OCR A-Level Biology 2.1.2 Biological Molecules

Complete on spec points 2.1.2 a-r (not including Thin Layer Chromatography)

Cation

an atom or molecule that has lost electrons to gain a positive charge

anion

an atom or molecule that has gained electrons to have a negative charge

role of Calcium (Ca2+)

nerve impulse transmission and muscle contraction

role of sodium (Na+)

nerve impulse transmission and kidney function

role of potassium ions (K+)

nerve impulse transmission and stomatal opening

role of hydrogen ions (H+)

catalysis of reactions and pH determination

role of ammonium ions (NH4+)

production of nitrate ions by bacteria

role of nitrate ions (NO3-)

nitrogen supply to plants for amino acid and protein formation

role of hydrogencarbonate ions (HCO3-)

maintenance of blood pH

role of chloride ions (Cl-)

balances positive charge of sodium and potassium in cells

role of phosphate ions (PO4 3-)

cell membrane formation, nucleic acid and ATP formation and bone formation

role of hydroxide ions (OH-)

catalysis of reactions and pH determination

polymer

long-chain molecule made by linking of many smaller molecules (monomers) in a repeating pattern

polar molecules

molecules with regions of negativity and positivity due to unequal sharing of electrons in covalent bonds

Hydrogen bonds

interaction between positive and negative regions of polar molecules

characteristics of water

has a high boiling point because of many hydrogen bonds requiring a large energy to break

is less dense as a solid because hroge

cohesion

water molecules being attracted to each other; this is due to hydrogen bonding and is important for plants that draw water up their stems

adhesion

water molecules sticking to other surfaces rather than running off

why does water have surface tension

water's cohesive properties mean water molecules are more attracted to each other than to air

uses of water in life

a solvent - any polar molecules can dissolve in water, and it acts as a medium for chemical reactions to take place and for transport of dissolved substances

a transport medium - the effects of cohesion and adhesion cause capillary action, necessary in xylem tissue of plants

a coolant - buffering temperature changes in organisms due to its high specific heat capacity - which is important for maintaining optimum temperature for enzyme activity

a stable environment - water does not change state or temperature easily, so provides a stable environment for aqueous organisms. Ice floating also insulates water below, preventing it from freezing. some organisms use the surface tension of water to move or reproduce

capillary action

the process by which water can rise up a narrow tube against the forces of gravity, due to its properties of cohesion and adhesion

glucose

a simple sugar with 6 carbons (a hexose monosaccharide) and the formula C6H12O6. one of the most important monomers in biology

difference between alpha and beta glucose

alpha glucose has OH group on carbon 1 below the plane, whereas beta has it above

glycosidic bond

bond formed between two sugars when one OH group from each reacts

Condensation reaction

Polymerisation reaction where water is formed as a byproduct

Fructose

Hexose monosaccharide found in fruit. Often bonds with glucose to form sucrose, commonly known as cane sugar

Ribose and deoxyribose

Pentose monosaccharides found in RNA and DNA respectively

Amylose

Polysaccharide made of alpha glucose with only 1-4 glycosidic bonds. Twists to form a helix further strengthened by hydrogen bonds. More compact and less soluble than glucose molecules used to make it

Amylopectin

Polysaccharide made of alpha glucose with both 1-4 and 1-6 glycosidic bonds. These form branches, with 1-6 branching points roughly every 25 glucose subunits

Starch

Made of amylase and amylopectin, made from converted glucose. Used as a chemical energy store in plants

Glycogen

Animal equivalent of starch - chemical energy store. Made of alpha glucose subunit but with more branches than amylopectin, making it more compact (ideal in animals). Branching also provides many free ends so it easy to add/remove subunit as necessary. Also insoluble

Hydrolysis of saccharides

Water is added across glycosidic bond between glucose subunit to release them in starch and glycogen so they can be used in respiration

Cellulose

Polymers of beta glucose subunit found in plants. Straight chains, which form hydrogen bonds with other chains to form microfibrils, which make macrofibrils,which make fibres used to make cell walls. Cellulose forms fibre necessary in our diet

How to do Benedicts test for reducing sugars

Add a few drops of Benedicts reagent, heat mixture for several minutes in water bath. Reagent will change colour from light blue if reducing sugars are present,and will be brick red if there is a high concentration and yellow/green if the concentration is lower

