Protein Structure Flashcards
Define secondary structure
Relationships between amino acids close in sequence
Is there rotation around the planar protein bond?
Does the other part of the chain have to be rhythmically flexible?
No rotation around planar protein bond // resonance gives partial double bond
Yes the other parts of the chain have to be rhythmically flexible
Which bonds in an amino acid are available for bonding?
Amine group ( Phi bond ) and Carboxyl group ( Psi bond)
Structure must have ____ between residues
Structures must have maximal number of stabilising forces between residues (H bonds)
Describe the structure of the Alpha helix
How long is a complete turn?
How many A per residues?
- 4 A per complete turn which is 3.6 amino acids
1. 5 A per residue
Describe the structure of the Alpha helix
Is the helix right or left handed?
Side chains point where?
Each side chain is how many degrees relative to its neighbour
N-C heliex is right handed
Side Chains point outwards
Each side chain is 100 degrees relative to its neighbour
What 2 amino acids can disrupt the folding of the alpha helix?
No Glycine or proline
What is the perfect helix’s phi and psi angles?
Phi- 60 degrees
Psi - 60 degrees
Why does proline disrupt the perfect alpha helix
The cyclic sidechain restricts rotation of angle phi (Φ) to about -50
There is no H atom on the N of the peptide bond and therefore this cannot H bond to
another peptide bond (X + 4) in the chain
Why does glycine disrupt the perfect alpha helix
Glycine does not have an alpha carbon so more flexible
What are the two types of beta sheets?
parallel ( C=O bonds to H) and antiparallel ( alternating C=O and N-H
Describe the Chou Fatma prediction for alpha structure?
For an α–helix, 4/6
contiguous residues
should have α–helix
values >100
Describe the Chou Fatma prediction for beta structure?
For a β-sheet 3/5
contiguous residues
should have β-sheet
values >100
What is the use of the Ramachandran Plot?
A plot with Psi on Y axis and Phi on the X with both from -180 to 180 degrees \+180 is when R-groups are at most extended • Plot bond angles of each residue following X-ray crystallography
Why is no structure sometimes important for proteins?
Disordered regions are highly important for
protein structure and function:
- Act to help bind ligands
- Connect two domains allowing flexible
linkages
- Intrinsically disordered proteins (IDPs) or
proteins with intrinsically disordered regions
(IDRPs) make up ~30% of the human
proteome
Name some examples of structural motifs
DNA binding
Helix-loop helix
EF hand
CA2+ binding
What is the relationship between cysteines and disulphide bridges
Cysteines are oxidised together to form a disulphide bridge.
Disulphide bridges are reduced to cysteines
What is the equation for the oxidation of cystines?
2 Cysteines-> cystine + 2H+ + 2e
What is the functional group of cysteine?
CO(CHCH2SH)NH
What is the disulphide bridge?
bond between the sulphur
Define tertiary structure?
folding of the polypeptide where the R groups interact
Is the tertiary structure thermodynamically stable and kinetically stable?
yes
Name 4 types of non-covalent bonds
and one type of covalent bond in the tertiary structure
Non covalent= hydrophobic interactions, hydrogen bonds, Van der Waal interactions, Electrostatic bonds
Covalent- disulphide bridge
What did the Anfisen Experiment show about proteins and folding?
The folded active form of a protein has the lowest free energy
All information to fold is in the primary structure
Some proteins require protein disulphide isomers which make and break disulphide bonds until correct confirmations are achieved
What is Levinthal paradox?
There are 99 peptide bonds and it would take 9.36 x10^77 years to sample every possible structure
What bonds occur in the protein molecule?
Hydrogen bonds/ Hydrophobic collapse
Pi bonds in aromatic proteins
Clusters of non polar amino acids are broken by what?
Organic solvents or denaturing enzymes
What is the prime driving force of protein interactions/.
Hydrophobic collapse
What is the relationship between Enthalpy change of the folded and unfolded state of the protein?
Delta H of the folded= unfolded
What is the relationship between Entropy change of the folded and unfolded state of the protein?
In water
in the protein
in H2O, entropy change of the unfolded< folded
in proteins, entropy change of unfolded > folded
Describe Pi-bond interactions in proteins
Also known as pi-stack of pi-overlap
Aromatic amino acids only
mixing of clouds of pi electrons
disrupted by heat
Hydrogen bonds
What bonds does this involve?
What breaks them?
Involves non charged R groups
Broken by heat, denaturing agents
Exposed H bonds are also disrupted by H20
What are electrostatic bonds between?
Charged residues either acidic or basic
Cysteine and tyrosine are also ionisable
Define pKa
the pH when 50% of the side chains have been ionised ( removed H+)
What equation links ph and pKA and concentration?
pH=pKa + log ( [A-] / [HA] )
What equation links A- H+ and HA
A- + H+ -> pH
Which two side chains absorb strongly at 280nm and can be used to measure protein concentration?
amino acids tyrosine and tryptophan have a very specific absorption at 280 nm, allowing direct A280 measurement of protein concentration.
