Biochemistry
Using Organic chemistry for Life
Clicker
Why are organic molecules important to biology?
A.
B.
C.
D.
Living objects are constructed mostly of organic
molecules.
Organic molecules are so varied that they are
capable of many different functions.
Only God knows for sure and she’s not saying.
Look, I’m here, isn’t that good enough?
Organic molecules are Life
If you think of all the different things an organism needs to do:
A.
Create energy
B.
Repair itself.
C.
Grow
D.
Transport materials
E.
Hold its structure
F.
Fend off invaders
G.
Protect from hostile nature (heat, light, storms, electricity…)
H.
Reproduce
I.
Store blueprints
J.
Store memories
K.
Acquire sensory data
L.
Process sensory data
Lots of functions require lots of molecules
Lipids
Lipids are water-insoluble components of cells
including fats, fatty acids, oils, phospholipids,
glycolipids, and steroids.
Your body is mostly water (aids transport, temperature
control), so if every molecule in your body were
water soluble, you’d melt into a salty puddle!!!
Lipids, among other uses, make up cell membranes –
to keep you from collapsing into a puddle!
Fatty Acids
Guess what kind of acid?
Carboxylic acid!!!
A fatty acid is a long alkane/alkene chain with a
carboxylic acid on the end!
O
CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2CH2 CH2 CH2 C OH
Myristic acid (common name)
Tetradecoic acid (IUPAC name)
Butterfat or coconut oil
Oleic acid (common name)
cis-octadec-9-enoic acid)
In olive oil, peanut oil
CH3 CH2 CH2 CH2 CH2 CH2 CH
O
CHCH2 CH2CH2 CH2 CH2 CH2 CH2 CH2 CH2 C OH
What does the “cis” mean?
It means the two H are on the same side!
CH3 CH2 CH2 CH2CH2 CH2
CH2 CH2CH2 CH2 CH2 CH2 CH2 CH2 CH2 C OH
C
H
O
C
H
Fatty Acids
Stearic Acid – C18H36O2 a saturated fatty acid
O
CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 C OH
Oleic Acid – C18H36O2 a monounsaturated fatty acid
O
CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH
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CH CH2 CH2 CH2 CH2 CH2 CH2 CH2 C OH
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Fatty Acids
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Structure and Melting Point


MP
Larger fatty acid = Higher
Class
Name
°C
melting point
Myristic Acid 58 Sat., 14 C
Double bonds decrease
Palmitic Acid 63 Sat, 16 C
the melting point




More DB = lower MP
Stearic Acid
71 Sat, 18 C
16 1 DB, 18 C
Oleic Acid
Saturated = no DB
Monounsaturated = 1 DB Linoleic Acid -5 2 DB, 18 C
Polyunsaturated = many Linolenic Acid -11 3 DB, 18 C
DB
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It’s all about the solubility
The alkane/alkene portion of the molecule is water
insoluble. Why?
It’s non-polar. Water is polar. Remember, “like
dissolves like”.
The carboxylic acid portion is water soluble. Why?
The carboxylic acid (C=0 and –OH) is polar, and so is
water.
If I throw oleic acid in water…
What happens?
It forms little micelles (beads) with the
hydrophobic tails all mixed together and the
hydrophilic acid portion facing the water.
This is why “oil and water don’t mix”…
Lipid Bilayer
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Fats and oils
“Triglycerides”
You’ve heard the term, what does it mean? A triglyceride is actually
a combination of glycerol (a triol) and 3 fatty acids. It’s actually a
tri-ester!
glycerol
OH
O
Myristic acid
OH
CH2 CH CH2
+
3 CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2CH2 CH2 CH2 C OH
O
O
OH
CH3 (CH2)11 C O
O C(CH2)11CH3
CH2 CH CH2
CH3 (CH2)11 C O
O
Trimystirin
Fats and oils
This a “saturated” fat – the hydrocarbon chain
is an alkane, no double bonds.
O
O
CH3 (CH2)11 C O
O C(CH2)11CH3
CH2 CH CH2
CH3 (CH2)11 C O
O
Trimystirin
Fats and oils
An “unsaturated” fat would have double bonds.
If we did the same reaction with oleic acid.
Oleic acid
glycerol
OH
CH2 CH CH2
+
3 CH3 (CH2)4 CH
O
OH
CH3 (CH2)4 CH
CH(CH2)7 C
CH(CH2)7 C OH
O
OH
O
O
O C (CH2)7 CH
CH2 CH CH2
CH3 (CH2)4 CH
CH(CH2)7 C O
Triolein
CH (CH2)4 CH3
Tristearin
a simple triglyceride found in lard
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Triglycerides
Saturated triglycerides tend to be
room temperature.
A.
B.
C.
D.
at
Solid
Liquid
Gas
All of the above, it depends on the type.
Triglycerides
Saturated triglycerides tend to be solids at
room temperature because of:
A.
B.
C.
D.
E.
Van der Waal’s forces
Hydrogen bonding
Dipole-dipole interactions
A and B
B and C
Triglycerides
Unsaturated triglycerides tend to be
room temperature.
A.
B.
C.
D.
Solid
Liquid
Gas
All of the above, it depends on the type.
at
Triglycerides
Unsaturated triglycerides (oils) tend to be
liquids at room temperature because of:
A.
B.
C.
D.
E.
Van der Waal’s forces
Hydrogen bonding
Dipole-dipole interactions
A and B
B and C
Triglycerides
They are big molecules. They tend to form
solids due to a combination of Van der
Waal’s forces and dipole forces. BUT,
unsaturated molecules can be sterically
hindered so that the polar parts can’t get near
the other polar parts. That leaves us with just
Van der Waal’s forces and it reduces the
melting point relative to saturated molecules.
Triolein
a simple triglyceride found in olive oil
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Other Lipids
Phospholipids – take a triglyceride and replace one of
the fatty acids with a phosphate group.
Glycolipids – Use glucose instead of glycerol.
These are ideal for cell walls: they are strong and have
a polar end and non-polar end. The polar end faces
the inside (aqueous) part of the cell and the nonpolar ends are internal.
Phospholipids




