AS Biology

1. AS Biology Module 1 Section 1.1 Molecules

2. Specification

3. Specification

4. Water • 75% of the human body is water • Between 70 to 90% of your cells is water • Water is a polar molecule • That is, one end is a bit positive, and one end is a bit negative • This means it acts as a solvent for polar compounds • Hydrogen bonding between oxygens and hydrogens is possible due to this dipolar character and allows water to form a complex network

5. Water as a solvent • Due to the polar nature of water, anything dissolved in water is surrounded by the water molecules and this aids in dissolution. Once dissolved, the chemicals are free to react and so many of the bodies reactions require water to take place. • Non-polar compounds such as lipids and some proteins do not dissolve in water and so cluster together. This is due to the hydrophobic nature of these compounds and this property is highly important in the function of some proteins. • As water is ubiquitous throughout the body, water is the primary transport medium found throughout the body.

6. Water: Concentration trick question • Water with a volume of One litre • What is its molarity (concentration)? • 1 litre = 1 kg = 1000 grams (as water has a density of 1) Moles = mass/RFM Moles = 1000/18 (the RFM of water is 18) Moles = 55.555555 The number of moles in 1 litre is called the Molarity 55.555 mol/l is the same as 55.555 M

7. Inorganic ions and compounds • K+ - Potassium • Involved in nervous transmission and in plant guard cell turgidity • Ca2+ - Calcium • Involved in nervous transmission and muscle contraction and calcium phosphate is important in bone and teeth structure. In plants makes up calcium pectate in the middle lamella of membranes. • PO43- - Phosphate • Highly important in cellular signalling and in construction of DNA nucleotides, also a part of calcium phosphate important for teeth and bones. ATP and phospholipids are also phosphate dependent • Mg2+ - Magnesium • Important in the structure of chlorophyll and some enzymes utilise magnesium in their active site and it can also form part of DNA tertiary structure • Fe2+/3+ - Iron • Important in the structure of haemoglobin as a carrier of oxygen • HCO3- - Hydrogen Carbonate • Present in the blood as a buffering agent responsible for keeping blood pH within a narrow biological range • NO3- - Nitrate • Important in formation of proteins • Na+ - Sodium • Involved in nervous transmission and in the kidney to reabsorb water and produce urine

8. Past-Paper Questions

9. Carbohydrates • Cn(H2O)n • i.e. Glucose is C6H12O6 • Carbohydrate – carbon and hydrate (water)! • Primarily used as short-term energy storage • Secondary function is intermediate-term energy storage • i.e. starch or glycogen • Other functions include cell signalling, protein aging and cell wall components of plants

10. Carbohydrates - Monosaccharides • The simplest of the sugars and the major ones are; α-Glucose and β-Glucose Fructose

11. Condensation Reaction • This is a reaction between two or more molecules that ends up with formation of a bond and the removal of water • The opposite reaction is a hydrolysis reaction, where you use water to break a bond

12. Carbohydrates - Disaccharides • The bond formed between the condensation of two monosaccharides is called a GLYCOSIDIC LINKAGE • Sucrose and Maltose are two of the most common disaccharides + +

13. Sucrose • Glucose and fructose combined by condensation results in sucrose • Bonded by a α(1-2) glycosidic bond • Has structural formula C12H22O11 • Sometimes called saccharose • Common table sugar

14. Maltose • Glucose plus glucose results in formation of maltose • Bonded by a α(1-4) glycosidic linkage • Formed when amylase breaks down starch

15. Carbohydrates - Polysaccharides • Monosaccharides are single sugars • Disaccharides are two monosaccharides joined together • Polysaccharides are chains of tens to thousands of monosaccharides

16. Carbohydrates - Polysaccharides • The structure of starch, cellulose and glycogen are all different even though are all made of the same basic block (glucose)

17. Carbohydrates - Polysaccharides • Cellulose Consists of thousands of β(1-4) linked glucose Present in plant cell walls due to its rigidity and strength A straight chain polymer full of hydrogen bonds • Starch Consists of α(1-4) linked glucose Present in plant cells as a storage molecule Consists of linear and helical amylose and branched amylopectin • Glycogen Consists of α(1-4) linked glucose and also α(1-6) glucose at branch points Present in animal cells as a storage molecule Primarily made and stored in muscles and the liver

18. Starch • Amylose • Amylopectin

19. Glycogen

20. Carbohydrates - Pentose sugars • Pentose sugars have FIVE sugars present • Structurally they look like pentagons • HIGHLY important class of sugars as ribose forms the backbone of RNA (ribose nucleic acid)and deoxyribose forms the backbone of DNA (deoxyribose nucleic acid)

21. Tests for carbohydrates • Iodine test to look for the presence of STARCH • Add a solution of iodine and potassium iodide to a sample you think contains starch. A blue/black colours means you have starch present, due to the presence of amylose that allows the colour to form. If no starch is present the colour remains yellow/orange. • Clinistix test for GLUCOSE • Tests for glucose and glucose ONLY. Reagents in the stick result in a colour change when glucose is oxidised by the immobilised enzyme present on the stick. The more glucose present the darker the colour becomes.

