BCEM 393 Chapter Notes - Chapter 4: Frederick Sanger, Amine, Cystine
20 May 2018
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Protein Three-Dimensional Structure
4.1 PRIMARY STRUCTURE: AMINO ACIDS ARE LINKED BY PEPTIDE BONDS TO FORM
POLYPEPTIDE CHAINS
- The 3D structure of proteins depends on their primary structure, which is simply linear
polymers formed by linking the alpha-carboxyl group of one amino acid to the alpha-amino
group of another amino acid
- The linkage joining amino acids is called a peptide bond (or amide bond)
- The formation of a dipeptide from two amino acids is accompanied by the loss of a water
molecule. The equilibrium of this reaction lies on the side of hydrolysis rather than synthesis
under most conditions. Hence, the biosynthesis of peptide bonds requires an input of free
energy
- Peptide bonds are kinetically stable because the rate of hydrolysis is extremely slow
- A series of amino acids joined by peptide bonds form a polypeptide chain, and each amino
acid unit in a polypeptide is called a residue
- A polypeptide chain has directionality, sometimes called polarity, because its ends are
different: an alpha-amino group is at one end, and an alpha-carboxyl group is at the other
- By convention, the amino end is taken to be the beginning of the polypeptide chain, and so
the sequence of amino acids in a polypeptide chain is written starting with the amino (N)
terminal residue
- A polypeptide chain consists of a regularly repeating part, called the main chain or backbone
and a variable part, comprising the distinctive side chains
- The polypeptide backbone is rich in hydrogen-bonding potential
- Each residue contains a carbonyl group (C=O), which is a good hydrogen bond acceptor, and
with the exception of proline, an amino group (N-H), which is a good hydrogen bond donor
- The largest protein known is the muscle protein titin, which serves as a scaffold for almost
27,000 amino acids
- Peptides consisting of less than or equal to 10 amino acids are called oligopeptides, or simply
peptides
- In some proteins, the linear polypeptide chain is covalently cross-linked
- The most common cross-links are disulphide bonds, formed by the oxidation of a pair of
cysteine residues. The resulting unit of two linked cysteines is called cystine
- Disulfide bonds can form between cysteine residues in the same polypeptide chain, or they
can link two separate chains together
- Rarely, non-disulfide cross-links derived from other side chains are present in proteins
- Proteins Have Unique Amino Acid Sequences Specified by Genes
- Frederick Sanger determined the amino acid sequence of insulin, a protein hormone. This
work is a landmark in the field of biochemistry because it showed, for the first time, that a
protein has a precisely defined amino acid sequence consisting only of L amino acids
linked by peptide bonds
- Knowing amino acid sequence is very important, for several reasons
- Firstly, amino acid sequences determine the 3D structures of proteins
- Second, knowledge of the sequence of a protein is usually essential to elucidating its
function (eg. the catalytic mechanism of an enzyme)
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- Third, alterations in amino acid sequence can produce abnormal function and disease.
Severe, sometimes fatal, diseases can result from a change in a single amino acid within
a protein
- Fourth, the sequence of a protein reveals much about its evolutionary history. Proteins
resemble one another in amino acid sequence only if they have a common ancestor.
