Good Morning Class - WordPress.com · Kinetics The Belousov-Zhabotinsky reaction, a chemical...
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Good Morning Class !
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To guideTo ask the right questions ?
To find the right answer ?
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17 %Exam?
Close-book Exam 10 %1 week after Assignment have done!
Assignment 7 %Your protein of interest• Structure• Function• Metabolism• Latest report about your
protein• 15-20 min Presentation
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Lecture 1- Basic knowledge for Biochemistry- Cell: Structure and Function- WaterLecture 2 - Amino acid Peptide and PolypeptideLecture 3 - Protein Structure and FunctionLecture 4 - Metabolism of Protein and Amino acid- Protein structure determination (If time allow)
Content
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Lecture 1- Basic knowledge for Biochemistry- Cell: Structure and Function- WaterLecture 2 - Amino acid Peptide and PolypeptideLecture 3 - Protein Structure and FunctionLecture 4 - Metabolism of Protein and Amino acid- Protein structure determination (If time allow)
Content
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Today objective:
- To review some essential background in Chemistry and Biology
- To introduce basic idea of Biochemistry
- To get your attention on Biochemistry
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Biochemistry
Biological chemistry
ชีวเคมี
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Biochemistry
Biological chemistry
ชีวเคมี
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Biology + Chemistry
Biochemistry
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Chemistry / เคมี
Study of mattersMatter:- atom and molecule- element- substance- compound- etc.
Biology / ชีววิทยา
Study of life or living things (organisms) Organisms: - animals- plants- fungi- bacteria- archaea- viruses?
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Biology / ชีววิทยา
Study of life or living things (organisms) Organisms: - animals- plants- fungi- bacteria- archaea- viruses?
- Structure- Function- Growth- Origin- Evolution- Distribution- Taxonomy- Ecology- etc.
Organ: brain, heart, stomach, skin, eye, leave, root, flower, etc.
Tissue: adipose, connective tissue, epithelial, phloem, xylem, etc.
Cell /particle: - Prokaryotes (bacteria)- Eukaryotes (animals,
plants, yeast and fungi) - viruses
Organelle & cellular components: nucleus, mitochondria, chloroplast, etc.
Sub organelle: lipid bilayer membrane, microfilament, microtubule, intermediate filament, etc.
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Biology / ชีววิทยา
Study of life or living things (organisms) Organisms: - animals- plants- fungi- bacteria- archaea- viruses?
- Structure- Function- Growth- Origin- Evolution- Distribution- Taxonomy- Ecology- etc.
Organ: brain, heart, stomach, skin, eye, leave, root, flower, etc.
Tissue: adipose, connective tissue, epithelial, phloem, xylem, etc.
Cell /particle: - Prokaryotes (bacteria)- Eukaryotes (animals,
plants, yeast and fungi) - viruses
Organelle & cellular components: nucleus, mitochondria, chloroplast, etc.
Sub organelle: lipid bilayer membrane, microfilament, microtubule, intermediate filament, etc.
Chemistry
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Structure Function Bonding Reaction
- Thermodynamic“How far it can go?”
- Kinetics“How fast it can go?”
Chemistry / เคมี
Study of mattersMatter:- atom & molecule- element- substance- compound- etc.
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Laws of Thermodynamics
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Kinetics
The Belousov-Zhabotinsky reaction, a chemical reaction that oscillates in time and space. When a very thin layer of an acidic solution containing potassium bromate (KBrO3), cerium ammonium nitrate [(NH4)2Ce(NO3)6], malonic acid (HO2CCH2CO2H), and an indicator is poured into a shallow dish, local fluctuations in the concentration of the reactants and a complex series of reactions cause striking geometric patterns of concentric circles and spirals to propagate across the dish.0
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The study of chemical processes in livingthings, including, but not limited to, livingmatter, dealing with structures, functions andinteractions of biomolecules
Biochemistry
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Chemical processes in living things (Biochemical process): Chemical reactions (using enzyme as catalyst) occur in living things dealing with structures, functions and interactions of biomolecules.
Biomolecules; Any organic molecule that is produced by a living organism, including large polymeric molecules (macromolecules) such as proteins, lipids, carbohydrates, and nucleic acids as well as small molecules such as primary metabolites (amino acid, nucleotide, organic acid, vitamin, etc.), secondary metabolites (alkaloids, terpenoids, glycosides, etc. ) and natural products.
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Examples of biochemical process
- Genetic information transferred: replication, transcription, translation, etc.
