F212 Module 1 Biological Molecules

Module 1Module 1Biological MoleculesBiological Molecules

F212 Molecules, F212 Molecules, biodiversity, food and biodiversity, food and healthhealth

Module 1 TopicsModule 1 Topics

• Biological Biological moleculesmolecules– Water– Intro to biologic

al molecules– Proteins– Carbohydrates– Lipids– Practical bioche

mistry

• Nucleic acids• Enzymes

Learning OutcomesLearning Outcomes

• describe how hydrogen describe how hydrogen bonding occurs between water bonding occurs between water molecules, and relate this, and molecules, and relate this, and other properties of water, to other properties of water, to the roles of water in living the roles of water in living organisms organisms

DefinitionsDefinitions

• Covalent bondCovalent bond– Formed when atoms share electronsFormed when atoms share electrons– Strong bondsStrong bonds

• Hydrogen bondHydrogen bond– Weak interaction that occurs when a Weak interaction that occurs when a

negatively charged atom is bonded to a negatively charged atom is bonded to a positively charged hydrogenpositively charged hydrogen

WaterWater

• 60 – 70 % of mammals60 – 70 % of mammals• About 90% of plantsAbout 90% of plants• Life originated in waterLife originated in water• Good solventGood solvent

• What else do you know about What else do you know about little old dihydrogen monoxide little old dihydrogen monoxide (DHMO)(DHMO)

Water is a liquidWater is a liquid

• A polar moleculeA polar molecule• Made up of two positively charged Made up of two positively charged

hydrogen atoms and one negatively hydrogen atoms and one negatively charged oxygencharged oxygen

• Covalent bonds form between oxygen and Covalent bonds form between oxygen and hydrogen with electrons shared between hydrogen with electrons shared between them.them.

• Hydrogen bonds form between water Hydrogen bonds form between water moleculesmolecules

• Up to four may form clusters which break Up to four may form clusters which break and reform all the timeand reform all the time

Water moleculeWater molecule

Hydrogen Bonds in Hydrogen Bonds in waterwater

Hydrogen bonds

Key features of waterKey features of water

• Key features of water as a Key features of water as a constituent of living organismsconstituent of living organisms– Good solventGood solvent– High specific heat capacityHigh specific heat capacity– High latent heat of vaporisationHigh latent heat of vaporisation– High cohesionHigh cohesion– ReactiveReactive– IncompressibilityIncompressibility


• To be able to To be able to – Define metabolismDefine metabolism– State the functions of biological State the functions of biological

moleculesmolecules– Name monomers and polymers of Name monomers and polymers of

carbohydrates, fats, proteins and carbohydrates, fats, proteins and nucleic acidsnucleic acids

– Describe general features of Describe general features of condensation and hydrolysis condensation and hydrolysis reactionreaction

Biological MoleculesBiological Molecules

• Molecular biology Molecular biology – the study of structure and the study of structure and

functioning of biological functioning of biological molecules.molecules.

• Metabolism Metabolism – sum total of all biochemical sum total of all biochemical

reactions in the body.reactions in the body.

Nutrients and HealthNutrients and Health

• To maintain a healthy bodyTo maintain a healthy body– CarbohydratesCarbohydrates– LipidsLipids– ProteinsProteins– Vitamins and mineralsVitamins and minerals– Nucleic acidNucleic acid– WaterWater– fibrefibre

Key Biological Key Biological MoleculesMolecules

• There are 4 key biological There are 4 key biological moleculesmolecules– CarbohydratesCarbohydrates– lipidslipids– proteinsproteins– nucleic acidsnucleic acids

Building blocks of lifeBuilding blocks of life

• 4 most common elements in 4 most common elements in the living organismsthe living organisms– hydrogenhydrogen– carboncarbon– oxygenoxygen– nitrogennitrogen

Biochemicals and Biochemicals and bondsbonds

• Covalent bonds join atoms together Covalent bonds join atoms together to form moleculesto form molecules

• Carbon is able to make 4 covalent Carbon is able to make 4 covalent bondsbonds

• Carbon can bond to form chains or Carbon can bond to form chains or rings with other atoms bonded to rings with other atoms bonded to the chainthe chain

• Carbon can also form double bonds Carbon can also form double bonds – E.g. C=C or C=OE.g. C=C or C=O

PolymersPolymers

• ““poly” means “many” = polymerspoly” means “many” = polymers

• Macromolecules are made up of Macromolecules are made up of repeating subunits that are joined end repeating subunits that are joined end to end, they are easy to make as the to end, they are easy to make as the same reaction is repeated many times. same reaction is repeated many times.

• Polymerisation is the making of Polymerisation is the making of polymers.polymers.

MacromoleculesMacromolecules

MacromoleculeMacromolecule Subunit (monomer)Subunit (monomer)

polysaccharidepolysaccharide monosaccharidemonosaccharide

proteinsproteins amino acidsamino acids

nucleic acidsnucleic acids nucleotidesnucleotides

MetabolismMetabolism

• Metabolism is the sum of all of the Metabolism is the sum of all of the reactions that take place within reactions that take place within organismsorganisms– AnabolismAnabolism

• Build up of larger, more complex molecules Build up of larger, more complex molecules from smaller, simpler onesfrom smaller, simpler ones

• This process requires energyThis process requires energy

– CatabolismCatabolism• The breakdown of complex molecules into The breakdown of complex molecules into

simpler onessimpler ones• This process releases energyThis process releases energy

Condensation reactionsCondensation reactions

• In a condensation reactionIn a condensation reaction– A water molecule is releasedA water molecule is released– A new covalent bond is formedA new covalent bond is formed– A larger molecule is formed by A larger molecule is formed by

bonding together of smaller bonding together of smaller moleculesmolecules

Hydrolysis ReactionsHydrolysis Reactions

• In hydrolysis reactionsIn hydrolysis reactions– A water molecule is usedA water molecule is used– A covalent bond is brokenA covalent bond is broken– Smaller molecules are formed by Smaller molecules are formed by

the splitting of a larger moleculethe splitting of a larger molecule

Hydrolysis and condensationHydrolysis and condensation

O

OH HO

CONDENSATIONHYDROLYSIS


• describe, with the aid of describe, with the aid of diagrams, the structure of an diagrams, the structure of an amino acids amino acids

• describe, with the aid of describe, with the aid of diagrams, the formation and diagrams, the formation and breakage of peptide bonds in breakage of peptide bonds in the synthesis and hydrolysis of the synthesis and hydrolysis of dipeptides and polypeptides dipeptides and polypeptides

Introduction to proteinIntroduction to protein

• 50% of the dry mass of cells is 50% of the dry mass of cells is proteinprotein

• Important functions includeImportant functions include– Cell membranesCell membranes– HaemoglobinHaemoglobin– Anti-bodiesAnti-bodies– EnzymesEnzymes– Keratin (hair and skin)Keratin (hair and skin)– collagencollagen

Structure of proteinsStructure of proteins

• All proteins are made up of the All proteins are made up of the same basic components same basic components amino amino acidsacids

• There are 20 different amino acids, There are 20 different amino acids, which alter by having different which alter by having different residual groups (residual groups (R groupsR groups))

• A single chain of amino acids A single chain of amino acids makes amakes a polypeptide polypeptide

Structure of an amino Structure of an amino acidacid

• Amino acids containAmino acids contain– Amine group (NHAmine group (NH22))

– Carboxylic acid group (COOH)Carboxylic acid group (COOH)

Joined at the same C atomJoined at the same C atom

Structure of an amino Structure of an amino acidacid

H

H OHN

H

R

C C

O

Amine group

Carboxylgroup

R group varies in different amino acids

TEST TIMETEST TIME

• Build an amino acid using the Build an amino acid using the molymod modelsmolymod models

• Glycine is an amino acid where the Glycine is an amino acid where the R group is hydrogen – change you R group is hydrogen – change you molecule into glycinemolecule into glycine

• Build a dipeptide using the Build a dipeptide using the molymod modelsmolymod models

Different Amino AcidsDifferent Amino Acids

• GlycineGlycine R group = HR group = H• AlanineAlanine R group = CHR group = CH33

• ValineValine R group = CR group = C33HH77

• You will be expected to learn how You will be expected to learn how to draw the basic structure of an to draw the basic structure of an amino acid. Remember that each amino acid. Remember that each Amino acid has it’s own specific R Amino acid has it’s own specific R groupgroup


• explain, with the aid of explain, with the aid of diagrams, the term ‘primary diagrams, the term ‘primary structure’ structure’

• explain, with the aid of explain, with the aid of diagrams, the term ‘secondary diagrams, the term ‘secondary structure’ with reference to structure’ with reference to ‘hydrogen bonding’ ‘hydrogen bonding’

Peptide bondPeptide bond

H

H

N

H

R

C C

O H

N

H

R

C C

O

OHPeptidebond

Building a polypeptideBuilding a polypeptide

• Peptide bonds are formed in Peptide bonds are formed in condensation reactionscondensation reactions

• Primary structurePrimary structure– The primary structure of a The primary structure of a

polypeptide is its amino acid polypeptide is its amino acid sequencesequence

– This is determined by the gene This is determined by the gene that codes for the polypeptidethat codes for the polypeptideAmino

acid

Peptide Bond

Secondary StructureSecondary Structure

• Polypeptides become twisted or Polypeptides become twisted or coiledcoiled

• They fold into one of two They fold into one of two structuresstructures– Alpha helix (right handed helix)Alpha helix (right handed helix)– Beta-pleated sheetBeta-pleated sheet

• Hydrogen bonds hold coils in placeHydrogen bonds hold coils in place– Weak but give stability to the parts of Weak but give stability to the parts of

a protein molecule.a protein molecule.C O H N


• explain, with the aid of explain, with the aid of diagrams, the term ‘tertiary diagrams, the term ‘tertiary structure’ with reference to structure’ with reference to hydrophobic and hydrophilic hydrophobic and hydrophilic interactions, disulphide bonds interactions, disulphide bonds and ionic interactionsand ionic interactions

Tertiary StructureTertiary Structure

• Folding of the polypeptide to Folding of the polypeptide to give a more complex 3-D give a more complex 3-D shape, the shape is specific to shape, the shape is specific to the function of the polypeptide.the function of the polypeptide.

