Aspects of Biochemistry PDF

Aspects of Biochemistry MODULE 1: CELL AND MOLECULAR BIOLOGY  Objectives To discuss how the structure and properties of water relate to the role that water plays as a medium of life. To explain the relationship between the structure and function of glucose. To e...

Aspects of Biochemistry MODULE 1: CELL AND MOLECULAR BIOLOGY  Objectives To discuss how the structure and properties of water relate to the role that water plays as a medium of life. To explain the relationship between the structure and function of glucose. To explain the relationship between the structure and function of sucrose. To discuss how the molecular structure of starch, glycogen and cellulose relate to their functions in living organisms. To describe the molecular structure of a triglyceride and its role as a source of energy.  Objectives cont’d To describe the structure of phospholipids and their role in membrane structure and function. To describe the generalised structure of an amino acid, and the formation and breakage of a peptide bond. To explain the meaning of the terms: primary, secondary, tertiary and quaternary structures of proteins. To outline the molecular structure of haemoglobin, as an example of a globular protein, and of collagen, as an example of a fibrous protein. To carry out tests for reducing and nonreducing sugars, starch, lipids and proteins. To investigate and compare quantitatively reducing sugars and starch.  Introduction All life on Earth shares a common chemistry. This provides indirect evidence for evolution. Despite their great variety, the cells of all living organisms contain only a few groups of carbon-based compounds that interact in similar ways. There are 4 major classes of biomolecules: Carbohydrates Lipids Proteins Nucleic acids  Introduction cont’d Carbohydrates are commonly used by cells as respiratory substrates. They also form structural components in plasma membranes and cell walls. Lipids have many uses, including the bilayer of plasma membranes, certain hormones and as respiratory substrates. Proteins form many cell structures. They are also important as enzymes, chemical messengers and components of the blood. Introduction cont’d Nucleic acids carry the genetic code for the production of proteins. The genetic code is common to viruses and to all living organisms, providing evidence for evolution. The most common component of cells is water; hence our search for life elsewhere in the universe involves a search for liquid water. Water and Mixtures Aspects of Biochemistry – Part A  Structure of water Solvent Properties pH properties Water and Temperature Regulation Heat capacity Heat of fusion Mixtures Heat of vaporization Surface Tension Capillarity Solutions Dispersions: Colloids suspensions  Objectives To describe with diagrams the structure of water molecule. To describe how water molecules are affected by pH and temperature. To explain the terms surface tension, capillarity and solvent. To explain the relationship between the properties of water and its role in living organisms. To differentiate homogenous & heterogenous dispersions systems To define colloid and emulsion.  Water Abundant on earth. Covers ~3/4 of the earth’s surface Molecular structure ~70% of human body weight. 1. size 2. polarity Makes life possible. 3. angle of the bonds Structure facilitates function 4. forms hydrogen bonds Elements, Size, Polarity & Angle of bonds Molar mass = 18.01528 g/mol Composed of 2 elements – Oxygen and Hydrogen O more electronegative than H So - electrons stay closer to nucleus of O atom than of H atom Therefore - H has partial positive charge & O has partial negative charge.  Ability to form Hydrogen bonds A partially +ve charged H atom lies between two partially -ve charged O atoms the H atom is attracted to both O atoms and is considered to be acting as a bond between them H bonding influences arrangement of water molecules Water’s influence on life Solvent ionic salts polar compounds Effect on nonpolar compounds Fluidity Surface tension Capillarity Temperature Regulation Specific Heat Capacity Heat of Vaporization Heat of Fusion pH properties  Properties - Affecting Non-polar Compounds O influences non-polar substances like lipids. Non-polar hydrophobic substances mixed with H2O tend to aggregate to form micelles reduce exposure of non-polar to polar surroundings. Hydrophobic interactions holding cell membranes together protein and nucleic acid molecular structures.  Properties of water Solvent properties O - excellent solvent due to polarity. Solvent - substance in which another substance (solute) can dissolve by dispersing as individual molecules or ions. Aqueous environment (water solvent) for all chemical/ metabolic reactions in cells.  