Biological molecules Flashcards
What about water gives its properties?
It is dipolar, meaning it can form hydrogen bonds.
Properties of water
High specific heat capacity.
High latent heat of vaporisation.
Cohesion and surface tension
What does high specific heat capacity mean for organsims?
Because of hydrogen bonding, water has a higher boiling point than usual so it is found as a liquid at common temps and can harbour life. Also water can act as a buffer against sudden temp variations so aquatic environments are stable and means water in terrestrial organisms are stable.
What does high latent heat mean for organisms
Evaporation of water such as sweat is effective means of cooling (body heat used).
What does cohesion mean for organisms
Allows water to be pulled up xylem vessels as water molecules stick together.
Surface tension for organsims
Where water molecules meet air, they are pulled back into body of water, meaning water surface acts as skin and pond skaters can live on it.
Water in metabolism role
Breaks down complex molecules via hydrolysis and produced in condensation reaction.
Chemical reactions happen in aqueous medium.
Raw material of photosynthesis.
Water as solvent importance
Water dissolves O2 and CO2, wastes (urea and ammonia), inorganic ions, amino acids, monosaccharides and ATP and enzymes.
Roles of inorganic ions
Fe used in haemoglobin.
Phosphate ions used in structure of DNA and stores energy in ATP.
Hydrogen ions determine pH.
Sodium ions are important in transport of glucose and amino acids across plasma membranes.
General formula of monosaccharide
(C H2 O)n where 2 < n < 8
Difference between alpha glucose and beta glucose
Arrangement of OH and H groups around carbon 1.
Test for reducing sugar
Benedict’s test: Add Benedict’s reagent and then heat, positive result: green, yellow, red, brick red (increasing conc.)
Negative result: remain blue.
Test for non-reducing sugar
Negative Benedict’s test (blue). Add HCl to hydrolyse solution to monosaccharide and then neutralise solution. Test with Benedict’s reagent again for orange-brown colour.
Condensation reaction between two monosaccharides
Glyosidic bond
How is maltose formed?
Condensation reaction between glucose and glucose.
How is sucrose formed?
Condensation reaction between glucose and fructose.
How is lactose formed?
Condensation reaction between glucose and galactose.
How is glucose and starch formed
Condensation of alpha glucose
How is cellulose formed
Condensation of beta glucose
Test for starch
Changes iodine solution from yellow to blue-black.
How is starch suited for storage
Insoluble, does not affect water potential (water not drawn in cells via osmosis).
Large and insoluble, does not diffuse out of cells.
Compact so can be stored in small place.
Forms a-glucose when hydrolysed, easily transported and used for respiration.
Branched form has many ends for enzymes to act on simultaneously, glucose released rapidly.
How is glycogen suited for storage
Insoluble, does not draw water via osmosis and does not diffuse out of cells.
Compact, a lot stored in small space.
More highly branched than starch, can be acted on simultaneously by enzymes to break down rapidly, important for animals with higher metabolic rate than plants.
How is cellulose suited for providing support and rigidity
Made up of B-glucose so forms long unbranched chains.
Chains run parallel and are crossed linked by H bonds to add strength.
Molecules are grouped to form microfibrils which are groups to form fibres to give strength.
What are the main two types of lipids
Triglycerides and phospholipids.
Structure of triglyceride
Three fatty acids that have formed ester bond each with glycerol.
Structure of phospholipid
Two fatty acids that have formed ester bond each with glycerol and a phosphate molecule.
Hydrophilic head and hydrophobic tail.
Roles of lipids
Source of energy (and release water).
Waterproofing (waxy cuticle layer)
Insulation
Protection
What is a saturated fatty acid?
All carbon atoms linked to max number of H.
Structure of triglyceride relating to properties
High ratio of high energy carbon-hydrogen bonds to carbon bonds - good source of energy.
Low mass to energy ratio, good storage molecule, reduces mass animal carries.
Insoluble in water, does not affect water potential of cells or osmosis.
High ratio of hydrogen to oxygen atoms, release water when broken down, good source of water in dry conditions.
Structure of phospholipid to properties
Polar molecules, form bilayer in cell-surface membrane in aqueous environment, hydrophobic barrier.
Phosphate heads of phospholipids hold at the surface of cell-surface membrane.
Can emulsify.
Structure allows them to form glycolipids by combining with carbohydrates within cell-surface membrane (important for cell recognition).
