3.3.1 Biological molecules

Monomers and polymers

Monomers - smaller units from which larger molecules are made e.g. monosaccharides (glucose etc.), amino acids, nucleotides

Polymers - molecules made from many monomers joined together

Condensation reaction - joins 2 molecules together with the formation of chemical bond and involves the elimination of a molecule of water

Hydrolysis reaction - breaks a chemical bond between 2 molecules and involves use of a water molecule

Carbohydrates

Carbohydrates are used as a source of energy as well as used as structural materials in cells. All carbohydrates are soluble and contain carbon, hydrogen and oxygen

Monosaccharides

All monosaccharides have the formula C6H12O6

  • Glucose (2 isomers = alpha and beta)

Alpha and beta glucose diagram

  • Galactose

  • Fructose

Disaccharides

2 monosaccharides joined together in a condensation reaction by a GLYCOSIDIC bond (water removed)

  • Maltose = glucose + glucose

    • reducing sugar

  • Sucrose = glucose + fructose

    • NON REDUCING SUGAR

  • Lactose = glucose + galactose

    • reducing sugar

Polysaccharides

Many monomers joined together via condensation reaction

  • Starch = alpha glucose

    • storage molecule in plants

    • insoluble - doesn’t change water potential of cells so no uptake of water via osmosis

    • compact and dense - coils into helix so large amounts can be stored in small spaces

    • branched - large surface area so can be acted on simultaneously by enzymes

    • hydrolysed by amylase to use glucose for respiration

  • Glycogen = alpha glucose

    • animal storage and short term energy store

    • insoluble - doesn’t change water potential of cells so no uptake of water via osmosis

    • compact - large amounts stored in small spaces

    • branched - can be acted on simultaneously - more rapidly broke down

    • hydrolysed by glucagon into glucose for respiration (insulin condenses glucose into glycogen)

  • Cellulose = beta glucose

    • used in cell walls in plants for structure

    • alternating inverted beta glucose molecules = rigid/inflexible, straight chain

    • chains linked together by hydrogen bonds to form microfibrils - which are very strong

    • bonds cannot be hydrolysed by amylase - requires specific enzyme














Biochemical tests (for sugars)

Test for reducing sugars:

  • add benedicts reagent and shake

  • place in hot water bath and heat mixture

  • negative = remains blue, positive = brick red

  • (Colour change due to presence of copper oxide as reducing sugar has donated electrons which reduce blue copper sulphate to red copper oxide)

  • all monosaccharides and disaccharides are reducing sugars with the only exception of sucrose

Test for non reducing sugars:

  • perform test for reducing sugar and observe negative result

  • boil with hydrochloric acid to hydrolyse glycosidic bond

  • neutralise the solution using alkaline

  • add benedicts and heat - positive = brick red

  • (unable to donate electrons and doesn’t reduce other chemicals)

Test for starch

  • add iodine solution to starch

  • negative = orange, positive = blue-black








Lipids

All lipids contain carbon, hydrogen and oxygen. They are insoluble.

Lipids are hydrolysed by lipase into fatty acids and glycerol

Triglycerides

triglycerides = 1 glycerol, 3x fatty acids joined by a condensation reaction to form an ester bond

Saturated lipids - no double carbon bonds

Monounsaturated lipids - 1 double carbon bond (weaker)

Polyunsaturated lipids - more than 1 double carbon bond

Double carbon bonds cause a change in shape so the lipids cannot fit together as closely (liquid)

Phospholipids

Hydrophobic tails, hydrophilic heads

Form phospholipid bilayer (cell membrane)

Biochemical test

  • crush food

  • add ethanol and SHAKE

  • add water

  • lipid = white emulsion formed

Proteins

Amino acids

Amino acid diagram

20 different amino acids - only part that differs is the R group

Dipeptides are formed in a condensation reaction between amine group of 1 amino acid and carboxyl group of another - forming a peptide bond

Made up of carbon, hydrogen, oxygen and nitrogen

Protein structure

  • Primary structure - sequence of amino acids

  • Secondary structure - hydrogen bonds form between amine group of 1 amino acid and carboxyl group of another - folding the polypeptide chain into alpha helices and beta sheets. (R group not involved)

  • Tertiary structure - polypeptide is folded into unique 3D shape forming a globular structure. Forming hydrogen bonds, ionic bonds and disulphide bridges between the R groups

  • Quaternary structure - more than one polypeptide chain to form globular proteins (enzymes) or fibrous proteins (more structural e.g. keratin)

Enzymes

Enzymes are biological catalysts for anabolic and catabolic reactions by lowering activation energy. They form enzyme substrate complexes and are affected by pH and temperature

Induced fit model:

  • substrate binds to active site of the enzyme

  • enzyme brings substrate molecules close together and puts stress on the bonds and bends them

  • active site changes shape slightly by changing the tertiary structure making it complimentary to substrate

  • this lowers activation energy

Rate of reaction:

  • temperature:

    • increases kinetic energy - more frequent collisions so more enzyme substrate complexes = increased rate of reaction

