General Chemistry PDF

General Chemistry Physical chemistry Dr. Eman M. Abd El-Maksoud Lecturer of Biochemistry  Matter An Insight Into The Structure and Properties of Matter  What Is Matter? Matter is anything that has mass and volume. A cup, pen, and eraser are made up of matt...

General Chemistry Physical chemistry Dr. Eman M. Abd El-Maksoud Lecturer of Biochemistry  Matter An Insight Into The Structure and Properties of Matter  What Is Matter? Matter is anything that has mass and volume. A cup, pen, and eraser are made up of matter  What Is Matter? The definition of matter is often taken to mean anything composed of atoms and molecules. Thus, matter is anything made of protons, neutrons, and electrons.  Structure Of Matter The atom is the “building block of matter”. All substances are composed of invisible particles called atoms. Atoms are the building blocks of matter and are in constant motion. The combination of atoms leads to millions of materials with different properties.  Atoms Atoms are composed of three types of particles: protons, neutrons, and electrons.  Nucleus Atoms are made up of a positively charged center, the nucleus, containing: - Protons with a positive charge - Neutrons with no charge (neutral) Nucleus O = Neutron w/ O Neutral Charge = Proton w/ + + Positive Charge  Atom The electrons of an atom are found orbiting the nucleus of the atom Electrons have a negative charge  Structure of Atom http://www.ehs.utoronto.ca/services/radiation/radtraining/module1.htm  Phases of Matter Matter is classified into four phases or states – Solid – Liquid – Gas – Plasma  STATES OF MATTER Based upon particle arrangement Based upon energy of particles Based upon distance between particles  Solid Solids have definite: – Mass – Volume – Shape Particles of solids are tightly packed, vibrating about a fixed position. Liquid Liquids have definite – Mass – Volume No definite shape.  Particles of liquids are tightly packed, but are far enough apart to slide over one another.  Gas Gases have NO definite – Mass – Volume – Shape Particles of gases are very far apart and move freely. But what happens if you raise the temperature to super-high levels… between 1000°C and 1,000,000,000°C ? Will everything just be a gas?  PLASMA  A plasma is an ionized gas.  A plasma is a very good conductor of electricity and is affected by magnetic fields.  Plasmas, like gases Plasma is the have an indefinite common state shape and an indefinite volume. of matter  Plasma Plasma is the form of matter that exists when the atoms are in an excited state. When a neutral gas is heated such that some of the electrons are freed from the atoms or molecules, it changes state and becomes a plasma. It consists of a partially-ionized gas, containing ions, electrons, and neutral atoms.  Some examples of plasma found on Earth are: lightning, auroras, and neon.  Plasma globe fluorescent lamps neon Lightning polar aurorae Stars  States of Matter A sample of matter can be a gas, a liquid, a solid or a plasma.  Comparison between states of matter Properties Solid Liquid Gas Plasma Molecules are Molecules are Intermolecular More space Particles are far very close to too far apart space than solids apart as in a gas each other from each other Intermolecular Not as strong Very Strong Negligible Negligible Force as solids Shape Fixed shape No fixed shape No fixed shape No fixed shape No fixed No fixed No fixed volume – Do volume - volume - Volume Fixed Volume not expand to expand to fill expand to fill fill the the container the container container. Flow from Flow in all Flow in all Fluidity Do not flow higher level to directions directions lower level Effect of Not Slightly Highly Highly Pressure compressible compressible compressible compressible  PHASE CHANGES Description of Term for Phase Heat Movement During Phase Change Change Phase Change Heat goes into the Solid to Melting solid as it melts. liquid Liquid to Heat leaves the Freezing solid liquid as it freezes.  PHASE CHANGES Description of Term for Phase Heat Movement During Phase Change Change Phase Change Vaporization Heat goes into the Liquid to gas liquid as it vaporizes. includes boiling and evaporation Heat leaves the gas as Gas to liquid Condensation it condenses. Heat goes into the Solid to gas Sublimation solid as it sublimates. Melting change of a solid into a liquid when heat is applied. In a pure crystalline solid, this process occurs at a fixed temperature called the melting point Freezing Freezing is a phase transition in which a liquid turns into a solid when its temperature is lowered below its freezing point. freezing means the solidification phase change of a liquid or the liquid content of a substance, usually due to cooling. What is Vaporization? Vaporization can be defined as the process in which the liquid state changes into the vapour state. As a result of an increase in temperature, the kinetic energy of the molecules increases. Due to the increase in kinetic energy, the force of attraction between the molecules reduces. As a result, they escape into the surrounding in the form of vapours. This process involves the consumption of heat energy. Vaporization includes boiling and evaporation Boiling Boiling is a state to bring the liquid into the vaporization form. A liquid is heated till it reaches the vaporization state, known as the boiling state of that liquid. The temperature, at which the boiling state of the liquid is achieved, is known as the boiling point of the liquid. Evaporation Evaporation is a kind of vaporization that by which an element or compound transitions from its liquid state to its gaseous state below the temperature at which it boils; in particular, the process by which liquid water enters the atmosphere as water vapour in the water cycle. Evaporation, mostly from the oceans Condensation Process Condensation is a physical process in which water is changed from its vapour form to its liquid form. Water in its vapour form is hot (about 100℃) and cooling the water vapours below its boiling point is called condensation process. In condensation process water vapour cools down immediately and water droplets are formed. Sublimation is the conversion between the solid and the gaseous phases of matter, with no intermediate liquid stage. An example is the vaporization of frozen carbon dioxide (dry ice) at ordinary atmospheric pressure and temperature into water vapor without first melting into water.  Intermolecular (non-covalent bonds) influence the physical properties of liquids Forces and solids. Intermolecular forces (or van der Waals forces): refer to the forces between individual particles (atoms, molecules, ions) of a substance. These forces are quite weak relative to intramolecular forces, that is, covalent and ionic bonds within compounds. kinetic energy form of energy that an object or a particle has by reason of its motion. If work, which transfers energy, is done on an object by applying a net force, the object speeds up and thereby gains kinetic energy. The kinetic molecular theory of gases gives a reasonably accurate description of the behavior of gases. The state of a substance depends on the balance between the kinetic energy of the individual particles (molecules or atoms) and the intermolecular forces. Properties of Gases A collection of widely separated molecules The kinetic energy of the molecules is greater than any attractive forces between the molecules The lack of any significant attractive force between molecules allows a gas to expand to fill its container Properties of Liquids The intermolecular attractive forces are strong enough to hold molecules close together Liquids are more dense and less compressible than gasses The attractive forces are not strong enough, however, to keep neighboring molecules in a fixed position and molecules are free to move past or slide over one another. liquids can be poured and assume the shape of their containers Properties of Solids The intermolecular forces between neighboring molecules are strong enough to keep them locked in position Solids (like liquids) are not very compressible due to the lack of space between molecules If the molecules in a solid adopt a highly ordered packing arrangement, the structures are said to be crystalline Due to the strong intermolecular forces between neighboring molecules, solids are rigid.  Types of Intermolecular Forces  Permanent Dipole-Permanent Dipole (Kessom Forces)  Permanent Dipole-Induced Dipole (Debye Forces)  Induced Dipole – Induced Dipole (London or Dispersion Forces)  Hydrogen Bonding Permanent Dipole-Permanent Dipole Permanent dipole–dipole interactions occur between polar covalent molecules because of the attraction of the δ+ atoms of one molecule to the δ- atoms of another molecule. Due to the difference in electronegativity between two atoms bonded by covalent bond, a dipole moment originates due to presence of δ+ on the atom with the lowest electronegativity and δ- on the atom with the highest electronegativity. Permanent Dipole-Induced Dipole A polar molecules causes a disruption in the arrangement of electron for the neighboring molecules and induce a dipole moment.  