"He said science was going to discover the basic secret of life someday," the bartender put in. He scratched his head and frowned. "Didn't I read in the paper the other day where they'd found out what it was?"
"I missed that," I murmured.
"I saw that," said Sandra. "About two days ago."
"That's right," said the bartender.
"What is the secret of life?" I asked.
"I forget," said Sandra.
"Protein," the bartender declared. "They found out something about protein."
"Yeah," said Sandra, "that's it."

-Kurt Vonnegut, Jr. Cat's Cradle

Assignment
Audesirk, Audesirk & Byers Chapter 3

Today's musical selection
Bush The chemicals between us

ORGANIC CHEMISTRY
is the chemistry of carbon (C) which makes 4 bonds.
In "Star Trek" (the first movie), people were called "carbon based units" by the alien.

Hydrocarbon

(Hydro-carbon - prefix suggests hydrogen, suffix suggests carbon).
They are hydrophobic and nonpolar.
CH4 methane, - natural gas
Fossil fuel, but also in primordial atmosphere, oddly
Gasoline has typically 8 carbons (octane) and is fluid. Long chains are thick, like oil and vasoline.
nonpolar, hydrophobic

Carbohydrate

Figure 3-4
(Carbo-hydrate is also sort of a compound word, carbon, but note that "hydrate" suggests water, not hydrogen) - the general formula is Cn(H2O)n
Monosaccharides
Hexose (hex = 6 [carbons], "-ose" always means sugar)- glucose, the most famous monosaccaccharide, is good to illustrate that monosaccharides usually assume a ring structure

Figire 3-6
Pentose - ribose, deoxyribose (that are in RNA and DNA) are famous

Figure 3-7
Compound dehydration synthesis, hydrolysis (hydro-water, lysis-breakdown)
In digestion, macromolecules are broken down to monomers.
Disaccharide - sucrose, lactose (milk)

Lactose
in milk, so all babies can digest it
Europeans evolved with dairy husbandry and so can enjoy milk as adults
Many Asians and Africans cannot
later we will see that the lac operon controls enzymes for lactose utilization in bacteria

Figure 3-8
Polysaccharides starch (plant), glycogen (glyco-sugar, gen-give birth to) (animal)
alpha 1-4 linkage
Carbohydrates are used for energy.

Figure 3-9
Carbohydrates are used for structure: cellulose (beta-1,4 glucoses), the most plentiful biological molecule on Earth,
Carbohydrates are used for bulk since people cannot digest fiber, but termites & cattle can. This introduces the topic of symbiosis (living together) and mutualism (where it is to the benefit of both organisms since, for termites, zooflagellates, which are protozoa, break down cellulose and for cattle, bacteria do the job.

Other functions
Carbohydrates are used for structure in some proteins
Carbohydrates contribute to exoskeleton in arthropods, a polymer called chitin that has some nitrogen and is also in cell walls of fungi

Lipids

(fats) store more energy (2x sugar) 1 tablespoon of sugar is 50, fat 100 "Calories" = kilocaloriies

Figure 3-11
Glycerol & 3 fatty acids (16-24 C long) - triglyceride ester bonds
note the dehydration synthesis
The -COOH defines an organic acid such as a fatty acid, otherwise the molecule is a hydrocarbon.
C-C (single bond) vs. C=C (double bond) unsaturated (vs saturated with H's), with several, it is referred to as "polyunsaturated" PUFA = polyunsaturated fatty acid
Animal fats tend to be saturated, bad for arteries leads to atherosclerosis; vs vegetable fats better.

Figure 3-15
Polar phospholipids - contribute to membranes because polar group is hydrophilic and fatty acid (acyl) tail is hydrophobic
polar-glycerol-FA1-FA2 (more double bonds, fluidity)
Here are some famous fatty acids: stearic C18, Oleic-18:1
There are also glycolipids with sugar attached to lipid in membranes.

Figure 3-16
Steroids-cholesterol - fit into membranes and serve as precursors for hormones,
especially "sex hormones" like testosterone, progesterone, estrogen
Howard Cossel "anabolic steroids" (metabolic: catabolic vs anabolic) - androgens, the hormones like testosterone that favor nitrogen retention (muscle growth)
Salts of cholesterol are in bile (from liver) that acts like a detergent to emulsify fats to aid in digestion.
Interestingly, cholesterol is required in animals and is an "essential" nutrient in insects that cannot synthesize it; too much bad in people, and that can be controlled by diet though people also biosynthesize cholesterol.

Other functions
Waxes: fatty acid + long chain alcohol (instead of glycerol) prevent water loss also used for structure in nbee hive.
Blubber, especially in warm blooded cetaceans, serves as insulation.
In summary, lipids are used for energy, structure, hormones, insulation, water loss, digestion

Proteins

Proteins and nucleic acids make up 2/3 of dry weight of the body
short = "Peptides", medium = polypeptide, long = "protein" (hundreds, thousands)
Proteins are very important because chains of amino acids can be very complex

Figure 3-18
Amino acid
The general formula is NH2-CR-COOH - amino ( -NH2 ) and acid ( -COOH ).

