Lecture 5.1: Proteins Flashcards
Proteins play crucial roles in virtually all biological processes, as:
• 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.)
What are proteins?
They are macromolecules (polypeptides) made of monomers called amino acids
What is orientation of peptide bonds?
They are planar
Ionization states of Amino Acids
Unionised State (NH2. COOH)
Zwitterion (NH3+, COO-)
Ionization states of Amino Acids
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.
How does pH of solution affect pKa?
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
pKa values of ionizable side chains: positive pKa’s
Lysine 10.5
Arginine 12.5
Histidine 6.0
pKa values of ionizable side chains: negative pKa’s
Glutamate 4.3
Aspartate 3.7
What is the Isoelectric Point (pI) of a protein?
The isoelectric point of a protein is the pH at which the protein carries no net charge
How does the pH of a protein affect Isoelectric Point?
If pH < pI protein is protonated
If pH > pI protein is deprotonated
What size (in aa) are peptides/oligopeptides?
2-50 aa
What size (in aa) are proteins?
50-34350 aa
Titin (a spring-like protein in skeletal muscle, 34350 aa, the largest human protein)
Conjugated Proteins
Some proteins require the binding of non-polypeptide prosthetic groups in order to function
Why are clinicians so interested in amino acids and proteins? (3)
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)
Protein Structure
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)
Which AA residues support the formation of alpha helix?
Small hydrophobic residues such as Ala and Leu are strong helix formers
Which AA residues break the formation of alpha helix?
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
β -sheet structure
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
Globular Proteins (role, structure, properties)
Role: catalysis, regulation
Compact shape
Soluble in water
Several types of secondary structure
EXAMPLE: Haemoglobin
Fibrous Proteins (role, structure, properties)
Role: structure/support, shape, protection
Long strands or sheets
Insoluble in water
Single type of repeating secondary structure
EXAMPLE: Collagen and α-keratin
Collagen
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)
Variety of Tertiary Structures of Globular Proteins
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)
Folding of water soluble proteins
Polypeptide chains fold to so that hydrophobic side chains are buried
Polar, charged chains are on the surface
Folding of membrane proteins
Membrane proteins often show “inside out” distribution of amino acids (with
hydrophobic residues on the outside)
EXAMPLE: Aquaporins
Forces involved in maintaining protein structure (6)
H-Bonds
Ionic Bonds
Disulphide Bridges (covalent bonds)
Van der Waals
Electrostatic interactions (salt bridges)
Hydrophobic effect
What is Protein Denaturation?
Proteins are not very stable
Disruption of protein structure is known as denaturation
Caused by breaking of forces that hold proteins together
What causes Protein Denaturation?
Heat (increased vibrational energy)
pH (alters ionisation states of amino acids- changes ionic/H-bonds)
Detergents/Organic Solvents (disrupt hydrophobic interactions)
How do proteins fold?
All the information needed for folding is contained in the primary sequence
Some proteins need molecular chaperones to assist in folding (e.g. TRiC)
What are the effects of mis-folded proteins?
Can cause disease
Diseases include but are not limited to: Transmissible spongiform
encephalopathies like Creutzfeldt-Jakob disease, Amyloidoses
Creutzfeldt-Jakob Disease
Altered conformation of the normal human prion protein (PrP)
Amyloidosis
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.
Formation of amyloid fibres
- 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
How many amino acids are there in one turn of an α-helix?
3.6
How can small, hydrophobic aromatic compounds can block the formation of amyloid fibrils?
Aromatic compounds have been shown to interfere with amyloid fibril formation by blocking the interaction of the aromatic side chains
