Macromolecules, Water, Acids and Bases

Question 1

Describe the molecular hierarchy of the 4 main macromolecules

Answer 1

• Macromolecules have three levels, monomer, polymer and cell structure
• AA - polypeptide - protein filament - membrane (peptide)
• Nucleotide - DNA - chromatin / chromosome
• Monosaccharide - starch - starch granules (glycosidic)
• Fatty acid - triacly-glycerol - fat (ester)

Question 2

Name and describe key functional groups

Answer 2

• Part of the structure of molecule however the structure of the group provide various functional properties
• Hydroxyl (OH)
• Amino (NH3)
• Acetyl (COO) - middle
• Carboxyl (COO) - end
• Methyl (CH3)
• Ketone (CO) - middle
• Aldehydes (CO) - end

Question 3

What is the relationship between structure and function of molecules

Answer 3

• Structure determines function and can influence how receptors interact with cells
• Interaction between molecules is specific

Question 4

What is the difference between stereo and geometric (cis / trans) isomers

Answer 4

• Stereo: Different chemical structure, different physical properties
• Geometric: Same chemical structure, different physical and chemical properties, cis (same side, kink) and trans (different sides, straight)

Question 5

What is biochemistry

Answer 5

• Chemistry of living matter
• Basis of all life is chemical reactions that take place within the cell
• Initiation and acceleration of reactions
• Organisation and specificity of metabolism
• Signalling, storage and transfer of information / energy

Question 6

What is the role of water and H bonds in human systems

Answer 6

• Water can serve as both H donor and acceptor
• H bonds give water anomalously high BP and MP
• Large surface tension
• Source of unique properties

Question 7

What is the biological importance and relevance of H bonds

Answer 7

• Strong dipole-dipole interactions
• Arise between a covalently bound H and lone pair of e
• Involve two electronegative atoms
• Strongest when bonded molecules allow for linear bonding patterns
• Source of unique properties of water, S / F of proteins, DNA and polysaccharides
• Binding of hormones to receptors and substrates to enzymes
• Matching of mRNA and tRNA

Question 8

List and describe the 4 main non-covalent bonds and their role in biological systems

Answer 8

• Non-Covalent: No sharing electrons, exchange
• Ionic: Electrostatic attraction between charged ions or ion and dipole, ataractic / repulsive
• H: Electrostatic attraction between uncharged polar or neutral groups
• Van der Waals: Weak but complementary interaction between all atoms, attractive (longer) and repulsive (shorter),
• Hydrophobic: Non-polar molecules in aqueous solution (polar), avoidance

Question 9

What is ionisation

Answer 9

• Ionisation is when an atom or molecule gains either a positive or negative charge

Question 10

What is equilibrium, pH and associated constants

Answer 10

• Equilibrium: Relationship between concentrations of participating species in an equilibrium process
• pH: The negative logarithm of the hydrogen ion concentration (pH = -log[H+])
• Ka: Determines the extent of dissociation of weak electrolytes, we can calculate the pH if the Ka is known
• pKa: Measures acidity (-log Ka), low (strong, fully dissociates) and high (weak)

Question 11

What is the importance of buffers (pH)

Answer 11

• Buffers: Resist change in pH, at pH = pKa, there is a 50:50 mixture of acid and anion forms of compound
• Buffering Capacity: Of an acid/anion system is greatest at pH = pKa, capacity is lost when the pH differs from pKa by more than 1 pH unit

Question 12

What are biological buffer systems

Answer 12

• Intracellular pH: Enzyme-catalysed reactions have optimal pH, solubility of polar molecules depends on H-bond donors and acceptors, equilibrium between CO2 gas and dissolved HCO3– depends on pH
• Blood Buffer: Resists decreasing pH (high H) through carbonic anhydrase, facilitates production of H2O and CO2 from HCO3 + H

Question 13

What is the structure and function of fats / FA

Answer 13

• Structurally diverse, organic
• Low solubility in water (hydrophobic), glycerol or sphingosine backbone, ester linkages (glycerol and FA)
• Storage of energy, insulation, water repellent
• Either contain (complex) or don’t contain FA
• Fatty Acids: Carboxylic acids with hydrocarbon chains containing4-36 C, saturated, monounsaturated, polyunsaturated
• Undergo oxidation to produce energy / ATP

