L19: Amino Acid side chain and primary structure

• Who is the author of the LF130 Cellular and Molecular Biology course?

  1. Katrine Wallis
• What are the invariant groups of amino acids?

  Hydrogen, amino group, and carboxylic acid
• How many commonly found amino acids are there in proteins?

  20
• What are the classifications of side chains in amino acids?

  • Hydrophilic
  • Hydrophobic
  • Polar
  • Non-charged
  • Charged
  • Ionizable groups
  • Positive (basic)
  • Negative (acidic)
• What determines the solubility of proteins?

  The properties of hydrophilic amino acids
• What is the pKa value of Arginine?

  ~10.0
• What is the pKa value of Histidine?

  ~6
• At what physiological pH are Lysine and Arginine positively charged?


  At physiological pH
• What is the pKa value of Aspartic acid?

  ~4.4
• What are the two polar amino acids mentioned?

  Asparagine and Glutamine
• What is the significance of the rules of thumb regarding pKa?

  They indicate the buffering capacity of a solution
• How does Tyrosine behave in terms of hydrophilicity or hydrophobicity?

  It can be hydrophilic or hydrophobic depending on the context
• What is the significance of Cysteine in protein structure?

  Cysteine can form disulfide bonds, providing stability
• Where are hydrophobic amino acids typically found in proteins?

  In the center of globular proteins
• Which amino acid has a branched chain structure?

  Valine
• What is the difference between Phenylalanine and Tryptophan?

  Tryptophan has an indole ring, while Phenylalanine does not
• What are the properties of Glycine and Proline?

  • Glycine: smallest amino acid, provides flexibility
  • Proline: forms a 5-membered ring, "stiff" in proteins
• In which environment is cysteine more stable?

  In the hydrophobic core of a protein
• What key information should you know about the 20 amino acids?

  • Names
  • 3-letter code
  • 1-letter code
  • Structure
  • Properties
  • pKa values of ionizable groups
• What are the names and codes for the amino acids listed?

  • Glycine (Gly, G)
  • Alanine (Ala, A)
  • Valine (Val, V)
  • Leucine (Leu, L)
  • Isoleucine (Ile, I)
  • Methionine (Met, M)
  • Proline (Pro, P)
  • Threonine (Thr, T)
  • Serine (Ser, S)
  • Cysteine (Cys, C)
  • Histidine (His, H)
  • Arginine (Arg, R)
  • Phenylalanine (Phe, F)
  • Tyrosine (Tyr, Y)
  • Tryptophan (Trp, W)
  • Aspartic acid (Asp, D)
  • Glutamic acid (Glu, E)
  • Asparagine (Asn, N)
  • Glutamine (Gln, Q)
  • Lysine (Lys, K)
• How are the amino acids ordered in the previous slides?

  • Hydrophobic/hydrophilic
  • Polar/charged
  • Positive/negative
  • Aliphatic/Aromatic
  • Hydrogen bonding acceptors and donors
  • Ionizable groups
• What is the recommendation for memorizing amino acid structures?


  Memorize the structures of the amino acids
• What is the pKa value of cysteinyl residues?

  8.3
• What are the key aspects to know about the 20 amino acids?

  Names, 3 letter code, 1 letter code, structure, properties, and pKa values of ionizable groups
• What are the names and codes for the amino acids glycine, alanine, and valine?

  • Glycine (Gly, G)
  • Alanine (Ala, A)
  • Valine (Val, V)
• What are the names and codes for the amino acids leucine, isoleucine, and methionine?

  • Leucine (Leu, L)
  • Isoleucine (Ile, I)
  • Methionine (Met, M)
• What are the names and codes for the amino acids proline, threonine, and serine?

  • Proline (Pro, P)
  • Threonine (Thr, T)
  • Serine (Ser, S)
• What are the names and codes for the amino acids cystine, histidine, and arginine?

  • Cystine (Cys, C)
  • Histidine (His, H)
  • Arginine (Arg, R)
• What are the names and codes for the amino acids phenylalanine, tyrosine, and tryptophan?

  • Phenylalanine (Phe, F)
  • Tyrosine (Tyr, Y)
  • Tryptophan (Trp, W)
• What are the names and codes for the amino acids aspartic acid, glutamic acid, asparagine, and glutamine?

  • Aspartic acid (Asp, D)
  • Glutamic acid (Glu, E)
  • Asparagine (Asn, N)
  • Glutamine (Gln, Q)
• What is the one-letter code for lysine?

  K
• How were the previous slides ordered regarding amino acid properties?

  According to hydrophobic/hydrophilic, polar/charged, positive/negative, aliphatic/aromatic, and ionizable groups
• What is the pKa value of the amino group in lysine?

  Between 9 and 10
• What is the process of joining amino acids called?

  • Condensation reaction
  • Forms peptide bonds
  • Cleaved by hydrolysis
• What is the backbone structure of peptides and proteins?

  N-Cα-C-N-Cα-C
• What is the difference between a dipeptide, tripeptide, oligopeptide, and polypeptide?

  A dipeptide has 2 AAs, a tripeptide has 3, an oligopeptide has 2-50, and a polypeptide has more than 50 AAs
• What defines a protein?

  A protein is a polypeptide or complex of polypeptides that has attained a stable three-dimensional structure and is biologically active
• What happens to the amino and carboxy groups when amino acids are bound together?

  They disappear except for the N and C terminus, becoming amino acid residues
• How many dipeptides can be formed from 20 amino acids?

  400
• How many tripeptides can be formed from 20 amino acids?

  8000