• ExamplesExamples– Hormone must fit into the Hormone must fit into the

hormone receptor in a target cellhormone receptor in a target cell– Enzymes have a complementary Enzymes have a complementary

active site to it’s substrateactive site to it’s substrate

Tertiary Structure - Tertiary Structure - bondsbonds

• Four types of bond help to hold Four types of bond help to hold the folded proteins in their the folded proteins in their precise shape.precise shape.– Hydrogen BondsHydrogen Bonds– Disulphide bondsDisulphide bonds– Ionic bonds Ionic bonds – Hydrophobic interactionsHydrophobic interactions

Hydrogen BondsHydrogen Bonds

• Between polar groupsBetween polar groups– Electronegative oxygen atoms of the Electronegative oxygen atoms of the

–CO–CO– Electropositive H atoms on either Electropositive H atoms on either

the –OH or –NH groupsthe –OH or –NH groups..

Disulphide bondsDisulphide bonds

• Between sulfur-containing R Between sulfur-containing R groups of the amino acid cysteine.groups of the amino acid cysteine.

• Covalent bondsCovalent bonds• Form strong links which make the Form strong links which make the

tertiary protein structure very tertiary protein structure very stable.stable.

• This bond can be broken by This bond can be broken by reducing agentsreducing agents

Ionic BondsIonic Bonds

• Between R groups, which Between R groups, which ionise to form positively and ionise to form positively and negatively charged groups that negatively charged groups that attract each other.attract each other.

Hydrophobic InteractionsHydrophobic Interactions

• These are interactions between the These are interactions between the non-polar side chains of a protein non-polar side chains of a protein molecule. molecule.

• The bond forms between non-polar, The bond forms between non-polar, hydrophobic R groups on the amino hydrophobic R groups on the amino acids.acids.

• Once the two hydrophobic molecules Once the two hydrophobic molecules are close together the interaction is are close together the interaction is reinforced by Van der Waals attractions reinforced by Van der Waals attractions (which provide the weak bond).(which provide the weak bond).

Van der Waals attractionsVan der Waals attractions

• Electrons are always in motion, Electrons are always in motion, and are not always evenly and are not always evenly distributed about a molecule. distributed about a molecule.

• This results in areas of positive This results in areas of positive and negative charge, which are and negative charge, which are continuously changing, and continuously changing, and enables molecules to “stick” to enables molecules to “stick” to one another.one another.

Denaturing ProteinDenaturing Protein

• The Polar R groups of proteins interact The Polar R groups of proteins interact with water forming hydrogen bonds with water forming hydrogen bonds that face outwards, This creates a that face outwards, This creates a hydrophobic core to the moleculehydrophobic core to the molecule

• When proteins are heated these bonds When proteins are heated these bonds break, the tertiary structure changes break, the tertiary structure changes and the protein does not function.and the protein does not function.

• The destruction of shape or loss of The destruction of shape or loss of function is function is denaturationdenaturation..

Denaturing ProteinsDenaturing Proteins

• Frying an eggFrying an egg


• explain, with the aid of explain, with the aid of diagrams, the term ‘quaternary diagrams, the term ‘quaternary structure’, with reference to structure’, with reference to the structure of haemoglobin the structure of haemoglobin

Quaternary StructureQuaternary Structure

• Association of different Association of different polypeptide chains bonded polypeptide chains bonded together to form intricate together to form intricate shapesshapes

• Sometimes contain Sometimes contain prosthetic prosthetic groupsgroups, which are a permanent , which are a permanent part of a protein molecule but part of a protein molecule but not made of amino acidsnot made of amino acids

Quaternary StructureQuaternary Structure

• Globular proteinGlobular protein– Molecules curl up into a “ball” shapeMolecules curl up into a “ball” shape– Examples – myoglobin, haemoglobinExamples – myoglobin, haemoglobin– Metabolic rolesMetabolic roles

• Fibrous ProteinsFibrous Proteins– Form long strandsForm long strands– Usually insolubleUsually insoluble– Have a structural roleHave a structural role– Examples – keratin, collagenExamples – keratin, collagen

HaemoglobinHaemoglobin

• Function – oxygen carrying pigment Function – oxygen carrying pigment found in red blood cellsfound in red blood cells

• StructureStructure– 4 polypeptides4 polypeptides

• 2 x 2 x αα-globin-globin• 2 x β-globin2 x β-globin

– Each polypeptide has a 3Each polypeptide has a 3oo structure structure stabilised by hydrophobic interactions stabilised by hydrophobic interactions in the centrein the centre

– In the middle each polypeptide in a In the middle each polypeptide in a haemhaem group group

OK so let’s summarise OK so let’s summarise proteinsproteins

Protein structure and Protein structure and diversity diversity

• It is difficult to describe in a simple It is difficult to describe in a simple sentence the role of proteins. sentence the role of proteins. – when there is something to do, it is a protein when there is something to do, it is a protein

that that doesdoes it. it. • Therefore proteins areTherefore proteins are

– important important – numerous numerous – very diverse very diverse – very complex, very complex, – able to perform actions and reactions able to perform actions and reactions

under some circumstances under some circumstances

Some examples of Some examples of proteinsproteins

• Antibodies:Antibodies: – they recognise molecules of invading they recognise molecules of invading

organisms. organisms.

• Receptors:Receptors: – part of the cell membrane, they recognise other part of the cell membrane, they recognise other

proteins, or chemicals, and inform the cell... proteins, or chemicals, and inform the cell...

• Enzymes:Enzymes: – assemble or digest. assemble or digest.

• Neurotransmitters Neurotransmitters and some and some hormones:hormones: – Trigger the receptors...Trigger the receptors...

• Channels and pores:Channels and pores:– holesholes in the cell membrane in the cell membrane

Summary of levels of Summary of levels of protein structureprotein structure

• Primary Structure– Amino acids linked in a linear sequence

• Secondary Structure– folding or coiling of polypeptide

• Tertiary structure– Folding of polypeptide by disulphide

bonds, ionic bonds, hydrogen bonds or hydrophobic interactions

• Quaternary structure– Two or more polypeptides bonded Two or more polypeptides bonded

togethertogether


• describe, with the aid of describe, with the aid of diagrams, the structure of a diagrams, the structure of a collagen molecule collagen molecule

• compare the structure and compare the structure and function of haemoglobin (and function of haemoglobin (and example of a globular protein) example of a globular protein) and collagen (an example of a and collagen (an example of a fibrous protein) fibrous protein)

Collagen (a fibrous Collagen (a fibrous protein)protein)

• Collagen is found in skin, teeth, Collagen is found in skin, teeth, tendons, cartilage, bones and tendons, cartilage, bones and the walls of blood vessels, the walls of blood vessels, making it an important making it an important structural protein.structural protein.

Structure of collagenStructure of collagen

• 3 identical polypeptide chains 3 identical polypeptide chains wound into a triple helix; this is wound into a triple helix; this is a left-handed helix.a left-handed helix.

• Each polypeptide is about 1000 Each polypeptide is about 1000 amino acids longamino acids long

• Primary structurePrimary structure• Every 3 amino acids = glycineEvery 3 amino acids = glycine

CollagenCollagen

• Sequences of polypeptide chains are Sequences of polypeptide chains are staggered so that glycine is found at staggered so that glycine is found at every position along the triple helix. every position along the triple helix.

• The three polypeptide chains are The three polypeptide chains are held together by hydrogen bonds.held together by hydrogen bonds.

• Adjacent molecules of collagen are Adjacent molecules of collagen are held together by covalent bonds held together by covalent bonds formed between the carboxyl group formed between the carboxyl group of one amino acid and the amine of one amino acid and the amine group of another.group of another.

