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Note On Molecules

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Published in: Biology
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As level Biology

Areesha A / Dubai

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Qualification: IGCSE-AS Level-A level

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  1. : :?.?. ?- ? S3TD210W : IV(lDO1Ol8 ????? ???
  2. Biological molecule Living organisms are made up of atoms which combine to form biological molecules. Biological molecules like protein and carbohydrate, may be made up of small molecules like amino acids and glucose which are soluble, easily transported and often involved in metabolism.
  3. Molecular Biology Molecular biology is the study of life at a molecular level. Closely linked to biochemistry (chemical reactions of biological reactions).
  4. Atom is the building block of the element of a biological molecule, for instance hydrogen or oxygen. Hydrogen Oxygen
  5. ii. iv. The four most common elements in living organisms: Hydrogen (H) Carbon (C) Oxygen (O) Nitrogen (N) E.g. Hormones/Food Protein amino acid carbon, oxygen, nitrogen, hydrogen
  6. Polymers are large molecules composed of many similar smaller molecules linked together. The individual smaller molecules are called monomers. When small organic molecules are joined together, giant molecules are produced. (polymerisation) These giant molecules are known as macromolecules. CH3 al anine
  7. PROTONS ucleotide *OLECOLAR NEUTRONS ATOM MOLECULES Gl cerol Monosaccharide ELECTRONS Condensation Hydrolysis Fatt Acids Amino aci Water Lipids Polynucleotides (Nucleic acids) Polysaccharides (Carbohydrates) Polypeptides (Protein)
  8. 2. Polymers: Biological Macromolecules Carbohydrates - composed of sugar monomers and necessary for energy storage. Lipids - include fats, phospholipids and steroids. Lipids help to store energy, cushion and protect organs, insulate the body and form cell membranes.
  9. 1. 2. Proteins - composed of amino acid monomers and have a wide variety of functions including molecular transport and muscle movement. Nucleic Acids - include DNA and RNA. Nucleic acids contain instructions for protein synthesis and allow organisms to transfer genetic information from one generation to the next.
  10. PROTONS ucleotide *OLECOLAR NEUTRONS ATOM MOLECULES Gl cerol Monosaccharide ELECTRONS Condensation Hydrolysis Fatt Acids Amino aci Water Lipids Polynucleotides (Nucleic acids) Polysaccharides (Carbohydrates) Polypeptides (Protein)
  11. Made of carbon, hydrogen and oxygen. Molecular Construction of Glucose H—O—C—H H C—O H é/O—HH C Hydrogen Carbon Oxygen
  12. Polysaccharide Monosaccharide Carbohydrate Disaccharide
  13. All carbohydrates contain the elements carbon, hydrogen and oxygen. The 'hydrate' pan of the name comes from the fact that hydrogen and oxygen atoms are present in the ratio Of 2 : l, as they are in water ('hydrate' refers to water). The general formula for a carbohydrate can therefore be written as Carbohydrates are divided into three main groups, namely Monosaccharides Disaccharides and Polysaccharides. refers to a sugar or sweet The word •saccharide' substance
  14. Single sugar molecule General formula (CH20)n There ar three ypes Glucose Hexose (6C) Triose (3C) Pentose
  15. sugars. •9 Monosaccharides are •9 Sugars dissolve easily in water to form sweet-tasting solutions. •9 Monosaccharides have the general formula (CH20)n and consist of a Single SUgar ('mono' means one). •9 The main types of monosaccharides, if they are classified according to the number of carbon atoms in each molecule, are (3C), and OSE •9 The names of all sugars END WITH - + Common hexosesare glucose, fructose and galactose. + Two common pentoses are ribose and deoxyribose
  16. The formula for a hexose can be written as C6 H 12 06 This is known as the molecular formula. It is also useful to show the arrangements of the atoms, which can be done using a diagram known as the structural formula. The picture shows the structural formula of glucose, a hexose, which is the most common monosaccharide. HO sinwn as C —O—H Structural formula Of glucose. hydroxyl group. There are five in glucose. —OH is known as a
  17. One important aspect of the structure of pentoses and hexoses is that the chain of carbon atoms is long enough to close up on itself and form a more stable ring structure. CHO H CH20H
  18. STRUCTURE •This can be illustrated using glucose as an example. •When glucose forms a ring, carbon atom number 1 joins to the oxygen on carbon atom number 5. + The ring therefore contains oxygen, and carbon atom number 6 is not part of the ring. Structural formulae for the straight- chain and ring forms of glucose. Chemists often leave out the C and H atoms from the structural formula for simplicity
  19. + The hydroxyl group, —OH, on carbon atom 1 may be above or below the plane of the ring. •The form of glucose where it is below the ring is known as a-glucose (alpha- glucose) and the form where it is above the ring is ß-glucose (beta- glucose). switch The same molecule can between the two forms. *Two forms of the same chemical are known as ISOMERS, and the extra variety provided by the existence of a- and ß-isomers has important biological consequences, as we shall see in the structures of starch, glycogen and cellulose OH a-Glucose H OH ß-GIucose
  20. Monosaccharides have two major functions - they are commonly used as a source of energy in respiration. This is due to the large number of carbon— hydrogen bonds. These bonds can be broken to release a lot of energy, which is transferred to help make ATP (adenosine triphosphate) from ADP (adenosine diphosphate) and phosphate. The most important monosaccharide in energy metabolism is glucose. Secondly, monosaccharides are important as BUILDING BLOCKS FOR LARGER MOLECULES. •9 For example, glucose is used to make the polysaccharides starch, glycogen and cellulose. Ribose (a pentose) is one of the molecules used to make RNA (ribonucleic acid) and ATP. Deoxyribose (also a pentose) is one of the molecules used to make DNA.
