Module 1 Biological Molecules F212 Molecules, biodiversity, food and health

Module 1 Topics Biological molecules Biological molecules Water Water Intro to biological molecules Intro to biological molecules Intro to biological molecules Proteins Proteins Carbohydrates Carbohydrates Lipids Lipids Practical biochemistry Practical biochemistry Practical biochemistry Nucleic acids Nucleic acids Enzymes

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

Definitions Covalent bondCovalent bond Formed when atoms share electrons Strong bonds Hydrogen bondHydrogen bond Weak interaction that occurs when a negatively charged atom is bonded to a positively charged hydrogen

Water 60 70 % of mammals 60 70 % of mammals About 90% of plants About 90% of plants Life originated in water Life originated in water Good solvent Good solvent What else do you know about little old dihydrogen monoxide (DHMO) What else do you know about little old dihydrogen monoxide (DHMO)

Water is a liquid A polar molecule A polar molecule Made up of two positively charged hydrogen atoms and one negatively charged oxygen Made up of two positively charged hydrogen atoms and one negatively charged oxygen Covalent bonds form between oxygen and hydrogen with electrons shared between them. Covalent bonds form between oxygen and hydrogen with electrons shared between them. Hydrogen bonds form between water molecules Hydrogen bonds form between water molecules Up to four may form clusters which break and reform all the time Up to four may form clusters which break and reform all the time

Water molecule

Hydrogen Bonds in water Hydrogen bonds

Key features of water Key features of water as a constituent of living organisms Key features of water as a constituent of living organisms Good solvent High specific heat capacity High latent heat of vaporisation High cohesion Reactive Incompressibility

Learning Outcomes To be able to To be able to Define metabolism State the functions of biological molecules Name monomers and polymers of carbohydrates, fats, proteins and nucleic acids Describe general features of condensation and hydrolysis reaction

Biological Molecules Molecular biology Molecular biology the study of structure and functioning of biological molecules. Metabolism Metabolism sum total of all biochemical reactions in the body.

Nutrients and Health To maintain a healthy body To maintain a healthy body Carbohydrates Lipids Proteins Vitamins and minerals Nucleic acid Water fibre

Key Biological Molecules There are 4 key biological molecules There are 4 key biological molecules Carbohydrates lipids proteins nucleic acids

Building blocks of life 4 most common elements in the living organisms 4 most common elements in the living organisms hydrogen carbon oxygen nitrogen

Biochemicals and bonds Covalent bonds join atoms together to form molecules Covalent bonds join atoms together to form molecules Carbon is able to make 4 covalent bonds Carbon is able to make 4 covalent bonds Carbon can bond to form chains or rings with other atoms bonded to the chain Carbon can bond to form chains or rings with other atoms bonded to the chain Carbon can also form double bonds Carbon can also form double bonds E.g. C=C or C=O

Polymers poly means many = polymers poly means many = polymers Macromolecules are made up of repeating subunits that are joined end to end, they are easy to make as the same reaction is repeated many times. Macromolecules are made up of repeating subunits that are joined end to end, they are easy to make as the same reaction is repeated many times. Polymerisation is the making of polymers. Polymerisation is the making of polymers.

Macromolecules Macromolecule Subunit (monomer) polysaccharidemonosaccharide proteins amino acids nucleic acids nucleotides

Metabolism Metabolism is the sum of all of the reactions that take place within organisms Metabolism is the sum of all of the reactions that take place within organisms Anabolism Build up of larger, more complex molecules from smaller, simpler ones Build up of larger, more complex molecules from smaller, simpler ones This process requires energy This process requires energy Catabolism The breakdown of complex molecules into simpler ones The breakdown of complex molecules into simpler ones This process releases energy This process releases energy

Condensation reactions In a condensation reaction In a condensation reaction A water molecule is released A new covalent bond is formed A larger molecule is formed by bonding together of smaller molecules

Hydrolysis Reactions In hydrolysis reactions In hydrolysis reactions A water molecule is used A covalent bond is broken Smaller molecules are formed by the splitting of a larger molecule

Hydrolysis and condensation O OHHO CONDENSATION HYDROLYSIS

Learning Outcomes describe, with the aid of diagrams, the structure of an amino acids describe, with the aid of diagrams, the structure of an amino acids describe, with the aid of diagrams, the formation and breakage of peptide bonds in the synthesis and hydrolysis of dipeptides and polypeptides describe, with the aid of diagrams, the formation and breakage of peptide bonds in the synthesis and hydrolysis of dipeptides and polypeptides

Introduction to protein 50% of the dry mass of cells is protein 50% of the dry mass of cells is protein Important functions include Important functions include Cell membranes Haemoglobin Anti-bodies Enzymes Keratin (hair and skin) collagen

Structure of proteins All proteins are made up of the same basic components amino acidsAll proteins are made up of the same basic components amino acids There are 20 different amino acids, which alter by having different residual groups ( R groups )There are 20 different amino acids, which alter by having different residual groups ( R groups ) A single chain of amino acids makes a polypeptideA single chain of amino acids makes a polypeptide

Structure of an amino acid Amino acids contain Amino acids contain Amine group (NH 2 ) Carboxylic acid group (COOH) Joined at the same C atom

Structure of an amino acid H H OH N H R CC O Amine group Carboxyl group R group varies in different amino acids

TEST TIME Build an amino acid using the molymod models Build an amino acid using the molymod models Glycine is an amino acid where the R group is hydrogen change you molecule into glycine Glycine is an amino acid where the R group is hydrogen change you molecule into glycine Build a dipeptide using the molymod models Build a dipeptide using the molymod models

Different Amino Acids GlycineR group = H GlycineR group = H AlanineR group = CH 3 AlanineR group = CH 3 ValineR group = C 3 H 7 ValineR group = C 3 H 7 You will be expected to learn how to draw the basic structure of an amino acid. Remember that each Amino acid has its own specific R group You will be expected to learn how to draw the basic structure of an amino acid. Remember that each Amino acid has its own specific R group

Learning Outcomes explain, with the aid of diagrams, the term primary structure explain, with the aid of diagrams, the term primary structure explain, with the aid of diagrams, the term secondary structure with reference to hydrogen bonding explain, with the aid of diagrams, the term secondary structure with reference to hydrogen bonding

Peptide bond H H N H R CC O H N H R CC O OH Peptide bond

Building a polypeptide Peptide bonds are formed in condensation reactions Peptide bonds are formed in condensation reactions Primary structurePrimary structure The primary structure of a polypeptide is its amino acid sequence This is determined by the gene that codes for the polypeptide Amino acid Peptide Bond

Secondary Structure Polypeptides become twisted or coiled Polypeptides become twisted or coiled They fold into one of two structures They fold into one of two structures Alpha helix (right handed helix) Beta-pleated sheet Hydrogen bonds hold coils in place Hydrogen bonds hold coils in place Weak but give stability to the parts of a protein molecule. COHN

