chapter 1 the foundations of biochemistry. why do we study biochemistry? 21 st century: integrated...
TRANSCRIPT
![Page 1: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/1.jpg)
Chapter 1
The Foundations of Biochemistry
![Page 2: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/2.jpg)
Why do we study biochemistry?
21st Century: Integrated (fusion) Science
BIO is the core !
BIO
Physics
Chemistry
Mathematics
Nanotechnology
IT & ETEngineering
![Page 3: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/3.jpg)
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
![Page 4: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/4.jpg)
Contents
The foundations of biochemistry Chapter 1
Cellular foundations
Chemical foundations
Physical foundations
Genetic foundations
Evolutionary foundations
![Page 5: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/5.jpg)
1.1 Cellular Foundations
![Page 6: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/6.jpg)
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
![Page 7: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/7.jpg)
Universal Features of Living Cells
![Page 8: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/8.jpg)
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
![Page 9: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/9.jpg)
Classification of Life
Three domains (kingdoms) Eukaryotes Prokaryotes
Eubacteria Archaebacteria
![Page 10: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/10.jpg)
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
![Page 11: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/11.jpg)
Structure of E. coli
Most-studied bacterium
15,000 ribosomes ~1,000 enzymes Circular DNA Plasmids
![Page 12: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/12.jpg)
Gram Staining
![Page 13: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/13.jpg)
Cell Envelopes of Prokaryotes
![Page 14: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/14.jpg)
Animal Cell
![Page 15: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/15.jpg)
Plant Cell
![Page 16: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/16.jpg)
Subcellular Fractionation of Tissue
![Page 17: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/17.jpg)
Organization of Cytoplasm
Cytoskeleton Actin filaments, microtubules, intermediate filaments
Highly dynamic structureAssembly and disassembly of subunits
FunctionsStructural organization of cytoplasmMolecular & organellar transport
![Page 18: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/18.jpg)
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
![Page 19: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/19.jpg)
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
![Page 20: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/20.jpg)
Cells Build Supramolecular Structures
In vitro studies vs. in vivo reality Gel-like cytosol High concentration, limited diffusion, uneven distribution
![Page 21: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/21.jpg)
1.2 Chemical Foundations
![Page 22: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/22.jpg)
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.
![Page 23: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/23.jpg)
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
![Page 24: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/24.jpg)
![Page 25: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/25.jpg)
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
![Page 26: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/26.jpg)
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
![Page 27: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/27.jpg)
3D Structure
Stereoisomers
Same chemical bonds but different configuration
Geometric (cis-, trans-) isomers Double bonds
Enantiomers or diastereomers Compounds with chiral centers
![Page 28: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/28.jpg)
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
![Page 29: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/29.jpg)
1.3 Physical Foundations
![Page 30: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/30.jpg)
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
![Page 31: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/31.jpg)
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
![Page 32: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/32.jpg)
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
![Page 33: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/33.jpg)
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)
![Page 34: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/34.jpg)
Energy Coupling in Mechanical & Chemical processes
![Page 35: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/35.jpg)
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
![Page 36: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/36.jpg)
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
![Page 37: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/37.jpg)
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
![Page 38: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/38.jpg)
1.4 Genetic Foundations
![Page 39: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/39.jpg)
Inheritance of Genetic Information
DNA contains encoded genetic information DNA replication Expression of genetic information
DNA RNA protein
![Page 40: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/40.jpg)
1.5 Evolutionary Foundations
![Page 41: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/41.jpg)
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
![Page 42: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/42.jpg)
Biological Evolution
Chemoheterotroph Photosynthetic
bacteria Aerobic bacteria Eukaryotic cells
Endosymbiosis of aerobic or photosynthetic bacteria
Muticellular eukaryotes
![Page 43: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/43.jpg)
Endosymbiosis
![Page 44: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/44.jpg)
Molecular Anatomy Reveals Evolutionary Relationships
Homologs
Genes with sequence similarity Paralogs
Homologs in the same species
Gene duplication Orthologs
Homologs in different species
![Page 45: Chapter 1 The Foundations of Biochemistry. Why do we study biochemistry? 21 st Century: Integrated (fusion) Science BIO is the core ! BIO Physics Chemistry](https://reader035.vdocuments.site/reader035/viewer/2022062304/56649eb15503460f94bb7a7a/html5/thumbnails/45.jpg)
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