  21. @ 1 monosaccharide + 1 monosaccharide = disaccharide A molecule of water is released Two monosaccharides are joined together to form disachharide in a process called condensation.
  22. sugars. They are FORMED BY TWO MONOSACCHARIDES joining together. The three most common disaccharides are maltose (glucose + glucose), lactose (glucose + (glucose + fructose) and galactose). Sucrose is the transport sugar in plants and the sugar commonly bought in shops. Lactose is the sugar found in milk and is therefore an important constituent of the diet of young mammals. The joining of two monosaccharides takes place by a process known as
  23. G/-YCOSRORC *Formation of a disaccharide from two monosaccharides by condensation. *This can be repeated many times to form a polysaccharide. *The GLYCOSIDIC BOND is formed between carbon atoms I AND 2 of neighboring glucose molecules. *Sucrose is made from an a-glucose and a ß-fructose molecule Formatbn Of glycoskiic bond by removal Of reaction) "-Glucose SCHPH OH ß-F nxtose OCHPH C ondensation o 1 Glycositic bond
  24. a-Glucose 6CH2 OH OH HO (a) Formation Of glycosidic bond by removal Of water (condensation reaction) 6CH OH • OH a-Glucose 6CH2 OH OH OH Condensation OH 6CH2 OH OH HO Maltose Glycosidic bond 6CH2 OH OH OH H20 OH An oxygen bridge is formed between the 2 molecules to form a disaccharide (b) Breaking Of glycosidic bond by addition Of water (hydrolysis reaction) 6CH2 OH OH OH OH Maltose H20 OH Hydrolysis OH OH a-Glucose 6CH2 OH OH OH OH OH a-Glucose OH OH OH OH OH OH
  25. (a) Formation of glycosidic bond by removal of water (condensation reaction) a-Glucose 6CH2 OH OH HO OH a-Glucose 6CH2 OH OH Hic) Condensation OH OH
  26. 6??2 ?? ?? ?? Maltose 1,4 Glycosidic bond ?? ?? ?? ??
  27. ???? 2 Glu COSe Sucrose FruCtose ??? ? 2 ???? 2 GIucose ?? ??20? ?? Examples of disaccharides GaIactose 2 Lactose GIucose Maltose 2 ?? GIucose
  28. *YOROSYSRS The reverse of condensation is the addition of water, which is known as hydrolysis. •This takes place during the digestion of disaccharides and polysaccharides, when they are broken down to monosaccharides Breaking Of glycosidic bond by additbn Of water (hydrolyss reaction) Sucrose a-Glucose •CHPH o 'CH20-i '-W crolysis 'CH20H ß•-Fructose o 'CH.O-I HO OH 6CH20H
  29. CH20H CH20H O OH 4 OH H a + OH H 1 H20 CH20H 4 OH H + Formation OH of CH20H O OH OH H OH OH HO H OH a-linkage a-Glucose ß-Glucose a-G lucose ß-Glucose ß-Maltose CH20H O OH 4 CH20H OH H OH CH20H CH2 OH H OH ß-Fructose OH CH20H o 0 OH H OH H H OH ß-Glucose a-Glucose Sucrose ß-Galactose ß-Lactose
  30. ALL OF THE CARBOHYDRATES!!!!
  31. SUGARS The reducing sugars include all monosaccharides, such as glucose, and some disaccharides, such as maltose. + THE ONLY COMMON NON-REDUCING SUGAR IS SUCROSE. Reducing sugars are so called because they can carry out a type of chemical reaction REDUCTION. known as In the process they are oxidized. This is made use of in the Benedict's test using Benedict's reagent. Benedict's reagent is COPPER(II) SULFATE IN AN ALKALINE SOLUTION AND HAS A DISTINCTIVE BLUE COLOR.
  32. SUGARS Reducing sugars reduce soluble blue copper sulfate, containing copper(ll) ions, to insoluble brick red copper oxide, containing copper(l). + The copper oxide is seen as a brick-red precipitate. reducingsugar+Cu2+ •oxidisedsugar+Cu• blue red-brown
  33. TEST FOR SUGAR A Bene ict s reagent tot e so ution you are testing and heat it In a water bath. Af a reducing syr is resent, the solution will gradually turn t roug green, yellow and orange to red-brown as the insoluble copper(l) oxide forms a precipitate. As long as you use excess Benedict's reagent (more than enough to react with all of the sugar present), the intensity of the red color is related to the concentration of the reducing sugar. > You can then estimate the concentration using color standards made by comparing the color against the colors obtained in tests done with reducing sugar solutions of known concentration. You could also measure the time taken for the color to change. Alternatively, you can use a colorimeter to measure subtle differences in color precisely. reen I yellow Traces of reducing sugar Orange Moderate Laree of red u blue —i green —i yellow —i red —i brown
  34. 2 3 with distilled water (control) with 0.1% glucose solution with 1.096 gluccse solution 5 with s solution with glucose solution
  35. soc,AR Some disaccharides, such as sucrose, are NOT REDUCING SUGARS, so you would get a negative result from Benedict's test. If both a reducing sugar and a non-reducing sugar are present, the precipitate obtained in the test will be heavier than the one obtained in Benedict's test. Oln the non-reducing sugars test, the disaccharide is first broken down into its two monosaccharide constituents. Q The chemical reaction is hydrolysis and can be brought about by hydrochloric acid. UThe constituent monosaccharides will be reducing sugars and their presence can be tested for using Benedict's test after the acid has been neutralized.
