Protein chemistry Flashcards
Amino acid residue
Chemical groups left behind after two or more amino acids have undergone condensation reactions
Amino terminus
End of a protein whose amino acid has not condensed with a carboxyl group (H3N+) (on the left)
Carboxyl terminus
End of a protein whose carboxyl group has not undergone condensation (COO-) (on the right)
Peptide
Short protein
Peptide bond
Another name for the amide bond found in a protein
Peptide backbone
All of the amide bonds and the alpha carbon atom in a peptide (everything except ‘R’ groups/sidechains)
Sequence
Order of arrangement of amino acid residues in a protein, from amino to carboxyl terminal
Primary structure
Order of amino acid residues (sequence)
Amino acid structure
Carboxylic acid group, Amine group, Alpha carbon (attached to both the amine and carboxylic acid group- protein backbone), ‘R’ group- substituent that makes each amino acid different (eg. alanine has a methyl group, sidechain)
Acid and base reaction of amino acids
Acid + base —> salt + water, Acting as an acid the H+ is taken from the COOH group making COO-, Some are diprotic meaning you need 2 moles of base to react, Acting as a base the H+ is added to the H2N group making H3N+ (put + on top of N), Some have more than one amine meaning you need 2 moles of acid to react
Zwitterion (dipolar salt)
When both a positive and negative charge are present making the overall charge 0, Amino acids can be an acid and base at the same time as they groups involved are on different functional groups, Around pH of 7, High melting and boiling point
Aliphatic side chain
Hydrophobic, CH3 group, non-polar, dispersion forces
Basic side chain
NH2 group, ionic bonds, can accept a proton
Neutral side chain
amide group, polar, dipole-dipole, hydrogen bonding and dispersion forces
Acidic side chain
Can donate a proton, can make ionic bonds with a basic side chain
Cysteine and sulfur side chains
Cysteine can make a covalent bond with another cysteine side chain, Sulfur makes the side chain polar
Types of side chains
Aliphatic, basic, neutral, acidic, aromatic
Forming proteins
Amino acids undergo a condensation reaction (endothermic reaction, water is a product) , n Amino acids —> 1 protein + n-1 H2O, Acid-base chemistry of resulting protein is determined by the amino terminus, carboxyl terminus and functional groups on the ‘R’ portions of its amino acid residues
Primary structure
Sequence of amino acid residues coded by the DNA in living systems, Involves covalent bonds in the peptide (amide) bonds between amino acid residues
Secondary structure
Caused solely by the hydrogen bonding between the oxygens and nitrogens in the amide bond (backbone), Nature of the R group (it its bulky and prevents movement of the peptide chain) affects the type of secondary structure present
Types of secondary structure
Alpha helix, beta sheet (parallel), antiparallel beta-sheet, random coil
Alpha helix
Formed when residues in the same region of a peptide undergo hydrogen bonding, Oxygen atoms from an amide bond form hydrogen bonds with a NH4 amino acid residues further along the chain
Beta pleated sheet
Occurs when there is hydrogen bonding between =O and HN- on the peptide backbone of the protein, Hydrogens and oxygens on ‘R’ groups don’t participate in beta sheet formation as they are in the wrong geometric plan to do this, Two forms: Parallel- where the hydrogen bonds are zig-zag, Anti-parallel- where hydrogen bonds line up straight (more stable as there is less stress on the hydrogen bonds)
Random coil
“No” secondary structure, No hydrogen bonds
