Biological molecules ocr A level biology

Biological molecules

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

• Carbohydrates - C,H,O

• Lipids - C,H,O

• Proteins -C,H,O,N,S

• Nucleic acids - C,H,O,N,P,S

(calcium ions)

Cations

• (Ca2+)

• involved in muscle contraction and nerve impulse transmission

sodium ions

Cation

• Na+

• Involved in co - transport

• reabsorption of water in the kidney

• nerve impulse transmission

Potassium ions

cation

• (K+)

• involved in stomatal opening

• nerve impulse transmission

Hydrogen ions

cation

• (H+)

• very important for catalyzing enzyme-controlled reactions

ammonium ions

• Cation

• (NH4 +)

• Useful in nitrogen cycle, bacteria converts ammonium ions to nitrate ions

nitrate

anion

• (NO3 –)

• Mineral ions absorbed by plants to provide nitrogen for amino acids

phosphate

• anion

• PO43-

• Formation of phospholipids for cell membranes

• creating nucleic acid

• ATP for making bones

Chloride

Anion

• (Cl –)

• Provide a negative charge to balance positive sodium ions and positive ions in cells

hydrogencarbonate

anion

• Maintains pH of blood

• HCO3-

Water charge

• Oxygen and hydrogen chemically bonded with covalent bond

• Oxygen is slightly negative Hydrogen is slightly positive

• Water is a polar molecule

• Opposite charges form hydrogen bonds

Specific Heat capacity

• Water has a very high specific heat capacity ( a lot of energy is required to change temperature)

• Heat energy go into breaking hydrogen bonds not kinetic energy of molecules so water is a buffer to instant temp change - allowing organism to live in water

• Ice is less dense than water and insulates water below so it doesn’t freeze - organism can live in water

latent heat of vaporization

• Very high latent heat of vaporization ( a lot of heat energy to evaporate water)

• Organisms can cool themselves without losing a lot of water

• Sweating - water evaporates allowing organism to cool down

Water as a solvent

• Water is an excellent solvent - contain dissolved oxygen used for organisms in respiration

• Can be used to transport CO2, glucose, amino acids in blood

• Also used in xylem e.g. magnesium

• Cohesion - surface tension allows surface of water to a habitat for insects e.g. pondskaters

Water metabolic reactions

• Used in hydrolysis reactions

• Used Photosynthesis

• Produced in condensation reactions

• Produced in respiration

Glucose

• Hexose sugar

• Monosccharide - single sugar molecule

• A store of chemical energy - very soluble in water -Have many hydroxyl groups which are polar can form hydrogen bonds with water molecules

• Hydrophilic

Why do plant cells store glucose as starch?

• As glucose is so soluble

• If a cell contains high amounts of glucose - water will move into cell by osmosis

Starch

• Made of Amylose and Amylopectin

• Store of glucose - very compact

• Insoluble in water - does not make water enter through osmosis

• Too large too diffuse out cell membrane

• When glucose is needed water breaks glycosdic bonds in (hydolysis reactions)

Amylose

• Polymer of α glucose molecules

• Chain of alpha glucoses with 1,4 glycosdic bonds - produce water

• Twists into compact helix held in place by hydrogen bonds between glucose molecules

• Tightly packed storage molecule

Amylopectin

• Polymer of α glucose joined by 1,4, glycosidic bonds

• Amylopectin is branched with another 1,4 chain between carbon 1’ of one a glucose molecules and carbon 6’ of another (every 25 - 30 molecules)

• 1,6 glycosdic bond

• Enzymes break glycosidic bonds at ends of molecules - very branched - many ends - enzymes can break down starch rapidly into glucose

Glycogen

• Animals store glucose as glycogen found in liver, muscle cells

• Polymer of α glucose joined by 1,4, glycosidic bonds

• Branched with 1,6, glycosidic bonds

• More branched than amylopectin - very compact - many free ends - enzymes can convert glycogen to glucose very rapidly

Cellulose

• Polymer of β glucose

• Unbranched straight chain - cellulose molecules can get close together with hydrogen bonds chains form microfibrils