  36. TEST FOR SOC,ARS ZHeat the sugar solution with hydrochloric acid. C] This will release free monosaccharides. QBenedict's reagent needs alkaline conditions to work, so you need to neutralize the test solution by adding an alkali such as sodium hydroxide. CIAdd Benedict's reagent and heat as before and look for the color change. Olf the solution goes red now but didn't in the first stage of the test, there is non- reducing sugar present. Olf there is still no color change, then there is no sugar of any kind present. C12 822 + 06 Glucose Sucrose
  37. Sugars, starches and cellulose are all examples of carbohydrates. are white, crystalline and sweet tasting solids which in water. They can be classified according to the number of atoms present in the molecule. Sucrose and maltose are formed when two monosaccharides join together in a reaction. The bond that forms between them is called the bond. Sucrose is formed when a molecule of bonds with a molecule of formed from 2 molecules of Maltose is Dissacharides can be converted back to monosaccharides in a reaction.
  38. CARBOHYORÅVE: POLYSACCHARROE Not sugars Polymers with monomers/subunits that are monosaccharide. Glucose is the main source of energy for cells it is stored in the form of olysaccharide hich is a convenient, compact, Inert and insoluble molecule. 1. Starch 2. Glycogen 3. Cellulose
  39. CARB: STARCH Mix f two substances amylose nd amylopectin. Made up of many 1 ,4-linked a-glucose, but shorter and branch out to the sides. The branches are formed by 1 ,6-linkages Condensation of a-glucose molecules, forming a long unbranching chain of 1 ,4-linked glucose
  40. Amylose Unbranched helical chain Amylose. an unbranched starch Amylopectin Branched chain CFI , inkage inkage Sng• end Structure of amylopectin, a branched starch
  41. Randy Dennä Clar*. and Durell Botany Viuai R—owce Libruy@ The McGraw-Hin inc. An r.t8 re«ved. Amylose Amylose and Amylopectin linkage linkage Amylopectin
  42. FOR Y tarc mo ecu esten to cur up nto ong sp ra s. •T The hole that runs down the middle of this spiral is just the right size for iodine molecules to fit into. To test for starch, you use something called 'iodine solution'. In fact, iodine won't dissolve in water, so the 'iodine solution' is actually iodine in potassium iodide solution. V The starch—iodine complex that forms has a strong blue-black color. Procedure Iodine solution is orange-brown. Y Add a drop of iodine solution to the solid or liquid substance to be tested. A blue-black color is quickly produced if starch is present.
  43. FOR Iodine molecule in the centre of the amylose helix Amylose helix formed by (I-glucose molecules (6 per turn of helix). The dimensions of the centre are just sufficient to fit iodine molecules within it The blue black coloration is due to the iodine molecules becoming fixed in the center of the helix of each starch molecule iodine starch chain
  44. GLYCOGEN Found in animal cells. Used as a storage carbohydrate instead of amylopectin. Like amylopectin, glycogen is made up of 1 ,4-linked a-glucose with 1,6-linkages forming branches. Glycogen is more branched
  45. Glycogen @ The chains also coil up into helical structures, making their final structure more compact (useful for storage). oc;'O 000
  46. amylopectin - found in plants glycogen - found in animals @glycogen has more glucose units than amylopectin. amylopectin - branches separated by 12 to 20 glucose units (less branched) glycogen - branching occurs every 8 to 12 glucose units. (more branched)
  47. @ CELLULOSE The structural polysaccharide in plant cell walls. Found in vegetables and fruits. Polymer of B-glucose units linked together by 1 ,4-glycosidic bond. Plant
  48. The main difference between cellulose and the other two storage molecules you've seen is that cellulose is a polymer of beta-glucose, whereas the other two are from alpha- glucose.
  49. ß-Glucose 6012 OH 042 OH Portion of cellulose molecule ß-Glucose 6042 OH Condensation ß-Glucose 6CH2 OH OH OH CH2 OH OH OH The hydroxyl group (-0H) in carbon 1 of B glucose projects above the ring. In order to form a 1,4-glycosidic bond with the adjacent B glucose (with the -OH of carbon 4 below the ring, one of these two B glucose need to be upside down relative to the other (i.e. 1800 )
  50. ß-Glucose 6012 OH 042 OH Portion of cellulose molecule ß-Glucose 6042 OH Condensation ß-Glucose 6CH2 OH OH OH CH2 OH OH OH Hence, in the polymer of B glucose, the hydroxyl groups (-0H) project outwards from each chain in all directions and form hydrogen bonds with neighboring chains. The cross-linking binds the chains rigidly together.
