Amino Acids

Principle of Macromolecular Organisation.

Concept 1: Biopolymers are formed from monomeric units.

• proteins from amino acids
• nucleic acids from nucleotides

Concept 2: macromolecules have different orders of structure.

• primary structure is the sequence of monomers
• secondary structure is the local folding of the primary structure
• tertiary structure is the 3-D folding of the macromolecule

Concept 3: Macromolecules associate non-covalently to form supramolecular structures, organelles, cells.

What are the biological function of proteins?

• enzymes, biological catalysts
• transport (myoglobin, hemoglobin transport oxygen)
• storage proteins (seeds)
• structural components, support and shape, extracellular matrix, tendons, cartilage, hair
• molecular motors (contraction, flagellae, muscle)
• regulation, information transfer, signals, hormones
• protection, defense (immunoglobulins, blood clotting)

What is the basic structure of an amino acid?

• They are alpha amino acids: they have a carboxyl group and an amine on the same C which is alpha to the carboxyl group, or the first C in the molecule.

How many amino acids are commonly found in proteins?

• 20

How many different classes of amino acid are there?

• charge-charge, acids and bases, -COO^-.....-NH3^+
• H-bond, electronegative atoms, -O-H...N-
• Dipole, electronegative atoms, >C=O
• induced dipole, van der Waals, hydrophobic interactions

• Three: they are classified by polarity
  • non-polar, hydrophobic group, containing aliphatic and aromatic groups
  • uncharged but polar group, containing either hydroxyl or amide groups
  • charged group, containing extra carboxyl or amine groups

Why do amino acids all have the same properties?

• Because they all have a-amine and a-carboxyl groups
• they all have the same acid and base properties
• they are all ampholytes, and buffers.

Why do amino acids all have different properties?

• Because they all have different side chains, differencies in polarity

What are the properties shared by all amino acids?

• optical properties
• acid and base, ampholytes, buffers

Why do amino acids have optical properties?
What is the structural feature that bestows optical properties?

• The alpha C is chiral, asymmetric -- it has different groups attached to each of its 4 bonds

What would be the structure of an amino acid without optical properties?
Which amino acid does not have optical properties?

• it would not have a chiral C, it would have the same two groups attached to the alpha-C
• glycine is the only amino acid that does not have optical properties (R = H). It's structure is NH2-CH2-COOH

How many titratable protons do amino acids contain?
What does the titration curve look like?

• All amino acids have at least 2: some amino acids have 3.

Why do amino acids all have different properties?

• The side chains are all different and impart different and unique physical and chemical properties to each amino acid.
• These differences are based on polarity.
• This will have important consequences for protein function, the binding of other molecules through non-covalent bonds.
  • important in protein function
  • acidic and basic properties important in catalysis
  • non-covalent interactions important in binding molecules

• alanine (R = hydrophobic methyl group)
• asparagine (R = polar but uncharged amide group)
• aspartic acid (R= charged carboxylic acid group)

What are some examples of modified amino acids or derivatives?

• Some are found in proteins, but modified after the protein is assembled.
  blood clotting, structure, seleno-cysteine
• Others modified to act as signal molecules: amines
  Histamine (allergic response) derived from the amino acid histidine
  Epinephrine (adrenaline, fight-or-flight hormone) derived from the amino acid tyrosine
• Others are products of metabolism:
  homocysteine, high serum concentrations correlate with an increased incidence of heart attacks (myocardial infarction)

Reprise: Principle of Macromolecular Organisation.

• Concept 1: Proteins are formed from amino acids.

Two amino acids are linked by an amide bond or peptide bond.
What is a peptide bond?
What are the functional groups involved in its formation?

• condensation of an acid with an amine gives an amide
• for 2 amino acids --> dipeptide, and multiple amino acids --> protein
• R-COOH + H2N-R' <--> R-CO-NH-R' + H20
• when an amide link joins two amino acids it is called a peptide bond.

Draw a peptide bond in a dipeptide

• 2 amino acids form a dipeptide
• 3 amino acids form a tripeptide
• several amino acids form an oligopeptide
• many amino acids form a protein
• an oligopeptide has an ill defined 3-D structure, whereas a protein has a well defined 3-D structure

Note there are two regions to the peptide bond:

• constant region, which is the peptide bond itself
• variable regions, which are the side chains (R = hydrophobic, polar, charged)

Note that peptides have polarity, a vector

• they have an N-terminal end with a free alpha-amine group and a C-terminal end with a free alpha-carboxyl group.
• nucleic acids also have a vector, a 5-end and a 3-end to the phosphodiester backbone

What are the characteristics of a peptide bond?

• From our study of essential chemistry:
  • double bond character
  • planar
  • restricted rotation
  • trans

Principle of Macromolecular Organisation.

• Concept 1: Biopolymers are formed from monomeric units: proteins from amino acids.
  • All macromolecules have constant and variable regions:
    the constant zone gives rise to regular repeating structures,
    the variable zone, irregular and unique structures.
  
  
• Concept 2: macromolecules have different orders of structure.
  • primary = sequence of monomers
  • secondary = local folding,eg double helix
  • tertiary = 3D-folding of the macromolecule
  
  
• Concept 3: Macromolecules associate non-covalently to form supramolecular structures, organelles, cells.

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Bich 107 lecture notes on Amino Acids were last updated 09/25/03

Comments to Martyn Gunn