Induced Dipole – Induced Dipole Dispersion Forces Dispersion forces are the only kind of intermolecular forces present among symmetrical nonpolar substances such as CO2, O2, N2, Br2, H2, and monatomic species such as the noble gases. Dispersion forces result from the attraction of the positively charged nucleus of one atom for the electron cloud of an atom in nearby molecules. This induces temporary dipoles in neighboring atoms or molecules. Dispersion forces. “Snapshots” of the charge distribution for a pair of helium atoms at three instants. Molecular shape affects intermolecular attraction  Hydrogen Bonding Hydrogen bonds are a special case of strong dipole– dipole interaction. They are not really chemical bonds in the formal sense. Strong hydrogen bonding occurs among polar covalent molecules containing H bonded to one of the three small, highly electronegative elements—F, O, or N. Typical hydrogen-bond energies are in the range 15 to 20 kJ/mol, which is four to five times greater than the energies of other dipole–dipole interactions. Intramolecular hydrogen bond -Helix in proteiin Intramolecular hydrogen bond Double Helix DNA SOLUTIONS  MATTER Matter: is anything that has mass and volume (occupies space).  The classical states of matter are solid, liquid and gas Matter Pure Substance Mixture A type of matter with a fixed composition Homogeneous Heterogeneous Element Compound Composed of Composed of 2 or more only one type CHEMICALLY of atom (Gold) combined elements (water)  MIXTURES Mixtures  a combination of two or more substances that do not combine chemically, but remain the same individual substances; can be separated by physical means  Two types: Heterogeneous Homogeneous “Hetero” means different “Homo” means the same. Consists of visibly different It has a constant composition substances or phases (solid, liquid, gas). throughout. The parts of the mixture are A mixture in which the components are noticeably different from one another. evenly distributed among each other. A suspension is a special type of You cannot see the component parts. heterogeneous mixture of larger Commonly referred to as solutions particles that eventually settle. Examples: Examples: Salt dissolved in water. Sand water, sugar dissolved in water Milk  Mixtures can be classified based on the size of their particles into three categories: Suspension Colloid Solution Heterogeneous Heterogeneous Homogeneous Medium particles. Large particles. Well-mixed (uniform) – single They do not separate in phase. Component parts can be layers distinguished by eye. Small particles. Cannot be separated by Component parts cannot be Separates into layers over filter. time. distinguished by eye. Particles can be trapped by Do not separate on standing filter paper. Cannot be separated by filter  CHARACTERISTICS OF SOLUTIONS, SUSPENSIONS, AND COLLOIDS PROPERTY SOLUTIONS COLLOIDS SUSPENSIONS Small Medium Large Particle Size (0.1 – 1 nm) (1-1000 nm) ( > 1000 nm) Scatter light? (Tyndall Effect) No Yes No Effect of Gravity Do not settle out Do not settle out Settle out (settle while standing?) Cannot be Cannot be Can be separated Filtration separated separated Uniformity Homogeneous Heterogeneous Heterogeneous  SOLUTIONS Solution:  A mixture of two or more substances that is identical throughout (homogeneous)  Composed of: solutes solvents the substance that dissolves the substance being dissolved. the solute. the substance(s) present in the the substance present in the larger smaller amount(s). amount When substances dissolve to form a solution solution, the properties of the mixture change. SOLUTES CHANGE SOLVENTS  The amount of solute in a solution determines how much the physical properties of the solvent are changed.  Examples: Lowering the Freezing Point Raising the Boiling Point The freezing point of a liquid solvent The boiling point of a solution is higher decreases when a solute is dissolved in it. than the boiling point of the solvent. Therefore, a solution can remain a liquid at Ex. Pure water freezes at 320F (00C), but when salt is a higher temperature than its pure solvent. dissolved in it, the freezing point is lowered. Ex. The boiling point of pure water is 2120F (1000C), but when salt is dissolved in it, the boiling point is higher. This is why it takes salt water longer to boil than fresh water.  CONCENTRATION (A measure of solute-to-solvent ratio)  The amount of solute that dissolves can vary. Concentration: The amount of solute dissolved in a solvent at a given temperature.  Hence, solutions can be described as:  Types of solutions Types of Solution Physical state Solute solvent Examples of solutions Gas in gas Gas air ( N2, O2, CO2 , other gases) liquid in gas Gas Liquid Gas Water steam in air Solid in gas Solid Naphthalene steam in air Gas in liquid Gas soda pop (CO2 in Liquid water) Liquid Liquid in liquid Liquid Vinegar in water Solid in liquid Solid Salt in water Gas in solid Gas H2 in platinum or palladium Liquid in solid Liquid dental amalgams Solid Solid (mercury in silver) Solid in solid Solid alloys ( brass, (Cu/Zn), Steel (Fe/C )) SOLUBILITY Definition The amount of a substance which will dissolve in a given amount of a particular solvent under certain conditions (i.e., temperature and pressure. Solute Generally, the solubility of solid solutes in liquid solvents increases with increasing temperature. solvent  FACTORS AFFECTING SOLUBILITY Temperature Shaking increased temperature causes solids to dissolve faster Shaking (Stirring) causes solids to dissolve faster Particle Size Smaller particles dissolve Faster because they have more surface area Note: Increasing the amount of solute DOES NOT increase the rate of dissolving TYPES OF LIQUID SOLUTIONS ACCORDING TO SOLUBILITY  Miscible solutions: liquids can easily dissolve in one another such as water and ethanol or water and acetone.  Semi Miscible solutions: liquids can dissolve in one another but under certain conditions such as water and phenol or water and ether.  Immiscible solutions: liquids are not soluble in each other such as water and benzene or water and chloroform. Immiscible Miscible solution solution Fore example: Miscible - will dissolve Immiscible – will not dissolve  SOLUBILITY AND CONCENTRATION Solutions can be described as:  Unsaturated if it has a low concentration of solute dissolved under certain conditions. (Not much solute in the solution) Solution  Saturated when as much solute is dissolved as possible under the existing conditions. (Has the maximum concentration of solute dissolved)  Supersaturated if contains more dissolved solute than normally possible (Lots of solute in the solution) Solution equilibrium: is the physical state in which the opposing processes of dissolution and crystallization of a solute occur at the same rates.  OSMOSIS AND DIFFUSION  Aqueous solutions are found inside and outside cells. The concentration of these solutions is highly controlled by the cells.  These solutions are separated by a semipermeable membrane called the cell membrane.  A semipermeable membrane allows some molecules to pass through the barrier.  Osmosis Diffusion of water through a selectively permeable membrane from an area of high to an area of low concentrations. (High solute; Low water) (Low solute; High water)  Solutions can be classified according to osmosis into 3 types: The solution in which the The solution has a lower The solution has a higher concentration of solutes in the concentration of solutes and concentration of solutes and solution is equal to the a higher concentration of a lower concentration of concentration of solutes inside water than inside the cell. water than inside the cell. the cell. (Low solute; High water) (High solute; Low water) Result: Water moves equally in Result: Water moves from Result: Water moves from both directions and the cell the solution to inside the inside the cell into the remains same size! (Dynamic cell): Cell Swells and bursts solution: Cell shrinks Equilibrium) open (cytolysis)! (Plasmolysis)!  Diffusion and Dialysis Diffusion Random movement of particles from an area of high concentration to an area of low concentration.  Fore example: Kidney Dialysis (treatment for kidney failing)  Kidneys act to remove water molecules out of blood through diffusion across the membranes in the kidneys.  Larger molecules, like proteins, are too large to pass the membrane and get reabsorbed in the blood.  Smaller molecules like urea diffuse out of the blood and move into urine in a process known as dialysis.  A person whose kidneys have failed can undergo artificial dialysis called hemodialysis.  Hemodialysis  During hemodialysis, blood is removed from the patient and passes through one side of a semipermeable membrane in contact on the opposite side with a dialyzing solution that is isotonic with normal blood solute concentrations.  Waste products in the blood will then diffuse out of the passing blood and into the dialyzing solution, and the dialyzed blood returns to the patient.  COLLOIDS Colloid is a heterogeneous mixture in which particles are spread, or dispersed, throughout the dispersion medium, which can be a solid, liquid, or gas. Fore example: milk, Fog and smoke Properties: Contain some particles that are intermediate in size (particles smaller than those in suspensions and larger than those in solutions). They do not separate in layers (They do not settle out with time). You can’t use a filter to separate the parts of a colloid The scattering of light property can be used to separate them from other mixtures Types of Colloids  Gels: colloidal mixtures of liquid dispersed in solid  Sols: colloidal mixtures of a solid dispersed in a liquid  Emulsions: colloidal mixture of a liquid dispersed in a liquid  Aerosols: colloidal mixture of a liquid dispersed in a gas  Foam: colloidal mixture of a gas dispersed in a liquid  Examples of Colloids Colloid Type Dispersed Dispersing Examples Substance Medium Aerosol Liquid Gas Fog, aerosol sprays Aerosol Solid Gas Smoke, airborne bacteria Foam Gas Liquid Whipped cream, soap suds Emulsion Liquid Liquid Milk, mayonnaise Sol Solid Liquid Paint, clays, gelatin Solid foam Gas Solid Marshmallow, Styrofoam Solid Liquid Solid Butter, cheese emulsion Solid sol Solid Solid Ruby glass  Some examples of Colloids from our daily life Blue color of the sky and sea water Food products Due to the scattering of light Food products such as Cake, by colloidal dust particles in air and bread, milk, cream, butter, ice impurities present in sea water. cream, margarine, fruit juices, (Tyndall effect). whipped cream, etc. are colloidal in nature. Blood Is a colloidal solution and the stoppage of bleeding on applying ferric chloride solution is due to coagulation of blood forming a clot.  