CHAPTER 19CHAPTER 19AMINO ACIDS AND PROTEINS

The Importance of ProteinsThe 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 AcidsA. 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 ionizedThere 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.

20 Amino Acids20 Amino Acids……

Now, letNow, let’’s think.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!)

Proteins and Amino AcidsProteins 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.

B. Amino Acids as Acids and BasesB. 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.

Zwitterions and pIZwitterions 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

ElectrophoresisElectrophoresis

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.

An Electrophoresis SetupAn Electrophoresis Setup

C. Formation of PeptidesC. 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

Peptide Bond Between Gly and AlaPeptide Bond Between Gly and Ala

Naming PeptidesNaming 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: alanylglycylserineHowever… we typically use 3 letter abbreviations out of convenience (Ala-Gly-Ser)

D. Protein Structure: Primary and D. Protein Structure: Primary and Secondary LevelsSecondary LevelsLarger 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

Alpha helixAlpha helix

Beta pleated sheetBeta pleated sheet

E. Protein Structure: Tertiary and E. Protein Structure: Tertiary and Quaternary Levels 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)

Tertiary Structure in a ProteinTertiary Structure in a Protein

Protein StructureProtein 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.

An Example of Quaternary An Example of Quaternary StructureStructure

Overview: Levels of Protein Overview: Levels of Protein StructureStructure

Thought questionThought question……

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

F. Protein Hydrolysis and F. Protein Hydrolysis and DenaturationDenaturationA 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”.

DenaturationDenaturation

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

DenaturationDenaturation

One more timeOne more time…… let let’’s thinks 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?