Protein Structure & Functions

Question 1

What are the functions of a protein?

Answer 1

➼ Carrier functions: transporting O2
➼ Metabolic functions: as enzymes using and producing energy
➼ Forms parts of cellular machinery: spliceosomes and ribosomes
➼ Makes up structural scaffold: microtubules, nucleosomes
➼ Sensing molecules: ligands and receptors

Question 2

How do we differentiate between L (levo) and D (dextro) forms of amino acids?

Answer 2

An L isomer reads Co-R-N CLOCKWISE, while a D isomer reads Co-R-N ANTICLOCKWISE.

Question 3

How is a peptide bond formed?

Answer 3

➼ By a condensation reaction
➼ A covalent bond is formed between the carboxyl group of one aa and the amino group fo the adjacent aa
➼ This releases a H20 molecule
➼ The amino group and the terminal carboxyl groups pf the first and last aa remain
➼ They are referred to the amino and carboxyl terminus

Question 4

Which chiral forms of aa have all organisms evolved to use? (L or D forms)

Answer 4

L-form

Question 5

Which aa does not have both L and D isoforms? Why

Answer 5

➼ Glycine

➼ Glycine does not have a chiral centre

Question 6

What is a zwitterion

Answer 6

➼ An aa that is charged but the charges balance out so the aa has no net charge

Question 7

What is a residue?

Answer 7

A residue is each repeating unit in a polypeptide chain.

Question 8

aa residues normally arranged in a trans-configuration?

Answer 8

➼ True

➼ The cis arrangement is less energetically stable

Question 9

Describe the levels of protein structure

Answer 9

➼ Primary structure: covalent bonds forming a polypeptide chain - ie. the order of amino acids residue

➼ SECONDARY STRUCTURE: regular folded form, eg. α helices, β sheets and β turns

➼ TERTIARY STRUCTURE: overall 3D structure, stabilised by non-covalent bonds and forces, and sometimes by intra-chain covalent bonds

➼ QUATERNARY STRUCTURE: organisation of polypeptide chains into assemblies, stabilised by non-covalent bonds and forces (like tertiary), and sometimes by intra-chain covalent bonds

Question 10

What are the 3 secondary structural folds?

Answer 10

➼ α helice
➼ β sheets
➼ β turns

Question 11

Describe secondary structure in detail including the arrangement of the variable side chains

Answer 11

➼ β sheets and β turns:
➼ They are formed by H bonds between the β strands.
➼ In sheets, the H bonds are between the strands.
➼ In turns, there are loops or turns linking the β sheets.

α helix:
➼ right-handed helix
➼ stablilized by H bonds between two amino acids four residues apart.

The arrangement of the variable side chains is important for structure and function. The side chains of both the α and β (sheets) protrude outwards from the structures.

Question 12

Describe the tertiary structure

Answer 12

➼ The secondary structure is then folded into more densely packed, generally globular structures.

➼ The formation of these structures depends on weak chemical bonds between the side chains.

Question 13

Describe quaternary structure

Answer 13

➼ 2 or more folded polypeptides may be combined to form a mature protein.

➼ The same bonds used in the tertiary structure are used to hold the subunits together.

Question 14

Give examples of cofactors proteins require to function

Answer 14

➼ Haem group in haemoglobin
➼ FAD & NAD to convert pyruvate to lactate by lactate dehydrogenase
➼ Vitamin K in the carboxylation of glutamic acid during blood clotting
➼ Zn2+ in the hydration of CO2 by carbon anhydrase to produce HCO3-

Question 15

Describe water soluble proteins

Answer 15

➼ Globular in shape
➼ Hydrophilic residues mostly on the external surface
➼ Hydrophobic residues usually buried inside the protein

Question 16

Describe membrane soluble proteins

Answer 16

➼ Hydrophilic residues usually buried inside the protein

➼ Hydrophobic residues usually on the external surface

Question 17

What are some techniques used to understand and determine protein structure?

Answer 17

➼ X ray crystallography
➼ NMR
➼ Cryoelectron Microscopy
➼ Circular dichroism