amino acids, proteins and DNA

• What is the general structure of an α amino acid?

  NH2-CH-CO2H-R
• What is the simplest amino acid?

  Glycine
• Why are all amino acids except glycine considered chiral?

  They have four different groups around the carbon atom.
• What do amino acids do to plane polarized light?

  They rotate it.
• What classifies an amino acid as acidic or basic?

  Presence of an extra carboxylic acid or amine group on the R group.
• What is the IUPAC name for aspartic acid?

  1. aminobutanedioic acid
• What is the IUPAC name for glycine?

  (2-)aminoethanoic acid
• What is a zwitterion?

  A dipolar form of an amino acid with both positive and negative charges.
• Why do amino acids have relatively high melting points?

  Due to ionic interactions between zwitterions.
• What are the acidic and basic properties of amino acids?

  The amine group is basic and the carboxylic acid group is acidic.
• How do amino acids act as weak buffers?

  They gradually change pH when small amounts of acid or alkali are added.
• What happens to the extra carboxylic acid or amine groups on the R group in different pH conditions?

  They react and change form in alkaline and acid conditions.
• What does the alpha in ‘α’ amino acid signify?

  Both NH2 and COOH groups are joined to the same carbon.
• What are dipeptides?

  Simple combination molecules of two amino acids with one amide link.
• How many combinations can be made from two different amino acids in a dipeptide?

  Two possible combinations.
• What reactions can the carboxylic acid and amine groups in amino acids undergo?

  They can undergo the usual reactions of these functional groups.
• What happens to proteins when heated with concentrated hydrochloric acid?

  They can be hydrolyzed and split back into their constituent amino acids.
• How can the composition of a protein molecule be deduced?

  By using TLC chromatography after hydrolysis.

  
• What is the method for thin-layer chromatography of amino acids?

  1. Draw a pencil line on a TLC plate.
  2. Add drops of each amino acid solution.
  3. Place the plate in a solvent chamber.
  4. Allow the solvent to rise and mark the solvent level.
  5. Dry the plate and spray with ninhydrin.
  6. Calculate Rf values.

  
• What is the Rf value formula in chromatography?

  Rf value = distance moved by amino acid / distance moved by the solvent
• Why is it important to wear gloves during chromatography?

  To prevent contamination from hands to the plate.
• What happens when ninhydrin is sprayed on an amino acid and heated?


  Red to blue spots appear.
• Why are amino acids transparent and need ninhydrin for visualization?

  Because they cannot be seen without it.
• What is the significance of Rf values in chromatography?

  Each amino acid has its own Rf value for identification.
• What is the primary structure of proteins?

  The sequence of the 20 different naturally occurring amino acids joined by peptide links.
• What is the secondary structure of proteins?

  The folding of the polypeptide chain into α-helices or β-pleated sheets.

  
• How are hydrogen bonds involved in the secondary structure of proteins?

  They hold the α-helix and β-pleated sheets in shape.

  
• What is the tertiary structure of proteins?

  The complex folding of the secondary structure held by interactions between R-side groups.
• What are the types of secondary structures in proteins?

  • α-helix: R-groups point outward.
  • β-pleated sheet: Protein chain folds into parallel strands.

  
• What are the key features of proteins?

  • Polymers made from amino acids.
  • Linked by peptide (amide) bonds.
  • Have primary, secondary, tertiary, and quaternary structures.
• What are the interactions that stabilize tertiary structures of proteins?

  • Hydrogen bonds
  • Ionic bonds
  • Hydrophobic interactions
  • Disulfide bridges

  
• What is the primary structure of proteins?

  The primary structure is the sequence of 20 different amino acids joined by peptide links.
• What type of reactions join amino acids in the primary structure of proteins?

  Condensation reactions with peptide links.
• What are the two types of secondary structures in proteins?

  • α-helix
  • β-pleated sheet

  
• In the α-helix secondary structure, where are the R-groups located?

  The R-groups are pointed to the outside of the helix.
• How does the β-pleated sheet structure form?

  The protein chain folds into parallel strands side by side.

  
• What holds the β-pleated sheet structure in place?

  Hydrogen bonds between the H of –N-H group and the –O of C=O of amino acids further along the chain.

  
• What is the tertiary structure of proteins?

  The tertiary structure is the folding of the secondary structure into more complex shapes.
• What interactions hold the tertiary structure in place?

  Interactions between the R-side groups of distant amino acids, including hydrogen bonding, sulfur-sulfur bonds, and ionic interactions.
• How can hydrogen bonds form in the tertiary structure?

  Hydrogen bonds can form between two serine side chains in different parts of the folded chain.