Learning Outcomes explain, with the aid of diagrams, the term tertiary structure with reference to hydrophobic and hydrophilic interactions, disulphide bonds and ionic interactions explain, with the aid of diagrams, the term tertiary structure with reference to hydrophobic and hydrophilic interactions, disulphide bonds and ionic interactions

Tertiary Structure Folding of the polypeptide to give a more complex 3-D shape, the shape is specific to the function of the polypeptide. Folding of the polypeptide to give a more complex 3-D shape, the shape is specific to the function of the polypeptide. Examples Examples Hormone must fit into the hormone receptor in a target cell Enzymes have a complementary active site to its substrate

Tertiary Structure - bonds Four types of bond help to hold the folded proteins in their precise shape. Four types of bond help to hold the folded proteins in their precise shape. Hydrogen Bonds Disulphide bonds Ionic bonds Hydrophobic interactions

Hydrogen Bonds Between polar groups Between polar groups Electronegative oxygen atoms of the CO Electropositive H atoms on either the OH or NH groups.

Disulphide bonds Between sulfur-containing R groups of the amino acid cysteine. Between sulfur-containing R groups of the amino acid cysteine. Covalent bonds Covalent bonds Form strong links which make the tertiary protein structure very stable. Form strong links which make the tertiary protein structure very stable. This bond can be broken by reducing agents This bond can be broken by reducing agents

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

Hydrophobic Interactions These are interactions between the non- polar side chains of a protein molecule. These are interactions between the non- polar side chains of a protein molecule. The bond forms between non-polar, hydrophobic R groups on the amino acids. The bond forms between non-polar, hydrophobic R groups on the amino acids. Once the two hydrophobic molecules are close together the interaction is reinforced by Van der Waals attractions (which provide the weak bond). Once the two hydrophobic molecules are close together the interaction is reinforced by Van der Waals attractions (which provide the weak bond).

Van der Waals attractions Electrons are always in motion, and are not always evenly distributed about a molecule. Electrons are always in motion, and are not always evenly distributed about a molecule. This results in areas of positive and negative charge, which are continuously changing, and enables molecules to stick to one another. This results in areas of positive and negative charge, which are continuously changing, and enables molecules to stick to one another.

Denaturing Protein The Polar R groups of proteins interact with water forming hydrogen bonds that face outwards, This creates a hydrophobic core to the molecule The Polar R groups of proteins interact with water forming hydrogen bonds that face outwards, This creates a hydrophobic core to the molecule When proteins are heated these bonds break, the tertiary structure changes and the protein does not function. When proteins are heated these bonds break, the tertiary structure changes and the protein does not function. The destruction of shape or loss of function is denaturation. The destruction of shape or loss of function is denaturation.

Denaturing Proteins Frying an egg Frying an egg

Learning Outcomes explain, with the aid of diagrams, the term quaternary structure, with reference to the structure of haemoglobin explain, with the aid of diagrams, the term quaternary structure, with reference to the structure of haemoglobin

Quaternary Structure Association of different polypeptide chains bonded together to form intricate shapes Association of different polypeptide chains bonded together to form intricate shapes Sometimes contain prosthetic groups, which are a permanent part of a protein molecule but not made of amino acids Sometimes contain prosthetic groups, which are a permanent part of a protein molecule but not made of amino acids

Quaternary Structure Globular proteinGlobular protein Molecules curl up into a ball shape Examples myoglobin, haemoglobin Metabolic roles Fibrous ProteinsFibrous Proteins Form long strands Usually insoluble Have a structural role Examples keratin, collagen

Haemoglobin Function oxygen carrying pigment found in red blood cells Function oxygen carrying pigment found in red blood cells Structure Structure 4 polypeptides 2 x -globin 2 x -globin 2 x -globin 2 x -globin Each polypeptide has a 3 o structure stabilised by hydrophobic interactions in the centre In the middle each polypeptide in a haem group

OK so lets summarise proteins

Protein structure and diversity It is difficult to describe in a simple sentence the role of proteins. It is difficult to describe in a simple sentence the role of proteins. when there is something to do, it is a protein that does it. Therefore proteins areTherefore proteins are important numerous very diverse very complex, able to perform actions and reactions under some circumstances

Some examples of proteins Antibodies:Antibodies: they recognise molecules of invading organisms. Receptors:Receptors: part of the cell membrane, they recognise other proteins, or chemicals, and inform the cell... Enzymes:Enzymes: assemble or digest. Neurotransmitters and some hormones:Neurotransmitters and some hormones: Trigger the receptors... Channels and pores:Channels and pores: holes in the cell membrane

Summary of levels of protein 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 together

Learning Outcomes describe, with the aid of diagrams, the structure of a collagen molecule describe, with the aid of diagrams, the structure of a collagen molecule compare the structure and function of haemoglobin (and example of a globular protein) and collagen (an example of a fibrous protein) compare the structure and function of haemoglobin (and example of a globular protein) and collagen (an example of a fibrous protein)

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

Structure of collagen 3 identical polypeptide chains wound into a triple helix; this is a left- handed helix. 3 identical polypeptide chains wound into a triple helix; this is a left- handed helix. Each polypeptide is about 1000 amino acids long Each polypeptide is about 1000 amino acids long Primary structure Primary structure Every 3 amino acids = glycine Every 3 amino acids = glycine

Collagen Sequences of polypeptide chains are staggered so that glycine is found at every position along the triple helix. Sequences of polypeptide chains are staggered so that glycine is found at every position along the triple helix. The three polypeptide chains are held together by hydrogen bonds. The three polypeptide chains are held together by hydrogen bonds. Adjacent molecules of collagen are held together by covalent bonds formed between the carboxyl group of one amino acid and the amine group of another. Adjacent molecules of collagen are held together by covalent bonds formed between the carboxyl group of one amino acid and the amine group of another.