Pupil Activity Pupil Activity

• Using your brains and what you Using your brains and what you have been taughthave been taught– compare the structure and compare the structure and

function of haemoglobin and function of haemoglobin and collagencollagen

• Try to make a bullet point list of at Try to make a bullet point list of at least 10 things least 10 things

Collagen vs Collagen vs HaemoglobinHaemoglobin

• CollagenCollagen– Repeating sequence Repeating sequence

of amino acidsof amino acids– Most of molecule Most of molecule

has left handed has left handed helix structureshelix structures

– Does not contain Does not contain prosthetic groupprosthetic group

– Insoluble in waterInsoluble in water– Metabolically Metabolically

unreactiveunreactive– Structural roleStructural role

• HaemoglobinHaemoglobin– Precise 1Precise 1oo structure structure– 22oo structure wound structure wound

into alpha helixinto alpha helix– Contains prosthetic Contains prosthetic

groupgroup– Soluble in waterSoluble in water– Metabolically Metabolically

reactivereactive


• describe, with the aid of describe, with the aid of diagrams, the molecular diagrams, the molecular structure of alpha-glucose as structure of alpha-glucose as an example of a an example of a monosaccharide carbohydratemonosaccharide carbohydrate

• state the structural difference state the structural difference between alpha and beta between alpha and beta glucoseglucose

CarbohydratesCarbohydrates

• contain carbon, hydrogen & contain carbon, hydrogen & oxygenoxygen

• organic compoundsorganic compounds• general formula Cgeneral formula Cxx(H(H22O)O)yy

– glucose Cglucose C66HH1212OO66

• 3 main groups3 main groups– monosaccharidesmonosaccharides– disaccharidesdisaccharides– polysaccharidespolysaccharides

MonosaccharidesMonosaccharides

• dissolve easily in water to form dissolve easily in water to form sweet solutionsweet solution

• general formula (CHgeneral formula (CH22O)O)nn, where , where n is the number of carbonsn is the number of carbons

• 3 main types 3 main types – TriosesTrioses (3C) (3C) – PentosesPentoses (5C)(5C)– HexosesHexoses (6C)(6C)

Glucose - a hexoseGlucose - a hexose

• Glucose is made of a chain of Glucose is made of a chain of atoms long enough to close up atoms long enough to close up upon itself and form a stable upon itself and form a stable ring structure. ring structure.

• Carbon atom 1 (Carbon atom 1 (11C) joins to the C) joins to the O on O on 55C. C.

• The six sided structure formed The six sided structure formed is known as a is known as a pyranosepyranose ring. ring.

Chain for a glucoseChain for a glucose

1C2C

3C4C5C6CH2OH

OH

OH

OH

OH H

H

O

H

H

H

αα-glucose ring form-glucose ring form

1C

2C3C

4C

5C

6CH2OH

OH OH

OH

OH

HH

O

H

H H

Making the drawing Making the drawing easiereasier

OH

OH

Glucose – a hexoseGlucose – a hexose

• Isomers Isomers – possess the same molecular possess the same molecular

formula but differ in arrangement formula but differ in arrangement of atoms.of atoms.

• αα-glucose and -glucose and ββ-glucose are -glucose are isomers of glucose. isomers of glucose. – Depending on whether the OH of Depending on whether the OH of

1C is above or below the plane of 1C is above or below the plane of the ring.the ring.

The IsomersThe Isomers

• αα-glucose-glucose • ββ-glucose-glucose

OOH

H

OH

OH


• describe, with the aid of describe, with the aid of diagrams, the formation and diagrams, the formation and breakage of glycosidic bonds in breakage of glycosidic bonds in the synthesis and hydrolysis of the synthesis and hydrolysis of a disaccharide (maltose) and a a disaccharide (maltose) and a polysaccharide (amylose) polysaccharide (amylose)

Disaccharides and the Glycosidic Bond

• Monosaccharides combine in pairs Monosaccharides combine in pairs to give a disaccharide, this involves to give a disaccharide, this involves the loss of a single water molecule the loss of a single water molecule

• This reaction is called This reaction is called condensationcondensation • The bond formed is known as a The bond formed is known as a

glycosidic bond.glycosidic bond.• To break a disaccharide the To break a disaccharide the

addition of water is needed, this addition of water is needed, this reaction is called reaction is called hydrolysis.hydrolysis.

Formation and Formation and breakage of the breakage of the glycosidic bondglycosidic bond

PolysaccharidesPolysaccharides

• Final molecules maybe 1000’s of Final molecules maybe 1000’s of monosaccharides, the size of these monosaccharides, the size of these molecules make them insoluble.molecules make them insoluble.

• Polysaccharides are NOT sugarsPolysaccharides are NOT sugars• The most important polysaccharides The most important polysaccharides

are built up entirely of glucose are built up entirely of glucose molecules. molecules.

• These are starch, glycogen and These are starch, glycogen and cellulose.cellulose.


• describe, with the aid of describe, with the aid of diagrams, the structure of diagrams, the structure of starchstarch

• describe, with the aid of describe, with the aid of diagrams, the structure of diagrams, the structure of glycogenglycogen

StarchStarch

• A mixture of two substances A mixture of two substances amylose and amylopectin.amylose and amylopectin.

• Starch granules are insoluble in Starch granules are insoluble in water. water.

• The form of carbohydrate used for The form of carbohydrate used for storage in plants.storage in plants.

• Starch grains build up in Starch grains build up in chloroplasts, or in storage organs chloroplasts, or in storage organs such as potato tubers.such as potato tubers.

AmyloseAmylose

• Long unbranching chains Long unbranching chains • 1-4 glycosidic bonds1-4 glycosidic bonds• formed by condensation formed by condensation

reactions.reactions.• The chains curve and coil into The chains curve and coil into

helical structures.helical structures.

AmylopectinAmylopectin

• 1,4 linked 1,4 linked αα-glucose molecules -glucose molecules form chains form chains

• shorter shorter • branch out to the sides. branch out to the sides.

– The branches form by 1-6 The branches form by 1-6 linkageslinkages

Comparison of the structure of Comparison of the structure of amylose and amylopectin amylose and amylopectin

moleculesmolecules

GlycogenGlycogen

• The form in which carbohydrate is stored The form in which carbohydrate is stored in the animal body.in the animal body.

• Glucose is converted to glycogen in the Glucose is converted to glycogen in the liver and muscles, liver and muscles, – it is kept until requiredit is kept until required– then it is broken down again into glucose.then it is broken down again into glucose.

• Formed by Formed by αα-glucose molecules joining in -glucose molecules joining in 1-4 and 1-6 links1-4 and 1-6 links

• There are more branches containing a There are more branches containing a smaller number of glucose moleculessmaller number of glucose molecules than than amylopectinamylopectin

Structure of glycogenStructure of glycogen

Starch and glycogenStarch and glycogen

• Starch and Glycogen are Starch and Glycogen are energy storage moleculesenergy storage molecules

• which take up little space due which take up little space due to their compact shapesto their compact shapes

• They help to prevent too high They help to prevent too high concentrations of glucose in concentrations of glucose in cells.cells.

Learning outcomesLearning outcomes

• describe, with the aid of describe, with the aid of diagrams, the structure of diagrams, the structure of cellulosecellulose

CelluloseCellulose

• Most abundant organic molecule on the Most abundant organic molecule on the planet due to its presence in cell walls.planet due to its presence in cell walls.

• Slow rate of breakdown in nature.Slow rate of breakdown in nature.• Polymer of about 10,000 β-glucose Polymer of about 10,000 β-glucose

molecules in a long unbranched chain.molecules in a long unbranched chain.• Many chains run parallel to each other Many chains run parallel to each other

and have cross linkages between them, and have cross linkages between them, giving increased stability.giving increased stability.

• hydrogen bonds form these links between hydrogen bonds form these links between chains, which collectively give the chains, which collectively give the structure increased strength.structure increased strength.

Structure of celluloseStructure of cellulose

CelluloseCellulose

• To join together one β-glucose To join together one β-glucose molecule must be rotated at 180molecule must be rotated at 18000 relative to the other. relative to the other.

• Successive glucose molecules are Successive glucose molecules are linked at 180linked at 18000 to each other. to each other.

• Cellulose molecules become tightly Cellulose molecules become tightly cross-linked with each other to form cross-linked with each other to form bundles called micro fibrils. bundles called micro fibrils.

• Micro fibrils form cellulose fibres by Micro fibrils form cellulose fibres by hydrogen bonding giving a high hydrogen bonding giving a high tensile strength similar to steel.tensile strength similar to steel.


