Welcome to
General Biochemistry
BCH 3033
CHAPTER 1
Review of Basic Cellular Biology and Chemistry
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.
Prokaryote and Eukaryote Cells
End of Chapter (EOC) Problem 1 puts these into 3D: what size
you see in a microscope? what’s its volume and how much
actin and mitochondria could it hold? how many molecules?
Prokaryotic Cell
EOC Problem 2: calculate
the length of DNA in a
bacterial cell…here it is all
folded up!
Bacterial Cytoplasm Is Full of Molecules
Prokaryotic Cell Envelope
Eukaryotic Cell
Muscle Cells
Eukaryotic Cytoskeleton: Actin (red), Microtubules (green)
Surround the Nucleus (blue). Fluorescence Microscopy.
Cytoskeleton Elements
Bacteria also have filaments (actin like) and
microtubules to organize their cytoplasm.
Biological Monomers
What to Look For = What’s Important:
Functional Groups: amino, carboxyl, carbonyls
(both), alcohol, methyl, phosphate,
sulfhydryl, and others.
Covalent Bonds – single, double, triple.
Ionization state, or not.
Solubility
How Monomers are Polymerized
Weak Bonds = H-bonds, Ionic bonds,
hydrophobic interactions, van der Waals
forces.
The Monomers
Structure to Molecular Hierarchy
Periodic Chart
Carbon Bonding
Carbon Bonding
Bond Angles and Rotation
Common Functional Groups of Biological Molecules
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
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 >1million D = 1,000kD
(Titin a muscle protein ~3 million D)
Cis and Trans
Cis and Trans – Conformational Change
Chirality
EOC Problem 11 is about two pharmacological drugs and
fits right in here with chirality and drug dosage.
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.
Chiral Rotation
Rectus (right)
Sinister (left)
Rotation by Priorities
Priorities of Some Biochemical Functional Groups
-OCH2 > -OH > -NH2 > -COOH > -CHO > -CH2OH > -CH3 > -H
Interactions between biomolecules are specific
Stereoisomers Have Different Biological Effects
ATP
Thermodynamics You Already Know
Endothermic vs Exothermic
ΔG = ΔH – T ΔS
ΔG is related to the Equilibrium Constant
ΔG = G products – G reactants
Reactants = Substrates
ΔGo = standard free energy change (we will change this
later)
for aA + bB  cC + dD
ΔG = ΔGo + RT ln K eq
AAA
: Hexokinase Rxn
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
Series of related enzymatically catalyzed
reactions forms a pathway
Metabolic Pathway
• produces energy or valuable materials
Signal Transduction Pathway
• transmits information
Pathways are controlled in order to
regulate levels of metabolites
Example of a negative regulation:
Product of enzyme 5 inhibits enzyme 1
Anabolism and Catabolism
Metabolic Diversity
Information Codes
Prism of Sennacherib
~700 BC, Assyrian
Bacterial DNA
DNA Replication
Central Dogma
DNA code Transcription  Translation  Protein
A
Miller and Urey
Experiment
in a Garage,
1953
RNA World to
DNA/RNA/Protein
World
Current Year
Endosymbiotic Origin of Mitochondria and
Chloroplasts
From Darwin to Orthologous and
Paralogous Genes
Paralogous Selection Required Gene Duplication
End of Chapter Problems
These are really easy…because 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
It’s a valuable review to make you a great biochemical
problem solver!
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 biomolecule’s
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