Chapter 1 The Foundations of Biochemistry
Jan 13, 2016
Chapter 1
The Foundations of Biochemistry
Why do we study biochemistry?
21st Century: Integrated (fusion) Science
BIO is the core !
BIO
Physics
Chemistry
Mathematics
Nanotechnology
IT & ETEngineering
Properties of Life
Biochemistry – Molecular Logic of Life Understanding the physical and chemical laws governing life
Simple elements and compounds
Biomolecules Life
Properties of life Chemical complexity and microscopic organization
Systems for extracting, transforming, and using energy from the environment
Self replication and self assembly
Sensing and responding to environmental changes
Defined functions for each components and their regulated interactions
Evolution
Contents
The foundations of biochemistry Chapter 1
Cellular foundations
Chemical foundations
Physical foundations
Genetic foundations
Evolutionary foundations
1.1 Cellular Foundations
Cells
Structural & functional units of living organisms Structure of cells
Plasma membrane Structural barrier from the surroundings Barrier of molecular transport Composed of lipids and proteins
Cytoplasm Cytosol: concentrated aqueous solution
– Enzymes, coenzymes, RNA, building blocks, metabolites, inorganic ions, proteasomes
Particles and organelles– Ribosome, ER, mitochondria, lysosomes, chloroplasts
(plants)
Nucleus (eukaryotes) or nucleoid (prokaryotes) Storage of genome and replication
Universal Features of Living Cells
Cellular Dimensions
Cell sizesBacteria: 1 ~ 2 mAnimal cells : 5 ~100 m
Limitations of cell sizeLower limit
Minimum number of biomolecules required by the cell
– Micoplasma: 300 nm– c.f. ribosome : 20 nm
Upper limitOxygen diffusionBacteria: small size high surface/volume ratio
Classification of Life
Three domains (kingdoms) Eukaryotes Prokaryotes
Eubacteria Archaebacteria
Classification of Life
Classification of prokaryotes depending of the habitats Aerobic : O2 as electron acceptor Anaerobic : nitrate( N2), sulfate (H2S), CO2 (CH4) as e-
acceptors Classification according to carbon & energy sources
Structure of E. coli
Most-studied bacterium
15,000 ribosomes ~1,000 enzymes Circular DNA Plasmids
Gram Staining
Cell Envelopes of Prokaryotes
Animal Cell
Plant Cell
Subcellular Fractionation of Tissue
Organization of Cytoplasm
Cytoskeleton Actin filaments, microtubules, intermediate filaments
Highly dynamic structureAssembly and disassembly of subunits
FunctionsStructural organization of cytoplasmMolecular & organellar transport
Types of Cytoskeleton
Actin filaments Microfilaments, 8-9 nm in diameter
Determine cell shape with membrane-binding proteins
Intermediate filaments 10 nm
Support nuclear membrane
Tissue formation through cell-cell, cell-matrix interactions
Microtubules Hollow tube-like structure, 24 nm
Organization of certain subcellular structures
Vasicular transport
Cells Build Supramolecular Structures
Macromolecules
Linkage of monomeric subunits by covalent bonds Amino acids (e.g. ala: 0.5 nm) Assembled into proteins (e.g.
hemoglobin, 5.5 nm in diameter) by ribosome (20 nm in diameter)
Interactions of macromolecules
Noncovalent interactions Hydrogen bonds Ionic interactions Hydrophobic interactions Van der Waals interactions
Cells Build Supramolecular Structures
In vitro studies vs. in vivo reality Gel-like cytosol High concentration, limited diffusion, uneven distribution
1.2 Chemical Foundations
Elements Essential to Life
Bulk elements : structural components of cells H, O, N, C
Most abundant elements : > 99% of cell mass
P,S, Na, Cl, K, Ca Trace elements
Fe, Cu, Zn etc.
Carbon in Biomolecules
Carbon Major component of biomolecules
Most biomolecules are derivatives of hydrocarbons
Bonding versatility Single or double bonds Bonding with diverse functional groups
Small Molecules
Primary metabolites (Mr ~100 to ~500)
Evolutionarily conserved in all types of cellsAmino acids, nucleotides, sugars, mono-,
di-, and tricarboxylic acids Secondary metabolites
Specific to cell typese.g. morphine in plant, antibiotics in bacteria
Metabolome
Macromolecules are the Major Constituents of Cells
Proteins Enzyme, structural function,
transport, signal transduction etc.