• compare and contrast the compare and contrast the structure and functions of structure and functions of starch (amylose) and cellulose starch (amylose) and cellulose

• explain how the structures of explain how the structures of glucose, starch (amylose), glucose, starch (amylose), glycogen and cellulose glycogen and cellulose molecules relate to their molecules relate to their functions in living organisms functions in living organisms

Comparing polysaccharidesComparing polysaccharides

Characteristic

amylose

amylopectin

glycogen cellulose

Found in

Found as

Function

Monomer

Bonds

chain

Homework QuestionHomework Question

• Discuss the structures of Discuss the structures of glucose, starch, glycogen and glucose, starch, glycogen and cellulose in relation to their cellulose in relation to their functions; include diagrams to functions; include diagrams to illustrate your answerillustrate your answer

Learning outcomesLearning outcomes

• compare, with the aid of compare, with the aid of diagrams, the structure of a diagrams, the structure of a triglyceride and a phospholipidstriglyceride and a phospholipids

• explain how the structure of a explain how the structure of a triglyceride, phospholipids and triglyceride, phospholipids and cholesterol molecules relate to cholesterol molecules relate to their functions in living their functions in living organisms organisms

Lipids Lipids are notare not polymers polymers

• Large molecules Large molecules • few oxygen atoms few oxygen atoms • many carbon and hydrogen many carbon and hydrogen

atomsatoms• hydrophobichydrophobic• Less dense than waterLess dense than water

LipidsLipids

• Two important groupsTwo important groups– Triglycerides Triglycerides

• Fats – solid at room temperatureFats – solid at room temperature• Oils – liquid at room temperatureOils – liquid at room temperature

– phospholipidsphospholipids

Lipids - functionsLipids - functions

• A source of energyA source of energy• Store of energy (adipose tissues)Store of energy (adipose tissues)• Biological membranesBiological membranes• Thermal insulators / insulationThermal insulators / insulation• BuoyancyBuoyancy• ProtectionProtection

– Cuticle of a leafCuticle of a leaf– Internal organsInternal organs

• Metabolic source of waterMetabolic source of water• hormoneshormones

Glycerol and fatty acidsGlycerol and fatty acids

• glycerolglycerol • Fatty acidFatty acid

H

H

C

C

C

H

H

H

OH

OH

OH

CHC

H

HC

H

HC

H

HC

H

HC

H

O

HO

H

OHO

C

Fatty AcidsFatty Acids

• Fatty acids have Fatty acids have – an acid group at one end (COOH)an acid group at one end (COOH)– Hydrocarbon chain (2 Hydrocarbon chain (2 20 20

carbons long)carbons long)

• Fatty acids can beFatty acids can be– SaturatedSaturated– Unsaturated Unsaturated

Saturated fatty acidSaturated fatty acid

• All possible bonds are made All possible bonds are made with hydrogenwith hydrogen

HO

CHC

H

HC

H

HC

H

HC

H

HC

H

O

H

Unsaturated fatty acidUnsaturated fatty acid

• One or more double bond One or more double bond between carbon atomsbetween carbon atoms

HO

CHC

H

C

H

C

H

HC

H

HC

H

O

H

Saturated and Saturated and unsaturated fatty acidsunsaturated fatty acids

• PolyunsaturatedPolyunsaturated– more than one double bondmore than one double bond

• Monounsaturated Monounsaturated – only one double bondonly one double bond

• Animal lipids are often Animal lipids are often saturated and occur as fatssaturated and occur as fats

• plant lipids are often plant lipids are often unsaturated and occur as oilsunsaturated and occur as oils

TriglyceridesTriglycerides

• Most common form of lipidMost common form of lipid• Combination of 3 fatty acid Combination of 3 fatty acid

molecules and one glycerol molecules and one glycerol molecule. molecule. – Glycerol is a type of alcoholGlycerol is a type of alcohol– Fatty acids are organic molecules Fatty acids are organic molecules

with a COOH group attached to a with a COOH group attached to a hydrocarbon tail.hydrocarbon tail.


• Each of the glycerol molecules Each of the glycerol molecules 3 -OH groups reacts with the 3 -OH groups reacts with the carboxyl group of a fatty acid.carboxyl group of a fatty acid.

• This is a This is a condensation reactioncondensation reaction, , and an and an ester bondester bond is is established.established.

Structure of a Structure of a triglyceridetriglyceride

• Glycerol Glycerol + + 3 fatty acids 3 fatty acids

H

H

C

C

C

H

H

H

OH

OH

OH

HO

HO

HO

C

O

C

O

C

O

Condensation reaction and Condensation reaction and formation of an ester bondformation of an ester bond

H

H

C

C

C

H

H

H

O

O

O

C

O

C

O

C

O

Ester bond


• Triglycerides are Triglycerides are – insoluble in water, insoluble in water, – soluble in some organic solvents, soluble in some organic solvents,

e.g. ether or ethanol. e.g. ether or ethanol. – non-polar non-polar – hydrophobic.hydrophobic.

Roles of triglyceridesRoles of triglycerides

• Energy reserveEnergy reserve• Insulator against heat lossInsulator against heat loss• BuoyancyBuoyancy• Protection (vital organs)Protection (vital organs)• Metabolic source of water.Metabolic source of water.

PhospholipidsPhospholipids

• Special type of lipidSpecial type of lipid• one of the fatty acid groups is one of the fatty acid groups is

replaced by phosphoric acid.replaced by phosphoric acid.• phosphoric acid is hydrophilic phosphoric acid is hydrophilic

(attracts water)(attracts water)• Biological significance of this Biological significance of this

molecule is its role in the cell molecule is its role in the cell membrane.membrane.

Simplified structure of Simplified structure of phospholipidphospholipid

Structure of a phopholipidStructure of a phopholipid

H

H

C

C

C

H

H

H

O

O

O

P

O

C

O

C

O

Phosphate group

OH

Structure of a Structure of a phospholipidphospholipid

Cholesterol - structureCholesterol - structure

• Small moleculeSmall molecule• -OH group is polar-OH group is polar• 4 carbon rings and 4 carbon rings and

hydrocarbon tail are non polarhydrocarbon tail are non polar

Cholesterol - StructureCholesterol - Structure

Cholesterol - functionCholesterol - function

• Found in biological membranesFound in biological membranes• Steroids e.g. testosterone, Steroids e.g. testosterone,

oestrogen and progesterone oestrogen and progesterone are made from cholesterolare made from cholesterol

• Excess cholesterolExcess cholesterol– Form gallstones in bileForm gallstones in bile– Cause atherosclerosis in blood Cause atherosclerosis in blood

vesselsvessels


• describe how to carry out describe how to carry out chemical tests to identify the chemical tests to identify the presence of the following presence of the following molecules: protein (Biuret molecules: protein (Biuret test), reducing and non-test), reducing and non-reducing sugars (Benedict’s reducing sugars (Benedict’s test), Starch (iodine solution) test), Starch (iodine solution) and lipids (emulsion test) and lipids (emulsion test)

Chemical Tests Chemical Tests

• Chemical tests can be done to Chemical tests can be done to confirm the presence of various confirm the presence of various biological molecules within a biological molecules within a samplesample

• These tests are These tests are qualitative testsqualitative tests– They indicate presence of a They indicate presence of a

molecule not how much is presentmolecule not how much is present

Testing for presence of Testing for presence of a carbohydratea carbohydrate

• StarchStarch• Reducing sugarReducing sugar• Non reducing sugarNon reducing sugar

starchstarch

• Iodine solution Iodine solution – iodine in potassium iodideiodine in potassium iodide– Add to solution will turn blue-Add to solution will turn blue-

black quickly if comes into black quickly if comes into contact with starch.contact with starch.

StarchStarch

• Starch molecules curl up into Starch molecules curl up into long spirals, with a hole down long spirals, with a hole down the middle of the spiral, just the middle of the spiral, just the right size for an iodine the right size for an iodine molecule. molecule.

• The starch-iodine complex The starch-iodine complex forms a strong blue-black forms a strong blue-black colour.colour.

Reducing sugarReducing sugar

• Benedict’s Reagent (copper II Benedict’s Reagent (copper II sulphate in alkaline solution)sulphate in alkaline solution)– Add benedict’s reagent to the Add benedict’s reagent to the

solution testingsolution testing– Heat in a water bath (80Heat in a water bath (80ooC) for 3 C) for 3

minutesminutes

Reducing sugarsReducing sugars

• If added to a reducing agent CuIf added to a reducing agent Cu2+2+ ions are ions are reduced to Cureduced to Cu++, and the change in colour to , and the change in colour to red of Copper (I) sulphate. red of Copper (I) sulphate.

• All monosaccharides are reducing sugars; All monosaccharides are reducing sugars; • Reducing sugars have an aldehyde group Reducing sugars have an aldehyde group

(H-C=0) somewhere in their molecule, (H-C=0) somewhere in their molecule, which contribute an electron to the copper. which contribute an electron to the copper.

• Reducing sugars become oxidised.Reducing sugars become oxidised.

Reducing sugar + CuReducing sugar + Cu2+2+ = oxidised sugar + Cu = oxidised sugar + Cu++

Non reducing sugarNon reducing sugar

• Heat sugar solution with acid to Heat sugar solution with acid to hydrolyse any glycosidic bonds hydrolyse any glycosidic bonds presentpresent

• Neutralise solution by adding Neutralise solution by adding sodium hydroxidesodium hydroxide

• Add benedict’s reagentAdd benedict’s reagent• Heat in a water bathHeat in a water bath• If it goes orange/red a non-reducing If it goes orange/red a non-reducing

sugar is present.sugar is present.

Non-reducing sugarsNon-reducing sugars

• Not all disaccharides are reducing Not all disaccharides are reducing sugars. sugars.

