UNIT 1 CHAPTER 1: THE BIOCHEMICAL BASIS OF LIFE KHANT MIN PHYO SBI4U Date: 23/12/2024 1.1 The Fundamental Chemistry of Life TERMS Matter • • • • Substance with mass and volume Substance occupies space Made up of atoms Ex. Solid, Liquid, Gas and Plasma Element • • • Pure substance that cannot be broken down into simplest substance Only make up of one type of atom Ex. Hydrogen, Carbon, Oxygen and etc … Atom • • Smallest unit of the element Made up of three main subatomic particles (proton, neutron and electron) Isotope • • Same element which has same number of protons but different number of neutrons Having same chemical properties due to same number of electrons Radioisotope • • Unstable isotope which emits radiation Mainly used in radiotherapy to kill the cancerous cells TYPE OF CHEMICAL BONDS Two different interactions of molecules: 1. Intramolecular bonds (interaction within molecules) 2. Intermolecular bonds (interaction between molecules) Intramolecular bonds Intermolecular bonds Covalent bonds Hydrogen bonds Ionic bonds Van Der Waal forces Polar covalent bonds Other Van Der Waal forces Ionic Bonds • • • Electrostatic force of attraction between oppositely charged ions such as cation and anion This attraction mostly forms between metal and non-metal Having strong attraction force and requires high energy to overcome Ex. Sodium Chloride Covalent Bonds • • • Electrostatic force of attraction between share pair of valence electrons and nuclei from each atom to create stability This attraction mostly forms between two or more non-metal The strength of the bond is determined by the electronegativity of the atoms Two types of covalent bonds: 1. Polar covalent bonds (Soluble in water) 2. Non-polar covalent bonds (Not soluble in water) Polar covalent • • Unequal sharing of valence electrons The stronger the electronegativity, the strong pull of shared electrons Ex. HCL • • Different ends have different electric charged Cl has more electronegativity so it has strong attraction force Non-polar covalent • • Equal sharing of valence electrons Ex. H2, Cl2 Electronegativity • The measure of an atom’s attraction to shared electrons Type of bonds Electronegativity difference Non-polar 0-0.5 Polar 0.5-1.7 Ionic bond >1.7 Van Der Waal Force • • • • Having very weak attraction between the molecules Intermolecular force Provide interaction between water molecules Force strength determined the solubility, melting and boiling point Type of Van Der Waal Force: 1. London Dispersion 2. Dipole-Dipole Force 3. Hydrogen Bonds London Dispersion • • • • Weakest intermolecular force Temporary force which let the atoms to form temporary dipoles Hold non-polar molecules together Ex. CH4, Helium, Neon Dipole-Dipole • • • • This force only occurs between the polar molecules Partially positive end of one molecule is attracted to the partially negative end of another molecule This force is stronger than London Dispersion force Ex. Attraction between two HCL molecule Hydrogen bonds • • • Special type of dipole-dipole interaction that one hydrogen atom (partially positive) in water molecule is bonded to another partially electronegative atom(oxygen) in other water molecule Having a strongest intermolecular force Ex. Attraction between water molecules How to find the electronegativity of each element? This is Pauling Scale find the electronegativity of the element Chemical reaction Dehydration • Reaction that joins two molecules together by removing a water molecule (H2O) to form a larger molecule • Also known as condensation reaction Hydrolysis • Reaction which split larger molecule into smaller molecules by using water (H2O) Neutralization • Reaction which an acid and base combine to product a salt and water Redox reaction • • • Oxidation is the loss of electrons Reduction is the gain of electrons Both reduction and oxidation occurred at the same time mean it is redox reaction 1.2 Water: Life’s solvent Properties of the water 1. Cohesion 2. Adhesion 3. High specific heat capacity 4. High solubility 5. Has range of densities Cohesion in water • Water molecules are bonded