5
Proteins &
Amino Acids
Many of the most important macromolecules in living systems are polymers.
Goal To understand how common
and dissimilar features of These polymers are composed of small building blocks that are linked
amino acids determine together in long, linear chains. Three of the most important biological
the chemical and physical polymers are polysaccharides, polynucleotides, and polypeptides (Figure
properties of proteins.
1). Polysaccharides, such as starch, are composed of sugar subunits whereas
polynucleotides, such as DNA and RNA (the subject of Chapter 8), are built
Objectives from nucleotides. Here and in the next chapter we focus on polypeptides.
After this chapter, you should be able to Polypeptides are chains of subunits called amino acids that are joined
together by peptide bonds. Short polypeptides are called peptides, and
• explain why peptide bonds are polar
long polypeptides are typically called proteins. Proteins are composed of
and prefer the trans configuration.
20 kinds of amino acids, which are at once alike and dissimilar. They share
• explain how side chains confer distinct common features that allow them to form peptide bonds with each other
chemical and physical properties on
amino acids.
while also exhibiting distinctive chemical features. This diversity of amino
acids and the sheer number of possible combinations in their linear order
• draw a peptide of a given sequence at a
allow for tremendous dissimilarity in the chemical and physical properties
specified pH.
of proteins (Figure 2). Furthermore, proteins do not exist as unstructured
chains. Rather, they fold in on themselves to form three-dimensional
architectures with unique features.
Proteins have diverse functions
Owing to their enormous diversity, cells employ proteins to perform
numerous tasks (Figure 3). Some proteins function as enzymes, which
catalyze chemical reactions by reducing ΔG‡. Nearly all enzymes are
proteins, and as we saw in the previous chapter, cells are able to carry
,Chapter 5 Proteins & Amino Acids 2
Figure 1 Polymers are Monomer Polymer
macromolecules composed of
small-molecule monomers linked
Carbohydrate
OH HO HO
O HO
together in chains HO
O
O O HO
O
HO O OH O OH O
OH HO OH O
HO
Carbohydrates, proteins, and nucleic acids OH HO HO
OHO
are examples of biological polymers. Each Sugar Starch
class of molecule is made of monomer
subunits covalently linked together in
S
chains.
Protein
O
O O O
H H
HO OH N N
N N N
NH2 H H H
O O
Amino acid OH
Protein
H2N N H
NH2 O N NH2
N H
N N O N O N
O N
Nucleic acid
O N N
P N N N
O N
O
O O O O
O O O
O P O O P O O P O O
OH
O O O
Deoxyucleotide
DNA
Figure 2 Proteins exhibit unique (A) (B)
structures and chemical properties
Surface charge representation of the
proteins actin (A) and HIV protease (B).
Even though both proteins are chains of
amino acids, they each feature distinct
three-dimensional shapes with unique
chemical properties, as evidenced by the
unique distribution of surface charges on
each molecule. Blue represents positive
charge, red negative charge, and white actin HIV protease
neutral.
out controlled chemical reactions because they use enzymes to modulate
reaction rates and couple favorable processes with unfavorable ones. In fact,
nearly all transformations that occur in the cell are mediated by enzymes,
and without them, living systems would carry out virtually no chemistry.
Enzymes catalyze a wide variety of reactions and are often categorized
according to the chemistry that they perform. Most enzymatic reactions
involve either the transfer of electrons (oxidation and reduction reactions),
the transfer of functional groups, the cleavage or formation of bonds, the
rearrangement of bonds within individual molecules, or the use of ATP to
covalently connect molecules. We will have more to say about how enzymes
lower ΔG‡ in subsequent chapters.
While enzymes come in many shapes and sizes and facilitate a vast number
of specific chemical reactions, proteins as a whole are even more diverse.
Not all proteins are enzymes; some proteins play structural roles. Hair is
made of such proteins, as are fingernails and the outer layers of the skin.
Many familiar materials, such as wool, silk, and leather are also made of
protein. These structural proteins have evolved to withstand particular
, Chapter 5 Proteins & Amino Acids 3
Structural Proteins
These proteins have evolved to withstand mechanical stress. These include
proteins like keratin that make up your hair and skin, as well as proteins like actin
and tropomyosin that enable muscle contraction.
Tubulin
Tubulin is a cytoskeletal protein that provides the
internal scaffold required for cell division.
Enzymatic Proteins
These proteins speed up chemical reactions
involved in digestion, blood clotting,
replication, transcription, translation, etc.
DNA Polymerase
DNA polymerase catalyzes the elongation of the
growing DNA strand during DNA replication.
Regulatory Proteins
These proteins coordinate the events within and between
cells. They turn various cellular processes “on” and “off.”
Src Kinase
Src kinase is a regulatory protein whose
misfunction is found in many types of cancer.
Carrier Proteins
These proteins help deliver molecules to different parts of cells and
organisms. These proteins are involved in processes such as
respiration, metabolism, and nerve stimulation.
Hemoglobin
Hemoglobin is found in red blood cells,
where it carries O2 throughout the body.
Figure 3 Proteins have a broad range of structures and functions
Example proteins are displayed using a surface representation. Proteins are colored by polypeptide chain.
mechanical stresses and afford protection to the organisms that produce
them. On a cellular level, structural proteins contribute to the physical
integrity of the cell and are responsible for much of the organization and
compartmentalization found in living systems. For example, cytoskeletal
Proteins &
Amino Acids
Many of the most important macromolecules in living systems are polymers.
