Biology Paper 2 - 2.2 Biological Molecules

Forms between non metals. Electrons shared to fill outer shells.

Carbon: 4
Nitrogen: 3
Oxygen: 2
Hydrogen: 1

Weak interaction between a slightly positive hydrogen atom and a slightly negative oxygen atom.

Any slightly negatively charged atom.

The joining of two molecules by the removal of water.

An OH group is removed from one molecule and a H from the other.

Allows light through for photosynthesis.
Different depths of water = different wavelengths of light.
Predators/prey can see to hunt/evade.

Platform to hunt from/hide beneath.

Insulates water beneath - stable environment reduces freezing.

Habitat for life - within and on surface.
Site of reactions.
Hydrolysis reactions.
Reactant in photosynthesis.
Transport medium - blood, vascular tissue in plants, food and gametes for sessile organisms.

Ionic solutes dissolve - positive/negative interactions between dipoles of water.
Ions transported around cells/systems/media, e.g. reactions in cytoplasm, ions in blood, minerals for coral.

Cohesion - attraction between molecules pulls them together into sphere.
Adhesion - attraction between water and other surface.
Attractions pull molecules together to form surface tension.
Habitat for pond skaters.
Unbroken column of water in xylem.

Thermally stable - lots of energy in/out to raise/cool.
Stable temperature for enzyme catalysed reactions.
Stable environment for aquatic organisms.

Evaporation of water requires high energy so heat is removed from organism.
Cooling through panting/sweating in animals.
Evaporation of water form mesophyll cells.

Substances composed of large amounts of hydrogen and carbon but fewer carbons than carbohydrates.
Insoluble in water but soluble in ethanol.
Oils, fats and waxes.

Add iodine (potassium iodide) to a sample. Blue-black colour means starch is present.

Heat sample with excess Benedict’s reagent at 80°C for 5 minutes.

Observe colour change from blue to:

Green 0.5%

Yellow 1.0%

Orange 1.5%

Brick red 2.0%

Test for reducing sugars first.

Take a fresh sample.

Boil sample with dilute HCl to hydrolyse glycosidic bond if present.

Cool.

Add alkali to solution (i.e. NaOH).

Carry out standard reducing sugars test.

Mix a sample with ethanol, then filter into a test tube containing water. A cloudy white precipitate means a lipid is present.

Add biuret reagent (equal volumes of sodium hydroxide and copper sulphate) to a sample. Lilac colour means a protein is present.

Energy source, energy store, structural units.

Energy source, monomer of polymers (including amylose, amylopectin and glycogen).

Energy source, monomer of cellulose in plant cell walls.

Component of RNA, ATP and NAD.

Component of DNA.

Glycosidic bond.
Formed through a condensation reaction.
One hydroxyl, OH, group from each molecule align.
HOH removed, bond formed between remaining oxygen.
Bond forms between carbon 1 and carbon 4 or carbon 1 and carbon 6.

Hydrolysis reaction.
Water split into H and OH.
Used to break glycosidic bond.

Amylose: energy store in plants, combines with amylopectin to form the complex starch, 1,4 glycosidic bonds, coils held by hydrogen bonds, C2 OH groups held within spiral make it less soluble.
Amylopectin: energy store in plants, combines with amylose to form the complex starch, 1,4 and 1,6 glycosidic bonds, coils held by hydrogen bonds, 1,6 bonds form branches.
Glycogen: energy store in animals, stored in liver and muscles, 1,4 and 1,6 glycosidic bonds, more highly branched than amylopectin.

Compact for storage, insoluble so do not affect water potential of cells, readily hydrolysed to free monomers for energy source.

Made of β-glucose monomers.
To form a glycosidic bond, each β-glucose must rotate 180° compared to its neighbour.
β-glucose monomers are joined by 1,4 glycosidic bonds.
Forms straight chains that run parallel to each other.
Hydrogen bonds form between chains, many H bonds add considerable strength.