  51. amylose (a starch) cellulose 000 oo The B-linkages make the chains straight unlike starch a glucose linkages which cause the chain to be curved.
  52. amylose (a starch) cellulose 00000 Cellulose chain run parallel to one another. Unlike amylopectin and glycogen molecules, there are no side chains in cellulose.
  53. This allows the linear chains to lie close together. Many hydrogen bonds are formed between the hydroxyl groups on adjacent chains.
  54. C Between 60 and 70 cellulose molecules become tightly cross-linked to form bundles called microfibrils. OMicrofibrils are in turn held together in bundles called fibers by hydrogen bonding.
  55. AA cell wall typically has several layers of fibers, running in different directions to increase strength. @CeIIuIose makes up about 20 — 40% of the average cell wall; other molecules help to cross- link the cellulose fibers, and some form a glue- like matrix around the fibers, which further increases strength. @Cellulose fibers have a very high tensile strength, almost equal to that of steel. @This means that if pulled at both ends they are very difficult to stretch or break, and makes it possible for a cell to withstand the large pressures that develop within it as a result of osmosis. SEM of cellulose
  56. åWithout the wall, the cell would burst when in a dilute solution. f These pressures help provide support for the plant by making tissues rigid, and are responsible for cell expansion during growth. The arrangement of fibers around the cell helps to determine the shape of the cell as it grows. Despite their strength, cellulose fibers are freely permeable, allowing water and solutes to reach or leave the cell surface membrane. glucose molecules form straight, unbranched chains electron micrograph of cellulose in a plant cell wall (XISOO) cellulose strands packed together to form fibrik fibres of cellulose laid down at different angles
  57. Cellulose Fibers from Print Paper (SEM xl,080). This image is copyright Dennis Kunkel , used with permission at uuusaanß(cakeicom
  58. How does amylose and cellulose differ from one another?
  59. ????? ??? ? ?? ????? ????? ?? ?? ????? ?? ????? ?? ????? ?? ????? ?????
  60. PROTONS ucleotide *OLECOLAR NEUTRONS ATOM MOLECULES Glycerol ELECTRONS Fatty Acids Amino aci Water Monosacc ari e Polynucleotides Polysaccharides (Nucleic acids) (Carbohydrates) Lipids Polypeptides (Protein)
  61. Describe the molecular structure of a triglyceride and a phospholipid and relate these structures to their functions in living organism.
  62. *Lipids contain the elements carbon, hydrogen and oxygen, as do carbohydrates. *However, in lipids the proportion of oxygen is much less. * Lipids are insoluble in water. fact they generally behave as •water-hating' molecules, a property described as hydrophobic.
  63. Lipids are a mixed group of hydrophobic compounds composed of the elements carbon, hydrogen and oxygen. They contain fats and oils (fats are solid at room temperature, whereas oils are liquid) Ljpids ridyceride complex Phospholipids Waxes Steroid s simple Te rpenes
  64. *Lipids can be dissolved in organic solvents such as alcohol (for example, ethanol), propanone and ether. *This property is made use of in the emulsion test for lipids. * Lipids occur in living things as animal fats and plant oils. *They are also present as the phospholipids of cell membranes. * In addition, there are other, more unusual forms of lipid. * For example, the steroids from which many growth and sex hormones are produced are lipids. * The waxes found on plants and animals are also lipids.
  65. @ Insoluble in water but soluble in organic solvents. Non-polar (leading to the absence of H- bond), and hence is hydrophobic. I.e., not soluble in water. STRUCTURE OF A TRIGLYCERIDE Fatty acid atty acid Fatty acid
  66. The three fatty acids may all be the same, thereby forming a simp e triglyceride, or they may be different, in which case a mixed triglyceride is produced, In either case it isa condensation reaction. Glycerol 3 fatty acids Triglyceride +3 wate Composed of 3 fatty acids and 1 glycerol Each FA has a -COOH attached to the hydrocarbon tail. Glycerol is a type of alcohol
  67. CHAH CHAH Glycerol HOOC HOOC Fatty acid 2 + 3H20 HOOC 3 fatty acids Triglyceride +3 water
  68. Fatty acids are a series of acids, some of which are found in fats (lipids). f They contain the acidic group —COOH, known as a carboxyl group. The larger molecules in the series have long hydrocarbon tails attached to the acid 'head' of the molecule. As the name suggests, the hydrocarbon tails consist of a chain of carbon atoms combined With hydrogen. The chain is often 15 or 17 carbon atoms long.
  69. + The difference between saturated' and "unsaturated" fat lies in the number of double bonds in the fatty acid chain. •to Saturated fatty acids lack double bonds between the individual carbon atoms, while in unsaturated fatty acids there is at least one double bond in the fatty acid chain. Animal lipids are often saturated (no double bonds) and occur as fats, whereas plant lipids are often unsaturated and occur as oils, such as olive oil and sunflower oil. taa
  70. Fatty acids ??? be satu- rated ?? unsaturated. Satumta fatty acid ? ? ? ? ? ? ? ? ??? ? ? ? ??-? ? ? Saturated tats, such as butter, are solid at room temperature. Unsatumt•d ???? acid ??????? ? ? ? ? ? ? ? ? Unsaturated fats, such as olive oil, ??? liquid at ???? temperature.
