Amino Acids, Peptides, Proteins, and Enzymes

Amino Acids

Amino acids are the building blocks of proteins.

 

Amino acid structure:

• Contain 2 functional groups:  an amino (-NH₂) group and a carboxylic acid (-COOH) group.
• R group = amino acid side chain.  This is what distinguishes one amino acid from another.
• If the amino group, carboxylic group, R-group, and hydrogen are bonded to a central carbon atom (a-carbon), they are termed a-amino acids.
• Only 20 different amino acids are present in the human body (TABLE 16.2).  Their names are abbreviated with 3 letters.
• All of the a-amino acids (except glycine) are chiral because the a-carbon is attached to 4 different groups.  In biological systems, only L-amino acids are incorporated into proteins.

Classification of amino acids:

• Nonpolar = contains an alkyl or aromatic side chain; hydrophobic
• Polar = have side chains with polar groups (e.g., -OH, -SH, -CONH₂, heterocyclic amines); hydrophilic
• Acidic  = side chains contain a carboxylic acid group
• Basic = side chains contain an amino group
• With the exception of proline, all amino acids are primary amines

Essential amino acids = cannot be synthesized by the human body and must be obtained from the diet.  The essential amino acids are:

Arg

His

Ile

Leu

Lys

Met

Phe

Thr

Trp

Val

 

 

Zwitterion structure:

• At the pH of most bodily fluids, the carboxyl group will loose H⁺ and the amino groups accepts an H⁺
• This is a dipolar form of the amino acid
• At a certain pH called the isoelectric point (pI), the positive and negative charges on the amino acid are equal (as in the diagram above), and the overall charge is zero. 
• In a solution that is more basic than pI, the -NH₃⁺ group will loose H⁺, and the overall charge will be negative.
• In a solution that is more acidic than pI, the -COO^- accepts an H⁺, and the overall charge will be positive.
• Zwitterioins for polar and nonpolar amino acids typically exit at pH values of 5.0-6.0
• Zwitterions for acidic amino acids typically exist at pH values of ~3
• Zwitterions for basic amino acids typically exit at pH 7.6-10.8

 

Peptides

The linking of 2 or more amino acids forms a peptide.

A peptide bond is an amide bond that forms when the –COO^- group of one amino acid reacts with the –NH₃⁺ group of the next amino acid.

·        The amino acid on the left end of a peptide with an unreacted free amino group is the N-terminal amino acid.

·        The amino acid on the right end of a peptide with an unreacted free carboxyl group is the C-terminal amino acid.

Classification of peptides:

·        Dipeptide = 2 amino acids linked together

·        Tripeptide = 3 amino acids linked together

·        Oligopeptide = 4-9 amino acids linked together

·        Polypeptide = 10-50 amino acids linked together

How to name a peptide:  Each amino acid beginning from the N-terminal is named with a –yl ending, followed by the name of the amino acid at the C-terminal.

Ala-Gly-Ser

Alanylglycylserine

 

 

Proteins

Protein = polypeptide chain of more than 50 amino acids.

Functions of proteins:

·        Structural components

·        Regulation of biological reactions

·        Oxygen transport

 

Structural levels of proteins:

·        Primary = amino acid sequence

·        Secondary = results from hydrogen bonding between peptide bonds along the chain.  There are 3 main types of secondary structures:

o       a-helix

o       b-pleated sheet

o       triple helix

·        Tertiary = folding of protein into a compact, 3-D shape.  Results from hydrogen bonding between R groups of amino acids.

o       Globular proteins = have compact spherical shapes.  Responsible for cell work.

o       Fibrous proteins = have long, thin, fiber-like shapes.  Responsible for structure of cells and tissues.

