3.4 The Structure of Proteins: Primary Structure Lecture
SUMMARY 3.4 The Structure of Proteins: Primary Structure
■ Differences in protein function result from differences in amino acid composition and
sequence. Some variations in sequence may occur in a particular protein, with little or
no effect on its function.
■ Amino acid sequences are deduced by fragmenting polypeptides into smaller
peptides with reagents known to cleave specific peptide bonds, determining the amino
acid sequence of each fragment by the automated Edman degradation procedure, and
then ordering the peptide fragments by finding sequence overlaps between fragments
generated by different reagents. A protein sequence can also be deduced from the
nucleotide sequence of its corresponding gene in DNA or by mass spectrometry.
■ Short proteins and peptides (up to about 100 residues) can be chemically
synthesized. The peptide is built up, one amino acid residue at a time, while tethered to
a solid support.
■ Protein sequences are a rich source of information about protein structure and
function, as well as the evolution of life on Earth. Sophisticated methods are being
developed to trace evolution by analyzing the slow changes in amino acid sequences of
homologous proteins.
Structure
Purification of a protein is usually only a prelude to a detailed biochemical dissection of
its structure and function. What is it that makes one protein an enzyme, another a
hormone, another a structural protein, and still another an antibody? How do they differ
chemically? The most obvious distinctions are structural, and to protein structure we
now turn.
FIGURE 3-23 Levels of structure in proteins. The primary structure consists of a
sequence of amino acids linked together by peptide bonds and includes any disulfide
bonds. The resulting polypeptide can be arranged into units of secondary structure,
such as an α helix. The helix is a part of the tertiary structure of the folded polypeptide,
which is itself one of the subunits that make up the quaternary structure of the
multisubunit protein, in this case hemoglobin.
The structure of large molecules such as proteins can be described at several levels of
complexity, arranged in a kind of conceptual hierarchy. Four levels of protein structure
are commonly defined (Fig. 3-23). A description of all covalent bonds (mainly peptide
bonds and disulfide bonds) linking amino acid residues in a polypeptide chain is its
, primary structure. The most important element of primary structure is the sequence
of amino acid residues. Secondary structure refers to particularly stable
arrangements of amino acid residues giving rise to recurring structural patterns.
Tertiary structure describes all aspects of the three-dimensional folding of a
polypeptide. When a protein has two or more polypeptide subunits, their arrangement
in space is referred to as quaternary structure. Our exploration of proteins will
eventually include complex protein machines consisting of dozens to thousands of
subunits. Primary structure is the focus of the remainder of this chapter; the higher
levels of structure are discussed in Chapter 4.
Differences in primary structure can be especially informative. Each protein has a
distinctive number and sequence of amino acid residues. As we shall see in Chapter 4,
the primary structure of a protein determines how it folds up into its unique three-
dimensional structure, and this in turn determines the function of the protein. We first
consider empirical clues that amino acid sequence and protein function are closely
linked, then describe how amino acid sequence is determined; finally, we outline the
many uses to which this information can be put.
The Function of a Protein Depends on Its Amino Acid
Sequence The bacterium Escherichia coli produces more than 3,000 different proteins; a
human has ~20,000 genes encoding a much larger number of proteins (through genetic
processes discussed in Part III of this text). In both cases, each type of protein has a
unique amino acid sequence that confers a particular three-dimensional structure. This
structure in turn confers a unique function.
Some simple observations illustrate the importance of primary structure, or the amino
acid sequence of a protein. First, as we have already noted, proteins with different
functions always have different amino acid sequences. Second, thousands of human
genetic diseases have been traced to the production of defective proteins. The defect
can range from a single change in the amino acid sequence (as in sickle cell disease,
described in Chapter 5) to deletion of a larger portion of the polypeptide chain (as in
most cases of Duchenne muscular dystrophy: a large deletion in the gene encoding the
protein dystrophin leads to production of a shortened, inactive protein). Finally, on
comparing functionally similar proteins from different species, we
find that these proteins often have similar amino acid sequences. Thus, a close link
between protein primary structure and function is evident.
Q: Glucose is the major energy-yielding nutrient for most cells. Assuming a cellular
concentration of 1 M (that is, 1 millimole/L), calculate how many molecules of glucose
would be present in our hypothetical (and spherical) eukaryotic cell. (Avogadro’s
number,
Is the amino acid sequence absolutely fixed, or invariant, for a particular protein? No;
some flexibility is possible. An estimated 20% to 30% of the proteins in humans are
polymorphic, having amino acid sequence variants in the human population. Many of
these variations in sequence have little or no effect on the function of the protein.
Furthermore, proteins that carry out a broadly similar function in distantly related
species can differ greatly in overall size and amino acid sequence.
