BCH 3000

PRINSIP BIOKIMIA

(Semester 1 -2012/13)

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Kod/Nama Kursus : BCM 3000 (4+0) (Biokimia Asas)

Nama Pensyarah : Prof. Dr. Mohd Arif Syed (MAS) -Penyelaras

Puan Zetty

Jabatan : Biokimia

Jadual Kuliah ( Masa dan Tempat) : SK 10-12; DKBiotek 1.1

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(This course encompasses the main biomolecule

components in biochemistry. Metabolism

involving the anabolism and catabolism of

major biomolecules are also explained)

Sinopsis

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1. Membezakan struktur dan fungsi biomolekul yang terdapat dalam sistem biologi (C4)

2. Menyatakan pelbagai proses metabolisme yang utama (P2)

3. Menerangkan tindakbalas biokimia (A3)

4. Menyelesaikan masalah dalam metabolisme biomolekul dengan menggunakan maklumat dari pelbagai sumber (CTPS, LL)

Learning Outcome

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1. Introduction-Biochemistry? Contributions? Important life components

2. Carbohydrates – Classification – mono, di polysaccharides – Structure –configuration & stereochemistry; reactions – glucose and other sugars

3. Amino acid & protein – biological roles, structure, classification, reactions, analysis. Peptides – primary, secondary, tertiary and quaternary structures

4. Lipid –functions & distribution, characteristics of fatty acids-saturated & unsaturated f/acids. Structures & characteristics of triacylglycerols, phospholipids, sphingolipids, terpenes & steroids

Brief Lecture Contents

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5. Nucleic acids – components – purines, pyrimidines. Structure, reactions & importance of nucleosides, nucleotides & polynucleotides. DNA, RNA – structure, functions & types

6. Enzymology – Classification, naming, active sites. Enzyme kinetics. Factors affecting enzyme activity- enzyme & substrate concentration, pH, temperature . Substrate specificity – single & multiple substrate. Enzyme inhibitors – competitive, con-competitive, uncompetitive. Control of enzyme reactions – product inhibition, Isoenzymes, multienzyme system and allosteric enzymes

Brief Lecture Contents

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7. Carbohydrate metabolism – Metabolic energy cycle –Bioenergetics: ATP other high energy compounds. Storage & energy transfer. Glycolysis & fermentation. Electron transport system. Compartmentation & mitochondria. Phosphorylation & production of ATP. Anaplerotic reactions. Glyoxylate cycle. Gluconeogenesis. Pentose phosphate pathway. Integration and control.

8. Photosynthesis – Fixation of CO2 during photosynthesis. Chlorophyll, components of photosynthesis. Photosystem I & II. Photophosphorylation. Calvin cycle. Hatch-Slack cycle.

Brief Lecture Contents

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9. Lipid metabolism – Lipid oxidation- Enzymes involved, energy production. Oxidation of saturated & branched fatty acids. Formation of ketone bodies. Lipid biosynthesis –mitochondrial system and extra-mitochondrial. Cycle & enzymes involved. Synthesis of saturated & unsaturated fatty acids. Cholesterol synthesis & control.

10. Protein & amino acid metabolism – Degradation of amino acids- transamination, deamination, decarboxylation. Cycle involved- intermediates for the TCA cycle. Ammonia and urea metabolism. Biosynthesis of amino acids- role in the metabolism of porphyrin and nucleic acids. Nitrogen fixation.

Brief Lecture Contents

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11. Nucleic acid metabolism – synthesis of mononucleotides – purines, pyrimidines – cycle and enzymes involved; control. Biosynthesis of ribo & deoxyribonucleotides. Characteristics of genetic materials – chromosomes. Genetic code, base sequence. DNA replication. DNA repair. Protein synthesis – ribosome, co-factor involved & phase of synthesis. Inhibition and control of synthesis.

12. Membrane Biochemistry – Modification & structure. Model for membrane structure. Transport mechanism across membrane – passive & active transport.

Brief Lecture Contents

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13. Hormones- Introduction to plant & animal hormones. Reactions & control of endocrine hormones. Hormone reactions at the molecular level.