Solvent Properties - Dissolving ionic salts O can dissolve ionic substances E.g., NaCl. Ions of salt attract opposite charge in O molecule. The pull to (bond with) the O is greater than the bond between the ions, so the ions get separated and go into solution (dissolve) H2O molecules cluster around separated ions preventing rejoining. In solution, ions move about more freely, making them more reactive. dissolve).  Solvent properties of water – dissolving polar compounds Dissolving Polar compounds Polar molecules that associate with O are hydrophilic. Dissolve non-ionic polar substances e.g., sugars, amino acids, alcohols which are essential in structures and physiological reaction of life.  Properties of water - Fluidity Fluidity (in liquid and gaseous state) O molecules easily yield to pressure and easily move and change their relative position without a separation of the mass (due to H bonds; also size). Osmosis Excellent transport medium (e.g., blood, lymph, phloem sap) in organisms because it not only dissolves substances but carries them as it flows.  Properties – Surface Tension "The property of the surface of a liquid that allows it to resist an external force, due to the cohesive nature of its molecules.” The molecules at the surface of a glass of water do not have other water molecules on all sides of them. Consequently, they cohere more strongly to those directly associated with them (in this case, next to and below them, but not above).  Properties – Surface Tension cont’d Cohesive forces at the surface of a liquid result in surface tension. the surface of the liquid occupies the least possible surface area & behaves as if a film is present which resists being separated. Water has a higher surface tension than any other liquid due to hydrogen bonding. It takes force to overcome this molecular attraction and break the water’s surface.  Properties – Surface Tension cont’d Many small organisms rely on surface tension to settle on water or to skate over its surface. Basilisk ‘Jesus’ lizard, Pond skaters, Water Striders. Properties – Surface Tension cont’d  Properties of water Capillarity the rise of water in narrow tubes due to H bonds. Water is attracted to hydrophilic substances such as glass (adhesion). The force is greater than gravity and water ‘crawls’ up the tube. As it moves it pulls along adjacent molecules to which they are H-bonded (cohesion). Eventually, the water in the centre of the tube also rises. Movement of water along cell walls, through soil, and through the xylem in plants.  Properties of water - Temperature regulation Water has high thermal capacity due to H bonding Raising the temperature of a liquid involves increasing the average kinetic energy (rate of motion) of its molecules; rate of motion is resisted by H bonds. Prevent large fluctuations of temperature in cells and in environment (keeping the temperature relatively constant) thus making it ideal for animal and plant life.  Properties of water - Heat capacity Much heat energy absorbed by water is therefore used to break H bonds before molecular motion of water molecules can be increased and temperature raised. Therefore, it takes a lot of heat to raise temperature of a given amount of water. Biochemical processes in organisms can tolerate small temperature ranges; are affected by extremes & even a little fluctuation in may be detrimental.  Properties of water - Heat capacity cont’d Constant temperature environment important for enzymes which catalyze chemical reactions. Readily absorbs heat generated by metabolic activity without greatly increasing the cell’s temperature.  Properties of water - Conductivity Temp: thermal conductivity O can readily transfer heat from molecule to molecule due to H bonds. Since O is distributed throughout an organism’s tissues, it can readily transfer heat from one part of the body to another, thus maintaining a relatively constant temperature throughout. Phase of Matter  Properties of water Temp: Heat of vaporization Highest for liquid O because the hydrogen bonds have to be broken first to convert liquid O to steam. At its boiling point (100℃ at a pressure of 1 atm) it takes 540 calories of heat to evaporate 1g H2O. Properties of water - Heat of vaporization When gaseous O breaks free from liquid O, energy is lost because the vapor takes away heat energy resulting in a cooling effect on the liquid left behind. Sweating and panting allow some animals to dissipate body heat through evaporation  Properties of water Temp: Heat of Fusion With its high heat capacity, ice requires relatively large amounts of heat energy to thaw. Liquid water must also lose a relatively large amount of heat energy to freeze. Contents of cells and their environments are also less likely to freeze since it requires so much heat loss to convert liquid water to solid water. Ice crystals cause great damage to plasma membrane and organelles if they develop inside cells.  