1. Biological Molecules Many organic compounds are large molecules called MACROMOLECULES. Macromolecules are usually polymers – molecules made up of repeating subunits called monomers. monomer polymer

2. Making and Breaking Macromolecules 4 main types of chemical reactions involved in building macromolecules (anabolism) and breaking them down (catabolism).

3. 1. Redox reactions – aka: oxidation – reduction reactions - involve the transfer of electrons between molecules “LEO the lion” says “GER” ElectronsElectrons ReductionReduction GainGain LoseLose ElectronsElectrons OxidationOxidation

4. O xidation I sI s L ose electrons R eduction I sI s G ain electrons Oxidation reactions Lose e - Remove H Add oxygen Release energy Reduction reactions: Gain e - Add H Remove Oxygen Require energy

5. Oxidation-Reduction Reaction (Redox Rxn) LEO the lion says GER Cu + 2Ag +  Cu 2+ + 2Ag

6. 2. condensation reaction – aka dehydration synthesis – enzyme aided reaction where a hydroxyl group from one molecule & a hydrogen from another molecule are removed, producing H 2 O and a new (larger) molecule ← C H HO C→ C + C ← C OH H C→ enzyme: takes OH out of 1 and H out of other ← C H C→ C O C ← C H C→ ‘O’ joins 2 molecules H 2 O comes out -

7. 3. cleavage – aka hydrolysis - the components of a water molecule (H + and OH) are added to a molecule to break it into 2 molecules - Opposite of dehydration synthesis H 2 O H OH C H C→ C O C C H C→ H & OH break O bond C H HO C→ C + C C OH H C→ 2 separate molecules

8. Dissolved Ions and the pH Scale many substances come apart (dissociate) into ions when they dissolve in water Water dissociates into: H 2 O ↔ H + + OH - * reversible reaction hydrogen ions hydroxide ions A higher [H + ] = stronger acid 4. acid-base – aka neutralization reactions – transfer hydrogen ions (H + ) between molecules.

9. pH Scale Summary: If….. [H + ] < [OH - ]  base [H + ] = [OH - ]  neutral [H + ] > [OH - ]  acid NOTE: pH scale is a logarithmic one. Each consecutive pH unit is separated by a factor of 10X.

10. Blood pH? 7.4 A slight change in pH (± 0.1) can lead to coma, paralysis and DEATH What helps to control fluctuations in pH? BUFFERS – help to keep the pH in different parts of your body constant by absorbing or releasing H + as needed

11. how? buffers release H + in basic solutions, but can accept H + in an acidic solution e.g. bicarbonate ion (HCO 3 - ) buffering an acid: H + + HCO 3 - ↔ H 2 CO 3 ↔ H 2 O + CO 2 carbonic acid decomposes into

12. If blood too acidic (  H + ), rxn moves left CO 2 H2OH2O H+H+ H+H+ H 2 CO 3 (aq) H+H+ H+H+ carbonic acid H+H+ surplus hydrogen ion If blood too basic (  H + ), rxn moves right HCO 3 - (aq) H+H+ bicarbonate ion

13. CarbohydrateslipidsProteinsWater MOST LEAST

14. Types of Biological Molecules

15. 1. Carbohydrates – contain C, H, O in 1:2:1 ratio a) simple sugars – monosaccharides - formula is C 6 H 12 O 6 or (CH 2 O) 6 - not usually in a chain but in a 6 carbon ring called a hexose i. glucose O C1C1 C2C2 C3C3 C4C4 C6C6 C5C5 OH HO – OH H H H H H – H - locations of OH are important for dehydration synthesis or hydrolysis reactions * simple sugars are chains in solids, rings in sol’n * Disc-OH Down Up Down

16. http://www.stolaf.edu/people/giannini/flashanimat/carbohydrates/gl ucose.swf

17. O C1C1 C2C2 C3C3 C4C4 C6C6 C5C5 OH – OH OHHO H H H –H – H HH ii. galactose isomers – are compounds with the same molecular formula but a different arrangement of atoms e.g. galactose & fructose are glucose isomers – iii. fructose C1C1 C6C6 C2C2 C4C4 C3C3 C5C5 – OH O HO – HO OH H – H– H H-H- H H H H – found in fruits Disc –OH Up Down Up Disc –OH Up Down

