Protein Structure and Folding Flashcards
What are proteins?
Polypeptides - macromolecules made up of amino acids joined covalently to give the sequence of the protein
What does the folding of proteins depend on?
The physical and chemical properties of the amino acids
What determines the amino acid sequence of a protein?
The nucleotide sequence of a gene
What do amino acids consist of?
A central carbon atom covalently bonded to an amino group, a carboxyl group, a hydrogen atom and an R group
How many amino acids found in our body?
20
How are amino acids classified?
According to the chemical properties of the R groups
What is an amino acid residue?
An amino acid residue is what remains of an amino acid after it has been joined by a peptide bond to form a protein
What is the primary structure of a protein?
The linear amino acid sequence of the polypeptide chain
What is the secondary structure of a protein?
Polypeptide chains are organised into structures such as alpha helices and beta sheets.
What is the tertiary structure of a protein?
The overall 3D configuration of the protein with disulfide, ionic and hydrogen bonds
What is the quaternary structure of a protein?
Association between different polypeptides to form a multi-subunit protein
How are peptide bonds formed?
The linking of two amino acids is accompanied by the abstraction of a molecule of water - condensation reaction
What conformation will peptide bonds always exhibit?
Trans
What does the amino acid sequence of a protein determine?
The way in which the polypeptide chain folds and the physical characteristics of the protein
What is the isoelectric point of proteins?
This is the pH at which there is no overall net charge
What if pH < pI?
Protein is protonated
What if pH > pI?
Protein is deprotonated
What are fibrous proteins?
These proteins provide support, shape and protection.
- Long strands or sheets
- Single type of repeating secondary structure
Eg Collagen
What are globular proteins?
These proteins are involved in catalysis and regulation
- Compact shape
- Several types of secondary structure
Eg enzymes
How do water soluble proteins fold?
They fold so that hydrophobic side chains are buried and polar, charged chains are on the suface
What is the Pi of basic proteins?
> 7
Contain many positively charged basic amino acids
What is the Pi of acidic proteins?
< 7
Contain many negatively charged acidic amino acids
What happens if the pK value is less than the pH of the solution?
The group is deprotonated
What happens if the pK value is greater than the pH of the solution?
The group is protonated
For example, at physiological pH, is lysine (pK = 10.5) protonated or deprotonated?
Protonated because pK value (10.5) is greater than pH (7.4)
For example, at physiological pH, is aspartate (pK = 2.8) protonated or deprotonated?
Deprotonated because pK value (2.8) is less than pH (7.4)
What are conjugated proteins?
A conjugated protein is a protein that functions in interaction with other (non-polypeptide) chemical groups eg Haemoglobin (iron)
How many amino acids per turn of an alpha helix?
3.6
What is the pitch of an alpha helix?
vertical distance between consecutive turns of the helix
0.54nm
What stabilises the structure of the alpha helix?
Hydrogen bonds between N-H and CO
The backbone –C=O group of one residue is H-bonded to the –NH group of the residue how many amino acids away?
Four
Why does proline act as a helix breaker?
Because the rotation around the N-C bond is impossible
Why does glycine act as a helix breaker?
because the tiny R group supports other conformations
What are two strong helix formers?
Small hydrophobic residues such as Alanine and Leucine
How many nanometres are between adjacent amino acid in the extended conformation (beta strand)?
0.35nm (also R groups alternate between opposite sides of chain)
What do side by side arrangements of beta strands make?
Beta sheet
What is the native state of a protein?
A normally folded protein that is functional
What can break forces holding proteins together?
Heat - increased vibrational energy
pH - alters ionisation states of amino acids
Detergents/organic solvents - can disrupt hydrophobic interactions
Where is all the information needed for folding contained?
In the primary structure
What are amyloid fibres?
Could be misfolded, insoluble form of a normally soluble protein
Which forces are involved in maintaining protein structure?
Primary - Covalent (peptide)
Secondary - Hydrogen bonds and covalent
Teriary - Ionic, disulphide, hydrogen bonds, van der waals, hydrophobic
Quaternary - same as tertiary
What are disulphide bonds formed between?
Cysteine residues
What can disulphide bonds be broken by?
Reducing agents eg b-mercaptoethanol
What happens to most proteins with disulphide bonds?
They are secreted eg ribonuclease
What is the bond strength of disulphide bonds?
214 kJ/mol
What are electrostatic interactions formed between?
Charged groups
What is the bond strength of electrostatic interactions?
10-30 kJ/mol
What are hydrogen bonds formed between?
Formed between
electronegative atom and a
hydrogen bound to another
electronegative atom
What is the bond strength of hydrogen bonds?
10-30 kJ/mol
What is the bond strength of hydrophobic bonds?
~ 10 kJ/mol
What is the bond strength of van der waals?
4 kJ/mol
What are amyloidoses?
Amyloidoses are group of rare but serious conditions caused by deposits of abnormal protein, called amyloid, in tissues and organs throughout the body.
Why are some amino acid side chains charged at physiologcal pH?
Different side chains have different pK values at physiological pH
What does the pKa value of an amino acid side chain tell you about that chemical group?
Whether the amino acid is protonated or deprotonated - if the pKa value is low, the chemical group is more acidic so becomes deprotonated, if the pKa value is high, the chemical group is more basic so becomes protonated.
For example, the side chain of histidine can exist in two different ionized forms. The pKa for the equilibrium between the protonated and deprotonated forms of histidine (pkR) is appoximately 6.0. Which is the predominant form of histidine and physiological pH?
pKr is lower than the pH so there are less hydrogen ions in the mixture. Histidine therefore gives up hydrogen ions in an attempt to restore equilibrium so becomes deprotonated.
pKa less than pH so deprotonated is the predominant form
At pKa of 6.0, there will be equal amount of the protonated form (on the left) and deprotonated form (on the right). If we add more H+ ions (decrease pH) the equibilbrium shifts to the left and the pprotonated form predominantes. If we take away H+ ions or add OH- ions equibilibrium shifts to the right and the deprotonated form predominates.
The protein serum albumin has an isoelectric point of 5.0. If this protein was placed in an electric field at physiological pH, would it move towards the positive or negative electrode?
Physiological pH = 7
No net charge at pH of 5
Low pI is acidic so it has a negative chage
Therefore it moves to the positive electrode
Histones have an isoelectric point of 10.8. What charge will they have under physiological conditions?
Isoelectric point (10.8) is higher than pH (7)
Protein is more basic as solution is more acidic
Histones take H+ ions from solution, become protonated
Positively charged