• To check for the presence of a To check for the presence of a reducing sugar, the disaccharide reducing sugar, the disaccharide needs to be broken down into its needs to be broken down into its constituent monosaccharides,constituent monosaccharides,

• monosaccharides are reducing monosaccharides are reducing sugars and will react with sugars and will react with benedict’s solution.benedict’s solution.

Testing for the Testing for the presence of proteinspresence of proteins

ProteinsProteins

• Biuret reagent Biuret reagent – copper sulphate and potassium or copper sulphate and potassium or

sodium hydroxidesodium hydroxide– Add Biuret solution to the Add Biuret solution to the

substancesubstance– If protein present get a purple If protein present get a purple

colourcolour

proteinsproteins

• All proteins have several All proteins have several amine, NHamine, NH22, groups within their , groups within their molecules. molecules.

• These groups react with copper These groups react with copper ions to form a complex that has ions to form a complex that has a strong purple colour.a strong purple colour.

Testing for the Testing for the presence of lipidspresence of lipids

lipidslipids

• ““Emulsion test”Emulsion test”– Shake substance (lipid) with Shake substance (lipid) with

absolute ethanol absolute ethanol – Pour ethanol into a tube Pour ethanol into a tube

containing watercontaining water– If no lipid is present mixture looks If no lipid is present mixture looks

transparenttransparent– If lipids are present – looks white If lipids are present – looks white

and cloudy.and cloudy.

lipidslipids

• Lipids are insoluble in water, but Lipids are insoluble in water, but soluble in ethanol. soluble in ethanol.

• As the ethanol mixture is poured As the ethanol mixture is poured into water, lipid molecules cannot into water, lipid molecules cannot remain mixed in water and clump remain mixed in water and clump together to form little groups. together to form little groups.

• The lipid molecules impede light The lipid molecules impede light and we see an emulsion (white and we see an emulsion (white cloudiness).cloudiness).


• describe how the concentration describe how the concentration of glucose in a solution may be of glucose in a solution may be determined by using determined by using colorimetrycolorimetry

Banana QualitativeBanana Qualitative

• Bananas, at each of five different stages of Bananas, at each of five different stages of ripeness.ripeness.– The stages must range from very green The stages must range from very green

(inedible) to very ripe (brown skin).(inedible) to very ripe (brown skin).– Each student will require an approximately 5 cm Each student will require an approximately 5 cm

length of each banana.length of each banana.– The bananas must be labelled or presented on The bananas must be labelled or presented on

labelled watch glasses.labelled watch glasses.

• 50cm50cm33 fresh iodine in potassium iodide fresh iodine in potassium iodide solution in a beaker labelled iodine solution in a beaker labelled iodine solution.solution.

• 50cm50cm33 fresh Benedict’s solution in a beaker fresh Benedict’s solution in a beaker labelled Benedict’s solution.labelled Benedict’s solution.

Nucleic AcidsNucleic Acids

Module 1 Biological Module 1 Biological MoleculesMoleculesUnit 2 Molecules, Biodiversity, food and Unit 2 Molecules, Biodiversity, food and healthhealth


• state that deoxyribonucleic acid state that deoxyribonucleic acid (DNA) is a polynucleotide, usually (DNA) is a polynucleotide, usually double stranded and made up of the double stranded and made up of the nucleotides adenine (A), thymine nucleotides adenine (A), thymine (T), cytosine (C) and guanine (G)(T), cytosine (C) and guanine (G)

• state that ribonucleic acid (RNA) is state that ribonucleic acid (RNA) is a polynucleotide usually single-a polynucleotide usually single-stranded and made up of the stranded and made up of the nucleotides adenine (A), uracil (U), nucleotides adenine (A), uracil (U), cytosine (C) and guanine (G)cytosine (C) and guanine (G)

Nucleic Acids – DNA and Nucleic Acids – DNA and RNARNA

• The nucleic acids haveThe nucleic acids have– The ability to carry instructionsThe ability to carry instructions– The ability to be copiedThe ability to be copied

• DNA and RNA are polymers; the DNA and RNA are polymers; the individual nucleotides are the individual nucleotides are the monomers that build up the monomers that build up the polynucleotides.polynucleotides.– DNA = deoxyribonucleic acidDNA = deoxyribonucleic acid– RNA = ribonucleic acidRNA = ribonucleic acid

NucleotidesNucleotides

• Nucleotides are made up of three smaller Nucleotides are made up of three smaller componentscomponents– Nitrogen containing baseNitrogen containing base– Pentose sugar (5 carbon atoms)Pentose sugar (5 carbon atoms)– Phosphate groupPhosphate group

Phosphate sugar

base

Bases Bases

• There are 5 different nitrogen-There are 5 different nitrogen-containing bases:containing bases:– A A AdenineAdenine– T T Thymine (DNA only)Thymine (DNA only)– U U Uracil (RNA only)Uracil (RNA only)– G G GuanineGuanine– CC CytosineCytosine

• DNA DNA – A, G, C and T– A, G, C and T• RNA RNA - A, G, C and U- A, G, C and U

BasesBases

• Purines (larger) Purines (larger) – These have double rings of carbon and nitrogen These have double rings of carbon and nitrogen

atomsatoms– adenineadenine– GuanineGuanine

• Pyrimidines (smaller)Pyrimidines (smaller)– These have a single ring of carbon and nitrogen These have a single ring of carbon and nitrogen

atomsatoms– ThymineThymine– uraciluracil– cytosinecytosine

PolynucleotidesPolynucleotides

• Polynucleotides strands Polynucleotides strands are formed of are formed of alternating sugars and alternating sugars and phosphatesphosphates

DNADNA

• Cut and paste activityCut and paste activity– Cut out the nucleotides and stick Cut out the nucleotides and stick

them down to form a double them down to form a double stranded DNA moleculestranded DNA molecule


• describe, with the aid of describe, with the aid of diagrams, diagrams, – how hydrogen bonding between how hydrogen bonding between

complementary base pairs (A-T, complementary base pairs (A-T, G-C) on two anti-parallel DNA G-C) on two anti-parallel DNA polynucleotide leads to the polynucleotide leads to the formation of a DNA molecule,formation of a DNA molecule,

– how the twisting of DNA produces how the twisting of DNA produces it’s ‘double-helix’ shape outline, it’s ‘double-helix’ shape outline, with the aid of diagrams, with the aid of diagrams,

DNADNA

• 2 strands 2 strands side-by-side side-by-side running in running in opposite opposite directions directions (antiparallel(antiparallel))

• The two The two strands are strands are held held together by together by hydrogen hydrogen bonds.bonds.

Complementary base pairsComplementary base pairs

• A purine in one strand is always A purine in one strand is always opposite a pyramidine in the other opposite a pyramidine in the other strand. strand. – Adenine – thymineAdenine – thymine– Guanine - cytosineGuanine - cytosine

• DNA forms a double helix, the strands DNA forms a double helix, the strands are held in place by hydrogen bonds. are held in place by hydrogen bonds.

• These bonds can be broken relatively These bonds can be broken relatively easily, this is important for protein easily, this is important for protein synthesis and DNA replication.synthesis and DNA replication.

Pupil ActivityPupil Activity

• Build your own DNA moleculeBuild your own DNA molecule• Equipment needed:Equipment needed:

– 2 purple pipe cleaners2 purple pipe cleaners– 2 white pipe cleaners2 white pipe cleaners– 6 red beads6 red beads– 6 yellow beads6 yellow beads– 12 aqua beads12 aqua beads– 12 purple beads12 purple beads

• Follow the instructions on the Follow the instructions on the handouthandout

DNA – a double helixDNA – a double helix

• Two polynucleotides held together Two polynucleotides held together by hydrogen bondsby hydrogen bonds

• Complementary base pairs Complementary base pairs – AAT (2 hydrogen bonds)T (2 hydrogen bonds)– GGC (3 hydrogen bonds)C (3 hydrogen bonds)

• Polynucleotides are anti-parallelPolynucleotides are anti-parallel– Parallel but with chains running in Parallel but with chains running in

opposite directionsopposite directions• 3’ to 5’direction3’ to 5’direction• 5’ to 3’direction5’ to 3’direction

Structure to functionStructure to function

• Information storageInformation storage– Long moleculesLong molecules– replication replication

• Base-paring rulesBase-paring rules• Hydrogen bondsHydrogen bonds

– StableStable


• how DNA replicates semi-how DNA replicates semi-conservatively, with reference conservatively, with reference to the role of DNA polymerase to the role of DNA polymerase

DNA ReplicationDNA Replication

• Each polynucleotide acts as a Each polynucleotide acts as a template for making a new template for making a new polynucleotidepolynucleotide

• This is known as This is known as semi-semi-conservative replicationconservative replication

Experimental Evidence for the semi-Experimental Evidence for the semi-conservative replication of DNAconservative replication of DNA

• Three ways were suggested for Three ways were suggested for DNA replicationDNA replication– Conservative replicationConservative replication– Semi-conservative replicationSemi-conservative replication– Dispersive replicationDispersive replication

• Scientists thought that semi-Scientists thought that semi-conservative replication was most conservative replication was most likely likely butbut there was no evidence to there was no evidence to support this theory.support this theory.