Properties of water As temperature falls, movement of O molecules slow; they get closer to each other; a crystalline structure forms. O therefore gets denser as it gets colder. O is densest at 4℃ (390F). If temp. continues to fall, O starts to expand and becomes less dense (H bonds cause water molecules to move apart and form crystal lattices).  Properties of water - Freezing properties Temp: Freezing Water not densest in the solid state. At 0℃ when ice less dense than liquid O forms and floats on water.  Properties of water - Freezing properties The fact that ice floats, facilitates aquatic life during winter. Solid ice floats on liquid water; frozen crust provides insulation against additional heat loss; water beneath ice stays warm enough to remain liquid; aquatic life live in liquid instead of freezing death in ice. If ice was dense it would sink to the bottom of lakes and rivers and force more water to the surface, to in turn freeze and sink; most of our planet’s water supply would be solid & unavailable.  Properties of water Acids and Bases The pH of a solution is measured by the conc. of H+ The pH scale ranges from 0 to 14; Below pH 7 is acidic; above pH 7 basic A base/alkaline is a H+ (Proton) acceptor; An acid is proton donor Pure water has a pH of 7 (neutral); produces equal amounts of H+ and OH– ions. Intracellular spaces of most organisms range from pH 7.2 to 7.4 Water dilutes acids or bases  Properties of water – pH Water dilutes acids or bases If pure water is added to an acid, equal ion and ion concentration is added; the solution remains acidic (pH increase). Conversely, if pure water is added to a base, equal ion and ion concentration is added; the solution is less basic (pH decreases). Biological processes are sensitive to pH changes; Even slight changes in pH can impede the chemical reactions on which life depends. Organisms protect themselves from pH fluctuations with buffers – substances which combine with free hydrogen and hydroxide, to resist changes in pH.  Dispersion systems - Mixtures Mixtures May be of variable composition (differ from molecules & compounds). Common in nature; most materials found in nature are not pure. Separated by physical processes (as opposed to a chemical reaction).  Mixtures/ Dispersion systems Mixture examples sodium chloride in water. variable volumes of O and variable weights NaCl in the mix. If left to evaporate (physical separation); water will be leaving the salt; even as it gets more concentrated it is still a mixture. circulatory fluids variable numbers of cells, nutrients and volume of water  Dispersion systems- Solutions Common in nature Extremely important for life processes. Body fluids of all life forms are solutions: intracellular, circulatory, tissue, excretory. (cytoplasm, blood, haemolymph, sap, urine) Concentrations of the solutes give valuable clues on the state of health of organisms.  Dispersion systems- Solutions Solutions Solutions = solvent + ≥ 1 solutes Solvent – dispersing medium in which the solutes are dissolved. H2O in biological systems Solutes - usually molecules or ions. dispersed phase Proportions of solute and solvent vary from one solution to another (whereas pure substances have fixed composition). Liquids, solids, or gases can act as either a solvent or solute. Liquids - most common solvent – water in biological systems  Dispersion systems - Homogenous mixtures. True solutions Solute molecules relatively small in comparison to the solvent molecules and dissolve. Non-liquid solvents of homogenous mixtures: Gases – in which other gases are dissolved air solutions. Solid metals - in which a non-metal may be dissolved Dental fillings: silver, copper & mercury. Steel: iron & graphite (C) Solid metals - in which other solid metals may be dissolved to form alloys Brass: copper & zinc Bronze: copper & tin Dispersion systems- heterogeneous mixture Suspensions Solute-like particles are large and immediately settle out after mixing with the solvent. E.g., Sand stirred into water; sand solute does not dissolve in water solvent. Colloids Solute-like particles are suspended in the solvent-like phase Intermediate kind of mixture (between homogenous solution & heterogeneous, suspension. E.g., clay in water; clay particles disperse throughout the water, but are visible, and eventually settle out.  