Chapter 3: Protein Structure and Function
Proteins are made of amino acids. Amino acids vary in structure and function because their side chains vary in
Proteins vary widely in structure. The structure of a protein can be analyzed at four levels that form a hierarchy
—the amino acid sequence, substructures called α-helices and β-pleated sheets, interactions between amino
acids that dictate a protein’s overall shape, and combinations of individual proteins that make up larger,
Proteins vary widely in function. In cells, most proteins are enzymes that function as catalysts. Chemical
reactions occur much faster when they are catalyzed by enzymes. During enzyme catalysis, the reactants bind to
an enzyme’s active site in a way that allows the reaction to proceed efficiently.
Section 3.1 Outline:
What Do Proteins Do?
The diverse functions of proteins include: defense, movement, catalysis, signaling, structure, and transport
Section 3.2 Outline:
Early Origin-of-Life Experiments
To test whether the first steps of chemical evolution could have occurred on ancient Earth, Stanley Miller
combined methane (CH
), ammonia (NH
), and hydrogen (H
) in a closed system with water, and applied heat
and electricity as an energy source (Figure 3.1).
The products that resulted from Miller’s experiment included hydrogen cyanide (HCN) and formaldehyde
CO), important precursors for more-complex organic molecules and amino acids.
Section 3.3 Outline:
Amino Acids and Polymerization
More recent experiments, similar to Miller’s, have confirmed that the second step in chemical evolution
occurred early in Earth’s history. Amino acids and other organic molecules form easily under conditions that
accurately simulate those on ancient Earth.
The Structure of Amino Acids
All proteins are made from just 21 amino acids. All
have a central
carbon atom that bonds to NH
(an amino functional group), COOH (a carboxyl functional group), H (a
hydrogen atom), and a variable side chain (Figure 3.2).
In water (
), the amino and carboxyl groups ionize to NH
, respectively, which helps amino acids
stay in solution and makes them more reactive.
The Nature of Side Chains
The 21 amino acids differ only in the variable side chain or R-group attached to the
central carbon (Figure 3.3). R-groups differ in their size, shape, reactivity, and interactions with water.
R-groups cannot form hydrogen bonds with water and tend to coalesce in aqueous
solution, whereas polar
R-groups interact readily with water (Table 3.2).
The nature of the side chain influences chemical reactivity. Amino acids with hydroxyl, amino, carboxyl, or