- Cell communication / signaling: intercellular, intracellular, multicellular
- Bioenergetics: synthesis , transfer and use of energy carrier such as ATP
- Metabolism: catabolism and anabolism- Regulation of metabolism: hormone (in blood) and
pheromone (excrete from animals)- Etc.
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ชีวเคมีCarbohydrate Nucleic acid ProteinLipid
Anabolism Catabolism
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Nucleic acids = ????
Biochemistry / Nutrition
Carbohydrate LipidProtein
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Malaria Toxin, Beverage
Biochemistry / Medicine & IndustryEPEC
Enteropathogenic Escherichia coli
Amanita muscaria
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GABA, Vitamin Effective substances (2nd metabolite)
Biochemistry / Herb & Pharmacy
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Cathinone,Amphetamine-like compound
CNS- Stimulant- Replace MDMA
khat
cannabis, weed, Pot, marijuana; bhang cocaine
Alkaloid / Pros & Cons
korth khat opium
Benzoylmethylecgonine (Cocaine)
CNSstimulant
cocaine
Mitragynine (indole alkaloid)
CNSstimulant
korth Morphine
CNS- Pain killer- Addict
opium
Tetrahydrocannabinol (THC)
CNS- G-protein couple receptor1 stimulant- G-protein couple receptor2 immune
cannabis, weed, Pot, marijuana; bhang
Biochemistry / secondary metabolites
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Where is Biochemistry in the Universe?
Stored in compound
….. ATP
4 Forces …Affinity,
…
Where is Biochemistry in the Universe?Big bangs………………………………….!!!!!!!Universes: galaxies, the stars, planets, draft planets, asteroids, etc.The solar system: the sun, the earth, the moon and other planets, etc.The earth: reducing to oxidizing condition, living and non living things; Life: animals, plants, archaea, bacteria, virusesSubstances/compounds/ions: H2, H2O, CO2, biomolecules, Ca2+, K+, etc. Elements: H, He, O, etc. Subatomic particle: e-, p+, n0, quarks, leptons, hadrons, etc.Force and Energy: F=ma and E=mc2
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W H A T A R E W E ?
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Multicellular organism ≈ 120 trillion cells
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General interesting Questions ?
How the biomolecules synthesized? which one came first RNA, DNA,Protein, Carbohydrate, Lipid?
How the life began on earth?
How does the first cell form?
How does the species evolved?
???????????????????...........
Down to Biochemistry
&Molecular
level
Biology
Chemistry
Biochemistry
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Function
Proteins Gene
Biology is an experimental science.
Biochemistry
Molecular Biology
Genetics
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B A C K T O T H E B A S I C
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The The earth’s Human CellsUniverse crust bodies
H (75%) O (46.6%) O (65%) H (59%)He (25%) Si (27.2%) C (18%) O (24%)O (<1%) Al (8.1%) H (10%) C (11%)etc. Fe (5.0%) N (3%) N (4%)
Ca (3.6%) P (1.5%) P, S (2%)Na (2.8%) K (1%) etc.K (2.6%) S (.035%)Mg (2.1%) Na (0.15%)etc. Mg (0.05%)
Cu, Se, Mo, F, Cl, I, Mn, Co, Fe (0.70%)Li, Sr, Al, Si, Ld, V, As, Br (trace amounts)etc.
H2O (65-90%)+
BiomoleculesProteins (50%)Nucleic acids (15 %)Carbohydrates (15%)Lipids (10%)Small Biomolecules (10%)
Chemistry of life / Chemical composition
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H2O (65-90%)+
BiomoleculesProteins (50%)Nucleic acids (15 %)Carbohydrates (15%)Lipids (10%)Small Biomolecules (10%)
The The earth’s Human CellsUniverse crust bodies
H (75%) O (46.6%) O (65%) H (59%)He (25%) Si (27.2%) C (18%) O (24%)O (<1%) Al (8.1%) H (10%) C (11%)etc. Fe (5.0%) N (3%) N (4%)
Ca (3.6%) P (1.5%) P, S (2%)Na (2.8%) K (1%) etc.K (2.6%) S (.035%)Mg (2.1%) Na (0.15%)etc. Mg (0.05%)
Cu, Se, Mo, F, Cl, I, Mn, Co, Fe (0.70%)Li, Sr, Al, Si, Ld, V, As, Br (trace amounts)etc.
Chemistry of life / Chemical composition
This course will focus onBiochemical processes of….
