Welcome to General Biochemistry BCH 3033

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Welcome toGeneral BiochemistryBCH 3033
CHAPTER 1 Review of Basic Cellular Biology and
Chemistry
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Learning Objectives to KNOW

1. Prokaryotic and eukaryotic cell structure and
   functions of each structure.
2. Organic chemical bonds and functional groups.
3. Stereoisomers and cis-trans conformations.
4. Basics of Thermodynamics and Chemical Kinetics.
5. Basics of Catabolism and Anabolism.
6. Biochemical hierarchy from monomers?polymers?cell
   structure.
7. Evolution of cells endosymbiosis vertical and
   horizontal gene transfer.
8. Evolution of proteins orthologs and paralogs.

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Prokaryote and Eukaryote Cells
End of Chapter (EOC) Problem 1 puts these into
3D what size you see in a microscope? whats
its volume and how much actin and mitochondria
could it hold? how many molecules?
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Prokaryotic Cell
EOC Problem 2 calculate the length of DNA in a
bacterial cellhere it is all folded up!
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Bacterial Cytoplasm Is Full of Molecules
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Prokaryotic Cell Envelope
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Eukaryotic Cell
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Muscle Cells
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Eukaryotic Cytoskeleton Actin (red),
Microtubules (green) Surround the Nucleus (blue).
Fluorescence Microscopy.
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Cytoskeleton Elements
Bacteria also have filaments (actin like) and
microtubules to organize their cytoplasm.
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Biological Monomers
What to Look For Whats Important Functional
Groups amino, carboxyl, carbonyls (both),
alcohol, methyl, phosphate, sulfhydryl, and
others. Covalent Bonds single, double,
triple. Ionization state, or not. Solubility Ho
w Monomers are Polymerized Weak Bonds H-bonds,
Ionic bonds, hydrophobic interactions, van
der Waals forces.
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The Monomers
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Structure to Molecular Hierarchy
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Periodic Chart
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Carbon Bonding
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Carbon Bonding
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Bond Angles and Rotation
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Common Functional Groups of Biological Molecules
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Biological molecules typically have several
functional groups
EOC Problems 8 and 12 are all about functional
groups and recognizing them. Great practice and
review of Organic Chem
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Molecular Weight or Mass
Biochemistry uses both Molecular Weight (Mr) or
Molecular Mass (m) in Daltons Carbon has Mr
12 or m 12D Very Small Proteins have a mass
of 10,000D 10kD Very Large ones have mass of
gt1million D 1,000kD (Titin a muscle protein 3
million D)
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Cis and Trans
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Cis and Trans Conformational Change
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Chirality
EOC Problem 11 is about two pharmacological drugs
and fits right in here with chirality and drug
dosage.
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This is Pasteur Looking at Dried Rabbit Spinal
Chord.used as a Rabies Vaccine
Tartaric acid precipitates out of aging wine into
two types of crystals that Pastuer separated with
tweezers and determined the optical rotation of
polarized light.
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Chiral Rotation
Rectus (right) Sinister (left)
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Rotation by Priorities
Priorities of Some Biochemical Functional
Groups -OCH2 gt -OH gt -NH2 gt -COOH gt -CHO gt -CH2OH
gt -CH3 gt -H
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Interactions between biomolecules are specific
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Stereoisomers Have Different Biological Effects
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ATP
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Thermodynamics You Already Know
Endothermic vs Exothermic ?G ?H T ?S ?G
is related to the Equilibrium Constant ?G G
products G reactants Reactants
Substrates ?Go standard free energy change (we
will change this later) for aA bB ? cC dD ?G
?Go RT ln K eq
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AAA
Hexokinase Rxn
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How to speed reactions up
Higher temperatures Stability of macromolecules
is limiting Higher concentration of
reactants Costly as more valuable starting
material is needed Change the reaction by
coupling to a fast one Universally used by
living organisms Lower activation barrier by
catalysis Universally used by living organisms
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Series of related enzymatically catalyzed
reactions forms a pathway

• Metabolic Pathway
• produces energy or valuable materials
• Signal Transduction Pathway
• transmits information

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Pathways are controlled in order to regulate
levels of metabolites
Example of a negative regulation Product of
enzyme 5 inhibits enzyme 1
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Anabolism and Catabolism
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Metabolic Diversity
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Information Codes
Prism of Sennacherib Bacterial DNA 700 BC,
Assyrian
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DNA Replication
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Central DogmaDNA code ?Transcription ?
Translation ? Protein
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A
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Miller and Urey Experimentin a Garage, 1953
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RNA World to DNA/RNA/Protein World
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Current Year
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Endosymbiotic Origin of Mitochondria and
Chloroplasts
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From Darwin to Orthologous and Paralogous Genes
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Paralogous Selection Required Gene Duplication
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End of Chapter Problems
These are really easybecause you have already
mastered the bio- and chemical-logic of problem
solving from your prerequisites. Please do
them and then after that check your answers at
the end of the text Abbreviated Solutions to
Problems (after page 1198) or Appendix B in the
5th Ed. Problems to do and know before the
class 1, 3, 5, 8, 11, 12 Its a valuable
review to make you a great biochemical problem
solver!
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Things to Know and Do Before Class

• To understand what defines living organisms and
  how biochemists isolate cell structures
• To know cell structures and their functions
• To know the organic structure of biomolecules
  functional groups and bonds
• To grasp principles of bioenergetics and chemical
  kinetics
• To know basics of catabolism and anabolism and
  biochemical hierarchy
• To review the forces driving evolution and know
  the difference between orthologous and paralogous
  evolution of proteins.
• To be able to do End of Chapter Problems 1, 3, 5,
  8, 11, 12