Revision Activity Revision Activity compare the structure and function of haemoglobin and collagen Try to make a bullet point list of at least 10 things Try to make a bullet point list of at least 10 things

Collagen vs Haemoglobin Collagen Collagen Repeating sequence of amino acids Most of molecule has left handed helix structures Does not contain prosthetic group Insoluble in water Metabolically unreactive Structural role Haemoglobin Precise 1 o structure 2 o structure wound into alpha helix Contains prosthetic group Soluble in water Metabolically reactive

Learning Outcomes describe, with the aid of diagrams, the molecular structure of alpha- glucose as an example of a monosaccharide carbohydrate describe, with the aid of diagrams, the molecular structure of alpha- glucose as an example of a monosaccharide carbohydrate state the structural difference between alpha and beta glucose state the structural difference between alpha and beta glucose

Carbohydrates contain carbon, hydrogen & oxygen contain carbon, hydrogen & oxygen organic compounds organic compounds general formula C x (H 2 O) y general formula C x (H 2 O) y glucose C 6 H 12 O 6 3 main groups 3 main groups monosaccharides disaccharides polysaccharides

Monosaccharides dissolve easily in water to form sweet solution dissolve easily in water to form sweet solution general formula (CH 2 O) n, where n is the number of carbons general formula (CH 2 O) n, where n is the number of carbons 3 main types 3 main types Trioses(3C) Pentoses(5C) Hexoses(6C)

Glucose - a hexose Glucose is made of a chain of atoms long enough to close up upon itself and form a stable ring structure. Glucose is made of a chain of atoms long enough to close up upon itself and form a stable ring structure. Carbon atom 1 ( 1 C) joins to the O on 5 C. Carbon atom 1 ( 1 C) joins to the O on 5 C. The six sided structure formed is known as a pyranose ring. The six sided structure formed is known as a pyranose ring.

Chain for a glucose 1C1C 2C2C 3C3C 4C4C 5C5C 6 CH 2 OH OH H H O H H H

-glucose ring form 1C1C 2C2C 3C3C 4C4C 5C5C 6 CH 2 OH OH H H O H H H

Making the drawing easier O H OH

Glucose a hexose Isomers Isomers possess the same molecular formula but differ in arrangement of atoms. -glucose and -glucose are isomers of glucose. -glucose and -glucose are isomers of glucose. Depending on whether the OH of 1C is above or below the plane of the ring.

The Isomers -glucose -glucose -glucose O OH H O H

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

Disaccharides and the Glycosidic Bond Monosaccharides combine in pairs to give a disaccharide, this involves the loss of a single water molecule Monosaccharides combine in pairs to give a disaccharide, this involves the loss of a single water molecule This reaction is called condensation This reaction is called condensation The bond formed is known as a glycosidic bond. The bond formed is known as a glycosidic bond. To break a disaccharide the addition of water is needed, this reaction is called hydrolysis. To break a disaccharide the addition of water is needed, this reaction is called hydrolysis.

Formation and breakage of the glycosidic bond

Polysaccharides Final molecules maybe 1000s of monosaccharides, the size of these molecules make them insoluble. Final molecules maybe 1000s of monosaccharides, the size of these molecules make them insoluble. Polysaccharides are NOT sugars Polysaccharides are NOT sugars The most important polysaccharides are built up entirely of glucose molecules. The most important polysaccharides are built up entirely of glucose molecules. These are starch, glycogen and cellulose. These are starch, glycogen and cellulose.

Learning Outcomes describe, with the aid of diagrams, the structure of starch describe, with the aid of diagrams, the structure of starch describe, with the aid of diagrams, the structure of glycogen describe, with the aid of diagrams, the structure of glycogen

Starch A mixture of two substances amylose and amylopectin. A mixture of two substances amylose and amylopectin. Starch granules are insoluble in water. Starch granules are insoluble in water. The form of carbohydrate used for storage in plants. The form of carbohydrate used for storage in plants. Starch grains build up in chloroplasts, or in storage organs such as potato tubers. Starch grains build up in chloroplasts, or in storage organs such as potato tubers.

Amylose Long unbranching chains Long unbranching chains 1-4 glycosidic bonds 1-4 glycosidic bonds formed by condensation reactions. formed by condensation reactions. The chains curve and coil into helical structures. The chains curve and coil into helical structures.

Amylopectin 1,4 linked -glucose molecules form chains 1,4 linked -glucose molecules form chains shorter shorter branch out to the sides. branch out to the sides. The branches form by 1-6 linkages

Comparison of the structure of amylose and amylopectin molecules

Glycogen The form in which carbohydrate is stored in the animal body. The form in which carbohydrate is stored in the animal body. Glucose is converted to glycogen in the liver and muscles, Glucose is converted to glycogen in the liver and muscles, it is kept until required then it is broken down again into glucose. Formed by -glucose molecules joining in 1-4 and 1-6 links Formed by -glucose molecules joining in 1-4 and 1-6 links There are more branches containing a smaller number of glucose molecules than amylopectin There are more branches containing a smaller number of glucose molecules than amylopectin

Structure of glycogen

Starch and glycogen Starch and Glycogen are energy storage molecules Starch and Glycogen are energy storage molecules which take up little space due to their compact shapes which take up little space due to their compact shapes They help to prevent too high concentrations of glucose in cells. They help to prevent too high concentrations of glucose in cells.

Learning outcomes describe, with the aid of diagrams, the structure of cellulose describe, with the aid of diagrams, the structure of cellulose

Cellulose Most abundant organic molecule on the planet due to its presence in cell walls. Most abundant organic molecule on the 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 -glucose molecules in a long unbranched chain. Polymer of about 10,000 -glucose molecules in a long unbranched chain. Many chains run parallel to each other and have cross linkages between them, giving increased stability. Many chains run parallel to each other and have cross linkages between them, giving increased stability. hydrogen bonds form these links between chains, which collectively give the structure increased strength. hydrogen bonds form these links between chains, which collectively give the structure increased strength.

Structure of cellulose

Cellulose To join together one -glucose molecule must be rotated at 180 0 relative to the other. To join together one -glucose molecule must be rotated at 180 0 relative to the other. Successive glucose molecules are linked at 180 0 to each other. Successive glucose molecules are linked at 180 0 to each other. Cellulose molecules become tightly cross- linked with each other to form bundles called micro fibrils. Cellulose molecules become tightly cross- linked with each other to form bundles called micro fibrils. Micro fibrils form cellulose fibres by hydrogen bonding giving a high tensile strength similar to steel. Micro fibrils form cellulose fibres by hydrogen bonding giving a high tensile strength similar to steel.