Nucleic acids : DNA, RNA Storage and transmission of
genetic information Structural and catalytic role
(RNA) Polysaccharides
Energy storage Extracellular structural element
for cellular signaling Lipids
Constitution of membrane Energy storage
3D Structure
Stereoisomers
Same chemical bonds but different configuration
Geometric (cis-, trans-) isomers Double bonds
Enantiomers or diastereomers Compounds with chiral centers
Interactions Between Biomolecules are Stereospecific
Usually one chiral formAmino acids : L isomersGlucose : D isomer
Biological reactions and interactions are stereospecific
Binding of argininamide to HIV RNA genome
1.3 Physical Foundations
Energy is a central theme in biochemistry. 1. No equilibrium 2. Dynamic steady state 3. Exchange energy and matter 4. Energy conservation 5. Enzymes promote sequences of chemical reactions. 6. Metabolism in balance and economy
Thermodynamics of Living Organism
Dynamic steady state Maintaining cellular constituents by balancing the
rate of production and consumption Open system
Exchanging energy and matter with its surroundings First law of thermodynamics: Energy conservation
Energy transduction in cells Flow of electrons along the electrochemical
potential gradient Sunlight energy transfer of e- from H2O to CO2
Production of energy-rich products (e.g glucose) 6CO2 + 6 H2O + light C6H12O6 + 6O2
Oxidation of energy-rich products transfer of e- to O2 to form H2O Production of energy
C6H12O6 + O2 6CO2 + 6 H2O + energy
Thermodynamics of Living Organism
Energy transduction in cells
Flow of electrons along the electrochemical potential gradient Sunlight energy transfer of e- from
H2O to CO2 Production of energy-rich products (e.g glucose)
6CO2 + 6 H2O + light C6H12O6 + 6O2
Oxidation of energy-rich products transfer of e- to O2 to form H2O Production of energy
C6H12O6 + O2 6CO2 + 6 H2O + energy
Free Energy Change for Biological Reactions
G = H –TS G: free-energy change H: enthalpy S: entropy
Coupling of energy-requiring (endergonic) reaction with reactions liberating free energy (exergonic) to make negative G Polymerization reaction: G1 is positive (endergonic) Hydrolysis of ATP: G2 is negative (exergonic) G1 + G2 is negative (exergonic)
Energy Coupling in Mechanical & Chemical processes
Measurement of Reactions Tendency to Proceed Spontaneously
aA + bB cC + dD
Equilibrium constant [Ceq]c [Deq]d
[Aeq]a [Beq]b
Go : standard free energy change (joules/mole)
[Ci]c [Di]d
[Ai]a [Bi]b
At equilibrium, G=0
Go = -RT ln Keq
Spontaneous reaction Keq >>1 Go : large and negative
Keq =
G = Go + RT ln
Enzymes
Functions of enzymes
Increasing reaction rate (kinetics) without affecting thermodynamics
Decreasing activation energy G‡
Better fit for transition state Binding of reactants with proper stereospecific orientations
Metabolism
Catabolism
Degrading pathways
Free-energy-yielding reactions Anabolism
Synthetic pathways
Energy-consuming reactions ATP is the major connecting link Tight regulation to achieve
balance and economy
e.g. feed back inhibition
1.4 Genetic Foundations
Inheritance of Genetic Information
DNA contains encoded genetic information DNA replication Expression of genetic information
DNA RNA protein
1.5 Evolutionary Foundations
Evolution
Mutation
Provides opportunity for evolution
Survival of the fittest under selective pressure
Chemical evolution
Generation of organic compounds under primitive atmospheric conditions
RNA world scenario RNA as initial self-replicating and
catalytic molecule
Miler and Urey, 1953
Biological Evolution
Chemoheterotroph Photosynthetic
bacteria Aerobic bacteria Eukaryotic cells
Endosymbiosis of aerobic or photosynthetic bacteria
Muticellular eukaryotes
Endosymbiosis
Molecular Anatomy Reveals Evolutionary Relationships
Homologs
Genes with sequence similarity Paralogs
Homologs in the same species
Gene duplication Orthologs
Homologs in different species
Information from Genome Sequences
Genome annotation Deduction of the function of each genes by
sequence comparison with known genes Construction of evolutionary phylogeny
Based on sequence homology Functional genomics
Allocations of genes to specific cellular processes Complex organisms has higher portion of genes
involved in regulation Human biology and medicine
Identification of human-specific genes Use genetic information to diagnosis and treatment
of diseases