    • however if temperature too high the bonds are disrupted - changing tertiary structure therefore changing active site shape so substrate no longer complimentary and enzyme is denatured

  • pH:

    • at extreme pH bonds are disrupted - changing tertiary structure therefore changing active site shape so substrate no longer complimentary and enzyme is denatured

    • amino acid charge is altered in active site, preventing formation of ESC

  • concentration

    • substrate concentration increases = rate of reaction increases

    • until saturation point reached then concentration has no effect as it has already reached maximum

Enzyme inhibition:

These reduce enzyme activity by directly or indirectly interfering with active site

  • Competitive inhibition - shape is similar to substrate so will fit into active site (direct) preventing substrate from binding - however does not permanently bind to active site. Effectiveness depends on how much inhibitor and substrate is present - adding more substrate overcomes inhibition

  • Non-competitive - attach to enzyme at a site away from the active site (allosteric site) (indirect) which permanently changes active site shape so substrate cannot bind. Effectiveness does not depend on how much substrate present

Biochemical test (proteins)

  • add biuret solution to a sample of crushed food

  • positive = purple, negative = blue

DNA

DNA structure

Monomer of DNA is a nucleotide - these join together in a condensation reaction between phosphate group of 1 amino acid and deoxyribose sugar of another forming a PHOSPHODIESTER bond

Nucleotide diagram

Nitrogenous bases: Adenine - Thymine, Cytosine - Guanine

Adenine and Guanine are purines which are slightly larger bases - Thymine and Cytosine are pyrimidines which are slightly smaller - small and large base are always paired to form an even structure (bases join together with hydrogen bonds)

RNA structure

RNA transfers genetic information from DNA to ribosomes

RNA has the same structure as DNA but with ribose sugar instead of deoxyribose sugar - also has a uracil base instead of thymine

RNA is a short and single stranded whereas DNA is long and double stranded

3 types of RNA:

  • messenger RNA (transfers DNA code from nucleus to cytoplasm to make proteins)

  • transfer RNA (used in making proteins and in translation)

  • ribosomal RNA (form ribosomes which are the site of protein synthesis)

Genetic code:

  • 3 bases in a row = codon

  • genetic code is universal (4 bases are same in all organisms)

  • genetic code is degenerate (different codons specify same amino acids)

  • genetic code is non overlapping (each base is only part of 1 codon)

DNA replication

SEMI-CONSERVATIVE REPLICATION:

  • DNA helicase unwinds the double helix and breaks hydrogen bonds between strands (‘unzipping DNA’)

  • Strands act as a template

  • Pool of free nucleotides attracted to complimentary bases (AT, GC)

  • DNA polymerase reforms hydrogen bonds

  • This produces 2 new DNA strands - each contain half original and half new - therefore semi conservative

Meselson and Stahl ultracentrifuge:

  • centrifuge DNA - more dense DNA forms band at bottom of tube (15N)

  • Add 15N DNA into a 14N growth medium - semi conservative replication forms 14.5N DNA - band appears further up

  • 2nd generation forms half 14N and half 14.5N DNA etc.

ATP

ATP = adenine triphosphate - provides energy to drive processes inside living cells

Synthesised during respiration and photosynthesis

ATP is a small soluble molecule that provides a short term store of chemical energy that cells can use in processes such as active transport, muscle contraction etc.

ATP diagram

ATP is converted (hydrolysed) into ADP (adenine diphosphate) in a hydrolysis reaction using enzyme ATP hydrolase - also releasing an inorganic phosphate (Pi) and energy.

ADP is converted into ATP in a condensation reaction using enzyme ATP synthase

Why use ATP:

  • soluble

  • energy released in small, manageable amounts

  • broken down easily in a single step

  • energy available rapidly

  • can be reformed from ADP and Pi

  • It phosphorylates substances making them more reactive

Water

5 key properties of water:

  • it is a metabolite - involved in chemical reactions e.g. respiration, protein synthesis - any condensation/hydrolysis reaction

  • it is an important solvent - allows chemical reactions to occur faster and allows transport of substances

  • high specific heat capacity - can absorb large amounts of heat energy without changing temperature - maintains stable environment acting as a buffer to minimise fluctuations in temperature which is important for aquatic organisms

  • high latent heat of vaporisation - water evaporates heat energy away from body causing a cooling effect (sweat)

  • strong cohesion between water molecules - hydrogen bonds allow water to be held together so it can flow as a continuous column of water - allows it to be pulled up in xylem

Inorganic ions

Inorganic ions (without carbon) occur in solution in the cytoplasm and body fluids of organisms

Sodium ions:

  • involved in co transport of glucose and amino acids across membranes (large molecules)

Phosphate ions:

  • DNA and RNA contain phosphate groups which allow nucleotides to bond with phosphodiester bonds to form polynucleotides

  • ATP contains phosphate group which acts as energy source (phosphorolysis other substances)

Iron ions:

  • bind to oxygen in haemoglobin so it can be carried around body

Hydrogen ions:

  • pH level determined by concentration of hydrogen ions (more hydrogen ions present = lower pH)