to each other due to hydrogen bond, so this bond keep the water molecule compactly and prevent separation. • Water molecules stick together by the hydrogen bond • Water has high surface tension due to cohesion Adhesion in water • Water molecules are polar so that they can attach with others polar surface by dipoledipole attraction • Ex. In plant xylem the water is attach to the wall by adhesion. • This figure show that water is cohesive and adhesive. Water has high specific heat capacity • As water has a high specific heat capacity, so water can absorb a lot of heat to break the hydrogen bond and change form liquid state to gas state Water has a range of density • Water has different density at different temperature and different state. 1.3 The Carbon Chemistry of Life Functional group 1. 2. 3. 4. 5. 6. Hydroxyl (-OH) Carbonyl (C=O) Carboxyl (-COOH) Amino group (NH2) Sulfhydryl (-SH) Phosphate (-PO4) Hydroxyl group (-OH) • • • Has OH group Hydrophilic Commonly found in alcohols. Ex. Ethanol Carbonyl group (C=O) • • • • • Has C=O Ketone (found in middle) Aldehyde (found at end) Hydrophilic Commonly found in nail polish remover Carboxyl group (-COOH) • • • • Has carbon double bonded with oxygen and a hydroxyl group Acidic (proton donor) Hydrophilic Commonly found at organic acid (fatty acid, amino acid) Amino group (-NH2) • • • Has -NH2 bond Base (proton acceptor) Commonly found at amino acid Sulfhydryl group (-SH) • • • • • -SH Non-polar Acidic Hydrophilic Commonly found in rubber and amino acid Phosphate group (-PO4) • • • • • -PO4 Non-polar Acidic Hydrophilic Commonly found in nucleic acid Carbohydrates • Made up of Carbon, Hydrogen, Oxygen Structure of the Carbohydrate 1. Monosaccharides 2. Disaccharides 3. Polysaccharides Monosaccharides (single sugar) • • • • Simplest form of carbohydrates Building block for carbohydrate Soluble in water Ex. Glucose, fructose Disaccharides (two sugars) • Two monosaccharides joined by a glycosidic bond through dehydration • Ex. Sucrose, Lactose, Maltose Glycosidic bond Polysaccharides • • • • Many single sugars bonded together by glycosidic bond and form polysaccharides Ex. Glycogen, cellulose, starch Insoluble in water Very polar Lipids • • • • Made up with carbon, hydrogen, and oxygen, nitrogen, sulfur, and phosphorus. Non polar Insoluble in water Used as energy store Main type of lipid: fatty acid, fats, phospholipids, steroids, waxes, triacylglycerol 1. Fatty acid • • • • • Consists of two main parts hydrocarbon chain and carboxyl group (-COOH) Typically has rage from 4 to 22 carbon atoms Solubility decreases as the chain length increases Ex. Stearic acid_ Saturated fatty acid_ no double bond Ex. Oleic acid_ Unsaturated fatty acid_ contain double bonds 2. Fats • • • Made up of a glycerol molecule and fatty acid Formed by dehydration synthesis One glycerol molecule attached to three fatty acids via ester bond (Triglycerides) Triacylglycerols 3. Phospholipids • • Made up of two fatty acid, one glycerol and phosphate group Phosphate group is hydrophilic and fatty acid is hydrophobic 4. Steroids • Composed of four carbon rings • Most steroid contain sterol structure • Cholesterol is the simplest form of steroids • Sex hormone such as testosterone, progesterone are steroids 5. Waxes • • • Made up of long hydrocarbon chains attached either carbon rings and alcohol groups Hydrophobic Not soluble in water Ex. Cutin of the leaves Protein • • Protein is made up of many amino acid Function: for muscle growth and repair There are 20 amino acids but 9 of them are essential (which can only get form diet and not supply by the body 1. 2. 3. 4. 5. 6. 7. 8. 9. Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan Valine Function of the protein • • • • To produce antibodies Produce enzyme Muscle building Produce hemoglobin Structure of the protein • • 4 levels of structures (Primary, Secondary, Tertiary and Quaternary) Amino acids join together by peptide bonds by removal of H2O molecule Primary Structure • Amino acids join together by peptide bond Secondary Structure • • Containing hydrogen bond Become Alpha-helix and Beta-pleated or sheeted Tertiary Structure • • • Protein starts to work at this level Ex. Myoglobin (monomer), Hemoglobin (tetramer) Containing hydrophobic interaction, ionic bond, disulfide bond and hydrogen bond Quaternary Structure • • Final state of protein Folded polypeptide chains interact and arrange together to form this structure Nucleic Acids • • • Nucleotide made up of nitrogen base, sugar, phosphate group Dehydration reaction bonds these nucleotides together Linked by Phosphodiester bond Two categories of nitrogenous bases • • Pyrimidines Purines DNA • • • • • Contain genetic information Has double strands Contain deoxyribose sugar The bases are linked by hydrogen bonds according to complementary base paring Base paring is (A-T) (G-C) RNA • • • • For protein synthesis Contain only single strand Contain ribose sugar Base pairing is (A-U) (C-G) Enzyme • • • • • Biological catalyst which speeds up the reaction Having unite shape and shape determines which reaction it catalyzes Having a specific site for particular substrate (reactant) Enzyme-substrate complex Enzymes can break molecule into two parts (products) Induced-fit Enzyme Model • • The enzyme active site is not perfect with the substrate initially. The enzyme confirms the shape of substrate and change in the enzyme shape and become fit between the enzyme and the substrate. How enzyme speed up the reaction. • It provides the alternative route with lower activation energy and increase the rate of reaction. Anabolic reaction and catabolic reaction • • Anabolic occur when two molecules join together due to enzyme-substrate complex Catabolic occurs when two molecules split apart due to enzyme-substrate complex Cofactors and Coenzymes Cofactor • • Non-protein which binds to an enzyme to assist in catalytic activity Ex. Iron, Magnesium Coenzyme • Organic compounds which required by many enzymes for catalytic activity. Allosteric activator and allosteric inhibitor (bind to others site of the enzyme) Allosteric activator • Bind to other site of enzyme can change the shape of enzyme to activate the reaction of enzyme Allosteric inhibitor • Bind to other site of enzyme can change the shape of enzyme to stop the reaction of enzyme Feedback inhibition • • • A regulatory mechanism where the end product of a reaction pathway controls its own production by acting as a regulator. Acts as an inhibitor, slowing or stopping the first enzyme, if the product is in excess Reduces inhibition and speed up the pathway if the product in scarce Enzyme inhibition • Process to stop or slow the enzyme activity Competitive inhibitor and Non-competitive inhibitor Competitive inhibitor • • Inhibitor resemble the substrate and binds to the active site Prevent the substrate from binding Non-competitive inhibitor • • Inhibitor binds to different site of the enzyme Change the active site shape and prevent substrate form binding Enzyme inhibition • Binding strength affects the inhibitor’s impact on the enzyme. Reversible inhibition • • Weak binding by the inhibitor (not-permanent) Enzyme regains normal function and characteristic when the inhibitor is released. Irreversible inhibition • • • Strong binding by the inhibitor (permanent) Enzyme can’t regain normal function and characteristic Enzyme become disable. Factor Affecting Enzyme Activity 1. 2. 3. 4. Concentration of enzyme Concentration of substrate pH Temperature Enzyme and substrate concentration • • • • Rate of reaction increase with substrate concentration when enzyme levels are constant Enzyme concentration limits the reaction rate. If substrate increase, rate of reaction increase If the substrate excess, enzyme become saturated and the rate levels off. pH • • Each enzyme works at their own optimum pH If pH is different from their enzyme will denature and slow down the rate of reaction. Temperature • • • Enzymes are work best at 37C which is body temperature (optimum temperature) If beyond the optimum temperature, the enzyme will become denature. Some enzymes have different optimum temperature
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