Protein Structure And Functions

Question 1

Amino acids form the building blocks from which proteins are made, these building blocks have four chemical groups covalently linked to a central alpha carbon. During protein synthesis amino acids are joined end to end via the formation of peptide bonds giving rise to polypeptides.

True or false?

Answer 1

True

Question 2

Amino acids occur in two forms, the D (Dextro-rotationary) and L (Levo-rotationary) forms these different forms equate to the “handedness” of the molecule around the so called chiral center.
All organisms have evolved to use only one of the chiral forms of amino acids in protein synthesis.

So all naturally occurring proteins contain the D or Dextro-rotationary form.

True or false?

Answer 2

False - the protein machinery has evolved to use the L-chiral form of amino acids and so all naturally occurring proteins in eukaryotes contain the L-form. It is true that D-amino acids are found in biological systems but this is restricted for example to their use by bacteria as components of the bacterial cell walls.

Question 3

The L or levo-rotationary and the D or dextro-rotationary forms of amino acids are so called because they cause the rotation of a plane of polarized light passed through a solution in either an anti-clockwise or clockwise direction, whilst this in itself is not necessary to know or remember, it explains the term L and D.

All amino acids except Glycine have a chiral center and so Glycine is the only amino acid that does not have both L and D isoforms

Answer 3

Levo or L form spells CO-R-N in a clockwise direction

Dextro or D form spells CO-R-N in an anti clockwise direction

Question 4

What does the carboxylic group on amino acid behave as?

Answer 4

Proton donor - it becomes ionised and forms a negative charge COO-

Question 5

What does the amino group on an amino acid behave as?

Answer 5

Proton accepter - it ionises and forms a positive charge NH3+

Question 6

A molecule that is charged but that the charged groups balance to have no overall net charge is termed a …?

Answer 6

Zwitterion

Question 7

Amino acid residues in a polypeptide are normally arranged in a trans configuration such that the variable side chain is alternately orientated and the cis arrangement is in fact less energetically stable.

true or false?

Answer 7

True - cis arrangement is less energetically stable. Because of this rarely in 0.1% of polypeptides are the amino acids and thus the R groups arranged in cis arrangement where the side chain is located on the same side. The arrangement as you can see also comprises of a invariable repearting unit of amide (NH), alpha carbon and carbonyl groups (C=O) joined by the peptide bond.

Question 8

Describe the primary structure of proteins

Answer 8

Covalent bonds forming polypeptide chain

Question 9

Describe the secondary structure of proteins

Answer 9

Regular folding form

Question 10

Tertiary structure?

Answer 10

Overall 3D shape

Question 11

Quaternary structure?

Answer 11

Organisation of polypeptides into assemblies

Question 12

There are three secondary structural folds including the alpha helix and beta sheets which enable the formation of complex tertiary structures the other is a…?

Answer 12

• turn
• beta turn
• beta bend
• Beta turns are short loops that allow the change of direction of the protein backbone.
• A beta turn allows a 180 turn and is stabilised by a hydrogen bond between amino acids comprising the turn ie residue 1 and 4 of the chain, this is the same as one amino acid and the next three amino acids along the chain

Question 13

Some proteins require cofactors to perform their normal function. Give some examples of proteins and their cofactors.

Answer 13

Nicotinamide adenine dinucleotide (NAD/NADH) in the reduction of Pyruvate to Lactate by Lactate dehydrogenase

Zinc in the hydration of carbon dioxide by carbonic anhydrase to produce bicarbonate ions

Heme in the binding of oxygen to hemaglobin

Vitamin K in the carboxylation of glutamic acid residues during clotting

Question 14

There are a number of commonly used techniques to understand and determine protein structure. These include:

Answer 14

• cryoelectron microscopy
• circular dichroism
• x-ray defraction crystallography
• nuclear magnetic resonance

Question 15

Describe the hydrophilic and hydrophobic interactions in water soluble proteins / globular form

Answer 15

Hydrophilic residues mostly on the external surface.

Hydrophobic residues usually buried inside the protein.

Question 16

Describe the hydrophilic and hydrophobic interactions in membrane proteins

Answer 16

Membrane spanning regions have externally located hydrophobic residues that interact with the membrane lipids.
They may have hydrophilic central channels.

Question 17

Describe the structural and general nature of amino acids and how this influences the chemical properties of a protein

Answer 17

—

Question 18

Define the nature of the peptide bond and how this contributes to protein structure

Answer 18

-

Question 19

Describe the complexity of proteins and the requirement for some proteins to associate with with other complex molecules, cofactors or ions

Answer 19

-

Question 20

Define how the structural organisation of the polypeptide chain relates to its functionality and cellular location

Answer 20

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