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Piamsook Pongsawasdi
Somporn Kamolsiripichaiporn
August 2015

Lehninger Principles of Biochemistry (2008)
Nelson, D.L. and Cox, M.M., 5th edition,
W.H. Freeman and Company, New York
(2557)
Course Material http://www.sc.chula.ac.th/department/Biochemistry/
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 The field describes “Life in molecular terms”
- Structures, mechanisms, and chemical processes
(metabolism) in living organisms
 Biochemistry is important for basic knowledge
 Biochemistry is important for applications in medicine, food and agriculture, industry, and environment
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Main Features of Living Organisms
 A high degree of chemical complexity and microscopic organization
 Systems for extracting, transforming, and using energy from the environment
 Defined functions for components ( macroscopic : stem, heart; microscopic : nucleus, biomolecules)
 Mechanisms for sensing and responding to alterations in surroundings
 Self-replication and self-assembly
 Ability to evolve over time
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Important Foundations for
Biochemistry
 Cellular Foundations
 Chemical Foundations
 Physical Foundations
 Genetic Foundations
 Evolutionary Foundations
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Cells: Structural and Functional Units of all Living Organisms
Organisms:
Unicellular smallest organism, microscopic, contain single cell
Multicellular contain various cell types with different size, shape, and function
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Universal Features of Living Cells
Cells of all kinds share the same structural features
plasma membrane
(lipid bilayer/protein)
cytoplasm
(biomolecules/small metabolites
/supramolecular structure)
nucleus (Eukaryotes) or nucleoid (Prokaryotes, no nuclear membrane)
(genes)
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Cellular Dimensions of Cells
Most cells are microscopic
- animal and plant cells
≈
5-100
µ m in diameter
- unicellular microorganism
≈
1-2
µ m long
- smallest cell is Mycoplasma (bacteria)
≈
300 nm in diameter
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3 Distinct Domains of Life
 3 large groups of living organisms evolve from common ancestor
Prokaryotes:
Bacteria inhabit soil, surface water, living tissues, decay organisms
Archaea inhabit extreme environment: salt lakes, hot springs, ocean depths
Eukaryotes :
* Amoeba, yeast, diatom
**Fungi, plant, animal
(*single **multi-cell)
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Subgroups of Bacteria and Archaea
Subgroups are characterized by their habitats
Aerobic – with plentiful supply of O
2
(obtain energy by electron transfer from fuel molecules to O
2
)
Anaerobic – devoid of O
2
(obtain energy by electron transfer to nitrate/sulfate/CO
2
, forming N
2
/H
2
S/CH
4 respectively)
Obligate anaerobes – die when exposed to O
2
Facultative anaerobes – able to live with/without O
2
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Classification of Organisms according to
Energy and Carbon Sources
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E.Coli - the Best Studied Bacterium
 Bacterial cells share certain common structural features , but also show group-specific specializations
(e.g. cell envelope)
 E.coli
is a usually harmless inhabitant of human intestinal tract
(1
µ m diameter x 2
µ m length)
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Differences in Cell Envelope of Bacterial Cells
Bact./Arch.
Gram -ve bact
Gram +ve bact
Archaea
Cyanobact
Inner*
+
+
+ (a)
+(b)
Cell envelope
Peptidoglycan Outer*
+ + thicker pseudo tougher
-
-
+
Gram-stain
Red
Blue
Red
* plasma membrane, peptidoglycan layer cell shape and rigidity
(a) different lipid structure compared to bact and eukaryotes, p. 352-353
(b) extensive, with photosynthetic pigments
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Differences in Cell Envelope of Bacterial Cells
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Cytoplasm and Nucleoid of E.coli
 Cytoplasm of E.coli - contains
≈
15,000 ribosomes ,
1,000 different enzymes , 1,000 small metabolites and inorganic ions,
≥
1 small, circular DNA called plasmids
 Nucleoid of E.coli contains a single long circular DNA
Plasmids
- usually confer resistance to toxins and antibiotics in the environment
- powerful tools for genetic engineering experiment
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Features of Eukaryotic Cells
Much larger than bacterial cells (10 3 - 10 5 times)
cell diameter of animal cell: 5-30
µ m, plant cell: 10-100
µ m
Distinct characteristics :
nucleus (nuclear membrane, chromatin structure)
cytoskeleton (protein filaments in cytoplasm providing structure, organization or motion)
membrane-enclosed organelles with specific functions e.g. mitochondria, lysosome (animal), chloroplast (plant)
starch/fat granules
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 Fig 1-7 continue
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Cells Build Supramolecular Structures
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Differences in Size and Interactions
Monomeric unit (building block): amino acid, nucleotide
(base, ribose/deoxyribose, phosphate), monosaccharide
[Alanine 0.5 nm long, covalent bond ]
Macromolecules: protein, enzyme, nucleic acid, carbohydrate,
[Hemoglobin 5.5 nm in diameter, 4 subunits, covalent and non-covalent interactions]
Supramolecular structure : chromatin, plasma membrane
[some are visible under light microscope, macromolecules are joined mostly by noncovalent interactions]
Organelles : ribosomes ( 20 nm , diameter), mitochondria ( 1
µ m )
Cells: Unicellular 1-2
µ m , Multicellular 5-100
µ m
Noncovalent: H-bond, ionic, hydrophobic, van der Waals interactions
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Study Approach to Understand a Biological Process
In Vitro (in test-tubes)
Cells isolation purification
Biomolecules
Properties Study *
In Vivo (in living cells)
Study biomolecules in intact cells
* Precautions: different environment in test-tubes and in cells e.g. concentrations, interactions between molecules
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Subcellular Fractionation
Tissue homogenate fractionation by size or density subcellular fractions
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Summary of Cellular Foundations
 Phototrophs use sunlight , chemotrophs oxidize fuels energy work
 All cells are bounded by plasma membrane, have cytosol, and genes
 Bacteria and archaea cells have nucleoid and plasmids.
Eukaryotic cells have nucleus, are multi-compartmented with specific organelles
 Cytoskeletal proteins cell shape and rigidity and serves as rails along which organelles move within cells
 Supramolecular complex - held by non-covalent interactions, form a hierarchy structure
 Removal of a component for in vitro study may lead to loss of important interactions in living cells
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