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Review / Important background2. Biology- Living things- Cell components and Organelles and functions
- Membrane
3. Water:- Physical: structure, as solvent, Hydrophobic effect, Osmosis and diffusion
- Chemical: ionization, acid/base/buffer
1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, redical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon; hybridization, stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
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Review / Important background2. Biology- Living things- Cell components and Organelles and functions
- Membrane
3. Water:- Physical: structure, as solvent, Hydrophobic effect, Osmosis and diffusion
- Chemical: ionization, acid/base/buffer
1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, redical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon; hybridization, stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
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1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, radical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon; hybridization, stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
Carbon12
6 electrons6 protons6 neutrons
Nucleus
orbital
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1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, radical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon; hybridization, stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
The process of converting an atom or molecule into an ion by adding or remov-ing charged particles such as electrons or ions.
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CH2NH3+ COOH CH2NH2 COO -
CH2NH3+ COO -
CH2NH2 COOH
Ionization: amino acid (Glycine)
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1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, radical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon; hybridization, Stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
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Radical (often referred to as free radicals) are atoms, molecules, or ions with unpaired electrons or an open shell configuration. Free radicals may have positive, negative, or zero charge. With some exceptions, these unpaired electrons cause radicals to be highly chemically reactive.
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Redical : Reactive Oxygen Species (ROS)
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- The most electronegative of all elements. - Each Fluorine atom has the ability to strip electrons from any
surrounding substance in - order to become the Fluoride ion F-. This is the most stable state for
Fluorine and the only state it is found in in the natural environment.
Fluoride on ROS Generation
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1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, redical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon; hybridization, stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
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Chemical bonds/interactions
WEAK BONDS
STRONG BONDSA. Ionic
B. Covalent
D. Ion - Permanent Dipole
F. Ion - Induced Dipole
G. Permanent Dipole - Induced Dipole
H. Induced Dipole - Induced Dipole
E. Permanent Dipole - Permanent Dipole (H)
C. Metallic
kJ/mol1000
900
500
NaCl
NaNO3
LiCl
NaF
MgCl2
N___N
N___C
CC
C__C
O__O
O__C
C_ O
Si _C
C_ H
C_N
C_ C
N_O
O_O
W
Hg
800
600
400
300
200
100
B
700
CA D E F G H
___
10
Which ones are important in Biological system ?
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1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, radical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon; hybridization, Stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
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Acid-base (pH, H+, OH-)
Brønsted–Lowry definition : Protonation of bases through the de-protonation of acids• Acid donates proton (H+)• Base accepts proton (H+)
2 NaOH + H2SO4 → Na2SO4 + 2 H2O
CH3COOH + NH3 → NH+4 + CH3COO−
Svante Arrhenius definition :• Acid is a substance that dissociates in water to form hydrogen ions (H+)• Base is a substance that dissociates in water to form hydroxide ions (OH-)
Reaction
Reaction
Lewis definition : Accepting or Donating electron pair
• Acid can accept a lone pair electron, completing its stable form.• Base can donate a lone pair electron, to a Lewis acid to form a Lewis adduct
ReactionH-N-H + H+ → H-N-H
H HII
..H
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Acid-base (pH, H+, OH-)
pH is a measure of the concentration of hydrogen ions( H+ or protons) in a solution
concentration of H+
(mole/liter)
pH
concentration of OH-
(mole/liter)7 140
01 x 10-701 x 100
01 x 10-14
01 x 10-14
01 x 10-7 01 x 100
pH stand for power of Hydrogen
pH = -log10[H+]
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1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, redical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon;
hybridization, stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
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Carbon and organic compounds
Carbon has the ability to form very long chains of interconnecting C-C bonds. This property is called catenation. Carbon-carbon bonds are strong, and stable. This property allows carbon to form an almost infinite number of compounds.
Almost all organic compounds contain carbon and hydrogen.
6
Carbon12.0107
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1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, redical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon;
hybridization, stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
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Hybridization of carbon
Sp3Tetrahedral
Sp2Trigonal Planar
SpLinear
Methane = Tetrahedral L -and D-isoform
Ethyne = LinearEthane = Trigonal planarCis- and Trans-isoform
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1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, redical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon; hybridization, stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
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L-isoform (left) / D-isoform (right)
CisTrans
Optical isomer / Enantiomer
Geometric isomer
1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, redical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon; hybridization, stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
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CH3-CH2-CH2-CH2- CH2-CH3
Hexane (C6H14)
Benzene (C6H6)
Cyclohexane (C6H12)
1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, redical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon; hybridization, stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
Absorption
Resonance
Fluorescent
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1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, redical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon; hybridization, stereoisomerism, polymer,aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
Lipid ?