Goal To understand how common
and dissimilar features of These polymers are composed of small building blocks that are linked
amino acids determine together in long, linear chains. Three of the most important biological
the chemical and physical polymers are polysaccharides, polynucleotides, and polypeptides (Figure
properties of proteins.
1). Polysaccharides, such as starch, are composed of sugar subunits whereas
polynucleotides, such as DNA and RNA (the subject of Chapter 8), are built
Objectives from nucleotides. Here and in the next chapter we focus on polypeptides.
After this chapter, you should be able to Polypeptides are chains of subunits called amino acids that are joined
together by peptide bonds. Short polypeptides are called peptides, and
• explain why peptide bonds are polar
long polypeptides are typically called proteins. Proteins are composed of
and prefer the trans configuration.
20 kinds of amino acids, which are at once alike and dissimilar. They share
• explain how side chains confer distinct common features that allow them to form peptide bonds with each other
chemical and physical properties on
amino acids.
while also exhibiting distinctive chemical features. This diversity of amino
acids and the sheer number of possible combinations in their linear order
• draw a peptide of a given sequence at a
allow for tremendous dissimilarity in the chemical and physical properties
specified pH.
of proteins (Figure 2). Furthermore, proteins do not exist as unstructured
chains. Rather, they fold in on themselves to form three-dimensional
architectures with unique features.
Proteins have diverse functions
Owing to their enormous diversity, cells employ proteins to perform
numerous tasks (Figure 3). Some proteins function as enzymes, which
catalyze chemical reactions by reducing ΔG‡. Nearly all enzymes are
proteins, and as we saw in the previous chapter, cells are able to carry
,Chapter 5 Proteins & Amino Acids 2
Figure 1 Polymers are Monomer Polymer
macromolecules composed of
small-molecule monomers linked
Carbohydrate
OH HO HO
O HO
together in chains HO
O
O O HO
O
HO O OH O OH O
OH HO OH O
HO
Carbohydrates, proteins, and nucleic acids OH HO HO
OHO
are examples of biological polymers. Each Sugar Starch
class of molecule is made of monomer
subunits covalently linked together in
S
chains.
Protein
O
O O O
H H
HO OH N N
N N N
NH2 H H H
O O
Amino acid OH
Protein
H2N N H
NH2 O N NH2
N H
N N O N O N
O N
Nucleic acid
O N N
P N N N
O N
O
O O O O
O O O
O P O O P O O P O O
OH
O O O
Deoxyucleotide
DNA
Figure 2 Proteins exhibit unique (A) (B)
structures and chemical properties
Surface charge representation of the
proteins actin (A) and HIV protease (B).
Even though both proteins are chains of
amino acids, they each feature distinct
three-dimensional shapes with unique
chemical properties, as evidenced by the
unique distribution of surface charges on
each molecule. Blue represents positive
charge, red negative charge, and white actin HIV protease
neutral.
out controlled chemical reactions because they use enzymes to modulate
reaction rates and couple favorable processes with unfavorable ones. In fact,
nearly all transformations that occur in the cell are mediated by enzymes,
and without them, living systems would carry out virtually no chemistry.
Enzymes catalyze a wide variety of reactions and are often categorized
according to the chemistry that they perform. Most enzymatic reactions
involve either the transfer of electrons (oxidation and reduction reactions),
the transfer of functional groups, the cleavage or formation of bonds, the
rearrangement of bonds within individual molecules, or the use of ATP to
covalently connect molecules. We will have more to say about how enzymes
lower ΔG‡ in subsequent chapters.
While enzymes come in many shapes and sizes and facilitate a vast number
of specific chemical reactions, proteins as a whole are even more diverse.
Not all proteins are enzymes; some proteins play structural roles. Hair is
made of such proteins, as are fingernails and the outer layers of the skin.
Many familiar materials, such as wool, silk, and leather are also made of
protein. These structural proteins have evolved to withstand particular
, Chapter 5 Proteins & Amino Acids 3
Structural Proteins
These proteins have evolved to withstand mechanical stress. These include
proteins like keratin that make up your hair and skin, as well as proteins like actin
and tropomyosin that enable muscle contraction.
Tubulin
Tubulin is a cytoskeletal protein that provides the
internal scaffold required for cell division.
Enzymatic Proteins
These proteins speed up chemical reactions
involved in digestion, blood clotting,
replication, transcription, translation, etc.
DNA Polymerase
DNA polymerase catalyzes the elongation of the
growing DNA strand during DNA replication.
Regulatory Proteins
These proteins coordinate the events within and between
cells. They turn various cellular processes “on” and “off.”
Src Kinase
Src kinase is a regulatory protein whose
misfunction is found in many types of cancer.
Carrier Proteins
These proteins help deliver molecules to different parts of cells and
organisms. These proteins are involved in processes such as
respiration, metabolism, and nerve stimulation.
Hemoglobin
Hemoglobin is found in red blood cells,
where it carries O2 throughout the body.
Figure 3 Proteins have a broad range of structures and functions
Example proteins are displayed using a surface representation. Proteins are colored by polypeptide chain.
mechanical stresses and afford protection to the organisms that produce
them. On a cellular level, structural proteins contribute to the physical
integrity of the cell and are responsible for much of the organization and
compartmentalization found in living systems. For example, cytoskeletal
