intro to proteins Flashcards
water
• the “solvent of life” • H2O • electrophilic oxygen attracts electrons in bonding pairs O partial negative charge (-) H partial negative charge (+) H2O forms electrical dipole
hydrogen bonds
- - 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
hydronium and hydroxyl ions
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
pH
• 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)
acids and pH
- an acid releases a proton
- reversible
- a conjugate base is formed on release of proton e.g. organic acids, carboxylic acids
bases and pH
- a base binds a proton
- reversible
- a conjugate acid is formed on release proton binding e.g. amino groups in biomolecules
buffers
- 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
pH in the body
- 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
biomolecules
• 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)
biomolecules: isomers
• 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)
enantiomers
• 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
proteins
- 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
studying proteins: techniques
- 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)
amino acids
Amino group (NH3+); positive charge at pH 7
Carboxyl group (COOH); negative charge at pH 7
D and L amino acids
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