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2 CHEMICAL FOUNDATION OF LIFE

2.1 Properties of water

•biological medium on Earth•Cells surrounded by water (70- 95%)•main reason the Earth is habitable

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2.1.1 Polarity of water and hydrogen bonding

• a polar molecule

• form hydrogen bonds with each other

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• Oxygen is more electronegative than hydrogen

• Oxygen – 2 partial negative charge (-)• Hydrogen - partial positive charge (+)• negative and positive attract each other.• forces of attraction (between water

molecules) = hydrogen bonds. (pg.47-48)

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2.1.2 Heat Capacity

• Specific heat - amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1ºC

• minimizes temperature fluctuations• Heat is absorbed • Heat is released

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Importance• heats up more slowly & hold its

temperature longer • major component in bodies of living

organisms • Biochemical reactions • Aquatic environments have relatively

stable temperatures. (previous notes)

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2.1.3 Heat of vaporization

• transformation of a substance from liquid to gas

• the heat a liquid must absorb for 1 gram to be converted to gas

• remaining surface cools - evaporative cooling

• helps stabilize temperatures

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Importance• cooling mechanism during sweating and

during transpiration.• Large amount of heat is lost during

evaporation - minimal lost of water (previous notes)

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2.1.4 Density

• Ice floats - hydrogen bonds more “ordered,” making ice less dense

(Figure 3.5, pg.50 - 51)

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• Density of water decreases - between 4C and 100C.

• density of water increases - between 0C and 4C.

• Maximum density is at 4C • liquid water - hydrogen bonds are not

stable, constantly break and reform• Below 0ºC (H bonds are more stable); H

bonds are locked into crystal latticework (molecules relatively far) to form ice (less dense and float) (previous notes)

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2.1.5 Solvent Properties

• versatile solvent due to its polarity• an effective solvent - forms hydrogen

bonds • ion is surrounded by a sphere of water

molecules, a hydration shell (Figure 3.6, pg.51)• dissolve nonionic polar molecules• Hydrophilic- has an affinity for water• Hydrophobic- does not have an affinity for

water

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2.1.6 Adhesion and Cohesion

• Cohesion- hydrogen bonds hold water molecules together

• Plants- helps transportation of water against gravity

• Adhesion of water to plant cell walls also helps to counter gravity

• Surface tension - measure of how hard it is to break the surface of a liquid

• related to cohesion (Figure 3.3 & 3.4, pg.48-49)

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Importance• aquatic organisms to land and “walk” on water.

– Water sticks strongly to most surfaces.Capillary action- glass tube with a narrow diameter is placed in

a beaker of water, the water will rise in the tube.

– Adhesion of water to the glass surface pulls the water upward because an adhesive force is stronger than the force of gravity.

(previous notes)

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2.1.7 Viscosity

• a measure of a fluid's resistance to flow• very low viscosity.Importance• Transport systems of living organisms.• For example, blood is mostly water - can

flow easily through vessels.• flow of water in xylem and phloem to

transport substances.• Less energy used by aquatic organisms

when swimming in water.

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2.1.8 Other properties

• Colorless and transparent: Transmission of sunlight is possible – aquatic plants can photosynthesize.

• Difficult to compress: Important structural agent - hydrostatic skeleton.

• Involved in many chemical reactions: Major raw material for photosynthesis; takes part in digestive reactions, breaking down food molecules by hydrolysis.

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2.2 The Chemistry of Carbon2.2.1 Definition of organic compound

• Organic compounds = compound containing carbon, can come from living and non-living sources

• Cells- carbon-based compounds• unparalleled • ability to form large, complex, and diverse

molecules• Proteins, DNA, carbohydrates

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2.2.2 Structure of carbon and formation of covalent bond in carbon• Electron configuration • four valence electrons - can form four

covalent bonds• tetravalence makes large, complex

molecules possible• covalent compatibility with many different

elements• Carbon chains - skeletons of most organic

molecules

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• vary in length and shape (Figures 4.3, 4.4, 4,5, pg. 60-61)

• properties of organic –carbon skeleton & component attached to it

• Functional groups- components of organic molecules involved in chemical reactions

• The number and arrangement of functional groups- unique properties (Figure 4.10, pg. 64-65)

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2.2.3 Macromolecules

• larger molecules• composed of thousands of covalently connected

atoms• Polymer- long molecule consist of building blocks

called monomers• polymers:

– Carbohydrates– Proteins– Nucleic acids

• Monomers form larger molecules- condensation (dehydration reaction)

• Polymers are disassembled to monomers- by hydrolysis (Figure 5.2, pg. 69)