Applications of Colloids Thickening agents Photography A colloid is used as thickening A colloidal solution of silver agents in industrial products such as bromide in gelatin is applied lubricants, lotions, toothpaste, on glass plates or celluloid films coatings, etc. or paper to from sensitive plates in photography. Paints and inks Purification In ball-point pens, the ink used of water is a gel (liquid-solid colloid). The colloidal impurities present in water can be removed by Smoke screen adding certain electrolytes like alum etc. the negatively charged colloidal particles of impurities get In warfare smoke screens are neutralized by the Al3+ ions and used which are nothing but colloidal settle down and pure water can dispersion of certain substances be decanted off. in the air.  Medicines Sewage disposal Colloidal particles of the dirt, Medicines in colloidal form are mud etc. carry electric charge, easily adsorbed by the body tissues hence when sewage water is passed and hence are more effective. through the plates kept at a high potential, the colloidal particles are coagulated due to electrophoresis and the suspended matter gets removed. Cleansing action of soap Soap solution is colloidal in nature. It removes the dirt particles either by adsorption or by emulsifying Artificial rain the greasy matter sticking to the cloth. Artificial rain can be caused by spraying oppositely charged colloidal dust or sand particles over a cloud. The colloidal water particles present In the cloud will be neutralized and coagulate to from bigger water drops causing artificial rain.  SOME PROPERTIES OF COLLOIDS THE TYNDALL EFFECT The scattering of visible light by colloidal particles is called the Tyndall effect. Solution Colloid  Colloids scatter light, making a beam visible.  Solutions do not scatter light (particles are too small to scatter light).  Suspensions also May exhibit the Tyndall effect but after shaking well (they settle out after a while)  BROWNIAN MOTION - The zig-zag movement of colloidal particles continuously and randomly.  This brownian motion arises due to the uneven distribution of the collisions between colloid particle and the solvent molecules.  These collisions help prevent the colloidal particles from setting. - Brownian movement was more rapid for smaller particles. - It decrease with increase the viscosity of the medium.  SUSPENSIONS A heterogeneous mixture in which the solid particles are spread throughout the liquid without dissolving in it.  The particles are dispersed but are big enough to settle out or be filtered out. Fore example: sand and water Prosperities: Separates into layers over time Particles can be trapped by filter paper Are cloudy in appearance  APPLICATIONS OF SUSPENSIONS Pharmaceutical applications of suspensions  Suspension can improve chemical stability of certain drug.  Drug in suspension exhibits higher rate of bioavailability than other dosage forms.  Duration and onset of action can be controlled  Suspension can mask the unpleasant/ bitter taste of drug. Food suspensions Fruit juices, chocolate drinks, coffee creamer, etc. ANY QUESTIONS ??? THANK YOU  Carbohydrate chemistry D/ Eman Abd elmaksoud Lecturer of Biochemistry Naming or nomenclature of monosaccharides: 1- According to the presence of aldehyde or ketone group. 2- According to the number of carbon atoms. 3- According to both presence of aldehyde or ketone group and number of carbon atoms. 1- According to the presence of aldehyde or ketone group: *Aldoses (aldo sugar): monosaccharides containing aldehyde group (-CHO). The suffix -ose means sugar. *Ketoses (keto sugar): monosaccharides which containing ketone group (-C=O).  2- According to the number of carbon atoms: Trioses: monosaccharides containing 3 carbon atoms. Tetroses: monosaccharides containing 4 carbon atoms. Pentoses: monosaccharides containing 5 carbon atoms. Hexoses: monosaccharides containing 6 carbon atoms. Heptoses: monosaccharides containing 7 carbon atoms. 3-According to both presence of aldehyde or ketone group and number of carbon atoms: Aldotrioses and ketotrioses. Aldotetroses and ketotetroses. Aldopentoses and ketopentoses. Aldohexoses and ketohexoses. Classification of monosaccharides: 1- Triosese: monosaccharide containing 3 carbon atoms. Aldotrioses: Glyceraldehyde (glycerose).parent sugar Ketotrioses: Dihydroxyacetone. 2- Tetroses: monosaccharide containing 4 carbon atoms. Aldotetroses: Erythrose. Ketotetroses: Erythrulose. Erythulose Erythrose 3-Pentoses: monosaccharide containing 5 carbon atoms. Aldopentoses: Ribose, arabinose, xylose and lyxose. Ketopentoses: Ribulose and xylulose. 4- Hexoses: monosaccharide containing 6 carbon atoms. Aldohexoses: Glucose, galactose and mannose. Ketohexoses: Fructose.  Ring (cyclic) structure of sugars: The simple open chain formula of sugars fails to explain some reactions e.g. glucose which has aldehyde group, doesn't give all the reactions of aldehyde. This indicates that the –CHO group must be masked or combined in some way. In solution, the sugar which has an aldehyde group undergoes the following: 1- Hydration of aldehyde group to form aldenol group (alcohol). 2- Condensation between one of the –OH of aldenol group and the –OH group of C4 or C5 to form ring structure (hemiacetal structure). 3- If the remaining –OH is on the right side, so it is α- sugar. 4- If the remaining –OH is on the left side, so it is β-sugar. 5- Pyranose and furanose: a) The 1-5 ring form is called pyranose as it resembles an organic compound named pyran e.g. α and β glucopyranose. b) The 1-4 ring form is called furanose as it resembles an organic compound named furan e.g. α and β glucofuranose. 5- Haworth and chair forms:  Asymmetric carbon atom: It is that carbon atom which is attached to 4 different groups or atoms. Any substance containing asymmetric carbon atom shows two properties; optical activity and optical isomerism. (ɗ) or (+) (ℓ) or (-)  If the concentration of the substance and the length of the tube are fixed, the angle of rotation will depend only on the nature of the substance and it is called specific rotation. Specific rotation: it is the angle of rotation specific for each optically substance when the concentration of substance is 100 g/dl and the length of measuring tube is 10 cm using sodium light at 20 ₒC. Example of specific rotation for glucose is (+52.5) and for fructose is (-91).  B- Optical isomerism: It is the ability of substance to present in more than one form (isomer). A substance containing one asymmetric carbon atom has 2 isomers. A substance containing 2 or more asymmetric carbon atoms can exist in a number of isomers = 2n where n is the number of asymmetric carbon atoms. e. g. glucose has 4 asymmetric carbon atoms so the number of its isomers equal 16 isomers.  1- D and L isomers (Enantiomers): Enantiomers are pairs of compounds that have the same structural formulas but differ in spatial configuration. one of them is the mirror image of the other and they rotate the plane of polarized light equally but in opposite directions. The simplest monosaccharide glyceraldehyde has one asymmetric carbon. So it has 2 optically active forms: L and its mirror image D form  They are classified into D and L forms according to the position of –OH attached to the carbon atom next to last –CH2OH e.g. carbon atom number 5 in glucose. 2- Anomeric carbon and anomers: Anomeric carbon: is the asymmetric carbon atom obtained from active carbonyl sugar group: carbon number 1 in aldoses and carbon number 2 in ketoses. Anomers: these are isomers obtained from the change of position of OH attached to the anomeric carbon e.g. α and β glucose are 2 anomers.  Mutarotation: It is a gradual change of specific rotation of any optically active substance having free aldehyde or ketone group. -α-glucose freshly dissolved in water, has specific rotation of +112. -β-glucose when freshly dissolved in water, has specific rotation of +19. When both anomers are left for sometimes α and β sugars slowly change into an equilibrium mixture which has specific rotation of +52.5  3- Aldose-Ketose isomerism: Fructose has the same molecular formula as glucose but differs in structure formula. One contains keto group (fructose) and the other contains aldehyde group (glucose). Both are isomers. Other examples of aldoses-ketose isomers include: D-glyceraldehyde and dihdroxyacetone, D-ribose and D-ribulose, D-xylose and D-xylulose.  4- Epimeric carbon and epimers: Epimeric carbon is the asymmetric carbon atom other than carbon of aldehyde or ketone group e.g. carbons number 2, 3 and 4 of glucose. Epimers: are isomers due to difference in configuration at a single carbon atom (epimeric carbon atom). so, D-glucose and D-galactose are epimers (C4). D-glucose and D-mannose are also epimers (C2). but D-galactose and D-mannose are not epimers since they differ at C2-4.  Properties of monosaccharides: A) Physical properties: 1. All monosaccharides are soluble in water. 2. All monosaccharides show the property of optical activity. 3. All monosaccharides can exist in α and β forms. 