Test for lipids
Emulsion test: add sample, add ethanol, shake, then add water, white emulsion = positive, clear = negative.
Structure of an amino acid
Central carbon, an amino group (NH2), carboxyl group COOH, hydrogen, R group (up to 20).
Condensation reaction between two amino acid is which bond and how
Peptide bond, bond between nitrogen and carbon of carboxyl group, OH and H lost to form water.
How does a change in one amino acid affect the protein?
A change in an amino acid changes the primary structure, changing the hydrogen bonds, altering tertiary structure.
What is primary structure of protein?
The sequence of amino acids that form the polypeptide chain.
Secondary structure of protein
C=O and NH can form hydrogen bonds to cause the long polypeptide chain to twist into 3D shape (alpha helix).
Tertiary structure of protein and bonds involved
Alpha helix twists even more to form a specific 3D structure of protein. Disulphide bridges (not easily broken). Ionic bonds (easily broken). Hydrogen bonds (easily broken).
Why is the 3D structure of protein important?
It makes each protein distinctive and can be recognise and recognise other molecules and interact in specific ways.
Quaternary structure of protein
Individual polypeptide chains linked with non-protein groups such as haem groups.
Test for protein
Biuret test: sample in test tube and equal amount of sodium hydroxide at room temp.
Few drops of 0.05% copper (II) sulfate and mix.
Purple = positive and remains blue if no protein.
What is an enzyme and how does it work?
Globular protein that acts as a catalyst by lowering activation energy for specific reaction it catalyses without undergoing permanent change.
Enzyme structure
Active site made up of small number of amino acids that is a depression in the large molecule. The enzyme-substrate complex is formed here.
Amino acids that are not part of active site.
Induced fit of enzyme action
Proximity of complementary substrate causes change in enzyme that forms functional active site. As enzyme changes shape, it puts strain on substrate molecule that distorts particular bonds in substrate to lower activation energy.
Why is lock and key not used?
Proposes that enzyme has rigid structure when enzymes have been observed to have other molecules bind to places other than active site (suggested shape of enzyme was altered by molecule).
Why does rate of enzyme controlled reaction slow down?
As reaction progresses, conc of substrate molecules decreases, meaning that there is less chance of a collision between enzyme and substrate molecules. Eventually no change in conc measured because so little substrate.
Effect of temp on enzyme action
Temp up, kinetic energy up, enzyme and substrate move more rapidly and combine more often. More effective collisions, more enzyme-substrate complexes being formed, rate of reaction increases.
At around 45C, hydrogen in enzyme molecule breaks, meaning that substrate fits less easily into changed active site, slowing rate of reaction.
At ~60C, enzyme is denatured, permanent change in shape of active site and molecule.
Why is body temp 37C if below optimum
Extra food to maintain high temp.
Other proteins would denature.
Illnesses that raise body temp would denature all enzymes.
Effect of pH on enzyme action
Change of pH away from optimum reduces enzyme action, extreme change in pH denatures.
Change in pH affects charges on amino acids that make up active site, substrate can no longer attach and e-s complex cannot form, reducing action.
Can also break bonds maintaining tertiary structure and changes active site shape.
How to find pH
pH = -log(H+)
Effect of enzyme conc on enzyme action
Enzymes not used up, can work well in low conc. As long as there is excess of substrate, an increase in enzyme conc, increases enzyme action. Addition of further enzyme molecules has no effect as there are enough active sites to accommodate all available substrate molecules.
Effect of substrate conc on enzyme action
Rate of reaction increases in proportion to conc of substrate. At low substrate concentration, limited number of substrate molecules to collide with and active sites not working at full capacity. As more subs added, active sites fill until all of them working at max capacity (when there is excess of substrate).
Competitive inhibition of enzymes
Have molecular shape similar to complementary substrate so occupy active site of enzyme. Compete with substrate for available active sites. Is not permanent so increase substrate conc reduces effect of inhibitor until all substrate molecules will occupy active site.
Non-competitive inhibitor
Attach to enzyme not at active site and alters shape of enzyme and active site so no substrate molecules can occupy and enzyme does not function. Increasing substrate concentration does not decrease effect of inhibitor.
Use of non-competitive inhibitors in end-product inhibition of metabolic pathways.
To keep steady conc of chemical in cell, same chemical acts as inhibitor at the start of the metabolic pathway. If conc of end product increases beyond normal, less end product produced and conc returned to normal.
If conc decreases beyond normal, less inhibition and more end product produced.