  71. Saturated Fatty Acid Unsaturated Fatty Acid o OH o OH H H Double bonds produce a bend in the fatty acid molecule (see diagram above). Molecules with many of these bends cannot be packed as closely together as straight molecules, so these fats are less dense. As a result, triglycerides composed of unsaturated fatty acids melt at lower temperatures than those with saturated fatty acids.
  72. Glycerol is an alcohol with t ree ydrox groups. The reaction between an acid and an alcohol produces a chemical known as an ester. The chemical link between the acid and the alcohol is known as an ester bond ester linkage. or an * The —COOH group on the acid reacts with the —OH group on the alcohol to form the ester bond , —COO— . * This is a condensation reaction because water is formed as a product. * The resulting ester can be converted back to acid and alcohol by the reverse reaction of adding water, a reaction known as hydrolysis. Ester linkage H H
  73. Fantastic energy reserves - rich in carbon- hydrogen bonds ready to be oxidised for energy. The same mass of lipid will have more energy than the same mass of carbohydrate. Provides buoyancy in the form of blubber for sea mammals - whilst providing insulation, as it does for all mammals. @ Metabolic source of water -o energy converts them to carbo water. This is useful for animal desert that do not have much
  74. Have a similar structure to triglycerides, but with a phosphate group in place of one fatty acid chain. have a polar hydrophilic "head" (the negatively-charged phosphate group) and two non-polar hydrophobic "tails" (the fatty acid chains). H— O Phosphatå i fatw acid _ _ _QT_Ö— O — acid CH —(CH2) gycerol
  75. Have both hydrophobic and hydrophilic properties. Polar Group Phosphate Glycerol Hydrophilic Head (Polar) Hydrophobic Tails (Non Polar) An important component of the cell's plasma membrane , by forming the phospholipid bilayer.
  76. Water G—Hydrophilic (polar) head Hydrophobic (non polar) tails Hydrophilic (polar) head Water Maintains fluidity of the plasma membrane
  77. FOR *Lipids are insoluble in water, but soluble in ethanol (alcohol). *This fact is made use of in the emulsion test for lipids. * The substance that is thought to contain lipids is shaken vigorously with some absolute ethanol (ethanol with little or no water in it). *This allows any lipids in the substance to dissolve in the ethanol. * The ethanol is then poured into a tube containing water. *If lipid is present, a cloudy white suspension is formed.
  78. * If there is no lipid present, the ethanol just mixes into the water. *Light can pass straight through this mixture, so it looks completely transparent. * But if there is lipid dissolved in the ethanol, it cannot remain dissolved when mixed with the water. * The lipid molecules form tiny droplets throughout the liquid. * This kind of mixture is called an emulsion. *The droplets reflect and scatter light, making the liquid look white and cloudy. Add 2an20t Shake rixüe Add2cm20t iqüd
  79. Fig _ 5.1 shows a diagram of tho phosphatidylcholine (a phospholipid). tristoarin molecular Fig. 5.1 structures tristoarin (a trig lycoride) H phosphatidylcholino CH3 (a) Table 5.1 shows a structural difference between the two molecules shown in Fig. 5.1 Complete Table 5.1 With further Structural differences Other than in numbers Of different Of atom S. structural feature length Of fatty acid chains Table 5.1 tristoarin the Same length phosphatidylcholino different lengths
  80. structural feature phosphate (group)/ contains phosphorus nitrogen charged / polar (number of) fatty acids number of ester bonds number of phosphate ester bonds triglyceride 3 3 phospholipid 2 2 1 award one mark for any of the following comparisons number of double bonds (in hydrocarbon chain) number of saturated fatty acids / ORA presence of double bonds presence of unsaturated fatty acids 3 1 1
  81. PROTONS ucleotide *OLECOLAR NEUTRONS ATOM MOLECULES Monosacc ar Lipids Polynucleotides Polysaccharides (Nucleic acids) (Carbohydrates) ELECTRONS Water o aci Polypeptides (Protein)
  82. ACROS) Proteins are the most complex and most diverse group of biological compounds. They have an astonishing range of different functions: 2. 3. 4. 5. 6. 7. 8. 9. 10. structure e.g. collagen (bone, cartilage, tendon), keratin (hair), actin (muscle) enzymes e.g. amylase, pepsin, catalase, etc others) transport e.g. haemoglobin (oxygen), transferrin (iron) pumps e.g. Na+K+ pump in cell membranes motors e.g. myosin (muscle), kinesin (cilia) hormones e.g. insulin, glucagon receptors e.g. rhodopsin (light receptor in retina) antibodies e.g. immunoglobulins storage e.g. albumins in eggs and blood, caesin in milk blood clotting e.g. thrombin, fibrin
  83. Describe the structure of an amino acid and the formation and breakage of a peptide bond.
  84. Proteins are made of amino acids. Amino acids are made of the five elements All amino acids have a central carbon atom which is bonded to an amine group, —NH2, and a carboxylic acid group, -COOH. It is these two groups which give amino acids their name. *The third component that is always bonded to the carbon atom is a hydrogen atom. Side chain (R group) N Amino group c ct carbon o c OH Carboxyl group
  85. This group varies in different amino acids. It is known as the R group or side-chain. amine group glycine o carboxylic acid group o OH Structure of the simplest amino acid, glycine, in which the R group is H, hydrogen.
