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
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Substance with mass and volume
Substance occupies space
Made up of atoms
Ex. Solid, Liquid, Gas and Plasma
Element
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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
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Smallest unit of the element
Made up of three main subatomic particles (proton, neutron and electron)
Isotope
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Same element which has same number of protons but different number of neutrons
Having same chemical properties due to same number of electrons
Radioisotope
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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
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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
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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
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Unequal sharing of valence electrons
The stronger the electronegativity, the strong pull of shared electrons
Ex. HCL
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Different ends have different electric charged
Cl has more electronegativity so it has strong attraction force
Non-polar covalent
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Equal sharing of valence electrons
Ex. H2, Cl2
Electronegativity
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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
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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
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Weakest intermolecular force
Temporary force which let the atoms to form temporary dipoles
Hold non-polar molecules together
Ex. CH4, Helium, Neon
Dipole-Dipole
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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
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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
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Reaction which split larger molecule into smaller molecules by using water (H2O)
Neutralization
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Reaction which an acid and base combine to product a salt and water
Redox reaction
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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.
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This figure show that water is cohesive and adhesive.
Water has high specific heat capacity
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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
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Water has different density at different temperature and different state.
1.3 The Carbon Chemistry of Life
Functional group
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Hydroxyl (-OH)
Carbonyl (C=O)
Carboxyl (-COOH)
Amino group (NH2)
Sulfhydryl (-SH)
Phosphate (-PO4)
Hydroxyl group (-OH)
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Has OH group
Hydrophilic
Commonly found in alcohols.
Ex. Ethanol
Carbonyl group (C=O)
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Has C=O
Ketone (found in middle)
Aldehyde (found at end)
Hydrophilic
Commonly found in nail polish remover
Carboxyl group (-COOH)
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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)
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Has -NH2 bond
Base (proton acceptor)
Commonly found at amino acid
Sulfhydryl group (-SH)
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-SH
Non-polar
Acidic
Hydrophilic
Commonly found in rubber and amino acid
Phosphate group (-PO4)
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-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)
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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
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Many single sugars bonded together by glycosidic bond and form polysaccharides
Ex. Glycogen, cellulose, starch
Insoluble in water
Very polar
Lipids
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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
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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
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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
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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
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Made up of long hydrocarbon chains attached either carbon rings and alcohol groups
Hydrophobic
Not soluble in water
Ex. Cutin of the leaves
Protein
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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
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Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine
Function of the protein
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To produce antibodies
Produce enzyme
Muscle building
Produce hemoglobin
Structure of the protein
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4 levels of structures (Primary, Secondary, Tertiary and Quaternary)
Amino acids join together by peptide bonds by removal of H2O molecule
Primary Structure
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Amino acids join together by peptide bond
Secondary Structure
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Containing hydrogen bond
Become Alpha-helix and Beta-pleated or sheeted
Tertiary Structure
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Protein starts to work at this level
Ex. Myoglobin (monomer), Hemoglobin (tetramer)
Containing hydrophobic interaction, ionic bond, disulfide bond and hydrogen bond
Quaternary Structure
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Final state of protein
Folded polypeptide chains interact and arrange together to form this structure
Nucleic Acids
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Nucleotide made up of nitrogen base, sugar, phosphate group
Dehydration reaction bonds these nucleotides together
Linked by Phosphodiester bond
Two categories of nitrogenous bases
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Pyrimidines
Purines
DNA
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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
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For protein synthesis
Contain only single strand
Contain ribose sugar
Base pairing is (A-U) (C-G)
Enzyme
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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
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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.
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It provides the alternative route with lower activation energy and increase the rate of
reaction.
Anabolic reaction and catabolic reaction
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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
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Non-protein which binds to an enzyme to assist in catalytic activity
Ex. Iron, Magnesium
Coenzyme
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Organic compounds which required by many enzymes for catalytic activity.
Allosteric activator and allosteric inhibitor (bind to others site of the enzyme)
Allosteric activator
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Bind to other site of enzyme can change the shape of enzyme to activate the reaction of
enzyme
Allosteric inhibitor
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Bind to other site of enzyme can change the shape of enzyme to stop the reaction of
enzyme
Feedback inhibition
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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
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Process to stop or slow the enzyme activity
Competitive inhibitor and Non-competitive inhibitor
Competitive inhibitor
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Inhibitor resemble the substrate and binds to the active site
Prevent the substrate from binding
Non-competitive inhibitor
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Inhibitor binds to different site of the enzyme
Change the active site shape and prevent substrate form binding
Enzyme inhibition
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Binding strength affects the inhibitor’s impact on the enzyme.
Reversible inhibition
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Weak binding by the inhibitor (not-permanent)
Enzyme regains normal function and characteristic when the inhibitor is released.
Irreversible inhibition
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Strong binding by the inhibitor (permanent)
Enzyme can’t regain normal function and characteristic
Enzyme become disable.
Factor Affecting Enzyme Activity
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Concentration of enzyme
Concentration of substrate
pH
Temperature
Enzyme and substrate concentration
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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
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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
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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