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CHAPTER 19. AMINO ACIDS AND PROTEINS. The Importance of Proteins …. Many functions in the body! (supportive, enzymes, hormones, antibodies…) Can be small or very large (hemoglobin: molar mass 64,000) Composed of individual amino acids. A. Proteins and Amino Acids.

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The importance of proteins l.jpg

The Importance of Proteins…

  • Many functions in the body! (supportive, enzymes, hormones, antibodies…)

  • Can be small or very large (hemoglobin: molar mass 64,000)

  • Composed of individual amino acids

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A. Proteins and Amino Acids

  • Amino acid: the building block of a protein

    • Contain two functional groups: amino (-NH2) and carboxylic acid (-COOH)

    • At physiological pH, the carboxyl group and the amino group are usually ionized

  • There are 20 naturally occurring amino acids. The R group gives each its unique characteristics.

  • Based on R group, amino acids can be classified as nonpolar, polar, acidic, or basic.

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20 Amino Acids…

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Now, let’s think.

  • The pI of cysteine is 5.1. Draw the predominant form of this amino acid at pH 1, and at pH 12. (you will have two different drawings!)

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Proteins and Amino Acids

  • Except for glycine, all amino acids are chiral.

  • We can also write Fischer projections for amino acids -- just place the carboxyl group (the most highly oxidized carbon) at the top.

    • L isomer: amino group on the left

    • D isomer: amino group on the right

  • In biological systems, only L amino acids are incorporated into proteins.

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B. Amino Acids as Acids and Bases

  • The form of the amino acid at physiological pH (with amino and carboxyl groups ionized) is called a zwitterion

  • For a given amino acid, there is a pH where the positive and negative charges are equal. This is called the pI -- isoelectric point. Here, the amino acid has a net charge = 0.

    • When the solution pH < pI, the -COO- group accepts a proton.

    • When the solution pH > pI, the -NH3+ group donates a proton.

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Zwitterions and pI

  • For polar and nonpolar amino acids, the pI is typically in the pH 5.0-6.0 range.

  • For acidic amino acids, the pI is around pH 3 due to the presence of a carboxyl group in the side chain

  • For basic amino acids, the pI is in the pH 7.6-10.8 range due to amino groups in the side chain

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  • A method to separate a mixture of amino acids (also used to separate mixtures of proteins and nucleic acids)

  • Place a mixture of amino acids in the center of a chamber between a positive and negative electrode. Start an electric current.

  • Amino acids with zero net charge will not move; those with a positive charge will migrate toward the negative electrode; those with a negative charge will migrate toward the positive electrode.

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An Electrophoresis Setup

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C. Formation of Peptides

  • Peptide: two or more amino acids linked together

  • Peptide bond: amide bond between the -COO- of one amino acid and the -NH3+ of another amino acid

  • In a long peptide chain, one end is called the N terminal, and the other end is called the C terminal

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Peptide Bond Between Gly and Ala

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Naming Peptides

  • Starting with the N terminus… name each amino acid in sequence with a -yl ending.

  • Until you get to the amino acid at the C terminus, and you use the full name of that amino acid.

  • Example: alanylglycylserine

    However… we typically use 3 letter abbreviations out of convenience (Ala-Gly-Ser)

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D. Protein Structure: Primary and Secondary Levels

  • Larger peptides are called proteins (usually >50 amino acids)

  • Primary structure refers to the sequence of amino acids in a protein.

  • The secondary structure refers to the first level of folding. The primary structure curls back in upon itself, initially in a few very regular patterns. The most common types of secondary structure = alpha helix, beta-pleated sheet, and triple helix.

  • Secondary: hydrogen bonds between backbone

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Alpha helix

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Beta pleated sheet

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E. Protein Structure: Tertiary and Quaternary Levels

  • Tertiary structure: additional folding above and beyond that of secondary structure. May involve:

    • Hydrophobic interactions between nonpolar R groups

    • Hydrophilic interactions between polar/ionized R groups and aqueous environment

    • Salt bridges between ionized basic/acidic R groups

      How might a change in pH affect this?

    • Hydrogen bonds between polar amino acid R groups

    • Disulfide bonds between R groups that contain sulfur (cysteine)

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Tertiary Structure in a Protein

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Protein Structure

  • Quaternary structure: protein consisting of two or more peptide subunits

    • Example: hemoglobin -- two alpha chains, two beta chains. Four chains all together.

    • Quaternary structure is held together by the same forces that hold tertiary forces together.

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An Example of Quaternary Structure

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Overview: Levels of Protein Structure

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Thought question…

What kind of interaction would you expect between a glutamic acid and a lysine, in the tertiary structure of a peptide?

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F. Protein Hydrolysis and Denaturation

  • A protein or peptide can be hydrolyzed into individual amino acids. (This is what happens in the stomach…)

  • Denaturation occurs when secondary, tertiary, or quaternary structure is disrupted. Primary structure is not affected. The protein unfolds “like a loose piece of spaghetti”.

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  • How do various denaturing agents work?

    • Heat breaks hydrogen bonds

    • Acids/bases protonate/deprotonate key areas, affecting hydrogen bonding and disrupting any ionic bonding

    • Organic compounds destroy hydrophobic interactions by forming their own hydrophobic interactions with the protein

    • Heavy metals disrupt ionic bonding and disrupt disulfide bonds

    • Agitation stretches polypeptide chains

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One more time… let’s think

What structural level of a protein is affected by denaturation? How is this different from the structural level of a protein affected by hydrolysis?

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