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Note to myself for Lec. 1:

Web site is required reading (at least twice a week) Problem bookProblem bookWeb lecturesEmail questions, Q&A database, office hoursEvening vs. morning lecturesRecitation sign-upNote exam dates and times (drop an exam); note final dateTransparencyExam topics, nature

What is expected of you as a student

1) Repeat what you have heard exactly as it was presented, know all the terms and the definitions we or the texts have provided

Probably fail

2) Repeat what you have heard in your own words, showing you have some understanding of the concepts and not just the words

Probably pass with up to a B-

3) Apply what you have learned to a new situation you have never seen before thus proving that you have understood the concept and not just learned how to describe it.

B to A

4) Synthesize a new application yourself or extend what you have learned to a new situation of your own design

A

If you can: then you will:

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Physics

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Hydrogen atom

Schrodinger equation:

Probability of finding an electron at a given position

Chemical Physics

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http://www.wou.edu/las/physci/ch336/lecture/lect10.htm

Chemistry

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ΔGo = - RTln(Keq)ΔG = ΔGo + RTln(Q)

Predicting the amount of energy released in a chemical reaction

Biology

[products]

[reactants]Q =

9Chemistry 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

10Characteristics of living things

1) Structure = complex

2) Metabolism = chemical interaction with the environment

3) Reproduction = duplication of the complex, metabolizing structure

11Artificial rubber plant vs. a real one:

1. complexity

Artificial:

polypropylenepolyester5 dye molecules_____ 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

2. Chemical interaction with the environment

NO3-

dust





153. Reproduction

Cannot reproduce itself Can reproduce itself

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Darwin’s finches

1. Focusing on differences to learn about nature

Consider 2 approaches to studying biology:

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} } Commondenominator?

2. Focusing on similarities to learn about nature

Reductionism

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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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??

?

20Cell 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+nuc

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Mem+nuc+org

Organelles

“mitochondria”

“lysosomes”

“ribosomes”

etc.

Organelles with membranes

Organelles 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 nucleus (DNA is in the cytoplasm)No 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, wine, 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 E. coli 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 these molecules and whence do they come?

The newly synthesized stuff must come from the stuff that’s in the medium . . .

~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 (OK, and salts) in one hour”

~5000 types of molecules

Net synthesis of an E. coli cell

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• 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

Large molecules

Small molecules

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1cell

Exponential growth

37• 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: 21=2, 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 = 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

N = No10kt

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Growth: semilog

A semi-log plot

N=No10kt N/No = 10kt log(N/No) = kt

Note: just used k here not k’, k defined in context in general

logN876543210

N

log(N/No) = kt

Got this far

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Growth phases

Real life

(linear on a semi-log plot)

42Use calculus if you know it, it’s 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: ln2=ktD, or k=ln2/tD,

so the constant comes out exactly as before as well. See exponential growth handout

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water

E. coli molecule #1

H2O

HOH

OH

H105o

Our first “functional group”:hydroxyl, -OH

Covalent bond(strength = ~100 kcal/mole)

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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“H-bond”

(strength = ~ 3 kcal/mole)

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Ethanol and Water

3

2

3 2

hydroxyl group again

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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 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.

“carboxyl”

Me You

O ||-C -- OH

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