Biochem-L1- Amino Acids and Peptide Bonds

why is protein structure important to study? explain an example

• structure of a protein determines the function- tissues, organelles and proteins and DNA

• carbon and diamonds have the same composition but the structure gives them different physical properties

how do we study proteins structure?

• x ray crystallography- shooting X-rays at molecules and look at the defraction pattern- see individual atoms- seen in NaCl

• NMR spectroscopy- works in solution and uses properties of atoms- determine distance

• light microscopy- cant see atoms

explain the central dogma

• DNA stores the information and RNA acts as a messenger

• ribosome reads 3 bp codons to add specific amino acids

• DNA is stable and proteins are chemically reactive and diverse

what is a chiral protein? what amino acid isn’t chiral?

a chiral protein is one that has a central atom and has 4 groups different attached to it. they cannot be superimposed, like hands have different parts can be flipped but won’t be the same.

• all aa are L form

• only glycine isn’t chiral

what is a zwitteron amino acid?

an amino acid, at physiological pH has both positive and negative charges

name the hydrophobic amino acids

• don’t donate H bonds

• - FAMILY VW

• non polar

• phenylalanine, alanine, methionine, isoleucine, leucine, tyrosine, valine, tryptophan

name the special cases of amino acids

GPC

• glycine- isn’t chiral

• proline- rigid ring and breaks helices

• cysteine- can form disulphide bonds

name the charged amino acids

DE RKH

• acidic- negatively charged

• aspartate, glutamate,

• basic- positively charged

• arginine, lysine, histidine

name the polar molecules

• uncharged

• STNQ

• serine, threonine, asparagine, glutamine

• form hydrogen bonds

what joins amino acids? how is a peptide bond formed?

dehydration reaction

• make a covalent bond with alpha carbonyl of 1 amino acid and the alpha nitrogen of a second amino acids

name the 3 polypeptide angles

omega

• C-N bond

• 180 degrees and is trans

• non rotatable

phi

• N-C alpha- rotatable

psi

• C alpha and C

• rotatable

what determines 3d structures?

each residue adopts a specific phi and psi angles which determines the 3D structure. forms alpha, beta turns

why is the peptide bond rigid? what happens then? what is this called?

as oxygen is very electronegative and pulls electron density towards itself. pulls electrons from the C=O bond and C-N bond. because of the electronegative of oxygen, C-N behaves like a partial double bond

OMEGA angle- 180 degrees

what is a dihedral angle?

A dihedral angle is a twist angle- 2 planes and 4 atoms. tells you how a chain twists to determine the 3D structure of a protein. psi and phi angles

what parts of a polypeptide CAN rotate? what does this determine

• Phi angle around N- alpha carbonyl

• psi angle around C alpha and C

• determines the 3D fold of the protein