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2.3 Important Organic Compounds2.3.1 Carbohydrates

• sugars and the polymers of sugars• Simplest- monosaccharides, or single sugars• Macromolecules- polysaccharides• Monosaccharides - molecular formulas (CH2O)• Glucose- common monosaccharide• classified by carbonyl group location and number

of carbons • major fuel for cells and raw material for building

molecules • linear skeleton• Ring form

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glucose maltoseglucose

glucose fructose sucrose

Dehydration reaction in synthesis of maltose

Dehydration reaction in synthesis of sucrose

•A disaccharide - dehydration reaction joins two monosaccharides •covalent bond - glycosidic linkage

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• Polysaccharides - polymers of sugars• storage and structural roles• determined by its monomers and positions

of glycosidic linkages• storage polysaccharide1 plants- starch - consists entirely of glucose

monomers (- glycosidic) 2 animals- glycogen (- glycosidic) (Figure 5.6, pg.72)

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• Cellulose- component of plant cell wall• polymer of glucose, but the glycosidic linkages

differ (- glycosidic)• Difference - based on two ring forms for glucose:

alpha () and beta ()• alpha glucose are helical• beta glucose are straight• straight structures, H atoms on one strand can

bond with OH groups on other strands• Parallel cellulose- grouped into microfibrils, - strong building materials for plants

(Figure 5.7 & 5.8, pg. 73)

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• Enzymes that hydrolyzing alpha linkages can’t hydrolyze beta linkages in cellulose

• Cellulose- insoluble fiber• Herbivores -have symbiotic relationships

with microbes to digest cellulose• Chitin - exoskeleton of arthropods• provides structural • cell walls of many fungi• used as surgical thread

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2.3.2 Lipids• large biological molecules • not form polymers• little or no affinity for water• Hydrophobic- hydrocarbons, nonpolar

covalent bonds• Lipids - fats, phospholipids, and

steroids• Fats - constructed from two types of

smaller molecules: glycerol and fatty acids

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• Glycerol- three-carbon alcohol with a hydroxyl group attached to each carbon

• fatty acid- a carboxyl group attached to a long carbon skeleton

• Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats

• triacylglycerol, or triglyceride - three fatty acids joined with glycerol by an ester linkage (Figure 5.11, pg.75)

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Use of Triglycerides• Energy source; Energy used as ATP during

respiration.• Energy store; 38 kJ per g.• Stored as insoluble droplets inside cells or

in adipose tissues (mammals).• Adipose tissue – heat insulator.• Fats – bad conductor of heat.• Shock absorption.• Buoyancy for aquatic organisms.• Fats – relatively low density (previous notes)

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• Saturated fatty acids - maximum number of hydrogen atoms possible and no double bonds

• Unsaturated fatty acids - one or more double bonds

• Function - energy storage• Fats made from saturated fatty acids -

saturated fats

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• animal fats - saturated• solid at room temperature• diet rich in saturated fats- cardiovascular

disease • Fats made from unsaturated fatty acids -

unsaturated fats• Plant fats and fish fats- unsaturated• liquid at room temperature (oil) (Figure 5.12, pg. 75)

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• Phospholipid - two fatty acids and a phosphate group are attached to glycerol

• fatty acid tails – hydrophobic• phosphate group and its attachments -

hydrophilic head

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• structure of phospholipids - bilayer arrangement

• Phospholipids- major component of all cell membrane

• Example of phospholipid in cell membrane : lecithin

(Figure 5.14, pg.77)

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• Steroids- a carbon skeleton consisting of four fused rings

• important steroid- cholesterol• component in animal cell membranes• essential in animals• high levels in the blood may contribute to

cardiovascular disease

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Importance:• Raw material for manufacturing of vitamin D• Component of mammalian membrane cells –

strengthens membranes at high body temperatures.

• Steroid abuseExample: Anabolic steroids • Synthetic androgens (male reproductive

hormones)Used especially by sportsmen to increase:• Muscle mass (to “bulk up”)• Physical strength• Endurance• Aggressiveness

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Signs of abuse: • Mood swings • Suicidal thoughts or suicide attempts • Restlessness • Fatigue, sleeplessness • Loss of appetite Changes in physical appearance: • In males - baldness, impotence, Shrinking testes and

development of breasts• In females - growth of facial hair, deepening of the

voice, and reduction of breast size • In both sexes - acne, oily hair and skin, cysts, jaundice

(yellowing of the skin) swelling of feet and ankles, aching joints, bad breath, nervousness and trembling

