1. Intro Bio Lecture 2 Announcements:
Recitations start on Monday, Sept. 11; times will be posted ~soon
Exams will be in afternoon, but there will be multiple start times.
Office hours:
LAC: T Th 1-2pm (912 Fairchild)
DM: T Th 1:30-2:30 pm (Mudd 744D or 744E)

2. 1. What’s an E. coli cell? What is it made of? Polysaccharides,
Lipids,
Nucleic Acids,
Proteins,
Small molecules
2. How do we get those chemicals starting with 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.
large molecules
(macromolecules)
organic
chemicals
small molecules

3. Flow of glucose in E. coli
Macromolecules
Polysaccharides
Lipids
Nucleic Acids
Proteins
mono-
mers
biosynthetic
pathway
intermediates
glucose
Each arrow is a specific chemical reaction.
Each chemical reaction is catalyzed by a different enzyme.
Each enzyme is a protein.

4. Exponential growth generation 1 generation 2
Observe: 1, 2, 4, 8, 16, etc. so, number of cells = 2generations

5. N =No10k10*t, log(N/No) =k10*t; if t=tD, N/No=2: k10=log(2)/tD= 0.3/tD
Exponential growth
For a more detailed explanation, see handout on exponential growth.
N = 1 x 2g N = 100 x 2g
N = No x 2g
g = t/tD where tD = the doubling time, or generation time.
N = No2t/tD
define k 1/tD, then N = No2kt
One can change the base of the exponential relation:
N = Noeke*t, ln(N/No) = ke*t; if N/No=2, t=tD: ke= ln(2)/tD =0.69/tD
N =No10k10*t, log(N/No) =k10*t; if t=tD, N/No=2: k10=log(2)/tD= 0.3/tD
and k2 = 1/tD, as above 5

6. Growth of E. coli (generation time of 1 hour, initial cell number = 1)
Number of Cells
Time (hours)

7. Growth of E. coli (generation time of 1 hour, initial cell number = 1)
A semi-log plot
Growth of E. coli (generation time of 1 hour, initial cell number = 1)
logN 8 7 6 5 4 3 2 1
100000
10000
1000
100 10 1
log(N/No) = k10t
Number of Cells 1 5 10 15 20 25
Time (hours)
N=No10k t N/No = 10k t log(N/No) = k10t 10

8. E. coli cultures in real life
“stationary” phase
Log of cell number
Exponential growth: “log” phase
(linear on a semi-log plot)
“lag”
phase
Time
Note: The cells do not have to be dividing synchronously to generate these curves, and usually are not. We are just seeing the average for the whole population.

9. our first “functional group”:
The molecules of E. coli: what needs to be made or provided
Molecule #1: water
water
H2O
HOH
our first “functional group”:
hydroxyl, -OH
105o . O H
Covalent bond
(strength = ~100
kcal/mole, the energy required to break the bond)
water molecule
hydrogen
atom
oxygen

10. δ+ = partial charge, not quantified NOT “ + ” , a full unit charge,
as in the formation of ions by NaCl in solution:
NaCl  Na+ + Cl-
The O-H bond is a polar bond (partial charge separation)
Water is a POLAR molecule (has 2 opposite poles)
Negative pole
Positive pole
So, a “dipole”

11. 180o
hydrogen bond
(3 kcal/mole)

12. Ethanol (CH3—CH2—OH) and water12

13. Amide group R = any group of atoms (the rest of the molecule)
Note: carbon atoms always make 4 bonds
R-CONH2 is an “amide”, CONH2 is an amide group
(another functional group)
Note: Don’t think of the amide as a C=O and an –NH2; the whole thing is one functional group, the amide. It is highly polar but with no full charges

14.  NH2 Some functional groups
glucosamine
acrylamide O
O-H | | | C
glucose |
CH2 |
Some functional groups
The structures and names and properties of the functional groups that we use in class must be memorized.
CH2 |
H2N C
COOH | | | H
glutamic acid

15. Hydrogen bonds between 2 organic molecules
ethanol, an alcohol
an amide
But they face formidable competition from water
And: weak bonds are ephemeral.

