BCH 560( H ORMONES ) M ASTERS Dr. Samina Hyder Haq Dept. Of Biochemistry King Saud University.
Welcome to General Biochemistry BCH 3033 CHAPTER 1 Review of Basic Cellular Biology and Chemistry.
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Transcript of Welcome to General Biochemistry BCH 3033 CHAPTER 1 Review of Basic Cellular Biology and Chemistry.
Welcome toGeneral 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 monomerspolymerscell
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 Chem
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 temperaturesStability of macromolecules is limiting
Higher concentration of reactantsCostly as more valuable starting material is needed
Change the reaction by coupling to a fast oneUniversally used by living organisms
Lower activation barrier by catalysisUniversally used by living organisms
Metabolic Pathway• produces energy or valuable materials
Signal Transduction Pathway• transmits information
Series of related enzymatically catalyzed reactions forms a pathway
Example of a negative regulation:Product of enzyme 5 inhibits enzyme 1
Pathways are controlled in order to regulate levels of metabolites
Anabolism and Catabolism
Metabolic Diversity
Information Codes
Prism of Sennacherib Bacterial DNA
~700 BC, Assyrian
DNA Replication
Central DogmaDNA code Transcription Translation Protein
A
Miller and Urey Experimentin 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