14. Integration & control o f metabolism. Relationship between carbohydrate, lipid and protein metabolism.

Brief Lecture Contents

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BCH3000 - SKEDUL KULIAH

Sep-12 Oct-12 Nov-12MINGGU 1 2 3 4 5 6 7 8 9 10 11 12

Monday 3 10 17 24 1 8 15 22 29 5 12 19 26

Tuesdsay 4 11 18 25 2 9 16 23 30 6 13 20 27

Wednesday 5 12 19 26 3 10 17 24 31 7 14 21 28

Thursday 6 13 20 27 4 11 18 25 1 8 15 22 29

Friday 7 14 21 28 5 12 19 26 2 9 16 23 30

Saturday 1 8 15 22 29 6 13 20 27 3 10 17 24

Sunday 2 9 16 23 30 7 14 21 28 4 11 18 25

Dec-12 Jan-13 Feb-13MINGGU 13 14 15

Monday 31 3 10 17 24 7 14 21 28 4 11 18 25

Tuesdsay 4 11 18 25 1 8 15 22 29 5 12 19 26

Wednesday 5 12 19 26 2 9 16 23 30 6 13 20 27

Thursday 6 13 20 27 3 10 17 24 31 7 14 21 28

Friday 7 14 21 28 4 11 18 25 1 8 15 22

Saturday 1 8 15 22 29 5 12 19 26 2 9 16 23

Sunday 2 9 16 23 30 6 13 20 27 3 10 17 24

KuliahCuti- AlexandriaCuti Pertengahan SemesterPeperiksaan AkhirCuti Umum

● Part of curriculum

● Explain a lot of the controversies in the news at the moment.

Stem cell study

Cloning of the human being

Diseases (defect in metabolism)

GM food and organisms (genetically modified)

Why study biochemistry?

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Biochemistry = the chemistry of life.

● bridges the gap between chemistry (the study of the structures and interactions of atoms and molecules) and biology (the study of the structures and interactions of cells and organisms).

● Since living things are composed of inanimate molecules, life, at its most basic level, is a biochemical phenomenon.

Inert; not living; not lively

BIOCHEMISTRY: A PROLOGUE

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● diverse in their macroscopic properties

● BUT remarkable similarity in their biochemistry that provides a unifying theme with which to study them.

◊ For example, hereditary information is encoded and expressed in an almost identical manner in all cellular life

◊ the series of biochemical reactions= metabolic pathways, as well as the structures of the enzymes that catalyze them are, for many basic processes, are nearly identical from organism to organism.

Living organisms

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This strongly suggests that all known life forms are descended from a single primordial ancestor in which these biochemical features first developed

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Although biochemistry is a highly diverse field, it is largely concerned with a limited number of interrelatedissues. These are

1. What are the chemical and three-dimensional structures of biological molecules and assemblies, how do they form these structures, and how do their properties vary with them?

2. How do proteins work?- what are the molecular mechanisms of enzymatic catalysis, how do receptors recognize and bind specific molecules, and what are the intramolecular and intermolecular mechanisms by which receptors transmit information concerning their binding states?

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3. How is genetic information expressed and how is it transmitted to future cell generations?

4. How are biological molecules and assemblies synthesized?

5. What are the control mechanisms that coordinate the myriads of biochemical reactions that take place in cells and in organisms?

6. How do cells and organisms grow, differentiate, and re­produce?

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● fairly new field of science -the 20th century

● first landmark of biochemistry - Friedrich Wohler (1828) synthesized the organic compound urea from the inorganic compound ammonium cyanate

● building blocks of life were the same as those of non-living things

● The role of enzymes as catalyst - Buchner showed that a process of biochemistry, catalysis, could occur independently from living cells (enzymes in yeast extracts and fermentation)

History of Biochemistry

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● Fischer developed the lock and key model (enzyme as rigid lock, substrate as key) A modified version of this model (induced fit) is still used today

● The second part of the 20th century saw advances in structural biology especially the structure of proteins

● The first protein structures were determined by John C. Kendrew and Max Perutz in the 1950s and 1960s.

● Now have determined the structures of more than 1000 proteins.

History of Biochemistry

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● The role of nucleic acid as information molecules

In 1944 Oswald Avery et al extracted DNA from a toxic strain of a bacteria and when added to a nontoxic strain resulted in the bacteria being transformed into a virulent strain.

Watson and Crick (1950) deduced the 3D structure of DNA.

Crick predicted that information encoded in DNA is transcribed to ribonucleic acid and then translated to protein.

This unidirectional information flow is referred to as the central dogma of molecular biology

History of Biochemistry

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Living things are enormously complex.

● simple E. coli cell contains some 3 to 6 thousand different compounds, most of which are unique to E. coli ; Homo sapiens (human beings), may contain 100,000 different types of molecules, although only aminor fraction of them have been characterized.