4. All monosaccharides can undergo mutarotation. Carbohydrate chemistry D/ Eman Abd elmaksoud Lecturer of Biochemistry  Chemical Properties 1-Oxidation 2-Reduction 3-Action of Alkalis 4-Action of Acids 5-Fermentation 6-Osazone formation  1- Oxidation A- Oxidation aldehyde group to aldonic acid B- Oxidation last alcoholic group to uronic acid C- Oxidation of both aldehyde & last alcoholic group to Saccharic acid Oxidation  2- Reduction Reduction of aldehyde or ketone groups of Sugars into corresponding alcohols  Ex. Glyceraldehyde to glycerol Glucose to sorbitol  Galactose to galactitol or dulcitol  Mannose to mannitol  Fructose to sorbitol + mannitol  2- Reduction Free aldehyde or ketone group act as reducing agents which can reduce cupric ions of benedict reagent into cuprous ions  3-Action of Alkalis  Weak alkalis result in isomerization eg. glucose to fructose & mannose. Strong alkalis result in polymerization of sugar (aldol condensation) 1.Aldol Reaction of aldehyde (or ketone) enolate with another molecule of the aldehyde (or ketone) in the presence of NaOH or KOH to form β- hydroxy aldehyde (or ketone). 2. Dehydration/Elimination reaction — Involves removal of a water molecule from the β-hydroxy aldehyde (or ketone) to form an α,β- unsaturated aldehyde or an α,β-unsaturated ketone.  4-Action of Acids A- Phosphoric acid gives phosphate esters eg glucose6phosphate & fructose6phosphate B- Sulfuric acid is a dehydrating agent removes 3 molecules of (H2O) from sugar forming furfural condensed with α naphthol into violet ring (Molisch,s test)  5- Fermentation Action of bacteria or yeast on sugar resulting in formation of ethyl alcohol + CO2 All monosaccharides except Pentoses are fermented (D form only) All disaccharides are fermentable except lactose polysaccharides are non-fermentable sugars  6- Osazone formation Osazones are yellow crystals compounds Reaction of sugar with phenylhydrazine Reaction depends on presence of free aldehyde or ketone group All monosaccharides form osazone crystals Lactose and Maltose form osazone crystals Sucrose & Polysaccharides not form osazone crystals  Monosaccharide derivatives 1 Sugar acids 2Sugar alcohols 3-Deoxy sugars 4-Amino sugars 5 Amino sugar acids 6 Glycosidic bond & glycosides 1-2 Sugar acids & alcohols sugar acids: the aldehyde at C1, or OH at C6, or both of them is oxidized to a carboxylic acid; e.g., gluconic acid, glucuronic acid and glucaric acid sugar alcohols: lacks an aldehyde or ketone groups glycerol, galactitol, mannitol & sorbitol C H 2 O H COOH CHO H C OH H C OH H C O H HO C H HO C H H C O H H C OH H C OH H C O H H C OH H C OH C H 2 O H CH2OH COOH D - r i b i t o l D-gluconic acid D-glucuronic acid  3- Deoxy sugars Sugars in which one of the hydroxyl groups has been replaced by a hydrogen atom (one oxygen atom is missed) Deoxyribose in nucleic acid L-fucose (6 deoxy galactose) in glycoproteins  4- Aminosugars An amino group substitutes for a hydroxyl group. The amino group may be acetylated, as in N-acetylglucosamine.  Glucosamine in heparin & hyaluronic acid  Galactosamine in chondritin sulphate  Mannosamine in neuraminic ad and sialic cid C H 2 O H C H 2 O H H O H H O H H H O H H O H H O H O H O H O O H H N H 2 H N C C H 3 H -D-glucosamine -D-N-acetylglucosamine  5- Aminosugar acids Condensation of aminosugars and some acids occurs in glycoproteins Neuraminic acid: (D-mannosamine + Pyruvic acid) building unit of structural polysaccharides Sialic acid: N-acetyl neuraminic acid (NANA) present in glycolipids  6- Glycosidic bond and glycosides Glycosidic bond: is the bond between a carbohydrate and another compound This bond is between the hydroxyl group of anomeric carbon of monosaccharide and another compound which may be:  Another monosaccharide to form disaccharide glycosides  Aglycone: non carbohydrate to form glycosides Glycosides: are naturally occurring substances present in plants and animal bodies; which are extracted and used as drugs.  Examples of glycosides 1-Disaccharides 2-Sugar nucleotides as ATP &GTP ( aglycone is purine & pyrimidine) 3-Glycolipids & glycoproteins  Cardiac glycosides as digitalis ( aglycone is steroid)  Formed by condensation of two molecules of monosaccharides bound together by glycosidic bond Maltose (αglucose+ αglucose (α1-4 glycosidic bond) Isomaltose (αglucose+ αglucose (α1-6 glycosidic bond) Lactose (βgalactose+βglucose (β1-4 galactoosidic bond)  Sucrose (αglucose+βfructose (α1-β2 glycosidic bond) Cellobiose (βglucose+βglucose (β1-4glycosidic bond) Trehalose(αglucose+ αglucose (α1-1glycosidic bond)  Naming of glycosidic bonds According to: Number of connected carbons Position of anomeric carbon of sugar: if it is in α position ,the linkage is an α bond if it is in β position ,the linkage is a β bond Maltose : a cleavage product of starch (by amylase enzyme), formed of 2 molecules of α-D glucopyranose linked together by (1 4) glycosidic bond.  Contains free active group It is a reducing sugar  Can present in α and β forms  Can show mutarotation  Forms sun flower shape osazone crystals  Fermented by yeast enzymes  Hydrolyzed by acid or maltase into 2 glucose  Formed from β-D galactopyranose+β-D glucopyranose linked by β1-4 galactosidic bond Contains free active group Reducing sugar  Can present in α and β forms  Can show mutarotation  Forms cotton ball shape osazone crystals  Non-Fermented by yeast enzymes (yeast Lack lactase enzyme)  Formed of α-Dglucopyranose+β-D fructofuranose linked together by α1-β2 glycosidic bond Contains no free active group: as both anomeric carbons; carbon 1 of α glucose and carbon 2 of β fructose are involved in glycosidic bond so: Non-reducing sugar No osazone crystals No mutarotation & No α andβ forms Fermentable by yeast enzymes  Sucrose is dextrorotatory on hydrolysis by invertase (sucrase) enzyme it gives a mixture of equal number of glucose and fructose and the mixture called invert sugar and it is levorotatory  Sucrose Invert sugar Source Sugar of cane & beet Sugar of bee honey Structure Formed of D glucose Formed of a mixture and fructose linked contains equal by 1α-2β glycosidic number of glucose bond and fructose (not linked) Optical activity Dextrorotatory Levorotatory Proprieties No free active group Free active group Polysaccharides They are polymers of more than 10 units of monosaccharides or their derivatives linked together by glycosidic linkage They are classified into homopolysaccharides and heteropolysaccharides Polysaccharides 1- Homopolysaccharides: contain repeated same sugar units A- Pentosans: Xylans in plant cell wall B- Hexosans: Glucosans (Starch, glycogen & cellulose) Galactosans: agar agar (bacterial culture) Fructosans: inulin (GFR) (onion-garlic) Mannosans: yeast wall Glucosaminosans: chitin (exoskeleton of insect) Galactouronicans: pectin Polysaccharides 2- Heteropolysaccharides (mixed) two or more different repeated monosaccharide units A- Acidic : contain uronic acid + aminosugar may or may not sulfated (GAGS) sulfate free : hyaluronic acid Sulfated: chondritin sulfate, heparin, dermatan sulfate, keratin sulfate & heparin sulfate B- Neutral: no uronic acid or sulfuric acid blood groups & glycoprotein hormones (LH, FSH & TSH) Polysaccharides 1- Homopolysaccharides : Glucosans (Starch, glycogen & cellulose) A- Starch : polysaccharides of plants (storage form of glucose in plants) composed of inner layer (amylose) and outer layer (amylopectin). -Gives blue color with iodine test Amylose is a glucose polymer with (14) linkages. CH2OH 6CH OH 2 CH2OH CH2OH CH2OH O 5 O H O H O H H O H H H H H H H H H H H OH H 1 4 OH H 1 OH H OH H OH H O O O O OH OH 3 2 H OH H OH H OH H OH H OH amylose  Amylopectin is a glucose polymer with mainly (14) linkages, but it also has branches formed by (16) linkages. Starch dextrin Maltose Glucose (by amylase E) Blue Violet Colorless Colorless (Iodine test) B- Glycogen, the glucose storage polymer in animals, is similar in structure to amylopectin. But glycogen has more (16) branches. Highly branched chain homopolysaccharides. Each branch comopsed glucose units linked together by α 1-4 glycosidic bond and α 1-6 glycosidic bond at branching point The highly branched structure permits rapid glucose release from glycogen stores, e.g., in muscle during exercise which is more essential to animals than to plants. Gives red color with iodine test  CH2OH 6CH OH 2 CH2OH CH2OH CH2OH O 5 O O H O H O OH H H H H H H H H OH H 1 O 4 OH H 1 O OH H O OH H O OH H OH H H H H 3 2 H H OH H OH H OH H OH H OH cellulose C- Cellulose, a major constituent of plant cell walls, consists of long linear chains (non-branched) of glucose with (14) linkages. No color with iodine test Humans cannot digest cellulose due to absence of hydrolase enzyme that attack β-linkage but used as source energy for herbivores as their gut contain bacterial enzyme attack β-linkage. Carbohydrate Chemistry  2-Heteropolysaccharides A- Acidic sulfate free: Hyaluronic acid Repeated disaccharide units of glucuronic acid + N-acetyl glucosamine (β 1-3 linkage).The unit attached to the next by (β 1-4 linkage) Present in synovial fluid, vitreous body of eye, embryonic tissue & cartilages. Forms highly viscous solution act as lubricant  Hyaluronic acid Functions:  It permits cell migration during wound repair.  It makes extracellular matrix loose because of its ability to attract water.  It makes cartilage compressible because of its high concentration in this tissue.  It forms highly viscous solution act as lubricant and shock absorbent in synovial fluid of joints, vitreous body of the eye and loose connective tissues.  