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Raffles Institution Raffles Programme Secondary Three Raffles Academy Biology Unit 3: Chemicals of Life Name: _____Suggested answers_________ Class: _________ ( ) Date: _______ Worksheet 1: Introduction to Biochemistry & Amino Acids Exercise 1 4. 4 Exercise 2 4. –NH3+ 5. No, molecular formula shown. 6. O 7. Yes, structural formula shown 8. The components of organic molecules that are most commonly involved in chemical reactions. 6 10. phenylalanine, glycine, aspartic acid 11. 14 12. a. enzymes (catalyse chemical reactions); b. transport; c. structural, e.g. collagen 15. C H N O 16. a. molecules that are mirror images of each other b. carbon bonded to four different groups c. different enantiomers have different biological effects d. 2n , n = number of asymmetric carbons Review Questions 1. Amino acids/proteins 2. Amino acids 3. 20 4. A large number, order and number can vary Worksheet 2: Proteins Exercise 1 1. Ionized/dissociated, exist as zwitterions 2. Campbell: non-polar, polar, electrically charged Biomodel: non-polar aliphatic; polar uncharged, aromatic, basic, acidic Differentiate between aliphatic (open carbon chains) and aromatic (benzene rings); acidic and basic 3. Depends on side chain 4. High electronegativity of O or N attached covalently to H 5. Central carbon atom in amino acid/first carbon after carbon attached to functional group; no, e.g. glycine 6. Peptide bond; amino and carboxyl groups 7. Monomer = molecules that can combine to give polymer; dimer = molecule consisting of 2 monomers joined together 1 8. Condensation/dehydration synthesis, covalent bond formed with loss of 1 molecule of water 9. Hydrolysis, break covalent bond with addition of 1 molecule of water 10. Dipeptide = two amino acids bonded together by peptide bond; oligopeptide = a few (3-40) amino acids bonded together by peptide bonds; peptone = water soluble compounds formed by partial hydrolysis of proteins; polypeptide = string of amino acids; protein = 1 or more polypeptides folded together/macromolecule that is the end product of transcription and translation 11. No, N-terminus and C-terminus, protein synthesis move from N to C direction 12. Sticks out, interact to give conformation 13. Bonds between parts of chain; determines its function (emergent property) 14. Describe complex architecture (superimposed levels) 15. Sequence of amino acids, may change interactions, e.g. sickle cell anemia 16. E.g. α-helix and β-pleated sheet, structure formed due to hydrogen bonds between atoms of backbone (not side chain); ribbons/arrows 17. Irregular contortions; due to interactions between side chains of amino acids (hydrogen bonds, disulphide bonds, ionic bonds, hydrophilic interactions, van der Waal’s interactions) 18. Aggregation of polypeptide subunits 19. Loss of native conformation, biologically inactive Exercise 2 Comparison Found in HIV Protease HIV Collagen Connective tissue, skin tendon, internal organs, bone Function Cuts pre-protein synthesised by human host into pieces which assemble to make new HIV Provides structure, protection and support; holds us together, strong and flexible, provides flexible strength, underlying structure for bones and teeth Structure Small, dimer of 2 identical polypeptides (each 99 amino acids long); assemble to form long tunnel covered by two flexible flaps, active site in centre 3 strands of polypeptides twisted together to form tropocollagen (~1400 amino acids long), right-handed triple helix, repeated proline, hydroxyproline and glycine (glycine in centre occupy minimum space as only glycine small enough to pack); Pro and Hpr form hydrogen bonds; 5 tropocollagen molecules twisted to form fibre 2 Medical significance (or how does understanding of the structure help mankind?) Design HIV protease inhibitor (e.g. ritonivir) added together with 2 anti-HIV drugs; difficult for HIV to develop resistance Rare genetic diseases and scurvy (vitamin C deficiency) due to defects in collagen; need oxygen and vitamin C to produce hydroxyproline from proline Worksheet 3 Lipids Exercise 1 4. 3: palmitic, oleic, stearic acid 5. 2 (palmitic and stearic); 1 (oleic) 7. saturated – molecule straight, unsaturated – molecule kinked; prevents molecules from packing together 8. geometric isomers 9. polyunsaturated – many double bonds; monounsaturated – 1 double bond; 2 families of essential fatty acids (EFAs) with double bond in ω3 and ω6 positions, respectively; ω3 in fish oils (e.g. α-linolenic acid/ALA 18C, eicosapentaenic acid/EPA 20C, docosahexaenoic acid/DHA 22C); ω6 in vegetable oils (e.g. linoleic acid, arachidonic acid) 10. convert liquid oil into solid, prevent rapid rancidity; produces trans fat, artificial, cannot be metabolized, linked with cancer, diabetes, heart disease, low birth rate, obesity Exercise 2 2. fat – solid at room temperature; oil – liquid at RT; triglyceride = triacylglycerol = glycerol + 3 fatty acids 3. ester bond; COOH and OH; condensation 5. non-polar; consists of non-polar C-H bonds in hydrocarbon chain of the fatty acids 6. insoluble because non-polar, water molecules hydrogen bond to each other and exclude the fats Exercise 3 1. Triglyceride = glycerol + 3 fatty acids; phospholipid = glycerol + 2 fatty acids + 1 phosphate/choline 2. Hydrophilic = substance with affinity for water; hydrophobic = substance without affinity for water 3. Form major components of all membranes Exercise 4 3. point to double bond 5. 