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Zumdahl’s Chapter 23
Biochemistry
Chapter Contents
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CHON
Proteins
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Amino acids
Peptides
Structure
Enzymes
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Carbohydrates
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Lipids
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Nucleic Acids
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Sugars
Starches
Cellulose
Micelles
Cellular membranes
Steroids
C H O N and beyond
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The elements of Life
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C, the hybridizer
H, placeholder and
water builder
O, the oxidizer and
hydrogen bonder
N, protein builder
Ca, the skeletizer
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Fe, the O2 carrier
Na,K depolarizers
P, the energy carrier
Cl, the neutralizer
S, the linker
Mg, Zn, Cu, Ni, Mo
enzyme coordinators
Proteins for kinetic control
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“Active sites” accelerate or decelerate the
biochemical reactions, holding equilibrium
at bay.
3-D shape structures active site and guides
target molecules thereto.
All accomplished with chains, hydrogen
bonding, and coordinate covalency.
glycine
valine
Chain Links
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 amino acids
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(NH2)CH(CO2H)R
 numerous since R can be anything.
Nature uses only 20 R’s for Earthly Life.
Simplest, R=H, glycine
 Other non-polar R include sec-propyl, valine
 Polar R include -CH2SH, cysteine
 Only cyclic sec-amine R, proline
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cysteine
proline
Peptide bonds
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Condensation reaction between amino acid
links to create the chain.
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Splits out water.
Bonds amino acids.
Leaves an amino acid to continue the chain!
–(NH)CHR(CO)(NH)CHR’(CO)– etc.
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(CO)—(NH) is the peptide bond.
Different R closely spaced to rule geometry.
Protein Structure
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Primary
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Secondary
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Folding of the chain by hydrogen bonding
between the backbone carbonyl and amide’s H.
Tertiary
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Simply the chain sequence of amino acids.
Overall shape of a single chain.
Quaternary
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Aggregation of more than one chain.
Secondary Structures
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 helix
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collagen
E.g., insulin
Pleated sheet
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Silk
(click for sheets)
View down the
insulin helix.
Tertiary Structure
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Elongated ribonuclease-A
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Globular myoglobin
Quaternary Structure
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The same hydrogen-bonding and sulfur
linkages that hold secondary and tertiary
structures together can bind multiple
strands into a single protein.
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Of course heat and a change of solvent can undo
these weak bonds to “denature” proteins.
The 4 strands of hemoglobin (carbon
monoxylated) are shown on the next slide.
CO
Heme
Non-enzyme Proteins
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While a critical function of proteins is to
form biological catalysts called enzymes,
other proteins are structural.
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Collagen’s fibers weave us skin.
Keratin’s longer pitch (screw repeat as the
monomers intertwine) form horn (triceratops)
and beak and talon.
acetylcholine
Enzymes
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Polypeptides (proteins) need not be
enzymes (take hen egg albumin, for
example), but when they are, they can be
not only very effective but very specific.
Acetylcholinesterase is a polypeptide
designed to hydrolyze acetylcholine, a
neurotransmitter (opens the Na+ gates).
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“Hydrolysis” reverses “condensation.”
Acetylcholinesterase
All this …
to hydrolyze this.
Click for ribbons
World’s Most Important Enzyme
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Without carbon, Life
would be a whole lot
different.
And inorganic carbon
is not the useful form!
Enter RUBISCO, the
Mg-based enzyme in
greatest abundance on
Earth to fix carbon.
Carbohydrates, (CH2O)n
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While proteins provide enzymatic activity
and extracellular structural materials,
carbohydrates provide cell energy sources.
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Sugars are the body’s fastest fuel.
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The brain runs exclusively on glucose which is
small enough to cross the blood–brain barrier.
Starches, high polysaccharides, not only
retain food value but are tissue materials.
Sucrose
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C12H22O11
Table sugar is not the simplest.
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fructose
It is the disaccharide condensation of the
simpler C6H12O6 isomers, fructose and
glucose, monosaccharides.
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Fructose is the “sweetness” of sugar
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Glucose is brain food
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and a ketone sugar or ketose.
and a aldehyde sugar or aldose.
Both are 6-carbon hexoses.
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Another critical class is pentose.
glucose
Reversible Cyclization
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Both ketoses & aldoses of at least 3
carbons can cyclize, closing on an OH’s
oxygen with its H going to the carbonyl.
–D–glucose
Glucose Polymers
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Sucrose is a disaccharide of glucose and
fructose, but the monomers don’t have to
be different to polymerize.
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–D–glucose polymerizes to amylose, the
major polysaccharide of starch.
–D–glucose polymerizes
to cellulose, a fiber.
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This is cellubiose…
Polymers as a Strategy
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Man builds large, expensive plants to
polymerize alkenes to plastics because the
latter have tweakable properties.