Dispersion systems - Colloids Particles of dispersed solute are large compared to solvent but small enough to remain suspended; settling is negligible. Solute neither dissolves nor sediments Solute particles large enough to make mixture appear cloudy (or opaque) because light is scattered as it passes through. Suspension therefore heterogenous. If left for a long time, flocculation occurs, that is, the particles come together then settle out.  Dispersion systems- Colloids Hydrophobic Colloids Hydrophobic solutes need emulsifying agents in order to exist in polar solvents (to form colloids). Emulsions Two liquids are immiscible and there do not dissolve in each other. E.g., oil in water. – hydrophobic interaction. both liquids separate. How to form a colloid? Emulsifiers coat the solute to prevent its coagulation into a separate phase. Eg., Mayonnaise: vegetable oil (hydrophobic solute) emulsified in water (polar solvent) by egg yolk (emulsifying agent). Eg. Milk: fat emulsified in water by casein.  Colloids Colloidal particles suspended in a solution may adsorb much of the solvent. E.g., Charcoal mixture; used in industry to remove colors from solutions, since it adsorbs many dyes and carry these with it when separated from the solution. Adsorption - Adhesion of the molecules of liquids, gases and dissolved substances to the surfaces of solids (as opposed to absorption, in which the molecules actually enter the absorbing medium). Carbohydrate Structure and Function Aspects of Biochemistry Part B Objectives – On successful learning of this topic you will be able to: Levels of organization Monosaccharides e.g., glucose Disaccharides e.g., sucrose Polysaccharides e.g., starch, cellulose, glycogen Isomerism – structural & stereoisomeris Roles in energy transfer, structural frameworks, storage  Carbohydrates Etymology: carbohydrate - hydrate of C Elements are in a ratio of roughly one carbon atom (C) to one water molecule. Biological molecules made of elements: C, H and O.  Carbohydrates cont’d In biochemistry, carbohydrates are often referred to as ‘saccharides’ (= ‘sugars’) Saccharides comprise a group that includes sugars, starch, and cellulose. The saccharides are divided into three chemical groups: monosaccharides, e.g., glucose disaccharides, e.g., sucrose polysaccharides, e.g., starch, cellulose. Monosaccharides and disaccharides, the smallest (lower molecular weight) carbohydrates, are commonly referred to as ‘sugars’.  Carbohydrates cont’d Functions of carbohydrates: 1. Storage and release of energy 2. Structural roles within the cell  Monosaccharides Carbohydrate molecule containing one sugar unit Simple, sweet sugars Soluble in water Cannot be broken down into smaller carbohydrate units by hydrolysis (splitting of a larger molecule into smaller ones by the chemical addition of water). No. C atoms range from 3 to 7.  Monosaccharides cont’d Classified according to the number of carbon atoms in each molecule. No. of Category Name Carbons 3 Triose 4 Tetrose 5 Pentose 6 Hexose 7 Heptose  Monosaccharide Structure Glucose, galactose, and fructose: same molecular formula different connections / Organization of their atoms isomers. Types of Isomers structural isomers stereoisomers  Monosaccharide Structure cont’d Structural isomers Glucose: Aldehyde or aldose sugar. Carbonyl group on C #1. Fructose: Ketone or keto sugar. Both functional Carbonyl group on C #2 groups are Functional groups collectively called carbonyls  Monosaccharide Structure cont’d Aldehydes & ketone groups act as reducing agents; donate electrons to other atoms or molecules. Principle of reducing sugar test using Benedict’s or Fehling’s solutions. Benedict’s or Fehling’s solutions have CuSO4 () – blue and soluble. When reduced by the sugar, they change to CuO () - red- brown and insoluble. 2 + 2 e- = 2  Monosaccharide Structure cont’d Straight chain structures Structural formulae glyceraldehyde ribose fructose glucose Molecular formulae  Monosaccharide Structure cont’d Pentose (5C) and Hexose (6C) sugars can flip into ring form, in which the chain links up with itself. Sides branches: some terminate as H atoms; others as OH (hydroxyl) groups. α-glucose and β-glucose are stereoisomers (same formula but different spatial arrangements of atoms).  Monosaccharide Structure cont’d α-glucose: the OH group on C1 projects downwards β-glucose: the OH group on C1 projects upwards, above the plane of the ring. These molecules that are nonsuperimposable mirror images of one another, like left and right gloves.  