Hence, molecular events in evolution can be traced from amino acid sequences
- Polypeptide Chains Are Flexible Yet Conformationally Restricted
- Certain characteristics of the peptide bond are important in determining the primary
structure, and thus the 3D structure:
- First, the peptide bond is essentially planar. Thus, for a pair of amino acids linked by a
peptide bond, 6 atoms lie in the same plane: the alpha-carbon atom and CO group of the
first amino acid
- Second, the peptide bond has considerable double-bond character owing to resonance
structures: the electrons resonate between a pure single bond and a pure double bond
- The partial double-bond character prevents rotation about this bond and thus
constrains the conformation of the peptide backbone
- The double bond character is also expressed in the length of the bond between the
CO and the NH groups
- Finally, the peptide bond is uncharged, allowing polymers of amino acids linked by
peptide bonds to form tightly packed globular structures that would otherwise be
inhibited by charge repulsion
- Two configurations are possible for a planar peptide bond
- In the trans configuration, the two alpha-carbon atoms are on opposite sides of the
peptide bond
- In the cis configuration, these groups are on the same side of the peptide bond
- Almost all peptide bonds in proteins are trans. This preference for trans over cis ca nee
explained by the fact that there are steric clashes between R groups in the cis
configuration but not in the trans configuration
- The bonds between the amino group and the alpha carbon atom and between the alpha
carbon atom and the carbonyl group are pure single bonds. The two adjacent rigid
peptide units may rotate about these bonds, taking on various orientations. This freedom
of rotation about two bonds of each amino acid allows proteins to fold in many different
ways
- The rotations about these bonds can be specified by torsion angles
- The angle of rotation about the bond between the nitrogen atom and the alpha carbon
atom is called phi
- The angle of rotation about the bond between the alpha carbon atom and the carbonyl
carbon atom is called psi
- A clockwise rotation about either bond as viewed toward the alpha carbon atom
corresponds to a positive value. The phi and psi angles determine the path of the
polypeptide chain
- Gopalasamudram Ramachandran, and Indian biophysicist, recognized that many
combinations are not found in nature because of steric clashes between atoms. He
generated a 2D plot, now called a Ramachandran plot, of the phi and psi values of
possible conformations
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- 3 quarters of the possible (phi, psi) combinations are excluded simply by local steric
clashes
- Steric exclusion, the fact that two atoms cannot be in the same place at the same time,
restricts the number of possible peptide conformations and is therefore, a powerful
organizing principle
4.2 SECONDARY STRUCTURE: POLYPEPTIDE CHAINS CAN FOLD INTO REGULAR STRUCTURES
- Linus Pauling and Robert Corey proposed that certain polypeptide chains have the ability to
fold into two periodic structures called the alpha helix and the beta pleated sheet
- Subsequently, other structures such as turns and loops were identified
- Alpha helices, beta pleated sheets, and turns are formed by a regular pattern of hydrogen
bonds between the peptide NH and CO groups of amino acids that are often near one
another in the linear sequence, or primary structure. Such regular folded segments are called
secondary structures
- The Alpha Helix Is a Coiled Structure Stabilized by Intrachain Hydrogen Bonds
- The side chains of the amino acids composing the alpha helix structure extend outward in
a helical array
- The alpha helix is stabilized by hydrogen bonds between the NH and CO groups of the
main chain
- The CO group of each amino acid forms a hydrogen bond with the NH group of the amino
acid that is situated four residues ahead in the sequence
- Except the amino acids near the ends of an alpha helix, all the main chain CO and NH
groups are hydrogen bonded
- Each residue is related to the next one by a rise, also known as a translation, of 1.5
angstroms along the helix axis and a rotation of 100°, which gives 3.6 amino acid residues
per turn of helix
- Amino acids spaces two apart in the sequence are situated on opposite sides of the helix
and so are unlikely to make contact
- The pitch of the alpha helix is the length of one complete turn along the helix axis and is
equal to the product of the translation (1.5 angstroms) and the number of residues per turn
(3.6, 5.4 angstroms)
- The screw sense of a helix can be right handed (clockwise) or left handed
(counterclockwise)
- Right handed helices are more energetically favourable because there are fewer steric
clashes between the side chains and the backbone
- Essentially, all alpha helices found in proteins are right handed
- Alpha helices are depicted as twisted ribbons or rods
- Beta Sheets Are Stabilized by Hydrogen Bonding Between Polypeptide Strands
- Beta sheets are different from alpha helices in appearance and in bond structure
- Instead of a single polypeptide strand, the beta sheet is composed of two or more
polypeptide chains called beta strands
- A beta strand is almost fully extended rather than being tightly coiled as in the alpha helix
- The distance between adjacent amino aids along a beta strand is approximately 3.5
angstroms
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Document Summary
4. 1 primary structure: amino acids are linked by peptide bonds to form. The 3d structure of proteins depends on their primary structure, which is simply linear polymers formed by linking the alpha-carboxyl group of one amino acid to the alpha-amino group of another amino acid. The linkage joining amino acids is called a peptide bond (or amide bond) The formation of a dipeptide from two amino acids is accompanied by the loss of a water molecule. The equilibrium of this reaction lies on the side of hydrolysis rather than synthesis under most conditions. Hence, the biosynthesis of peptide bonds requires an input of free energy. Peptide bonds are kinetically stable because the rate of hydrolysis is extremely slow. A series of amino acids joined by peptide bonds form a polypeptide chain, and each amino acid unit in a polypeptide is called a residue.