● biochemical understanding of any organism would be a hopelessly difficult task ??

No !!!! - Why ????

BIOLOGICAL STRUCTURES

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Living things have an underlying regularity that derives from their being constructed in a hierarchical manner.

Multicellular organisms

Organizations of organs

Tissues

Cells

Subcellular organelles

Supramolecular assemblies of macromolecules 23

An example of hierarchical organization of biological structures

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What makes a living thing?

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● Only six nonmetallic elements make up 97% of the weight of most organisms – carbon, oxygen, hydrogen, nitrogen, phosphorous and sulfur.

● All form stable covalent bonds.

● here are also 5 common ions found in all organisms: - Calcium (Ca2+), Potassium (K+) Sodium (Na+), Magnesium (Mg2+), Chloride (Cl-)

● Water is a major component of cells.

● Altogether, a total of 29 different elements are commonly found in living organisms.

The Chemical Elements of Life

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Brown – important elementspurple – essential ionsdark blue – more common trace elementslight blue – less common trace elements

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● Most of the solid material of cell consists of carbon-containing compounds (organic compounds).

● The organic compounds of interest is shown

Organic compounds

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● These organic compounds have own specific

functional groups

Functional Groups

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● The elements of life are assembled into molecules with common structures and patterns – how ?? –

via linkages (bonds)

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The polymeric organization of proteins, nucleic acids an dpolysaccharides

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● they are formed from smaller molecules called monomers that are linked together in a sequential way to form long chains

● After being joined together, the individual monomers in a chain are referred to as residues

● There are various levels in the hierarchy of life i.e. atoms, molecules, biopolymers, organelles, cells, tissues, organs and whole organisms

BIOPOLYMERS

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An example of a biopolymer

● polymers formed from the condensation of individual monomers called amino acids

● Twenty amino acids are incorporated into proteins in all cells

● Each amino acid contains an amino group and a carboxylate group and a side chain (R group).

● The amino group from one amino acid reacts with the carboxylate group of the other to form an amide linkage that is referred to as a peptide bond

PROTEINS

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● Many amino acids joined in this manner is called a polypeptide ( have N and C terminal

● The amino acids are combined in a specific sequence to produce proteins consisting of hundreds or thousands of amino acid residues

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● A functional protein consist of one polypeptide or several different polypeptides tightly bound together.

● Proteins function as either enzymes or structural components of cells and organisms.

● The function of a protein depends on the 3D structure or conformation.

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BCM 3000

PRINSIP

BIOKIMIA

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● Composed basically of carbon, oxygen and hydrogen.

● Monosaccharides – simple sugars, polysaccharides –polymers.

● Fischer projection – linear molecule.

● Haworth projection – ring form (usual biochemical form).

● Ribose – approx. 20 conformations

POLYSACCHARIDES

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● Glucose –

o most abundant six-carbon sugar

o Monomer for cellulose, glycogen and starch

o Differ in bonding between C-1 of the monomer to the next

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● Biopolymers of monomers called nucleotides.

● Nucleotides – five-carbon sugar, heterocyclic nitrogen base and at least one phosphate.

o Five – carbon sugar (ribose and deoxyribose).

o Base (purines and pyrimidines).

Purines – adenine (A) and guanine (G).

Pyrimidines (cytosine ( C), thymine (T) and Uracil (U)

Nucleic acids

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Nucleic acids are polymers formed from monomers called nucleotides that are joined in a phosphodiester linkage

Polynucleotide-formed by linking phosphate group to C-3 oxygen atom of another nucleotide

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1. DNA

● uses deoxyribose sugars

● Usually double stranded

2. RNA

● Uses ribose sugars

● Usually single stranded

● 4 types of RNA :

i. mRNAii. tRNAiii. rRNAiv. heterogenous RNA.

Examples of nucleic acids

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● Diverse class of compounds rich in carbon and hydrogen (low in oxygen).

Fatty acids, glycerophospholipids, wax and beeswax.

● Most lipids not soluble in water.

● In membranes lipid are polar - hydrophilic water loving head and hydrophobic (water fearing) tail.

● Form bi-layer membrane system.

Lipids and Membranes

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● Life requires input of energy – ultimately from the sun

● Metabolism

Describes the numerous reactions in which organic compounds are synthesized and degraded and useful energy is extracted, stored and used.