Learning Outcomes compare and contrast the structure and functions of starch (amylose) and cellulose compare and contrast the structure and functions of starch (amylose) and cellulose explain how the structures of glucose, starch (amylose), glycogen and cellulose molecules relate to their functions in living organisms explain how the structures of glucose, starch (amylose), glycogen and cellulose molecules relate to their functions in living organisms

Comparing polysaccharides Characteristicamyloseamylopectinglycogencellulose Found in Found as Function Monomer Bonds chain

Practice Long Answer Question Discuss the structures of glucose, starch, glycogen and cellulose in relation to their functions; include diagrams to illustrate your answer Discuss the structures of glucose, starch, glycogen and cellulose in relation to their functions; include diagrams to illustrate your answer

Learning outcomes compare, with the aid of diagrams, the structure of a triglyceride and a phospholipids compare, with the aid of diagrams, the structure of a triglyceride and a phospholipids explain how the structure of a triglyceride, phospholipids and cholesterol molecules relate to their functions in living organisms explain how the structure of a triglyceride, phospholipids and cholesterol molecules relate to their functions in living organisms

Lipids are not polymers Large molecules Large molecules few oxygen atoms few oxygen atoms many carbon and hydrogen atoms many carbon and hydrogen atoms hydrophobichydrophobic Less dense than water Less dense than water

Lipids Two important groups Two important groups Triglycerides Fats solid at room temperature Fats solid at room temperature Oils liquid at room temperature Oils liquid at room temperature phospholipids

Lipids - functions A source of energy A source of energy Store of energy (adipose tissues) Store of energy (adipose tissues) Biological membranes Biological membranes Thermal insulators / insulation Thermal insulators / insulation Buoyancy Buoyancy Protection Protection Cuticle of a leaf Internal organs Metabolic source of water Metabolic source of water hormones hormones

Glycerol and fatty acids glycerol glycerol Fatty acid H H C C C H H H OH C H C H H C H H C H H C H H C H O HO H OHO C

Fatty Acids Fatty acids have Fatty acids have an acid group at one end (COOH) Hydrocarbon chain (2 20 carbons long) Fatty acids can be Fatty acids can be Saturated Unsaturated

Saturated fatty acid All possible bonds are made with hydrogen All possible bonds are made with hydrogen HO C H C H H C H H C H H C H H C H O H

Unsaturated fatty acid One or more double bond between carbon atoms One or more double bond between carbon atoms HO C H C H C H C H H C H H C H O H

Saturated and unsaturated fatty acids Polyunsaturated Polyunsaturated more than one double bond Monounsaturated Monounsaturated only one double bond Animal lipids are often saturated and occur as fats Animal lipids are often saturated and occur as fats plant lipids are often unsaturated and occur as oils plant lipids are often unsaturated and occur as oils

Triglycerides Most common form of lipid Most common form of lipid Combination of 3 fatty acid molecules and one glycerol molecule. Combination of 3 fatty acid molecules and one glycerol molecule. Glycerol is a type of alcohol Fatty acids are organic molecules with a COOH group attached to a hydrocarbon tail.

Triglycerides Each of the glycerol molecules 3 - OH groups reacts with the carboxyl group of a fatty acid. Each of the glycerol molecules 3 - OH groups reacts with the carboxyl group of a fatty acid. This is a condensation reaction, and an ester bond is established. This is a condensation reaction, and an ester bond is established.

Structure of a triglyceride Glycerol + 3 fatty acids Glycerol + 3 fatty acids H H C C C H H H OHOH OHOH OHOH HO C O C O C O

Condensation reaction and formation of an ester bond H H C C C H H H O O O C O C O C O Ester bond

Triglycerides Triglycerides are Triglycerides are insoluble in water, soluble in some organic solvents, e.g. ether or ethanol. non-polar hydrophobic.

Roles of triglycerides Energy reserve Energy reserve Insulator against heat loss Insulator against heat loss Buoyancy Buoyancy Protection (vital organs) Protection (vital organs) Metabolic source of water. Metabolic source of water.

Phospholipids Special type of lipid Special type of lipid one of the fatty acid groups is replaced by phosphoric acid. one of the fatty acid groups is replaced by phosphoric acid. phosphoric acid is hydrophilic (attracts water) phosphoric acid is hydrophilic (attracts water) Biological significance of this molecule is its role in the cell membrane. Biological significance of this molecule is its role in the cell membrane.

Simplified structure of phospholipid

Structure 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 phospholipid

Cholesterol - structure Small molecule Small molecule -OH group is polar -OH group is polar 4 carbon rings and hydrocarbon tail are non polar 4 carbon rings and hydrocarbon tail are non polar

Cholesterol - Structure

Cholesterol - function Found in biological membranes Found in biological membranes Steroids e.g. testosterone, oestrogen and progesterone are made from cholesterol Steroids e.g. testosterone, oestrogen and progesterone are made from cholesterol Excess cholesterol Excess cholesterol Form gallstones in bile Cause atherosclerosis in blood vessels

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

Chemical Tests Chemical tests can be done to confirm the presence of various biological molecules within a sample Chemical tests can be done to confirm the presence of various biological molecules within a sample These tests are qualitative tests These tests are qualitative tests They indicate presence of a molecule not how much is present

Testing for presence of a carbohydrate Starch Starch Reducing sugar Reducing sugar Non reducing sugar Non reducing sugar

starch Iodine solution Iodine solution iodine in potassium iodide Add to solution will turn blue-black quickly if comes into contact with starch.

Starch Starch molecules curl up into long spirals, with a hole down the middle of the spiral, just the right size for an iodine molecule. Starch molecules curl up into long spirals, with a hole down the middle of the spiral, just the right size for an iodine molecule. The starch-iodine complex forms a strong blue-black colour. The starch-iodine complex forms a strong blue-black colour.

Reducing sugar Benedicts Reagent (copper II sulphate in alkaline solution) Benedicts Reagent (copper II sulphate in alkaline solution) Add benedicts reagent to the solution testing Heat in a water bath (80 o C) for 3 minutes

Reducing sugars If added to a reducing agent Cu 2+ ions are reduced to Cu +, and the change in colour to red of Copper (I) sulphate. If added to a reducing agent Cu 2+ ions are reduced to Cu +, and the change in colour to red of Copper (I) sulphate. All monosaccharides are reducing sugars; All monosaccharides are reducing sugars; Reducing sugars have an aldehyde group (H- C=0) somewhere in their molecule, which contribute an electron to the copper. Reducing sugars have an aldehyde group (H- C=0) somewhere in their molecule, which contribute an electron to the copper. Reducing sugars become oxidised. Reducing sugars become oxidised. Reducing sugar + Cu 2+ = oxidised sugar + Cu +

Non reducing sugar Heat sugar solution with acid to hydrolyse any glycosidic bonds present Heat sugar solution with acid to hydrolyse any glycosidic bonds present Neutralise solution by adding sodium hydroxide Neutralise solution by adding sodium hydroxide Add benedicts reagent Add benedicts reagent Heat in a water bath Heat in a water bath If it goes orange/red a non-reducing sugar is present. If it goes orange/red a non-reducing sugar is present.

Non-reducing sugars Not all disaccharides are reducing sugars. Not all disaccharides are reducing sugars. To check for the presence of a reducing sugar, the disaccharide needs to be broken down into its constituent monosaccharides, To check for the presence of a reducing sugar, the disaccharide needs to be broken down into its constituent monosaccharides, monosaccharides are reducing sugars and will react with benedicts solution. monosaccharides are reducing sugars and will react with benedicts solution.