PolymerBuilding block
Monosaccharide StarchGlycogen
Nucleotide DNARNA
Amino acid Protein
Organic compound
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1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, redical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon; hybridization, Stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups, alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
WIKI !!
Review / Important background
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Example of Functional groups in Biomolecules
SteroidAmino acid
Nucleotide
Glucose
Cholesterol
Fatty acid
Triglyceride
Phopholipid
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Oxidation-reduction (redox) Hydrolysis vs. Condensation Precipitation Addition Elimination Rearrangement Polymerization Substitution Polymerization vs.
Depolemerization etc.
1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, redical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon; hybridization, stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
Review / Important background
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Reduction Cu2+(aq) + 2e-
Cu(s)OxidationZn(s) Zn2+(aq) + 2e-
Oxidation-reduction reactionZn(s) + Cu2+(aq) Zn2+(aq) + Cu(s)
(reduce Oxidation No.)
Oxidation-reduction / Redox reaction
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H in is reduction the compound is reduced
Oxidation-reduction / Redox reaction
H out or O in is oxidation the compound oxidized.
O2 is the strongest oxidizing agent: energy / (ATP) production.
H
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Condensation
Hydrolysis
Hydrolysis vs. Condensation
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Hydration ≠ Hydrolysis
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Elimination
Addition
CH2 CH2Pt
Br2+ CH2 CH2BrBr
CH2 CH2alcohol HCl+CH2 CH2
ClH
KOH
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Substitution
A.
B. enzyme
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Polymerization vs. Depolymerization
Deoxyribonucleic acids
Protein
DNA,
Enzymes
Deoxy-ribonucleotides
Amino acids
Depolymerization
Enzymes
Enzymes
Enzymes
monomer (building block)
monomer (building block)
(polymer)
(polymer)
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Review / Important background2. Biology- Living things- Cell components and Organelles and functions
- Membrane
3. Water:- Physical: structure, as solvent, Hydrophobic effect, Osmosis and diffusion
- Chemical: ionization, acid/base/buffer
1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, redical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon; hybridization, stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
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Living things = Object that can undergometabolism, maintain homeostasis, possess acapacity to grow, respond to stimuli, reproduceand, through natural selection, adapt to theirenvironment in successive generations. Morecomplex living organisms can communicatethrough various means.
Biology
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The smallest object that can undergoes those properties is
Biology
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PLant cell
Viral particle
Animal cell
Bacterial cell& Archaea
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Textbook drawings of the cell’s largest organelle might need to be updated based on new images. Supe-resolution shots of the endoplasmic reticulum reveal tightly packed tubes where previouspictures showed plain flat sheets, scientists report in the Oct. 28 Science.
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BiochemistryChemical composition of the cell componentsExample:Cell wall : Plant cellulose and hemicelluloseBacteria PeptidoglycanYeast Glucan-Manoprotein +Chitin
Cell Membrane: Different composstion in cell types, or Organelles
Phospholipid Head group Fatty acid compositionProtein, Carbohydrate and Glycerol content
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LUCA, last universal common ancestor(life / the first cell)
Bacteria Archaea Eukarya
DiplomonadsMocrosporidia
Trichomonads
Flageellates
CiliatesPlants
Diatoms
Slime moldsEntoamoebae
Animala
Aquifex
ThermotogalesFlavobacteria
CyanobacteriaChloroplast
Purple bacteria
Chloroflexus
PyrodictuimThermoproteus
ThermococcusMethanococcus
Methanothermus Halophiles
Where does the first cell come from?
Evolution of Cell
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How does chemistrybecomes life?
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Early life is an anaerobe.
Photosynthesis /Cyano bacteria
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Results (after 1 week)Aldehydes, carboxylic acids formedGlycine and alanine formedAmino acidsSugarsPurines & pyrimidinesNB: Chirality 50/50 %
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A possible pathways for the synthesis of the cell(a spontaneously-replicating membrane by Szostak, 2001)
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Review / Important background2. Biology- Living things- Cell components and Organelles and functions
- Membrane
3. Water:- Physical: structure, as solvent, Hydrophobic effect, Osmosis and diffusion
- Chemical: ionization, acid/base/buffer
1. Chemistry- Atom: isotope, orbital, octet theory- Ionization, redical, oxidation number, - Chemical bonds/interactions- Acid-base (pH, H+, OH-)- Carbon and Hydrocarbon; hybridization, stereoisomerism, polymer, aliphatic & aromatic, cyclization
- Functional groups; alcohol, aldehydeketone, carboxylic acid, ester, amine, amide
- Chemical reactions - Thermodynamics, kinetics
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WaterPhysical properties: Chemical properties:- Structure - Ionization of water- Polarity - Acid-base chemistry- Acting as Solvent - Buffers- The hydrophobic effect - H-bond- Osmosis and diffusion
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Formation of Water
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Structure of water
O-H = Covalent bond with bond strength = 460 kJ/mol
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Distribution of electron in water
Note that the average electron density around the oxygen atom is about 10x that around the hydrogen atoms.