It can be hydrolyzed by hyaluronidase enzyme (spreading factor) present in bacteria, sperm and some snake poisons  2-Heteropolysaccharides B-Acidic sulfated 1-Chondritin 4 and 6 sulfate Usually found with protein (proteoglycan) Repeated disaccharide units of glucuronic acid + N-acetyl galactosamine with sulfate on either carbon 4 or 6 by (β 1- 3 linkage).The unit attached to the next by (β 1-4 linkage) The most abundant GAGS in the body, it is found in caritlages, tendons, ligaments and other tissues  Chondritin sulfate Form strong network in cartilage Maintain shape of skeletal system Compress cartilage in weight bearing 2-Keratan sulfate (kerato = cornea): -It consists of repeated disaccharide units of galactose (no uronic acid) with sulfate on carbon 6 and N- acetylglucosamine with sulfate on carbon 6. -It present in cornea and it is found as proteoglycan in cartilage. -Functions: It plays an important role in corneal transparency. 3- Dermatan sulfate: In cornea, it plays together with keratin sulfate, an important role in corneal transparency.  Heparin Repeated disaccharide unit consists of uronic acid with sulfate on C2 and glucosamine with sulfate on C 2 and C6 by (α1-4 linkage) the units are attached together by (α 1-4 linkage) Present in mast cell Act as anticoagulant 2- Proteoglycans and glycoproteins: Proteoglycans and glycoproteins are proteins containing carbohydrates. They differ from each other in that they present in different sites, contain different sugars and have different shape and size. A- Proteoglycans: These are chains of GAGS attached to protein molecule. They serve as a ground substance and associated with structure elements of tissues as bone. the carbohydrate part is present in very long unbranched chains (more than 50 monosaccharide molecule) attached to protein core. B- Glycoproteins (mucoproteins): consist of: a. Protein core. b. Carbohydrate chains which are branched short chain (from 2-15 Monosaccharide units) such chains are usually called oligosaccharide chains.  Hexoses: galactose and mannose.  Acetylhexosamines: N-acetylglucosamine.  Pentoses: arabinose and xylose.  Methylpentoses: L-fucose.  Sialic acid.  They contain no uronic acids or sulfate groups. Functions: 1. Glycoproteins are components of extracellular matrix. 2. components of mucins of GIT and UG tracts, where they act as protective biologic lubricants. 3. Glycoproteins are components of cell membrane as: a. Blood group antigens (A, B, AB). b. Cell surface recognition receptors: for hormones, other cells and viruses. c. Plasma proteins: globular proteins except albumin present in plasma are glycoproteins. d. Most secreted enzymes and proteins (as hormones) are glycoproteins. Chemistry of lipids Dr/ Eman Abdelmaksoud Component: Def Biological importance Def of FA Classification of fatty acid Nomenclature of F.A Physical& Chemical properties of simple lipid Def: Lipids are a heterogeneous group of organic compounds, mainly composed of hydrocarbon chains. Soluble in nonpolar (organic) solvents and insoluble in water. Lipids are the esters of fatty acids with alcohol.  Lipids ARE LIPIDS BAD? DO THEY HAVE ANY FUNCTION? Biological importance: Diet Depot fat Constant fat Signaling Highest source -storage form of energy (9.3 of energy -enter in structure of cell membrane Supply bod w KCal/g). -thermal cholesterol ess insulator and mitochondria -contain for and bile a essential fatty -Protect against hormone acids trauma -enterin structure of -contain fat -support internal myelin sheath soluble Second organ vitamins (A, D, messanger K and E). 1-Fatty acids: FA Def: Fatty acids are water insoluble long chain hydrocarbons. having one carboxylic group at the end of the chain (-COOH). They are mostly aliphatic (not branched). Fatty acids present as free fatty FFA acids in the plasma. FA 10 carbon >10 carbon Lower FA higher FA Nomenclature of FA 4 3 2 1 (Arabic numbers) CH3-………CH2-CH2-CH2-COOH γ β α (Greek numbers) ω1 ω2 ω3 ω4 (Omega numbers) Fatty acids Classification: 1- Saturated fatty acids 2- Unsaturated fatty acids 3- Sulfur containing fatty acids 4- Hydroxy containing fatty acids 5- Branched chain fatty acids 6- Cyclic fatty acids IUPAC numerical multiplier 1- Saturated fatty acids: Have no double bonds in the chain. The general formula is CH3-(CH2)n-COOH (n) equals the number of methylene (-CH2) groups. CH3-………CH2-CH2-CH2-COOH Their systemic name ends by the suffix (-anoic) Stearic acid (18 C) Octadecanoic acid (Octa = 6, Deca = 10). Name Formulae Occurrence Acetic acid (2C) CH3-COOH vinegar Butyric acid (4C) CH3-CH2-CH2-COOH butter Caproic acid (6C) CH3-(CH2)4-COOH butter, palm oil, coconut Caprylic acid (8C) CH3-(CH2)6-COOH butter, palm oil Capric acid (10C) CH3-(CH2)8-COOH butter, palm oil, coconut Lauric acid (12C) CH3-(CH2)10-COOH cinnamon, palm, coconut oils Myristic acid (14C) CH3-(CH2)12-COOH nutmeg, palm oil, coconut oil Palmitic acid (16C) CH3- (CH2)14-COOH butter, palm oil Stearic acid (18C) CH3- (CH2)16-COOH butter, vegetable oils Arachidic acid (20C) CH3-(CH2)18-COOH peanut Behanic acid (22C) CH3-(CH2)20-COOH seeds Lignoceric acid (24C) CH3-(CH2)22-COOH peanut, cerebrosides 2- Unsaturated FA -General formula : CH3(CH2)nCH=CH(CH2)nCOOH. -Systemic name ends by the suffix (-enoic) oleic acid (18C) Octadecenoic acid (Octa=8, Deca =10). Linoleic acid (18C) Octadeca-9,12dienoic acid (cis,cis-9,12-  Unsaturated fatty acids A- Monounsaturated fatty acids B-Polyunsaturated fatty acids (PUFA) MUFA (monoethenoic, monoenoic) (polyethenoic, polyenoic) essential fatty acids containing one double bond containing two or more double bonds 9 9,12 palmitoleic (16: 1 ∆ ) linoleic (18:2∆ ) 9 9,12,15 oleic acid (18: 1 ∆ ) linolenic (18:3∆ ) 15 5,8,11,14) nervonic acid (24: 1 ∆ ). arachidonic acids (20:4∆ C-Eicosanoids: they are cyclic compounds which derived from arachidonic acid (20 C). Position of double bonds in unsaturated fatty acids A-The delta (∆) numbering system: 9 palmitoleic acid C 16:1∆ B-Omega (ω) numbering system: 7 palmitoleic acid C 16:1 ω MUFA 9 Palmitoleic (16: 1 ∆ ) CH3-(CH2)5-CH=CH-(CH2)7-COOH 9 Oleic acid (18: 1 ∆ ) CH3-(CH2)7-CH=CH-(CH2)7-COOH 15 Nervonic acid (24: 1 ∆ ) CH3-(CH2)7-CH=CH-(CH2)13-COOH PUFA 9,12 Linoleic (18:2∆ ): CH3-(CH2)4-CH=CH-CH2-CH=CH-(CH2)7-COOH 9,12,15 Linolenic (18:3∆ ): CH3-CH2-CH=CH-CH2-CH=CH-CH2-CH=CH-(CH2)7-COOH 5,8,11,14 Arachidonic acids (20:4∆ ): CH3-(CH2)4-CH=CH-CH2-CH=CH-CH2-CH=CH-CH2-CH=CH-(CH2)3-COOH Omega-3 fats: Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) come mainly from fish, called marine omega-3s. Alpha-linolenic acid (ALA), found in vegetable oils and nuts. Function: -prevent heart disease and stroke -control lupus, eczema, and rheumatoid arthritis. Omega-6 fats: linoleic acid (LA), arachidonic acid come from vegetable oils (sunflower, corn, soybean, and cottonseed) -stimulate skin and hair growth, maintain bone health, reproductive system, regulate metabolism. -reduced rates of heart attacks and other heart diseases -has role in inflammation, fever promotion, blood pressure regulation. Most of us get 14 to 25 times more omega-6 mor than omega-3s. 3- Sulfur containing FA: Lipoic acid (6,8 dithiooctanic acid) is a water soluble vitamin and it is one of the hydrogen carriers that act as coenzymeCH in2 – the CHbody. 2 – CH – (CH2)4 – COOH SH SH 4- Hydroxy containing FA: OH group is attached to α-carbon atom of FA. Cerebronic acid (hydroxy Lignoceric acid): CH3 – (CH2)21 – CHOH – COOH  Function of essential fatty acids: Vegetable oils (corn seed, soybean and linseed oils) are rich in essential fatty acids -Normal growth. - Enter in the structure of phospholipids and cholesterol esters. -Treatment of atherosclerosis because they lower the blood cholesterol level. -Maintenance of normal structure and function of skin. Eicosanoids: comprise prostanoids and leukotriens. Prostanoids include prostaglandins, prostacyclins and thromboxanes.. -work like hormones, but they do not like to travel.. 'local hormones' -They act on the cells that produce them or on neighboring cells. can be classified as autocrine/paracrine hormones. -Prostaglandins: mediate the inflammatory response to infection and injury. -leukotriens play roles in acute and chronic inflammation and allergic diseases. 5- Branched chain FA: common constituents of the lipids of bacteria and to a much lesser extent of animals and plants. -primarily saturated fatty acids (FA) with a methyl branch or more on the carbon chain. branched chain fatty acid called phytanic acid (18 C). formed by bacterial degradation of chlorophyll in the intestinal tract of ruminants. Refsum′s disease is caused by inability of alpha oxidation of phytanic acid. This leads to accumulation of it in plasma and tissues. Cause neurodegeneration and muscle dystrophy. 6- Cyclic FA: -unusual class of minor fatty acids generally produced by bacteria and less frequently by plants. Bacteria (lactic acid bacteria) synthetize cyclopropane FA. -omega-cyclohexyl fatty acids, present in milk produced by rumen bacteria. Cyclopropane and omega-cyclohexyl fatty acids found in bovine meat and dairy products Classifying FA acc.to sources Non essential fatty acids Essential fatty acids -Synthesized in the body -Can't be synthesized in the -Can be synthesized from body. acetyl COA (active acetate) - not necessary to be -They must be obtained from obtained from the diet. the diet. ex: saturated, MUFA. Ex:PUFA Physical properties of fatty acids: A. Solubility: 1. Short chain fatty acids. (acetic acid and butyric acid) are soluble in water. 2. Long chain fatty acids are soluble in nonpolar solvents. B. Melting point: depends on the length of the chain of fatty acids and the degree of unsaturation 1. Short chain and unsaturated fatty acids are liquid at room temperature. 