1A: Biological Molecules


Molecules of Life

Theory of Evolution: Everyone descended from one or a few common ancestors and that they have changed and diversified over time. Evidence: Shared biochemistry, carbon-based compounds that interact using the same nucleic and amino acids. These suggest that animals and plants have a common ancestor.

Monomers: Small, basic molecular units. Monosaccharides, amino acids, nucleotides.

Polymers: Large, complex molecules made of long chains of monomers joined together.

Formed via condensation reactions that form a chemical bond between monomers, releasing a molecule of water.

(Insert diagram)

Polymers can be broken down into monomers via hydrolysis reactions. It breaks the chemical bond between monomers using a water molecule.

(Insert diagram)

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Monosaccharides (M's) and Disaccharides (D's). M's are simplest sugars, and are building blocks of carbohydrates.

Carbohydrates contain: C, H, O. Made from M's - Glucose, Fructose, Galactose

Glucose: Hexose sugar, 6 C atoms. Two isomers (Same molecular formula, but atoms connected in a different way) of glucose are Alpha (A) and Beta (B) glucose. (Insert diagram)

D's are formed from 2 M's via a condensation reaction. A glycosidic bond is formed as a molecule of water is released. (Insert diagram)

(A) glucose + (A) glucose = Maltose

Glucose + Fructose = Sucrose

Glucose + Galactose = Lactose

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Benedict's Test

Reducing Sugars: All monosaccharides + Maltose, Lactose

Add Benedict's solution (Blue) to sample and heat in water bath that has been brought to boil. If RS present then coloured precipitate will form. Colour changes based on amount present. Blue (negative)>Green>Yellow>Orange>Brick Red.

Other ways: Filter solution and weigh precipitate, or remove precipitate and use a colorimeter to measure absorbance of remaining Benedict's reagant.

Non-Reducing Sugars: Sucrose. If original test blue, could be NRS present. Have to break down into M first. Add dilute HCl to new sample of test solution and carefully heat in water bath that has been brought to boil. Neutralise by adding sodium hydrogencarbonate. Then re-carry out Benedict's test.

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Carbohydrates. 2+ M's joined via condensation reaction. (Insert examples) Can be broken down into constituent M's via hydrolysis reactions.

Starch: Cells get energy from glucose. Plants store excess glucose as starch. Made of 2 polysaccharides of (A) glucose - Amylose, Amylopectin. Is insoluble in water so no effect on water potential, so no water enters cells by osmosis, which could make them swell; makes it good for storage.

> Amylose: Long, unbranched chain. Angles of glycosidic bonds give coiled structure. Makes compact, good for storage because more can fit in smaller space.

> Amylopectin: Long, branched chain. Side branches allow enzymes that break down molecule to access glycosidic bonds easier. Means glucose can be released easily.

Glycogen: Animals store excess glucose as this. (A) glucose. Many more side branches than Amylopectin. Means stored glucose can be released quickly, important for energy release in animals. Very compact molecule; good for storage.

Celluose: Long, unbranched chains of (B) glucose. When (B) glucose bonds, forms straight celluose chains. Linked by H bonds to form strong fibres - microfibrils. Strong fibres means celluose provides good structural support for cells.

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Iodine Test for Starch

Add Iodine dissolved in Potassium Iodide solution to the test sample.

If there is starch present, sample changes from brown-orange to a dark, blue-black colour.

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Lipids (1): Triglycerides

Fats or oils found in all cells. Made from variety of components, but all contain hydrocarbons (only H and C atoms). 2 types of lipid need to know - Triglycerides + Phospholipids. (Insert diagrams)

Triglycerides: 1 glycerol, 3 fatty acids. Fatty acids have long "tails" made of hydrocarbons. Tails are hydrophobic. Tails make lipids insoluble in water. Fatty acids either saturated or unsaturated.

Saturated: No double bonds between C atoms. The fatty acid is saturated with H.

Unsaturated: Double bonds between C atoms, causes chain to kink.

