Lecture 5.1: Proteins

Question 1

Proteins play crucial roles in virtually all biological processes, as:

Answer 1

• Catalysts – enzymes
• Transporters (e.g. O2, Fe)
• Structural support (e.g., collagens in skin and bone)
• Machines (e.g., muscular contraction and motion)
• Immune protection (e.g. immunoglobulins)
• Ion channels
• Receptors (for hormones, neurotransmitters, etc.)
• Ligands in cell signalling (growth factors etc.)

Question 2

What are proteins?

Answer 2

They are macromolecules (polypeptides) made of monomers called amino acids

Question 3

What is orientation of peptide bonds?

Answer 3

They are planar

Question 4

Ionization states of Amino Acids

Answer 4

Unionised State (NH2. COOH)
Zwitterion (NH3+, COO-)

Question 5

Ionization states of Amino Acids

Answer 5

Unionised State (NH2. COOH)
Zwitterion (NH3+, COO-)

Amino acids that lack an ionisable R- group exist as zwitterions when dissolved in water at pH 7.0

The relative amounts amount of the zwitterion, the fully protonated or fully deprotonated forms are dependent upon pH.

Question 6

How does pH of solution affect pKa?

Answer 6

If the pH of the solution < the group pKa value, then the group will be protonated

If the pH of the solution > the group pKa value, then the group will be de-protonated

Question 7

pKa values of ionizable side chains: positive pKa’s

Answer 7

Lysine 10.5
Arginine 12.5
Histidine 6.0

Question 8

pKa values of ionizable side chains: negative pKa’s

Answer 8

Glutamate 4.3
Aspartate 3.7

Question 9

What is the Isoelectric Point (pI) of a protein?

Answer 9

The isoelectric point of a protein is the pH at which the protein carries no net charge

Question 10

How does the pH of a protein affect Isoelectric Point?

Answer 10

If pH < pI protein is protonated
If pH > pI protein is deprotonated

Question 11

What size (in aa) are peptides/oligopeptides?

Answer 11

2-50 aa

Question 12

What size (in aa) are proteins?

Answer 12

50-34350 aa

Titin (a spring-like protein in skeletal muscle, 34350 aa, the largest human protein)

Question 13

Conjugated Proteins

Answer 13

Some proteins require the binding of non-polypeptide prosthetic groups in order to function

Question 14

Why are clinicians so interested in amino acids and proteins? (3)

Answer 14

Proteins are the building blocks of cells, and are the target for the majority of therapies (channels, receptors, antibodies)

Tertiary structure of proteins is determined by amino acid sequence (protein formation, drug binding thus treatment effectiveness)

Understanding acid-base disturbances (urinary, respiratory and CVS system)

Question 15

Protein Structure

Answer 15

Primary structure: The linear amino acid sequence of the polypeptide chain (covalent peptide bonds)

Secondary structure: Local spatial arrangement of the polypeptide backbone (H-Bonds, a-helix or beta pleated sheet)

Tertiary structure: Three-dimensional arrangement of all atoms in polypeptide (H-Bonds, Ionic Bonds, Disulphide Bridges)

Quaternary structure: Three-dimensional arrangement of protein subunits (multiple polypeptide chains, prosthetic groups)

Question 16

Which AA residues support the formation of alpha helix?

Answer 16

Small hydrophobic residues such as Ala and Leu are strong helix formers

Question 17

Which AA residues break the formation of alpha helix?

Answer 17

Pro acts as a helix breaker because the rotation around the N-Ca bond is impossible

Gly acts as a helix breaker because the tiny R-group supports other conformations

Question 18

β -sheet structure

Answer 18

In a β-strand R groups alternate between opposite sides of chain

Side-by-side arrangement of β-strands makes a β -sheet

Antiparallel β-sheet: adjacent β-strands run in opposite directions, with multiple inter-strand H-bonds stabilising the structure

Question 19

Globular Proteins (role, structure, properties)

Answer 19

Role: catalysis, regulation
Compact shape
Soluble in water
Several types of secondary structure

EXAMPLE: Haemoglobin

Question 20

Fibrous Proteins (role, structure, properties)

Answer 20

Role: structure/support, shape, protection
Long strands or sheets
Insoluble in water
Single type of repeating secondary structure

EXAMPLE: Collagen and α-keratin

Question 21

Collagen

Answer 21

Triple-helical arrangement of collagen αchains containing a ‘Gly – X – Y’
repeating sequence

H-Bonds stabilise interactions between α-chains (rope-like structure)

Covalent cross-links further-stabilise α-chains to allow the formation of collagen microfibrils (then fibrils and then fibres)

Question 22

Variety of Tertiary Structures of Globular Proteins

Answer 22

Motifs: folding patterns containing one or more elements of secondary structure (β-α-β loop, β-barrel)

Domains: part of a polypeptide chain that fold into a distinct shape. Often have a highly-specific functional role (calcium-binding domains of troponin C)

Question 23

Folding of water soluble proteins

Answer 23

Polypeptide chains fold to so that hydrophobic side chains are buried

Polar, charged chains are on the surface

Question 24

Folding of membrane proteins

Answer 24

Membrane proteins often show “inside out” distribution of amino acids (with
hydrophobic residues on the outside)

EXAMPLE: Aquaporins

Question 25

Forces involved in maintaining protein structure (6)

Answer 25

H-Bonds
Ionic Bonds
Disulphide Bridges (covalent bonds)
Van der Waals
Electrostatic interactions (salt bridges)
Hydrophobic effect

Question 26

What is Protein Denaturation?

Answer 26

Proteins are not very stable
Disruption of protein structure is known as denaturation
Caused by breaking of forces that hold proteins together

Question 27

What causes Protein Denaturation?

Answer 27

Heat (increased vibrational energy)
pH (alters ionisation states of amino acids- changes ionic/H-bonds)
Detergents/Organic Solvents (disrupt hydrophobic interactions)

Question 28

How do proteins fold?

Answer 28

All the information needed for folding is contained in the primary sequence

Some proteins need molecular chaperones to assist in folding (e.g. TRiC)

Question 29

What are the effects of mis-folded proteins?

Answer 29

Can cause disease

Diseases include but are not limited to: Transmissible spongiform
encephalopathies like Creutzfeldt-Jakob disease, Amyloidoses

Question 30

Creutzfeldt-Jakob Disease

Answer 30

Altered conformation of the normal human prion protein (PrP)

Question 31

Amyloidosis

Answer 31

Amyloidosis is a rare disease that occurs when an abnormal version of a protein, called amyloid, builds up in your organs and interferes with their normal function.

Question 32

Formation of amyloid fibres

Answer 32

• Mis-folded, insoluble form of a normally soluble protein is formed
• Highly-ordered with a high degree of β-sheet
• Core β-sheet forms before the rest of the protein
• Inter-chain assembly stabilised by hydrophobic interactions between aromatic amino acids

Question 33

How many amino acids are there in one turn of an α-helix?

Answer 33

3.6

Question 34

How can small, hydrophobic aromatic compounds can block the formation of amyloid fibrils?

Answer 34

Aromatic compounds have been shown to interfere with amyloid fibril formation by blocking the interaction of the aromatic side chains