1. 2 2 growth: linear n = no10 kt 3 3 growth: semilog a semi-log plot n=n o 10 kt n/no = 10 kt...
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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
44
Growth phases
Real life
(linear on a semi-log plot)
55Use 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)
1010
Ethanol and Water
3
2
3 2
hydroxyl group again
1111
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
1212
an amide
ethanol, an alcohol
Hydrogen bonds between 2 organic moleculesWater often out-competes this interaction (but not always)
1313
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
14Waterdeltas
Water is a POLAR molecule, a dipole
Positivepole
Negativepole
15waterHbonds
Hydrogen bond
1616Ethanol and Water
3
2
3 2
17R= any group of atoms(the rest of the molecule)
amide3
R-CONH2 is an “amide”, -CONH2 is an amide group (another functional group)Note: Don’t break down the amide into a C=O and an –NH2; the whole thing is one functional group, the amide. It is highly polar but with no full charges
Note: carbon atoms always make 4 bonds
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an amide
ethanol, an alcohol
They face formidable competition from water
Hydrogen bonds between 2 organic molecules
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CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH3
X
Not all molecules are polar; e.g. octane, a non-polar, or apolar
H H H H H H H H
| | | | | | | |
H-C-C-C-C-C-C-C-C-H Note the absence of δ’s
| | | | | | | |
H H H H H H H H
20Chemical Bonds
Bond:
Energy needed
to break:
Comments:
Strength class-
ification:
Covalent
~100kcal/mole
Electrons shared
strong
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• 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
22Chemical Bonds
Bond:
Energy needed
to break:
Comments:
Strength class-
ification:
Covalent
~100kcal/mole
Electrons shared
strong
Hydrogen
~3
Water-water;Organic-water;Organic-organic(having polar functional groups)
weak
23Ionic bonds
• Full loss or capture of an electron
• 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)
• But: weak in aqueous solution
• 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”
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BASES = amines
Gain a proton
R-NH2 + H+ R-NH3+
(net charge ≈ +1 at pH 7)
Example: ethyl amine:CH3-CH2-NH2
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
Where does the base get the proton? Are there any protons around in water at pH7?
Carboxyl group = -COOH Amine group = -NH2
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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 these weak bonds are VERY important for biological molecules …….
26Chemical Bonds
Bond:
Energy needed
to break:
Comments:
Strength class-
ification:
Covalent
~100kcal/mole
Electrons shared
strong
Hydrogen
~3
Water-water;Organic-water;Organic-organic
weak;orientation dependent
Ionic
~5
Full charge transfer;Can attract H-bond;Strong in crystal
weak
27Van der Waals bonds• Can form
between ANY two atoms that approach each other
• “Fluctuating induced dipole”
• Very weak (~ 1 kcal/m)
• Effective ONLY at very close range (1A)(0.1 nm)
First molecule
“ “
28Chemical Bonds
Bond:
Energy needed
to break:
Comments:
StrengthClass-
ification:
Covalent
~100kcal/mole
Electrons shared
strong
Hydrogen
~3
Water-water;Organic-water;Organic-organic
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?
29Chemical Bonds
Bond:
Energy needed
to break:
Comments:
Strength class-
ification:
Covalent
~100kcal/mole
Electrons shared
strong
Hydrogen
~3
Water-water;Organic-water;Organic-organic
weak
Ionic
~5
Full charge transfer;Can attract H-bond;Strong in crystal
weak
Van der Waals
~1
Fluctuating induced dipole;Very close range only
weak
Hydro-phobic forces~3
Not a bond per se;entropy driven;only works in water
weak
30Consider octane, C8H18, or:
CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH3
Electro-negativities of C and H are ~ equal
No partial charge separation
Non-polar, cannot H-bond to water, = “hydrophobic”
Contrast: polar compounds = “hydrophilic”
C CCCCC CCH H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
HI
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I – – – – – – – – –
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Octane in water
(These numbers are made up.)
32(These numbers are made up.)
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• ENTROPY: related to the number of different states possible
• The water molecules around the non-polar molecule have a LOWER entropy (less choices, more ordered).
• Systems tend to change to maximize entropy (different states possible to occupy).
• Aggregation of the non-polar molecules with each other minimizes the number of water molecules that are on their surface, thus maximizing the entropy of the system
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• 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.