22. Tests for carbohydrates • Benedicts test to test for REDUCING SUGARS • Reducing sugars like glucose can reduce copper hydroxide present in the reagent in the presence of heat resulting in a positive brick red colour seen.

23. Past-Paper Questions

24. Past-Paper Questions

25. Past-Paper Questions

26. Lipids • Lipids are things such as fats and oils • They do not mix with water (immiscible) • They are formed from the condensation of GLYERCOL and FATTY ACIDS • The structural building block is a TRIGLYCERIDE

27. Saturated and unsaturated lipids • The fatty acid chains that makeup the lipid can be either; • saturated • unsaturated • poly-unsaturated (just means more unsaturated than most) • The number of double bonds present leads to a decrease in melting temperature

28. Fatty-acids in water • In water, some lipids can dissolve and form monolayers on the surface • Other molecules may form circular structures called micelles that sequester the hydrophobic tails away from the water, encased within the outward facing hydrophilic heads

29. Phospholipids • A special kind of lipid • Special properties allow it to form double layered membranes • Hydrophobic tail • Hydrophilic head

30. Phospholipids in water • Phospholipids contain two fatty acid chains • Like fatty-acids they can form monolayers on the surface of water • Or form double membrane structures called LIPOSOMES

31. Phospholipid membranes • Cholesterol is also an important constituent of membranes • It aids in permeabilising the membrane • The cell membrane and all the membranes of the organelles are made from phospholipid double membranes • Due to the hydrophobic centre and hydrophilic external regions of the membrane, this explains why membranes show mixed permeability

32. Past-Paper Questions

33. Past-Paper Questions

34. Proteins • No matter how complex (and proteins can get VERY complex), they are all formed from basic building blocks called Amino Acids • Condensation reactions between amino acids make PEPTIDES • Combining peptides is responsible for PROTEIN formation • Hydroylsis reactions of proteins results in peptide and amino acid formation

35. The peptide bond • CO-NH • Peptide linkage • Formed by condensation reaction • Results in a dipeptide • This has an N and C terminus

36. Protein Primary (1o) Structure • The amino acid sequence of a polypeptide involving peptide bonds • The amino acids can either be given as their full names of by their one letter abbreviations • Just a string of amino acids arranged in a polypeptide chain

37. Protein Secondary (2o) Structure • Secondary structure elements are held together by hydrogen bonds • There are many more types of secondary structure available though • Local regions of structure; • α-helix • β-pleated sheet

38. Protein Tertiary (3o) Structure • The folding of a polypeptide upon itself into a complex 3D structure • Regions of the polypeptide are held together by; • Disulphide bonds • Ionic bonds • Hydrogen bonds • Hydrophobic interactions

39. Protein Quaternary (4o) Structure • Not all proteins have this level of structure • Formed by a collection of polypeptides interacting in a 3D structure • Haemoglobin is an example of a protein displaying quaternary structure

40. Shape in relation to function • Protein shape is a major determinant of protein function • Globular proteins • Such as enzymes are more compressed and rounded in shape • Water soluble • Contain 3o and 4o structure organisation • Fibrous proteins • Such as collagen and other structural proteins are drawn out in shape • Water insoluble • Consists of repeating 2o structure elements

41. Shape in relation to function

42. Conjugated Proteins • A protein that functions through an interaction with other chemical groups attached by covalent bonds or other types of bonding • The non-amino-acid group attached to conjugated proteins is called the PROSTHETIC GROUP • Usually this is a vitamin or vitamin derivative • Examples include haemoglobin and glycoproteins found on cell membranes. Glycoproteins contain carbohydrate as the prosthetic group.

43. Haemoglobin and chlorophyll • Haem is the prosthetic group found in haemoglobin. It is the iron that carries the oxygen around the body, not the rest of the protein. • Chlorophyll is a pigment found in the chloroplasts of plants. Magnesium is required for synthesis of this group.

44. Chromatography of amino acids • Using a piece of chromatography paper, mark a line a few centimetres up from the bottom of the page. Using a capillary tube, spot on small volumes of amino acids or samples for analysis. • Once dry, lower the page carefully into a chamber full of the resolving agent you are to use. BE CAREFUL NOT TO SHAKE THE VESSEL OR GET SOLVENT PAST THE LINE YOU MARKED. • Once the page is securely in the vessel, close the lid and leave the chromatogram to run until the solvent is a few centimetres from the top of the page (half an hour to a few hours, it caries).

45. Analysing the chromatogram • Once the run is complete, mark the solvent front and allow the paper to dry. Once fully dry, spray the paper with ninhydrin to visualise the amino acid spots. Mark the centre of the spots and measure the distance travelled using a ruler. Also measure the solvent front distance. Calculate the Rf values.

46. Tests for proteins • Biuret test • Detects the presence of peptide bonds and can be used to quantitate the amount of protein present. In the presence of peptides, copper (II) ion formation leads to the formation of a violet/purple coloured coordination complex in alkaline solution. • A sample is treated with an equal volume of 1% potassium or sodium hydroxide (strong base) followed by a few drops of aqueous copper (II) sulphate and a stabilising reagent. It will turn from blue to violet in the presence of proteins.