Protein Structure Flashcards
Give some example of functions of proteins.
Catalysts (enzymes) Transporters (O2, Fe) Structural support (collagens in skin and bone) Machines (contraction and motion) Immune protection (immunoglobulins) Ion channels Receptors Ligands in cell signalling
What is the subunit of proteins?
Polypeptides
What is the subunit of polypeptides?
Amino acids
How are amino acids linked?
By covalent bonds
What is folding of a protein?
A polypeptide chain folds into a complex 3D structure that is highly specific.
What is folding determined by?
The chemical and physical properties of the amino acid.
What is the general structure of an amino acid?
An amino group (NH2) A carboxyl group (COOH) A hydrogen atom (H) A distinctive R group (side chain) and a carbon in the middle. All of these are joined by covalent bonds.
What different forms of an amino acids are there?
Unionised form and ionised.
What groups of the amino acid can ionise?
Both the carboxyl group and the amino group.
COOH and COO- + H+) and (NH2 + H+ and NH3+
What can be found at the N-terminal end of an amino acid?
The NH3+ amino group.
What can be found at the C-terminal end of an amino acid?
The COO- carboxyl group.
What is an amino acid residue?
What remains of an amino acid after it has been joined by a peptide bond to form a protein.
How can amino acids be classified?
Hydrophobic or hydrophilic
Polar or non-polar
Acidic or Basic or Neutral
Aliphatic or aromatic
What is pK values?
How likely something is to ionise.
If the pH of a solution is less than the pK value of the amino acid, what will happen?
The R-group of the amino acid will be protonated
If the pH of a solution is more than the pK value of the amino acid, what will happen?
The R-group of the amino acid will be deprotonated
Give some examples of amino acid with positively charged R groups.
Lysine
Arginine
Histidine
Give some examples of amino acids with negatively charged R groups.
Glutamate
Aspartate
What is the predominant form of lysine with a pK of 10.5 at physiological pH?
Lysine will be protonated since pH
What is the predominant form of Aspartate with a pK of 2.8 at physiological pH?
Aspartate will be deprotonated since pH>pK.
What are the different structures of proteins?
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
What is the primary structure?
The linear amino acid sequence of the polypeptide chain formed by covalent bonds and peptide bonds.
What is the secondary structure?
The alpha helix or beta-pleated sheet formation of proteins. Here hydrogen bonds come into play to make it stable.
What is the tertiary structure?
A spatial arrangement which involves the folding of alpha helices and beta-pleated sheets. They can be either fibrous like collagen or globular like myoglobin. This is formed by disulphide bridges and hydrogen bonds.
What is the quaternary structure?
When several of tertiary structures join together to form a complex.
How are two amino acids linked together?
By peptide bonds. The the carboxyl group and amino group (COO- and NH3+) join together. H2O is formed and released and a peptide bond between the C-N is formed.
Peptide bonds are rigid. What does this mean?
They have partial double bond characteristics so they are unable to rotate.
Do peptide bonds exhibit a trans or cis conformation?
Trans
Why is the amino acid sequence important?
Because it determines how the polypeptide chain will fold.
It determines the physical characteristics of the protein.
Explain what the isoelectric point (pI) of a protein is.
pI of a protein is the pH at which there is no overall net charge and equilibrium is achieved.
What value of pI do basic proteins have?
A pI > 7
What value of pI do acidic proteins have?
A pI < 7
What happens if pH < pI?
The protein is protonated
What happens if pH > pI?
Protein is deprotonated
Regarding secondary structure, what does proline do?
Proline acts as a helix break because the rotation around the N-C bond is impossible.
Regarding secondary structure, what does glycine do?
Glycine acts as a helix breaker because the tiny R-group supports other conformations.
What are strong helix formers?
Small hydrophobic residues such as alanine and leucine.
What are fibrous proteins?
Tertiary structures with the role of support, shape and protection.
Long strands or sheets
A single type of repeating secondary structure (either helix or beta-pleated sheets) like collagen.
What are globular proteins?
Tertiary structures with the role of catalysis and regulation.
A compact shape with several types of secondary structures.
Briefly describe the structure of collagen.
Fibrous protein with triple helical arrangement.
Contains a repeating sequence of Glycine - X - Y.
Hydrogen bonds stabilise interactions between chains.
How are water soluble proteins folded?
So that the hydrophobic side chains are buried and polar, charged chains are on the surface.
Give some examples of quaternary structured proteins.
Haemoglobin with 2 alpha subunits and 2 beta subunits
Ribosomes
What are the bonds of primary structure?
Covalent (peptide)
What are the bonds of secondary structure?
H-bonds
What are the bonds of tertiary structure?
Covalent, Ionic, disulphide, H-bonds, van Der Waals and hydrophobic (not really a bond).
What are the bonds of quaternary structure?
Covalent, ionic, disulphide, h-bonds, van Der Waals and hydrophobic (not really a bond).
How can proteins denature?
By excessive heat or pH altercation.
Also detergents and organic solvents can denature proteins by disrupting the hydrophobic interactions.
How does heat denature proteins?
Increased vibrational energy
How does pH denature proteins?
Alters ionisation states of amino acids and changes ionic/h-bonds.
What happens if there is protein misfolding?
This can cause disease such as Transmissible spongiform encephalopathies such as Creutzfeldt Jakob’s disease.
What is amyloidosis?
A group of diseases which involves misfolded proteins. For example an insoluble form of a normally soluble protein.