16. Octane, a non-polar, or apolar, molecule
CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH3
H—C—C—C—C—C—C—C—C—H | H
Note the absence of d’s X
no interactions with water

17. Chemical bonds
Bond:
Energy needed to break:
Comments:
Strength
Classification:
Covalent
~100
kcal/mole
Electrons
shared
strong
1 calorie = amount of energy needed to raise the temperature of 1 gram of water (1 cc or ml of water) one degree C
1 Calorie = dietary calorie = 1000 calories
1 kilocalorie (kcal) = 1000 calories

18. Chemical bonds Bond: Energy needed to break: Comments:
Strength Classification:
Covalent
~100
kcal/mole
Electrons
shared
strong
Hydrogen ~3
Water-water;
Organic-water;
Organic-organic (having polar functional groups)
weak

19. Ionic Bonds Full loss or capture of an electron H
Full charge separation
Full positive charge, or full negative charge (= charge of one electron)
E.g. NaCl = Na+:::Cl Strong bond between the ions in a crystal (e.g., rock salt, solid)
But: weak in aqueous solution: water surrounds the ions
So the ionic bond of NaCl becomes weak in water
Is the bond between an Na+ ion and water ionic or an H-bond? Some characteristics of each:
a “polar interaction” or an “ion-dipole interaction” H O
Na+

20. Organic ions = acids and bases
ACIDS = carboxylic acids
Lose a proton
O O || ||
R-C-OH  R-C-O H+
(net charge ≈ -1 at pH 7)
Example: acetic acid:
CH3-COOH
BASES = amines
Gain a proton
R-NH2 + H R-NH3+
(net charge ≈ +1 at pH 7)
Example: amphetamine:
Carboxyl group = -COOH
Amine group = -NH2
Where does the base get the proton from? Are there any protons around in water at pH7?

21. Ionic bonds O || R–C–O- - - - - - +H3N–R O | | Weak, ~ 5 kcal/mole.
Under the right conditions (to be seen later), two oppositely charged organic ions can form an ionic bond:
O ||
R–C–O H3N–R
Weak, ~ 5 kcal/mole.
But all these weak bonds are VERY important for biological molecules, as we will see later O | |

22. Functional groups
Again: The names, chemical structures and properties of the functional groups used in this course must be memorized, as well as their characteristics.
See the Functional Groups handout.
Those are the ones to be memorized.
This is one of very few memorizations required.
“carboxyl” Me
You O ||
-- ─C─O _ O | |

23. Chemical bonds Bond: Energy needed to break: Comments:
Strength Classification:
Covalent
~100
kcal/mole
Electrons
shared
strong
Hydrogen ~3
Water-water;
Organic-water;
Organic-organic (having polar functional groups)
weak
Ionic ~5
Full charge transfer;
Can attract H-bond;
Strong in crystal
weak

24. Van der Waals interactions
Can form between ANY two atoms that approach each other
“Fluctuating induced dipole”
Very weak
(~ 1 kcal/m)
Effective ONLY at very close range (1Å) (0.1 nm)
first molecule
chance charge separation
fluctuating dipole
a second molecule
charge separation induced by first molecule

25. Chemical Bonds Bond: Energy needed to break: Comments:
Strength Classification:
Covalent
~100
kcal/mole
Electrons
shared
strong
Hydrogen ~3
Water-water;
Organic-water;
Organic-organic (having polar functional groups)
weak
Ionic ~5
Full charge transfer;
Can attract H-bond;
Strong in crystal
weak
Van der Waals ~1
Fluctuating
induced
dipole;
close range
only
weak
Why are we doing all this now?

26. Octane (C8H18) H H—C—C—C—C—C—C—C—C—H CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH3| H
CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH3
Electro-negativities of C and H are ~ equal
No partial charge separation
Non-polar (apolar), cannot H-bond to water, = “hydrophobic”
Contrast: polar compounds = “hydrophilic”

27. Entropy 8 Octane in water octane
Number of water molecules that are relatively ordered: 8
Octane in water
octane
water
(These numbers are made up.)

28. Entropy 8 + 8 = 16 vs. 10 vs. Water has less entropy vs. more entropy.
Number of water molecules that are relatively ordered:
8 +
8 = vs
octane
vs.
water
Water has less entropy vs more entropy.

