Medic_Summaries (IMS) Topic 2
Proteins and Enzymes
Disease is caused by:
- Lack of/non-functional proteins (haemophilia)
- Insufficient amount of protein synthesised (thalassaemia)
- Presence of malformed protein (Alzheimer’s disease, Duchenne muscular dystrophy)
- External proteins (cholera)
- External prion proteins (mad cow disease)
Proteins are very diverse:
- Catalysis: phenylketonuria (phenylalanine hydroxylase); haemophilia (clotting factors)
- Transport/storage: haemoglobin, ferritin
- Motion: dystrophin (Duchenne muscular dystrophy)
- Communication: hormone receptors, neurotransmitters
- Structure: keratin, collagen (osteogenesis imperfecta, scurvy)
- Channels/transporters: CFTR Cl- channels (cystic fibrosis)
- Regulation: cell division, protein synthesis, hormones
- Immunity: antibodies, self-recognition (myasthenia gravis)
Genome: full set of genes in an organism (30,000-40,000 protein coding genes)
Proteome: full set of proteins encoded by the human genome
30,000 genes gives ca. 200,000 proteins, which gives ca. 1 million modified proteins.
Alpha amino acids:
- Alpha carbon with four bonds to:
- Hydrogen atom
- Alpha amino group
- Alpha carbonyl group
- R-group
- Named according to the R-group
- 20 common amino acids found in proteins:
- Sulphur-containing: cysteine, methionine
- Imino: proline (not an amino acid)
- Non-polar: glycine, alanine, valine, leucine, proline, isoleucine, phenylalanine,
tryptophan, methionine
- Polar: serine, threonine, cysteine, tyrosine, asparagine, glutamine
- Electrically charged (-ve): aspartate, glutamate
- Electrically charged (+ve): arginine, histidine
Aliphatic: straight-chained
Aromatic: cyclic
Amino acids can be more than one grouping eg. methionine is non-polar, sulphur-containing and
aliphatic.
- All alpha amino acids have OPTICAL ACTIVITY (CHIRAL), except for glycine
- Only L-isomers (L-amino acids) are present in proteins
- Amino acids are building blocks for proteins
- The arrangement of amino acids in proteins affects the structure/function of the protein
Primary structure: amino acid sequence
Secondary structure: local spatial arrangements of amino acids in the peptide chain
Tertiary structure: overall 3D protein shape
Quaternary structure: arrangement of different subunits in a protein
1 Adapted from Lectures at the University of Leeds Medical School
, Medic_Summaries (IMS) Topic 2
Amino acids:
- Sequences are defined by genes
- Joined by peptide bonds (to form a polypeptide chain)
- Natural proteins contain ca. 50-2,000 amino acids
AA chain = BACKBONE
AA within chain = RESIDUE
Different R-groups = SIDE CHAINS
- N terminus (amino-end) to C terminus (carboxyl-end)
- The reaction for linking amino acids occurs on ribosomes (CONDENSATION reaction)
Peptide bonds:
- Contain partial double-bond characteristics
- Resonate (this makes the bond more RIGID)
Secondary structure: alpha helix
- Side chains extend outwards
- Hydrogen bonds between NH and C=O stabilise the helix (intrachain H-bonds)
- Each C=O oxygen is H-bonded to NH, four residues ahead in the linear sequence
- Rod structure
- H-bonds nearly parallel to helix axis (increased ELASTICITY)
Secondary structure: beta pleated sheet
- H-bonds between adjacent strands:
- Intrachain: two parts of the same chain
- Interchain: between different amino acids
- NO elasticity
- Zigzag/pleated shape (parallel or antiparallel)
- R-groups lie outside the plane of the sheet
Tertiary structure: close packing of secondary structural elements
- Interior: HYDROPHOBIC (Leu, Val, Met, Phe - SOLUBLE proteins)
- Exterior: HYDROPHILIC (Arg, His, Lys, Asp, Glu - CHARGED residues)
- Tertiary structure gives the ACTIVE SITE
Quaternary structure: some proteins contain more than one polypeptide chain
- Subunits: individual polypeptide chains
- Quaternary structure is the arrangement, IN SPACE, of the subunits
- Monomer proteins: myoglobin, insulin
- Multi-subunit proteins:
- Structural proteins (collagen fibres)
- Multi-enzyme complexes (mitochondrial ATPase)
- Immune system proteins (antibodies)
- Transport proteins (haemoglobin)
- Motility proteins (myosin)
- Subunits contain closely packed non-polar side chains, H-bonds, disulphide bonds
- Proteins stabilised by side chains:
- Covalent: disulphide bonds
- Non-covalent: weak interactions (electrostatic, VdW, H-bonds, hydrophobic)
Disulphide bonds:
- Oxidation between Cys (cysteine to cystine), adjacent in space
Electrostatic interactions:
- Stabilise tertiary and quaternary interactions (oppositely charged side chains)
- Oppositely charged side chains form a SALT BRIDGE
- Same charge side chains OPPOSE one another
2 Adapted from Lectures at the University of Leeds Medical School
Proteins and Enzymes
Disease is caused by:
- Lack of/non-functional proteins (haemophilia)
- Insufficient amount of protein synthesised (thalassaemia)
- Presence of malformed protein (Alzheimer’s disease, Duchenne muscular dystrophy)
- External proteins (cholera)
- External prion proteins (mad cow disease)
Proteins are very diverse:
- Catalysis: phenylketonuria (phenylalanine hydroxylase); haemophilia (clotting factors)
- Transport/storage: haemoglobin, ferritin
- Motion: dystrophin (Duchenne muscular dystrophy)
- Communication: hormone receptors, neurotransmitters
- Structure: keratin, collagen (osteogenesis imperfecta, scurvy)
- Channels/transporters: CFTR Cl- channels (cystic fibrosis)
- Regulation: cell division, protein synthesis, hormones
- Immunity: antibodies, self-recognition (myasthenia gravis)
Genome: full set of genes in an organism (30,000-40,000 protein coding genes)
Proteome: full set of proteins encoded by the human genome
30,000 genes gives ca. 200,000 proteins, which gives ca. 1 million modified proteins.