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• Risks from taking steroids: – Possibility of heart attack and stroke.– Increase in anger, hostility and violent

behavior. – Increased risk of getting AIDS from

sharing needles

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2.3.3 Protein• 50% of the dry mass of most cells• structural support, storage, transport,

cellular communications, movement, and defense against foreign substances

• consists of one or more polypeptides• Polypeptides - polymers of amino acids• organic molecules with carboxyl and

amino groups• properties due to differing side chains,

called R groups• Cells use 20 amino acids to make

thousands of proteins

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Amino Group

Carboxyl Group

α carbon

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Example of amino acid based on the side chain:• polar, eg: Serine• non polar, eg: glycine• acidic, eg: aspartic acid• basic, eg: lycine

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Properties of Amino Acids• Amphoteric - both acidic and basic

properties.• zwitterions in water. • carries both positive charge (-NH3+) and

negative charge (-COO-) at a specific pH(7.4)

Amino and carboxyl groups ionization in solution:• -COOH ↔ -COO- + H+ (donates H+)• -NH2 + H+ ↔ -NH3+ (accepts H+)

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• Amino acids- linked by peptide bonds• Polypeptide- polymer of amino acids• range in length • Each polypeptide - unique linear sequence

of amino acids (Figure 5.18, pg.80)

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Protein Structure• primary structure - sequence of amino

acids• Secondary structure - found in most

proteins, coils and folds in the polypeptide chain

• Tertiary structure - interactions among various side chains (R groups)

• Quaternary structure - consists of multiple polypeptide chains

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• Primary structure - inherited genetic information

• coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone

• a coil - alpha helix • a folded - beta pleated sheet

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• Tertiary structure - interactions between R groups

• include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions

• Strong covalent bonds- disulfide bridges may reinforce the protein’s conformation

• Quaternary structure - two or more polypeptide chains form one macromolecule

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• Collagen - fibrous protein consisting of three polypeptides coiled like a rope

• Hemoglobin - globular protein consisting of four polypeptides: two alpha and two beta chains

(Diagram: Levels of protein structure, pg.82-83)

Types of bond in protein structure:• hydrogen bonds, ionic bonds, disulphide

bonds, hydrophobic interactions & van der Waals interactions

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Fibrous and Globular Protein• Fibrous - elongated molecules,

secondary structure - dominant structure.

• insoluble, supportive role in the body, and involved in movement (as in muscle and ciliary proteins). 

• often have regular repeating structures.Example: i.Keratin which is a helix of helices (2

pairs of α-helices wound around one another) consisting of 7repeating amino acid

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ii.Silk which is composed of only -sheets (glycine-alanine-serine repeats)• Globular - soluble and form spheroidal

molecules in water• typically consist of relatively straight

runs of secondary structure joined by stretches of polypeptides that abruptly change direction. 

Example:– Enzymes, transport proteins and

receptor proteins– Myoglobin

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• physical and chemical conditions can affect conformation

• pH, salt concentration, temperature, or other environmental factors - protein to unravel

• denaturation• protein is biologically inactive

Denaturation

Denatured proteinRenaturationNormal protein

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2.3.4 Nucleic Acid– Deoxyribonucleic acid (DNA)– Ribonucleic acid (RNA)

• polynucleotides• made of monomers called nucleotides• Each nucleotide - a nitrogenous base, a

pentose sugar, and a phosphate group• without the phosphate group -nucleoside

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• Nucleotide monomers - nucleosides and phosphate groups

• Nucleoside = nitrogenous base + sugar• two families of nitrogenous bases:

– Pyrimidines - single six-membered ring– Purines - six-membered ring fused to a

five-membered ring• DNA - deoxyribose• RNA - ribose

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• Nucleotides - phosphodiester linkages between the —OH group on the 3’ carbon of one nucleotide and the phosphate on the 5’ carbon of the next.

• Refer these as the 5’ end and the 3’ end,

respectively.

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The DNA double Helix

• 1953 - James Watson and Francis Crick, proposed the double helix as the three-dimensional structure of DNA

• DNA double helix - two backbones run in opposite 5´ to 3´ directions from each other - antiparallel

• sugar-phosphate backbones are on the outside of the helix, and the nitrogenous bases are paired in the interior of the helix.

• two polynucleotides, or strands, held together by hydrogen bonds between the paired bases and by van der Waals interactions between the stacked bases.

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Chargaff’s rules of complimentary base pairing:

• A with T: the purine adenine (A) always pairs with the pyrimidine thymine (T)

• C with G:  the pyrimidine cytosine (C) always pairs with the purine guanine (G)

• 2 H bonds between A–T; 3 H bonds between C–G

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RNA (structure mRNA & tRNA, pg.320-321)• mRNA - delivers the information encoded

in genes from DNA to ribosome, a specialized structure, or organelle, where that information is decoded into a protein.