Formed by condensation reactions. Ester bond forms between fatty acid and glycerol, releasing a molecule of water. Happens 2 more times to form a triglyceride.

Used as energy storage molecules because long hydrocarbon tails of fatty acids contains lots of chemical energy - loads of energy released when broken down. 2x as much energy per gram as carbohydrates. Insoluble in water, no effect on water potential of cell so no water entering cell by osmosis. They bundle together as insoluble droplets because fatty acid tails are hydrophobic - tails face inwards, shielding themselves from water with glycerol heads.

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Lipids (2): Phospholipids

1 phosphate group, 1 glycerol molecule, 2 fatty acid molecules. Phosphate group is hydrophilic. Fatty acid tails are hydrophobic. Important in the cell membrane.

They make up the bilayer of cell membranes, control what goes in and out of cells. Because of the properties of the heads and tails, the phospholipids form a double layer with heads facing outward towards the water on either side. Centre of bilayer is hydrophobic, water-soluble substances can't easily pass through - membrane acts as a barrier to those substances.

Emulsion test for presence of lipids: Shake the test substance with ethanol for a minute/until dissolved, then pour solution into water. (Can shake again) Lipid shows up as milky emulsion. More lipid = more noticeable milky colour.

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Proteins (1)

Monomers of proteins are amino acids. 2 amino acids = dipeptide. 2+ amino acids = polypeptide. 1+ polypeptide = protein.

Amino acid: Carboxyll group, amine/amino group, R variable group (usually contain C), H atom, connected to C atom. Only exception is glycine - R group is one H atom. All living things share a bank of only 20 amino acids.

Bonds formed between amino acids by condensation are peptide bonds. Hydrolysis happens when dipeptides and polypeptides are broken down. 

Primary structure: Sequence of amino acids in the polypeptide chain.

Secondary structure: Chain doesn't remain flat and straight. H bonds form between amino acids in chain which makes it coil into an (A) helix or fold into (B) pleated sheet.

Tertiary structure: Coiled/folded chain is folded further. More bonds form between different parts of polypeptide chain, H bonds, ionic bonds. Disulphide bridges form when 2 cysteines come close together - sulphur atom in one bonds with the other. If single polypeptide chain, final 3D structure.

Quaternary structure: Proteins made of many various polypeptide chains are held together by bonds. Is the way they are assembled together. If more than 1 polypeptide chain, protein's final 3D structure.

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Proteins (2)

Shape determines function - makes them specialised to carry out particular jobs.

Enzymes: Roughly spherical due to tight folding of chains. Soluble, often have roles in metabolism, e.g. break down large food molecules, others help synthesise large molecules.

Antibodies: Involved in immune response and are found in blood. 2 light polypeptide chains and 2 heavy chains bonded together. Have variable regions, amino acid sequences in these vary greatly.

Transport proteins: Channel proteins contain hydrophobic and hydrophyllic amino acids, which cause the protein to fold up and form a channel. Transport molecules and ions across membranes.

Structural proteins: Physically strong. Long polypeptide chains lying parallel to each other with cross-links between them. Keratin and collagen. Collagen has 3 chains folded tightly together, which makes it strong. Great supportive tissue in animals.

Biuret test for proteins: Make test solution alkaline by adding sodium hydroxide solution. Add copper(II) sulphate solution. If protein present, solution turns purple. If not, stays blue.

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Enzymes (1)

Enzymes speed up chemical reactions by acting as biological catalysts. Catalyse metabolic reactions - cellular level (respiration), organism as whole (digestion). Can affect structures in organisms (collagen), as well as functions (respiration). Can be intracellular or extracellular. Have an active site, which has a specific shape. Substrate binds to it. Highly specific due to tertiary structure.

A certain amount of energy needs to be supplied to chemicals before reaction can start - activation energy (often heat). Enzymes lower amount of AE needed making reactions at a lower temperature than without an enzyme. This speeds up the rate of reaction.

