Peter's Section 1 Final Study Guide

From Biolk483


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.
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