Lecture Eight - Amino acids and proteins II Flashcards
What are the names of the four sequential structures of amino acids to proteins?
Primatry structure (1°).
Secondary structure (2°).
Tertiary structure (3°).
Quarternary structure (4°).
How can one figure out the structure of a protein?
Need to know which amino acids are present.
Need to know the amount (or number) of each amino acid.
Need to know the order (sequence) in which they are arranged.
Describe the primary structure of a protein.
The sequence of amino acids in a polypeptide chain, read from the N-terminal amino acid to the C-terminal amino acid.
Sequences are now widely determine by mass spec but can also be elucifated via:
Amino acid analysis:
- Hydrolysis of the polypeptide, most commonly carried out suing 6M HCl at elevated temperature (all amide bonds are broken, all -S-S- links reduced).
- Quantitative analysis of the hydrolysate by ion-exchange chromatography.
What is cyanogen bromide?
Cyanogen bromide, BrCN, is specific for cleavage of peptide bonds formed by the carboxyl group of methonine.
What can enzyme catalysis be used for the hydrolysis of particular peptide bonds?
A group of protein cleaving enzymes can be used to catalyze the hydrolysis of specific peptide bonds. Often referred to as peptidases.
Enzyme - catalyzes hydrolysis of the peptide bond at the carboxyl end.
Trypsin - arginine, lysine.
Chymotrypson - phenylalanine, tryptophan, tyrosine.
What is a method of sequencing amino acids?
Use partial hydrolysis, which breaks peptides into smaller fragments.
Identify the fragments.
Fit the fragments back togehter.
Edman Degradation:
Most widely used method.
Idenifies the N-terminal end of the peptide by attaching a chemical marker.
N-terminal amino acid + marker split off and identified.
Process repeated.
Describe the secondary structure of a protein.
The secondary structure refers the ordered arrangements (conformations) of the amino acids in regions of the polypeptide. To understand this, we first need to look at peptide bond geometry.
The four atoms of a peptide bond and the two alpha carbons joined to it lie in a plane with bond angles of 120° about C and N.
To account for this geometry, Linus Pauling proposed that a peptide bond is most accurately represented as a hybrid of two contributnig resonance structures.
The hybrid has considerable C double bond N character and rotation about the peptide bond is restricted.
Which two conformations are possible for the secondary structre of a palanar peptide bond (secondary structure)?
Two conformatinos are possible for a planar peptide bond.
Vitrually all peptide bonds in naturally occurring proteins studied to date have the S-trans conformation.
To determine from models which conformations would be most stable, Pauling and Corey assume:
1) All six atoms of each peptide lie in the same plane and have the s-trans conformation.
2) There is hydrogen bonging between the N-h of one peptide bond and the C=O of another peptide bond.
Describe the alpha helices and beta pleated sheets of the secondary structure in a protein.
On the basis of model building, Pauling and Carey proposed that two types of secondary structure should be particularly stable.
The alpha helix and the beta pleated sheet.
Alpha helix: A type of secondary structure in which a section of polypeptide chain coils into a spiral, most ommonly a right-handed spiral.
There are 3.6 amino acids per turn of the helix.
Each peptide bond is s-trans and planar.
N-H groups of all peptide bonds point in the same direction, which is roughtly parallel to the axis of the helix.
C=O groups of all peptide bonds point in the opposite direction to the N-H bonf, and also parallel to the acis of the helix.
The C=O group of each peptide bond is hydrogen bonded to the N-H group of the peptide bond four amino acid units away fro it.
All R groups point outwards from the helix.
Describe the tertiary structure of a protein.
Tertiary structure is the overall folding pattern and arrangements of all the atoms.
This pattern is often held in 3D space by the -S-S- linkages.
Non-polar side chains point to the inside of the mulecule.
Polae side chains point to the outside, so these proteins may be water soluble.
Describe the quarternary structure of proteins.
SOme proteins, more complicated, have a fourth level of structure.
Quarternary (e.g. haemoglobin).
The arrangement of polypeptide chains into a non-covalently bonded aggregation.
Additional molecules may also be incuded (i.e. Haem).
- The makor factor stabilizing the aggragation of polypeptide subunits is the hydrophobic effect.
Hydrophobic effect = The tendancy of non-polar groups to cluster together in such a way as to be shieled from contact with an aqueous environment.
- If two polypeptide chains each have one hydrophobic patch, each patch can be shielded from contact with water if the chains form a dimer.