• 1958 Matthew Meselsohn and 1958 Matthew Meselsohn and Franklin Stahl demonstrated that Franklin Stahl demonstrated that DNA replication was semi-DNA replication was semi-conservative following experiments conservative following experiments with with E. Coli.E. Coli.

Stage 1Stage 1

• E. ColiE. Coli were grown in a medium were grown in a medium containing a heavy isotope containing a heavy isotope nitrogen (nitrogen (1515N). N).

• The bacteria used 15N to make The bacteria used 15N to make the purine and pyrimidine the purine and pyrimidine bases in its DNA.bases in its DNA.

Stage 2Stage 2

• After many generations, they After many generations, they were then transferred to light were then transferred to light isotope nitrogen (isotope nitrogen (1414N)N)

Stage 3Stage 3

• Bacteria were taken from the Bacteria were taken from the new medium after one new medium after one generation, two generations generation, two generations and later generations.and later generations.

• DNA was extracted from each DNA was extracted from each group of bacteria, group of bacteria,

• samples were placed in a samples were placed in a solution of caesium chloride solution of caesium chloride and spun in a centrifuge.and spun in a centrifuge.

ResultsResults

Generation 1 2 3

ConclusionsConclusions

1.1. Explain why the band of DNA in the first Explain why the band of DNA in the first generation is higher than that in the parental generation is higher than that in the parental generation.generation.

2.2. If replication were conservative what results If replication were conservative what results would you expect in the first generation?would you expect in the first generation?

3.3. If the DNA had replicated dispersively what If the DNA had replicated dispersively what results would you expect in the first results would you expect in the first generation?generation?

4.4. Explain how the second generation provides Explain how the second generation provides evidence that the DNA has reproduced semi-evidence that the DNA has reproduced semi-conservatively and not dispersivelyconservatively and not dispersively

5.5. What results would you expect to see from a What results would you expect to see from a third generation, draw a diagram of the third generation, draw a diagram of the results?results?

Explanation of resultsExplanation of results

• Parental generation - both Parental generation - both strands made with strands made with 1515NN

• First generation – DNA made of First generation – DNA made of one strand one strand 1515N and one strand N and one strand 1414NN

• Second generation – some DNA Second generation – some DNA made of 2 strands of made of 2 strands of 1414N and N and some made of some made of 1515N and N and 1414N.N.

DNA ReplicationDNA Replication

• Double helix unwinds and the DNA Double helix unwinds and the DNA “unzips” as hydrogen bonds break“unzips” as hydrogen bonds break

• Existing polynucleotides acts as a Existing polynucleotides acts as a template for assembly of nucleotidestemplate for assembly of nucleotides

• Free nucleotides move towards exposed Free nucleotides move towards exposed bases of DNAbases of DNA

• Base pairing occurs between free Base pairing occurs between free nucleotides and exposed basesnucleotides and exposed bases

• Enzyme DNA polymerase forms covalent Enzyme DNA polymerase forms covalent bonds between free nucleotidesbonds between free nucleotides

• Two daughter DNA molecules form Two daughter DNA molecules form separate double helices.separate double helices.


• state that a gene is a sequence state that a gene is a sequence of DNA nucleotides that codes of DNA nucleotides that codes for a polypeptide for a polypeptide

• outline the roles of DNA and outline the roles of DNA and RNA in living organisms (the RNA in living organisms (the concept of protein synthesis concept of protein synthesis must be considered in outline must be considered in outline only) only)

RNARNA

• single strand, containing single strand, containing – uraciluracil notnot thymine thymine– Ribose sugarRibose sugar

• There are 3 forms of RNAThere are 3 forms of RNA– Messenger RNAMessenger RNA mRNAmRNA– Transfer RNATransfer RNA tRNAtRNA– Ribosomal RNARibosomal RNA rRNArRNA

DNA and Protein SynthesisDNA and Protein Synthesis

• All chemical reactions are All chemical reactions are controlled by enzymes, all enzymes controlled by enzymes, all enzymes are proteins, DNA codes for are proteins, DNA codes for proteins, therefore DNA controls all proteins, therefore DNA controls all the activities of a cell.the activities of a cell.

• The shape and behaviour of a The shape and behaviour of a protein depends on the exact protein depends on the exact sequence of amino acids in the sequence of amino acids in the primary structure (polypeptide). primary structure (polypeptide).

The Genetic CodeThe Genetic Code

• DNA determines the exact order in DNA determines the exact order in which amino acids join together.which amino acids join together.

• The genetic codeThe genetic code– sequence of bases along the DNA sequence of bases along the DNA

molecule, molecule, – There are 20 different amino acids, only 4 There are 20 different amino acids, only 4

bases, bases, – a sequence of 3 bases codes for an amino a sequence of 3 bases codes for an amino

acid. acid. – This is called the This is called the triplet codetriplet code. .

• A A genegene is the part of a DNA molecule, is the part of a DNA molecule, which codes for just one polypeptide.which codes for just one polypeptide.

Protein SynthesisProtein Synthesis

• The process of protein The process of protein synthesis occurs in four stages:synthesis occurs in four stages:– transcription of DNA to make transcription of DNA to make

messenger RNA (mRNA)messenger RNA (mRNA)– movement of mRNA from the movement of mRNA from the

nucleus to the cytoplasmnucleus to the cytoplasm– amino acid activationamino acid activation– translation of mRNA to make a translation of mRNA to make a

polypeptidepolypeptide

TranscriptionTranscription

• This is the process by which mRNA is This is the process by which mRNA is built up against one side of an built up against one side of an opened up piece of DNA. opened up piece of DNA.

• The relevant section of DNA unwinds, The relevant section of DNA unwinds, the hydrogen bonds between base the hydrogen bonds between base pairs are broken and the two strands pairs are broken and the two strands split apart.split apart.

• Free nucleotides then assemble Free nucleotides then assemble against one strand of DNA. against one strand of DNA.

• The enzyme RNA polymerase moves The enzyme RNA polymerase moves along the DNA adding on RNA along the DNA adding on RNA nucleotide at a time. nucleotide at a time.

Movement of mRNA to Movement of mRNA to ribosomesribosomes

• mRNA leaves the nucleus mRNA leaves the nucleus through a nuclear pore into the through a nuclear pore into the cytoplasm, and attaches to a cytoplasm, and attaches to a ribosome.ribosome.

Amino Acid ActivationAmino Acid Activation

• Enzymes attach amino acids to Enzymes attach amino acids to their specific tRNA molecule. their specific tRNA molecule.

• This needs energy supplied by This needs energy supplied by ATP. ATP.

• An anti-codon is a triplet of An anti-codon is a triplet of bases forming part of a tRNA bases forming part of a tRNA molecule and it is molecule and it is complementary to a codon.complementary to a codon.

TranslationTranslation

• Amino acid attaches to the ribosomeAmino acid attaches to the ribosome• Adjacent amino acids are joined Adjacent amino acids are joined

together by peptide bonds and a together by peptide bonds and a polypeptide chain is built up.polypeptide chain is built up.

• This carries on until the ribosome This carries on until the ribosome reaches a stop codon, the reaches a stop codon, the polypeptide breaks loose from the polypeptide breaks loose from the ribosome and translation is complete.ribosome and translation is complete.

EnzymesEnzymes


• state that enzymes are state that enzymes are globular proteins, with a globular proteins, with a specific tertiary structure, specific tertiary structure, which catalyse metabolic which catalyse metabolic reactions in living organisms; reactions in living organisms;

RecapRecap

• What is metabolism?What is metabolism?– sum total of all biochemical sum total of all biochemical

reactions in the body.reactions in the body.

EnzymesEnzymes

• All enzymes are All enzymes are – globular proteinsglobular proteins– catalystscatalysts– SpecificSpecific– affected by temperature and pHaffected by temperature and pH

More about enzymesMore about enzymes

• Two basic functions within cells:Two basic functions within cells:– Act as biological catalystsAct as biological catalysts– Provide a mechanism whereby Provide a mechanism whereby

individual chemical reactions can be individual chemical reactions can be controlledcontrolled

• Enzyme molecules have a Enzyme molecules have a specific 3D shape and all possess specific 3D shape and all possess an active site.an active site.


• Follow the progress of an Follow the progress of an enzyme-catalysed reaction; enzyme-catalysed reaction;

CatalaseCatalase

• The enzyme The enzyme catalasecatalase breaks down breaks down hydrogen peroxide into water and oxygen.hydrogen peroxide into water and oxygen.

2H2H22OO22 => 2H => 2H22O + OO + O22

• Hydrogen peroxide is formed continually Hydrogen peroxide is formed continually as a bi-product of various chemical as a bi-product of various chemical reactions in living cells. reactions in living cells.

• It is toxic and if the cells did not It is toxic and if the cells did not immediately break it down it would kill immediately break it down it would kill them. them.