·        Quaternary = combination of 2 or more proteins to form a larger, biologically active protein.  Example = hemoglobin

Denaturation of a protein occurs when there is a disruption in any of the bonds that stabilize the secondary, tertiary, or quaternary structures.  The primary structure is not affected.  Proteins can be denatured by:

·        Heat = disrupts hydrogen bonds and hydrophobic attractions between R groups

·        Acids and bases = disrupt hydrogen bonds and salt bridges

·        Organic compounds = disrupt hydrophobic interactions between R groups

·        Heavy metal ions = disrupt disulfide bonds

·        Agitation = disrupts hydrogen bonds and hydrophobic interactions between R groups by stretching the polypeptide chain.

 

 

Enzymes

Catalyst = substance that increases the rate of a reaction by changing the way a reaction takes place, but the substance itself is not altered during the reaction.

Catalysts function by lowering the activation energy of a reaction.  The activation energy is analogous to a hill that must be climbed in order to reach a certain location.  The higher the hill the longer it takes to get over it.  FIGURE 16.13

Enzymes = biological catalysts that catalyze nearly al the chemical reactions that take place in the body.

The name of an enzyme describes the compound or the reaction that it catalyzes.  The names of all enzymes end in –ase.

Some classes of enzymes that you should be familiar with are:

• Oxidoreductases = catalyze oxidation-reduction reactions.
• Transferases = catalyze transfer of a group between 2 compounds.
• Lyases = catalyze the addition or removal of groups to a double bond without hydrolysis.
• Isomerases = catalyze the rearrangement of atoms in a molecule to form an isomer.
• Ligases = catalyze the formation of bonds between molecules using ATP. 

 

Models of enzyme action:

Most enzymes are globular proteins.

 

Substrate = group of molecules that fit the 3D shape of a particular enzyme; this is the substance the enzyme acts upon.

 

Active site = region of the enzyme to which the substrate binds.  It’s usually a small portion of the enzyme.  In the active site, the side chains of the amino acids interact with the side chains of the amino acids of the substrate.

 

Enzymes are very specific about the type of substrate they will bind—only a few substrates have the correct shape and/or amino acid sequence that will fit into the active site.

 

When the substrate and enzyme are properly aligned, they form an enzyme-substrate complex (ES).  This complex provides the alternate pathway that lowers the activation energy of the reaction.

Step 1                         E + S                          ES

 

Step 2                                                             ES                   E + P

 

Overall                        E + S                          ES                   E +P

 

Lock-and-key model

• Active site is a rigid, nonflexible shape.
• Active site = lock; substrate = key
• Only those substrates that fit exactly into the active site are able to bind with the enzyme.

 

Induced-fit model

• Certain enzymes have a broader range of specificity than can be explained by the lock-and-key model.
• In this model, the enzyme and substrate interact.
• The active site adjusts to fit the shape of the substrate, while the substrate adjusts its shape to adapt to active site.

 

Factors that affect enzyme activity

Activity = how fast an enzyme catalyzes the reaction that converts a substrate to a product.

 

Three factors affect enzyme activity:

1. Temperature

·        At low temperatures, most enzymes show little activity because there isn’t sufficient energy to catalyze reaction.

·        At high temperatures, the enzyme becomes denatured and thus loses its enzyme activity.

·        Optimum temperature is 37 °C for most enzymes

 

2. pH

·        Most enzymes have an optimum pH that maintains the proper tertiary structure of the enzyme.  Any pH above or below this pH changes the shape of the enzyme.

·        Most enzymes have optimum pH of 7.2.  However, there are some enzymes that have different optimum pH’s (example pepsin = digestive enzyme).

 

3.      Substrate concentration

·        As long as the concentration of the enzyme exceeds that of the substrate, as you increase substrate concentration, you increase enzyme activity. 

·        At some point, the concentration of the substrate is equal to or exceeds that of the enzyme and adding more substrate cannot increase the activity any further.

 

Enzyme cofactors

Many enzymes are simple enzymes when their active forms are simply their tertiary structure.

Other types of enzymes require a coenzyme (organic molecule) or a cofactor (small molecules or metal ions) to become active.

 

Examples of cofactors are the water-soluble vitamins.