Transcript Gen Biochem-Foundations - Biochemistry

General Biochemistry
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Foundations of Biochemistry
Piamsook Pongsawasdi
Kanoktip Packdibamrung
August 2016
References
Lehninger Principles of Biochemistry (2008)
Nelson, D.L. and Cox, M.M., 5th edition,
W.H. Freeman and Company, New York
ชีวเคมี (2559) พิมพ์ครั้งที่ 2
คณาจารย์ ภาควิชาชีวเคมี
โรงพิมพ์ แห่ งจุฬาลงกรณ์ มหาวิทยาลัย
Course Material
http://blackboard.it.chula.ac.th
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What is Biochemistry?

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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CELLULAR
FOUNDATIONS
Animal
vs Plant Cell
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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 m in diameter
- unicellular microorganism  1-2 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 O2 (obtain energy by
electron transfer from fuel molecules to O2 )
Anaerobic – devoid of O2 (obtain energy by electron transfer
to nitrate/sulfate/CO2, forming N2/H2S/CH4 respectively)
- Obligate anaerobes – die when exposed to O2
- Facultative anaerobes – able to live with/without O2
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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 m diameter x 2 m length)
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Differences in Cell Envelope
of Bacterial Cells
Cell envelope
Bact./Arch.
Inner*
Peptidoglycan
Outer*
Gram-stain
Gram -ve bact
+
+
+
Red
Gram +ve bact
+
thicker
-
Blue
Archaea
+ (a)
pseudo
-
Cyanobact
+(b)
tougher
+
* plasma membrane, peptidoglycan layer
Red
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 (103 - 105 times)
- cell diameter of animal cell: 5-30 m, plant cell: 10-100 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 m)
Cells: Unicellular 1-2 m, Multicellular 5-100 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)
isolation
purification
Cells
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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