Found in plants.
Makes up the plant cell wall.
High tensile strength to prevent cells bursting under turgour pressure.
Allows ions and water to permeate.
Can be reinforced with additional substances. Suberin and cutin for waterproofing (e.g. Casparian strip). Lignin for strengthening (e.g. xylem vessels).

Starch: Stored in plants, insoluble, less branched, just 1,4 glycosidic bonds.
Glycogen: Stored in animals, less insoluble, more branched, 1,4 and 1,6 glycosidic bonds.

Peptidoglycan - bacterial cell walls, polysaccharide chains cross linked with protein bridges.
Chitin - exoskeleton of insects, beta-glucose with acetylamine group, cross links form between chains.

Glycerol head group, three fatty acid tails, joined by ester bonds formed through condensation reactions.

Condensation reaction between COOH of fatty acid and OH of glycerol, covalent bond forms, water is produced.

Saturated: No double bonds between carbon atoms.
Monounsaturated: A single carbon-carbon double bond.
Polyunsaturated: Many carbon-carbon double bonds.

Unsaturated: Tails 'stack', hydrogen bonds form between tails of triglycerides, solid at room temperature (e.g. animal fats).
Monounsaturated: Kinks in tail, less stacking, lipid more fluid at room temperature (e.g. avocado, fish oils).
Polyunsaturated: Many kinks, little/no stacking, lipid fluid at room temperature (e.g. plant oils).

Tail length. The longer the tail the higher the number of H bonds. More H bonds pull triglycerides closer. Decreases fluidity.

Energy source: hydrolysis yields high number of hydrogen atoms for synthesis of ATP during respiration.
Energy store: insoluble so do not affect water potential of cells.
Insulation: blubber in whales, myelin sheath in neurones.
Buoyancy: lipids less dense than water so enable organisms to float.
Protection: layer around delicate organs e.g. kidneys.
Neural development: essential fatty acids omega 3 and 6 used in brain development.

Glycerol head group.
Two fatty acid tails joined by condensation reaction to form two ester bonds.
Phosphate group joined by condensation reaction to form phosphodiester bond.

Phosphate group negative, polar, attracted to water, hydrophilic.
Fatty acid tail non-polar, repelled by water, hydrophobic.
Molecule is amphiphatic, has two distinct and different properties within one molecule.

Aqueous environment outside and within cells.
Hydrophilic phosphate heads attracted to water.
Hydrophobic fatty acid tails repelled by water.
Double/bilayer of phospholipids forms.

Highest percentage molecule in the plasma membrane of plants and animals.
Phospholipids free to move within bilayer, if tails not exposed.
Selectively permeable: small, non-polar molecules can diffuse through, e.g. oxygen and carbon dioxide.
Polar molecules require transport channels.

Steroid alcohol.
Four carbon rings.
Hydrophobic.

Sits within the fatty acid region of the bilayer.
Regulates fluidity.
Contributes to the formation of steroid hormones, oestrogen, progesterone and testosterone.
Contributes to the formation of vitamin D in animals.
Contributes to the formation of steroid phytohormones in plants.

Carry out the Benedict’s test on a sample (describe the test).
Filter the sample to remove the red copper oxide precipitate.
Zero the colorimeter using distilled water.
Place the supernatant (liquid) into a cuvette which is placed in a colorimeter.
Shine red light through the sample - any blue copper sulphate will absorb the red light.
Measure the transmission of red light through the supernatant.
If the glucose concentration is low there will be a high absorbance of red light so the % transmission will be low.
If the glucose concentration is high there will be a low absorbance of red light so the % transmission will be high.

Take a series of known reducing sugar glucose.
Carry out the Benedict's test and record the % transmission using a colorimeter.
Plot a graph of glucose concentration (x axis) against % transmission of light (y axis).
Carry out Benedict's test on unknown and record % transmission of light.
Draw a horizontal line from relevant % transmission on y axis to calibration curve.
From this point draw a vertical line down to x axis.
Where line crossed x axis this is concentration of unknown.