Monosaccharide Structure cont’d Fructose ( - structural isomer of glucose 5-membered ring Reacts differently from glucose α-fructose Sweeter than glucose Found in fruits, nectar and semen α-fructose and β-fructose are stereoisomers β-fructose  Monosaccharide Functions Monosaccharides are an energy source Most of them provide about 4 Calories (kilocalories) per gram, just like other carbohydrates. Glucose is the main fuel for the body cells. Fructose also participates in metabolism. Galactose is found in erythrocytes of individuals with B-type of blood. Ribose is part of ribonucleic acid (DNA, RNA) in cells. Monosaccharides are non-essential nutrients, which means your body can produce all of those it needs for proper functioning from other nutrients, so you do not need to get them from food.  Monosaccharide Functions cont’d Absorption of Monosaccharides: Effect on Blood Sugar Levels Monosaccharides, like most nutrients are absorbed in the small intestine. They can be absorbed without previously being broken down by the intestinal enzymes. Glucose and galactose are absorbed easily, completely; while fructose can be absorbed only slowly and incompletely. After ingestion, glucose and galactose quickly raise the blood sugar (they have high glycemic index), while fructose raises blood sugar only mildly and slowly (it has low glycemic index). During digestion, all carbohydrates have to be broken down into monosaccharides in order to be absorbed.  Disaccharides Two monosaccharide molecules link together form a disaccharide. Sweet Soluble in water and crystalizable Most commonly transported carbohydrate in invertebrate animals, plants and other organisms glucose most common in vertebrates Formed by the action of enzymes such as amylase on starch in vertebrate digestive system. E.g., Lactose: glucose + galactose  Disaccharides cont’d General formula. 2 monosaccharides join by condensation/ dehydration form a disaccharide (double sugar): 1 molecule removed (condensation/dehydration) from pair of monosaccharide molecules. Covalent glycosidic bond joins both monosaccharides. Reversible reaction: disaccharides may be hydrolysed to monosaccharide sub- units. Compound formed depends on the monosaccharides  Disaccharide - Sucrose Table sugar α glucose + β fructose =sucrose Main transport carbohydrate in plants, abundant in stem of sugar cane & sugar beet. H from C1 of glucose and OH 1, 2 glycosidic bond from C2 of fructose  Disaccharide – Sucrose cont’d Non-reducing sugar Carbonyl groups give carbohydrates their reducing property Sucrose’s Carbonyl group ‘tied up’ in the glycosidic bond (C #2 of fructose combines with C #1 of glucose). (c=o on C1 of glucose (aldehyde) but C2 of fructose (ketone)  Disaccharide - Maltose α glucose + α glucose = maltose Condensation reaction is removed. H from C1 and OH from C4 forming a 1, 4 glycosidic bond Maltose is a reducing sugar C1 on 2nd ring not bonded α α  Hydrolysis of Disaccharides When carbohydrates are digested - glycosidic bonds are broken This reaction is called hydrolysis – addition of Glycosidic bonds are broken down carbohydrase enzymes Enzymes are specific  Hydrolysis of Disaccharides cont’d Hydrolysis of sucrose produces the monomers. Sucrose α glucose + β fructose Sucrose is an important source of energy for humans. The enzyme sucrase hydrolyses sucrose to glucose and fructose. Fructose molecule is the rearranged (isomerised) to form glucose. Therefore, each sucrose molecule produces two glucose molecules that can be used in respiration.  Hydrolysis of Disaccharides cont’d Maltose α glucose + α glucose Using the enzyme maltase  Hydrolysis of Disaccharides cont’d Disaccharides such as sucrose would give a negative test with Benedict’s solution However, if HCl is added and the solution is heated The glycosidic bonds will break – separating sucrose to glucose and fructose. If an alkali such as NaOH is then added to neutralise the excess acid – we will get a positive Benedict's test due to the presence of carbonyl groups.  Polysaccharides General formula Insoluble or slightly soluble. Form colloidal dispersions. Not sweet Widely used for energy storage or structural materials (those with stable 3D architecture). E.g., starch, glycogen, cellulose and chitin Large molecules; long chains of monosaccharide units variable number folded or branched.  Polysaccharides cont’d By chaining free monosaccharide molecules into an insoluble polysaccharide, sugar can be stored in a compact form A polysaccharide sugar: Cannot diffuse out of the cell Exerts no osmotic action within cells. Can be hydrolyzed to release energy.  