Figure 3-20
Peptide bonds involves -NH2 and -COOH getting linked with a dehydration synthesis.

There are about 20 amino acids (alphabet of 20 letters)
R group varies
If you made a peptide 4 amino acids long, there would be 20 x 20 x 20 x 20 = 160,000 different possibilities, hence the complexity.
About half of the amino acids are "essential" meaning that they cannot be made by metabolic conversion from other molecules and thus need to be eaten - corn is notoriously low in tryptophan and methionine).

Structure:
primary (the sequence)
secondary (alpha helix, beta pleated sheet)
tertiary structure (disulfide and other bonds)
quaternary structure (chains interact with each other)
(here is a really important example - hemoglobin - which has 2 alpha subunits and 2 beta subunits.)

Beyond 4 levels
There are so many levels of protein structure above these 4, glycosylation (adding a sugar), phosphorylation, chopping fragments out of the protein, and other post-translational modifications, that you will have to wait until a more advanced course to really focus on them.

Protein diversity makes for individuality, and at the level of the immune system, proteins (antigens) determine self vs non-self.

Proteins can serve for:
Structure (example keratin which is in hair)
Enzymes - Their names end in the suffix -ase), that are catalysts (molecules that influece the rate of a reaction).
Antibodies (used against antigens)
Storage
Transport (example hemoglobin)
Motility and contraction
Hormones and neurotransmitters (often smaller fragments of a larger precursor, a prohormone)
Receptors (for hormones and neurotransmitter)
Energy - though the use of protein for energy is not efficient and NH3, released in catabolism of amino acids, is toxic and must be eliminated, sometimes as urea, sometimes as uric acid.
Venoms, toxins

Questions used in 2007 and 2008 relating to this outline

If it were in a polyunsaturated fatty acid, how many bonds does a carbon have?
(a) 1
(b) 2
(c) 3
*(d) 4
(e) 5

Explain "corn is not a good source of essential amino acids."
(a) It does not have all 15 amino acids.
(b) The proteins of corn have been hydrolyzed.
*(c) It does not have all the amino acids required in the human diet.
(d) These are the amino acids used for energy in catabolism.
(e) Corn is missing pyruvate, a very important amino acid.

The dehydration synthesis combines [A] to [B] in fat molecules
(a) [A] carbohydrate; [B] water
(b) [A] one amino acid; [B] another
(c) [A] one amino acid; [B] ammonia
(d) [A] glycogen; [B] glucose
*(e) [A] glycerol; [B] fatty acids

The lipids in membranes have two fatty acids. In place of the third, there is a
(a) glycerol.
(b) steroid.
*(c) polar group.
(d) hydrocarbon.
(e) saturated amino acid.

Lipids store twice as much energy as carbohydrates. How is that energy measured?
*(a) in "calories"
(b) by the length of the chain
(c) by tonicity (hypertonic, isotonic, hypotonic)
(d) by the first law of thermodynamics
(e) by oxidation - reduction

What is considered bulk or fiber for humans but can be used for energy by termites and cattle?
*(a) cellulose
(b) those amino acids that are not essential
(c) disaccharides
(d) long chain fatty acids
(e) It depends on whether the humans in question are lactose intolerant.

What kind of molecule is octane?
(a) a monosaccharide
*(b) a hydrocarbon
(c) glycogen
(d) a steroid
(e) a polypeptide

What kind of molecule is ribose?
*(a) a pentose
(b) an enzyme
(c) chitin
(d) a polysaccharide
(e) an anabolic steroid

Which of the following is NOT an organic molecule?
A) a polypeptide
B) nucleic acid
C) cellulose
*D H2O
E) a monounsaturated fatty acid

Macromolecules are synthesized by removing (what?) from the building blocks?
A) carbon.
B) covalent bonds.
*C) water.
D) oxygen.
E) peptides.

Which of the following correctly matches an organic polymer with its respective monomers?
*A) protein and amino acids
B) carbohydrates and polysaccharides
C) hydrocarbon and monosaccharides
D) polar phospholipid and steroids
E) glycerol and glycogen

The fiber in your diet is really
A) a polypeptide.
B) a polyunsaturated fatty acid.
C) starch.
D) keratin, a structural protein.
*E) a polysaccharide.

In a biological membrane, the phospholipids are arranged with the fatty acid chains facing the interior of the membrane. As a result, the interior of the membrane is
*A) hydrophobic.
B) hydrophilic.
C) charged.
D) polar.
E) filled with water.

