Peptides Flashcards
What is a property structure of amino acids ?
- amphoteric
- charge variability = changes with pH
what is the isoelectric point ?
- the pH at which an amino acid has no net charge because it exists in its “zwitterion” form
- pH 6.5–7.5
properties of non-polar, neutral amino acids ?
- no charge on side chains
- no H bonding = no electronegative atoms
- not soluble in water
properties of polar neutral amino acids ?
- soluble in water, can form H bonds
properties of charged amino acids ?
- either positive or negative charge
- can form H and ionic bonds
- soluble in water
chirality of amino acids ?
- all amino acids except glycine have chiral α-carbon
- Only L amino acids are found in proteins.
- Most L amino acids have an absolute
configuration of S
what is the human protein atlas ?
- map showing all the known proteins in the body and how they are distributed in tissues and organs
how do acidic side chains affect the (pI) isoelectric point of an amino acid?
- lower the pI compared to average pka due to side chain adding extra -ve charge
how do basic side chains affect the pI point of an amino acid ?
- higher than the average of pKa for amine and acid groups as the side chain introduces extra +ve charge
what are 3 methods for separating amino acids ?
- pI separation by electrophoresis ( Nonpolar travel faster)
- Chromatography
- Ion exchange chromatography
How are peptides synthesized from α-halo acids?
- carboxylic acid to α-halo acids = Br2,PBr, H2O
- react with excess NH3
- halogen replaced by NH3+
How are peptides synthesized via Strecker synthesis ?
- aldheyde converted to imine (C=N) using NH3
- imine reacts with cyanide ion to form aminonitrile
- hydrolysis of aminonitrile to form amino acid (CN hydrolysed to COOH using HCl)
What is the peptide bond?
- covalent bond formed between the carboxyl group (–COOH) of one amino acid and the amine group (–NH₂) of another
Why is the peptide bond resonance-stabilized?
- delocalization of electrons between the carbonyl oxygen (C=O) and the amide nitrogen (–NH)
- lone pair of electrons on the nitrogen
How are electrons distributed in the peptide bond ?
- unequally
- greater electron density on the carbonyl oxygen
- higher electronegativity than N
what is the primary structure of a protein ?
- sequence of amino acids in polypeptide chain
What is the secondary structure of a protein ?
- localized folding patterns within the polypeptide chain
- stabilized by H bonds
- α-helix and β-pleated sheets
What is the α-helix (𝛼-helix), and how is it structured?
- right-handed spiral structure
- each C=O forms a H bond with the NH of the amino acid four residues earlier
What is the β-pleated sheet (𝛃-sheet) ?
- 2 or more lengths of the polypeptide chain lie parallel to each other
- R groups of the amino acids point above and below the sheets
- NH and C=O parts of the peptide bond point towards each other
- H-bonds between these sections
Ramachandran Plot
- way to visualise dihedral angles ψ against φ of amino acid residues in protein structure
- recognised that many combinations of angles in a polypeptide chain are forbidden because of steric collisions between atoms
What is the tertiary structure of a protein?
- final 3D shape, which is determined by the interactions between the R-groups
What are the four main types of interactions that stabilize the tertiary structure of proteins?
- Ionic bonds
- Hydrophobic interactions
- Hydrogen bonds
- Disulphide bridges (covalent)
What is the quaternary structure of a protein?
- two or more polypeptide chains interact
- Forces between these chains, SAME AS TERTIARY structure
What are the two categories of proteins based on quaternary structure, and examples?
- Fibrous proteins: long linear structures providing support and strength (e.g., collagen).
- Globular proteins: compact, spherical shapes and often have functional roles, such as enzymes or transport (e.g., hemoglobin).
What is protein denaturation ?
- loss of structure + activity due to disruption to interactions
- denaturation can be reversible or irreversible
