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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

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

7Characteristics of living things

1) Structure = complex

2) Metabolism = chemical interaction with the environment

3) Reproduction = duplication of the complex, metabolizing structure

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

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

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

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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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

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.