Using Benedicts test for non-reducing sugars

If non-reducing sugars such as sucrose are first boiled with hydrochloric acid, they will break down into reducing sugars such as glucose and fructose, which will have a positive result when benedicts test is subsequently performed

Reducing sugars

Sugars that can reduce other substances by donating an electron. All monosaccharides and some disaccharides like maltose and lactose are reducing sugars

How does Benedicts test work

Cu2+ ions in Benedicts solution are reduced by reducing sugars to form copper. While copper sulfate appears blue, the copper element appears red. If all the copper ions were reduced, the solution will go strongly red, but if some remain, the red precipitate and blue solution will form a greenish appearance or some other colour in between

Iodine test

Add a few drops of iodine dissolved in potassium iodide to sample. If appearance changes from yellow-brown to blue-black, starch is present. If it remains yellow-brown, this is a negative result and starch is not present.

Reagent strips

Reagent straps can be used to detect the presence of reducing sugars, and with a colour coded chart, the concentration can be determined

Colorimetry to find concentration of sugars

Place a filter in the colorimetry and calibrate using distilled water. Perform Benedicts test and filter out any precipitate. Find % transmission of remaining solutions. Lower transmission means more copper ions were left behind and concentration of sugars was lower. Use known concentrations to plot a calibration curve and find the concentration of an unknown solution.

Colorimetry

Quantitative method of finding the concentration of a solution by measuring how much of a certain wavelength of light it absorbs and transmits. The more concentrated a solution is, the less light it will transmit.

Lipids

Polymers usually made of fatty acids and glycerol and containing carbon, hydrogen and oxygen. May be fats or oils. Nonpolar and therefore insoluble in water

Difference between fats and oils

Fats are usually solid at room temperature, whereas oils are usually liquid

Triglyceride

Lipid made by combining one glycerol molecule with three fatty acid chains. Glycerol is an alcohol and fatty acids are carboxylic acids. The reaction is called esterification and forms three water molecules

Saturated

Saturated fatty acids contain no double bonds between carbon atoms so each carbon forms bonds with the maximum number of hydrogen atoms. Saturated chains are usually found in fats

Unsaturated

Unsaturated fatty acids contain double bonds between carbon atoms. If only one double bond is present, they are monounsaturated, but if more are present they are called polyunsaturated. Double bonds cause the chains to kink and bend, so they cannot pack so closely together and are liquid at room temperature (oils)

Phospholipids

Phosphate ions (PO4 3-) replace one of the fatty acids in triglycerides. The phosphate head is polar and hydrophilic, whereas the fatty acid chains are insoluble and hydrophobic. Phospholipids are surfactants and play a key role in cell membranes

Phospholipid bilayer

A two layered sheet formationof phospholipids where all the hydrophobic tails point inwards to the centre of the sheet and the hydrophilic heads point outwards, protecting the insides. Play a key role in cell membranes as they allow separate aqueous environments to form

Reaction forming lipids

Esterification - a condensation reaction between a carboxylic acid and alcohol group

Biological uses of lipids

membrane formation and the creation of hydrophobic barriers

hormone production

electrical and thermal insulation

energy storage and source

protection of vital organs

waterproofing

buoyancy for aquatic animals

Essential fatty acids

fatty acids that can't be produced by our bodies and that we must eat in our diet

ampipathic

term meaning dual nature that can be used to describe phospholipids

surfactant

a substance which decreases the surface tension between a liquid and another substance

what happens when lipids are respired

Ester bonds are hydrolysed and lipid molecules are broken down into fatty acids and glycerol, and then CO2 and H2O

Sterols

A type of lipid based on a complex 4 carbon ring structure with an OH group at one end. Like phospholipids, they are amphipathic as the OH group is hydrophilic and the rest of the molecule is hydrophobic.

Cholesterol

A sterol made in the liver and intestines found in cell membranes. Helps to regulate the fluidity of the membrane in low and high temperatures. Vitamin D, steroid hormones and bile are manufactured using cholesterol

Emulsion test

test to identify lipids. Sample is mixed with ethanol and then water is added and the solution is shaken. If a white emulsion forms, a lipid is present, but if the solution remains clear, no lipids are present.