Repeat using a narrower range of increments eg 2%, 4%, 6%, 8% instead of 5%, 10%.

Repeat the data to narrow the range and remove anomalies before calculating a mean.

Use a colorimeter with more decimal places.

| Use concentrations with closer increments eg 1.5%, 2.0%, 2.5%.

Chemical or biological variable to be tested.
Binding of variable to receptor brings about a change, e.g. colour, product of the reaction.
Converted to electrical signal or digital display.
Used for water testing, bacterial contamination.
Canaries used to detect toxic, odorless gases during mining.

The monomer of all proteins and enzymes.

| Comprised of the same basic structure.

Contain carbon, hydrogen, nitrogen and oxygen.
Some contain sulphur.
All have a variable R group that confers specific properties to each amino acid.
Each amino acid has an amino group, NH2, and a carboxyl group, COOH.

Amino acids are water soluble.
This causes the amino and carboxylic groups to ionise.
The amino group gains a proton and acts as an acid, it becomes NH3+.
The carboxyl group loses an electron and acts as a base, becomes COO-.
An amino acid has basic and acidic properties.
R groups may also have acidic or basic properties.

In solution the NH3+ can neutralise hydroxyl groups in alkalis, OH-.
The COO- can neutralise protons in acids, H+.
By accepting and releasing H+ changes in pH and be modulated.

Condensation reaction. Carboxyl group of one amino acid loses OH. Amino group of the next amino acid loses H. Peptide bond is formed and water is released.

Peptide bond: formed between amino acids; bond forms between carboxyl group and amino group of next amino acid; polymer is a polypeptide.
Glycosidic bond: formed between alpha glucose monomers; formed between beta glucose monomers; bond forms between carbons 1,4 and 1,6; polymer is a polysaccharide.
Both: formed during a condensation reaction, broken during hydrolysis reaction.

Primary structure.
Secondary structure.
Tertiary structure.
Quaternary structure.

The sequence of amino acids in polypeptide chain.
Held by covalent, peptide bonds between amino acids.
Number and order of amino acids is determined the base sequence of the specific gene from which it is coded.
Changes in the base sequence may alter the order, number and type of amino acid in the primary structure.

The folding or coiling of the primary structure.

| Alpha helix or beta pleated sheet.

Primary structure twisted into a coil.
36 amino acids per 10 turns of the helix.
Held by hydrogen bonds between NH group of one amino acid and CO group of the amino acid four places along in the chain.
High in globular proteins.
Many weak hydrogen bonds give stability to the final protein structure.

Primary structure folded into a zigzag structure.
Zigzag folds back on itself to form beta pleated sheet.
Held in place by hydrogen bonds NH group of one amino acid and NH group from another amino acid further down the sheet.
High in fibrous proteins.
Many weak hydrogen bonds give stability to the final protein structure.

Folding and coiling of primary and secondary structures into specific 3D shape
3D shape specific to order and properties of amino acids in primary structure, determined by the base sequence in the gene

Two or more tertiary structures combined to make a functional protein.
Antibodies, collagen and haemoglobin all have a tertiary structure.

Primary - covalent, peptide bonds between amino acids.
Secondary - hydrogen bonds between amino acids in different parts of the polypeptide chain.
Tertiary - hydrogen bonds, ionic bonds between positive/negative R groups, disulphide bridges between R groups of sulphur containing amino acids e.g. cysteine and methionine.

Hydrophobic R groups avoid water and associate in the centre of the polypeptide.
Hydrophilic R groups are attracted to water and are found at the outer edges of the polypeptide.

Insoluble in water; regular, repeating amino acid sequences, often with small R groups (e.g. proline); secondary structures mostly beta pleated sheets; metabolically inactive; often long and relatively thin; structural; examples are collagen, keratin, elastin.

