Protein Structure Flashcards
Proteins are polypeptides; what are polypeptides?
Macromolecules made up of amino acids
Amino acids joined covalently to give the sequence of the protein
What determines the amino acid sequence of a protein?
The amino acid sequence of a protein is encoded by a gene
The nucleotide sequence of a gene determines the amino acid sequence of a protein
What does the folding of proteins depend on?
The polypeptide chain folds into a complex and highly specific three-dimensional structure, determined by the sequence of amino acids
The folding of proteins depends on the chemical and physical properties of the amino acids
Describe the structure of an amino acid
Amino acids consist of a central carbon atom (the a-carbon) covalently bonded to: • an amino group (-NH2) • a carboxyl group (-COOH) • a hydrogen atom (-H) • a distinctive R group (side chain)
Which two parts of an amino acid can ionise and how?
NH2 + H+ NH3+
COOH COO- + H+
Both the carboxyl and animo group can ionise
Define zwitterion
Molecule (esp AA) containing both a positively charged functional group and a negatively charged functional group
What are amino acids classified according to?
Chemical properties of the R groups - acid base behaviour determined by the R groups
What is an amino acid residue?
The part of an amino acid that remains after it has been joined by a peptide bond to form a protein
Name chemical properties of the R groups
Hydrophobic Hydrophilic Polar Non-polar Acidic Basic Neutral
Name physical properties of amino acids?
Aliphatic
Aromatic
What is Ka?
Acid dissociation constant
What is pKa?
-log Ka
The lower the pKa, the stronger the acid
When will a group of protonated/deprotonated in solution?
If the pH of the solution < the pK value then the group will be protonated
If the pH of the solution > the pK value then the group will be deprotonated
What is the primary structure?
The linear amino acid sequence of the polypeptide chain
What is the secondary structure?
Local spatial arrangement of polypeptide backbone - the conformation - e.g. Alpha helices/beta pleated sheets
What is the tertiary structure?
The overall 3D configuration of the protein
What is the quaternary structure?
Association between different polypeptides to form a multi-subunit protein
How is a peptide bond formed?
Condensation reaction: COOH of one AA forms bond with NH2 of another giving CONH and releasing H2O
Name properties of a peptide bond
Planar: C alpha, C, O, N, H and C alpha all lie in the same plane
Rigid: The C-N bond has partial double bond characteristics - unable to rotate - contributes to planarity
Exhibit a trans conformation: C alpha on opposite sides of peptide bond (cis would lead to steric clashes)
Bonds on either side of the peptide bond are free to rotate
What does the amino acid sequence o a protein determine
The way in which the polypeptide chain folds
The physical characteristics of the protein
What is the Isoelectric point?
The isoelectric point, pI, of a protein is the pH at which there is no overall net charge
I.e the pKa of entire protein
When are proteins protonated/deprotonated in terms of pI?
BASIC PROTEINS
pI > 7
Contain many positively charged (basic) amino acids
ACIDIC PROTEINS
pI < 7
Contain many negatively charged (acidic) amino acids
If pH < pI protein is protonated
If pH > pI protein is deprotonated
How long are peptides/ogliopeptides?
A few amino acids in length
How long are polypeptides/proteins?
Many amino acids - biologically active peptides and proteins come in a varying range of sized
Proteins are generally 100+AA