29. Entropy drives aggregation of nonpolar molecules
ENTROPY: related to the number of different states possible: more states, more entropy.
Systems tend to change to maximize entropy (max. no. of different states possible to occupy; occupy as many states as possible).
The water molecules around the non-polar molecule have a LOWER entropy (fewer choices, more ordered).
Aggregation of the non-polar molecules with each other minimizes the number of lower entropy water molecules that are on their surface, thus maximizing the entropy of the system.

30. Number of water molecules that are relatively ordered:
8 +
8 = vs
octane
vs.
water
Admittedly, the non-polar octane molecules lose entropy when they coalesce. That is, they are more disordered when they are separate.
However, this loss of entropy apparently* cannot counteract the gain in entropy of the system brought about by the freeing up of water molecule from the “cage” around the non-polar molecules.
* Gasoline and water do not mix.

31. Water cages around an apolar molecule 2 artists’ depictions
water molecules released into bulk solution
H-bonds
nonpolar
substance
highly ordered
water molecules
hydrophobic
aggregation
lower entropy
higher entropy

32. Chemical Bonds Bond: Energy needed to break: Comments:
Strength Classification:
Covalent
~100
kcal/mole
Electrons
shared
strong
Hydrogen ~3
Water-water;
Organic-water;
Organic-organic (having polar functional groups)
weak
Ionic ~5
Full charge transfer;
Can attract H-bond;
Strong in crystal
weak
Van der Waals ~1
Fluctuating
induced
dipole;
close range
only
weak
Hydrophobic forces ~3
Not a bond per se;
entropy driven;
only works in water
weak

33. Large vs. small molecules
≥ ~5000 daltons
Called macromolecules
Examples: proteins, polysaccharides, DNA, polypropylene, polyester
SMALL
≤ ~500 daltons (~ 50 atoms)
Called small molecules
Size differences are rough, there are gray areas
Examples:
water, ethanol, glucose, acetic acid, glutamic acid, amphetamine, glucosamine, acrylamide, acetamide, octane, NaCl

34. Polymers Propylene CH3-CH=CH2
Polypropylene, a polymer, a large molecule

35. Large molecules are built up from small molecules
One possibility:
Poly ?

36. Or from many different small molecules?No

37. Linear polymers in biology
A great simplification:
Large molecules are linear polymers of
small molecules.
O-O-O-O-O-O-O- ………

38. Nomenclature for polymers
monomer
O-O
dimer
O-O-O
trimer
O-O-O-O
tetramer
O-O-O-O-O-O-O
oligomer
a monomer
of the polymer
O-O-O-O-O-O-O-O-O-O-O
oligomer
polymer:

39. 4 categories of macromolecules
polysaccharides,
lipids,
 nucleic acids, and
proteins.
Many (not all) important cellular small molecules are the monomer constituents of these polymers.
There’s only about 50 of these monomers, a small number to learn about.
About another dozen important small molecules are not monomers of polymers. Mostly vitamins, whose role will become apparent later.

40. Monomers and polymers How does E. coli get these monomers Example 1
Macromolecule: polysaccharide
A monomer found in polysaccharides is glucose:
Present in our minimal medium
No problem. )
glucose

41. Getting the monomers Example 2:
Macromolecule: protein
Monomer: amino acids
One example amino acid at right = alanine
Looks nothing like glucose
Where does E. coli get alanine?
CH3 C
H2N
COOH H

42. E. coli makes all the monomers by biochemical transformations starting from glucose
H2N C
COOH H
glucose
glucose →A → B→C →D →E →alanine →protein
A, B, C, D, E, are “intermediates”:
i.e., intermediate chemical structures (molecules) between glucose and alanine.

44. Very rough estimate of the total number of different small molecules in an E. coli cell:
50 monomers
15 non-monomer important small molecules (e.g., like vitamins)
65 total “end products”
Average pathways to monomers and important small molecules starting from glucose: = ~ 10 steps, so ~9 intermediates per pathway
Must be 65 such pathways  65 x 9 = 585 intermediates
65 end-products intermediates = 650 total types of small molecules per E. coli cell
A manageable number, and we ~know them all