Alpha amino acids:
- Alpha carbon with four bonds to:
- Hydrogen atom
- Alpha amino group
- Alpha carbonyl group
- R-group
- Named according to the R-group
- 20 common amino acids found in proteins:
- Sulphur-containing: cysteine, methionine
- Imino: proline (not an amino acid)
- Non-polar: glycine, alanine, valine, leucine, proline, isoleucine, phenylalanine,
tryptophan, methionine
- Polar: serine, threonine, cysteine, tyrosine, asparagine, glutamine
- Electrically charged (-ve): aspartate, glutamate
- Electrically charged (+ve): arginine, histidine
Aliphatic: straight-chained
Aromatic: cyclic
Amino acids can be more than one grouping eg. methionine is non-polar, sulphur-containing and
aliphatic.
- All alpha amino acids have OPTICAL ACTIVITY (CHIRAL), except for glycine
- Only L-isomers (L-amino acids) are present in proteins
- Amino acids are building blocks for proteins
- The arrangement of amino acids in proteins affects the structure/function of the protein
Primary structure: amino acid sequence
Secondary structure: local spatial arrangements of amino acids in the peptide chain
Tertiary structure: overall 3D protein shape
Quaternary structure: arrangement of different subunits in a protein
1 Adapted from Lectures at the University of Leeds Medical School
, Medic_Summaries (IMS) Topic 2
Amino acids:
- Sequences are defined by genes
- Joined by peptide bonds (to form a polypeptide chain)
- Natural proteins contain ca. 50-2,000 amino acids
AA chain = BACKBONE
AA within chain = RESIDUE
Different R-groups = SIDE CHAINS
- N terminus (amino-end) to C terminus (carboxyl-end)
- The reaction for linking amino acids occurs on ribosomes (CONDENSATION reaction)
Peptide bonds:
- Contain partial double-bond characteristics
- Resonate (this makes the bond more RIGID)
Secondary structure: alpha helix
- Side chains extend outwards
- Hydrogen bonds between NH and C=O stabilise the helix (intrachain H-bonds)
- Each C=O oxygen is H-bonded to NH, four residues ahead in the linear sequence
- Rod structure
- H-bonds nearly parallel to helix axis (increased ELASTICITY)
Secondary structure: beta pleated sheet
- H-bonds between adjacent strands:
- Intrachain: two parts of the same chain
- Interchain: between different amino acids
- NO elasticity
- Zigzag/pleated shape (parallel or antiparallel)
- R-groups lie outside the plane of the sheet
Tertiary structure: close packing of secondary structural elements
- Interior: HYDROPHOBIC (Leu, Val, Met, Phe - SOLUBLE proteins)
- Exterior: HYDROPHILIC (Arg, His, Lys, Asp, Glu - CHARGED residues)
- Tertiary structure gives the ACTIVE SITE
Quaternary structure: some proteins contain more than one polypeptide chain
- Subunits: individual polypeptide chains
- Quaternary structure is the arrangement, IN SPACE, of the subunits
- Monomer proteins: myoglobin, insulin
- Multi-subunit proteins:
- Structural proteins (collagen fibres)
- Multi-enzyme complexes (mitochondrial ATPase)
- Immune system proteins (antibodies)
- Transport proteins (haemoglobin)
- Motility proteins (myosin)
- Subunits contain closely packed non-polar side chains, H-bonds, disulphide bonds
- Proteins stabilised by side chains:
- Covalent: disulphide bonds
- Non-covalent: weak interactions (electrostatic, VdW, H-bonds, hydrophobic)
Disulphide bonds:
- Oxidation between Cys (cysteine to cystine), adjacent in space
Electrostatic interactions:
- Stabilise tertiary and quaternary interactions (oppositely charged side chains)
- Oppositely charged side chains form a SALT BRIDGE
- Same charge side chains OPPOSE one another
2 Adapted from Lectures at the University of Leeds Medical School
