Good Morning Class - WordPress.com · Kinetics The Belousov-Zhabotinsky reaction, a chemical reaction that oscillates in time and space. When a very thin layer of an acidic solution

Good Morning Class !

To guideTo ask the right questions ?

To find the right answer ?

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

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

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

Today objective:

- To review some essential background in Chemistry and Biology

- To introduce basic idea of Biochemistry

- To get your attention on Biochemistry

Biochemistry

Biological chemistry

ชีวเคมี

Biochemistry

Biological chemistry

ชีวเคมี

Biology + Chemistry

Biochemistry

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?



- 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.



- 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

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.

Laws of Thermodynamics

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

The study of chemical processes in livingthings, including, but not limited to, livingmatter, dealing with structures, functions andinteractions of biomolecules

Biochemistry

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.

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.

ชีวเคมีCarbohydrate Nucleic acid ProteinLipid

Anabolism Catabolism

Nucleic acids = ????

Biochemistry / Nutrition

Carbohydrate LipidProtein

Malaria Toxin, Beverage

Biochemistry / Medicine & IndustryEPEC

Enteropathogenic Escherichia coli

Amanita muscaria

GABA, Vitamin Effective substances (2nd metabolite)

Biochemistry / Herb & Pharmacy

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

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

W H A T A R E W E ?

Multicellular organism ≈ 120 trillion cells

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

Function

Proteins Gene

Biology is an experimental science.

Biochemistry

Molecular Biology

Genetics

B A C K T O T H E B A S I C

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

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….

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


- Membrane






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



Carbon12

6 electrons6 protons6 neutrons

Nucleus

orbital

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



The process of converting an atom or molecule into an ion by adding or remov-ing charged particles such as electrons or ions.

CH2NH3+ COOH CH2NH2 COO -

CH2NH3+ COO -

CH2NH2 COOH

Ionization: amino acid (Glycine)

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



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.

Redical : Reactive Oxygen Species (ROS)

- 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




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 ?

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



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


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+]

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



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

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



Hybridization of carbon

Sp3Tetrahedral

Sp2Trigonal Planar

SpLinear

Methane = Tetrahedral L -and D-isoform

Ethyne = LinearEthane = Trigonal planarCis- and Trans-isoform




L-isoform (left) / D-isoform (right)

CisTrans

Optical isomer / Enantiomer

Geometric isomer




CH3-CH2-CH2-CH2- CH2-CH3

Hexane (C6H14)

Benzene (C6H6)

Cyclohexane (C6H12)




Absorption

Resonance

Fluorescent

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



Lipid ?

PolymerBuilding block

Monosaccharide StarchGlycogen

Nucleotide DNARNA

Amino acid Protein

Organic compound

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


WIKI !!

Review / Important background

Example of Functional groups in Biomolecules

SteroidAmino acid

Nucleotide

Glucose

Cholesterol

Fatty acid

Triglyceride

Phopholipid

Oxidation-reduction (redox) Hydrolysis vs. Condensation Precipitation Addition Elimination Rearrangement Polymerization Substitution Polymerization vs.

Depolemerization etc.




Review / Important background

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

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

Condensation

Hydrolysis

Hydrolysis vs. Condensation

Hydration ≠ Hydrolysis

Elimination

Addition

CH2 CH2Pt

Br2+ CH2 CH2BrBr

CH2 CH2alcohol HCl+CH2 CH2

ClH

KOH

Substitution

A.

B. enzyme

Polymerization vs. Depolymerization

Deoxyribonucleic acids

Protein

DNA,

Enzymes

Deoxy-ribonucleotides

Amino acids

Depolymerization

Enzymes

Enzymes

Enzymes

monomer (building block)

monomer (building block)

(polymer)

(polymer)


- Membrane






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

The smallest object that can undergoes those properties is

Biology

PLant cell

Viral particle

Animal cell

Bacterial cell& Archaea

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.

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

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

How does chemistrybecomes life?

Early life is an anaerobe.

Photosynthesis /Cyano bacteria

Results (after 1 week)Aldehydes, carboxylic acids formedGlycine and alanine formedAmino acidsSugarsPurines & pyrimidinesNB: Chirality 50/50 %

A possible pathways for the synthesis of the cell(a spontaneously-replicating membrane by Szostak, 2001)


- Membrane






WaterPhysical properties: Chemical properties:- Structure - Ionization of water- Polarity - Acid-base chemistry- Acting as Solvent - Buffers- The hydrophobic effect - H-bond- Osmosis and diffusion

Formation of Water

Structure of water

O-H = Covalent bond with bond strength = 460 kJ/mol

Distribution of electron in water

Note that the average electron density around the oxygen atom is about 10x that around the hydrogen atoms.

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.

The polarity also allows water interact with an electric field.

Water in electric field

Water as solvent

Physiological concentration of NaCl 150 mM

Watermolecules Chloride ion (Cl-)

Sodium ion (Na+)

Sodium chloride

Hydrophobic effect

The interactions can hold molecules together: avoiding hydrophobic groups of molecules to interaction with water.

Hydrophobic effect

The interactions can hold molecules together: avoiding hydrophobic groups of molecules to interaction with water.

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.

Effect of water on cellHypotonic solution Isotonic solution Hypertonic solution

Animal cell

Plant cell

Ionization and acid-base properties of water

(hydroxide ion)

(hydronium ion)2 x H2O

HO-

H3O+

auto-ionization of water

• 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.


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+]

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)

H-bond in water

-

-

-

++

+

+

Water : Water

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

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

ชีวเคมีCarbohydrate Nucleic acid ProteinLipid

Anabolism Catabolism

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

NEXT !

Next ! Amino acids and Proteins

Documents

Good Morning Class - WordPress.com · Kinetics The Belousov-Zhabotinsky reaction, a chemical reaction that oscillates in time and space. When a very thin layer of an acidic solution