3 6. point at OH group; wedged between phospholipid molecules, reduces membrane fluidity at moderate temperature by reducing phospholipid movement; hinders solidification at low temperatures by disrupting regular packing of phospholipids 3 Worksheet 4 Carbohydrates Exercise 1 2. yes 5. yes, -OH, C=O due to difference of electronegativity between O and H/C 6. C H O 8. a. both have carbonyl group, aldoses have aldehyde group, ketoses have ketone group b. pyranose = 6-membered ring; furanose = 5-membered ring c. triose – 3C, pentose – 5 C, hexose – 6 C 9. structural isomers 10. enantiomers 11. anomeric carbon = new asymmetric carbon formed by formation of ring structure a. α-glucose has OH group attached to anomeric carbon (C1) pointed down from plane of ring; β-glucose has OH group pointed up from plane of ring b. position of OH on asymmetric carbon farthest from aldehyde/ketone groups different 12. most commonly D sugars and L amino acids 15. condensation/dehydration synthesis, glycosidic bond 16. glucose + galactose 17. α(14) = glycosidic bond between α-anomeric C1 carbon of 1 glucose with C4 of second glucose Α(12) = glycosidic bond between α-anomeric C1 carbon of glucose with C2 of fructose 18. reducing sugars = sugars with aldehyde groups that can be oxidized to carboxylic acid groups, and reducing e.g. Cu2+ to Cu+ a. Both reducing, fructose is ketose but ketone group can isomerise to aldehyde group (tautomeric) b. Maltose reducing with free aldehyde group; sucrose non-reducing because aldehyde group used in glycosidic bond formation Exercise 2 1. Oligosaccharides = few monosaccharides joined together; polysaccharides = many monosaccharides joined together 2. Small changes in structure result in large difference in function (emergent properties) 3. Polysaccharide Monomer Type of Relate structure to property and glycosidic bond function Starch α-glucose α(14) Helical, unbranched, compact Amylose Starch – α-glucose α(14) Helical, branched, packed into Amylopectin α(16) at granules branches Glycogen α-glucose α(14) More extensively branched, α(16) at dense clusters of granules more branches Cellulose β-glucose β(14) Straight, unbranched, hydroxyl 4 group free to form hydrogen bonds with other cellulose molecules lying parallel forming microfibrils Worksheet 5 Cytology/Cell Biology Cell ultrastructure / organelle Rough endoplasmic reticulum Smooth endoplasmic reticulum Golgi body Structure Function Role of biochemicals in relation to function Network of membranous sacs and tubes studded with ribosomes, membrane separates lumen from cytosol, continuous with nuclear envelope Network of membranous sacs and tubes not studded with ribosomes, membrane separates lumen from cytosol, continuous with nuclear envelope Stacks of flattened membranous sacs; has polarity (cis and trans faces) Aids in synthesis of secretory and other proteins from bound ribosomes; adds carbohydrates to glycoproteins, produces new membranes Synthesis of lipids, metabolism of carbohydrates, Ca2+ storage, detoxification of drugs and poisons Phospholipids form membranes compartmentalizing protein synthesis for export out of cell. Modifications of proteins, adds carbohydrates on proteins and phospholipids; synthesis of many polysaccharides; sorting of Golgi products, which are then released in vesicles Cellular respiration Phospholipids form membranes which compartmentalizes metabolic reactions and forms vesicles which contain metabolites Mitochondria Bounded by double membrane; inner membrane has infoldings (cristae) Ribosomes Two subunits made of ribosomal RNA and proteins; can be free in cytosol or bound to ER Typically two membranes around fluid stroma, which contains membranous Chloroplasts Protein synthesis Photosynthesis 5 Phospohlipids form membranes compartmentalizing lipid synthesis from cytosol Phospholipids form membranes for compartmentalizing respiratory metabolic reactions, as well as barrier for ATPase to work RNA folded into conformation to carry out translation Phospholipids compartmentise organelle separating thylakoids stacked into grana Cell surface membrane Phospholipid bilayer with Form external barrier of cholesterol molecules; cell; control entry and exit integral proteins and of materials peripheral proteins within bilayer; carbohydrate side chains project from protein or lipid molecules Nuclear envelope Double membrane with associated proteins, surrounding nucleus, continuous with ER Centrioles A pair of nine sets of triplet Found in centrosomes microtubules arranged in which serves as a ring microtubule-organising centre, with a role in spindle formation in cell division Nucleus DNA organized as chromosomes/chromatin Carry genes Nucleolus Mass of densely stained granules and fibres Site where rRNA is synthesised and where proteins imported from cytoplasm is assembled into ribosomes Separates chromosomes and nuclear enzymes from cytosol 6 light and dark reaction, holds photosystem molecules in place Phospholipid form barrier, cholesterol determine fluidity of membrane, proteins serve as transport, receptor or carrier molecules, carbohydrates for cell signaling or recognition Phospholipids separate chromosomes from cytosol; compartmentalizes DNA and RNA synthesis from rest of cell; proteins form pore complex which regulates entry and exit of proteins and RNA Microtubules formed from globular protein tubulin (dimer of α and β-tubulin), assembled and disassembled to shape and support cell, serve as tracks for motor proteins to move. DNA contain hereditary information to direct protein synthesis through transcription DNA serve as template for transcription of rRNA