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
What are conjugated proteins?
Have covalently linked chemical components in addition to amino acids
What holds the primary structure together
Covalent bonds
Angles determine the conformation of the peptide backbone and hence the fold of the protein
What bonds are found in the alpha helix
Hydrogen bonds between N-H and C=O stabilise the structure.
The backbone -C=O group of one residue is H bonded to the -NH group of the residue 4 amino acids away
What affects the stability of the alpha helix?
Not all polypeptide sequences adopt a-helical
structures
• Small hydrophobic residues such as Ala and Leu are strong helix formers
• 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
Describe the arrangement of a beta strand
Beta strand:
Fully extended conformation
0.35nm between adjacent amino acids
R groups alternate between opposite sides of chain
What are the 2 types of beta pleated sheet?
Antiparallel b-sheet: adjacent b-strands run in opposite directions, with multiple inter-strand H-bonds stabilizing the structure - r groups on opposite side
Parallel b-sheet: strands run the same way, kinked H bonds
Describe fibrous proteins and give an example
Role - support, shape, protection
Long strands or sheets
Single type of repeating secondary structure
E.g. Collagen
Describe globular proteins and give an example
Role - catalysis, regulation
Compact shape
Several types of secondary structure
E.g. Carbonic anhydrase
Give examples of various tertiary structures o globular proteins
Beta-alpha-beta-loop
Beta barrel
Define motif
Motifs - folding patterns containing 1 or more elements of secondary structure
Define domains
Part of a polypeptide chain that folds into a distinct shape - often has a specific functional role
Describe the folding of water soluble proteins
Polypeptide chains old so that hydrophobic side chains are buried and the polar charged chains are on the surface
Describe the folding of membrane proteins
Often show inside out distribution of amino acids