Question 14

What is the structure and function of proteins / peptides

Answer 14

• Linear hetero-polymers of alpha amino acids
• Involved in catalysis (polymerase), transport (Hg), structure (collagen) and motion (actin / myosin)
• 3D conformation, native fold = protein is functional
• AA polymerise to form peptides, condensation product
• Peptides consist of AA, cofactors (non AA), co enzymes (organic) and prosthetic groups (non protein)

Question 15

What is the basic structure of an amino acid

Answer 15

• Linear hetero-polymers, a carbon has 4 substituents, tetrahedral, all chiral (except glycine)
• Peptide bonds
• All (except proline) have acidic carboxyl (COO), basic amino (NH3), alpha hydrogen and R substituent (unique)
• Well suited to carry out varies of functions
• 5 basic groups, non polar / aliphatic (7), aromatic (5), polar / uncharged (5), positively charged (3) and negatively charged (2)

Question 16

How do amino acids act as buffers

Answer 16

• Ionisable Proteins: Amino acids contain at least two ionisable protons each with its own pKa
• COOH: Acidic pKa, protonated at low pH
• NH3: Basic pKa, protonated at high pH
• Low pH: Amino acid exists in positively charged form (cation), carboxyl / amino groups are protonated
• High pH: Amino acid exists in negatively charged form (anion), carboxyl / amino groups are deprotonated

Question 17

What are the 4 levels of protein structure

Answer 17

• Primary: AA linked by peptide bonds, includes disulphide bonds, cannot rotate, resonance, less reactive, almost planar
• Secondary: Local spacial arrangement, a helices (H bonds of backbone and every 4th AA), b sheets (H bonds of backbone and amides in different strands, parallel / antiparallel)
• Tertiary: Overall spatial arrangement, weak interaction between side chains (hydrophobic / polar / disulphide)
• Quaternary: Assembly of individual polypeptides into a large functional cluster, ribbon / surface contour model

Question 18

How can proteins be separated / purified

Answer 18

• Chromatography: Separation of solutions, mobile and stationary phase, separated based on charge, size, affinity
• SDS PAGE: Separates proteins by molecular weight, SDS = -ve detergent, thus proteins have a uniform -ve charge, native shape doesn’t matter, unfolds

Question 19

What are the key principles of protein folding / denaturation

Answer 19

• Folding: Function depends on primary, secondary, tertiary and quaternary folds
• Fold to lowest energy fold in u secs, direction toward native structure is thermodynamically favourable
• Denaturation: Loss of integrity / structure and thus activity, changes in temp, pH, presence of chaotropic agents (disrupts H bonds of H2O)
• Mis-Folding: Promotes aggregation, basis of human diseases

Question 20

How does proteolysis result in irreversible degradation of a protein

Answer 20

• Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids
• Hydrolysis of peptide bonds
• Irreversible post translational modification

Question 21

What is the structure and function of carbohydrates and common ones

Answer 21

• Sugar
• Energy source / storage, structural component (cell wall), cell-cell signalling
• Glycosidic bonds
• Ribose (5), glucose (6), galactose / mannose (epimers of glucose), fructose (ketose of glucose)
• Disaccharide, polysaccharide (linear or branched)

Question 22

How are carbohydrates stored in humans

Answer 22

• Glycogen
• Branched homo-polysaccharide of glucose
• Compact, more complex

Question 23

What are the properties of water

Answer 23

• Dipolar, tetrahedral arrangement, H have localised partial +ve charges and O has a partial -ve charge
• Good solvent for charged polar substances (AA)
• Poor solvent for non-polar substances
• Able to dissolve salts by hydrating component ions

Question 24

What is entropy and when does it change

Answer 24

• Entropy: Thermodynamic quantity, degree of randomness
• Increases as temperature increases and as a substance changes from solid to liquid to gas
• High Entropy: Thermodynamically favourable, flickering clusters of H2O molecules in bulk phase
• Low Entropy: Thermodynamically unfavourable, highly ordered H2O form ‘cages’ around hydrophobic alkyl chains

Question 25

What is a zwitterion

Answer 25

• Predominate between pKa values of COOH (pK1) and NH3 (pK2)
• Single molecule has both +ve and -ve charge
• Isoelectric point is (pK1pK2)/2
• Net charge is 0, not soluble in water, does not migrate in electric field