Topic 2 - Protein structure and folding Flashcards
What is the primary structure?
Linear amino acid sequence of the polypeptide chain
Peptide bonds
What is the secondary structure
Local recurring arrangement of polypeptide backbone arranged in alpha chains or beta pleats
Alpha helix: hydrogen bonds stabilise the structure (right handed) - iron
Beta sheet: composed of beta strand anti parallel, stabilised by hydrogen bonds. Also in parallel and mixed - fatty acid
What is the tertiary structure
The final 3D structure of the protein Globular or fibrous Globular - compact, several types - enzymes Fibrous - extended, repeating - collagen All types of forces
What is the Quarternary structure
The different polypeptides that form a multi-subunit protein
Non covalent interactions
Eg: Hb - 2 alpha and 2 beta
Ribosome - 55 protein subunits and 3 RNA
What is a peptide bond
The linking of two amino acids at a ribosome by a condensation reaction thus accompanied by loss of water
Forms a carbonyl-oxygen amide
What are the key features of a peptide bond
Planar
C, O, N, H and C - all lie in the same plane
Possess a free amino terminus and a carboxyl terminus in a protein
Rigid, C-N has partial double bond characteristics
Trans conformation (C-O and N-H on opposite sides of bond), and so R groups on opposite side so does not interact
Bonds on either side are free to rotate
How do amino acids contribute to protein structure
The amino acid sequence determines:
- folding of polypeptide in primary sequence
- physical characteristics of the protein
- rotation about psi -C-C bind and Phi-C-N bond allows formation of 3D structure
- distribution of amino acid residues so hydrophobic buried and polar/charged on surface. In membrane, hydrophilic head, hydrophobic tail
Why protein structure is important to protein function
- Size - no of amino acid residues and molecular weight in kDa
- Isoelectric point - pH at which there is no overall charge
STRUCTURE DETERMINES FUNCTION
What does folding break and how? What happens if it goes wrong?
H bonds
Ionic
Dipole dipole
London forces
Ordered process involved localised folding and stable conformations maintained such as alpha helix so become most stable
Transmissible spongiform encephalopathies
Eg: CJD
If not disposed, mis folding can trigger diseases
What are the key features of proteins
Macromolecules
Made of amino acids joined covalently
The amino acid sequence of the protein is encoded by a gene…the nucleotide sequence of a gene - amino acid sequence of protein
What is the general structure of an amino acid
Central carbon atom covalently bonded to an amino group, carboxyl group, hydrogen atom, distinctive R group (determines function)
When protonated - COOH and NH3+
Zwitterion - NH3+ and COO-
Deprotonated - NH2 and COO-
Posses a NH3+ at N terminal and COO- at C terminal end
How are amino acids classified
According to chemical properties of the R groups, eg: acid base behaviour
Hydrophobic Hydrophilic Polar Non polar Acidic - negatively charged at physiological pH Basic - positively charged at physiological pH Aliphatic - C + H Aromatic - phenyl
If polar = hydrophilic. If strongly polar = acidic
Polar - oxygen or sulphur
What is an amino acid residue
What remains of an amino acid after it has been joined by a peptide bond to form a protein
Usually alpha helices- hydrophobic
What is the Henderson hasselnach equation
pH = pKa + log([A-]/[HA])
Why is an alpha helix particularly suited to existence in the hydrophobic environment of the interior of a membrane?
The hydrogen bonds formed in the backbones neutralise the polar residues making them more stable in this hydrophobic environment
