Transcript Document

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E. coli molecule #1
water
H2O
HOH
Our first “functional group”:
hydroxyl, -OH
H O
105o
H
Covalent bond
(strength = ~100
kcal/mole)
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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
waterHbonds
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Hydrogen bond
Ethanol and Water
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2
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5
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
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ethanol, an alcohol
an amide
Hydrogen bonds between 2 organic molecules
Water often out-competes this interaction (but not always)
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Hydrogen bonds between 2 organic molecules
ethanol, an alcohol
an amide
They face formidable competition from water
Not all molecules are polar; e.g. octane, a non-polar, or apolar molecule
CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH3
H H H H H H H H
| | | | | | | |
H-C-C-C-C-C-C-C-C-H
| | | | | | | |
H H H H H H H H
Note the absence of δ’s
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X
Chemical Bonds
Bond: Covalent
Energy
needed ~100
to break: kcal/mole
Comments: Electrons
shared
Strength
class- strong
ification:
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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
Chemical Bonds
Bond: Covalent
Hydrogen
Energy
~3
needed ~100
to break: kcal/mole
Comments: Electrons
shared
Strength
class- strong
ification:
Water-water;
Organic-water;
Organic-organic
(having polar
functional
groups)
weak
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Ionic 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+:::ClStrong 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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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
Carboxyl group = -COOH
BASES = amines
Gain a proton
R-NH2 + H+
R-NH3+
(net charge ≈ +1 at pH 7)
Example: ethyl amine:
CH3-CH2-NH2
Amine group = -NH2
Where does the base get the proton? Are there any protons around in water at pH7?
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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
…….
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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.
O
||
-C -- OH
“carboxyl”
Me
You
Chemical Bonds
Bond: Covalent
Hydrogen
Energy
~3
needed ~100
to break: kcal/mole
Comments: Electrons
shared
Strength
class- strong
ification:
Ionic
~5
Water-water;
Organic-water;
Organicorganic
Full charge
transfer;
Can attract
H-bond;
Strong in
crystal
weak;
orientation
dependent
weak
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Van der Waals bonds
• Can form
between
ANY two
atoms that
approach
each other
First molecule
• “Fluctuating
induced
dipole”
• Very weak
(~ 1 kcal/m)
• Effective
ONLY at
very close
range (1A)
(0.1 nm)
“
“
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Chemical Bonds
Bond: Covalent
Hydrogen
Ionic
Van der
Waals
~5
~1
Water-water;
Organic-water;
Organicorganic
Full charge
transfer;
Can attract
H-bond;
Strong in
crystal
Fluctuating
induced
dipole;
Close range
only
weak
weak
weak
Energy
~3
needed ~100
to break: kcal/mole
Comments: Electrons
shared
Strength
Class- strong
ification:
Why are we doing all this now?
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Chemical Bonds
Bond: Covalent
Hydrogen
Ionic
Van der
Waals
~5
~1
Water-water;
Organic-water;
Organicorganic
Full charge
transfer;
Can attract
H-bond;
Strong in
crystal
Fluctuating
induced
dipole;
Very close
range only
Not a bond
per se;
entropy
driven;
only works
in water
weak
weak
weak
weak
Energy
~3
needed ~100
to break: kcal/mole
Comments: Electrons
shared
Strength
class- strong
ification:
Hydrophobic
forces
~3
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Consider octane, C8H18, or:
H H H H H H H H
I I I I I I I I
H– C – C– C– C– C– C – C– C– H
I I I I I I I I
H H H H H H H 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”
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Octane in water
(These numbers are made up.)
(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
(no. ofdifferent states possible to occupy).
• 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
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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.
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
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Water cages around methane: CH4
3 artists’ depictions
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End of bonds, and water, our molecule #1
Now on to the next 4999 types of molecules found in an E.
coli cell:
First let’s categorize: Small vs. large molecules
LARGE
• >= ~5000 daltons
SMALL
• <= ~500 daltons (~ 50 atoms)
• Called macromolecules
• Called small molecules
• Examples:
proteins, polysaccharides,
DNA
• 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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Large molecules are built up from small molecules
One possibility:
Poly ?
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Or 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-………
Nomenclature for polymers
O
monomer
O-O
dimer
O-O-O
trimer
O-O-O-O
tetramer
O-O-O-O-O-O-O
oligomer
O-O-O-O-O-O-O-O-O-O-O
oligomer
polymer
a monomer of the polymer
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The large molecules, or macromolecules, of all
cells can be grouped into 4 categories:
•
•
•
•
polysaccharides,
lipids,
nucleic acids, and
proteins.
• Many important small molecules are the monomers of these polymers.
• 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.
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Monomers and polymers
Example 1.
Macromolecule:
polysaccharide
A monomer of many
polysaccharides is
glucose:
Present in our minimal
medium
.
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Getting the monomers
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Example 2:
Macromolecule: protein
CH3
Monomer: amino acids
Example at right = alanine
Looks nothing like glucose
Where does E. coli get alanine?
H2N
C
H
COOH
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E. 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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Flow of glucose in E. coli
Macromolecules
Polysaccharides
Lipids
Nucleic Acids
Proteins
yn
th
e
tic
pa
t
hw
ay
monomers
bi
os
intermediates
glucose
Each arrow = a specific chemical reaction
Very rough estimate of the total number of different
small molecules in an E. coli cell:
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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
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
Macromolecule 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
Abbreviated
C
With
numbering
C
Remember,
always 4 bonds to carbon;
Often even if not depicted
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anomeric
carbon
Fisher
view
Chair view
Haworth view
Handout 2-7
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10
7
6
5
89
3
1 24
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7
6
5
89
3
1 24
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beta-glucose
alpha-glucose
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anomeric
carbon
Fisher
view
Chair view
Haworth view
Handout 2-7
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5
3
4
1
Relationship between Haworth (flat ring) depiction and chair-form
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Flat ring (Haworth projection)  relative positions of
the H and OH at each carbon, one “above” the other.
But it does not tell the positions of the groups relative
to the ring plane (up, down or out). (No room “in.”)
Handout 2-8
Ball and stick models of glucose
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Alpha or beta?
You try it later.
Glucose
Gray = C
White = H
Red = O
}
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