18. Molecular Isomers: The same, yet different Carvone Optical isomers – mirror image The devastating case of Thalidomide

20. b) disaccharides – high energy monosaccharides are bound into more stable chains for/during transportation - Condensation (dehydration synthesis) reactions involved O C1C1 C2C2 C3C3 C4C4 C6C6 C5C5 OH HO – OH H H H H H –H – H glucose+ O C1C1 C2C2 C3C3 C4C4 C6C6 C5C5 OH HO – OH H H H H H –H – H α linkage is bottom-to- bottom condensation O C1C1 C2C2 C3C3 C4C4 C6C6 C5C5 OH HO – OH H H H H H –H – H O C1C1 C2C2 C3C3 C4C4 C6C6 C5C5 OH – OH H H H H H –H – H O Maltose + water  Condensation reaction

21. O C1C1 C2C2 C3C3 C4C4 C6C6 C5C5 OH HO – OH H H H H H –H – H glucose + O C1C1 C2C2 C3C3 C4C4 C6C6 C5C5 OH – OH OHHO H H H –H – H HH galactose  O C1C1 C2C2 C3C3 C4C4 C6C6 C5C5 OH HO – OH H H H H H –H – H Lactose + water O C1C1 C2C2 C3C3 C4C4 C6C6 C5C5 OH – OH OH H H H –H – H HH O β linkage is top-to- bottom condensation

22. O C1C1 C2C2 C3C3 C4C4 C6C6 C5C5 OH HO – OH H H H H H –H – H glucose+ C1C1 C6C6 C2C2 C4C4 C3C3 C5C5 – OH O HO – HO OH H – H– H H-H- H H H H fructose O C1C1 C2C2 C3C3 C4C4 C6C6 C5C5 OH HO – OH H H H H H –H – H C1C1 C6C6 C2C2 C4C4 C3C3 C5C5 O HO – OH H – H– H H-H- H H H H O sucrose Linkage??? α linkage

23. c) polysaccharides – are complex carbohydrates composed of hundreds-thousands of monosaccharide subunits - e.g. starch – long chains of carbohydrates, plants store glucose as starch glycogen – storage form of glucose in animals cellulose – is a structural carbohydrate that forms cell walls aka fibre – holds feces together - constipated, eat more fibre

24. Carbohydrates – Complex (Polysaccharides) What is the difference between starch and cellulose? Starch Cellulose

26. d) Chitin – sounds like “kite-in” - structural carbohydrate found in crustaceans like crabs and shrimp, the exoskeleton of insects - Strong, similar structure to cellulose - Used in medical industry – biodegradable stitches

27. Types of Biological Molecules - LIPIDS Glycerol Fatty acids 1 1 2 2 3 3 – include: fats, oils, phospholipids, waxes -do not readily dissolve in H 2 O (largely hydrophobic) a) Triglycerides – include fats and oils -Large molecules made up of 2 kinds of smaller molecules: glycerol and 3 fatty acid chains

28. 1 ENERGY STORAGE short-term main function Making and Breaking Lipids (fats) Fats and oils are called triglycerides because of their structure Condensation Synthesis Hydrolysis What functional groups are present on the glycerol and fatty acid molecules? + 3 H 2 O Ester linkage

29. Two types of fatty acids: saturated and unsaturated Unsaturated fats contain C to C double bonds- create “kinks”, keeps the fatty acid chains from packing close to one another – remain liquid at room temperature Saturated fats have no double bonds, more H atoms, solid at room temperature Hydrogenated fats – bad why?

30. b) phospholipids - composed of 2 fatty acid chains and a glycerol + phosphate group - Make up cell membrane

31. c) sterols – have 4 fused carbon rings as a backbone, no fatty acid chains -functional groups attached to carbon rings- different structure, different function -Include: cholesterol, steroids, (test., est., prog.) bile salts Double lipid bilayer – cell membrane

32. Proteins 8 Main types: Transport proteins - move molecules across cell membrane Enzyme proteins- biological catalysts – speed up reactions Antibody proteins - fight infections Contractile proteins -can change shape rapidly – found in muscle tissue, cilia, flagella Hormone proteins - some hormones are proteins (e.g insulin) Extra Storage Proteins -act as a storage supply of amino acids – used for building new proteins Receptor proteins - found on cell surface- bind hormones Structural proteins -make up skin, hair, fingernails bird feather, tendons, cartilage