Peptides

polymers made up of amino acid molecules (the monomers)

Proteins

biological molecules consisting of one or more polypeptides arranged as complex macromolecules and with specific biological funtions. always contain carbon, hydrogen, oxygen and nitrogen

structure of amino acids

all amino acids have an amine group (NH2), a carboxyl group (COOH), a hydrogen and an R group attached to one carbon. The R (residue) group varies depending on which amino acid it is, and is what affects the chemical properties and charges of the amino acid

synthesis of peptides

The hydroxyl (OH) in the carboxylic acid group of one amino acid reacts with a hydrogen in the amine group of another. This causes a peptide bond to form and produces water (making it a condensation reaction)

essential amino acids

amino acids which can't be produced by humans and must be obtained from what we eat. These are mostly found in meat and soya

Primary structure

the sequence in which amino acids are joined in a protein. The particular aminoa cids will influence how the polypeptide folds, which determines its function. The only bonds involved in the primary structure are peptide bonds

Secondary structure

The repeated oxygen, hydrogen and nitrogen atoms of the amino acids interact. Hydrogen bonds may form, creating coils called alpha helices. Polypeptides may lie parallel to each other joined by hydrogen bonds, forming beta pleated sheets.

Tertiary structure

the folding of a protein into its final shape. This is dependent on R groups as well as sections of secondary structures. The interactions R groups may have, in order of strength:

• hydrogen bonds

• hydrophilic and hydrophobic interactions - hydrophobic amino acids tend to cluster towards the core of a protein whereas hydrophilic (charged/polar) tend to be on the outside

• ionic bonds - positively and negatively charged R groups can interact with each other and form ionic bonds

• disulphide bonds/bridges - amino acids containing sulphur (cysteine and methionine) can have their sulphur atoms form a strong covalent bond with each other, holding a shape in place

Quaternary structure

The result of association of several polypeptide subunits to form a different protein molecule. Created by same interactions as for tertiary structure

Breakdown of polypetides

To break peptide bonds, water is added across the bond, reforming the amine and carboxylic acid groups. This is often catalysed by proteases

Biurets test for proteins

Add sodium hydroxide solution, then copper sulfate solution until the sample solution turns blue. Alternatively add biuret reagent (mixture of alkali and copper sulfate). Leave for 5 minutes. If protein is present, the solution will turn purple, as peptide bonds form violet coloured complexes with copper ions in alkali solutions

Globular proteins

Types of proteins which are compact, water soluble, and usually roughly spherical. Formed when hydrophobic R-groups cluser towards the centre of the protein to be kept way from the aqueous environment and hydrophilic R-groups remain on the outside.

insulin

a globular protein and hormone involved in regulation of blood glucose concentration. hormones are transported in the bloodstream so need to be soluble. They also have to fit into specific receptors to have an effect and so need specific shapes

Conjugated proteins

Proteins which contain a non-protein component called a prosthetic group. Proteins without a prosthetic group are called simple proteins. Haemoglobin and catalase are examples of conjugated proteins

Haemoglobin

A globular protein which carries oxygen around the blood and is what gives red blood cells their colour. Made of four polypeptides - 2 alpha and 2 beta subunits - each of which has a haem prosthetic group. This contains an Fe2+ ion which is what binds to O2 molecules.

Catalase

An enzyme which catalyses the breakdown of hydrogen peroxide (a by-product of metabolism) into water and oxygen. It contains four haem prosthetic groups which allow it to interact with hydrogen peroxide.

Fibrous proteins

Formed from long, insoluble molecules which have a high proportion of amino acids with hydrophobic R-groups. Often have small R-groups and a very repetitive primary structure, making them very organised. They form long, strong molecules which are not folded into complex 3D shapes like globular proteins

Keratin

A group of fibrous proteins present in hair, skin and nails. Has a large proportion of cysteine, resulting in strong disulfide bonds and inflexible materials. The degree of flexibility depends on the number of disulfide bonds - hair has fewer and so is more flexible than nails, which contain more.

Elastin

A fibrous protein found in elastic fibres. These are present in the walls of blood vessels and in the alveoli of lungs, giving them flexibility to expand when needed and return to their normal size. Elastin is a quaternary protein made from many stretchy molecules called tropoelastin.

Collagen

A fibrous protein and connective tissue found in skin, tendons, ligaments and the nervous system. Has several different forms, all of which are made up of three polypeptides wound together in a long and strong rope-like structure. Collagen proteins have staggered ends and form long fibrils called tropocollagen