Testing for the presence of proteins

Proteins Biuret reagent Biuret reagent copper sulphate and potassium or sodium hydroxide Add Biuret solution to the substance If protein present get a purple colour

proteins All proteins have several amine, NH 2, groups within their molecules. All proteins have several amine, NH 2, groups within their molecules. These groups react with copper ions to form a complex that has a strong purple colour. These groups react with copper ions to form a complex that has a strong purple colour.

Testing for the presence of lipids

lipids Emulsion test Emulsion test Shake substance (lipid) with absolute ethanol Pour ethanol into a tube containing water If no lipid is present mixture looks transparent If lipids are present looks white and cloudy.

lipids Lipids are insoluble in water, but soluble in ethanol. Lipids are insoluble in water, but soluble in ethanol. As the ethanol mixture is poured into water, lipid molecules cannot remain mixed in water and clump together to form little groups. As the ethanol mixture is poured into water, lipid molecules cannot remain mixed in water and clump together to form little groups. The lipid molecules impede light and we see an emulsion (white cloudiness). The lipid molecules impede light and we see an emulsion (white cloudiness).

Learning Outcomes describe how the concentration of glucose in a solution may be determined by using colorimetry describe how the concentration of glucose in a solution may be determined by using colorimetry Practice writing out this method Practice writing out this method

Nucleic Acids Module 1 Biological Molecules Unit 2 Molecules, Biodiversity, food and health

Learning Outcomes state that deoxyribonucleic acid (DNA) is a polynucleotide, usually double stranded and made up of the nucleotides adenine (A), thymine (T), cytosine (C) and guanine (G) state that deoxyribonucleic acid (DNA) is a polynucleotide, usually double stranded and made up of the nucleotides adenine (A), thymine (T), cytosine (C) and guanine (G) state that ribonucleic acid (RNA) is a polynucleotide usually single-stranded and made up of the nucleotides adenine (A), uracil (U), cytosine (C) and guanine (G) state that ribonucleic acid (RNA) is a polynucleotide usually single-stranded and made up of the nucleotides adenine (A), uracil (U), cytosine (C) and guanine (G)

Nucleic Acids DNA and RNA The nucleic acids have The nucleic acids have The ability to carry instructions The ability to be copied DNA and RNA are polymers; the individual nucleotides are the monomers that build up the polynucleotides. DNA and RNA are polymers; the individual nucleotides are the monomers that build up the polynucleotides. DNA = deoxyribonucleic acid RNA = ribonucleic acid

Nucleotides Nucleotides are made up of three smaller components Nucleotides are made up of three smaller components Nitrogen containing base Pentose sugar (5 carbon atoms) Phosphate group Phosphate sugar base

Bases There are 5 different nitrogen-containing bases: There are 5 different nitrogen-containing bases: A Adenine T Thymine (DNA only) U Uracil (RNA only) G Guanine CCytosine DNA A, G, C and T DNA A, G, C and T RNA - A, G, C and U RNA - A, G, C and U

Bases Purines (larger) Purines (larger) These have double rings of carbon and nitrogen atoms adenine Guanine Pyrimidines (smaller) Pyrimidines (smaller) These have a single ring of carbon and nitrogen atoms Thymine uracil cytosine

Polynucleotides Polynucleotides strands are formed of alternating sugars and phosphates Polynucleotides strands are formed of alternating sugars and phosphates

DNA Cut and paste activity Cut and paste activity Cut out the nucleotides and stick them down to form a double stranded DNA molecule

Learning Outcomes describe, with the aid of diagrams, describe, with the aid of diagrams, how hydrogen bonding between complementary base pairs (A-T, G-C) on two anti-parallel DNA polynucleotide leads to the formation of a DNA molecule, how the twisting of DNA produces its double-helix shape outline, with the aid of diagrams,

DNA 2 strands side-by-side running in opposite directions (antiparallel) 2 strands side-by-side running in opposite directions (antiparallel) The two strands are held together by hydrogen bonds. The two strands are held together by hydrogen bonds.

Complementary base pairs A purine in one strand is always opposite a pyramidine in the other strand. A purine in one strand is always opposite a pyramidine in the other strand. Adenine thymine Guanine - cytosine DNA forms a double helix, the strands are held in place by hydrogen bonds. DNA forms a double helix, the strands are held in place by hydrogen bonds. These bonds can be broken relatively easily, this is important for protein synthesis and DNA replication. These bonds can be broken relatively easily, this is important for protein synthesis and DNA replication.

Pupil Activity Build your own DNA molecule Build your own DNA molecule Equipment needed: Equipment needed: 2 purple pipe cleaners 2 white pipe cleaners 6 red beads 6 yellow beads 12 aqua beads 12 purple beads Follow the instructions on the handout Follow the instructions on the handout

DNA a double helix Two polynucleotides held together by hydrogen bonds Two polynucleotides held together by hydrogen bonds Complementary base pairs Complementary base pairs A T (2 hydrogen bonds) G C (3 hydrogen bonds) Polynucleotides are anti-parallel Polynucleotides are anti-parallel Parallel but with chains running in opposite directions 3 to 5direction 3 to 5direction 5 to 3direction 5 to 3direction

Structure to function Information storage Information storage Long molecules replication Base-paring rules Base-paring rules Hydrogen bonds Hydrogen bonds Stable

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

DNA Replication Each polynucleotide acts as a template for making a new polynucleotide Each polynucleotide acts as a template for making a new polynucleotide This is known as semi-conservative replication This is known as semi-conservative replication

Experimental Evidence for the semi- conservative replication of DNA Three ways were suggested for DNA replication Three ways were suggested for DNA replication Conservative replication Semi-conservative replication Dispersive replication

Scientists thought that semi-conservative replication was most likely but there was no evidence to support this theory. Scientists thought that semi-conservative replication was most likely but there was no evidence to support this theory. 1958 Matthew Meselsohn and Franklin Stahl demonstrated that DNA replication was semi-conservative following experiments with E. Coli. 1958 Matthew Meselsohn and Franklin Stahl demonstrated that DNA replication was semi-conservative following experiments with E. Coli.

Stage 1 E. Coli were grown in a medium containing a heavy isotope nitrogen ( 15 N). E. Coli were grown in a medium containing a heavy isotope nitrogen ( 15 N). The bacteria used 15N to make the purine and pyrimidine bases in its DNA. The bacteria used 15N to make the purine and pyrimidine bases in its DNA.

Stage 2 After many generations, they were then transferred to light isotope nitrogen ( 14 N) After many generations, they were then transferred to light isotope nitrogen ( 14 N)

Stage 3 Bacteria were taken from the new medium after one generation, two generations and later generations. Bacteria were taken from the new medium after one generation, two generations and later generations. DNA was extracted from each group of bacteria, DNA was extracted from each group of bacteria, samples were placed in a solution of caesium chloride and spun in a centrifuge. samples were placed in a solution of caesium chloride and spun in a centrifuge.