When hemoglobin is shown as two alpha chains linked to two beta chains, this represents which level of protein organization?
A) glycosylation
B) posttranslational modifications
C) primary structure
*D) quaternary structure
E) phosphorylation

What type of chemical reaction results in the breakdown of organic polymers into their respective subunits?
A) dehydration
B) oxidation
C) reduction
D) ionization
*E) hydrolysis

Where is glycogen stored in vertebrate animals?
A) brain and kidneys
*B) liver and muscles
C) heart and bones
D) pancreas and blood
E) adipose tissue

The group of biological molecules most diverse in structure is
A) disaccharides.
B) lipids.
*C) proteins.
D) polyunsaturated fatty acids
E) steroids


Questions used in 2002 relating to this outline (and other outlines)

One reason that membrane lipids are arranged the way they are is because of
(a) essential amino acids.
(b) ionic bonds.
*(c) hydrophobic fatty acids.
(d) hydrolysis of bonds.
(e) the half life.

Which would have the greatest potential for variability?
(a) a nucleotide 3 base pairs long
*(b) a peptide 3 amino acids long
(c) a hydrocarbon 3 carbons long
(d) a glycogen chain 3 glucose molecules long
(e) ATP

Those amino acids your metabolism cannot synthesize from other amino acids are called
(a) polyunsaturated.
(b) isotopes.
(c) vital.
(d) exerogonic.
*(e) essential.

Certain chemical modifications of a protein are called "post-translational."
(a) Post-translational modifications include "high" levels of structural organization such as alpha helix vs. beta pleated sheet.
(b) "Post-translational" would be the term applied to the association of two alpha subunits and two beta subunits in hemoglobin.
(c) "Post-translational" refers to the sequence of amino acids coded in that protein's "gene" (DNA coding sequence).
(d) For a protein to become an antigen (a non-self protein), it must be modified post-translationally.
*(e) "Post-translational" is after the manufacture of protein from a template of mRNA.

Steroids are
(a) hydrophilic.
(b) hydrocarbons.
(c) carbohydrates.
(d) triglycerides.
*(e) lipids.

In terms of biological reactions, what is the opposite of dehydration synthesis?
(a) transcription
(b) anabolic metabolism
(c) entropy
(d) photosynthesis
*(e) hydrolysis

Which does NOT have nitrogen in it?
(a) deoxyribonucleic acid
(b) chitin
*(c) starch
(d) protein
(e) urea

Kilocalories, those "calories" you count when you are dieting, are a measurement of
(a) water content of food and drink you consume.
(b) amino acid content of food.
*(c) energy available in food.
(d) relative fat content of food.
(e) relative carbohydrate content of food.

People with type I diabetes mellitus need to inject insulin
(a) because they have a mutation that puts valine in the 6th amino acid position of the beta chain of hemoglobin.
*(b) that is a protein hormone.
(c) because it is an enzyme used in digestion.
(d) to replace the missing gonadal steroids.
(e) to activate the sodium-potassium pump.

Enzymes are indicated by the suffix
(a) -ose.
*(b) -ase.
(c) -eic.
(d) -some.
(e) -karyote.

What type of molecule is cellulose?
(a) triglyceride
(b) nucleic acid
(c) polypeptide
(d) polyunsaturated fatty acid
*(e) carbohydrate

Vegetable oils would be higher (than animal fats) in
*(a) fatty acids with double bonds.
(b) triglycerides in which each acyl group is saturated with as many -H's as possible.
(c) all essential amino acids.
(d) uric acid.
(e) mutations.

Triglycerides with some double bonds are called
(a) enzymatic.
(b) ionic.
*(c) polyunsaturated.
(d) hydrolytic.
(e) radioactive.

Which does not have sugar in it?
(a) starch
(b) glycoproteins and glycolipids
(c) glycogen
*(d) testosterone
(e) sucrose

Which is not true about hemoglobin?
(a) It contains iron.
(b) It is in red blood cells.
(c) It is altered in sickle cell anemia.
*(d) It is an enzyme that makes DNA from a template of mRNA.
(e) It is a protein used for the transport of oxygen.

Reactions by which amino acids are used for energy, yielding nitrogenous wastes, might be referred to as:
*(a) catabolic.
(b) anabolic.
(c) prokaryotic.
(d) eukaryotic.
(e) autotrophic.

Which is NOT a carbohydrate?
(a) lactose
*(b) cholesterol
(c) glycogen
(d) Cn(H2O)n
(e) chitin

Enzymes function for
(a) motility.
(b) energy storage.
*(c) catalysis.
(d) attacking antigens.
(e) storage of hereditary information.

The liver bile salts that are secreted into the intestines are most closely related to
(a) cellulose.
(b) membrane glycolipids.
(c) ATP.
*(d) cholesterol.
(e) antibodies.

About how many different amino acids are used by living things?
(a) 10
*(b) 20
(c) 40
(d) 64
(e) 100

Arrangement of membrane lipids depends largely on
*(a) polar and hydrophobic portions of the molecules.
(b) ions.
(c) collagen.
(d) hydrolysis.
(e) radioactivity.

The term "unsaturated," as in "polyunsaturated" refers to
(a) whether all of the essential amino acids are there.
(b) whether an electron is missing.
(c) whether the third nucleotide in the codon is required to specify the amino acid.
(d) whether an element has an extra neutron.
*(e) whether there are double bonds.

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