  86. *The only way in which amino acids differ from each other is in the remaining fourth group of atoms bonded to the central carbon. This is called the *There are 20 different amino acids which occur in the proteins of living organisms, all with a different R group. carbon atom to whkh the functional groups are attached amino group (basic) carboxyl group OH
  87. glycine the R-groups of three adds ??? ? alanine ??? ?? ??? ? ?? leucine
  88. Amin( H bond: N The rl H molec condensation reaction Dipeptide formation —c — c—c —C—C —N N — c—c removal Of water polyn N N — c—c bond forms here H O H water H o
  89. Amino acid 1 RI group R2 group Amino acid 2 Condensation Hydrolysis Water molecule RI group R2 group Peptide bond Dipeptide When two amino acids join together a dipeptide is formed. Three amino acids form a tripeptide. Many amino acids form a polypeptide.
  90. A dehydration reaction links amino acids together in a polypeptide 12 / O H3N-c -C OH Parts of a polypeptide amide bond amino (N) *N-c c+N-f-c4 N-f-c N-c -c end or repeaüng uni backbone carboxyl (C) end
  91. we're BFF'S OF OUR peptide boNd! peptide BONd
  92. ii. Bonds used in protein structure Peptide bond (covalent bond) Ionic bond Disulphide bond Hydrogen bonds Hydrophobic interaction
  93. STROCV8mE Polypeptides are just a string of amino acids, but they fold up to form the complex and well-defined three-dimensional structure of working proteins. @ It is broken down into four levels: 2. 3. 4. Primary structure Secondary structure Tertiary structure Quartenary structure Fred Sanger, 1953
  94. Phated shet Primary protein structure is of i chain •f in-arc ace Arnino Acids Atma helix Secondary protein structure cc-cuts w Fen of •mim •cids _ Pleated sheet Tertiary protein structure when Alpha Quaternary protein structure is a grown Of mae than Image Source: National Human Genome Research institute (NHGRI) Talking s. image it Site.
  95. STRUCTURE OF A polypeptide or protein molecule may contain several hundred amino acids linked into a long chain. * The particular amino acids contained in the chain, and the sequence in which they are joined, is called the primary structure of the protein. *There are an enormous number of different possible primary structures. * Even a change in one amino acid in a chain made up of thousands may completely alter the properties of the polypeptide or protein. Notice that at one end of the amino acid chain there is an —NH3+ group, while at the other end there is a —COO- group. These are known as the amino and carboxyl ends, or the N and C terminals, respectively
  96. SECONOARY STRUCTURE OF *This secondary structure is due to hydrogen bonding between the oxygen of the —CO— group of one amino acid and the hydrogen of the —NH— group of the amino acid four places ahead of it. *These shapes are permanent, held in place by hydrogen bonds. * a helix, a delicate coil held together by hydrogen bonding between every fourth amino acid, as shown above. *The other main type of secondary structure is the pleated sheet. * In this structure two or more segments of the polypeptide chain lying side by side (called strands) are connected by hydrogen bonds between parts of the two parallel segments of polypeptide backbone
  97. Hydrogen bonds, although strong enough to hold the a- helix and ß-pleated sheet structures in shape, are easily broken by high temperatures and pH changes. position of amino acid residues and peptide linkages peptde chain gl hydrcgen bond
  98. SECONOARY STRUCTURE OF e secon ary structure o a protem develops when parts of the polypeptide chain take up a particular shape, immediately after formation at the ribosome. Parts of the chain become folded or twisted, or both, in various ways. Two MAJOR STRUCTURAL FORMS ARE PARTICULARLY STABLE AND COMMON. Either part or all of the peptide chain becomes coiled to produce an a helix or it becomes folded into ß sheets. a-helix ß-Sheet hydrogen bond
  99. *The way in which a protein coils up to form a precise three-dimensional shape is known as its tertiary structure. is precise, compact structure, unique to that protein that arises when the molecule is further folded and held in a particular complex shape. *This shape is made permanent by four different types of bonding, established between adjacent parts of the chain.
  100. Hydrogen bonds — between electronegative oxygen atoms on CO groups and electropositive H atoms on NH groups Rest of amino acid Rest of amino acid Rest of amino acid c 6- o Hydrogen Rest of bond amino acid
  101. Disulfide bridges — covalent bond between R groups of cysteine amino acids TYTosine Cysteine Asparagine Disutfide bridge Val ine Cysteine Aspartic acid Disulfide bonds form between two cysteine molecules, which contain sulfur atoms. strong covalent bonds. They can be broken by reducing agents. They are
  102. Ionic bonds — between NHa and COO— ions on basic amino acids such as asparagine and acid ones such as aspartic acid CH. c Tyrosine Cysteine Asparagine o o Valine Cysteine Aspartic acid Ionic bond Ionic bonds form between R groups containing ionized amine (NH3 +) groups and ionized carboxylic acid (COO— ) groups. They can be broken by pH changes.
  103. Hydrophobic interactions — between non-polar R groups such as those on the amino acids tyrosine and valine CHO Tyrosine 043 Cysteine Asparagine Hydrophobic interaction Valine Cysteine Aspartic acid Occur between non-polar R groups. Although the interactions are weak, the groups tend to stay together because they are repelled by the watery environment around them.