Esters of glycerol
Glycerol attached to 2 fatty acids and 1 phosphate
group
Phospholipids have a hydrophilic head due to
phosphate group, and a hydrophobic tail from the
fatty acid hydrocarbon chain
part of lipid bilayer found in animal cell
membranes
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Phosphatidyl Choline
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Glycolipids



similar structure and properties to the
phospholipids
the nonpolar part composed of a fatty acid
chain and a hydrocarbon chain
the polar part is a sugar molecule

e.g., glucose
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Glucosylcerebroside
(found in plasma membranes of
nonneural cells)
HO
CH2OH
HC
HC OH
C
HO H
O
O
H
CH C
H
C
CH N
C
CH2
O
CH
CH
OH
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Steroids
Steroids are lipids with a four-ring central
OH
structure.
CH3
CH3
O
Testosterone
Steroids
CH3 OH
CH3
CH3
CH3
CH3
O
CH3
testosterone
CH3
HO
CH3 OH
cholesterol
HO
estrogen
b-estradiol
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Carbohydrates
Structurally much simpler than lipids.
Carbohydrates are polyhydroxy aldehydes or
ketones.
H
HC
H H OH H
O
C C
C C CH
OH OH OH H OH
Glucose (C6H12O6) – a monosaccharide
Carbohydrates
You can actually string together
monosaccharides to make more complicated
carbohydrates.
But even monosaccharides have variety!
H
HC
H H OH H
O
C C
C C CH
OH OH OH H OH
Carbons 2, 3, 4, and 5 are all “chiral” – 4 different atoms are attached
Carbohydrates
But even monosaccharides have variety!
Mannose is an optical isomer of glucose – differing
only in the relative 3D orientation of the -OH
H
HC
H H OH H
O
C C
C C CH
OH OH OH H OH
Glucose
H
HC
H H OH OH
O
C C
C C CH
OH OH OH H H
Mannose
Intramolecular rearrangement
H
HC
H H OH H
O
C C
C C CH
OH OH OH H OH
Glucose can actually react with itself by addition to the carbonyl to
form a 6 membered ring (5 or 6 membered rings are more stable
and, therefore more likely)
OH
H
OH
C
H
C
C
C
OH
C
H
H
O
OH
H
CH2
OH
Intramolecular rearrangement
H
HC
H H OH H
O
C C
C C CH
OH OH OH H OH
OH
H
OH
C
H
C
C
C
OH
C
H
H
O
OH
H
CH2
OH
Equivalent representations of glucose. Similar pairs of structures
exist for all sugar.
Glucose is an example of one type of sugar, called an “aldose”
because of the aldehyde group in the linear structure.
Fructose (C6H12O6)
Fructose is a ketose. It’s structure is similar to aldoses
(like glucose) but it is a ketone in the linear
representation rather than an aldehyde.
Notice: Fructose is a structural isomer of glucose!
H
HC
H H OH O
C C
C C CH2
OH OH OH H
OH
Dehydration returns!
Monosaccharides can be linked together via
dehydration reactions to form “glycosidic
linkages”.
A glycosidic linkage is really just an ether
linkage created by dehydration of 2 alcohols!
Dehydration returns!
While it might seem that we can create the linkage
using multiple different alcohol (-OH) sites to form
the bond, there is one –OH that is more reactive
than all the others!
OH
H
OH
C
H
C
C
C
OH
C
H
H
O
OH
H
CH2
OH
Because of the presence of the O next to it, this C-OH bond is more reactive!
Dehydration returns!
The dehydration reaction that creates the
“glycosidic linkage” occurs preferentially at
this site!
OH
C
H
OH
H
OH
CH2
H
OH
C
C
C
C
O
OH
H
H
H
OH
OH
C
H
C
C
C
OH
C
H
H
O
OH
H
CH2
OH
Dehydration returns!
OH
C
H
OH
H
OH
H
C
C
C
C
CH2
OH
C
O
OH
H H
HH
O
C
H
C
C
C
OH
C
H
H
OH
H
CH2
O
OH
OH
H
C
C
OH
H
H
H
C
H
OH
OH
O
OH
OH
H
OH
C
CH2
OH
H
C
C
H
C
C
OH
H
+ H2O
C
O
CH2
OH
Size matters..
If 2 sugar molecules can form a glycosidic
linkage, then the most reactive site is used.
BUT, there’s no reason why you can’t use the
less preferred sites.
Carbohydrates are “polysaccharides” formed by
multiple glycosidic linkages between sugar
molecules.
Clicker Question
A.
B.
I’m here
I’m not here
Amino Acids
Amino Acids are building blocks of proteins.
Amino Acids are exactly what the name
suggests: amines AND carboxylic acids
