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PSU Molecular Biology Lectures

Lecture 1: Class Introduction and Review

Recorded: January 9, 2017
Viewed: August 20, 2020

Lecture 2: More Review

Recorded: January 11, 2017
Viewed: August 21, 2020

Review of these topics

  • Central Dogma: DNA replicates plus DNA –> mRNA –> tRNA –> protein
  • Genomes
  • Gene Families: paralogs are parallel within a single organism. Orthologs are homologous across taxons. All of the above are homologs. See also Alberts p. 20
  • Model Organisms (23:25). See table below:
Domain Species Common name # of base pairs (M) # of genes
Bacteria E. coli n/a 4.6 4,289
Archaea Sulfolobus solfataricus n/a 3 2,977
Eukarya S. cerevisiae baker’s yeast 12 ~6,300
Eukarya C. elegans nematode 130 ~21,000
Eukarya Arabidopsis thaliana mustard plant ~220 ~26,000
Eukarya Drosophila melanogaster fruit fly ~200 ~15,000
Eukarya Danio rerio zebrafish ~1,500 ~22,600
Eukarya Xenopus clawed frog ~3,100 ~20,000
Eukarya Mus musculus mouse ~2,700 ~22,600
Eukarya Felis silvestris catus domestic cat ~2,500 ~20,000
Eukarya Homo sapiens sapiens human ~3,200 ~20,000

Review of general chemistry

  • Noncovalent bonds: ionic bonds, van der Waals, hydrophobic interactions, hydrogen bonds
  • Acid-base chemistry
  • Chemical composition of life. 70% of water, 30% other. Of that 30%,
  • Review of hydrolysis (energetically favorable - ΔG) vs. condensation/dehydration synthesis which is energetically unfavorable and requires usage of ATP.
  • Catabolic vs. anabolic pathways
    • Catalysis aka catabolic pathways breakdown food into useful monomers of macromolecules as well as creating ATP.
    • Anabolic pathways use up ATP to synthesize large macromolecules through polymerization. Entropy decreases.
  • Dissasociation constant Kd important for binding of substrates and pharmacology drug-target interactions.

Lecture 3: Review of Proteins

Recorded: January 13, 2017
Viewed: August 22, 2020

  • Outline: amino acids, peptide bonds, secondary structure, protein folding, domains/motifs, mulltimers, protein families, modeling, allostery
  • Residue = particular side-chain for an amino acid
  • There are only 5 amino acids that are polar with a net electrical charge on their molecule: Lysine, Arginine, Histidine, Aspartate, and Glutamate.
  • Histidine is particularly interesting b/c unlike all the other amino acids, it is either neutral or positively charged (aka basic pH) depending on the surrounding environment. This is because histidine’s pKa = ~6.5. See this page for further info.
  • Main amino acids to be concerned about for this course (19:00):
    • Basic amino acids: Lysine (Lys, K) and Arginine (Arg, R). Both of these are polar and charged, with a net positive charge.
    • Acidic amino acids: Aspartic Acid (Aspartate, Asp, D) and Glutamic Acid (Glutamate, Glu, E). They are both polar and charged, with a net negative charge.
  • Protein structure. “Leucine zipper” creates a coiled coil. Note also that leucines are nonpolar sidechains (aka hydrophobic); so these leucines “hide” inthe interior of the coiled coil, away from the hydrophilic water environment. (36:31)
  • Domain is a separately folded subsection of a protein.
  • Structure prediction (43:00). Interesting principle that has been empirically determined. Let’s say we have two different DNA sequences (a and b) that code for two different proteins (A and B). Assume we know the protein structure of A but not of protein B. If the DNA sequence of a and b are at least 30% the same (measured by bp or nucleotides), then there is a 99% chance that the resultant A and B proteins have the same structure!
    • Example of Elastase compared to Chymotrypsin. See Figures 3-12 and 3-13 on Alberts 5e p. 138.
    • Often because of common ancestry. Typically caused more by divergent evolution orthologs from common ancestry rather than convergent evolution.
  • See also images of proteins in Alberts 5e, Fig. 3-23 and 3-24 on p. 144-145.
  • Multimers = multiple molecules interacting with each other. (50:00). See this passage from oligomer wikipedia page: “The term multimer is used in biochemistry for oligomers of proteins that are not covalently bound. The major capsid protein VP1 that comprises the shell of the polio virus is a self-assembling multimer of 72 pentamers held together by local electric charges.”

Lecture 4:

  • Recorded: January 15, 2017
  • Viewed: October 21, 2020
  • Initial discussion of GTPase, GAP, etc.

Molecular Biology Bi334 Winter 2019

  • Lecture 1: Introduction
  • Rest of 2019 lectures are missing?