  104. STRUCTURE *Many protein molecules are made up of two or more polypeptide chains. *Hemoglobin is an example of this, having four polypeptide chains in each molecule. *The association of different polypeptide chains is called the quaternary structure of the protein. The chains are held together by the same four types of bonds as in the tertiary structure. Quaternary structure
  105. ?????1??? ??-?• (Fe•pr0toporphyrin ?)
  106. a) b) Proteins with a 3D structure fall into two main types: Globular - spherical structures that are water soluble. They usually have metabolic roles, for example: enzymes in all organisms, plasma proteins and antibodies in mammals. Fibrous - elongated 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.
  107. Fibrous Protein Long parallel polypeptide chain with cross links Generally secondary structure most important in carrying out its structural and supporting function Insoluble in water Repetitive regular sequence of amino acids E.g. collagen, keratin An important structural protein, found in skin, tendons, cartilage, bones and teeth. Globular Protein Coiled and folded into globular shape(spherical) Tertiary structure determines its metabolic function Soluble in water Irregular amino acid sequences E.g. Haemoglobin Found in red blood cells
  108. Hemoglobin is the oxygen-carrying pigment found in red blood cells, and is : a globular protein. We have seen that it is made up of four polypeptide chains, so it has a • quaternary structure. Each chain is itself a protein known as Globin. Globin is related to myoglobin and so has a very similar tertiary structure. There are many types of globin — two types are used to make hemoglobin, : and these are known as alpha globin (a-gtobin) and bday-bhin (ß-ybhin) Two of the hemoglobin chains, called a chains, are made from a-globin, • and the other two chains, called ß chains, are made from ß-globin
  109. *The hemoglobin molecule is nearly spherical. *The four polypeptide chains pack closely together, their hydrophobic R groups pointing in towards the center of the molecule, and their hydrophilic ones pointing outwards. Structure of haemoglobin blvxu_' f æ-yth ) erytvrocyte (RBC) cmtau-vs —270
  110. e Interactions etweent e y rop o ic groups inside the molecule are important in holding it in its correct three-dimensional shape. *The outward-pointing hydrophilic R groups on the surface of the molecule are important in maintaining its solubility. the genetic condition known as sickle cell anemia, one amino acid which occurs in the surface of the ß chain is replaced with a different amino acid. *The correct amino acid is glutamic acid, which is polar. *The substitute is valine, which is nonpolar. * Having a non-polar R group on the outside of the molecule makes the hemoglobin much less soluble, and causes the unpleasant and dangerous symptoms associated with sickle cell anemia in anyone whose hemoglobin is all of this 'faulty' type. Normal hemo 10b in chain Nevmal red cell Sickled red cell Glutamic Glutamic acid Glutamic iotidi ni re-Oni Sickle cell anemia hemoglobin ß chain
  111. ac po ypeptl e c am o emogo In contams a haem group. A group like this, which is an important, permanent, part of a protein molecule but js not made of amino acids, is called a prosthetlC group. *Each haem group contains an iron atom and One oxygen molecule, 02, can bind with each iron atom. a complete hemoglobin molecule, with four haem groups, can carry four oxygen molecules (eight oxygen atoms) at a time. It is the haem group which is responsible for the color of hemoglobin. *This color changes depending on whether or not the iron atoms are combined with oxygen. If they are, the molecule is known as oxy hemoglobin, and is bright red, If not, the color is purplish. pup atm 02 loaded 02
  112. explain why haemoglobin is described as a globular protein with quaternary structure. ............................................[2] (ii) soluble/polar/hydrophilic (on outside)/compact/spherical/curled/ coiled/folded (into a ball)/metabolically active; 4 01 2
  113. *Collagen is the most common protein found in animals, making up 25% of the total protein in mammals. *It is an insoluble fibrous protein found in skin (leather is preserved collagen), tendons, cartilage, bones, teeth and the walls of blood vessels. * It is an important structural protein, not only in humans but in almost all animals, and is found in structures ranging from the body walls of sea anemones to the egg cases of dogfish.
  114. collagen molecule consists of three polypeptide chains, each in the shape of a helix. >These three helical polypeptides are wound around each other, forming a three-stranded 'rope' or 'triple helix'. > The three strands are held together by hydrogen bonds and some covalent bonds. Almost every third amino acid in each polypeptide is glycine, the smallest amino acid. >GIycine is found on the insides of the strands and its small size allows the three strands to lie close together and so form a tight coil. Any other amino acid would be too large. three Eng polypeptide molecules, coiled togetrer to form a triple helix every third Mliro acid is glycine (the smallest arnho acid) Mid the other two amino acids are mastly proline and hydroxyproine cwalent Donas form between the pclypeptlde chains— together with many t•ydrwl
  115. helix With three a miM acids turn 2.Three helices wind together to form a collagen molecule. These strands are held together by hydrogen bonds and some covalent bonds. 1.The polypeptides which make up a collagen molecule are in the shape of a stretched-out helix. Every third amino acid is glycine. 3. Many of these triple helices lie side by side, linked to each other by covalent cross-links between the side chains of amino acids near the ends of the polypeptides. Notice that these cross-links are out of step with each other; this gives collagen greater strength.
