Peter's Section 1 Final Study Guide

From Biolk483

Contents 1 Some numbers 2 Cell biology 3 Amino acids 3.1 Amino acid classification 4 Enzymes, etc.

Some numbers

• 16 chemical linkages
• 100,000 molecules in a human
• 6,000 molecules in an e. coli
• 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 4x10^6 AMUs.
• Composition of the cell:
  • 70-90% water
  • 22% macromolecules
  • 3% sugars
  • 2% lipids

Cell biology

• 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 Angstroms 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.

Amino acids

• 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 casein are two A.A. 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.

Amino acid classification

• The non-polar amino acids:
  • The aliphatic amino acids are: ala, leu, val, ile, and pro.
  • The aromatic amino acids are : phe, trp
    • Phe and His are good at blocking for porphyrins; they keep 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 as 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.
  • Histidine can be phosphorylated as in the 3phosphoglycerate -- phosphoglucomutase --> 2 phospho glycerate reaction.
  • From the Kreb cycle, the succinal coA -> succinate reaction occurs via a histidine with a phosphoramidate arm via the enzyme succinyl thiokinase.
• The negatively charged amino acids: glutamic acid and aspartic acid.
  • Asp can be used as a neurotransmitter.

Enzymes, etc.

• Use iodoacetate to keep di-sulfide 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.