Biochemistry

1
Biochemistry

• Foundations of Biochemistry
• Molecular Logic Cells
• Biomolecules Water

2
Molecular Logic of Life

• Living organisms extract, transform, and use
  energy from their environment (nutrients or
  sunlight)
• Work chemical, mechanical and osmotic
• Self-Replication and Self-Assembly

3
Biomolecules

• Same kinds of monomeric subunits
• Structure function
• Genus/Species defined by unique set of
  macromolecules

4
Energy Production and Consumption

• Living organisms not in equilibrium with their
  surroundings
• Constant flux of mass and energy (synthesis and
  degradation)
• Dynamic Steady State

5
Work

• Chemical synthesis of cellular components
• Osmotic accumulation and retention of salts and
  various organic compounds
• Mechanical contraction of muscle or motion of
  bacterium
• In any physical or chemical change, total energy
  in the universe remains constant, although form
  may change.

6
Bioenergetics

• Biological energy transducers do not rely on T
  and P differences must operate at same T and P.
• Heat flow not useful source of energy.

7
Energy Needs

• Provided directly or indirectly by solar energy
• Flow of electrons in redox reactions underlies
  energy transductions in cells
• Interdependent exchanging energy and matter via
  the environment.

8
Coupling of Reactions

• Free Energy (?G) amount of energy actually
  available to do work.
• Energy change as system moves from initial state
  to equilibrium, with no changes in T or P (rate
  of product formation rate of reactant
  formation).

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Reactions (Contd)

• Exothermic ?G of products less than ?G of
  reactants ? releases free energy to do work.
• Endothermic ?G of products greater than ?G of
  reactants ? input of energy.
• Glucose Pi ? G6P (endothermic, ?G)
• ATP ? ADP Pi (exothermic, -?G)
• Glucose ATP ?G6P ADP (exothermic)

10
Reactions (Contd)

• Endothermic cellular reactions are driven by
  coupling them to exothermic reactions or
  photochemical processes through shared
  intermediates.

11
Enzymes

• Enhance rate of reaction ? lower energy of
  activation.
• Enhance through binding effects
• a. proximityb. orientation
• Enhanced by a factor of 1010 - 1014

12
Enzymes (Contd)

• A ? B ? C ? D ? E ? F
• Catabolism degradation
• Anabolism synthesis
• ATP is universal carrier of metabolic energy,
• Linking catabolic and anabolic pathways

13
Biomolecules

• Review of chemistry of carbon
• Review of Functional Groups
• Review of Isomers
• a. geometric
• b. constitutional
• c. stereo
• 1. stereospecificity

14
Chemical Reactivity

• Bond Strength ?H (enthalpy)
• Five Classes of Chemical Transformations
• a. redox dehydrogenations (dehydrogenases),
  oxidations (oxidases, oxygenases)
• b. C-C bond cleavage and formation SN1, SN2
• c. Electron Transfers intramolecular
  rearrangements (isomerizations)
• d. Group Transfer Reactions activation of
  substrate
• e. Biopolymerizations (proteins, nucleic acids,
  and polysaccharides

15
Chapter 5 Amino Acids, Peptides, and Proteins