• microfibrils —→ macrofribils ——> cellulose fibres ——→ cellwall

• Huge number of hydrogen bonds makes cellulose strong

• Hydroxyl of carbon 1’ points above ring

• Every second β glucose molecule is flipped in cellulose as hydroxyl groups must be next to each other to form glycosidic bonds

How does cellulose structure help its function

• Cellulose cell wall is permeable to moleculues

• As water moves in via osmosis it pushes cellulose cell wall

• strength resists outward pressure

• prevents plant cell from bursting - makes plant turgid creating upright structure

Why do animals need glucose

• High rate of respiration

• Energy need can change rapidly -move quickly to escape predator - glycogen can be rapidly transferred into glucose to be used in respiration

• Glycogen is insoluble can not draw water in cell via osmosis

• Large molecule cannot diffuse out of cell

Glucose isomers

• Alpha glucose - Carobn 1’ hydroxyl group points below plane of ring

• Beta glucose Carbon 1’ hydroxyl group points above plane of ring

Ribose

• Pentose sugar

Monosaccharides

• Soluble in water - many hydroxyl groups - can form hydrogen bonds with water molecules

• These molecules are hydrophillic

• Can join to form disaccharides and polysaccharides

• more monosaccharides - glucose, galactose, fructose

Disaccharide

• Two monosaccharides react to form disaccharide

• Glucose + glucose ——> maltose

• Glucose + fructose ——> Sucrose

• Glucose + galactose——> lactose

• When a disaccharide is made a molecule of water is also produced from one hydrogen atom from one monsaccharide and a hydroxyl of another

• Condensation reaction - water molecule is formed

Glycosdic bond

• Bond formed by two monosaccharides (condensation reaction)

• Between carbon 1’ and carbon 4’

• Oxygen link

• 1,4 glycosidic bond

Condensation reaction

• Disaccharides and polysaccharides are formed when two hydroxyl groups (on different saccharides) interact to form a strong covalent bond called the glycosidic bond

• (the oxygen link that holds the two molecules together)

• Every glycosidic bond results in one water molecule being removed and formed as a product

• Thus glycosidic bonds are formed by condensation

Hydrolysis reaction

• Adding water will break glysosidic bond and revert disaccharide back to monsaccharide

Amino acid groups

• amine, carboxyl and R group

• R group changes in different amino acids

Peptide bond

• Amino acids form a peptide bond (takes place in ribosomes (condensation reaction) makes water

• peptide bond can be broken by adding water (hydrolsysis reaction) e.g. protease enzyme in digestive system

• many peptide bond between amino acids polypeptide

Differemce between polypetide and protein?

• Polypeptide needs to fold into complex 3d shape to become a protein

• Can carry out its function

Primary structure

• Primary structure - specific order of amino acids sequences in a polypeptide - helps to determine 3D shape - for function

Secondary structure

• C=O(oxygen small negative charged) groups and N-H (hydrogen small positive charge) groups

• These charges attract each other - hydrogen bonds form - make polypeptide chain twist and fold - secondary structure e.g. alpha helix

• Another type is beta pleated sheet - polypeptide chain folds into - flatter sheet like structure - hydrogen bonds between amino acids hold shape

• Some amino acids found in alpha helices others in beta pleated sheets

Tertiary structure

• Region of secondary structure fold into precise 3D shape - tertiary struucture

• Weak Hydrophobic an Hydrophillic interactions - between R groups

• Weak Hydrogen bonds

• Strong covalent Disulfide bonds - between two R groups (only if contains sulfur)

• ionic bonds between positively charged amine and negative R group

• In picture - 5 alpha helices very specific pattern around a beta pleated sheet. e.g. active site of enzyme relies on protein forming of specific tertiary structure

Quarternary strucutre

• Made from more than one polypeptide chain specific 3d structure

• e.g. Haemoglobin with 4 chains

• Haemoglobin has prosthetic haem group attached to each polypeptide chain

• Prosthetic group - no amino acids but iron

• Is a conjugated protein - non protein group added

Fibrous proteins

• Polypeptides form long twisted strands linked together - highly repetitive - strong