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Polarity of water
The approximate shape and charge distribution of water.Note that the average electron density around the oxygen atom is about 10x that around the hydrogen atoms.
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The polarity also allows water interact with an electric field.
Water in electric field
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Water as solvent
Physiological concentration of NaCl 150 mM
Watermolecules Chloride ion (Cl-)
Sodium ion (Na+)
Sodium chloride
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Hydrophobic effect
The interactions can hold molecules together: avoiding hydrophobic groups of molecules to interaction with water.
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Hydrophobic effect
The interactions can hold molecules together: avoiding hydrophobic groups of molecules to interaction with water.
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Osmosis and diffusion
Another important property of water is its ability to facilitate the transfer of molecules through osmosis. When 2 aqueous solutions are separated by a membrane that only allows the passage of water molecules, water will move from the less concentrated to the more concentrated side.
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Effect of water on cellHypotonic solution Isotonic solution Hypertonic solution
Animal cell
Plant cell
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Ionization and acid-base properties of water
(hydroxide ion)
(hydronium ion)2 x H2O
HO-
H3O+
auto-ionization of water
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• Expressed mathematically, the concentration of H+ = 1 x 10-7 mole/liter
• pH = -log10[H+] = -log10[10-7 ] = 7
H
H O
H
H O
HH
O
H
O
-
At room temperature 25 C, 1 in 555 million water moleculesIonization of water
H
H O
HH
O
H+
If the concentration of hydrogen ions goes up 10 time [H+] = 1 x 10-6, 100 time [H+] = 1 x 10-6.
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Acid-base (pH, H+, OH-)
pH is a measure of the concentration of hydrogen ions( H+ or protons) in a solution
concentration of H+
(mole/liter)
pH
concentration of OH-
(mole/liter)7 140
01 x 10-701 x 100
01 x 10-14
01 x 10-14
01 x 10-7 01 x 100
pH stand for power of Hydrogen
pH = -log10[H+]
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BufferBuffer solution - A solution is which resistant changes to pH.Your body uses buffers to maintain the pH of your blood.Blood pH 7.35 - 7.45Buffer system in body -1. Proteins2. Phosphates HPO4
2- / H2PO4- : 1.6 / 1
3. Carbonates H2CO3 / HCO3- : 10 / 1
Reaction:base neutralization: OH- + H2CO3⇔ HCO3
- + H2Oacid neutralization: H3O+ + HCO3
-⇔ H2CO3 + H2OH2CO3 →H2O + CO2 (exhale)
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H-bond in water
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Water : Water
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H-bond in biomolecule
A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group.
H-bond vs Protein folding
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Every chemical reaction that occurs in the human body occurs through water. All cells in the human body are soaked in water. Nutrients and oxygen are transported throughout the body using water and individual cells need water to bring the nutrients and oxygen into them. Water is used to cool the body down through the action of perspiration. Water lubricates joints and internal organs, such as the eyeballs.
Example:- Digestion - Hydrolysis- Waste - Electrolytes, - Warning - Nutrients
Water
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ชีวเคมีCarbohydrate Nucleic acid ProteinLipid
Anabolism Catabolism
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1). Berg JM, Timoczko JL & Stryer L, “Biochemistry”, W.H. Freeman & Co., New York (every edition)
2). Voet D & Voet GJ, “Biochemistry”, John Wiley & Sons (Asia) Pte, Ltd., Singapore (every edition)
3). Alberts B, Johnson A, Lewis J, Raff M, Roberts K & Walter P, “Molecular Biology of the Cell”(all edition)
4). David L. Nelson & Michael M. Cox “Lehninger Principles of Biochemistry”, W.H. Freeman & Co., New York (every edition)
References and suggest text books
5). ม.จุฬาลงกรณ์ 6). ม.ขอนแก่น 7). ม.มหดิล
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NEXT !
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Next ! Amino acids and Proteins