Results Generation123

Conclusions 1.Explain why the band of DNA in the first generation is higher than that in the parental generation. 2.If replication were conservative what results would you expect in the first generation? 3.If the DNA had replicated dispersively what results would you expect in the first generation? 4.Explain how the second generation provides evidence that the DNA has reproduced semi- conservatively and not dispersively 5.What results would you expect to see from a third generation, draw a diagram of the results?

Explanation of results Parental generation - both strands made with 15 N Parental generation - both strands made with 15 N First generation DNA made of one strand 15 N and one strand 14 N First generation DNA made of one strand 15 N and one strand 14 N Second generation some DNA made of 2 strands of 14 N and some made of 15 N and 14 N. Second generation some DNA made of 2 strands of 14 N and some made of 15 N and 14 N.

DNA Replication Double helix unwinds and the DNA unzips as hydrogen bonds break Double helix unwinds and the DNA unzips as hydrogen bonds break Existing polynucleotides acts as a template for assembly of nucleotides Existing polynucleotides acts as a template for assembly of nucleotides Free nucleotides move towards exposed bases of DNA Free nucleotides move towards exposed bases of DNA Base pairing occurs between free nucleotides and exposed bases Base pairing occurs between free nucleotides and exposed bases Enzyme DNA polymerase forms covalent bonds between free nucleotides Enzyme DNA polymerase forms covalent bonds between free nucleotides Two daughter DNA molecules form separate double helices. Two daughter DNA molecules form separate double helices.

Learning Outcomes state that a gene is a sequence of DNA nucleotides that codes for a polypeptide state that a gene is a sequence of DNA nucleotides that codes for a polypeptide outline the roles of DNA and RNA in living organisms (the concept of protein synthesis must be considered in outline only) outline the roles of DNA and RNA in living organisms (the concept of protein synthesis must be considered in outline only)

RNA single strand, containing single strand, containing uracil not thymine Ribose sugar There are 3 forms of RNA There are 3 forms of RNA Messenger RNAmRNA Transfer RNAtRNA Ribosomal RNArRNA

DNA and Protein Synthesis All chemical reactions are controlled by enzymes, all enzymes are proteins, DNA codes for proteins, therefore DNA controls all the activities of a cell. All chemical reactions are controlled by enzymes, all enzymes are proteins, DNA codes for proteins, therefore DNA controls all the activities of a cell. The shape and behaviour of a protein depends on the exact sequence of amino acids in the primary structure (polypeptide). The shape and behaviour of a protein depends on the exact sequence of amino acids in the primary structure (polypeptide).

The Genetic Code DNA determines the exact order in which amino acids join together. DNA determines the exact order in which amino acids join together. The genetic code The genetic code sequence of bases along the DNA molecule, There are 20 different amino acids, only 4 bases, a sequence of 3 bases codes for an amino acid. This is called the triplet code. A gene is the part of a DNA molecule, which codes for just one polypeptide. A gene is the part of a DNA molecule, which codes for just one polypeptide.

Protein Synthesis The process of protein synthesis occurs in four stages: The process of protein synthesis occurs in four stages: transcription of DNA to make messenger RNA (mRNA) movement of mRNA from the nucleus to the cytoplasm amino acid activation translation of mRNA to make a polypeptide

Transcription This is the process by which mRNA is built up against one side of an opened up piece of DNA. This is the process by which mRNA is built up against one side of an opened up piece of DNA. The relevant section of DNA unwinds, the hydrogen bonds between base pairs are broken and the two strands split apart. The relevant section of DNA unwinds, the hydrogen bonds between base pairs are broken and the two strands split apart. Free nucleotides then assemble against one strand of DNA. Free nucleotides then assemble against one strand of DNA. The enzyme RNA polymerase moves along the DNA adding on RNA nucleotide at a time. The enzyme RNA polymerase moves along the DNA adding on RNA nucleotide at a time.

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

Amino Acid Activation Enzymes attach amino acids to their specific tRNA molecule. Enzymes attach amino acids to their specific tRNA molecule. This needs energy supplied by ATP. This needs energy supplied by ATP. An anti-codon is a triplet of bases forming part of a tRNA molecule and it is complementary to a codon. An anti-codon is a triplet of bases forming part of a tRNA molecule and it is complementary to a codon.

Translation Amino acid attaches to the ribosome Amino acid attaches to the ribosome Adjacent amino acids are joined together by peptide bonds and a polypeptide chain is built up. Adjacent amino acids are joined together by peptide bonds and a polypeptide chain is built up. This carries on until the ribosome reaches a stop codon, the polypeptide breaks loose from the ribosome and translation is complete. This carries on until the ribosome reaches a stop codon, the polypeptide breaks loose from the ribosome and translation is complete.

Enzymes

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

Recap What is metabolism? What is metabolism? sum total of all biochemical reactions in the body.

Enzymes All enzymes are All enzymes are globular proteins catalysts Specific affected by temperature and pH

More about enzymes Two basic functions within cells: Two basic functions within cells: Act as biological catalysts Provide a mechanism whereby individual chemical reactions can be controlled Enzyme molecules have a specific 3D shape and all possess an active site. Enzyme molecules have a specific 3D shape and all possess an active site.

Learning Outcomes Follow the progress of an enzyme- catalysed reaction; Follow the progress of an enzyme- catalysed reaction;

Catalase The enzyme catalase breaks down hydrogen peroxide into water and oxygen. The enzyme catalase breaks down hydrogen peroxide into water and oxygen. 2H 2 O 2 => 2H 2 O + O 2 Hydrogen peroxide is formed continually as a bi- product of various chemical reactions in living cells. Hydrogen peroxide is formed continually as a bi- product of various chemical reactions in living cells. It is toxic and if the cells did not immediately break it down it would kill them. It is toxic and if the cells did not immediately break it down it would kill them.

Investigation 1 Catalase is the fastest enzyme known. Catalase is the fastest enzyme known. In this investigation you will be able to watch the action of catalase and compare it with an inorganic catalyst that catalyses the same reaction. In this investigation you will be able to watch the action of catalase and compare it with an inorganic catalyst that catalyses the same reaction. 1.Pour hydrogen peroxide into two test tubes to a depth of about 2cm. 2.Into one test tube sprinkle about 0.1g of manganese dioxide. 3.Into the 2nd test tube put in a 1cm 2 piece of potato. 4.Observe the two test tubes and record what happens.