Bioenergetics

o The study of the changes in metabolic energy

The Energetics of Life

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● DG – the free-energy change for a reaction is the difference between the free energy of the product and the free energy of the reactants.

DG = DH - T DS

where

DH is the change in heat content (enthalpy change)

DS is the change in randomness (entropy change)

T is the temperature in Kelvin.

DG < 0 reaction is spontaneous

DG > 0 reaction requires input of energy

DG = 0 reaction is at equilibrium.

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● Many many types of chemical reactions simultaneously occur in any living cell.

● Yet, these reactions follow a pattern that organizes

them into the coherent process we refer to as life.

o For instance, most biological reactions are members of a metabolic pathway - sequence of reactions that produce one or more specific products.

o Moreover, the rates of its reactions are so tightly regulated that there is rarely an unsatisfied need for a reactant in a metabolic pathway or an unnecessary buildup of some product.

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Metabolic Processes

Metabolism - traditionally divided into two major

categories:

1. Catabolism or degradation, in which nutrients and cell constituents are broken down so as to salvage their com­ponents and/or to generate energy.

2. Anabolism or biosynthesis, in which biomolecules are synthesized from simpler components

The energy required by anabolic processes is provided by catabolic processes largely in the form of adenosine triphosphate (ATP).

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● Deoxyribonucleic acid (DNA) is the cell's master repository of genetic information

● Genetic information is encoded in the sequence of these bases.

● The division of a cell must be accompanied by the replication of its DNA.

◊ each DNA strand acts as a template for the formation of its complementary strand

◊ every progeny cell contains a complete DNA molecule each of which consists of one parental strand and one daughter strand. Mutations arise when, through rare copying errors or damage

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Expression and Transmission of Genetic Information

repository is a place where data or specimens are stored and maintained for future retrieval.

Encoded - prearranged; programmed, determined, set,preset

Replication - duplication,copying, reproduction

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Cells are classified as eukaryotes or prokaryotes

1. Prokaryotes (bacteria)

Ubiquitous, no nucleus, only approx 1000 genes

2. Eukaryotes (plants, animals, fungi and protists)

Membrane bound nucleus, 1000 fold greater in volume.

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The cell is the basic unit of life

An animal cell53

A plant cell54

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● All living cells depend on water for their existence.

● Metabolic machinery of cells has to operate in an aqueous environment

● Water molecule – polar

● Water molecule is V-shaped with an angle of 104.5O

Properties

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Water

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Oxygen atom

● has 8 electrons with 6 in the outer shell

● The outer shell can accommodate 4 sp3 orbitals.

2 lone pairs containing 2 electrons each and 2 orbitals which can share their electron with the electron in hydrogen

an oxygen atom covalently bonded to two hydrogen atoms

It has a tetrahedral bond structure that results from 4 sp3 hybridized orbitals

● The oxygen nucleus attracts electrons more strongly than the single proton in hydrogen nucleus

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Tetrahedral bond structure of water 60

● There is a small negative charge on oxygen (d-) and a

small positive charge on the hydrogen (d+)

● Water forms hydrogen bonding (up to 4 hydrogen bondings)

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There are 4 types of noncovalent interactions.

1. Charge-charge interactions

● Electrostatic interactions between two chargedparticles e.g. NaCl

● The strongest noncovalent forces

● Also responsible for mutual repulsion of similarly charged ionic groups

Noncovalent Interactions in Biomolecules

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2. Hydrogen bonds

● A type of electrostatic interaction which occurs in many macromolecules

● Among the strongest noncovalent forces in biological systems

● Strong enough to confer structural stability but weak enough to be readily broken.

● Can form when a hydrogen covalently bonded to a strong electronegative atom, such as nitrogen, oxygen and sulfur

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Hydrogen bonding

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● Weak intermolecular forces produced between all neutral atoms by transient electrostatic interactions

● Have attractive and repulsive components

● forces that exist between MOLECULES of the same substance

3. Van der Waals Forces

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Van der Waals Forces

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● The association of a relatively nonpolar molecule or group in aqueous solution with other nonpolar molecules rather than with water

● The non-polar groups mutually repel water and other polar groups and results in a net attraction of the non-polar groups for each other. Hydrocarbon alkyl groups on ala, val, leu, and ile interact in this way

4. Hydrophobic interactions

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Hydrophobic interactions69

Ionization of Water

● Important property of water – slight tendency to ionize.

● Pure water consist of H2O and small quantity of hydronium ions (H3O+) and hydroxide ions (OH-)

● Important property of water – slight tendency to ionize.

