Protein structure and function

Question 1

Digestive enzyme/catalytic proteins …

Answer 1

Break down nutrients in food into small pieces that can be readily absorbed

Question 2

Transport proteins …

Answer 2

Carry substances throughout the body in blood or lymph

Question 3

Structural proteins…

Answer 3

Build different structures, like the cytoskeleton

Question 4

Hormone signalling proteins…

Answer 4

Coordinate the activity of different body systems

Question 5

Immunological proteins…

Answer 5

Protect the body from foreign pathogens

Question 6

Contractile proteins…

Answer 6

Muscle contraction

Question 7

Storage proteins…

Answer 7

Provide food for the early development of the embryo or the seedling

Question 8

Toxins proteins…

Answer 8

Used by pathogens or other organisms to cause disease

Question 9

Primary Structure

Answer 9

The unique sequence of amino acids of a protein.

This is entirely driven by the DNA sequence of the gene encoding the protein. We can very simply deduce the primary structure of a protein knowing only the DNA sequence of a gene.

Question 10

Secondary Structure

Answer 10

Localized folding of the polypeptide driven by hydrogen bonding interactions within the polypeptide backbone. Two common types are:

βsheet
αhelix

Question 11

β sheets

Answer 11

Can be parallel or anti-parallel

Driven by H bonding between a backbone Amine (N-H)group on one strand, and a backbone Carbonyl(C=O) group on another strand

Question 12

α helices

Answer 12

• Right handed helix.
• Normally each turn is 3.6 amino acids with a pitch of 5.4 Å (0.54 nm).
• Driven by H bonding between a backbone Amine (N-H)group a backbone Carbonyl(C=O) group 3 or 4 residues earlier.
• Tightly packed with almost no free space within the helix.
• Side chains protrude out from the helix.

Question 13

Secondary structure

Answer 13

• Different amino acids have a propensity to favour structures.
• Large aromatic residues (tyrosine, phenylalanine, tryptophan) and β-branched amino acids (threonine, valine, isoleucine) are favoured in βstrands. •Methionine, alanine, leucine, glutamate, and lysine like to form helices. Proline and glycine don’t.
• Due to these propensities we can fairly accurately predict regions of secondary structure in a protein knowing only the sequence.

Question 14

Tertiary structure

Answer 14

• The three-dimensional shape of a protein – primarily driven by the chemistry of the side chains (R groups) and interactions between them.
• A range of non-covalent interactions -hydrogen bonding, ionic bonding, dipole-dipole interactions, and Van der Waals forces
• Ionic: Oppositely charged R groups attract. Like charges can repel
• HydrophobicR groups of nonpolar amino acids cluster in the interior of the protein.
• HydrophilicR groups lie on the outside surface of the protein to interact with water.
• In membrane-spanning proteins HydrophobicR groups may be outside interacting with the membrane lipids.
• Cystines can form covalent linkages with each other –Disulfide bond
• Thiol (S-H) groups are oxidized removing the H and forming a covalent linkage between the two Sulphur atoms.
• Strength: Disulfide > Ionic > hydrogen > Van der Waals

Question 15

Tertiary structure – Cofactors

Answer 15

• Some proteins (particularly enzymes) can coordinate a cofactor or “prosthetic groups” within the protein using the R groups
• This may be essential for the structure and/or function of the protein
• Metal ions (Mg, Mn, Zn, Fe, Ca), organic molecules (heme), or vitamins

Question 16

Quaternary Structure

Answer 16

• Some proteins are comprised of more than one polypeptide chain.
• Multiple folded proteins subunits.
• Driven by Ionic interactions, hydrogen bonding, hydrophobic interactions.
• May be dynamic.
• Homooligomersor Heterooligomers.

Question 17

Proteins can be loosely categorized into several types

Answer 17

Globular
Fibrous
Membrane proteins

Question 18

Globular…

Answer 18

Typically soluble in water
Often enzymes, transport, immune
Often irregular sequence and secondary structure
Moderate or no Quaternary Structure
Lower stability
Enzymes, Hemoglobin, antibodies

Question 19

Fibrous

Answer 19

Typically insoluble in water
Often structural
Often repetitive primary and secondary structure
High level of Quaternary Structure
Highly stable (e.g. heat, pH)
Keratin, Actin, collagen, silk

Question 20

Membrane proteins

Answer 20

• Traverse through a lipid bilayer (membrane)
• Transport, receptors, signalling, adhesion
• TM region –single α-helix or α-helical bundle
• Mitochondria and Gram-negative bacterial also have β-barrel TM proteins
• Generally high degree of non-polar (hydrophobic) amino acids
• Non-polar (hydrophobic) side chains face out toward the membrane
• Polar (hydrophilic) side chains face inwards

Question 21

Which relatively weak type of bond helps stabilise the three-dimensional structure of large molecules like proteins and DNA?

Answer 21

Hydrogen bond