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Biochemistry Notes

The document discusses the structure of proteins at four levels - primary, secondary, tertiary, and quaternary. The primary structure refers to the specific sequence of amino acids in a protein, which is important as genetic diseases can result in abnormal sequences, altering protein folding and function. Amino acids are joined by peptide bonds, which link the carboxyl group of one amino acid to the amino group of the next. The peptide bond is rigid and planar, allowing the polypeptide chain flexibility to fold into complex three-dimensional shapes defined by its tertiary and quaternary structure.

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56 views3 pages

Biochemistry Notes

The document discusses the structure of proteins at four levels - primary, secondary, tertiary, and quaternary. The primary structure refers to the specific sequence of amino acids in a protein, which is important as genetic diseases can result in abnormal sequences, altering protein folding and function. Amino acids are joined by peptide bonds, which link the carboxyl group of one amino acid to the amino group of the next. The peptide bond is rigid and planar, allowing the polypeptide chain flexibility to fold into complex three-dimensional shapes defined by its tertiary and quaternary structure.

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ahm
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Biochemistry Notes

I. OVERVIEW
The 20 amino acids commonly found in proteins are joined together by peptide
bonds. The linear sequence of the linked amino acids contains the information
necessary to generate a protein molecule with a unique three-dimensional shape
that determines function. The complexity of protein structure is best analyzed by
considering the molecule in terms of four organizational levels: primary,
secondary, tertiary, and quaternary (Fig. 2.1). An examination of these
hierarchies of increasing complexity has revealed that certain structural elements
are repeated in a wide variety of proteins, suggesting that there are general rules
regarding the ways in which proteins achieve their native, functional form.
These repeated structural elements range from simple combinations of α-helices
and β-sheets forming small motifs to the complex folding of polypeptide
domains of multifunctional proteins (see p. 19).

Figure 2.1 Four hierarchies of protein structure.


II. PRIMARY STRUCTURE
The sequence of amino acids in a protein is called the primary structure of the
protein. Understanding the primary structure of proteins is important because
many genetic diseases result in proteins with abnormal amino acid sequences,
which cause improper folding and loss or impairment of normal function. If the
primary structures of the normal and the mutated proteins are known, this
information may be used to diagnose or study the disease.
A. Peptide bond
In proteins, amino acids are joined covalently by peptide bonds, which are
amide linkages between the α-carboxyl group of one amino acid and the α-
amino group of another. For example, valine and alanine can form the
dipeptide valylalanine through the formation of a peptide bond (Fig. 2.2).
Peptide bonds are resistant to conditions that denature proteins, such as
heating and high concentrations of urea (see p. 20). Prolonged exposure to a
strong acid or base at elevated temperatures is required to break these bonds
nonenzymically (see p. 14).

Figure 2.2 A. Formation of a peptide bond, showing the structure of the


dipeptide valylalanine. B. Characteristics of the peptide bond. [Note: Peptide
bonds involving proline may have a cis configuration.]
1. Naming the peptide: By convention, the free amino end (N-terminal) of
the peptide chain is written to the left and the free carboxyl end (Cterminal)
to the right. Therefore, all amino acid sequences are read from
the N- to the C-terminal end. For example, in Figure 2.2A, the order of
the amino acids in the dipeptide is valine, alanine. Linkage of ≥50 amino
acids through peptide bonds results in an unbranched chain called a
polypeptide, or protein. Each component amino acid is called a residue
because it is the portion of the amino acid remaining after the atoms of
water are lost in the formation of the peptide bond. When a peptide is
named, all amino acid residues have their suffixes (-ine, -an, -ic, or -ate)
changed to -yl, with the exception of the C-terminal amino acid. For
example, a tripeptide composed of an N-terminal valine, a glycine, and a
C-terminal leucine is called valylglycylleucine.
2. Peptide bond characteristics: The peptide bond has a partial double-bond
character, that is, it is shorter than a single bond and is rigid and planar
(Fig. 2.2B). This prevents free rotation around the bond between the
carbonyl carbon and the nitrogen of the peptide bond. However, the
bonds between the α-carbons and the α-amino or α-carboxyl groups can
be freely rotated (although they are limited by the size and character of
the R groups). This allows the polypeptide chain to assume a variety of
possible conformations. The peptide bond is almost always in the trans
configuration (instead of the cis; see Fig. 2.2B), in large part because of
steric interference of the R groups (side chains) when in the cis position.
3. Peptide bond polarity: Like all amide linkages, the −C = O and −NH
groups of the peptide bond are uncharged, and neither accept nor release
protons over the pH range of 2–12. Thus, the charged groups present in
polypeptides consist solely of the N-terminal (α-amino) group, the Cterminal
(α-carboxyl) group, and any ionized groups present in the side
chains of the constituent amino acids. The −C = O and −NH groups of the
peptide bond are polar, however, and are involved in hydrogen bonds
(for example, in α-helices and β-sheets), as described on pp. 16–

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