● Pure water consist of H2O and small quantity of hydronium ions (H3O+) and hydroxide ions (OH-)

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A logarithmic scale to measure the concentration of H+.

The pH Scale

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AIR – H2O

Medium for biological system

need to know the role in the degradation/dissociation of ions from biomolecules

Water = neutral molecule, but it can ionise –

AIR – H2O

From the dissociation/ionization of water equation

pH = -log [H+]

ie. pH = negative log of hydrogen ion (H+) concentration

pOH = negative log of hydroxyl ion (OH-) concentration

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= substance that donates proton

a substance which produces hydrogen ions (H+) by dissociation

For example

HCl H+ + Cl-

Hydrogen ions (H+) associate with water to form H3O+ (Hydronium ion)

ACID

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= Substances that receive proton

= can associate with H+ (e.g. NH3)

= may produce hydroxide ions (OH- ) either by direct dissociation or subsequent to reaction with water

i. KOH K+ + OH-

NH3 + H2O NH4OH NH4+ + OH-

BASE

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STRONG ACIDS are compounds that dissociate (ionize)

almost 100% in an aqueous solution.

HCl H+ + Cl-

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The common acids that are almost one hundred percent ionized are:

HNO3 - nitric acid

HCl - hydrochloric acid

H2SO4 - sulfuric acid

HClO4 - perchloric acid

HBr - hydrobromic acid

HI - hydroiodic acid

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WEAK ACIDS = Substances that dissociate

partially

HAc H+ + Ac-

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LiOH - lithium hydroxide

NaOH - sodium hydroxide

KOH - potassium hydroxide

RbOH - rubidium hydroxide

CsOH - cesium hydroxide

Mg(OH)2 - magnesium hydroxide

Ca(OH)2 - calcium hydroxide

Sr(OH)2 - strontium hydroxide

Ba(OH)2 - barium hydroxide

Examples of strong bases

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When a weak acid or base dissociates in an aqeous solution, will get an equilibrium between the acid and its conjugate base. This equilibrium is called

Using this equilibrium and taking into consideration the equation for the dissociation of weak acid, will get an important equation called the Henderson-Hasselbalch equation

pH = pKa + log [A-]

[HA]

Equilibrium constant = Ka

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H2O + H2O H3O + + OH-

H2O H+ + OH ………… (1)

Law of Mass Action to get equilibrium point

Keq = [H+] [OH-] ..................... (2) [H2O]

Keq = Equlibrium constant

[ ] = concentration in mole/liter (M)

(the rate of a chemical reaction is directly proportional to the molecular concentrations of the reacting substances )

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IONIZATION OF WATER

If we know the value of Keq pure water can determine the values of [H+] dan [OH-]

Keq for pure water = 1.8 x 10-16M

[Water] = 55.5M

1.8 x 10-16 = [H+] [OH-]55.5M

[H+] [OH-] = 1.0 x 10-14M .................... (3)

[H+] = [OH-] – equation (1)

[H+] = [OH-] = 1.0 x 10-14M

= 1.0 x 10-7M

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In exponential form - (1.0 x 10-7M) too small

Simpler method – use - Svenson – pH dan pOH

pH = -log [H+]

pOH = -log [OH-]

Equation (3) becomes

log [H+] + log [OH-] = -14

-log [H+] - log [OH-] = 14

i.e. pH + pOH = 14

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Because [H+] = [OH-]pH = pOH = 7

pH = pOH = 7, solution is neutral

pH = pOH < 7, solution is acidic

pH = pOH > 7, solution is basic

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For weak acid eg. CH3COOH (HA)

HA H+ + A-

In equilibrium conditions

Ka = [H+][A-]

[HA]

Ka = equilibrium constant

[H+] = Ka [HA]

[A-]

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HENDERSON-HASSELBALCH EQUATION

log [H+] = log Ka + log [HA][A-]

- log [H+] = - log Ka + log [A-][HA]

- log [H+] = pH ; -log Ka = pKa

pH = pKa + log [A-]

[HA]

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HENDERSON-HASSELBALCH EQUATION

pH = pKa + log [A-]

[HA]

pH = pKa + log [conjugate base]

[conjugate acid]

pH = pKa + log [proton acceptor]

[proton donor]

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This equation is useful to determine

1. the amount of acid

2. the amount of base or

3. the amount of salt required to prepare a

buffer with the pH that we want

This equation is called the HENDERSON-HASSELBALCH Equation

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