protein structure and function

Question 1

describe the functions of proteins

Answer 1

They are functional products of the genome providing

→ CARRIER FUNCTIONS: trafficking oxygen

→METABOLIC FUNCTIONS: enzymes producing and utilising energy

→FORM PARTS OF THE CELLULAR MACHINERY: spliceosomes, ribosomes

→ MAKE UP STRUCTURAL SCAFFOLD: microtubules, nucleosomes

→SENSING MOLECULES: receptors and their ligands

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

why do all amino acids have D and L isomers and what is the exception?

Answer 3

All amino acids except for Glycine have the two isomers due to them being tetrahedral in arrangement and due to the α carbon being chiral.

Question 4

in what form are amino acids incorporated into proteins and what is the other form used for?

Answer 4

→All amino acids incorporated into proteins by living organisms are in the L-form.

→D-amino acid residues comprise cell walls in bacteria and are often used in therapeutics.

Question 5

what is a residue?

Answer 5

A residue is each repeating unit in a polypeptide chain.

Question 6

describe the four levels of structure in a protein

Answer 6

→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 7

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

Answer 7

→ 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 8

describe the tertiary structure

Answer 8

→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 9

describe quaternary structure

Answer 9

→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 10

what are examples of two co-factors that proteins might need to work?

Answer 10

→FAD and NAD
→ Mg2+ and Zn2+
→haem in haemoglobin

Question 11

Describe water-soluble proteins

Answer 11

→Water-soluble proteins are often globular in shape.

→Some water-soluble proteins may arrange into: - filaments (actin) - tubes (tubulin) - coiled coils (cortexillin)

→The hydrophilic residues are mostly on the external surface while the hydrophobic residues are mostly buried inside.

→The membrane spanning region will have externally located hydrophobic residues that interact with membrane lipids.