• Stable (unreactive)

• insoluble in water

• Form H bonds with adjacent chains

• Very suitable for structural/ stability roles e.g. keratin - hair and nail

Outline 3 named fibrous proteins

• Collagen - makes skin, cartilage, ligaments - quarternary structure has 3 polypeptide chains wound

• Chains held by hydrogen and covalent bonds

• Keratin - makes hair, skin and nails - insoluble so these strucutres are not broken by water

• Elastin - makes elastic fibres of alveoli and arteries - stretch and g

Globular proteins

• Polypeptide chains form a spherical shape

• Unstable e.g. enzymes denatured

• Soluble in water - hydrophillic R groups

• Involved in metabolic functions e.g. enzymes, antibodies. hormones, haemoglobin

Outlined 3 named globular proteins

• Haemoglobin - 4 polypeptide chains 2 alpha/ 2 beta each bind to O₂

• Enzymes - Pepsin in stomach digests proteins using specific active site

• Insulin - produced by beta cells reduces blood glucoose conc - specific to muscle and liver cells

Lipids

• Made of fatty acids and glycerol

• Non - polar

• Insoluble in water

• Hydrophobic dissolve in ethanol

• Do not form polymers

Triglyceride

• Triglycerides are formed via condensation reactions

• one molecule of glycerol + three molecules of fatty acids ———> tryglycerides

• 3 Ester bond formed

Properties of tryglycerides

• Can transfer energy - large ratio of energy - storing carbon - hydrogen bonds compared to number of carbon atoms. A lot of Energy can be transferred when be broken down

• High ratio of hydrogen to oxygen atoms they can act as a metabolic water source. This is because triglycerides can release water if oxidised. Essential for desert animals e.g. camels

• Hydrophobic - Insoluble in water, do not affect osmosis

• Low in mass can be stored without increasing mass - decreasing movement like muscle does

Phospholipid

• Made of glycerol molecule, two fatty acids, phosphate group

• Two fatty acids also bind to glycerol via condensation reactions forming two ester bonds

Properties of phospholipids

• Hydrophilic head attracts water - as phosphate is charged repelling other fats

• “tail” fatty acid chain is not charged repels water but mixes with fats

• Forms phopsholipid bylayer which makes up structure for plasma cell membrane. hydrophillic head attracted to water hydrophobic tails repel from water

Ester bond

• Bond formed between fatty acids and glycerol to form tryglyceride

Fatty acids

• Saturated fatty acid - hydrocarbon chain has only single bonds between carbons

• Unsaturated fatty acid - hydrocarbon chain has a double bond between carbon atoms

Chloesterol

• Cholesterol is a sterol

• 4 carbon rings and a hydroxyl group

• Both hydrophobic and hydrophillic regions

• Imbedded in cell membranes to impact fluidity

• Reduce fluidity high temperatures

• Increase fluidity at low temperatures

• Help control movement across cell membrane

Test for starch

• iodine solution turns from orange to blue/black

Test for reducing sugars

• Add benedict’s solution and heat 5mins at 80^oC

• Positive test blue - green - orange - brick red

• can also use reagent test strips

Test for non reducing sugars

1. Following negative benedict’s test

2. Add acid and boil - hydrolysis

3. Cool solution then add alkali to neutralise

4. Add benedict’s solution and heat heat for 5mins 80^oC

5. Only orange and brick red as when hydrolysed sucrose create fructose and glucose is made doubling sugar content

Test for protein

• Add biurets solution

• blue → purple

Test for lipids

• Dissolve sample in ethanol

• Add distilled water

• Positive test white emulsion forms

Colorimeter method

• Set filter opposite on the colour spectrum

• Calibrate with distilled water to zero

• Insert sample with different concentrations of glucose

• Measure percentage transmission of light

• Create callibration curve

• As glucose conc increases benedict’s solution proportion decreases making solution less tinted and allows less light to be absorbed

Thin Layer Chromatography

• Molecules move based on solubility in solvent

• Calculate Rf value

• Distance moved by solute/ Distance moved by solvent