BIOL 151 Lecture 4: Bio 151 - Chapter 4

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7 Feb 2017
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BIO 151 - Chapter 4
4.1 Molecular Structure of Proteins
Amino acids differ in their side chains
o Amino acids contain a central carbon atom called the α (alpha) carbon,
connected by covalent bonds to four different chemical groups:
An Amino group (-NH)
A Carboxyl group (-COOH)
A hydrogen atom
A side chain/R Group
The side chain differs from one amino acid to the next
They are chemically diverse and are grouped according to their
properties, with a particular emphasis on whether they are
hydrophobic or hydrophilic, or have special characteristics that
might affect a protein’s structure
o The side groups of the basic and acidic amino acids are strongly polar and are also
hydrophilic
Basic amino acids tend to be positively charged at intracellular pH, and
acidic amino acids tend to be negatively charged
These amino acids are usually on the outside surface of the folded
proteins, while the hydrophobic ones are on the inside
o The rest of the side groups of amino acids can be said to be nonpolar and
hydrophobic
o Special Amino Acids:
Glycine
It’s R group is only a hydrogen
The small size of the amino acid also makes it flexible, allowing
more flexibility of the polypeptide backbone, which is important in
the folding of the protein
Proline
It is more rigid compared to glycine, therefore allowing it to
maintain protein structures
Cysteine
It makes a special contribution through it’s -SH group
The -SH group can help form a S-S disulfide bond, which can
form cross bridges that can connect different parts of the same
protein or even different protein
Successive amino acids in proteins are connected by peptide bonds
o Peptide Bond: the bond formed between two amino acids
In forming the peptide bond, the carboxyl group of one amino acid reacts
with the amino group of the next amino acid in line, and a molecule of
water is released
The C=O group in the peptide bond as a carbonyl group, and the N-H
group is an amide group
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BIO 151 - Chapter 4
o Polymers of amino acids ranging from as few as two to many hundreds share a
chemical feature common to individual amino acids, which is that the ends are
chemically distinct from each other
One end has a free amino group, and is known as the amino end of the
peptide
The other end has a free carboxyl group, which is the carboxyl end
A polymer of amino acids connected by peptide bonds is known as a
Polypeptide
The term protein is often used as a synonym for polypeptide
Amino acids that are incorporated into a protein are often referred to as
amino acid residues
The sequence of amino acids dictates protein folding, which determines function
o The structures of a protein
Primary Structure: the sequence of amino acids in a protein
This sequence determines how a protein will fold
Secondary Structure: the interactions between stretches of amino acids
in a protein
Tertiary Structure: the three-dimensional conformation of a single
polypeptide chain, usually made up of several secondary structure
elements
Quaternary Structure: some of the proteins are made up of several
individual polypeptides that interact with each other, with each
polypeptide having a tertiary structure
o Proteins have a wide range of functions in the cell, from serving as structural
elements to communicating with the external environment to accelerating the rate
of chemical reactions
o The sequence of amino acids in a protein (its primary structure) is usually
represented by a series of three-letter or one-letter abbreviations for the amino
acids
Secondary Structures result from hydrogen bonding in the polypeptide backbone
o The structure relies on interactions in the polypeptide backbone and is relatively
independent of the side chains
o Two types of secondary structures are found in many different proteins
α (alpha) helix
the helix is stabilized by hydrogen bonds that form between each
amino acid’s carbonyl group and the amide group four residues
ahead in the sequence
β (beta) sheet
the polypeptide folds back and forth on itself, forming a pleated
sheet that is stabilized by hydrogen bonds between carbonyl
groups on one chain and amide groups in the other chain across the
way
Tertiary structures result from interactions between amino acid side chains
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