Class 1 Flashcards
two common types of covalent bonds between amino acids in proteins
- the peptide bonds that link amino acids together into polypeptide chains
- disulphide bridges between cysteine R-groups.
how is a peptide bond formed?
peptide bond is formed between the carboxyl group of one amino acid and the alpha amino group of another amino acid with the loss of water
What is the backbone of the polypeptide?
NCCNCC
residue
an amino acid is termed residue when it is part of a polypeptide chain.
what do we know from thermodynamics about spontaneous reactions?
we know that free energy must decrease for a reaction to proceed spontaneously and that such a reaction will spontaneously move towards equilibrium.
Proteolysis
also known as proteolytic cleavage
it is the hydrolysis of a protein by another protein.
The protein that does the cutting is known as a proteolytic enzyme or protease.
Is proteolytic cleavage, a specific way of cleaving peptide bonds?
yes it is! Learn!
Many enzymes only cleave the peptide bond adjacent to a specific amino acid.
an example of trypsin cleavage is….
the protease trypsin cleaves on the carboxyl side of the positively charged (basic) residues arginine and lysine.
an example of chymotrypsin cleavage is…
chymotrypsin cleaves adjacent to hydrophobic residues such as phenylalanine.
What is Cysteine?
Cysteine is an amino acid with a reactive thiol (sulfhydryl, SH) in its side chain.
The thiol of one cysteine can react with the thiol of another cysteine to produce a covalent sulphur-sulphur bond known as disulphide bond.
Cystine Vs Cysteine
Once a Cysteine residue becomes disulphide-bonded to another cysteine residue , it is called cystine instead of cysteine.
Which is more oxidized, the sulphur in cysteine or the sulphur in cystine?
The sulphur in cysteine is bonded to a hydrogen and a carbon; the sulphur in cystine is bonded to a sulphur and a carbon (two hydrogens removed in the reaction).
Hence the sulphur is cystine is more oxidized.
antioxidants
Chemicals that prevent oxidation reactions
The inside of cells is known as a reducing environment because cells possess antioxidants. Where would disulphide bridges be more likely to be found, in extracellular proteins, under oxidizing conditions, or in the interior of cells, in a reducing environment?
In a reducing environment, the S-S group is reduced to two SH groups. Disulphide bridges are found only in extracellular polypeptides,where they will not be reduced. Examples of protein complexes held together by disulphide bridges include antibodies and the hormone insulin.
Primary structure :
The amino acid sequence
Secondary Structure :
Hydrogen bonds between backbone groups
Tertiary Structure :
Hydrophobic/ Hydrophilic interactions
Quaternary Structure :
Various Bonds Between Separate Chains
Denaturation
Denaturation refers to the disruption of a protein’s shape without breaking peptide bonds.
What denatures proteins?
Urea - which disrupts hydrogen bonding interactions
Extremes of pH
Extremes of Temperature
By changes in salt concentrations (tonicity)
Primary Structure description
- simplest level
- This is the linear ordering of amino acid residues
- Primary structure is the same as sequence
- The bond that determines the primary structure is the peptide bond
Secondary Structure
-Refers to the initial folding of a polypeptide chain into shapes stabilized by hydrogen bonds between backbone NH and CO groups.
What are the two most common secondary structures?
Alpha helix &
Beta-pleated sheet
How does hydrogen bonding occur in the Beta pleated sheets?
Hydrogen bonding occurs between residues distant from each other in the chain or even on separate polypeptide chains.