35 Hydrophobic “bonds” (forces)
• Affects NON-polar molecules that find themselves in an aqueous environment (i.e., must be in water)
• They cannot H-bond with water molecules
• The water molecules around the non-polar molecule are not able to constantly switch partners for H-bonding
• The water molecules around the non-polar molecule are in a MORE ordered state.
• Hydrophobic “forces”, not really “bonds” per se
36Water cages around methane: CH4
3 artists’ depictions
37End of bonds, and water, our molecule #1
Now for the next 4999 types of molecules found in an E. coli cell:First let’s categorize: Small vs. large molecules
LARGE• >= ~5000 daltons
• Called macromolecules
• Examples:proteins, polysaccharides, DNA
SMALL• <= ~500 daltons (~ 50 atoms)
• Called small molecules
• Size differences are rough, there are gray areas
• Examples:water, ethanol, glucose,acetamide, methane, octane
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Propylene CH3-CH=CH2
Polypropylene, a polymer, a large molecule
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Poly ?
Large molecules are built up from small molecules
One possibility:
40Or from many different small molecules?
No
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A great simplification:
Large molecules are linear polymers of
small molecules.
O-O-O-O-O-O-O-………
42Nomenclature for polymers
monomer
dimer
trimer
tetramer
oligomer
oligomer
polymer
O
O-O
O-O-O
O-O-O-O
O-O-O-O-O-O-O
O-O-O-O-O-O-O-O-O-O-O
a monomer of the polymer
43The large molecules, or macromolecules, of all cells can be grouped into 4 categories:
• polysaccharides, • lipids, • nucleic acids, and• proteins.
• Many of the important small molecules of the cell are the monomers of these polymers.
• There are only about 50 of these monomers, a very manageable number to learn about.
• There are about another dozen small molecules in an E. coli cell that are important but are not monomers of polymers (Most of these are related to vitamins).
44Monomers and polymers
Macromolecule: polysaccharide
A monomer of many polysaccharides is glucose:
Present in our minimal medium
)
.
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Polymer: protein
Monomer: amino acids
Example at right = alanine
Looks nothing like glucose
Where does E. coli get alanine?
Getting the monomers
For example:
CH3
C COOHH2N
H
46E. coli makes all the monomers by biochemical
transformations starting from 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.
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g l u c o s e
monomers
MacromoleculesPolysaccharides LipidsNucleic AcidsProteins
biosy
nthet
ic p
athw
ay
intermediates
F l o w o f g l u c o s e i n E . c o l i
E ac h a rro w = a sp e c ific c h em ica l re ac tio n
48Very rough estimate of the total number of different small molecules in an E. coli cell:
50 monomers15 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
65 such pathways 65 x 9 = 585 intermediates
65 end-products + 585 intermediates = 650 total types of small molecules per E. coli cell
A manageable number, and we ~ know them all
49Macromolecule class #1:
Polysaccharides
• Monomer = sugars
• Sugars = small carbohydrate molecules
• Carbohydrates ~= CnH2nOn
• Contain one C=O group and many –OH’s
• Can contain other functional groups as well (carboxyls, amines)
• Most common sugar and monomer is glucose
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Glucose, straight chain depictions
With numbering
C C
Remember, always 4 bonds to carbon; Often even if not depicted
Abbreviated
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anomeric carbon
Handout 2-7Haworth view
Fisher view
Chair view
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1 234567891011
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1 23456789
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Physical model ball and stick model of glucose ring closure/opening
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beta-glucose alpha-glucose
56Ball and stick models of glucose
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Glucose
}Gray = CWhite = HRed = O
Ring oxygen
C6 (-CH2OH)
C5
C1
hydr
oxyl
58Alpha glucoseAll the hydroxyls and the –CH2OH are sticking out equatorialExcept for the hydroxyl on the anomeric carbon 1
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From Handout 2-7
2
5
3
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From Handout 2-7
4
1
5
3
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Flat ring (Haworth projection) just gives the relative positions of the H and OH at each carbon, one is “above” the other. But it does not tell the positions of the groups relative to the plane of the ring (up, down or out)
Relationship between Haworth (flat ring) depiction and chair-form
Handout 2-8
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Glucose
}Gray = CWhite = HRed = O
Ring oxygen
C6 (-CH2OH)
C5
C1
hydr
oxyl
Alpha or beta?You try it later.