Lecture 8 Flashcards
Describe the quaternary structure
- some proteins contain more than 1 polypeptide chain
- interact through non covalent interactions and covalent bonds
- each polypeptide chain in a protein is called a subunit
- subunits can be identical or different
Name 2 proteins with a quaternary structure
- CAP: composed of 2 identical subunits
- Hemoglobin: composed of two identical a subunits and two identical b subunits
What are protein families? And give an example
- proteins that are grouped in protein families where each member has an amino acid sequence and 3D conformation that closely resembles each other
- arise over time during evolution
Ex. chymotrypsin and elastase (differ in substrate specificity)
How do proteins form large assemblies
- through subunits which bind to one another
What is a ligand?
- any substance bound by a protein
- protein ligand interactions are dictated by non-covalent bonds
What is a binding site?
- region of protein that associates with a ligand
- formed by a specific arrangement of amino acid side chains that may not immediately adjacent to one another in the polypeptide chain
What are antibodies
- Y shaped molecules that are composed of two heavy chain and two light chains
- binds very specifically to a target molecule called an antigen
- it has to antigen binding sites where the amino acid sequence is highly variable
- there are billions of different possible antibodies
Why are antibodies important?
- important for fighting infections
- important laboratory tool
(identification, quantification, localization)
What is an enzyme
- it is a biological catalyst which speeds up the rate of a reaction by lowering the activation energy
Enzyme bind to a _____________ forming a ________________. After the reaction has proceeded, the enzyme will be in contact with the product as an _________ and will eventually release a _______________
- substrate
- enzyme-substrate complex
- enzyme-product complex
- product
What is an active site
- the region of an enzyme that binds and catalyzes the substrate
Why are enzymes so large?
- to provide folding framework for active site
- precisely align active site residues
- optimize binding energy in the transition state
What is the activation energy
- the energy required to go from ground state to transition state
What is a transition state
- the maximum energy species formed on the reaction coordinate
How do enzymes lower the activation energy
- align substrate in favourable orientation
- rearrange the electron distribution
- physically strain the substrate to induce a reaction
What is a lysozyme
- an enzyme that severs polysaccharide chains that form cell walls in bacteria
- performs a hydrolysis reaction
- helps reaction overcome the activation energy
- multiple non covalent interactions are formed
- two amino aid residues (Glu35 and Asp52) are critical for this hydrolysis to take place
What are the properties of Glu and Asp
they are both negatively charged (acidic amino acids)
Which amino acids are more likely to be found in the active site
polar or charged amino acids
Give two examples of small nonprotein molecules that are necessary for a particular protein to perform its function.
- retinal: retinal binds to protein rhodopsin and changes shape upon absorption of protein
- heme: binds to protein hemoglobin and allows to reversible binding of oxygen