Nature does the same with  amino acids,
saccharides, and nucleotides.
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The evolutionary advantage is that a single
process (condensation, say) requires a simple
mechanism to produce great complexity.
Nucleic Acids
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Just as the side chains (proline notwithstanding) are
key to protein secondary structure, bases of
the nucleic acids are key to Life’s code.
But order is everything, and it’s obtained (in
nucleic acids) by esters of a pentose phosphate.
d–ribose
–d–ribose
Encoding Life
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The pentose is the same for every nucleic
acid, so we need a side group called a base.
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Containing amide groups, they are literally
basic, but it is their hydrogen bonding
capacity that is important instead.
adenosine
-D-ribofuranose
condense
adenine
+ H2O
Nucleic Acid Chain
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Phosphate linkages bind the backbone.
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Being polyprotic, H3PO4 can bind by
condensation to more than one nucleotide.
This is adenosine 5-phosphoric acid.
It has other sugar hydroxyls to
condense with another H3PO4.
Which can bind to yet another
nucleotide (not necessarily adenosine)
and so on …
Bases
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There are 5 bases in an earthly Life nucleic
acid chain:
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Adenine, Cytosine, Guanine, and Thymine or
Uracil. ( T appears in DNA but U in RNA. )
U
G
C
A
T
C
Base Pairs
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G
DNA and RNA are double helixes with the
two backbones held in place by hydrogen
bonds between the bases.
Geometry dictates that bases pair with their
respective mates: T
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C with G
A with ( T or U )
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The former in DNA and the latter in RNA.
A
As the Chains Turn …
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Since they don’t mate
with anything else,
even when the helix
strands are separated,
the bases can find one
another and reform.
The coding (3 bases at a
time = “1 codon”) is
preserved.
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Below is a fragment
of RNA helix. Note
the orientation of the
base planes.
DNA
only a snippet …
“deoxy-” refers to the unused –OH
on the sugars becoming –H instead.
Lipids
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Solubility in aqueous solution:
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Ions? Phenomenol! Due to hydration shell.
Sugars? Excellent! They hydrogen bond.
Acids? Not bad, if they’re small to present a
large fraction of the molecule as carboxylic.
Hydrocarbons? Forget it. They London
bond, and water refuses to give up its fine
hydrogen bonding to accommodate them.
Lipids are Schizoid
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Solubility of mixed mode molecules:
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octadecylphosphonate
Long chain organic acids, anions, or salts
have both hydrophilic and hydrophobic ends.
Who wins?
Everyone … if their tails can dissolve in one
another leaving only their hydrophilic heads
to interact with water!
Micelles and lipid bilayers know this trick.
Micelles
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This is how your laundry gets clean.
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Soap molecules are schizoid in the same way.
The hydrophobic tails hide in a sphere.
The hydrophilic heads face the water and
permit the least disruption of its organization.
Grease dissolve in the sphere and are flushed.
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It’s called emulsification.
The next slide shows such a formation.
Micelle Forming
GrayClick
is thetohydrocarbon
see a cutaway
“bubble”
Lipid Bilayer
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But instead of organizing as a sphere, a
lipid could minimize its disruption of water
by making a sandwich; hydrophilic bread
surrounding hydrophobic innards.
This is a lipid bilayer.
It could also close around an aqueous
interior space and look very, very
cell-surface-like.
Bilayer Model
H2O solution molecules
hydrophobic (hydrocarbon) nonpolar tails
hydrophilic polar head groups
Steroids
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Olympic Bane is anabolic steroid.
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These molecules, like testosterone, cause the
retention of nitrogen and thus encourage
muscle growth.
But this is only one class of steroid, all of
which stem from cholesterol and bear its
characteristic 6-6-6-5 fused rings.
Cholesterol
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 a good thing.
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But too much of a good thing fills the arteries with
lipids that kill.
That terminal –OH group makes it an alcohol.
Greek: kholē stereos “bile solid;” it is a
precursor to bile acids that emulsify fats.
It is essential in cell–membrane production.
And the precursor of hormones:
C18H24O2
Ladies First
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Estradiol
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Though the ’s don’t show, that leftmost ring
is a phenyl (benzene’s family) and so planar.
Estradiol eschews cholesterol’s fatty tail (it
was ever thus) for the greater functionality of
a second –OH, hence –diol.
Estrus means “coming into heat,” which is
one of this molecule’s proud duties in nonhuman females where estrus is cyclic.
Warped to the Core
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Testosterone
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(salacious etymology)
C19H28O2
The carbonyl makes it a ketone.
And the leftmost ring isn’t phenyl but a
warped cyclohexene.
Like estradiol, it is released at puberty to
control secondary sex characteristics and
behavioral expression.
But it converts to estradiol in the male brain!