Protein Structure Flashcards
Proteins play crucial roles in all biochemical processes
Catalysts - enzymes
Transporters (e.g. O2, Fe)
Structural support (e.g., collagens in skin and bone)
Machines – e.g., muscular contraction and motion
Immune protection (e.g., immunoglobulins)
Ion channels
Receptors (for hormones, neurotransmitters, etc.)
Ligands in cell signalling (growth factors etc.)
Key features of proteins
Proteins are polypeptides
Macromolecules made up of amino acids
Amino acids joined covalently to give the sequence of the protein
The amino acid sequence of a protein is encoded by a gene
The nucleotide sequence of a gene determines the amino acid sequence of a protein
The polypeptide chain folds into a complex and highly specific three-dimensional structure, determined by the sequence of amino acids
The folding of proteins depends on the chemical and physical properties of the amino acids
The amino acid sequence of a protein is encoded by a gene
The nucleotide sequence of a gene determines the amino acid sequence of a protein
Amino acids are the building blocks of proteins
Amino acids consist of a central carbon atom (the a-carbon) covalently bonded to: an amino group (-NH2) a carboxyl group (-COOH) a hydrogen atom (-H) a distinctive R group (side chain)
Ionisation statues of amino acids
Unionised form of AA has NH2 group and COOH group
Ionised form of AA has NH3+ group and COO- group (both carboxyl group and amino group can ionise)
What is an AA residue
An amino acid residue is what remains of an amino acid after it has been joined by a peptide bond to form a protein
Classification of AA
Classified according to the chemical and physical properties of the R groups
Chemical properties - hydrophobic/phillic, non-polar/polar, acidic/basic/neutral
Physical properties - aliphatic and aromatic
pk values of ionisable side chains
Amino acids and their respective pKr’s
Positively charged R groups - Lysine 10.5, Arginine 12.5,
Histidine 6.0
Negatively charged R groups - Glutamate 4.3 Aspartate 2.8
If the pH of the solution < the pK value then the group will be protonated
If the pH of the solution > the pK value then the group will be deprotonated
Proteins structure
Primary structure - the linear amino acid sequence of the polypeptide chain
Secondary structure - local spatial arrangement of polypeptide backbone – the conformations like helices
Tertiary structure the overall 3- dimensional configuration of the protein
Quaternary structure association between different polypeptides to form a multi-subunit protein
Peptide bond formation
The linking of two amino acids is accompanied by the abstraction of a molecule of water
Peptide bonds are planar: Calpha1, C, O, N, H and Calpha2 all lie in the same plane
Peptide bonds are rigid: The peptide bond C-N has partial double bond characteristics which means its unable to rotate – contributes to planarity
Peptide bonds exhibit a trans formation - Calphas are on opposite sides of the peptide bond - a cis formation is where they are on the same side of the peptide bond and this doesnt occur due to the Calphas causing steric clashes
Bonds on either side of the peptide bond are free to rotate - Psi rotation = is the rotation around the bond between Calpha and C, Phi rotation is the rotation around the bond between Calpha and N
Importance of AA in proteins
The amino acid sequence of a protein determines:
The way in which the polypeptide chain folds
The physical characteristics of the protein
Isoelectric point of protiens
The isoelectric point, pI, of a protein is the pH at which there is no overall net charge
BASIC PROTEINS - pI > 7 - Contain many positively charged (basic) amino acids
ACIDIC PROTEINS - pI < 7 - Contain many negatively charged (acidic) amino acids
If pH < pI protein is protonated
If pH > pI protein is deprotonated
Sizes of peptides and proteins
Peptides/oligopeptides - A few amino acids in length
Polypeptides/proteins - Many amino acids
Biologically active peptides and proteins come in a varying range
of sizes
e.g. angiotensin II Asp-Arg-Val-Tyr-Ile-His-Pro-Phe
Conjugated proteins
Some proteins contain covalently linked chemical components in addition to amino acids
Protein conformation
Covalent (peptide) bonds hold primary structure together
Angles determine the conformation of peptide backbone and hence the ‘fold’ of the protein
Secondary structure - the alpha-helix
3.6 aa / turn 0.54nm pitch Right-handed helix
Secondary structure
- the a-helix
H-bonds between N-H and C=O stabilise the structure of the a- helix
The backbone –C=O group of one residue is H-bonded to the –NH group of the residue four amino acids away
Sequence affects alpha-helix stability
Not all polypeptide sequences adopt a-helical
structures
Small hydrophobic residues such as Ala and Leu are strong helix formers
Pro acts as a helix breaker because the rotation around the N-C a
bond is impossible
Gly acts as a helix breaker because the tiny R- group supports other conformations
The extended conformation (the ß strand)
The extended conformation - describes the way that AA line up - R groups alternate between opposite sides of the chain
Side by side arrangement of ß strands makes ß sheets
2 different types of sheets - antiparallel and parallel
Antiparallel ß-sheet: adjacent ß-strands run in opposite directions, with multiple inter-strand H-bonds stabilizing the structure.
