Proteins
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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

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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

  • 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


Functions of Proteins


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

  • Amino acids can be classified by the nature of the side-chain as acidic, basic, polar neutral or nonpolar


Polar Neutral Amino Acids


Nonpolar 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

  • 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

  • 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 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 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

  • 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

  • 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

  • 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 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)

  • 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)

  • 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)

  • 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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