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

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 (M r ) or Molecular Mass (m) in “Daltons” Carbon has M r = 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 -OCH 2 > -OH > -NH 2 > -COOH > -CHO > -CH 2 OH > -CH 3 > -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 ΔG o = standard free energy change (we will change this later) for aA + bB  cC + dD ΔG = ΔG o + 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

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 SennacheribBacterial DNA ~700 BC, Assyrian

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 5 th 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