lehninger(sixth edition) ch 01: the foundations of biochemistry
TRANSCRIPT
CHAPTER-1
Adopted from Nilsen and cox – Lehninger principles of biochemistry (sixth edition)
Learning Objectives
• Prokaryotic and eukaryotic cell structure and functions of each structure.
• Organic chemical bonds and functional groups.• Stereoisomers and cis-trans conformations.• Basics of Thermodynamics and Chemical Kinetics.• Basics of Catabolism and Anabolism.• Biochemical hierarchy from monomerspolymerscell
structure.• Evolution of cells: endosymbiosis; vertical and horizontal
gene transfer.• Evolution of proteins: orthologs and paralogs.
Prokaryote and Eukaryote Cells
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
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
Geometry of carbon bonding
Common Functional Groups of Biological Molecules
several functional groups in single biomolecule.
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)
Representation of molecules
Ball-and-stick model
Space-filling modelStructural formula in perspective form
Cis and Trans(Configurations of geometric isomers)
Cis and Trans – Conformational Change
Chirality
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 ConstantΔG = 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
Things You must have to know• 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 Problems 1, 3, 5, 8, 11, 12