Protein structure and enzyme kinetics Flashcards
How many amino acids are there and what does the properties of amino acid help explain
20
Help explain many of the structural and functional properties of proteins
What is protein structure,
aa sequence + disulphidebonds
What is the secondary structure ?
single units of regular structure stabilised by H-bonds
What is tertiary structure
3D-fold of a single polypeptidechain
What is quaternary
many proteins function as complexes of more than one polypeptide chain
What are the three factors restricting the conformation available to the polypeptidechain:
- peptide bond has partial double bond character – there is no free rotation around peptide bond
- preferred orientation around the peptide bond is transconformation (apart from Proline (P)).
3.lack of free rotation around the C atom due to steric clashes.
What is Ramachandran Plot
gives the “allowed” (i.e. stable)conformations of the polypeptide chain around the C atoms -stable regions cluster in two regions of the Ramachandran plot:
What are the factors of the alpha helix
most common secondarystructure element in proteins –therefore very stable
right-handed helix
stabilised by H-bonds
3.6 aa / turn* pitch 5.4 Å* rise per aa 1.5 Å
What are the factors of the beta Strand?
The typical length of a beta-strand is ~ 6 - 8 aa (proteins typically contain from 2 to 15 strands). beta-sheets are stabilised by H-bonds between adjacent strands
What are the important information about loops?
Connecting regions joining alpha-helices and beta strands
various lengths and three-dimensional configurations ( and angles are irregular)
located on surface of the protein
variable in sequence and structure
tend to consists of charged and polar aa
LOOPS CAN BE FUNCTIONALLY VERY IMPORTANT Because they are on the surface of the protein and because they are rich in functional side-chain groups, loop regions often participate in BINDING SITES FOR LIGANDS and ENZYME ACTIVE SITES..
What makes up the active site residue?
D102, H57 & S195 make upthe key active site residuesthat allow the serine proteinaseto hydrolyse the peptide bond
Why is enzyme kinetics important?
1) Kinetic properties of enzyme can give insights into its mechanism of action (i.e., how it works at the molecular level).
2) Understanding kinetics of enzyme-catalysed reactions can help elucidate the physiological role of the enzyme – allowing a quantitative understanding of metabolism and metabolic regulation.
3) Most drugs are enzyme inhibitors - understanding enzymekinetics is essential for the development of new therapeutic drugs.
What is the primary protein structure?
- Sequence of amino acid that makes up a protein (amino acid = monomer building block)
- Amino acids are held together by peptide bond
- Genes determine the order a number of amino acids for the sequence as it is critical for protein structure and function.
- In protein synthesis, amino acid added to form, polypeptide, chains, and proteins are made of one or more polypeptide chain
What is secondary protein structure?
- Describe the localised confirmations of the polypeptide, meaning the folding pattern for the protein
- Stigma bonds freely rotate, so the side chains have a flexible confirmation
- Molecules with dipole will attempt to store energy by electrostatic interaction, so the backbone forwards, allowing the residue to interact with one another
- Beta pleated sheets have the backbone extended to form dipole dipole interactions
- The alpha helix backbone is spiral with all groups pointing out and the amide groups interact with the amide groups three residue above and below
What is tertiary protein structure?
- Complete the folding pattern
- Residue with hydrophobic side, chains =interior protein, so they cannot come in contact with aqueous solvent, residues with hydrophilic side chains = surface to make dipole dipole ion dipole interactions with water molecules
