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PRINSIP BIOKIMIA
(Semester 1 -2012/13)
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BCM 3000 (4+0) (Biokimia Asas) Prof. Dr. Mohd Arif Syed (MAS) -Penyelaras Puan Zetty
Jabatan
Biokimia
Sinopsis
(This course encompasses the main biomolecule components in biochemistry. Metabolism involving the anabolism and catabolism of major biomolecules are also explained)
Learning Outcome
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)
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
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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.
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14. Integration & control o f metabolism. Relationship between carbohydrate, lipid and protein metabolism.
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Kuliah Cuti- Alexandria Cuti Pertengahan Semester Peperiksaan Akhir Cuti Umum
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Stem cell study Cloning of the human being Diseases (defect in metabolism)
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BIOCHEMISTRY: A PROLOGUE
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.
Living organisms
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 interrelated issues. 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 re-produce?
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History of Biochemistry
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 nonliving 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)
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History of Biochemistry
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.
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History of Biochemistry
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.
BIOLOGICAL STRUCTURES
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 a minor fraction of them have been characterized. biochemical understanding of any organism would be a hopelessly difficult task ??
Living things have an underlying regularity that derives from their being constructed in a hierarchical manner.
Tissues
Cells Subcellular organelles Supramolecular assemblies of macromolecules
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Brown important elements purple essential ions dark blue more common trace elements light blue less common trace elements
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Organic compounds
Most of the solid material of cell consists of carboncontaining compounds (organic compounds). The organic compounds of interest is shown
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Functional Groups
These organic compounds have own specific functional groups
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The elements of life are assembled into molecules with common structures and patterns how ??
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BIOPOLYMERS
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
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PROTEINS
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
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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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POLYSACCHARIDES
Composed basically of carbon, oxygen and hydrogen. Monosaccharides simple sugars, polysaccharides polymers. Fischer projection linear molecule.
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Glucose o most abundant six-carbon sugar o Monomer for cellulose, glycogen and starch
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Nucleic acids
o
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Nucleic acids are polymers formed from monomers called nucleotides that are joined in a phosphodiester linkage
Polynucleotideformed by linking phosphate group to C-3 oxygen atom of another nucleotide
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4 types of RNA :
i. mRNA ii. tRNA iii. rRNA iv. heterogenous RNA.
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Bioenergetics
o The study of the changes in metabolic energy
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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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Metabolic Processes
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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Metabolism
categories:
1. Catabolism or degradation, in which nutrients and cell constituents are broken down so as to salvage their com-ponents 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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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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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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An animal cell
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A plant cell
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Water
Properties
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
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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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1. Charge-charge interactions
Electrostatic interactions between two charged particles e.g. NaCl The strongest noncovalent forces Also responsible for mutual repulsion of similarly charged ionic groups
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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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4. Hydrophobic interactions
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 nonpolar groups for each other. Hydrocarbon alkyl groups on ala, val, leu, and ile interact in this way
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Hydrophobic interactions
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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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The pH Scale
A logarithmic scale to measure the concentration of H+.
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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
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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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ACID
= substance that donates proton
a substance which produces hydrogen ions (H+) by dissociation For example
HCl H+ + ClHydrogen ions (H+) associate with water to form H3O+ (Hydronium ion)
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BASE
= can associate with H+ (e.g. NH3) = may produce hydroxide ions (OH- ) either by direct dissociation or subsequent to reaction with water
i.
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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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HAc
H+ + Ac-
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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
Equilibrium constant = Ka
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
IONIZATION OF WATER
H2O + H2O H2O H+ H3O + + OH+ OH (1)
Law of Mass Action to get equilibrium point (the rate of a chemical reaction is directly proportional to the molecular concentrations of the reacting substances ) Keq = [H+] [OH-] ..................... (2) [H2O]
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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Equation (3) becomes log [H+] + log [OH-] = -14 -log [H+] - log [OH-] = 14
i.e. pH + pOH
= 14
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Because
pH = pOH = 7, solution is neutral pH = pOH < 7, solution is acidic pH = pOH > 7, solution is basic
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HENDERSON-HASSELBALCH EQUATION
For weak acid eg. CH3COOH (HA)
HA H+ + A-
Ka = equilibrium constant
HENDERSON-HASSELBALCH EQUATION
log [H+] = log Ka + log [HA] [A-] - log [H+] = - log Ka + log [A-] [HA]
[HA]
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pH = pKa + log [A-] [HA] pH = pKa + log [conjugate base] [conjugate acid]
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This equation is called the HENDERSONHASSELBALCH Equation 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
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