• tRNA – serves as adapter molecule in protein synthesis; translates mRNA codons into amino acids.

• rRNA - are the structural components of the ribosome - active role in recognizing conserved portions of mRNAs and tRNAs - assist protein synthesis.

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2.4 Techniques of Analysis2.4.1 Chromatography• separate and analyze complex mixtures. • involves a sample (or sample extract)

being dissolved in a mobile phase (which may be a gas, a liquid or a supercritical fluid).

• mobile phase is then forced through an immobile, immiscible stationary phase.

• The phases are chosen such that components of the sample have differing solubilities in each phase.

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• A component which soluble in the stationary phase - take longer to travel through it than a component which is not very soluble in the stationary phase but very soluble in the mobile phase.

• differences in mobilities - sample components will become separated from each other as they travel through the stationary phase.

Paper chromatography (PC) • stationary phase is liquid soaked into a sheet or

strip of paper– mobile phase is a liquid solvent – some components spend more time in the

stationary phase than others – components appear as separate spots spread

out on the paper after drying or "developing"

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What is the Retention Factor, Rf?• The retention factor, Rf, is a quantitative

indication of how far a particular compound travels in a particular solvent.

• The Rf value is a good indicator of whether an unknown compound and a known compound are similar, if not identical.

• If the Rf value for the unknown compound is close or the same as the Rf value for the known compound then the two compounds are most likely similar or identical.

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• The retention factor, Rf, is defined asRf = distance the solute (D1) moves divided by the distance traveled by the solvent front (D2)

• Rf = D1 / D2 where D1 = distance that color traveled, measured from center of the band of color to the point where the food color was applied

• D2 = total distance that solvent traveled

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2.4.2 Electrophoresis• Electro refers to the energy of electricity.

Phoresis, from the Greek verb phoros, means "to carry across.“

• This technique uses a gel as a molecular sieve to separate nuclei acids or proteins by size

(Figure 20.8, pg.393)

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Cathode

Powersource

Anode

Mixtureof DNAmoleculesof differ-ent sizes

Gel

Glassplates

Longermolecules

Shortermolecules

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2.4.3 X-ray diffraction• used to determine crystalline compound in a

given sample. • The analysis is based on that X-ray will be

diffracted by crystal planed and minerals can be identified by measuring this diffraction at different angles.

• The diffraction pattern of unknown material is compared with that of the reference database in order to identify its chemical compound.

• Each crystalline compound has its unique characteristic X-ray pattern which may be used as a fingerprint for its identification.

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From diffraction patterns we can: • measure the average spacings between layers or

rows of atoms; • determine the orientation of a single crystal or

grain; • find the crystal structure of an unknown material;

and • measure the size, shape and internal stress of

small crystalline regions. (example : Figure 5.24, pg.86)

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2.4.4 Centrifugation• Cell fractionation takes cells apart and

separates the major organelles from one another

• Ultracentrifuges fractionate cells into their component parts

• enables scientists to determine the functions of organelles

(Figure 6.5, pg.97)

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HomogenizationTissuecells

Differential centrifugation

Homogenate

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1000 g(1000 times theforce of gravity)

10 minSupernatant pouredinto next tube

20,000 g20 min

80,000 g60 min

150,000 g3 hr

Pellet rich innuclei andcellular debris

Pellet rich inmitochondria (and chloro-plasts if cellsare from a plant)

Pellet rich in“microsomes”(pieces of plasmamembranes andcells’ internalmembranes) Pellet rich in

ribosomes

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2.4.5 MicroscopyLight Microscopy• visualize cells too small to see with the

naked eye• light microscope (LM) - visible light passes

through a specimen and then through glass lenses, which magnify the image

• minimum resolution- 200 nanometers (nm), the size of a small bacterium

(Figure 6.2, pg.95)

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• magnify effectively to about 1,000 times the size of the actual specimen

• Various techniques enhance contrast and enable cell components to be stained or labeled

• Most subcellular structures, or organelles, are too small to be resolved by a LM

(Figure 6.3, pg.96)

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Electron Microscopy• used to study subcellular structures • Scanning electron microscopes (SEMs)

focus a beam of electrons onto the surface of a specimen, providing images that look 3D

• Transmission electron microscopes (TEMs) focus a beam of electrons through a specimen

• TEMs are used mainly to study the internal ultrastructure of cells

(Figure 6.4, pg.96)

