alevel biology structure

Enzyme

Biological Catalyst which lowers activation energy by providing an alternate reaction pathway without being used up.
Globular protein with a depression in structure giving active site

1. Substrate in enzyme holds substance closer together, so easier to form bonds by minimising repulsion

2. Shape can strain bonds and allow molecule to be more easily broken

Induced fit
Lock and Key

Substrate binds to the active site of enzyme,
active site changes shape to be complementary to the enzyme

Enzyme active site is complementary to the substrate, and only the substrate can fit in the active site

Enzyme full functioning

Stress bonds to make/break polymers

1. Substrate in enzyme holds substance closer together, so easier to form bonds by minimising repulsion

2. Shape can strain bonds and allow molecule to be more easily broken

DNA

RNA

DNA and RNA are used to store genetic information in a cell

Consists of a double helix with two strands in antiparallel. With a pentose-phosphate backbone. strand goes from 3 prime end —> 5 prime end

RNA is shorter, single strand for translation, also has ribose sugars not deoxyribose.

DNA	RNA
Deoxyribose	Ribose
A-T, C-G	A-U, C-G
Double helix/ strand	Single stranded
Long	Short
Sugar-phosphate backbone	Sugar phosphate backbone

DNA structure

How structure of dna helps with function

Polynucleotide joined together with phosphodiester bonds between phosphate of one nucleotide and deoxyribose of another nucleotide via a condensation reaciton

Nucleotides consist of a: nitrogenous base bonded to a pentose sugar, and a phosphate.

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2 strands - both can act as templates for semi-conservative replication, hence saving energy

H-bonds → easily separated for replication

Many h-bonds → stable molecule

Sugar-phosphate backbone - protects h-bonds

Double helix - compact

ATP

Adenosine triphosphate.

ribose bonded to adenine, and 3 phosphates, via a condensation reaction between the adenosine, phosphate and ribose with ATP synthase.

Uses which make it suitable:

1. Inorganic phosphate is used for phosphorylation to produce more reactive substances

2. Little energy released as heat

3. Easily resynthesized

4. Energy can be used for metabolism, contraction, active transport, secretion, and molecule activation

5. Unstable bonds so releases energy instantly

6. cannot be transported out of cell

Semi-conservative replication

1. DNA helicase unwinds double helix, to form a dna fork, where both strands act as template for a new one

2. DNA primase attaches RNA primer to dna

3. Free floating nucleotides form hydrogen bonds to dna Bases via complementary base pairing

4. DNA polymerase III bonds the nucleotides of new strand by forming phosphodiester bonds.

5. Antiparallel causes one strand to be made continuously, whilst the other is made in okazaki fragments. with continuous primers being added, with bases bonded together

6. DNA exonuclease removes primers, polymerase I fills in gaps

7. DNA ligase joins the strands together

Enzyme Inhbition

Inhibitor - substance that interferes with the functioning of an active site, directly or indirectly.

Inhibition is required to control reactions by stopping specific enzymes in a reaction.

End point inhibition - final molecule of enzyme reactions series, inhibits the first enzyme, maintaining steady concentration
Non-competitive:

Bind to allosteric site, which changes the tertiary structure of the enzyme, causing denaturing of the active site, and active site is no longer complementary to substrate

Competitive:

Similar structure to substrate, so directly binds to active site, which prevents substrates from binding, therefore temporarily inhibiting the enzyme

Factor Affecting enzyme controlled reactions
1.Temperature
2. Ph
3. Enzyme Concentration
4. Substrate Concentration

1. More kinetic energy so substrate and enzyme collide more frequently, forming more enzyme-substrate complexes, increasing rate of reaction. Too high causes hydrogen bonds in chain to be broken losing active site shape.

2. Too high denatures, too many H+ ions effecting bonding, altering amino acids

3. More enzymes for substrate to collide with, so higher chance of enzyme substrate complex. More active sites to bind to.

4. More substrates to bind to enzymes, however reaches plateau as all enzymes have active site in use

Water (properties which make it useful), M,S,HL,HS,CO,LV,TE,AD

1. metabolite in respiration

2. solvent, metabollic reactions can take faster place within water

3. high latent heat of vaporisation, so cools organism upon evaporation

4. high specific heat capacity, can buffer temperature changes

5. cohesive, suitable for plant transport as can support water columns

6. low viscosity, flows easily through narrow

7. handles tension, so force can be applied

8. adhesive, so high surface tension, when ice forms can resist changes to environment below

Monosaccharides, disaccharides. (polysaccharide definition, bonding type, carbons bonded + effect, disaccharides to learn)

long chain made up of small repeating monosaccharide units

Disaccharides have either 1-4 bonds or 1-6 bonds

1-4 produces straight chain

1-6 produces branching

maltose (reducing)= 2 a-glucose

lactose (reducing)= a-glucose + galactose

sucrose (non-reducing) = a-glucose + fructose
cellulose = b-glucose + b-glucose

polysaccharides/ carbohydrates (starch, glycogen, cellulose) (properties, structure, uses)

Starch: storage of excess glucose in plants

Monomers: a-glucose, Amylose (straight chain, coils) Amylopectin ( 1-6 bonds, so branched and long)

Coiled so more compact storage, Branched so has a higher surface area, quicker to release energy, water can be stored inbetween coils

Glycogen: short term storage of excess glucose in animal

Long Branched chain of a-glucose

Larger sa, quicker release of energy,

Cellulose: cell walls of plants, B-glucose

Long straight chain of alternating glucose, microfibrils between chains

Very strong, resistant to excessive bending.

Testing for sugars

Reducing:

Add benedicts to liquid sample, Apply heat

Non-reducing:

Add benedicts, heat, no positive results = add dilute hcl, then neutralise with an alkali, add benedicts, heat.

Iodine: Presence of starch, brown —> blue-black

Lipids

Lipid: Biological molecules which are only soluble in organic solutions, used for long term energy storage, structure, insulation, protection

saturated = c-c bonds, unsaturated = c=c bonds

1. triglycerides

   Glycerol + 3 fatty acids

   Hydrophobic fatty acids, non-polar

2. phospholipids

   Glycerol + phosphate + fatty acids

   polar one end. Hydrophilic properties, means phosphate forces arrangement of fatty acids pointing inwards.

Proteins

Peptide bond - condensation reaction between amine group, and carboxyl groups of 2 amino acids, producing a water molecule.

Polypeptide, made up of multiple amino acids.
Protein can be made from multiple polypeptides

Primary structure: Sequence of bonded amino acids

Secondary structure: Amino acid chain bends into alpha helices, beta pleated sheets, as Hydrogen bonds form between charged hydrogens and charged Nitrogen, Oxygen

Tertiary structure: Twisting, and bending of chain,

additional hydrogen bonds, disulfide bridges between R groups, Ionic bonds, All between any unbonded charged atoms

Quaternary structure: Multipe polypeptide chains in a protein which work towards a function.

Chemical tests

Proteins:
Biuret, changes from blue-black to purple
Lipids:
Add ethanol, then water and shake, forms a white emulsion
Starch:
Add iodine blue-black colour change
Reducing sugar:
Add benedict’s and heat, forms red/orange/green colour precipitate