Zumdahl’s Chapter 23

Biochemistry

Chapter Contents C H O N Proteins

Amino acids Peptides Structure Enzymes

Nucleic Acids

Carbohydrates Sugars Starches Cellulose

Lipids Micelles Cellular membranes

Steroids

C H O N and beyond The elements of Life

C, the hybridizer H, placeholder and

water builder O, the oxidizer and

hydrogen bonder N, protein builder Ca, the skeletizer

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 “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.

Chain Links amino acids

(NH2)CH(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

glycine valine

cysteineproline

Peptide bonds Condensation reaction between amino acid

links to create the chain. Splits out water. Bonds amino acids. Leaves an amino acid to continue the chain!

–(NH)CHR(CO)(NH)CHR’(CO)– etc. (CO)—(NH) is the peptide bond. Different R closely spaced to rule geometry.

Protein Structure Primary

Simply the chain sequence of amino acids.

Secondary Folding of the chain by hydrogen bonding

between the backbone carbonyl and amide’s H.

Tertiary Overall shape of a single chain.

Quaternary Aggregation of more than one chain.

Secondary Structures helix

E.g., insulin Pleated sheet

Silk (click for sheets)

View down theinsulin helix.

collagen

Tertiary Structure Elongated ribonuclease-A

Globular myoglobin

Quaternary Structure The same hydrogen-bonding and sulfur

linkages that hold secondary and tertiary structures together can bind multiple strands into a single protein.

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 While a critical function of proteins is to

form biological catalysts called enzymes, other proteins are structural. Collagen’s fibers weave us skin. Keratin’s longer pitch (screw repeat as the

monomers intertwine) form horn (triceratops) and beak and talon.

Enzymes 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).

“Hydrolysis” reverses “condensation.”

acetylcholine

AcetylcholinesteraseAll this …

to hydrolyze this.

Click for ribbons

World’s Most Important Enzyme 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

While proteins provide enzymatic activity and extracellular structural materials, carbohydrates provide cell energy sources. Sugars are the body’s fastest fuel.

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 Table sugar is not the simplest.

It is the disaccharide condensation of the simpler C6H12O6 isomers, fructose and glucose, monosaccharides. Fructose is the “sweetness” of sugar

and a ketone sugar or ketose. Glucose is brain food

and a aldehyde sugar or aldose.

Both are 6-carbon hexoses. Another critical class is pentose.

C12H22O11

fructose glucose

Reversible Cyclization 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 Sucrose is a disaccharide of glucose and

fructose, but the monomers don’t have to be different to polymerize. –D–glucose polymerizes to amylose, the

major polysaccharide of starch. –D–glucose polymerizes to cellulose, a fiber.

This is cellubiose…

Polymers as a Strategy 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. The evolutionary advantage is that a single

process (condensation, say) requires a simple mechanism to produce great complexity.

Nucleic Acids 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 The pentose is the same for every nucleic

acid, so we need a side group called a base. Containing amide groups, they are literally

basic, but it is their hydrogen bonding capacity that is important instead.

-D-ribofuranose

adenine

adenosine

condense+ H2O

Nucleic Acid Chain Phosphate linkages bind the backbone.

Being polyprotic, H3PO4 can bind by condensation to more than one nucleotide.

This is adenosine 5-phosphoric acid.

It has other sugar hydroxyls tocondense with another H3PO4.

Which can bind to yet anothernucleotide (not necessarily adenosine)and so on …

Bases There are 5 bases in an earthly Life nucleic

acid chain: Adenine, Cytosine, Guanine, and Thymine or

Uracil. ( T appears in DNA but U in RNA. )

A

CG

T

U

Base Pairs 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: C with G A with ( T or U )

The former in DNA and the latter in RNA.

C

G

T

A

As the Chains Turn … 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.

Below is a fragment of RNA helix. Note the orientation of the base planes.

DNA

only a snippet …

“deoxy-” refers to the unused –OHon the sugars becoming –H instead.

Lipids Solubility in aqueous solution:

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 Solubility of mixed mode molecules:

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.

octadecylphosphonate

Micelles This is how your laundry gets clean.

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.

It’s called emulsification.

The next slide shows such a formation.

Micelle Forming Click to see a cutawayGray is the hydrocarbon “bubble”

Lipid Bilayer 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

hydrophilic polar head groups

hydrophobic (hydrocarbon) nonpolar tails

Steroids Olympic Bane is anabolic steroid.

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 a good thing.

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:

Ladies First Estradiol

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 non-human females where estrus is cyclic.

C18H24O2

Warped to the Core Testosterone (salacious etymology)

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!

C19H28O2