• molarity• stoichiometry• chemical equilibria• pH• etc.?
and:
• exponents• logarithms• algebra• no calculus
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7Characteristics 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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8Artificial rubber plant vs. a real one:
complexity
Artificial:
polypropylenepolyester5 dyes_____ 7 different distinguishable molecules
Real:
20,000 different distinguishable molecules
And each one is doing a job.
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CO2
H2O
O2
Artificial Real
Chemical interaction with the environment
NO3-
dust
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10Reproduction
Cannot reproduce itself Can reproduce itself
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Darwin’s finches
Focusing on differences to learn about nature
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} } Commondenominator?
Focusing on similarities to learn about nature
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Chemistry analogy: basic building block is the molecule
Corn syrup
sweet sweet
Take smaller bits
a molecule
+
Not glucose
not sweet(lost it)
2 different molecules
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Alive
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Cut
Alive
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C ut
Alive Alive?
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C ut
G ro wth m e d ium
Alive Alive?
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C ut
G ro wth m e d ium
Alive Alive?
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C ut
G ro wth m e d ium
Alive Alive? Alive
Kla us Be c ke r
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Cut
Growth
mediumShake
apart
Alive Alive Alive
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C ut
G ro wth m e d ium
Sha ke a p a rt
Alive Alive Alive Alive?
Kla us Be c ke r
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C ut
G ro wth m e d ium
Sha ke a p a rt
Ta ke one c e ll
Alive Alive Alive Alive?
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C ut
G ro wth m e d ium
G ro wth m e d ium
Sha ke a p a rt
Ta ke one c e ll
Alive Alive Alive Alive?
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Cut
Growth
medium
Growth
medium
Shake
apart
Take
one cell
Alive Alive Alive Alive Alive
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Cut
Growth
medium
Growth
medium
Shake
apart
Shake
harder (blender)
Take
one cell
Alive Alive Alive Alive Alive Alive?
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Cut
Growth
medium
Growth
medium
Shake
apart
Shake
harder (blender)
Take
one cell
X
Alive Alive Alive Alive Alive
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Cut
Growth
medium
Growth
medium
Shake
apart
Shake
harder (blender)
Take
one cell
X
Alive Alive Alive Alive Alive Dead
Cell theory end
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29Cell 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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Mem+nucOrganelles without membranes
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Mem+nuc+org
Organelles
“mitochondria”
“lysosomes”
“ribosomes”
etc.
Organelles with membranesOrganelles without membranes
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A cell
10 microns
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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. of cells in the whole organism = ~ 1 (unicellular)
Prokaryote, prokaryotic
No nucleusNo membrane-bound organelles
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Prokaryotes:
(mostly bacteria)
Pneumococcus (pathogen)Rhizobium (nitrogen fixation)Escherichia coli (lab)
Eukaryotes:
Amoeba (pond)Paramecium (pond)Plasmodium (malaria)Yeast (beer, bread, lab)
Prokaryotes:
Very few examples
Eukaryotes:Human beingWorm (C. elegans)Fruit fly (Drosophila)Zebra fishMustard plant (Arabidopsis)Mouse(these are all popular research organisms)
Unicellular Multicellular
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binfission
---------------------------------------------------- One hour --------------------------------------------
1 2One net bacterial cell in 1 hour (in minimal medium)
Escherichia coli
E. coli
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~10,000,000 molecules in 1 cell~5000 types of molecules
~20,000,000 molecules in 2 cells
Net increase = 10,000,000 organic molecules, synthesized in one hour
What are they and from whence do they come?
~5000 types of molecules
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C6H12O6 glucose, a sugar
KH2PO4
MgSO4
NH4Cl ammonium chloride
H2O water
+trace elements (e.g., Zn, Fe, Cu, Se, … )
potassium phosphate
magnesium sulfate
A minimal medium for E. coli
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C6H12O6 glucose, a sugar
KH2PO4
MgSO4
NH4Cl ammonium choride
H2O water
+trace elements (e.g., Zn, Fe, Cu, Se, … )
potassium phosphate
magnesium sulfate
A minimal medium for E. coli
MM with glucose
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~10,000,000 molecules in 1 cell~5000 types of molecules
~20,000,000 molecules in 2 cells
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”
~5000 types of molecules
Net synthesis of an E. coli cell
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43Preview
• 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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gu
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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.
• 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 = No10k’t , but here k’ = log(2)/tD rather than 1/tD (log = log base 10)
• Or we can use the natural log, e: N = Noek”t where k” = ln(2)/tD
• And if we take the log of both sides, we get (base 10 case):
log(N/No) = k’t (k’ = log(2)/tD = 0.3/tD)and ln(N/No) = k”t (k” = ln(2)/tD = 0.69/tD)
See exponential growth handout
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Growth: linear
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Growth: semilog
A semi-log plot
N=No10kt N/No = 10kt log(N/No) = kt
Note: just k used here not k’, k defined in context
logN876543210
N
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Growth phases
Real life
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56dN/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: 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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water
E. Coli molecule #1
H2O
HOH
OH
H105o
Our first “functional group”:hydroxyl, -OH
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Waterdeltas
δ+ = 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)
Negative pole
Positive pole
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waterHbonds
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waterHbonds
Hydrogen bond
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61Ethanol and Water
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R= any group of atoms
amide3
R-CONH2 is an “amide”, -CONH2 is an amide group (another functional group - the whole –CONH2 together)
O is more electronegative than C
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an amide
ethanol, an alcohol
Hydrogen bonds between 2 organic moleculesWater 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.