2. Long chain and saturated fatty acids are solid at room 11-Alcohols Include glycerol, cholesterol and higher alcohols (e.g. acetyl alcohol) usually found in the waxes. Glycerol: It is polyhydric alcohol containing 3 –OH groups. Numbering of carbons of glycerol is either: α, β and γ OR 1, 2 and 3  Simple lipid Def: it is esters of FA and alcohol. Classify acc.to type of alcohol Neutral fats or triacylglycerol Waxes (TAG) carry no charge. Fatty acids + glycerol Fatty acids + long chain (Storage form of fat in alcohol adipose tissue) (cholesterol ester) (bee wax)  Simple lipid: A-TAG -Human fat (TAG) is liquid at room temperature and contains high concentration of oleic acid. Dietary sources: Animals butter and lards. plants cotton seed oil, linseed oil, sesame oil and olive oil. Marine oils cod liver and shark liver oil. Types: Simple TAG: similar 3 fatty acids are attached to glycerol tripalmitin, tristearin, triolein. Mixed TAG: three different fatty acids are attached to glycerol 1-palmitodistearin, 1-2-distearopalmitin, 1-3-distearopalmitin. Physical properties of TAG: 1. Solubility: soluble in fat solvents. 2. Melting point: TAG rich (USFA) liquid at room temperature (oils). TAG rich (SFA) solid at room temperature (fats). lower fatty acids melt at lower temperature than those of higher fatty acids. N.B: -the membrane lipids must be fluid as it contains more unsaturated fat than storage lipids. -S/C fat is also softer than that serving as a protective layer around the internal organs. -Butter fat is softer than lard because butter contains large amount of short chain fatty acids which are butyric and Caproic. TAG Physical properties: 3. Specific gravity: it is less than 1 TAG float on the surface of water. 4. Grease stain test: TAG give positive grease stain test. 5. Pure fats are tasteless, odorless, colorless and neutral in reaction TAG Chemical properties: 1. Acrolein test: -all TAG contain glycerol, so all give positive acrolein test. -Glycerol give an aldehyde substance called acrolein by losing 2 water molecules. 2. Hydrolysis: lipase enzyme can hydrolyze TAG into fatty acids and glycerol TAG Chemical properties: 3. Saponification: Alkali +TAG glycerol and salts of fatty acids (soaps) -Soaps cause emulsification of oily material (i.e. breaking down large fat particles into small ones). helps easy washing the fatty materials away. Ordinary soap: Na and K salts of fatty acids are soluble in water. Hard soap: Ca and Mg salts of fatty acids are insoluble in water. hard water: Water containing calcium or magnesium ions. TAG Chemical properties: 4. Halogenations: presence of USFA in TAG. R – CH=CH – COOH I2 R – CH – CH – COOH I I 5. Hydrogenation: depends on the presence of USFA. Hydrogen is added at high temperature and this reaction is the base of conversion of oils into margarine (hardening of oils). TAG Chemical properties: 6. Oxidation or rancidity or rancidification:. this is a toxic reaction of TAG. It leads to unpleasant odor or taste of oils and fats developing after oxidation by oxygen of air, bacteria or moisture. small amount of unsaturated acids present in fats/oils gets oxidized by air to form peroxides which further break down into aldehydes having unpleasant smell and taste. Saturated fatty acids do not get rancid. Types of rancidity: 1- Oxidative rancidity: -by exposure to heat, light, moisture, copper, nickel and iron -The greater degree of unsaturation, the more liability to oxidative rancidity. -prevented by packing under vacuum, storage at low temperature Or using artificial antioxidants. Types of rancidity: 2. Ketonic rancidity: -oxidation of USFA by enzymes found in dry molds. give aldehyde and ketone with peculiar taste. R – CHO R – CH=CH –COOH R–C – CH2 – COOH It can be prevented by sterilization. Types of rancidity: 3. Hydrolytic rancidity: fats bacterial enzyme lipase glycerol and free fatty acids moisture, temp -It occurs in butter due to high content of water. -prevented by inactivation of enzymes and keeping fats away from moisture. Fat constants Purity and composition of oil depends upon the degree of unsaturation, acidity on hydrolysis, and its molecular weight. Each fat has a certain constant value or numbers which detect adulteration and quality of fats. include: 1-Saponification value (number) 2-Acid value (number) 3-Iodine value (number) 4-Acetyl value (number) 1-Saponification value (number) Def: the number of mg of KOH necessary to saponify (combined) all fatty acids present in 1 gram of fats after complete hydrolysis. -Fats with a high percentage of short chain fatty acids have a greater saponification number than that with high percentage of long chain fatty acids. -Butter has greater saponification number than lard. -It is used for determination of adulteration. 2- Acid value (number): Def: the number of mg of KOH necessary to neutralize the free fatty acids present in 1 gram of fats. -Acid value is important for the detection of rancidity. -Normally, the acid number is zero but after rancidity free fatty acids are produced in excess. 4- Acetyl value (number): Def: the number of mg of KOH needed to neutralize the acetic acid produced by the saponification of 1 gram of completely acetylated fat or oil -used to detect the presence of hydroxyl fatty acids. -It is high in caster oil. 3- Iodine value (number): Def: the number of grams of iodine necessary to saturate all unsaturated fatty acids present in 100 grams of fats. -Iodine number gives an idea about the degree of unsaturation of the fatty acids present in fat (quality of fats). N.B: oils have high iodine number than fats. B-Waxes: Acetyl alcohol is most present in waxes. The fatty acids present are long chain acids. The commonest wax in human bodies is cholesterol ester. Bee wax is palmitic acid ester with myricyl alcohol. wool fat is oleic or stearic acid ester with cholesterol. It is useful in manufacture of Waxes Properties: They have the same physical properties as fats. Give negative acrolein test. Not digested by lipase enzyme. so not utilized by the body. They are solids at room temperature. Complex (compound) lipids: FA+ALCOHOL+ other substance 1-Phospholipids Ⅱ- Glycolipids Ⅲ- lipoproteins Ⅳ- Sulfolipids Ⅴ-Aminolipids.  Compound lipid 1-Phospholipids or phosphatides or lipoids: Fatty acids +alcohol + phosphoric acid residues and nitrogenous base. They are classified acc.to alcohol content into: A- Glycerophospholipids: alcohol is glycerol. B- Sphingophospholipids: alcohol is sphingosine. A- Glycerophospholipids B- 1-Phosphatidic acid (diacylglycerol phosphate) Sphingophospholipids Sphingomyelin 2- Lecithin (phosphatidylcholine) 3- Lysolecithin 4- Cephalin (phosphatidylethanolamine) 5- Phosphatidylserine and phosphatidyl threonine 6-Lipositol (phosphatidylinositol) or myo-inositol 7- Plasmalogens 8- Cardiolipin (diphosphatidylglycerol)  A-Glycerophospholipids Saturated FA It is Constant fat Identified by acrolein test. Amphipathic lipids Unsaturated FA Glycerol Pophoric Nitrogenous base acid  A-Glycerophospholipids: 1. Phosphatidic acid (DAG phosphate): Precursor of this group Saturated FA UnSaturated FA Phosphoric acid A-Glycerophospholipids: 2-Lecithin (phosphatidylcholine) The most abundant phospholipids in cell membrane choline nerve transmission Dipalmitoyl lecithin: contain 2 palmitic acid act as surfactant in lung  A-Glycerophospholipids: 3- Lysolecithin: Formed by: -lecithin cholesterol acyl transferase (LCAT) -lecithinase enzyme (spreading factor) lecithinase enzyme lecithin lysolecithin A-Glycerophospholipids: 4- Cephalin (phosphatidylethanolamine) Saturated FA Glycerol Unsaturated FA Pophoric ethanolamine acid -It presents in cell membrane and myelin sheath of nerves. -Act as activator factor of coagulation mechanisms as it enters in composition of thromboplastin. 5- Plasmalogens -It is like cephalin but it contains unsaturated alcohol attached to glycerol at position 1 (α) by ether linkage instead of FA. -About 10% of the phospholipids present in brain, semen and muscles.  A-Glycerophospholipids: 6- Lipositol (phosphatidylinositol) or myo-inositol Saturated FA Glycerol Unsaturated FA Pophoric acid inositol It is present in cell membrane, brain, liver, heart and muscles. Diacylglycerol and inositol triphosphate both act as precursor of second messengers mediating hormonal action inside cells. A-Glycerophospholipids: 7- Phosphatidylserine and phosphatidyl threonine: 8- Cardiolipin:(diphosphatidylglycerol) -2 phosphatidic acids linked together by glycerol. -It is the major lipids in mitochondrial membrane of the heart.  B) Sphingophosphlipids: Sphingomyelin: Ceramide+ phosphoryl choline Niemann-Pick's disease: it is a genetic inborn error disease resulting from deficiency of sphingomyelinase enzyme lead to accumulation of sphingomyelin in liver and spleen which leads to II. Glycolipids (Glycosphingolipids) Fatty acid+ sphingosine+ carbohydrates. A) Neutral glycolipids (Cerebrosides): Ceramide + monosaccharide(glucose or galactose) Galactocerebroside: the major glycosphingolipids of the brain and other nervous tissues Glucocerebroside: the predominant simple glycosphingolipids of extra neural tissues (1) Nervon: the fatty acid is nervonic acid. (2) Kerasin: the fatty acid is lignoceric acid. (3) Oxynervon: the fatty acid is hydroxy nervonic acid. (4) Cerebron: the fatty acid is cerebronic acid. Functions of neutral glycolipids: Neutral glycosphingolipids are constituents of the outer plasma cell membrane, concerned with: Cell to cell communication and recognition. Tissue immunity. Species specificity. Blood group antigens. B) Acidic glycolipids (Gangliosides): Ceramide + glucose and galactose+ one or more sialic acid (NANA) Functions oF gangliosides: Highly concentrated ganglionic cell of nervous tissues especially nerve endings participate in transmission of nerve impulses across synapses. They are receptors to toxins (viruses and tetanus). They mediate cell-cell recognition. They act as tumor marker on surface of tumor cells. Tay-Sach's disease: It a genetic inborn error disease characterized by accumulation of large amount of gangliosides in brain and viscera due to absence of β-galactosidase enzyme leads to mental retardation, hepatomegaly, IV. Lipoproteins lipids conjugated with protein. -The plasma lipids are TAG, phospholipids, free cholesterol , esterified cholesterol and free fatty acids. conjugated with proteins synthesized by the liver forming lipoprotein -This facilitates transport of lipids between blood and different tissues.  