MCGB - Protein Structure And Function Flashcards
What is a polypeptide?
Macromolecules made up of amino acids (which are joint covalently).
What encodes the amino acid sequence of a protein?
The nucleotide sequence of a gene
What is the general structure of an amino acid?
Easier to draw this out - central carbon with a H, COOH, R and NH2 group all bonded to it
What does the base ionise to form?
NH2 and H+ form NH3+ (this is reversible)
What does the acid ionise to form?
COOH forms COO- and H+
Why are amino acids classified according to the chemical properties of the R groups?
All that is left of the amino acids once they have formed bonds is the side chains, so properties must be due to side chains.
What is an amino acid residue?
What remains of an amino acid after it has been joined by a peptide bond to forms protein
What is a pK value?
The logarithmic value of the dissociation constant, Ka, of a hydrogen atom present in a molecule.
If the pH of an amino acid solution is lower than the pK value then what will happen to the R group?
It will be protonated
If the pH of an amino acid solution is higher than the pK value then what will happen to the R group?
It will be deprotonated
Give some examples of positively charged R groups.
Lysine, arginine, histidine
Give some examples of negatively charged R groups.
Glutamate, aspartate
What is physiological pH?
7.4
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?
Local spatial arrangement of polypeptide backbone - eg helices
What is the tertiary structure of a protein?
Overall 3D configuration eg folding
What is the quaternary structure of a protein?
Association between different polypeptides to form a multi-subunit protein
What name is given to the bond where two amino acids are linked, accompanied by the loss of a molecule of water?
Peptide bond (condensation reaction)
True or false - peptide bonds are planar?
False
Why do peptide bonds always exhibit a trans configuration?
Otherwise “steric clashes” would occur - where atoms get too close and start to repel each other.
What are the folding of the polypeptide chain and the physical characteristics of the protein both determined by?
The amino acid sequence of the protein
What is the isoelectric point (pI) of a protein?
The pH at which there is no overall net charge.
If pH is lower than pI, what will happen to the protein?
Protein is protonated
If pH is higher than pI what will happen to the protein?
It will be deprotonated
True or false - peptides can vary hugely in size?
True - Titin, the largest in humans, has an Mr of almost 3 million
What sort of bond holds the primary structure of a protein together?
Covalent
Give one similarity between an alpha helix and a DNA helix.
They are both right handed helices.
What stabilises the structure of the alpha helix that forms the secondary structure of a protein?
H-bonds between N-H and C=O
Which two amino acids DON’T form alpha helices?
Proline (no rotation around bond) and glycine (R-group supports other conformations)
What is the other possible conformation for a secondary structure of a protein (other than alpha helix)?
Beta sheet (can be parallel or antiparallel)
What is the difference between globular and fibrous proteins?
Fibrous - long strands/sheets, single type of repeating secondary structure, for support/shape/protection
Globular - compact shape, several types of secondary structure, for catalysis/regulation
What are “motifs” and “domains” an example of in terms of proteins?
Tertiary structures of globular proteins
True or false - polypeptide chains fold so that hydrophobic side chains are buried and polar, and charged chains are on the surface?
True
Give some examples of proteins with quaternary structures.
Haemoglobin, ribosomes (and any more you can think of).
Which forces maintain the primary structure of a protein?
Covalent
Which forces maintain the secondary structure of a protein?
H-bonds
Which forces maintain the quaternary structure of a protein?
Covalent, ionic, H-bonds, van der Waals, hydrophobic
How strong are covalent bonds?
Very strong (214 kJ/mol)
Which is stronger - electrostatic interactions or hydrogen bonds?
They are about equal
Which is the weakest force involved in maintaining protein structure?
Van der Waals forces
What is the term used to describe disruption of protein structure?
Denaturation
Give some examples of things that can denature proteins.
Heat (increased vibrational energy), pH (alters ionisation states of amino acids and changes ionic/H-bonds), detergents/organic solvents (disrupts hydrophobic interactions)
True or false - protein binding is driven by the need to find the least stable conformation?
False - driven by desire to find MOST stable conformation.
What are amyloid fibres?
Misfolded, insoluble form of a normally soluble protein.