Results Describe the difference in reaction with the inorganic catalyst and the organic catalyst Describe the difference in reaction with the inorganic catalyst and the organic catalyst

Investigation 2 Graduated measuring cylinder 15ml Hydrogen peroxide water

Method Design a results table to record the oxygen produced every 10 seconds. Design a results table to record the oxygen produced every 10 seconds. cut up 4cm 3 piece of potato into this slices into the conical flask, and start recording results immediately. cut up 4cm 3 piece of potato into this slices into the conical flask, and start recording results immediately. Take a reading for the amount of oxygen produced every 10 seconds, until the oxygen is no longer being produced. Take a reading for the amount of oxygen produced every 10 seconds, until the oxygen is no longer being produced.

Extension If you have time, you could repeat the above experiment, but this time grind up the 4cm 3 of potato with some fine sand. How do the results compare? If you have time, you could repeat the above experiment, but this time grind up the 4cm 3 of potato with some fine sand. How do the results compare?

Results Draw a graph of oxygen produced against time. Draw a graph of oxygen produced against time. Describe the graph in terms of interaction between the molecules of catalase and hydrogen peroxide. Describe the graph in terms of interaction between the molecules of catalase and hydrogen peroxide. How could you adapt this experiment to investigate the effect of the following on the rate of the reaction. How could you adapt this experiment to investigate the effect of the following on the rate of the reaction. temperature pH substrate concentration enzyme concentration

Learning Outcomes state that enzyme action may be intracellular or extra cellular; state that enzyme action may be intracellular or extra cellular; describe, with the aid of diagrams, the mechanism of action of enzyme molecules, with reference to describe, with the aid of diagrams, the mechanism of action of enzyme molecules, with reference to specificity, active site, lock and key hypothesis, induced-fit hypothesis, enzyme-substrate complex, enzyme-product complex lowering of activation energy

Active Site The Active site is the region to which another molecule or molecules can bind. This molecule is the substrate of the enzyme. The Active site is the region to which another molecule or molecules can bind. This molecule is the substrate of the enzyme. The enzyme and substrate form an enzyme-substrate complex. The enzyme and substrate form an enzyme-substrate complex. When enzyme and substrate collide in the correct orientation, the substrate becomes attached and held temporarily in position at the active site. When enzyme and substrate collide in the correct orientation, the substrate becomes attached and held temporarily in position at the active site.

Substrate end products Enzyme and substrate molecules then interact so that a chemical reaction involving the substrates takes place and the appropriate products are formed. Enzyme and substrate molecules then interact so that a chemical reaction involving the substrates takes place and the appropriate products are formed. When the reaction is complete, the product or products leave the active site. When the reaction is complete, the product or products leave the active site.

Enzyme Specificity Active sites are specific for one type of moleculeActive sites are specific for one type of molecule Examples of specificityExamples of specificity Amylase breaks down glycosidic bonds in starch to form maltose Catalase breaks down hydrogen peroxide into water and oxygen Trypsin is a protease that only breaks peptide bonds next to the amino acids arginine and lysine

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

Induced fit Theory Active site is a cavity of a particular shape Active site is a cavity of a particular shape initially the active site is not the correct shape in which to fit the substrate. initially the active site is not the correct shape in which to fit the substrate. As the substrate approaches the active site, the site changes and results in being a perfect fit. As the substrate approaches the active site, the site changes and results in being a perfect fit. After the reaction has taken place and the products have gone. After the reaction has taken place and the products have gone. The active site returns to its normal shape. The active site returns to its normal shape.

Metabolism A catabolic reaction A catabolic reaction substrate has been broken down An anabolic reaction An anabolic reaction substrate used to build a new molecule

Lowering of Activation Energy Activation energy is the energy given temporarily to a substrate to convert it into a product. Activation energy is the energy given temporarily to a substrate to convert it into a product. The higher the activation energy the slower the reaction. The higher the activation energy the slower the reaction. Enzymes help to decrease activation energy by providing an active site where reactions can occur more easily than elsewhere. Enzymes help to decrease activation energy by providing an active site where reactions can occur more easily than elsewhere.

Lowering Activation Energy Activation energy without enzyme Activation energy with enzyme

Learning Outcomes To follow the progress of an enzyme- catalysed reaction; To follow the progress of an enzyme- catalysed reaction;

Experiments with enzymes Follow the time course of an enzyme-catalysed reaction by measuring Follow the time course of an enzyme-catalysed reaction by measuring rates of formation of products (for example using catalase), rate of disappearance of substrate (for example using amylase). When an enzyme and a substrate are mixed together, a reaction begins. Substrate molecules collide with the enzyme and bind to its active site; product molecules are formed. When an enzyme and a substrate are mixed together, a reaction begins. Substrate molecules collide with the enzyme and bind to its active site; product molecules are formed.

Experiments with enzymes As the reaction proceeds the number of substrate molecules decreases and the number of product molecules increase. The number of enzyme molecules remains constant. As the reaction proceeds the number of substrate molecules decreases and the number of product molecules increase. The number of enzyme molecules remains constant. We can measure the rate of a reaction by measuring either: We can measure the rate of a reaction by measuring either: Increasing product Decreasing substrate

Increasing Product Example: catalase breaks down hydrogen peroxide into water and oxygen

Decreasing Substrate Example: amylase breaks down starch into maltose

Explanations for the course of reaction As the reaction proceeds there is less substrate available, therefore less product gets released. As the reaction proceeds there is less substrate available, therefore less product gets released. Rate of reaction is quickest at the beginning when there is a high concentration of substrate. Rate of reaction is quickest at the beginning when there is a high concentration of substrate. Later the substrate becomes the limiting factor and the reaction slows down. Later the substrate becomes the limiting factor and the reaction slows down. Eventually all substrate is used up, so the reaction stops Eventually all substrate is used up, so the reaction stops

Learning Outcomes describe and explain the effects of pH, temperature, enzyme concentration and substrate concentration on enzyme activity; describe and explain the effects of pH, temperature, enzyme concentration and substrate concentration on enzyme activity; describe how the effects of pH, temperature, enzyme concentration and substrate concentration on enzyme activity can be investigated experimentally describe how the effects of pH, temperature, enzyme concentration and substrate concentration on enzyme activity can be investigated experimentally

Factors Affecting enzyme Activity Enzyme Concentration Enzyme Concentration Substrate concentration Substrate concentration Temperature Temperature pH pH

Enzyme Concentration The rate of reaction is directly proportional to the enzyme concentration The rate of reaction is directly proportional to the enzyme concentration assuming that there are plenty of substrate molecules and enzymes are the only limiting factors. assuming that there are plenty of substrate molecules and enzymes are the only limiting factors.

Enzyme Concentration

Substrate concentration For a given amount of enzyme, the rate of an enzyme controlled reaction increases with substrate concentration, up to a certain point. For a given amount of enzyme, the rate of an enzyme controlled reaction increases with substrate concentration, up to a certain point. This point is Vmax, which is the maximum rate of reaction; the amount of enzyme becomes the limiting factor. This point is Vmax, which is the maximum rate of reaction; the amount of enzyme becomes the limiting factor.