  116. Eac comp ete, t ree-stran e mo ecu eo co agen interacts wit ot er collagen molecules running parallel to it. Covalent bonds form between the R groups of amino acids lying next to each other. These cross-links hold many collagen molecules side by side, forming fibrils. *The ends of the parallel molecules are staggered; if they were not, there would be a weak spot running right across the collagen fibril. Finally, many fibrils lie alongside each other, forming strong bundles called fibers. *The advantage of collagen is that it is flexible but it has tremendous tensile strength, meaning it can withstand large pulling forces without stretching or breaking.
  117. FOR *All proteins have peptide bonds, containing nitrogen atoms. * These form a purple complex with copper(ll) ions and this forms the basis of the BIURET TEST. biuret reagent. *The reagent used for this test is called *You can use it as two separate solutions: a dilute solution of potassium hydroxide or sodium hydroxide, and a dilute solution of copper(ll) sulfate. *Alternatively, you can use a ready-made biuret reagent that contains both the copper(ll) sulfate solution and the hydroxide ready mixed.
  118. FOR *To stop the copper ions reacting with the hydroxide ions and forming a precipitate, this ready-mixed reagent also contains sodium potassium tartrate or sodium citrate. Procedure *The biuret reagent is added to the solution to be tested. *No heating is required. *A purple color indicates that protein is present. * The color develops slowly over several minutes. Biuret Test for Protein Biuret Reagent Food Sample Positive Negative Result
  119. Describe and explain the roles of water in living organisms and as an environment for organisms;
  120. END NEAR qickr.ccm
  121. I ifo ac SAVE WATER. SAVE LSE.
  122. charge 8+ charge Hydrogen Bonds
  123. Water molecules are charged, with the oxygen atom being slightly negative and the hydrogen atoms being slightly positive. These opposite charges attract each other, forming hydrogen bonds. These are weak, long distance bonds that are very common and very important in biology.
  124. Solvency Because it is charged, water is a very good solvent. Charged or polar molecules such as salts, sugars and amino acids dissolve readily in water and so are called hvdrophilic ("water loving"). Uncharged or non-polar molecules such as lipids do not dissolve so well in water and are called hydrophobic ("water hating"). Water is therefore an excellent medium for facilitating chemical reactions in cells.
  125. Transport medium Water is the transport medium in blood, lymphatic, excretory and digestive system of animals, and in the vascular system in plants (phloem and xylem) Water bst by Water by hüS re.aslonworld
  126. Density and freezing properties Below 40C, the density of water sfäitst decrease. Ice is less dense than water and h9nc floats on liquid water, insulating the water below: A large amount of energy is required to convert water to ice and thus water is less likely to freeze. Protecting marine life from freezing to death!
  127. CAPACRVV •Water has a high specific heat capacity meaning that it needs to gain a lot of energy to raise its temperature. Conversely it also needs to lose a lot of energy to lower its temperature. Water's specific heat capacity is 4.2 kJ/g/0C. *Specific heat capacity, is the amount of heat needed to raise the temperature of one gram of a substance by one degree Celsius
  128. Hydrogen bond restricts movement of water molecules Large amount of energy is needed to raise the temperature. Large bodies of water (sea, lake, ocean) are slow to change to temperature - more stable habitats. *Water has a high latent heat of vaporization which means a lot of energy is required to evaporate it. When it evaporates, water draws thermal energy out of the surface it's on, which can be observed in sweating.
  129. @ In an animal body as there is a high proportion of water, and so a stable body temperature is easier to attain. Also useful in the body is that the process of evaporation transfers a large amount of energy and this is why sweating is effective in cooling the body.
  130. TENSRON Water molecules have very high cohesion — in other words they tend to stick to each other. *This explains why water can move in long, unbroken columns through the vascular tissue in plants, and is an important property in cells. * High cohesion also results in high surface tension at the surface of water. * This allows certain small organisms, such as pond skaters, to exploit the surface of water as a habitat, allowing them to settle on or skate over its surface. Glass bie Water
  131. hesio dhesion polar or Charged Object
  132. The surface of a volume of water isn't easily broken, mainly because of the hydrogen bonds. The high surface tension of water allows for many organisms to walk on it without breaking through (below left is a water strider)or when you carefully place a needle (below right), paper clip, or other small object on top of the water and it doesn't break through. High surface tension and cohesion
  133. Water molecules, partially because of their polarity, have a tendency to stick together, a property known as cohesion. This provides a high surface tension which allows very light animals to use the surface of the water as a habitat. It also means that water can move in long unbroken columns through vascular tissue in plants and is an important property in cells. Glas tube Water
  134. Water takes part as a reagent in some chemical reactions inside cells. *For example, it is used as a reagent in photosynthesis. During photosynthesis, energy from sunlight is used to separate hydrogen from the oxygen in water molecules. *The hydrogen is then effectively used as a fuel to provide the energy needs of the plant — for example, by making glucose, an energy-rich molecule. *The waste oxygen from photosynthesis is the source of the oxygen in the atmosphere which is needed by aerobic organisms for respiration. Water is also essential for all hydrolysis reactions. * Hydrolysis is the mechanism by which large molecules are broken down to smaller molecules, as in digestion.
  135. N/A

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