Polysaccharides cont’d Starch Main food storage molecule of plants. potatoes & cereals are rich in starch. Not found in animals. Polymer of alpha glucose Mixture of polymers amylose (20%) & amylopectin (80%).  Polysaccharides – Starch Starch (20% amylose and 80% amylopectin) Amylose Alpha Glucose units linked by 1,4 glycosidic bonds Long and unbranched Amylopectin Alpha Glucose units linked in short chains by 1,4 glycosidic bonds Branched every 24-30 glucose units Branches formed by 1,6 glycosidic bonds Polysaccharides – Starch cont’d Polysaccharides – cont’d  Polysaccharides – Starch cont’d Starch molecules (Amylose) adopt a stable spiral/helical configuration. 6 glucose units per turn; spiral held together by hydrogen bonds Testing for starch The space in the middle of the helix (formed by amylose) fits iodine molecules which form a blue- coloured complex with starch (amylose). Polysaccharides – Starch cont’d Testing for starch Iodine is not very soluble in water Therefore, the iodine reagent is made by dissolving iodine in water in the presence of potassium iodide. This makes a linear triiodide ion complex with is soluble. The triiodide ion slips into the coil of the starch causing an intense blue- black color. Testing for Starch  Polysaccharides - Cellulose Polymer of β glucose by 1,4 glycosidic bonds Single chain may contain up to 10,000 sugar units with total length 5µm. Beta glucose forms parallel chains which interlink by H bonds to form microfibrils, then fibers Different from starch whose long chain is coiled into a helix and whose OH groups (which could form H bonds) are orientated to project inwards so there are no cross linkages. Glycosidic bonds, plus H bond cross linkages between adjacent chains makes it tough and stable. Polysaccharides – Cellulose cont’d  Polysaccharides - Cellulose Forms structures like plant cell walls Completely insoluble and hard to digest Cellulase (enzyme needed to hydrolyze cellulose) rarely in animals; they cannot digest cellulose. Microscopic cellulose decomposers break down dead plant material to re-release energy  Polysaccharide - Glycogen Storage polysaccharide of animals & fungi Stored mainly in liver & muscle cells Easily converted to glucose. Alpha Glucose units linked in short chain by 1,4 glycosidic bonds. Branched every 8-12 glucose units Branches formed by 1,6 glycosidic bonds Polysaccharide – Glycogen cont’d  Polysaccharide - Chitin Structural polysaccharide in arthropods (insects, spiders, crustaceans), nematodes & fungi Polymer of N-acetylglucosamine (2-acetamido-2- deoxy-D-glucose) Beta 1-4 glycosidic linkage Structure resembles that of cellulose, except that the hydroxyl groups on C# 2 have been replaced by acetylamino groups. Polysaccharide – Chitin cont’d  Polysaccharide Summary Carbohydrates perform numerous roles in living organisms. Monosaccharides e.g. glucose, fructose provide energy for living organisms e.g. animals Polysaccharides serve for the storage of energy (e.g. starch and glycogen) and as structural components e.g. cellulose in plants and chitin in arthropods). Polysaccharide Summary cont’d Protein structure and Function Aspects of Biochemistry Part C Objectives 1. To describe in words & diagrams the structure of amino acids. 2. To outline how proteins are formed by peptide bonds. 3. To explain how proteins are organized at primary, secondary, tertiary, quaternary levels. 4. To state the functions of proteins 5. To classify proteins according to structure/solubility, composition, function.  Introduction Proteins More than 50% of the dry mass of an organism. Numerous important functions Regulation of movement of substances into and out of cells (channel & carrier proteins). Regulation of gene expression Catalysis  Proteins Elements: C, H, O, N and sometimes S. Monomers: amino acids. Made from combinations of 20 amino acids the same 20 amino acids, in different arrangements, are present in all living organisms). Unique sequence of amino acids give each protein unique properties.  Amino acids - Basic structure A carbon atom (asymmetric) is bonded to: a carboxyl group (COOH) an amino group (HNH) a hydrogen atom and a variable group (‘R’)  Amino acid - Structure Bipolar COOH donates a proton to form COO- accepts a proton to form Type of ‘R’ group determines the property of the amino acid Extra in the ‘R’ group = basic proteins More COOH in the ‘R’ group = acidic proteins More C-H = non-polar More OH = polar  Can you Identify the four major parts of the 20 known amino acids?  