O
H2N CH2 C OH
Glycine
α - Amino Acids
Glycine is the simplest of the α - amino acids.
The α refers to the carbon immediately next
to the carbonyl group. To be an α - amino
acid, the amine must be bonded to this
carbon.
O
H2N CH2 C OH
Glycine
α
Different substituents,
different α - amino acid
If the α – carbon has different substituents
(besides the 2 H’s of glycine) it is a different
amino acid.
O
H2N CH2 C OH
O
O
H2N CH C OH
CH2
OH
H2N CH C OH
CH2
C=0
OH
Glycine
Serine
Aspartic acid
Let’s think together…
Amines are…
bases
Carboxylic acids are…
acids
What happens when you mix an acid and a
base together?
They neutralize each other!
How would that neutralization
occur?
The –COOH is an acid, the –NH2 is a base. Any –
COOH can donate a proton to any –NH2. Some
amino acids are stronger acids/bases than others
based on the side group, but they are all
acids/bases.
O
H2N CH2 C OH
Amphoteric form of Glycine
O
+
H3N CH2 C OH
Acid form of Glycine
O
H2N CH2 C O Base form of Glycine
O
+
H3 N CH2 C O Zwitterion form of Glycine
Which one is it?
If you had a beaker full of glycine in distilled
water at 25 C and 1 atm of pressure, which
one would be the dominant form?
O
H2N CH2 C OH
Amphoteric form of Glycine
O
+
H3N CH2 C OH
Acid form of Glycine
O
H2N CH2 C OBase form of Glycine
O
H2N CH2 C OH
Zwitterion form of Glycine
Which one is it?
Could you ever have any of the other forms?
Sure! Change the pH!
O
H2N CH2 C OH
Amphoteric form of Glycine
O
+
H3N CH2 C OH
Acid form of Glycine
O
H2N CH2 C OBase form of Glycine
O
H2N CH2 C OH
Zwitterion form of Glycine
What happens if I mix serine
and glycine?
Let’s make H2O!
O
H2 N CH C OH
CH2
O
OH
H2N CH2 C OH
Serine
Glycine
Dehydration…not always a bad
thing! [Called “condensation”]
O
O
H2 N CH C OH
+
H2N CH2 C OH
Glycine
CH2
OH
Serine
O
O
O
O
H2N CH2 C OH
H2 N CH C OH HNH CH2 C OH
CH2
OH
HNH CH C OH
OR
CH2
OH
Dehydration…not always a bad
thing! [Called “condensation”]
O
O
O
O
H2 N CH C OH HNH CH2 C OH
CH2
HNH CH C OH
H2N CH2 C OH
CH2
OR
OH
O
H2 N CH C
OH
O
O
NH CH2 C OH
O
H2N CH2 C NH CH C OH
Peptides
CH2
OH
CH2
+ H2O
+ H2O
OH
Protein structure
One way to look at protein “information” is in the
sequence of the amino acids.
Consider the alphabet, with 26 letters.
If you had 26 amino acids, how many 3 letter words
could you write?
17,576 (26x26x26)
456,976 Four letter words
11,881,376 Five letter words
141 trillion 10 letter words
Structure and Function
Unlike words, proteins are 3-D objects. The
function of a given protein is determined by
its “sequence”=which amino acid follows
which amino acid called the “primary
structure”, but it is also determined by the
secondary, tertiary, and even quarternary
structure.
Secondary structure
Once the amino acids are in a sequence, it is
possible for them to form “superstructures” by
hydrogen bonding with each other across
chains.
Secondary structure is a multi-amino acid
structure.
Secondary structure
An alpha helix (α-helix) is a right-handed
(clockwise) spiral in which each peptide is in
the trans conformation. The amine group of
each peptide bond runs upward and parallel
to the axis fo the helix; the carbonyl points
downward.
A β-pleated sheet consists of neighboring
chains that are anti-parallel to each other.
Each peptide bond is trans and planar. The
amine and carbonyl point toward each other.
Tertiary structure
Once the amino acid sequences are arranged
into secondary “superstructures”, these
secondary structures can be arranged
differently relative to each other. A kind of
“super-superstructure”.
This tertiary structure is usually constructed
largely by disulfide bonds between cysteine
amino acid groups.
Quarternary structures
Some proteins are made up of multiple
polypeptide subunits (different chains of
amino acids). Each subunit has its own
primary, secondary, and tertiary structure.
The subunits are arranged relative to each
other in “quarternary super-supersuperstructures”