Lecture 8

Question 1

Describe the quaternary structure

Answer 1

• 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

Question 2

Name 2 proteins with a quaternary structure

Answer 2

• CAP: composed of 2 identical subunits
• Hemoglobin: composed of two identical a subunits and two identical b subunits

Question 3

What are protein families? And give an example

Answer 3

• 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)

Question 4

How do proteins form large assemblies

Answer 4

• through subunits which bind to one another

Question 5

What is a ligand?

Answer 5

• any substance bound by a protein
• protein ligand interactions are dictated by non-covalent bonds

Question 6

What is a binding site?

Answer 6

• 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

Question 7

What are antibodies

Answer 7

• 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

Question 8

Why are antibodies important?

Answer 8

• important for fighting infections
• important laboratory tool
  (identification, quantification, localization)

Question 9

What is an enzyme

Answer 9

• it is a biological catalyst which speeds up the rate of a reaction by lowering the activation energy

Question 10

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 _______________

Answer 10

1. substrate
2. enzyme-substrate complex
3. enzyme-product complex
4. product

Question 11

What is an active site

Answer 11

• the region of an enzyme that binds and catalyzes the substrate

Question 12

Why are enzymes so large?

Answer 12

• to provide folding framework for active site
• precisely align active site residues
• optimize binding energy in the transition state

Question 13

What is the activation energy

Answer 13

• the energy required to go from ground state to transition state

Question 14

What is a transition state

Answer 14

• the maximum energy species formed on the reaction coordinate

Question 15

How do enzymes lower the activation energy

Answer 15

• align substrate in favourable orientation
• rearrange the electron distribution
• physically strain the substrate to induce a reaction

Question 16

What is a lysozyme

Answer 16

• 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

Question 17

What are the properties of Glu and Asp

Answer 17

they are both negatively charged (acidic amino acids)

Question 18

Which amino acids are more likely to be found in the active site

Answer 18

polar or charged amino acids

Question 19

Give two examples of small nonprotein molecules that are necessary for a particular protein to perform its function.

Answer 19

• 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