Substrate concentration

Temperature An increase in temperature affects the rate of reaction in two ways An increase in temperature affects the rate of reaction in two ways Factor 1 Factor 1 As the temperature increase the kinetic energy of the substrate and enzyme molecules increases and they move faster. The faster the molecules move the more often they collide and the greater the rate of reaction.

Temperature Factor 2 Factor 2 As temperature increases, more atoms which make up the enzyme molecules vibrate. This breaks down the bonds which hold the molecules in the precise shape. The enzyme becomes denatured and loses catalytic properties.

Temperature OPTIMUM TEMPERATURE OPTIMUM TEMPERATURE temperature at which an enzyme catalyses a reaction at a maximum rate.

Temperature

pH The precise 3-D shape of an enzyme is partly a result of hydrogen bonding. The precise 3-D shape of an enzyme is partly a result of hydrogen bonding. These bonds maybe broken down by high concentrations of H+ ions. These bonds maybe broken down by high concentrations of H+ ions. When pH changes from the optimum When pH changes from the optimum shape of enzyme changes affinity of substrate for the active site decreases

Online resources Online simulation of practical available at Online simulation of practical available at http://mvhs.mbhs.edu/coresims/enzyme/inde x.php http://mvhs.mbhs.edu/coresims/enzyme/inde x.php http://mvhs.mbhs.edu/coresims/enzyme/inde x.php Good simulation of the theory of temp/pH available at AS guru Good simulation of the theory of temp/pH available at AS guru www.bbc.co.uk www.bbc.co.uk Chemistry for biologists Chemistry for biologists www.chemsoc.org/networks/learnnet/cfb/ www.chemsoc.org/networks/learnnet/cfb/

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

Enzyme Inhibitors Inhibitors prevent enzymes from working Inhibitors prevent enzymes from working There are two types of inhibitor There are two types of inhibitor competitive non-competitive.

Competitive Inhibitors Have a similar shape to the normal substrate and are able to bind to the active site. Have a similar shape to the normal substrate and are able to bind to the active site. Do not react with the active site but leave after a time without any product forming. Do not react with the active site but leave after a time without any product forming. The rate of reaction decreases because the substrate molecules have to compete with the inhibitor for the active site. The rate of reaction decreases because the substrate molecules have to compete with the inhibitor for the active site. It is possible to reduce the effect of the inhibitor by adding more substrate It is possible to reduce the effect of the inhibitor by adding more substrate

Competitive inhibitor

Effect of concentrations of inhibitor and substrate on the rate of an enzyme controlled reaction No inhibitor With fixed concentration of competitive inhibitor Substrate concentration Rate of reaction

Examples Competitive inhibitor Competitive inhibitor Reversible Statins compete with a liver enzyme which helps to make cholesterol Statins compete with a liver enzyme which helps to make cholesterol Non-reversible Penicillin inhibits an enzyme that makes cell walls in some bacteria Penicillin inhibits an enzyme that makes cell walls in some bacteria

Non-competitive inhibitors Molecules bind to some part of an enzyme other than the active site. Molecules bind to some part of an enzyme other than the active site. This changes the active site so that the substrate can no longer fit. This changes the active site so that the substrate can no longer fit. If the concentration of this type of inhibitor is high enough, all enzymes maybe inhibited and the reaction slows to nothing. If the concentration of this type of inhibitor is high enough, all enzymes maybe inhibited and the reaction slows to nothing. Increasing the concentration of the substrate has no effect on this type of inhibition. Increasing the concentration of the substrate has no effect on this type of inhibition.

Non competitive inhibitor

Rate of an enzyme controlled reaction with and without a non-competitive inhibitor No inhibitor With non-competitive inhibitor Substrate concentration Rate of reaction

Examples Non-competitive inhibitor Non-competitive inhibitor Potassium cyanide bind to haem, which is part of cytochrome oxidase This is non-reversible

End product inhibition Metabolic reactions must be finely controlled and balanced; Metabolic reactions must be finely controlled and balanced; end product inhibition regulates certain enzyme-catalysed processes in organisms. end product inhibition regulates certain enzyme-catalysed processes in organisms.

End product inhibition

This is an example of non- competitive inhibition This is an example of non- competitive inhibition product 3 binds to another part of the enzyme other than the active site. It is also an example of a feedback mechanism. It is also an example of a feedback mechanism.

Learning Outcomes explain the importance of cofactors and coenzymes in enzyme-controlled reactions; explain the importance of cofactors and coenzymes in enzyme-controlled reactions; state that metabolic poisons may be enzyme inhibitors, and describe the action of one named poison; state that metabolic poisons may be enzyme inhibitors, and describe the action of one named poison; state that some medicinal drugs work by inhibiting the activity of enzyme state that some medicinal drugs work by inhibiting the activity of enzyme

Co-factor A non-protein component A non-protein component Required by enzymes to carry out reactions Required by enzymes to carry out reactions Examples Examples Metal ions in carbonic anhydrase Haem in catalase Chloride ions and amylase

Co-enzyme Organic, non protein molecules Organic, non protein molecules Role is to carry chemical groups between enzymes, linking together enzyme controlled reactions Role is to carry chemical groups between enzymes, linking together enzyme controlled reactions Examples Examples NAD, FAD and coenzyme A involved in respiration NADP involved in photosythesis

Prosthetic groups A coenzyme that is a permanent part of the enzyme A coenzyme that is a permanent part of the enzyme Example Example Carbonic anhydrase contains a zinc- based prosthetic group

Metabolic poisons Metabolic poisons can be enzyme inhibitors Metabolic poisons can be enzyme inhibitors Example Example Potassium cyanide inhibits cell respiration inhibits cell respiration Non-competitive inhibitor for the enzyme cytochrome oxidase Non-competitive inhibitor for the enzyme cytochrome oxidase Decreases the use of oxygen so that ATP can not be made Decreases the use of oxygen so that ATP can not be made The organism respires anaerobically and lactic acid builds up in the blood The organism respires anaerobically and lactic acid builds up in the blood

Medicines and enzymes Infection by viruses are treated by using chemicals that act as protease inhibitors which the virus needs to build new viral coats. Infection by viruses are treated by using chemicals that act as protease inhibitors which the virus needs to build new viral coats. Antibiotics Antibiotics Penicillin inhibits a bacterial enzyme which makes bacterial cell walls

Learning Outcomes Measure the effect of different independent variables and independent variable ranges on an enzyme-catalysed reaction; Measure the effect of different independent variables and independent variable ranges on an enzyme-catalysed reaction; Measure the effect of an inhibitor on an enzyme-catalysed reaction. Measure the effect of an inhibitor on an enzyme-catalysed reaction.

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Module 1 Biological Molecules F212 Molecules, biodiversity, food and health