Composition of lipoproteins in human plasma Fraction Source Protein% Main contents Chylomicrons Intestine 1-2% Triacylglycerol from chyle Pre-β-lipoprotein Liver and intestine 7-10% Triacylglycerol from (VLDL) liver β-lipoprotein Chylomicrons and VLDL 22% 60% cholesterol (LDL) 40% phospholipid α-lipoprotein Liver and intestine 56% 60% phospholipid (HDL) 40% cholesterol NEFA Adipose tissue 99% 1% free fatty acids  Derived lipids Sterols and steroids: cyclic compound that contains cyclopentano perhydrophenanthrene ring or steroid nucleus The most important steroids Cholesterol (animal origin). Ergosterol (plant origin). Vitamin D group (D2 and D3). Bile salts. Steroid hormones (male and female sex hormones, adrenocortical hormones). Digitalis glycosides. Cholesterol (animal sterol): It is often found as cholesterol ester. Function: It enters in the structure of everybody cell. It is the major constituent of the plasma membrane. It is the precursor of all steroid hormones. It is oxidized in the liver to give cholic acid which forms bile salts. It is oxidized to give 7-dehydrocholesterol, a provitamin present under the skin which gives vitamin D3 by ultraviolet rays. High level of cholesterol in blood will lead to atherosclerosis and gall stone. Vitamin D group: Vitamin D3 (cholecalciferol) is derived from 7- dehydrocholesterol by the rupture of second ring by ultraviolet rays. Vitamin D2 (ergocalciferol) is derived from ergosterol by the rupture of second ring by ultraviolet rays. Bile acids and salts: Bile acids (cholic acid): They are the end products of cholesterol catabolism in the body Bile salts: are bile acids conjugated with glycine or taurine. types of bile salts: sodium or potassium glycocholate and sodium or potassium taurocholate. Functions of bile salts: They activate pancreatic lipase. They have emulsifying and hydrotropic action; help in lipid digestion and absorption. They have choleretic action i.e. they stimulate liver cells to secrete bile. They help absorption of fat soluble vitamins Hormones of steroid nature: 1. Female sex hormones: a-Estrogens: b-Progesterone: 2. Male sex hormones (testosterone): 3. Adrenal cortical hormones (corticoids): Protein chemistry Dr. Eman abdelmaksoud  Protein Proteins are organic nitrogenous substances composed of carbon, hydrogen, oxygen and nitrogen. Proteins are made up of hundreds of smaller units called amino acids that are attached to one another by peptide bonds, forming a long chain  Amino acids General function 1. Building units of proteins e.g. tissue protein, plasma proteins, all enzymes and protein hormones. 2. Building units of peptides e.g. glutathione 3. Act as neurotransmitters i.e. glycine, glutamate, Serotonin (try) and acetylcholine (meth). 1. Used in detoxification reactions e.g. glycine. 2. Precursor for synthesis of important biological compounds e.g. histamine, ,γ-aminobutyric acid (GABA) , creatine, T3, thyroxine, epinephrine, melatonin, serotonin, S-adenosyl methionine.  Amino acids General structure All amino acids at a pH 7 are α and L-amino acids All amino acids at a pH 7 are amphoteric(act either as an acid or a base) All amino acids (except glycine) are optically active Although about 300 amino acids found in nature, only 20 enter in protein structure (primary). Each amino acid has a general structure that consists of the following components: 1.Central Carbon Atom (Cα): The core of the amino acid. 2.Amino Group (NH₂ or NH₃⁺): Attached to the central carbon, this group can exist in two forms depending on the pH of the environment: - At physiological pH (around 7.4), it typically exists as NH₃⁺ (protonated form). - In more basic conditions, it can exist as NH₂ (deprotonated form). 3.Carboxyl Group (COOH or COO⁻): Also attached to the central carbon, this group can also exist in two forms: - At physiological pH, it is usually in the COO⁻ (deprotonated form). - In more acidic conditions, it can exist as COOH (protonated form). 4.Hydrogen Atom (H): A single hydrogen atom is bonded to the central carbon. 5.R Group (Side Chain): This is a variable group that differs among amino acids and determines the specific properties and identity of each amino acid.  Classification of amino acids According to chemical structure I- Aliphatic amino acids: having no ring structure II- Aromatic amino acids : contain aromatic ring According to the nutritional value (biological value) Essential (indispensible) amino acids Non essential (dispensible) amino acids According to the metabolic fate 1- Ketogenic amino acids: 2- Glucogenic amino acids: 3- mixed amino acids  Classification of amino acids According to chemical structure I- Aliphatic amino acids: having no ring structure A- Neutral amino acids : contain one –COOH group and one –NH2 group Glycine: (Gly = G) Alanine: (Ala = A)  Classification of amino acids According to chemical structure I- Aliphatic amino acids: having no ring structure A- Neutral amino acids : contain one –COOH group and one –NH2 group Branched chain amino acids: 1. Valine: (Val =V) 2. Leucine: (Leu = L) 3. Isoleucine: (Ile) valine  Classification of amino acids According to chemical structure I- Aliphatic amino acids: having no ring structure A- Neutral amino acids : contain one –COOH group and one –NH2 group Hydroxy containing amino acids (OH): 1. Serine: (Ser = S) 2. Threonine: (Thr = T)  Classification of amino acids According to chemical structure I- Aliphatic amino acids: having no ring structure A- Neutral amino acids : contain one –COOH group and one –NH2 group Sulfur containing amino acids (S): 1- Cysteine (Cys = C) 2- Methionine: (Met = M)  Classification of amino acids I.According According totochemical chemicalstructure: structure I- Aliphatic amino acids: having havingno noring ringstructure structure: B- acidic amino acids : contain one amino group and more than one carboxylic group 1- Aspartic acid: (Asp = D) 2- Aspargine: (Asn = N) Amidic amino acid 3- Glutamic acid: (Glu = E) 4- Glutamine: Gln = Q  Classification of amino acids According to chemical structure I- Aliphatic amino acids: having no ring structure C- Basic amino acids : contain one carboxylic group and more than one amino group 1- Arginine: (Arg = R) guanito group 2- Lysine: (Lys = K)  Classification of amino acids According to chemical structure II- Aromatic amino acids : contain aromatic ring 1- Phenylalanine: (Phe = F) 2- Tyrosine: (Tyr= Y) OH containing a.a  Classification of amino acids According to chemical structure II- Aromatic amino acids : contain aromatic ring 3- Tryptophan: (Trp = W) precursor to the neurotransmitter serotonin, the hormone melatonin, and vitamin B3 (niacin). Indole ring 4- Histidine: (His = H) basic a.a 5- Proline : (Pro = P) imidazole ring imino group  Classification of amino acids According to the optical activity A. D-amino acids: with the amino group on the right of asymmetric carbon atom. B. L-amino acids: with the amino group on the left of asymmetric carbon atom. C. None optically active amino acid.  Classification of amino acids According to the nutritional value (biological value) Essential (indispensible) Non essential amino acids (dispensible) amino acids 10 a.a Can be synthesized in the body Can not be synthesized by body Their deficiency in diet affect Their deficiency in the diet doesn't growth and health affect growth and health They are valine, leucine, They include glycine, alanine, isoleucine, threonine, methionine, serine, cysteine, aspargine, Arginine, lysine, phenylalanine, aspartic acid, glutamic acid, tryptophan,and histidine glutamine, tyrosine and proline N.B. Arginine and histidine are called semi-essential  Classification of amino acids According to the metabolic fate 1- Ketogenic amino acids: Give rise to ketone bodies and fat during its catabolic pathways e.g. leucine. 2- Glucogenic amino acids: Give rise to glucose during its catabolic pathways e.g glycine, glutamine, proline, serine, alanine, threonine, aspartic acid, aspargine, glutamic acid, methionine, cysteine, arginine, valine and histidine. 3- Ketogenic and glucogenic (mixed) amino acids(5): Give rise to either fat or glucose during its catabolic pathways e.g isoleucine, lysine, tryptophan, phenylalanine and tyrosine.  Derived or modified amino acids Non- primary amino acids found in proteins After the synthesis of proteins, some of the amino acids are modified in post-translation processing. 1. 4-hydroxyproline found in collagen formed by hydroxylation of proline. 2. 5-Hydroxylysine found in collagen formed by hydroxylation of lysine.  