Zumdahl’s Chapter 23. Biochemistry. C H O N Proteins Amino acids Peptides Structure Enzymes Nucleic Acids. Carbohydrates Sugars Starches Cellulose Lipids Micelles Cellular membranes Steroids. Chapter Contents. The elements of Life C , the hybridizer
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Zumdahl’s Chapter 23 Biochemistry
C H O N Proteins Amino acids Peptides Structure Enzymes Nucleic Acids Carbohydrates Sugars Starches Cellulose Lipids Micelles Cellular membranes Steroids Chapter Contents
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 C H O N and beyond
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 glycine valine • 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 cysteine proline
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.
collagen View down the insulin helix. Secondary Structures • helix • E.g., insulin • Pleated sheet • Silk (click for sheets)
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.
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 acetylcholine • 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.”
to hydrolyze this. Acetylcholinesterase All this … Click for ribbons
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. World’s Most Important Enzyme
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 C12H22O11 • 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. glucose fructose
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
condense 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. adenosine -D-ribofuranose + H2O adenine
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 to condense with another H3PO4. Which can bind to yet another nucleotide (not necessarily adenosine) and so on …
U G C A T 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. )
C G T A 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.
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. As the Chains Turn …
DNA “deoxy-” refers to the unused–OH on the sugars becoming –H instead. only a snippet …
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 octadecylphosphonate • Solubility of mixed mode molecules: • Long chain organic acids, anions, or salts have both hydrophilicand 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 • 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 Gray is the hydrocarbon “bubble” Click to see a cutaway
It could also close around an aqueous interior space and look very, very cell-surface-like. 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.
Bilayer Model H2O solution molecules hydrophobic (hydrocarbon) nonpolar tails hydrophilicpolar head groups
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 C18H24O2 • 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.
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