Editing Peter's Section 1 Final Study Guide

<h3>Some numbers</h3>
*16 chemical linkages
*100,000 molecules in a human
*6,000 molecules in an <i>e. coli</i>
*Environmental precursors are generally less than 200 AMUs and include things like CO, CO2, H2S, N2, NH2, Na+, K+, Cl-, etc.
*Water has 1000g / 18AMU = 55.5 Molarity
*Energy sources converting precursors to organic materials include: light, heat, radioactivity, magnetism, sonic booms and ultraviolet light.
*1953 was a big year in biochem: Stanley Miller's primordial soup experiment, Watson and Crick define structure of DNA, Sanger sequences insulin.
*Pyruvate and citric acid are smaller than 300 AMUs
*Alanine is 5 Angstroms.
*Viruses are about 1000 Angstroms
*Mitochondria are about 20,000 Angstroms (two microns).
*Ribosomes are about 300 Angstroms and 4x10e6 AMUs.
*Composition of the cell:
**70-90% water
**22% macromolecules
**3% sugars
**2% lipids

<h3>Cell biology</h3>
*Nuclear zone is found in prokaryotes and is an area highly concentrated with genetic material.
*Mesosome is an invagination; a precursor to the cristae of the mitochondria.
*The nucleolus is found in eukaryotes and is an area enriched with RNA.
*Caveolai send signal into cell.
*Coated pits take things into the cell.
*Tight junction holds two cells together; a gap junction holds the cells together and allows passage of material between the two cells.
*Peroxisomes do oxidations to get rid of toxic things.  They put oxygens on to make the toxin sticky and digestible.
*The plasma membrane is ~100 Angstrums thick.
*Lipid rafts are cholesterol enriched.
*Smooth Endoplasmic Reticulum does drug metabolism; lipid synthesis.
*The mitochondria makes only 9 proteins.
*Lysosome has only one lipid bilayer membrane.

<h3>Amino acids</h3>
*We have d-aminoxidase to get rid of d amino acids.
*The L > D is explained by the catastrophe theory.
*Smallest proteins are about 5,000 AMU (generally between 50,000 and 100,000 AMU).
*Enzymes can speed reaction by a factor of 10^20.
*There are approximately 2000 different reactions in the human body.
*Ovalbumin and caselin are two storage proteins.
*Albumin, hemoglobin, calmodulin are all proteins that do intra-body transportation.
*Collagen is the most abundant protein in the human.
*We have alpha and beta amino acids but beta are relatively unimportant.
*Full +1 charge given if the pH is < the pKa of a Nitrogen atom's Hydrogen.
*Full -1 charge given if the pH is > the pKA of an Oxygen atom's Hydrogen.
*Proline shows up yellow with anhydrin.
*Non-polar amino acids are found on inside of protein and neutral/polar, anionic and cationic amino acids are found on outside.

<h4>Amino acid classification</h4>
*The non-polar amino acids:
**The aliphatic amino acids are: ala, leu, val, ile, and pro.
**The aromatic amino acids are : phe, trp
***Phe is good at blocking for porpherins; it keeps the metal from being oxidized.
**The sulphuric amino acids are: met
*The uncharged / polar amino acids:
**The alcoholic amino acids are: ser, thr, tyr
***These can be phosphorylated.  Serine is seen is glycogen phosphorylase and pyruvate dehydrogenase.
***Serine is also seen as a phospholipid.
***Tyrosine can protect flat molecules.
***Asparagine attaches sugars to proteins.
**The nitrogen amino acids are : asp, gln
**The sulphuric amino acids are: cys
**The odd-ball amino acid is   : gly
***Glycine can be a neurotransmitter.
*The positively charged amino acids: lys, arg, his.
**Lysine can form a schiff base as seen in aldolase.  This will show up purple when coupled with rhodopsin.
**Lysine can form amid linkages as in pyruvate carboxylate (with biotin, yielding oxaloacetate).
**Free argenine is used in the urea cycle.
**Histine can be used to protec porpherins.
**Histine can be phosphorylated as in the 3phosphoglycerate -- phosphoglucomutase --> 2 phospho glycerate reaction.
**From the kreb cycle, the succinal coA -> succinate reaction occurs via an histidine with a phosphoramidate arm arm succinyl thiokinase.
*The negatively charged amino acids: glutamic acid and aspartic acid.
**Asp can be used as a neurotransmitter.

<h3>Enzymes, etc.</h3>
*Use iodoacetate to keep dicisteine bonds apart.
*The alpha helix is formed by hydrogen bonding; it takes ~21 amino acids to cross the membrane.  Usually met and ala make up the alpha helix.
*Beta sheets made up of val, ile, tyr.
*We can determine the proportion of secondary structure components in a protein via ORD-CD.
*The native protein structure is the best thermodynamic structure.
*Cytochrome C is small (103-112 aa) and has 27 invariant aa.
*Ribosomes have 2 parts RNA and one part protein.
*Ribonuclease:
**cleaves RNA (cuts a phosphodiester bond)
**Small, easily isolated, easy to follow rate and product.
**Two Iodoacetates bind to ribonuclease.  They bind to two histidines.  So we know the active sites are His 12 and 119.
*Chymotripsin:'
**Cleaves to right of c-terminal on Trp, Tyr, and Phe
**Important aa: His57, Ser195, Asp102.