Derived or modified amino acids 3. Cystine formed by conjugation of two cysteines via disulfide linkage found in high concentrations in digestive enzymes  Non protein and Non α-amino acids: These are amino acids that do not occur in proteins Perform other functions in metabolism 1- β-alanine: a component of COA, carnosine NH2 Catabolic product of some pyrimidine bases. CH2 – CH2 – COOH 2- γ-aminobutyric acid (GABA) NH2 formed from glutamic acid CH2 - CH2 – CH2 – COOH Neurotransmitter  Non protein and Non α-amino acids: 3- Taurine: NH2 occurs in bile combined with bile acids CH2 – CH2 – SO3H 4- DOPA (3,4-dihydroxyphenylalanine) precursor for melanin pigment, epinephrine and norepinephrine 5- Monoiodotyrosine (MIT) and Diiodotyrosine (DIT) Precursors of thyroid hormones (T3 and T4) (MIT) (DIT)  Properties of amino acids I. Physical properties of amino acids 1. Solubility: All amino acids are soluble in water, diluted acids and alkalis 2. Optical activity: All amino acids except glycine are optically active 3. Amphoteric property: All amino acids behave as acids and alkalis (Zwitter ion)  Properties of amino acids Zwitter ion :is a compound with no overall electrical charge, but which contains separate parts which are positively and negatively charged. e.g. amino acids Isoelectric point (IEP or IP ) : The pH at which an amino acid carries equal positive and negative charge e.g. IP of glycine is pH 6.07  Properties of amino acids II. Chemical properties of amino acids: A. Reactions due to presence of amino group of amino acids: 1- Salt formation 2- Deamination a. Oxidative deamination α-keto acids b. Reductive deamination fatty acids c. Hydrolytic deamination Hydroxy fatty acids  Properties of amino acids II. Chemical properties of amino acids: A. Reactions due to presence of amino group of amino acids: 3- Carboxylation carbamine compounds 4- Methylation Amino acid can be methylated in the presence of methyl donners as methionine. Glycine can be methylated to betaine which by reduction gives rise to choline. 5-Action of nitrous acid Hydroxy fatty acid Amino acid reacts with nitrous acid give rise to corresponding fatty acid, nitrogen and water. It can be used for estimation of amino acid by determining the amount of nitrogen elevated and divided by 2 as 1/2 is derived from amino acid and the other 1/2 is derived from nitrous acid.  Properties of amino acids II. Chemical properties of amino acids: B. Reactions due to presence of carboxylic group of amino acids 1- Salt formation 2- Decarboxylation Amine Removal of CO2 from amino acids give rise to the corresponding amines histidine gives histamine and tryptophan gives tryptamine.  Properties of amino acids II. Chemical properties of amino acids: B. Reactions due to presence of carboxylic group of amino acids 3- Esterification Amino acids can react with alcohol to form ester. N.B: The last –COOH group in dicarboxylic amino acids can combine with ammonia to form the corresponding amide i.e. glutamic acid form glutamine and aspartic acid form aspargine. NH3  Properties of amino acids II. Chemical properties of amino acids: C. Reactions due to presence of side chain of amino acids (Color reactions of proteins) Reaction name Principle Resulting color Rosenheim indole group of tryptophan Purple color + conc. sulfuric acid + Rosenheim's reagent Millon phenolic group of tyrosine Red color after boiling. + Millon's reagent Xanthoproteic phenyl group of phenylalanine orange color + conc. sulfuric acid Sulfur sulfur of cysteine or cysteine Black color + lead acetate  Properties of amino acids II. Chemical properties of amino acids: C. Reactions due to presence of side chain of amino acids (Color reactions of proteins) Sulfur reaction: It is the reaction between sulfur of cysteine or cystine and lead acetate giving black color. N.B: Methionine does not give positive sulfur reaction test because its sulfur is masked by methyl group. Cys Sulfur test Met Black color No Black color  Properties of amino acids II. Chemical properties of amino acids: C. Reactions due to presence of both COOH and NH2 groups 1- Zwitterion formation 2- Reaction with ninhydrin Ninhydrin +Ninhydrin Blue color Amino acids NH3 complex CO2 H H2O The intensity of the blue color produced is used as a measure of the amount of amino acid present Therefore, Ninhydrin is used in amino acid analysis of proteins All amino acids, except proline, are hydrolyzed and react with ninhydrin  Properties of amino acids II. Chemical properties of amino acids: C. Reactions due to presence of both COOH and NH2 groups 3 - Formation of peptide bonds Peptide bond formation is a dehydration synthesis reaction (also known as a condensation reaction)  Peptides A peptide is short chains of amino acids linked by peptide (amide) bonds If 2 amino acids are linked together they form a dipeptide, if 3 amino acids are together linked they form tripeptide Polypeptides may contain more than 10 and up to 100 amino acids What Is the Difference Between a Peptide and a Protein? Peptides are smaller than proteins. peptides are defined as molecules that consist of between 2 and 50 amino acids, whereas proteins are made up of 50 or more amino acids  Peptides Examples of physiologically active peptides Peptide hormones i.e. insulin (51), glucagon (29), angeotensin I (10), angeotensin II (8) and gastrin (17) Antithrombotic peptides Inhibit the blood platelet aggregation i.e. Casoplatelins (bioactive peptides from bovine casein) Antioxidative peptides Inhibit lipid autooxidation process i.e. L-carnosine, Glutathione Neuropeptides act as neurotransmitters i.e. Acetylcholine, and GABA  Insulin ▪ is a peptide hormone produced by beta cells of the pancreatic islets ▪ Function is to maintain normal blood glucose level (keeps your blood sugar level from getting too high (hyperglycemia) or too low (hypoglycemia)) Insulin is described as a “key,” which unlocks the cell to allow sugar to enter the cell and be used for energy.  L-carnosine Naturally occurring dipeptide made by chemical combination of β-alanine and histidine. Present in meat, fish and poultry. Can be synthesized by carnosine synthetase enzyme in the brain and muscle. Biological importance: 1. Buffering function: 2. Antioxidant function: inactivate reactive oxygen species and scavenge free radicals. 3. Therapeutic uses : prevent signs of aging, improve muscle strength and exercise performance  Glutathione (GSH) a tripeptide comprised of three amino acids (cysteine, glutamic acid, and glycine) Produced naturally by the liver. Found in fruits, vegetables, and meats Can be present in reduced (GSH) and oxidized (GSSG) forms  Glutathione (GSH) Biological importance: 1. Powerful antioxidant (reducing) agent : preventing damage to important cellular components caused by reactive oxygen species 2. It activates many enzymes e.g. Glutathione peroxidase 3. Prevents hemolysis of the RBCs 4. It inactivate insulin hormone 5. Prevent rancidity of fat 6. Help in amino acids absorption Protein chemistry Dr. Eman abdelmaksoud  Protein ✓ Proteins are formed of amino acid residue (more than 100 amino acids) linked together by peptide bonds. ✓ They are of high molecular weight ,colloidal in nature , and heat labile. Each protein has a unique amino acids sequence Alteration in amino acid sequences result in abnormal function or diseases sickle cell anemia, Mutations in the HBB gene cause sickle cell disease. Hemoglobin consists of four protein subunits, typically, two subunits called alpha-globin and two subunits called beta-globin hemoglobin is replaced with hemoglobin S  Biomedical importance of proteins I- Structural functions Essential building blocks of the cells Essential for the repair of damaged tissues. II - Dynamic functions ❑ Catalytic function e.g. enzymes ❑ Regulation of metabolism e.g. hormones ❑ Movement function e.g. actin, tubulin ❑ Storage function Ferritin stores iron. Ceruloplasmin stores copper ❑Defense or protective function keratin found in skin cells protects against mechanical and chemical injury Blood clotting proteins fibrinogen and thrombin prevent blood loss Antibodies (Immunoglobulins) ❑Transport function Na-K ATPase and glucose transporter Hemoglobin Lipoproteins Albumin carries calcium, free fatty acids and bile pigments. Transferrin carries iron  Protein structure ❑Bonds responsible for protein structure are: I- Covalent (strong) bonds 1. Peptide bond It stabilizes the protein structure Prevent rotation of protein molecule broken only by enzymatic action or by strong acid or base at high temperature 2. Disulfide bond II- Non covalent or weak bonds 1. Hydrogen bonds 2. Hydrophobic interactions 3. Electrostatic bonds (ionic interaction or salt bridge) Hydrophobic interactions describe the relations between water and hydrophobes (low water- soluble molecules). Hydrophobes are nonpolar molecules and usually have a long chain of carbons that do not interact with water molecules. The non polar side chains of neutral amino acids tend to be introduced to the inside of the protein molecule exposed to water. They are not true bonds but interactions that help to stabilize the protein structure. Hydrogen bonds: It is formed when a sharing of hydrogen atom occurs between the nitrogen and the carbonyl oxygen of different peptide bonds. Hydrogen bonds may be formed between polar uncharged R groups e.g. – OH with each other or with water. Electrostatic bonds (ionic interaction or salt bridge): These bonds occur between the charged group of side chains of amino acids (NH3+ of basic amino acids and COO- of acidic amino acids).  Conformation of proteins ▪ Protein molecule has a characteristic three dimensional shape (primary, secondary and tertiary structure) ▪ Proteins formed of two or more polypeptide chains have quaternary structure  1. Primary structure of proteins Refers to the number and sequence (order) of amino acids in the polypeptide chain The free α-amino group, written to the left, is called the amino-terminal or N- terminal end. The free α-carboxyl group, written to the right, is called the carboxyl-terminal or C-terminal end.  2. Secondary structure of proteins Refer to Coiling, folding or bending of the polypeptide chain The most common types of secondary structures are α helix and the β pleated sheet These secondary structures are held together by hydrogen bonds. α-helix Is a right-handed helix that is held together by hydrogen bond The hydrogen bond is formed between the N-H on one amino acid and the C=O on another amino acid 4 residues away each turn of the helix containing 3.6 amino acids. typical α-helix is about 11 a.a. Exampl