Download 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
1
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.)
2
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!
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
A peptide with the same 7 amino acids in a different order would have completely different properties
(function) than the peptide above.
3
Protein structure
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
4
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 (-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.
5
Beta-sheet (-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 -sheet
Anti-parallel -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.)
6
Some proteins consist of beta sheets connected by loops (The sheets are represented by arrows in the
ribbon diagram.)
Many poteins have both alpha-helices and beta-sheets
7
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.
8