lehninger(sixth edition) Ch 01: The foundations of biochemistry
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Transcript of lehninger(sixth edition) Ch 01: The foundations of biochemistry
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CHAPTER-1
Adopted from Nilsen and cox – Lehninger principles of biochemistry (sixth edition)
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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.
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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?
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Prokaryotic Cell
calculate the length of DNA in a bacterial cell…here it is all folded up!
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Bacterial Cytoplasm Is Full of Molecules
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Prokaryotic Cell Envelope
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Eukaryotic Cell
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Muscle Cells
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Eukaryotic Cytoskeleton: Actin (red), Microtubules (green) Surround the Nucleus (blue). Fluorescence Microscopy.
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Cytoskeleton Elements
Bacteria also have filaments (actin like) and microtubules to organize their cytoplasm.
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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.
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The Monomers
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Structure to Molecular Hierarchy
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Periodic Chart
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Carbon Bonding
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Carbon Bonding
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Geometry of carbon bonding
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Common Functional Groups of Biological Molecules
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several functional groups in single biomolecule.
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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)
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Representation of molecules
Ball-and-stick model
Space-filling modelStructural formula in perspective form
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Cis and Trans(Configurations of geometric isomers)
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Cis and Trans – Conformational Change
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Chirality
Problem 11 is about two pharmacological drugs and fits right in here with chirality and drug dosage.
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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.
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Chiral Rotation
Rectus (right) Sinister (left)
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Rotation by Priorities
Priorities of Some Biochemical Functional Groups
-OCH2 > -OH > -NH2 > -COOH > -CHO > -CH2OH > -CH3 > -H
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Interactions between biomolecules are specific
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Stereoisomers Have Different Biological Effects
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ATP
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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
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AAA
: Hexokinase Rxn
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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
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Metabolic Pathway• produces energy or valuable materials
Signal Transduction Pathway• transmits information
Series of related enzymatically catalyzed reactions forms a pathway
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Example of a negative regulation:Product of enzyme 5 inhibits enzyme 1
Pathways are controlled in order to regulate levels of metabolites
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Anabolism and Catabolism
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Metabolic Diversity
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Information Codes
Prism of Sennacherib Bacterial DNA
~700 BC, Assyrian
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DNA Replication
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Central DogmaDNA code Transcription Translation Protein
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A
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Miller and Urey Experimentin a Garage,
1953
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RNA World to DNA/RNA/Protein
World
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Current Year
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Endosymbiotic Origin of Mitochondria and Chloroplasts
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From Darwin to Orthologous and Paralogous Genes
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Paralogous Selection Required Gene Duplication
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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