Chapter 3.4: Proteins Are Polymers with Variable Structures

Flashcards from Chapter 3.4 of Principles of Life, 3rd Edition.

Proteins

Polymers made up of tens to tens of thousands of monomers called amino acids, essential to the functioning of life due to their numerous abilities

Amino acid

A single monomer of a protein that contains an amino and carboxyl group; these can be classified into twenty different types with charge, polarity, size, shape, and functional differences

• Like nucleotides, these form proteins sequentially, with carboxyl groups chaining with incoming amino groups to form peptide bonds

• Some are required to be obtained from the diet

Peptide bond

The bond between amino acids in a protein, formed by a carboxyl and amino group with a water molecule loss

Alpha carbon

The central carbon in an amino acid that can form four covalent bonds

• Two are occupied by the carboxyl and amino groups

• A third is occupied by a hydrogen atom

• The fourth is occupied by the differing R group

R group

A functional group unique to each of the twenty amino acids

• Ten are hydrophilic, with five having an electric charge attracting ions and another five having polarity attracting hydrogen bonds

• Seven have nonpolar hydrocarbon chains, which can cluster together in the protein’s interior or interact with lipids

• Three remain in a special category due to structural features

Glycine

A special R group consisting of a hydrogen atom

• This allows for tight corners and flexibility in proteins

Cysteine

A special R group with a terminal SH group

• Can react with another side chain or molecule to form a stabilizing covalent disulfide bridge

Oligopeptides

Short polymers of 20 or fewer amino acids; includes some hormones and other signaling molecules

Polypeptides

Very long polymers with a unique sequence of amino acids that ultimately comprise proteins

Primary structure

The precise sequence of amino acids in a protein; there are many of these due to the 20 amino acids available

• Determined by covalent peptide bonds

Secondary structure

The stage of a protein’s structure that consists of regular, repeated spatial patterns in different regions of a polypeptide chain; the most common patterns are the alpha helix and beta pleated sheet

Alpha helix

A right-handed helical shape formed in secondary structures, with R groups coiling and extending from the peptide backbone to form hydrogen bonds within the coil

Beta pleated sheet

A secondary structure shape formed by extended and aligned amino acids, stabilized by hydrogen bonds between amino and carboxyl groups on the two chains

Tertiary structure

The stage of a protein’s structure that arises from the bending and folding of polypeptide chains, resulting in a three-dimensional structure with an interior and exterior capable of molecular interactions

Side chain interactions

These determine the shape of tertiary and quaternary structures, and include:

• Cystine covalent disulfide bridges

• Ionic interactions and bonds between charged side chains to ensure correct formations

• Hydrogen bonds

• van der Waals interactions between hydrophobic side chains

Subunits

Two or more polypeptide chains folded into a unique tertiary structure, these affect quaternary structure folding

Quaternary structure

These result from subunit binding and interactions as well as side chain interactions

• May form beta pleated sheets between separate polypeptide chains, which can lead to abnormalities if overly aggregated

Denaturing

Occurs when a protein is heated or has its molecular structure disrupted

• Can often be reversed if cooled or the disruptive force is removed, requiring the primary structure to remain intact and unbonded from unoriginal polypeptides

• May also occur due to pH, polar solutes, ionic bonds, and nonpolar substances that affect chemical reactions