Investigation 1Investigation 1

• Catalase is the fastest enzyme known. Catalase is the fastest enzyme known. • In this investigation you will be able to In this investigation you will be able to

watch the action of catalase and compare watch the action of catalase and compare it with an inorganic catalyst that it with an inorganic catalyst that catalyses the same reaction.catalyses the same reaction.1.1. Pour hydrogen peroxide into two test tubes to Pour hydrogen peroxide into two test tubes to

a depth of about 2cm. a depth of about 2cm. 2.2. Into one test tube sprinkle about 0.1g of Into one test tube sprinkle about 0.1g of

manganese dioxide. manganese dioxide. 3.3. Into the 2nd test tube put in a 1cmInto the 2nd test tube put in a 1cm22 piece of piece of

potato. potato. 4.4. Observe the two test tubes and record what Observe the two test tubes and record what

happens. happens.

ResultsResults

• Describe the difference in Describe the difference in reaction with the inorganic reaction with the inorganic catalyst and the organic catalyst and the organic catalystcatalyst

Investigation 2Investigation 2

Graduated measuring cylinder15ml

Hydrogen peroxide

water

MethodMethod

• Design a results table to record the Design a results table to record the oxygen produced every 10 seconds.oxygen produced every 10 seconds.

• cut up 4cmcut up 4cm3 3 piece of potato into this piece of potato into this slices into the conical flask, and slices into the conical flask, and start recording results immediately.start recording results immediately.

• Take a reading for the amount of Take a reading for the amount of oxygen produced every 10 seconds, oxygen produced every 10 seconds, until the oxygen is no longer being until the oxygen is no longer being produced.produced.

ExtensionExtension

• If you have time, you could If you have time, you could repeat the above experiment, repeat the above experiment, but this time grind up the 4cmbut this time grind up the 4cm33 of potato with some fine sand. of potato with some fine sand. How do the results compare?How do the results compare?

ResultsResults

• Draw a graph of oxygen produced Draw a graph of oxygen produced against time. against time.

• Describe the graph in terms of Describe the graph in terms of interaction between the molecules of interaction between the molecules of catalase and hydrogen peroxide.catalase and hydrogen peroxide.

• How could you adapt this experiment to How could you adapt this experiment to investigate the effect of the following on investigate the effect of the following on the rate of the reaction.the rate of the reaction.

– temperaturetemperature– pHpH– substrate concentrationsubstrate concentration– enzyme concentrationenzyme concentration


• state that enzyme action may be state that enzyme action may be intracellular or extra cellular; intracellular or extra cellular;

• describe, with the aid of diagrams, the describe, with the aid of diagrams, the mechanism of action of enzyme mechanism of action of enzyme molecules, with reference to molecules, with reference to – specificity, specificity, – active site, active site, – lock and key hypothesis, lock and key hypothesis, – induced-fit hypothesis, induced-fit hypothesis, – enzyme-substrate complex, enzyme-substrate complex, – enzyme-product complex enzyme-product complex – lowering of activation energy lowering of activation energy

Active SiteActive Site

• The The Active siteActive site is the region to which is the region to which another molecule or molecules can another molecule or molecules can bind. This molecule is the substrate bind. This molecule is the substrate of the enzyme. of the enzyme.

• The enzyme and substrate form an The enzyme and substrate form an enzyme-substrate complexenzyme-substrate complex..

• When enzyme and substrate collide in When enzyme and substrate collide in the correct orientation, the substrate the correct orientation, the substrate becomes attached and held becomes attached and held temporarily in position at the active temporarily in position at the active site.site.

Substrate Substrate end products end products

• Enzyme and substrate molecules Enzyme and substrate molecules then interact so that a chemical then interact so that a chemical reaction involving the substrates reaction involving the substrates takes place and the appropriate takes place and the appropriate products are formed. products are formed.

• When the reaction is complete, When the reaction is complete, the product or products leave the product or products leave the active site.the active site.

Enzyme SpecificityEnzyme Specificity

• Active sites are specific for one type of Active sites are specific for one type of moleculemolecule

• Examples of specificityExamples of specificity– Amylase breaks down glycosidic bonds in Amylase breaks down glycosidic bonds in

starch to form maltosestarch to form maltose– Catalase breaks down hydrogen peroxide Catalase breaks down hydrogen peroxide

into water and oxygeninto water and oxygen– Trypsin is a protease that only breaks Trypsin is a protease that only breaks

peptide bonds next to the amino acids peptide bonds next to the amino acids arginine and lysinearginine and lysine

Lock and Key TheoryLock and Key Theory

• Some part of the enzyme has Some part of the enzyme has an active site, which is exactly an active site, which is exactly the correct shape to fit the the correct shape to fit the substrate.substrate.– Active site Active site = lock= lock– Substrate Substrate = key= key

Induced fit TheoryInduced fit Theory

• Active site is a cavity of a particular Active site is a cavity of a particular shapeshape

• initially the active site is not the correct initially the active site is not the correct shape in which to fit the substrate. shape in which to fit the substrate.

• As the substrate approaches the active As the substrate approaches the active site, the site changes and results in site, the site changes and results in being a perfect fit.being a perfect fit.

• After the reaction has taken place and After the reaction has taken place and the products have gone. the products have gone.

• The active site returns to its normal The active site returns to its normal shape.shape.

MetabolismMetabolism

• A catabolic reaction A catabolic reaction – substrate has been broken downsubstrate has been broken down

• An anabolic reaction An anabolic reaction – substrate used to build a new substrate used to build a new

moleculemolecule

Lowering of Activation Lowering of Activation EnergyEnergy

• Activation energy is the energy Activation energy is the energy given temporarily to a substrate to given temporarily to a substrate to convert it into a product.convert it into a product.

• The higher the activation energy The higher the activation energy the slower the reaction. the slower the reaction.

• Enzymes help to decrease Enzymes help to decrease activation energy by providing an activation energy by providing an active site where reactions can active site where reactions can occur more easily than elsewhere.occur more easily than elsewhere.

Lowering Activation Lowering Activation EnergyEnergy

Activation energy without enzyme

Activation energy with enzyme


• To follow the progress of an To follow the progress of an enzyme-catalysed reaction; enzyme-catalysed reaction;

Experiments with Experiments with enzymesenzymes

• Follow the time course of an enzyme-Follow the time course of an enzyme-catalysed reaction by measuring catalysed reaction by measuring – rates of formation of products (for example rates of formation of products (for example

using catalase), using catalase), – rate of disappearance of substrate (for example rate of disappearance of substrate (for example

using amylase).using amylase).

• When an enzyme and a substrate are When an enzyme and a substrate are mixed together, a reaction begins. mixed together, a reaction begins. Substrate molecules collide with the Substrate molecules collide with the enzyme and bind to its active site; enzyme and bind to its active site; product molecules are formed.product molecules are formed.

Experiments with Experiments with enzymesenzymes

• As the reaction proceeds the As the reaction proceeds the number of substrate molecules number of substrate molecules decreases and the number of decreases and the number of product molecules increase. The product molecules increase. The number of enzyme molecules number of enzyme molecules remains constant.remains constant.

• We can measure the rate of a We can measure the rate of a reaction by measuring either:reaction by measuring either:– Increasing productIncreasing product– Decreasing substrateDecreasing substrate

Increasing ProductIncreasing ProductExample: catalase breaks down Example: catalase breaks down hydrogen peroxide into water and hydrogen peroxide into water and oxygenoxygen

Decreasing SubstrateDecreasing SubstrateExample: amylase breaks down Example: amylase breaks down starch into maltosestarch into maltose

Explanations for the Explanations for the course of reactioncourse of reaction

• As the reaction proceeds there is As the reaction proceeds there is less substrate available, therefore less substrate available, therefore less product gets released.less product gets released.

• Rate of reaction is quickest at the Rate of reaction is quickest at the beginning when there is a high beginning when there is a high concentration of substrate.concentration of substrate.

• Later the substrate becomes the Later the substrate becomes the limiting factor and the reaction limiting factor and the reaction slows down.slows down.

• Eventually all substrate is used up, Eventually all substrate is used up, so the reaction stopsso the reaction stops


• describe and explain the effects of describe and explain the effects of pH, temperature, enzyme pH, temperature, enzyme concentration and substrate concentration and substrate concentration on enzyme activity; concentration on enzyme activity;

• describe how the effects of pH, describe how the effects of pH, temperature, enzyme concentration temperature, enzyme concentration and substrate concentration on and substrate concentration on enzyme activity can be investigated enzyme activity can be investigated experimentally experimentally

Factors Affecting Factors Affecting enzyme Activityenzyme Activity

• Enzyme ConcentrationEnzyme Concentration• Substrate concentrationSubstrate concentration• TemperatureTemperature• pHpH

Enzyme ConcentrationEnzyme Concentration

• The rate of reaction is directly The rate of reaction is directly proportional to the enzyme proportional to the enzyme concentrationconcentration

• assuming that there are plenty assuming that there are plenty of substrate molecules and of substrate molecules and enzymes are the only limiting enzymes are the only limiting factors.factors.