Parallel ß sheets - adjacent ß strands run in the same direction - still with multiple inter strand H bonds stabilising the structure
Tertiary structures
The spatial arrangement of AA dictate the tertiary structure
2 simple protein structures
The alpha helix - the iron storage protein ferritin
The ß sheet - fatty acid binding protein
Globular and fibrous proteins
Fibrous Role – support, shape, protection
Long strands or sheets
Single type of repeating secondary structure e.g. collagen
Collagen - triple helical arrangement of collagen chains
contain Gly – X – Y repeating sequence
hydrogen bonds stablise interactions between chains
Collagen fibrils formed from covalently cross- linked collagen molecules
Globular Role – catalysis, regulation
Compact shape
Several types of secondary structure e.g. carbonic anhydrase
Globular protiens have a variety of tertiary structures
Motifs — these are folding patterns containing 1 or more elements of secondary structure e.g. a ß-alpha-ß loop
Domains - these are part of a polypeptide chains that fold into a distinct shape - these usually have a specific functional role - e.g. the calcium binding domain in Troponin C
Folding of water soluble proteins
Polypeptide chains fold to so that hydrophobic side chains are buried and polar, charged chains are on the surface
Proteins present in the PM usually are exposed to water in the centre of their channel (due to them being channel proteins - therefore membrane proteins often show inside out distribution of AA (hydrophilic AA in the centre and hydrophobic AA on the exterior)
Quaternary shape
The coming together of 2 or more tertiary structures
E.g. Hb contains 2 alpha subunits and 2 ß subunits
Forces involved in maintaining protein structure
At the primary level/structure - Covalent (peptide) bonds
At the secondary level/structure - H-bonds
At the Tertiary level/structure - Covalent (disulphide bonds), ionic, H bonds, VDWs forces and hydrophobic
At the quaternary level/ structure - Covalent (disulphide bonds), ionic, H bonds, VDWs forces and hydrophobic
Covalent bonds - formed between cysteine residues - can be broken with reducing agents - most proteins with disulphide bonds are secreted e.g. ribonuclease
H bonds - formed between electronegative atom and a hydrogen bound to another electronegative atom (usually H to O or N)
Hydrophobic effect - interaction between hydrophobic side chains due to the displacement of water - hydrophobic parts of molecules come together to form circular structures
VDWs forces - dipole dipole interactions - when 2 surfaces of 2 large molecules come together
Protein denaturation
Proteins are not very stable
A normally folded protein that is functional is said to be in the native conformation
Disruption of protein structure is known as denaturation
Caused by breaking of forces that hold proteins together
e.g. Heat - Increased vibrational energy
pH - Alters ionization states of amino acids which changes ionic/H-bonds
Detergents/Organic solvents Disrupt hydrophobic interactions
How do proteins fold
The folding process must be ordered
Each step involves localised folding and with stable conformations maintained
Driven by the need to find the most stable conformation
Protein misfolding can cause disease
Transmissible spongiform encephalopathies e.g. BSE, kuru, CJD
Altered conformation of a normal human protein promotes/converts existing protein into diseased state
Amyloidoses - group of brain diseases characterised by progressive misfolding and aggregation of proteins
Formation of amyloidoses fibers
Amyloid fibres - misfolded, insoluble form of a normally soluble protein
highly ordered with a high degree of b-sheet
core b-sheet forms before the rest of the protein
inter-chain assembly stabilised by hydrophobic interactions between aromatic amino acids
