Learning Objectives



Protein Structure and Function

Protein function

Proteins are giant molecules that carry out many of the important functions inside living cells. For example:

Proteins (enzymes) catalyze cellular reactions (a different protein catalyzes each reaction).

Proteins provide structural stability to a cells and tissues (cytoskeleton, cartilage, muscle, hair, etc.)

Proteins are important components of cellular membranes including membrane channels

Proteins store and transport metal ions, oxygen, nutrients, and other small molecules between cells

Proteins serve as motors that transport other molecules within a cell and cause muscle contraction.

Protein structure

Proteins are linear polyamides. The monomers are called amino acids. There are 20 different amino acids commonly found in proteins (several others are less common). A chain of amino acids ranging from 2 to 50 amino acids is called a polypeptide (or simply peptide). A protein is a polypeptide that has at least 50 amino acids. (The cut-off between peptide and protein is entirely arbitrary.)

Protein chain length can range from 50 to several thousand amino acids (molecular weights from 5000 to more than 1,000,000!!).

THE FUNCTION OF A PROTEIN IS DETERMINED BY ITS 3-DIMENSIONAL STRUCTURE.

THE STRUCTURE IS DETERMINED BY THE LINEAR SEQUENCE OF AMINO ACIDS.

THE SEQUENCE OF AMINO ACIDS IN A PROTEIN IS ENCODED WITHIN ITS GENE.

A DNA-binding protein wrapped around DNA

Amino acids: The building blocks of proteins

All amino have both amine and carboxylic acid functional groups (hence the name “amino acid”). Each of the 20 common amino acids has a different side chain (R in the figure below). It is the side chain that largely determines the chemical properties of an amino acid.

The amino and carboxyl groups are shown in their ionized form. (Carboxylic acids are weak acids and amines are weak bases.)

The polymerization reaction: Formation of peptide (amide) bonds

To form a protein, amino acids are linked together through amide bonds. The carboxyl group of one amino acid reacts with the amino group of another amino acid to form an amide bond (also called a peptide bond). This is a condensation reaction!

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Notice that the resulting “dipeptide” has a free amino group on one end and a free carboxyl group on the other. Thus, the condensation reaction can be repeated indefinitely.

Below is the heptapeptide: Asp-Lys-Gln-His-Cys-Arg-Phe

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A peptide with the same 7 amino acids in a different order would have completely different properties (function) than the peptide above.

Protein structure

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Primary structure: The linear sequence of amino acids (from N-terminus to C-terminus)

Secondary structure: 3-dimenional folding of relatively short stretches of amino acids. Generally described by tracing the path taken by the peptide backbone (excludes side chains). Stabilized by hydrogen bonding between backbone carboxylate and amino groups.

Tertiary structure: 3-dimensional folding of an entire protein. Involves interactions between various secondary structures. Described by indicating the position of every atom. In addition to interactions between along the backbone, also stabilized by interactions between side chains, and by binding of metal ions and small molecules.

Quarternary structure: Many proteins are composed of more than one peptide chain. These are called multi-subunit proteins. The quarternary structure describes how the various subunits fit together in the protein. Stabilized largely by London dispersion forces between subunits.

THE 3-DIMENSIONAL STRUCTURE OF A PROTEIN IS STABILIZED BY:

LONDON DISPERSION FORCES

DIPOLE-DIPOLE INTERACTIONS

HYDROGEN BONDING

ION-DIPOLE INTERACTIONS

ION-ION INTERACTIONS

Secondary structures

The two most common types of secondary structures found in proteins are the “alpha helix” and the “beta sheet”. Almost all proteins contain one or both of these types of structures. Both are stabilized by hydrogen bonding!

Alpha helix (α-helix)

An alpha helix is stabilized by hydrogen bonds. Every amino hydrogen is bonded to a carboxyl oxygen that is four amino acids down the chain.

Beta-sheet (β-sheet)

Beta-sheets are formed when two or more extended peptide chains align side by side. The strands are held together by hydrogen bonds.

Parallel β-sheet

Anti-parallel β-sheet

Tertiary structure

The tertiary structure of hemoglobin consists of multiple alph-helices connected by unstructured loops. Adjacent helices interact with each other through a variety of forces which stabilize the 3-dimensional fold. (The red planar molecule is a “heme” group bound to the protein. Oxygen binds to the iron atom that is in the center of the heme molecule.)

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Some proteins consist of beta sheets connected by loops (The sheets are represented by arrows in the ribbon diagram.)

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Many poteins have both alpha-helices and beta-sheets

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Quarternary structure

Hemoglobin has four subunits (two pairs of identical subunits). The subunits are held together primarily through London dispersion forces. Subtle changes in the arrangement of the subunits changes how tightly oxygen is bound.

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