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2.5 Enzyme• catalytic protein - speeds up a reaction

without being consumed by the reactionEndergonic• chemical reaction that consume/USE

energy• product contain more energy than

reactantExergonic• chemical reaction that release energy• product contain less energy than

reactant

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2.5.1 Properties of enzyme

• Specific• not destroyed by the reactions they

catalyzed• Sensitive to high temperature and pH• reversible• can be inhibited

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2.5.2 Catalysis and activation energy• chemical reaction- involves bond breaking

and bond forming• initial energy needed to start a chemical

reaction - activation energy (EA)

• in a form of heat from the surroundings• Enzymes catalyze reactions by lowering

the EA barrier

• Enzymes do not affect the change in free-energy (∆G)

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Progress of the reaction

Fre

e en

erg

yCourse ofreactionwithoutenzyme

Reactants

Course ofreactionwith enzyme

EA

without enzyme

EA withenzymeis lower

G is unaffectedby enzyme

Products

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2.5.3 Mechanism of action and kinetics• Substrate - reactant that an enzyme acts

on • enzyme binds to its substrate - enzyme-

substrate complex• active site - region on the enzyme where

the substrate binds• Induced fit of a substrate brings chemical

groups of the active site into positions that enhance their ability to catalyze the reaction

(Figure 8.16 & 8.17, pg.153)

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2.5.4 Factors affecting enzyme activity– General environmental factors, such as

temperature and pH– Chemicals that specifically influence the

enzyme• optimal temperature • optimal pH (Figure 8.18, pg.154)

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2.5.5 Inhibitor• interfere, reduce or destroy enzyme

activityCompetitive inhibitors• bind to the active site of an enzyme,

competing with the substrate• has shape resemble enzyme’s substrate • inhibitor occupy the site - prevent enzyme

from combine with substrate, no product is generating.

• Reversible (Figure 8.19, pg.155)

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Noncompetitive inhibitor• bind to another part of an enzyme -

enzyme to change shape and active site less effective

• Irreversible – example: toxin and poisons (bind permanently)

• Reversible – allosteric regulation• Allosteric regulation - protein’s function at

one site is affected by binding of a regulatory molecule at another site

• inhibit or stimulate an enzyme’s activity

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Example of allosteric inhibition: Feedback inhibition• end product of a metabolic pathway shuts

down the pathway• prevents a cell from wasting chemical

resources by synthesizing more product than is needed

(Figure 8.21, pg.157)

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2.5.6 Enzyme cofactors• Non-protein enzyme helpers (pg.155)

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2.5.7 Nomenclature of enzymes (IUB)• Produced by the Nomenclature Committee

of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), in consultation with the IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)

• Enzyme Nomenclature is a resource providing general information on enzyme nomenclature.

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2.5.8 Enzyme technology

• Biosensor- analytical device which converts a biological response into an electrical signal

• cover sensor devices used in order to determine the concentration of substances and other parameters of biological interest even where they do not utilise a biological system directly.

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• The biocatalyst must be highly specific for the purpose of the analyses, be stable under normal storage conditions.

• The reaction should be as independent of such physical parameters as stirring, pH and temperature as is manageable. This would allow the analysis of samples with minimal pre-treatment.

• The response should be accurate, precise, reproducible and linear over the useful analytical range, without dilution or concentration.

• The complete biosensor should be cheap, small, portable and capable of being used by semi-skilled operators.

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Schematic diagram showing the main components of a biosensor. The biocatalyst (a) converts the substrate to product. This reaction is determined by the transducer (b) which converts it to an electrical signal. The output from the transducer is amplified (c), processed (d) and displayed (e).

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• Immobilized enzyme - an enzyme that is physically attached to a solid support over which a substrate is passed and converted to product.

• advantages • Multiple or repetitive use of a single batch of

enzymes • The ability to stop the reaction rapidly by

removing the enzyme from the reaction solution (or vice versa)

• Enzymes are usually stabilized by bounding • Product is not contaminated with the

enzyme  (especially useful in the food and pharmaceutical industries)

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• Application: example, lactose hydrolysis• The main purpose of using immobilized enzymes

here is to convert the disaccharide lactose via hydrolysis into its monosaccharide components, glucose and galactose.

• Lactose is a disaccharide that occurs naturally in both human and cow's milk. It is widely used in baking and in commercial infant-milk formulas.

• One large problem with lactose is that many people are lactose intolerant - meaning that their body is incapable of digesting lactose.

• So it must be hydrolyzed into its monosaccharide components, allowing digestion which is the purpose of products today such as LACTAID.