SUMMARY 3.4 The Structure of Proteins: Primary Structure
■ Differences in protein function result from differences in amino acid composition and
sequence. Some variations in sequence may occur in a particular protein, with little or
no effect on its function.
■ Amino acid sequences are deduced by fragmenting polypeptides into smaller
peptides with reagents known to cleave specific peptide bonds, determining the amino
acid sequence of each fragment by the automated Edman degradation procedure, and
then ordering the peptide fragments by finding sequence overlaps between fragments
generated by different reagents. A protein sequence can also be deduced from the
nucleotide sequence of its corresponding gene in DNA or by mass spectrometry.
■ Short proteins and peptides (up to about 100 residues) can be chemically
synthesized. The peptide is built up, one amino acid residue at a time, while tethered to
a solid support.
■ Protein sequences are a rich source of information about protein structure and
function, as well as the evolution of life on Earth. Sophisticated methods are being
developed to trace evolution by analyzing the slow changes in amino acid sequences of
homologous proteins.
Structure
Purification of a protein is usually only a prelude to a detailed biochemical dissection of
its structure and function. What is it that makes one protein an enzyme, another a
hormone, another a structural protein, and still another an antibody? How do they differ
chemically? The most obvious distinctions are structural, and to protein structure we
now turn.
FIGURE 3-23 Levels of structure in proteins. The primary structure consists of a
sequence of amino acids linked together by peptide bonds and includes any disulfide
bonds. The resulting polypeptide can be arranged into units of secondary structure,
such as an α helix. The helix is a part of the tertiary structure of the folded polypeptide,
which is itself one of the subunits that make up the quaternary structure of the
multisubunit protein, in this case hemoglobin.
The structure of large molecules such as proteins can be described at several levels of
complexity, arranged in a kind of conceptual hierarchy. Four levels of protein structure
are commonly defined (Fig. 3-23). A description of all covalent bonds (mainly peptide
bonds and disulfide bonds) linking amino acid residues in a polypeptide chain is its
, primary structure. The most important element of primary structure is the sequence
of amino acid residues. Secondary structure refers to particularly stable
arrangements of amino acid residues giving rise to recurring structural patterns.
Tertiary structure describes all aspects of the three-dimensional folding of a
polypeptide. When a protein has two or more polypeptide subunits, their arrangement
in space is referred to as quaternary structure. Our exploration of proteins will
eventually include complex protein machines consisting of dozens to thousands of
subunits. Primary structure is the focus of the remainder of this chapter; the higher
levels of structure are discussed in Chapter 4.
Differences in primary structure can be especially informative. Each protein has a
distinctive number and sequence of amino acid residues. As we shall see in Chapter 4,
the primary structure of a protein determines how it folds up into its unique three-
dimensional structure, and this in turn determines the function of the protein. We first
consider empirical clues that amino acid sequence and protein function are closely
linked, then describe how amino acid sequence is determined; finally, we outline the
many uses to which this information can be put.
The Function of a Protein Depends on Its Amino Acid
Sequence The bacterium Escherichia coli produces more than 3,000 different proteins; a
human has ~20,000 genes encoding a much larger number of proteins (through genetic
processes discussed in Part III of this text). In both cases, each type of protein has a
unique amino acid sequence that confers a particular three-dimensional structure. This
structure in turn confers a unique function.
Some simple observations illustrate the importance of primary structure, or the amino
acid sequence of a protein. First, as we have already noted, proteins with different
functions always have different amino acid sequences. Second, thousands of human
genetic diseases have been traced to the production of defective proteins. The defect
can range from a single change in the amino acid sequence (as in sickle cell disease,
described in Chapter 5) to deletion of a larger portion of the polypeptide chain (as in
most cases of Duchenne muscular dystrophy: a large deletion in the gene encoding the
protein dystrophin leads to production of a shortened, inactive protein). Finally, on
comparing functionally similar proteins from different species, we
find that these proteins often have similar amino acid sequences. Thus, a close link
between protein primary structure and function is evident.
Q: Glucose is the major energy-yielding nutrient for most cells. Assuming a cellular
concentration of 1 M (that is, 1 millimole/L), calculate how many molecules of glucose
would be present in our hypothetical (and spherical) eukaryotic cell. (Avogadro’s
number,
Is the amino acid sequence absolutely fixed, or invariant, for a particular protein? No;
some flexibility is possible. An estimated 20% to 30% of the proteins in humans are
polymorphic, having amino acid sequence variants in the human population. Many of
these variations in sequence have little or no effect on the function of the protein.
Furthermore, proteins that carry out a broadly similar function in distantly related
species can differ greatly in overall size and amino acid sequence.
