Lecutre 7+8 Flashcards
The amide (peptide) bond
- amides may be formed by the reaction of the COOH group of one amino acid with the NH2 group of another
Peptide bond structure
- the amide nitrogen lone pair interacts with the C=O group
Two consequences
- amides are unreactive towards nucleophiles - hydrolysis requires heating with aqueous acid
- peptide bonds are rigid and planar
Peptides are…
Linear polymers of amino acids
Peptides directional sense and different ends
H2N- = N terminus
-COOH = C terminus
GLY = N terminus
ALA = C terminus
Bond rotation?
- bond rotation not possible about the amide bonds
- sequential a-C’s are usually in a trans relationship
Exeption to the possible rotation about the amide bonds
N of PROLINE
Peptide properties are defined by:
- terminal COOH and NH2 groups
- functional groups and physical character of side chains
- sequence of amino acid units
- gly-ala-ser-gly and gly-ala-gly-ser are different structures and have different properties
- for peptides and small proteins the molecules largely refueled the properties of the compete amino acids
Sickle cell anemia
- haemoglobin molecule uses are abnormal and have lower solubility causing haemoglobin to aggregate, causing red blood cells to distort/deform
- normal haemoglobin molecules are charged at physiological pH thus polar
- absnormal haeglobloin has been replaces by valine where it is non polar
Peptides are..
Too small to have a tertiary structure
Peptide or protien?
N>75 protien
N<75 peptide
4 levels of protien structure
Primary: sequence of aa’s
secondary: segments off structure along peptide chain e.g a-helix,turns,B-sheet
Teriary structure: how secondary structural elements fit together
Quanternary structure: how proteins or indipendent peptide chains come together
Why do peptides adopt secondary structures
- in aqueous environment =, the chain will adopt a configuration so as to expose the polar side chains (hydrophilic groups) and Burt the non polar side chains (hydrophobic groups) ie maximum favourable non-covalent interactions
- hydrogen bonding between amide links stablaises secondary structural elements
E.g - a-helix, B-sheet and well defines turns ( and off course water is competent for these H-bonding sites)
A-helicies and B-sheets
Self - disulphides bride
When the cystine residues are embedded in a peptide chain, the disulphides braindges may link otherwise remote parts of the molecule together
The structure of insulin e
- two otherwise Indipendent peptide chains joined together by disulphides bridges
Facts about peptide synthesis
- Fred Sanger
- two inidipendent peptide chains for a total of 51 amino acids
Peptide synthesis - how to selectively form only one produce
- TWO AMINO ACIDS CAN POTENTIALLY REACT TO FORM 4 POSSIBLE DIPEPTIDES (therefore protection needed)
- protect NH2 and COOH groups not required to react
- form peptide bond to combine protected amino acids
- remove protecting groups (deprotection
The synthesis of dipeptide Ala-Gly
BOC protects amino groups
Eserfying protects carbonyl groups
BOC- deprotected with mild acid
ESTERS - deprotected with base
Use ‘activator’ such as DCC to form a peptide bond between them
Specific steps in the synthesis of Ala-Gly
- make BOC-Ala (reaction one)
- make Gly-OMe (reaction two)
- react with DCC
- deprotect
Strategy for larger peptides
Why does peptide hydrolysis proceed with difficulty
- H20 is a poor nucleophile
- the C=O of an amide is unreactive towards nucleophiles
Can be achieved by heating with strong aqueous acid but even then the reaction proceeds slowly
General mechanism for amide hydrolysis in acid
- carbon cation intermediate is also resonance stabilised
- last step is irreversible
Protein digestion
- metabolism efficiently hydrolyses the peptide bonds to liberate amino acids - esp the ones we dont make
- this is achieved by low pH of our stomach
- effectiveness enzymes, proteases, that effect hydrolysis of the peptide bond e.g chymotrypsin and carboxypepridase
Proteases - base hydrolysis of an amide
Chymotrypsin
- a proteolytic enzyme (a serine protease) found in the digestive system of many organisms
- it catalyses the hydrolysis of peptide bonds, spefically the peptide bond on the carbonyl side of an aromatic - benzine like amino acids
How does chymotrypsin recognise aromatic ring
- chymotrypsin has a hdrophobic binding packer to recognise the aromatic ring (will also accept large hydrophobic R groups)
- thus I ding sire positions the peptide bond for preaccessing at the active site which contains a ‘ catalytic triad’
The catalytic triad at the active site of chymotrypsin
Chymotrypsin mechanism
Carboxypeptidase A
- a protease
- recognised carboxylare of the C terminal and hydrolyses ajecnet peptide bond - effectively clips off the C-terminal residue and exposes the next one for processing
- example of metalloenzyme, with Zn2+ playing an integral role at the active site
3 key factors of carboxypeptidase
- reactants are held close together
- Zn2+ makes C=O more susceptible to nucleopphillci attack
- H20 is deptrotoated to make better nucleophile
End of carboxypeptidase mechanism
- following merchandise allows us to get a tetrahedral intermendiate
- the slow step of the reaction is made much faster
- this then leads to the breaking of the C-N bond liberating he C-terminal amino acid and exposes the next amino acid
Why is the OH group if tyrosine able to act as a proton donor
- usually to proton of an alcohol group is not acidic
- however the OH group of tyrosine is attached to a benzene ring and this influences it’s acidity and reactivity thus having a lower pKa
Why is phenol acidic
- OH of phenol more acidic then aliphatic alcohol is due to the realities stability of its conjugate base due to resolve cue stablismation
Basicity of benzene type amines