When substrate binds to active site it forms enzyme-substrate complex which is what lowers AE. If 2 substrates need to be joined, being attached to enzyme holds them close together, reducing repulsion so they bond easier. If enzyme is catalysing a breakdown reaction, fitting into active site puts strain on substrate bonds, so they break up easier.

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Enzymes (2)

Lock and Key model: Enzymes only work with substrates that fit their active site (complementary shape), same way key fits into lock. Early scientists' theory. 

"Induced fit" model: Helps explain why enzymes are so specific and only bind to one particular substrate. Doesn't only have to be right shape, has to make active site change. Widely accepted.

Enzyme properties: Related to tertiary structure, which is determined by primary structure. This is determined by gene, so if mutation occurs, tertiary structure might change. Specific, usually only catalyse one reaction because only 1 complemetary substrate fits into active site. Each enzyme has a different tertiary structure. If this is changed, the active site of protein changes. Substrate won't fit, no ESC, enzyme won't carry out function. 

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Factors affecting enzyme activity

Measuring enzyme activity: How fast product is made; amount of end product present at different times, how fast substrate is broken down; amount of substrate molecules left at different times.

Temperature: More heat>more kinetic energy>molecules move faster>more likely to collide with enzymes' active sites. Energy of collisions increases, means each collision likely to result in reaction. Too high>enzymes molecules vibrate more>breaks bonds that hold enzyme in shape>active site changes shape>substrate no longer fits>reaction stops. Denatured.

pH: Most human enzymes work best at 7. Pepsin works best at 2 because it's found in the stomach. Above and below optimum, H+, OH- ions in acids/alkalis disrupt ionic/H bonds that hold tertiary structure in place. Enzyme denatures, active site changes shape.

Substrate concentration: Higher substrate, faster reaction. More substrate means collision is more likely, more active sites occupied. Only true up to "saturation". After, all active sites full, so adding more substrate has no effect as nothing to bind to.

Enzyme concentration: More enzyme molecules, more likely substrate collides to form ESC. Substrate is limited, so eventually more than enough enzyme to deal with it, so no further effect in adding more.

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Enzyme Inhibitors

Competitive: Similar shape to substrate. Compete with substrate to bind to active site, but no reaction. Block active site so no substrate molecule can fit. How much it is inhibited depends on concentration of inhibitor and substrate. High conc of inhibitor>takes up nearly all active sites>no substrate gets to enzyme. High conc of substrate>substrates chance of getting to enzyme before inhibitor increases.

Non-competitive: Bind to enzyme away from active site. Causes active site to change shape so substrate cant bing to it. Don't compete with substrate because different shape. Increasing conc of substrate won't make a difference, enzyme activity will still be inhibited.

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Enzyme controlled reactions (RQ1)

Catalase catalyses breakdown of hydrogen peroxide into water and oxygen. Different temperatures

1. Set up boiling tubes containing the same volume and concentration of hydrogen peroxide. To keep pH constant, add equal volumes of buffer solution to each boiling tube. 2. (Insert diagram). 3. Put each boiling tube in water bath at different temps, along with another tube containing catalase. Wait 5 mins for each to heat up. 4. Use pipette to add same volume and concentration of catalase to each boiling tube. Quickly attach bung and delivery tube. 5. Record O2 produced in 1st minute. 6. Repeat at each temp 3x and use mean. 7. Calculate mean rate of reaction at each temperature by dividing volume of O2 produced by time taken. Unit is cm(3)s(-1)

Amylase catalyses the breakdown of starch to maltose. Test for presence of starch using iodine in potassium iodide (Insert diagram)

1. Drop of iodine in each dip in spotting tile. Label the seconds. 2. Mix together known conc and volume of amylase and starch in test tube. 3. Pipette mixture into 1 of the dips at regular intervals. 4. Observe colour change from orange-brown to blue-black. 5. See how fast amylase works by how long it takes for iodine to no longer turn blue-black when mixture is added. 6. Repeat with different concentrations. 7. 3x at each amylase conc to find mean time. 

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