Protein Formation Proteins: polymers of amino acids Amino acids join by covalent peptide bonds between the carboxyl group of one amino acid and the amino group of the neighboring amino acid. Dehydration Synthesis/ Condensation Reaction. OH from the carboxyl end of one amino acid and H from the amino end of another. Dipeptide Protein Formation Continued condensation leads to the addition of further amino acids resulting in the formation of a long chain called a polypeptide. Levels of Protein Structures  Primary structure The specific linear sequence of amino acids in a polypeptide. Formed by: the linear chain of amino acids of which the polypeptide is composed, plus any disulphide bridges formed by the presence of >1 cysteine molecule  Primary structure Different proteins have different sequences Sequence determines function. is dependent on the genetic code in the DNA of the cell.  Secondary structure The organization of portions of the polypeptide chain based on how amino acids react with each other. Three major types of secondary structure: alpha helix, beta-pleated sheet a random coil.  Secondary structure - Alpha helix Formed by a polypeptide chain or part of a chain. Formed when hydrogen bonding occurs between the amino group in one peptide bond and the carbonyl (C═0) group (of the COOH) of another close by peptide bond. Found in alpha keratin; the major protein of wool, hair, nails, feathers, horns. Secondary structure - Beta pleated sheet Formed by a polypeptide chain or parts of the chain. Formed when two or more sections of a polypeptide chain lie side by side and hydrogen bonding occurs, holding them together. Found in Fibroin (silk protein) Less stretchable than alpha helix.  Tertiary structure Formed by further folding & coiling of the secondary structure of the polypeptide Strongly influenced by the interactions of R groups in different parts of the chain. Formed by hydrogen, ionic, disulphide, and covalent bonds or by hydrophobic interactions between R groups. Results in the final compact 3D shape. E.g., myoglobin, enzymes.  Tertiary structure cont’d Hydrogen bonds – forms between CO (of carboxyl) and NH (of amino group). Ionic bonds – formed between R groups with positive and negative charges. Disulphide bonds – links the S atoms of the sulphydryl group of two cysteine amino acids. Hydrophobic interactions –protein folds in such a way as to shield hydrophobic groups while exposing hydrophilic groups to aqueous surroundings.  Tertiary Interactions cont’d The secondary, tertiary and quaternary structures are not random, but highly specific, and precisely dictated by the primary structure that is by the sequence of amino acids in the chain.  Quaternary structure Interaction of more than one polypeptide chain Quaternary structures may be held together by a variety of bonds (similar to tertiary structure) E.g., haemoglobin consists of four polypeptide chains (two alpha and two beta). Summary of the Four Levels of Protein Structure Biuret test Biuret test - testing for proteins using copper (II) sulfate solution in an alkaline environment (NaOH). The copper ions reflect off closely clustered amide groups of proteins casting a violet color to a solution with proteins.  Properties of proteins Anything that affects the specific 3D structure of a protein will affect its properties. Disruption of structure is called denaturation The protein unfolds, losing its tertiary & secondary structure. Primary structure is unaffected. Under suitable conditions, reforming of the structure can occur (renaturation).  Classification of Proteins Structure and solubility: fibrous Globular intermediate  Classification of Proteins cont’d There are two main classes of protein tertiary structure: Fibrous proteins are generally composed of long and narrow strands and have a structural role (they are something) Globular proteins generally have a more compact and rounded shape and have functional roles (they do something) Fibrous and Globular Proteins  Fibrous and Globular Proteins cont’d Globular - These tend to form ball-like structures where hydrophobic parts are towards the centre and hydrophilic are towards the edges, which makes them water soluble. They usually have metabolic roles, for example: enzymes in all organisms, plasma proteins and antibodies in mammals. Fibrous - They proteins form long fibres and mostly consist of repeated sequences of amino acids which are insoluble in water. They usually have structural roles, such as: Collagen in bone and cartilage, Keratin in fingernails and hair.  Globular Protein - Haemoglobin Haemoglobin is a water-soluble globular protein which is composed of two α polypeptide chains, two β polypeptide chains and an inorganic prosthetic haem group. Its function is to carry oxygen around in the blood, and it is facilitated in doing so by the presence of the haem group which contains a ion, onto which the oxygen molecules can bind.  