Proteins Flashcards
Most proteins contain between _ and _ amino acids linked together via peptide bonds
50 and 200
What is the average molecular weight of an amino acid?
110
What is the average molecular weight of a protein (range)?
about 5,000 to 200,000
Peptide bonds form between _
The amino group of one amino acid and the carboxyl gorup of another
Oligopeptides are composed of up to
about 25 amino acid residues
What is the convention (lhs, rhs) in representation of polypeptide chains?
Free amino group to the left hand side
Free carboxyl group to the right hand side
Which configurartion is more common in polypeptide chains, trans or cis?
Trans. Hydrogen on amino grou opposite side of oxygen on carbonyl
What is the consequence of the presence of resonance structures in peptide bonds?
Conformational rigidity about that bond
What restricts the confromational range of torsion angles?
Steric hindrance
Which symbol represents the torsion angle of C-N bonds in polypeptides?
Phi
Which symbol represents the torsion angle of C-C bonds in polypeptides?
Psi
By convention, psi and phi are _ in a fully extended planar conformation
180 degrees
Psi an phi increase with
clockwise rotation
What kind of diagram shows the possible torsion angles?
Ramachandran plot
What structure contains informartion about crosslinks between amino acid residues like cysteine (disulfide bridges)
Primary structure
Crosslinks, such as disulfide bridges, are common in _, but rare in _
Common in extracellular prteins
Rare in intercellular proteins
Give an example of a protein with crosslinks between side chains of lysine residues
Collagen
Which structure represents the regular folding of regions of polypeptide chains?
Secondary
There are _ amino acids per turn of an alpha helix
3.6
A turn of an alpha helix covers a distance of _
0.54nm
In an alpha helix conformation, side chains are positioned _
On the outside of the helix
In an alpha helix arrangement, hydrogen bonding occurs between _
the carbonyl oxygen of each amino acid and the hydrogen on the amino group of the fourth amino away
In an alpha helix, the hydrogen bonds run _
parallel to the axis
Why is proline rarely found in alpha helical arrangements?
It cannot form the proper hydrogen bonding patterns due to its structure
The protein myoglobin has how many alpha helical structures along its polypeptide chain?
8
What function does proline have in alpha helices?
It changes the direction and terminates the helix
What quality of polypeptide chains forces the planarity/rigidity of the beta pleated sheet arrangement?
The rigidity of the peptide bond (due to resonance structure)
In beta pleated sheets, polypeptide chains are fully extended with a distance of _ between alpha carbon atoms
0.35nm
If enough polypeptide chains are involved, beta pleated sheets can close up to form _
A beta barrel
Describe the structure of silk fibroin
It has many stacks of antiparallel beta pleated sheets
What process can reverse the direction of chains and allow the connection of ends of antiparallel regions?
beta turns
Hydrogen bonds occur between _ in folded over beta pleated sheets
carbonyl group with the amino group of the 4th amino acid away
Which structure refers to the 3D spatial arrangement of proteins?
Tertiary
Give 4 interactions which stabilise the tertiary structure of proteins
Disulfide bonds between cysteine residues
Hydrogen bonds
Van der waals forces
salt bridges between oppositely charged side chains
Where are cysteine disulfide bonds usually formed?
In the oxidizing environment of the endoplasmic reticulum
In water soluble globular proteins, what is the ffect of hydrophobic forces on the structure?
Non polar regions are buried away from aqueous exterior
In beta pleated sheets, how are side chains positioned?
They protrude above and below the plane
In large proteins, chains may fold over and form distinc regions known as _
Domains
Domains are generally connected by _
Relatively unfolded sections
Give two examples of proteins with domains
Immunoglobulin(found in antibodies)
Zinc finger domain (DNA binding)
What does the quaternary structure refer to?
The spatial arrangement of polypeptide subunits and the interactions between them
What structure can be predicted from primary sequence of amino acids? What structure cannot?
Presence of alpha helices and beta pleated sheets can be predicted
Tertiary 3D native conformation cannot, special techniques must be used
Give 3 techniques used in determining the 3D structure of proteins
NMR spectroscopy
Cryoelectron microscopy
X-ray crystallography
What observation in x ray crystallography can be mathematically analysed in order to determine the 3D structure of proteins?
Diffraction patterns produced by the scattering of x-rays by a crystallized protein structure (aligned and rigid array of molecules)
What effect is measured in the use of NMR in determining protein structure?
The effect of radio frequencies on atomic spin. There is more perturbation in regions where atoms are closer together. Distance can be inferred
For what kind of protein is cryoelectron microscopy the mosr useful technique in determining structure?
Multi subunit proteins
For what kind of protein is NMR the most useful technique in determining structure?
Small proteins
Why is there no need for an external template in protein folding?
Proteins fold spontaneously, through ordered pathways which are encoded in the primary structure
What is the main driving force in protein folding?
Hydrophobic forces
Why can protein folding occur much faster in vivo than in vitro?
The presence of accesory proteins speeds up the process
What kind of mutations are unlikely to affect protein folding?
Alterations to surface residues - folding is driven mainly by internal residues
