Amino acids, proteins and DNA

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

  NH2-CH-CO2H-R
• What does the R group in an amino acid represent?

  The R group can vary depending on the specific amino acid.
• What is the simplest amino acid?

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

  They have four different groups around the central carbon atom.
• What is the effect of amino acids on plane polarized light?

  Amino acids rotate plane polarized light.
• What are acidic and basic amino acids characterized by?

  They have 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 zwitterion form of an amino acid?

  A dipolar form where the amino acid has both positive and negative charges.
• Why do amino acids have relatively high melting points?

  Due to ionic interactions between zwitterions.
• What is the acidity and basicity of amino acids attributed to?

  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 attached to the same carbon.
• What are dipeptides?

  Simple combinations of two amino acids linked by one amide bond.
• 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 esterification and other typical 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. Remove the plate when solvent reaches near the top.
  5. Spray with ninhydrin and heat to visualize spots.
  6. Calculate Rf values.

  
• What is the Rf value formula in chromatography?

  Rf value = distance moved by amino acid / distance moved by 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 amino acids?

  Red to blue spots appear after heating.
• Why might some substances not separate well in chromatography?

  Because similar compounds have similar Rf values.
• What is the primary structure of proteins?

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

  It can form α-helices or β-pleated sheets.

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

  They hold the protein chain in α-helices and β-pleated sheets.

  
• What defines the tertiary structure of proteins?

  The folding of the secondary structure into complex shapes held by interactions between R-side groups.
• What is the primary structure of proteins?

  The primary structure is the sequence of 20 different amino acids joined by peptide links.
• How are amino acids joined in the primary structure of proteins?

  Amino acids are joined together by condensation reactions with peptide links.
• What are the two forms of secondary structure in proteins?

  • α-helix
  • β-pleated sheet

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

  The R-groups on the amino acids 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 hold the structure.
• 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 R-side groups in distant amino acids hold the tertiary structure.
• What types of interactions can occur in the tertiary structure?

  Hydrogen bonding, sulfur-sulfur bonds, and ionic interactions can occur.
• 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.
• What are ionic interactions in the context of proteins?

  Ionic interactions occur between acidic amino acids and basic amino acids.
• What is a zwitterion in amino acids?

  A zwitterion is formed by the transfer of a hydrogen ion from the -COOH to the -NH2 group.
• What is a sulfur bridge in proteins?

  A sulfur bridge is a covalent bond formed between two cysteine side chains.