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Proteins. Proteins are long polymers made up of 20 different amino acid monomers They are quite large, with molar masses of around 5,000 g/mol to around 100,000 g/mol They have complex structures with unique 3-D shapes that determine their functions

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proteins
Proteins
  • Proteins are long polymers made up of 20 different amino acid monomers
  • They are quite large, with molar masses of around 5,000 g/mol to around 100,000 g/mol
  • They have complex structures with unique 3-D shapes that determine their functions
  • They are the most abundant organic compounds in the body, and also the most diverse in function
  • Proteins are involved in structure, transport, storage, metabolism, cell signaling and many other processes
amino acids
Amino Acids
  • Amino acids, as the name implies, have both an amine group and a carboxylic acid group
  • The 20 amino acids that make up our proteins have the amine group, the acid group, a hydrogen, and a variable group attached to a central carbon (called the  carbon)
  • The variable groups (called side chains) are what determine the individual characteristics of the amino acids

General structure of an amino acid:

acidic and basic amino acids
Acidic and Basic Amino Acids
  • Amino acids can be classified by the nature of the side-chain as acidic, basic, polar neutral or nonpolar
abbreviations for amino acids
Abbreviations for Amino Acids
  • Each amino acid has standard 3-letter and 1-letter abbreviations (shown in the table below)
d and l amino acids
D- and L-Amino Acids
  • All amino acids besides glycine are chiral
  • Each amino acid has two possible enantiomers

- these are classified as D or L as with sugars

  • Amino acids in nature are almost exclusively L-amino acids
  • When a Fischer projection is written with the acid at the top, and the R group at the bottom:

- if the amine group is on the right, it’s a D-amino acid

- if the amine group is on the left, it’s an L-amino acid

isoelectric points for amino acids
Isoelectric Points for Amino Acids
  • Because the amine group is basic, and the carboxylic acid group is acidic, amino acids often exist as zwitterions
  • A zwitterion is a dipolar ion with a net charge of zero
  • Because zwitterions act like salts, they have high melting points
  • The isoelectric point (pI) is the pH at which a zwitterion forms

- below pI the amino acid has a net positive charge

- above pI the amino acid has a net negative charge

  • Acidic amino acids have low pI values and basic amino acids have high pI values (due to side-chain ionization)
electrophoresis of amino acids
Electrophoresis of Amino Acids
  • Electrophoresis is a technique used to separate charged molecules with an electric field
  • The samples are loaded onto a support medium (usually an agarose or polyacrylamide gel) and separated by mobility

- mobility is affected by size, shape, charge and solubility

  • A buffered solution is used to conduct the charge and allow the charged molecules to move

- negatively charged amino acids move towards the anode (-)

- positively charged amino acids move towards the cathode (+)

peptides
Peptides
  • Peptides are two or more amino acids linked together by amide bonds (called peptide bonds)
  • A peptide bond is formed when the acid group of one amino acid reacts with the amine group of another amino acid
  • When writing the structure of a peptide:

- the amino acid with the free (unreacted) amine group is written on the left and is called the N terminal amino acid

- the amino acid with the free (unreacted) acid group is written on the right and is called the C terminal amino acid

  • Peptides are usually named using the 3- or 1-letter abbreviations for the amino acids, going from N terminal to C terminal
synthesis of peptides and proteins
Synthesis of Peptides and Proteins
  • In cells, peptides and proteins are synthesized using RNA catalysts (to be discussed in Chapter 22)
  • In the laboratory a variety of techniques are used

- most commonly the peptides are synthesized on resin beads using an automated peptide synthesizer

- smaller peptides, like dipeptides, are generally synthesized by hand in solution (not on resin)

- protecting groups must be used in order to prevent unwanted amino acid couplings

structure of peptide bonds
Structure of Peptide Bonds
  • Peptides are particularly stable and are also fairly rigid
  • This is due to the structure of the peptide amide bonds
  • Through resonance, the lone pair electrons on nitrogen and the pi electrons of the carbonyl are delocalized

- this gives some double bond character to the C-N bond, preventing free rotation around that bond

- this also makes the nitrogen less basic, since the lone pair is not very available for bonding, increasing peptide stability

primary structure of peptides and proteins
Primary Structure of Peptides and Proteins
  • A polypeptide containing 50 or more amino acids is usually called a protein
  • The primary structure of a protein is the sequence of amino acids in the peptide chain
  • The higher levels of structure, as well as the function, are derived from the primary structure

- even a single amino acid change can have drastic effects

  • For example, the nonapeptides oxytocin and vasopressin only differ in the amino acids at positions 3 and 8
insulin
Insulin
  • Insulin was the first protein whose primary structure was determined
  • Human, pig and cow insulin differ only at four amino acids
  • Bovine insulin (from cow pancreas) was used for diabetics, but now it’s made by genetically engineered E. coli
secondary structure of proteins the alpha helix
Secondary Structure of Proteins (the Alpha Helix)
  • The secondary structure of a protein indicates the conformation of the peptide chain in a given region
  • There are three main types of secondary structure: the alpha helix, the beta-pleated sheet and the triple helix

- all three are governed by hydrogen bonding

  • The alpha helix is coiled due to H-bonding between backbone N-H on one loop to backbone C=O group on next loop
  • The side chains are all on the outside of the helix, so larger side chain groups favor  helix
secondary structure of proteins the beta pleated sheet
Secondary Structure of Proteins (the Beta-Pleated Sheet)
  • Beta-pleated sheets consist of peptide chains side-by-side, held together by backbone H-bonding
  • All the side chains point out above and below the sheet

- smaller side chains favor -pleated sheets (larger ones would be too crowded)

secondary structure of proteins the triple helix
Secondary Structure of Proteins (the Triple Helix)
  • A triple helix consists of three peptide strands in a braid, held together by H-bonding, both backbone H-bonding and H-bonding between hydroxyl groups on adjacent peptide strands

- they contain large amounts glycine, proline, hydroxyproline and hydroxylysine that contain –OH groups for H-bonding

  • Triple helices are very strong, and are found in collagen, connective tissue, skin, tendons, and cartilage

- several triple helices can form a larger braid for increased strength

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