33. Proteins are made up of…. Amino acids Amino Acid Structure Amino Group Carboxyl (acid) Group Any one of the 20 different side-chains

34. … 20 different R chains …… 20 different amino acids 8 are essential – must get them in your diet Red meat gives you all 8 12 nonessential amino acids - can be synthesized by your body

36. Protein synthesis – occurs in ribosomes - long chains of amino acids are linked together by condensation reactions to create a polypeptide - condensation reaction forms a peptide bond

37. Protein structure -the sequence of amino acids in a protein determines the shape of the protein ( sequence = structure) 1. primary structure – the order of amino acids determined by DNA

38. H – bonds form btw the oxygen of the carboxyl group of one amino acid with the hydrogen of the amino group of a different amino acid creating a coiling pattern within the protein thread, called α (alpha) helix 2. secondary structure – forms spontaneously – as soon as polypeptide chain synthesized - sheet-like can also be formed, called a β (beta) pleated sheet

39. Alpha helixBeta (β) pleated sheet hydrogen bonds H bonds (dotted lines) in a polypeptide chain. Such bonds can give rise to a coiled chain or to a sheet like array of chains

40. 3. tertiary structure – involves highly specific looping and folding of the polypeptide chain to form a globular shape (semi-solid) - Results from interactions between the various side chains (R-groups) 4. quaternary structure – 2 or more polypeptide (amino acid) chains can interact to form a complex protein - this interaction is the quaternary structure Quaternary structure of human hemoglobin - made up of 4 polypeptide chains heme group Twisting and folding of the polypeptide chain

43. Protein denaturation – if a protein loses its quaternary or tertiary shape (due to bond breakage), the protein loses it structure and possibly, its function What can cause a protein to lose its shape?

44. Ignore the slides that follow (nucleic acids and nucleotides) We’ll cover this in Unit 3

45. 4. nucleic acids & nucleotides nucleotides - have:5 C sugars– ribose - deoxyribose - phosphate group - a single or double C ring structure which contains nitrogen, called a nitrogen base P deoxyribose or ribose O N e.g. i) ATP (adenosine triphosphate) - needed to deliver energy from one reaction site to another ii) coenzymes – assist enzymes by accepting H’s or electrons that are removed from a molecule by an enzyme e.g. NAD + (nicotinamide adenine dinucleotide) FAD (flavin adenine dinucleotide) iii) messengers – chemical messengers such as cyclic adenosine monophosphate (cAMP) - trigger parts of cells to become active

46. nucleic acids – RNA (ribonucleic acid) – single strand - DNA (deoxyribonucleic acid) – double strand - are long, twisted chains of nucleotides (G, C, A, T) - they contain genetic codes for cellular function - the sugars of one group covalently bond in the phosphate of another group to form a backbone with the N base free in RNA - in DNA, 1 N base hydrogen bonds with the 2 nd strand’s N base - the importance of nucleic acid is that they allow living organisms to reproduce - recall that there are 2 types: DNA & RNA, and each are polymers of nucleotides – each nucleotide has:i) a pentose (5 C sugar) ii) phosphate group iii) a nitrogen base

47. i. pentose a) ribose (RNA) O CH 2 OH OH b) deoxyribose (DNA) O CH 2 OH OH H One fewer ‘O’ ii. phosphate group - O – P – OH OH O - O – P – O - O-O- O or

48. iii. nitrogen bases a) pyrimidines– have a 6 member ring of C & N e.g. cytosine (c), thymine (T), uracil (U) In DNA only RNA only (replaces T’s) * RNA made of U,G,C,A * b) purines – have a double 6 member C & N ring e.g. adenine (A) & guanine (G)

49. - a nucleoside is a pentose connected to a nitrogenous base: ribose O N - a nucleotide is a nucleoside + a phosphate group: P ribose O N

50. A Arrangement of nucleotides in DNA A B 1 1 1 1 Deoxyribose 2 2 2 2 Phosphate 3 3 3 Paired Bases B Schematized double helix