intro to proteins

Question 1

water

Answer 1

•	the “solvent of life”
•	H2O
•	electrophilic oxygen attracts electrons in bonding pairs
O partial negative charge (-)
H partial negative charge (+)
H2O forms electrical dipole

Question 2

hydrogen bonds

Answer 2

• - of water oxygens attract + of hydrogens to form hydrogen bonds
• H-bonds are weak (29 kJ vs 410 kJ of O-H covalent bond)
• give water its physical properties
• can form between water and other molecules

Question 3

hydronium and hydroxyl ions

Answer 3

water dissociates freely to form hydroxyl and hydronium ions:
H2O + H2O OH- + H3O+

• the hydronium ion concentration, [H3O+], is usually expressed as the proton concentration, [H+]
• in pure water, there is minimal dissociation, with
[H+ ] = [OH-] = 10-7M

Question 4

pH

Answer 4

• therefore in aqueous solutions:
[H+] x [OH-] = 10-14
• [H+] in mol/L is commonly expressed as pH, the negative logarithm of [H+]
i.e. pH = -log [H+]

• low pH = high [H+]; acidic
• high pH = low [H+]; alkaline (basic)

Question 5

acids and pH

Answer 5

• an acid releases a proton
• reversible
• a conjugate base is formed on release of proton e.g. organic acids, carboxylic acids

Question 6

bases and pH

Answer 6

• a base binds a proton
• reversible
• a conjugate acid is formed on release proton binding e.g. amino groups in biomolecules

Question 7

buffers

Answer 7

• buffers resist pH change; i.e. maintain the status quo
• buffers are mixtures of a weak acid and the conjugate base
• adding acid shifts equilibrium to left (H+ taken up)
• adding alkali shifts equilibrium to right (H+ released)
• most effective when [HA] ≈ [A-] i.e. when pH ≈ pKa

Question 8

pH in the body

Answer 8

• cellular reactions are pH sensitive
• physiological pH is 7.25-7.45
• phosphate is an important intracellular buffer (pKa 6.8)
• carbonic acid is an important buffer in blood

Question 9

biomolecules

Answer 9

• there are more than a million different molecules in humans
• many are macromolecules (MW > 10^3)
- e.g. proteins, nucleic acids, complex carbohydrates
- these are all polymers formed by condensation reactions between functional groups
• other molecules found in the body have a range of functions, including:
- signalling (hormones, neurotransmitters)
- energy storage (glycogen, triglycerides)
- energy transfer (ATP, coenzymes)

Question 10

biomolecules: isomers

Answer 10

• shape (geometry) is important in biochemistry
• molecules with the same atomic composition can have different geometry (isomers)
- positional isomers differ in position of functional group (e.g. propan-1-ol & propan-2-ol)
- geometric isomers differ in arrangement of groups around a “rigid” bond (e.g. cis & trans isomers of compounds with double bonds)

Question 11

enantiomers

Answer 11

• optical isomers differ in orientation around an asymmetric carbon with four different substituents
• if there is only one asymmetric carbon, molecules are mirror images – enantiomers
- c.f. right and left hand, therefore chiral
- identical physical and chemical properties
- rotate plane-polarised light in different directions
- d (dextro rotatory; right) & l (levo rotatory; left)

• in biochemistry, the terms d and l are defined by reference to the two enantiomers of glyceraldehyde
• enzymes and receptors are usually specific for a particular enantiomer. Therefore only the correct enantiomer can be a substrate or ligand

Question 12

proteins

Answer 12

• proteins are polymers of amino acids
• 20 common l-amino acids found in proteins
• amino acids come from diet; some can be made in the human body
• proteins are not a primary energy store
• they are the main structural and functional polymers in all organisms
• constitute about 16% of body weight

Question 13

studying proteins: techniques

Answer 13

• techniques to study proteins include:
  • proteins are polymers of amino acids
  • 20 common l-amino acids found in proteins
  • amino acids come from diet; some can be made in the human body
  • proteins are not a primary energy store
  • they are the main structural and functional polymers in all organisms
  • constitute about 16% of body weight
• These can require separating (purifying) proteins from cellular components, including other proteins
• Separation methods rely on differences in physical properties, including size and overall charge; e.g.
• chromatography (separation using a solid phase with specific chemistry)
• electrophoresis (separation by an electrical field)
• dialysis (separation by diffusion through semi-permeable barrier)

Question 14

amino acids

Answer 14

Amino group (NH3+);
positive charge at pH 7

Carboxyl group (COOH); negative charge at pH 7

Question 15

D and L amino acids

Answer 15

amino acids exist as enantiomers.
Assignment of d and l is based on the absolute configuration of glyceraldehyde* Proteins are only made from l-amino acids

Question 16

amino acids: side chains

Answer 16

• “R” defines the amino acid’s
- size
- polarity i.e. hydrophobic or hydrophilic, charged or neutral
- reactivity
• There are 20 naturally occurring “amino acids”. Actually;
- 19 different “R” groups (including “H” for glycine)
- 1 imino acid (proline)
• Sequence of amino acids in protein determines its structure and function
• Amino acids can be grouped by side chain properties

Question 17

charge properties of amino acids

Answer 17

• the overall charge of an amino acid depends on:
- pH
- the side chain (R group)
• amino acids are zwitterions