Understanding Protein Structure, Enzymes, and Nucleic Acids

Proteins are composed of 20 amino acids.

Functional groups influence reactivity.

Nonpolar side chains are green.

Polar side chains are pink.

Electrically charged side chains:

• Acidic: red
• Basic: blue

Condensation reactions form a peptide bond by bonding the carboxyl group of one amino acid to the amino group of another. Multiple peptide bonds create a polypeptide. Polypeptides containing more than 50 amino acids are called proteins.

Protein Structure

Primary structure: The unique sequence of amino acids.

Secondary structure: Hydrogen bonds between the carbonyl group of one amino acid and the amino group of another form a protein's secondary structure.

Secondary structure depends on the primary structure.

Tertiary structure: Results from interactions between R-groups or between R-groups and the peptide backbone. These contacts cause the backbone to bend and fold.

R-group interactions include hydrogen bonds, hydrophobic interactions, covalent, and ionic bonds.

Quaternary Structure: Many proteins contain several distinct polypeptide subunits that interact to form a single structure; the bonding of two or more subunits produces a quaternary structure.

Folding and Function: Folded molecules are more energetically stable than unfolded molecules.

Denatured (unfolded) proteins are unable to function normally.

Enzyme Catalysis

Enzymes catalyze reactions by lowering activation energy.

Steps of Enzyme Catalysis

1. Initiation: Substrates are precisely oriented as they bind to the active site.
2. Transition state facilitation: Interactions between the substrate and active site R-groups lower activation energy.
3. Termination: Reaction products are released from the enzyme.

Competitive inhibition: Molecules similar in size and shape to the substrate compete with the substrate for access to the active site.

Allosteric regulation: Occurs when a molecule causes a change in enzyme shape by binding to the enzyme at a location other than the active site. This can activate or deactivate the enzyme.

Nucleic Acids

A nucleic acid is a polymer of nucleotide monomers.

A condensation reaction forms a phosphodiester linkage between the phosphate group on the 5' carbon and the -OH group on the 3' carbon.

DNA Structure

James Watson and Francis Crick determined:

DNA strands run in an antiparallel configuration. DNA strands form a double helix. Purines always pair with pyrimidines.

Strands form complementary base pairs: A-T, which have two hydrogen bonds, and G-C, which have three hydrogen bonds.

DNA has two different-sized grooves: the major groove and the minor groove.

DNA CONTAINS INFORMATION.

The difference between RNA and DNA is that RNA is single-stranded, while DNA is double-stranded.