Fibrous Protein- collagen Composed of three polypeptide chains wound around each other. Each of the three chains is a coil itself. Hydrogen bonds form between these coils, which gives the structure strength. This is important given collagen’s role, as structural protein.  Fibrous Protein- collagen cont’d This strength is increased as collagen molecules form further chains with other collagen molecules Collagen molecules also form Covalent Cross Links with each other Collagen molecules wrapped around each other form Collagen Fibrils which themselves form Collagen Fibres. Lipid structure and Function Aspects of Biochemistry Part D  Objectives Describe (in words and diagrams) the structure of triglycerides and their components Differentiate between saturated and unsaturated fatty acids Describe the structure of phospholipids, steroids State the function and properties of different types of lipids.  Lipids Elements: C, H and O; less O, more C-H bonds than carbohydrates. Non-polar; doesn’t dissolve in water vital component of membranes which separate aqueous compartments Will dissolve in non-polar substances alcohols, acetone, ether and chloroform.  Testing for Lipids Sudan Test Sudan IV is insoluble in water but soluble in lipids. Sudan IV Test for lipids: Dark red Sudan IV is added to a solution along with ethanol to dissolve any possible lipids. Positive test: Sudan IV will stain any lipids present reddish-orange. Testing for Lipids cont’d Emulsion Test  Lipids: Fats and Oils Fats & Oils are esters Loss of Condensation/dehydration In organisms, lipids are usually made from glycerol (a 3C alcohol) and fatty acids.  Lipid components: Glycerol Glycerol 3C molecule. C atoms form the ‘backbone’ of the lipid. Each C bears an OH (hydroxyl) group. 3 sites available to form ester linkages with fatty acids. Glycerol + 1 FA= monoglyceride (monoacylglycerol) Glycerol + 2 FA = diglyceride (diacylglycerol) Glycerol + 3 FA = triglyceride (triacylglycerol)  Lipid components: Fatty Acids Fatty acids: methyl group at one end hydrocarbon chain carboxyl group The shorthand chemical formula for a fatty acid is RCOOH Fatty acids can vary in two ways: Length of the hydrocarbon chain The fatty acid may be saturated (mainly in animal fat) or unsaturated (mainly vegetable oils, although there are exceptions e.g., coconut and palm oil)  Lipid components: Fatty Acids cont’d Saturated fatty acids: No double bonds between any C atoms. All possible bonds are used. Has maximum no. of H atoms possible Usually solid at room temperature.  Lipid components: Fatty Acids cont’d Unsaturated fatty acids Have ≥ 1 double bonds. Triglycerides have many. Tend to be oils at room temperature because They have a lower melting point The chains are harder to pack closer together due to kinks in the tail.  Lipid components: Fatty Acids cont’d FA are Amphipathic Carboxyl end of molecule is hydrophilic will dissolve in aqueous solutions in the cell Hydrocarbon chain is hydrophobic will attach to or dissolve in nonpolar organic compounds  Monoglycerides 1 fatty acid + glycerol = Monoglyceride. The fatty acid can be joined on any of glycerol’s 3C  Diglycerides Formed when two fatty acid are joined to glycerol. The fatty acids can be the same or different.  Triglycerides/ Triacylglycerols 1 molecule glycerol + 3 molecules fatty acid (same or different). The 3 OH groups of glycerol have reacted with COOH groups of 3 fatty acids. Ester Linkages 3 molecules of have been removed. Diagrammatic representations of Triglycerides  Triglycerides Solid or liquid at normal room temp. Solids are called “fats” or “butters” - Animals Liquids are called “oils” – Plants Less dense than water Animals in cold habitats usually have less saturated triglycerides to prevent their bodies becoming rigid at the low temperatures.  Triglyceride - Energy Storage As triglycerides are hydrophobic - they do not cause osmotic water uptake in cells so more can be stored. Plants store triglycerides, in the form of oils, in their seeds and fruits. If extracted from seeds and fruits these are generally liquid at room temperature due to the presence of double bonds which add kinks to the fatty acid chains altering their properties Mammals store triglycerides as oil droplets in adipose tissue to help them survive when food is scarce (e.g., hibernating bears)  Functions of lipids Energy source & storage Cell membrane structure Shock absorbers for internal organs Structural support Accentuates the body Insulation Waterproofing Carries fat soluble vitamins (A,D,E,K) Supplies essential fatty acids Hormones