Soluble in water; hydrophobic R groups in centre of polypeptide; hydrophilic R groups on edge of polypeptide; secondary structures mostly mostly alpha helices; rounded in structure; often enzymes; examples are haemoglobin, insulin.

A non-protein component needed for the functioning of a protein molecule.
E.g. iron ion in haem group of haemoglobin.

Collagen: Quaternary structure = 3 polypeptide chains; high in proline and lysine, small R group; high tensile strength; artery walls - prevents bursting; tendons -connects muscles to bone; bone - matrix reinforced with calcium phosphate; cartilage and connective tissues - holds layers together.
Elastin: Cross-linking and coiling - strong and extensible (stretchy); skin, lungs, bladder and blood vessels - allows stretch and recoil.
Keratin: High in cysteine - R group contains sulphur, disulphide bridges between cysteine amino acids; very stable, very strong; hair, skin, nails, hooves - mechanical protection, barrier, waterproof.

Haemoglobin: Quaternary structure - four polypeptide chains, 2x alpha, 2x beta; form one haemoglobin molecule, subunits held by hydrogen bonds, ionic bonds and disulphide bridges; each subunit contains haem prosthetic group - essential for function - conjugated protein; carriage of oxygen from alveoli to respiring cells and carbon dioxide from respiring cells to alveoli.
Insulin: Quaternary structure - two polypeptide chains; a chain begins with alpha helix, B chain ends with beta pleated sheet; joined by disulphide bridges; soluble -hydrophilic R groups on outside of molecule; insulin binds to receptors on outer surface of cells to aid uptake of glucose from blood.
Pepsin: Single polypeptide chain, 327 amino acids in length - 4 basic R groups, 43 acidic R groups - stable in acidic environment of stomach; symmetrical tertiary structure held by hydrogen bonds and disulphide bridges; digestive enzyme.

Ab initio: 3D modelling based on electrical and physical properties, provides more than one possible model from an amino acid solution.
Comparative protein modelling: Protein threading scans amino acid sequence, compare against known sequences in a data base, provides possible set of models to match sequence.

Calcium, Ca2+. Rigidity of bones and teeth; blood clotting; muscle contraction.
Sodium, Na2+. Regulation of osmotic pressure; absorption of carbohydrate; turgidity og plant vacuole.
Potassium, K+. Osmoregulation and pH; transport across cell membranes; generation of leaves and flowers in plants; transmission in nerves and muscle contraction.
Hydrogen, H+. Photosynthesis and respiration; transport of oxygen in blood; regulation of blood pH.
Ammonium; NH4+. Amino acids and proteins; hormones; nucleic acids; nitrogen cycle.
Nitrate, NO3-. Amino acids and proteins; nucleic acids; hormones; nitrogen cycle.
Hydrogencarbonate; HCO3-. Regulation of blood pH; transport of carbon dioxide in blood.
Chloride, Cl-. Urine production; osmoregulation; transport of carbon dioxide; carriage of oxygen; regulation of blood pH; root growth in plants.
Hydroxide, OH-. Regulation of blood pH.

Separation of molecules based on size.
Smaller molecules travel further than larger molecules.
Two stages: Stationary - the paper or TLC plate. Mobile - the solvent relevant for the specific biological molecule.

Draw line in pencil at bottom of paper/TLC plate.
Dot sample onto line, allow to dry between dots.
Place in solvent, cover, leave.
Run until solvent reaches just below top of paper.
Calculate Rf value.

Rf = x/y. x = distance travelled by molecule. y = distance travelled by front.

Ultraviolet light - TLC plates show fluorescence, spots mask glow.
Ninhydrin - binds to amino acids, visible as brown/purple dots.
Iodine - add crystals, seal container, vapour forms and binds molecules.

Rate of travel through plate determined by: size of molecule, solubility in given solvent.
Exposed -OH groups on surface of plate or paper form H bonds with molecules.
Highly polar molecules adsorbed to surface more easily than less polar molecules.
Less polar molecules move more easily up the paper or plate - less ‘stick’.