btw: turn on the recorder
DESCRIPTION
BTW: Turn on the recorder. Note to myself for Lec. 1: Web site is required reading (at least twice a week) Problem book Problem book Web lectures Email questions, Q&A database, office hours Evening vs. morning lectures Recitation sign-up - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/1.jpg)
BTW: Turn on the recorder
1
![Page 2: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/2.jpg)
![Page 3: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/3.jpg)
3
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
![Page 4: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/4.jpg)
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:
![Page 5: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/5.jpg)
5
Physics
![Page 6: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/6.jpg)
6
Hydrogen atom
Schrodinger equation:
Probability of finding an electron at a given position
Chemical Physics
![Page 7: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/7.jpg)
7
http://www.wou.edu/las/physci/ch336/lecture/lect10.htm
Chemistry
![Page 8: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/8.jpg)
8
ΔGo = - RTln(Keq)ΔG = ΔGo + RTln(Q)
Predicting the amount of energy released in a chemical reaction
Biology
[products]
[reactants]Q =
![Page 9: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/9.jpg)
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
![Page 10: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/10.jpg)
10Characteristics of living things
1) Structure = complex
2) Metabolism = chemical interaction with the environment
3) Reproduction = duplication of the complex, metabolizing structure
![Page 11: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/11.jpg)
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.
![Page 12: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/12.jpg)
12Characteristics of living things
1) Structure = complex
2) Metabolism = chemical interaction with the environment
3) Reproduction = duplication of the complex, metabolizing structure
![Page 13: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/13.jpg)
13
CO2
H2O
O2
Artificial Real
2. Chemical interaction with the environment
NO3-
dust
![Page 14: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/14.jpg)
14Characteristics of living things
1) Structure = complex
2) Metabolism = chemical interaction with the environment
3) Reproduction = duplication of the complex, metabolizing structure
![Page 15: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/15.jpg)
153. Reproduction
Cannot reproduce itself Can reproduce itself
![Page 16: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/16.jpg)
16
Darwin’s finches
1. Focusing on differences to learn about nature
Consider 2 approaches to studying biology:
![Page 17: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/17.jpg)
17
} } Commondenominator?
2. Focusing on similarities to learn about nature
Reductionism
![Page 18: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/18.jpg)
18
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
![Page 19: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/19.jpg)
19
??
?
![Page 20: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/20.jpg)
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.
![Page 21: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/21.jpg)
21
membonly
Outside Inside
‘ ‘
![Page 22: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/22.jpg)
22
Mem+nuc
![Page 23: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/23.jpg)
23
Mem+nuc+org
Organelles
“mitochondria”
“lysosomes”
“ribosomes”
etc.
Organelles with membranes
Organelles without membranes
![Page 24: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/24.jpg)
24
A cell
10 microns
![Page 25: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/25.jpg)
25
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)
![Page 26: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/26.jpg)
26
bactcell0
A bacterial cell
A bacterium
![Page 27: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/27.jpg)
27
bactcell1
No. of cells in the whole organism = ~ 1 (unicellular)
Prokaryote, prokaryotic
No nucleus (DNA is in the cytoplasm)No membrane-bound organelles
![Page 28: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/28.jpg)
28
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
![Page 29: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/29.jpg)
29
binfission
---------------------------------------------------- One hour --------------------------------------------
1 2One net bacterial cell in 1 hour (in minimal medium)
Escherichia coli
E. coli
![Page 30: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/30.jpg)
30
~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
![Page 31: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/31.jpg)
31
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
![Page 32: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/32.jpg)
32
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
![Page 33: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/33.jpg)
33
~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
![Page 34: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/34.jpg)
34Preview
• 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
![Page 35: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/35.jpg)
35
![Page 36: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/36.jpg)
36
1cell
Exponential growth
![Page 37: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/37.jpg)
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
![Page 38: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/38.jpg)
38
Growth: linear
N = No10kt
![Page 39: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/39.jpg)
39
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
![Page 40: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/40.jpg)
Got this far
![Page 41: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/41.jpg)
41
Growth phases
Real life
(linear on a semi-log plot)
![Page 42: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/42.jpg)
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
![Page 43: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/43.jpg)
43
water
E. coli molecule #1
H2O
HOH
OH
H105o
Our first “functional group”:hydroxyl, -OH
Covalent bond(strength = ~100 kcal/mole)
![Page 44: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/44.jpg)
44
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
![Page 45: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/45.jpg)
45
waterHbonds
![Page 46: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/46.jpg)
46
waterHbonds
Hydrogen bond“H-bond”
(strength = ~ 3 kcal/mole)
![Page 47: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/47.jpg)
47
Ethanol and Water
3
2
3 2
hydroxyl group again
![Page 48: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/48.jpg)
48
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
![Page 49: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/49.jpg)
49
an amide
ethanol, an alcohol
Hydrogen bonds between 2 organic moleculesWater often out-competes this interaction (but not always)
![Page 50: BTW: Turn on the recorder](https://reader035.vdocuments.us/reader035/viewer/2022062408/56813a28550346895da20c2f/html5/thumbnails/50.jpg)
50
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