Enzyme ConcentrationEnzyme Concentration

Substrate Substrate concentrationconcentration

• For a given amount of enzyme, For a given amount of enzyme, the rate of an enzyme controlled the rate of an enzyme controlled reaction increases with substrate reaction increases with substrate concentration, up to a certain concentration, up to a certain point. point.

• This point is V max, which is the This point is V max, which is the maximum rate of reaction; the maximum rate of reaction; the amount of enzyme becomes the amount of enzyme becomes the limiting factor.limiting factor.

Substrate Substrate concentrationconcentration

TemperatureTemperature

• An increase in temperature affects An increase in temperature affects the rate of reaction in two waysthe rate of reaction in two ways

• Factor 1Factor 1– As the temperature increase the kinetic As the temperature increase the kinetic

energy of the substrate and enzyme energy of the substrate and enzyme molecules increases and they move molecules increases and they move faster. faster.

– The faster the molecules move the The faster the molecules move the more often they collide and the greater more often they collide and the greater the rate of reaction.the rate of reaction.


• Factor 2Factor 2– As temperature increases, more As temperature increases, more

atoms which make up the enzyme atoms which make up the enzyme molecules vibrate. molecules vibrate.

– This breaks down the bonds This breaks down the bonds which hold the molecules in the which hold the molecules in the precise shape. precise shape.

– The enzyme becomes denatured The enzyme becomes denatured and loses catalytic properties.and loses catalytic properties.


• OPTIMUM TEMPERATURE OPTIMUM TEMPERATURE – temperature at which an enzyme temperature at which an enzyme

catalyses a reaction at a catalyses a reaction at a maximum rate.maximum rate.


pHpH

• The precise 3-D shape of an enzyme The precise 3-D shape of an enzyme is partly a result of hydrogen is partly a result of hydrogen bonding. bonding.

• These bonds maybe broken down by These bonds maybe broken down by high concentrations of H+ ions.high concentrations of H+ ions.

• When pH changes from the optimumWhen pH changes from the optimum– shape of enzyme changesshape of enzyme changes– affinity of substrate for the active site affinity of substrate for the active site

decreasesdecreases

pHpH

Online resourcesOnline resources

• Online simulation of practical Online simulation of practical available atavailable at– http://mvhs.mbhs.edu/coresims/enzyme

/index.php

• Good simulation of the theory of Good simulation of the theory of temp/pH available at AS guru temp/pH available at AS guru – www.bbc.co.uk

• Chemistry for biologistsChemistry for biologists– www.chemsoc.org/networks/learnnet/cfb/


• explain the effects of explain the effects of competitive and non-competitive and non-competitive inhibitors on the competitive inhibitors on the rate of enzyme-controlled rate of enzyme-controlled reactions, reactions, – with reference to both reversible with reference to both reversible

and non-reversible inhibitors; and non-reversible inhibitors;

Enzyme InhibitorsEnzyme Inhibitors

• Inhibitors prevent enzymes Inhibitors prevent enzymes from workingfrom working

• There are two types of inhibitorThere are two types of inhibitor– competitive competitive – non-competitive.non-competitive.

Competitive InhibitorsCompetitive Inhibitors

• Have a similar shape to the normal Have a similar shape to the normal substrate and are able to bind to the substrate and are able to bind to the active site.active site.

• Do not react with the active site but Do not react with the active site but leave after a time without any product leave after a time without any product forming.forming.

• The rate of reaction decreases because The rate of reaction decreases because the substrate molecules have to the substrate molecules have to compete with the inhibitor for the compete with the inhibitor for the active site.active site.

• It is possible to reduce the effect of It is possible to reduce the effect of the inhibitor by adding more substratethe inhibitor by adding more substrate

Competitive inhibitorCompetitive inhibitor

Effect of concentrations of Effect of concentrations of inhibitor and substrate on the inhibitor and substrate on the rate of an enzyme controlled rate of an enzyme controlled reactionreaction

No inhibitor

With fixed concentration of competitive inhibitor

Substrate concentration

Rate

of

react

ion

ExamplesExamples

• Competitive inhibitorCompetitive inhibitor– ReversibleReversible

• Statins compete with a liver enzyme Statins compete with a liver enzyme which helps to make cholesterolwhich helps to make cholesterol

– Non-reversibleNon-reversible• Penicillin inhibits an enzyme that Penicillin inhibits an enzyme that

makes cell walls in some bacteriamakes cell walls in some bacteria

Non-competitive Non-competitive inhibitorsinhibitors

• Molecules bind to some part of an Molecules bind to some part of an enzyme other than the active site.enzyme other than the active site.

• This changes the active site so that This changes the active site so that the substrate can no longer fit.the substrate can no longer fit.

• If the concentration of this type of If the concentration of this type of inhibitor is high enough, all inhibitor is high enough, all enzymes maybe inhibited and the enzymes maybe inhibited and the reaction slows to nothing.reaction slows to nothing.

• Increasing the concentration of the Increasing the concentration of the substrate has no effect on this type substrate has no effect on this type of inhibition.of inhibition.

Non competitive Non competitive inhibitorinhibitor

Rate of an enzyme controlled Rate of an enzyme controlled reaction with and without a non-reaction with and without a non-competitive inhibitorcompetitive inhibitor

No inhibitor

With non-competitive inhibitor

Substrate concentration

Rate

of

react

ion

ExamplesExamples

• Non-competitive inhibitorNon-competitive inhibitor– Potassium cyanide bind to haem, Potassium cyanide bind to haem,

which is part of cytochrome which is part of cytochrome oxidase oxidase

– This is non-reversibleThis is non-reversible

End product inhibitionEnd product inhibition

• Metabolic reactions must be Metabolic reactions must be finely controlled and balanced; finely controlled and balanced;

• end product inhibition end product inhibition regulates certain enzyme-regulates certain enzyme-catalysed processes in catalysed processes in organisms.organisms.



• This is an example of non-This is an example of non-competitive inhibitioncompetitive inhibition– product 3 binds to another part of product 3 binds to another part of

the enzyme other than the active the enzyme other than the active site. site.

• It is also an example of a It is also an example of a feedback mechanism.feedback mechanism.


• explain the importance of cofactors explain the importance of cofactors and coenzymes in enzyme-and coenzymes in enzyme-controlled reactions; controlled reactions;

• state that metabolic poisons may state that metabolic poisons may be enzyme inhibitors, and describe be enzyme inhibitors, and describe the action of one named poison; the action of one named poison;

• state that some medicinal drugs state that some medicinal drugs work by inhibiting the activity of work by inhibiting the activity of enzyme enzyme

Co-factorCo-factor

• A non-protein componentA non-protein component• Required by enzymes to carry Required by enzymes to carry

out reactionsout reactions• ExamplesExamples

– Metal ions in carbonic anhydraseMetal ions in carbonic anhydrase– Haem in catalaseHaem in catalase– Chloride ions and amylaseChloride ions and amylase

Co-enzymeCo-enzyme

• Organic, non protein molecules Organic, non protein molecules • Role is to carry chemical Role is to carry chemical

groups between enzymes, groups between enzymes, linking together enzyme linking together enzyme controlled reactionscontrolled reactions

• ExamplesExamples– NAD, FAD and coenzyme A – NAD, FAD and coenzyme A –

involved in respirationinvolved in respiration– NADP – involved in photosythesisNADP – involved in photosythesis

Prosthetic groupsProsthetic groups

• A coenzyme that is a A coenzyme that is a permanent part of the enzymepermanent part of the enzyme

• ExampleExample– Carbonic anhydrase contains a Carbonic anhydrase contains a

zinc-based prosthetic groupzinc-based prosthetic group

Metabolic poisonsMetabolic poisons

• Metabolic poisons can be enzyme Metabolic poisons can be enzyme inhibitorsinhibitors

• ExampleExample– Potassium cyanide Potassium cyanide

• inhibits cell respirationinhibits cell respiration• Non-competitive inhibitor for the enzyme Non-competitive inhibitor for the enzyme

cytochrome oxidasecytochrome oxidase• Decreases the use of oxygen so that ATP can Decreases the use of oxygen so that ATP can

not be madenot be made• The organism respires anaerobically and The organism respires anaerobically and

lactic acid builds up in the bloodlactic acid builds up in the blood

Medicines and enzymesMedicines and enzymes

• Infection by viruses are treated Infection by viruses are treated by using chemicals that act as by using chemicals that act as protease inhibitors which the protease inhibitors which the virus needs to build new viral virus needs to build new viral coats.coats.

• AntibioticsAntibiotics– Penicillin inhibits a bacterial enzyme Penicillin inhibits a bacterial enzyme

which makes bacterial cell wallswhich makes bacterial cell walls


• Measure the effect of different Measure the effect of different independent variables and independent variables and independent variable ranges independent variable ranges on an enzyme-catalysed on an enzyme-catalysed reaction; reaction;

• Measure the effect of an Measure the effect of an inhibitor on an enzyme-inhibitor on an enzyme-catalysed reaction. catalysed reaction.

Documents

F212 Module 1 Biological Molecules