BIOL 150 Chapter Notes - Chapter 4: Cysteine, Protein Structure, Hydrophile
Chapter 4: Translation and Protein Structure
➔Proteins are the most versatile of macromolecules- each has its own built-in ability to
carry out a cellular function.
◆Some proteins aggregate to form relatively stiff filaments that help define the
cell’s shape and hold organelles in position.
◆Others span the cell membrane and form channels or pores through which ion s
and small molecules can move.
◆Many others are enzymes that catalyze the thousands of chemical reactions
needed to maintain life.
◆Others are signaling proteins that enable cells to coordinate their internal activities
or to communicate with other cells.
➔Proteins are linear polymers of any combination of 20 amino acids- each has different
chemical characteristics.
4.1 MOLECULAR STRUCTURE OF PROTEINS
➔There are as many amino acids as there are letters in the alphabet, the order is important.
◆The exact order of amino acids in a protein determines the protein’s shape and
function.
Amino acids differ in their side chains.
➔ Consists of a central carbon atom- ɑ (alpha) carbon: connected by covalent bonds to 4
different chemical groups:
◆Amino group, carboxyl group, side chain (R group), hydrogen atom.
●All at equal angles- forms a tetrahedron.
➔In an environment of a cell, where pH is in a range 7.35-7.45 (physiological pH), the
amino group gains a proton to become -NH3+ and the carboxyl group loses a proton to
become COO-.
➔R groups of the amino acids differ from one amino acid to the next.
◆Amino acids differ in their chemical and physical properties.
◆Grouped according to their properties- particular emphasis on whether they are
hydrophobic or hydrophilic.
◆Hydrophobic- those that do not readily interact with water or form hydrogen
bonds.
●Most have nonpolar R groups composed of hydrocarbon chains or
uncharged carbon rings.
●Tend to aggregate with each other.
○Aggregation is also stabilized by weak van der Waals forces.
●Tend to be buried in the interior of folded proteins- kept away from water.
➔Amino acids with polar R groups have a permanent charge separation- one of the R group
is slightly more negatively charged than the other.
➔R groups of the basic and acidic amino acids are strongly polar.
◆At the pH of a cell, the R groups of the basic amino acids gain a proton and
become positively charged...those of the acidic amino acids lose a proton and
become negatively charged.
●They are charged so they are located on the outside surface of the folded
molecule.
●Charged groups can also form ionic bonds with each other and with other
charged molecules in the environment- negatively charged group or
molecule bonds with a positively charged group or molecule.
○Important way in which proteins can associate with each other or
with other macromolecules (such as DNA).
➔Properties of several amino acids are noteworthy, they have an effect on protein structure.
◆Glycine-
●its R group is hydrogen (different from the rest), not symmetric.
◆Proline-
● Distinctive,
● R group is linked back to the amino group, linkage creates a kink or bend
in the polypeptide chain and restricts rotation of the C-N bond, imposing
constraints on protein folding in its vicinity.
◆Cysteine
●Makes special contribution to protein folding through its -SH group.
●When two chains in the same or different polypeptides come into
proximity, they can react to form an S-S disulfide bond, covalently joins
the side chains.
Successive amino acids in proteins are connected by peptide bonds.
➔Peptide bond- the bond formed between the two amino acids.
◆In formation- the carboxyl group of one amino acid reacts with the amino group
of the next amino acid in line, a molecule of water is released.
●In the resulting molecule, the R groups of each amino acid point in
different directions.
➔Polymers of amino acids ranging from as few as 2 to many hundreds share a chemical
feature common to individual amino acids: the ends are distinct from each other.
◆One end- has a free amino group; amino end of the molecule.
◆Other end - has a free carboxyl group- carboxyl end of the molecule.
◆Polypeptide- a polymer of amino acids connected by peptide bonds.
●Typical polypeptides produced in cells consist of a few hundred amino
acids.
◆Protein- often used as a synonym for polypeptide, especially when the
polypeptide change has folded into a stable, 3D conformation.
◆Amino acids that are incorporated into a protein often referred to as amino acid
residues.
The sequence of amino acids dictates protein folding, which determines function.
➔Structures
◆Primary structure- sequence of amino acids in a protein.
●Sequence of amino acids ultimately determines how a protein folds.
◆Secondary structure- interactions between stretches of amino acids in a protein.
◆Tertiary structure- longer range interactions between secondary structures in turn
support the overall 3D shape of the polypeptide.
◆Quaternary structure- proteins that are made up of several individual polypeptides
that interact with each other.
➔Wide range of functions.
◆Serving as structural elements to communicating with the external environment.
◆Accelerating the rate of chemical reactions.
◆Ability to carry out this function depends on the 3D shape of the protein.
◆When fully folded, some proteins contain pockets with positively or negatively
charged side chains at just the right positions to trap small molecules.
●Others have surfaces that can bind another proteins or a sequence of
nucleotides in DNA or RNA
●Some form rigid rods for structural support
●Others keep their hydrophobic side chains away from water molecules by
inserting into the cell membrane.
➔Sequence of amino acids in a protein is usually represented by a series of 3-letter or
1-letter abbreviations for the amino acids.
Secondary structures result from hydrogen bonding in the polypeptide backbone.
➔Hydrogen bonds can form between the carbonyl group in one peptide bond and the amide
group in another, allowing localized regions of the polypeptide chain to fold.
◆Localized folding is a major contributor to the secondary structure of the protein.
➔ ɑ (alpha) helix, Β (beta) sheet.
◆Stabilized by hydrogen bonding along with the polypeptide backbone.
➔ (alpha) helices
◆Polypeptide backbone is twisted tightly in a right-handed coil with 3.6 amino
acids per complete turn.
◆Helix is stabilized by hydrogen bonds that form between each amino acid
carboxyl group and amide group, 4 residues ahead in the sequence.
◆R groups project outward from the ɑ helix.
●Chemical properties of the projecting R groups largely determine where
the ɑ helix is positioned in the folded protein, and how it might interact
with other molecules.
Document Summary
Proteins are the most versatile of macromolecules- each has its own built-in ability to carry out a cellular function. Some proteins aggregate to form relatively stiff filaments that help define the cell"s shape and hold organelles in position. Others span the cell membrane and form channels or pores through which ion s and small molecules can move. Many others are enzymes that catalyze the thousands of chemical reactions needed to maintain life. Others are signaling proteins that enable cells to coordinate their internal activities or to communicate with other cells. Proteins are linear polymers of any combination of 20 amino acids- each has different chemical characteristics. There are as many amino acids as there are letters in the alphabet, the order is important. The exact order of amino acids in a protein determines the protein"s shape and function. Consists of a central carbon atom- (alpha) carbon: connected by covalent bonds to 4 different chemical groups:
