Chapter 3- Protein Structure and Function

3.1 Amino Acids and Their Polymerization

Most of these molecules are composed of just 20 different building blocks, called amino acids.
In all 20 amino acids, a central carbon atom (referred to as the carbon) bonds covalently to four different atoms or groups of atoms:
- H-a hydrogen atom
- NH2-an amino functional group
- COOH-a carboxyl functional group
- a distinctive R-group”
The combination of amino and carboxyl functional groups is key to how these molecules behave.
The R-group, or side chain, represents the part of the amino acid core structure that makes each of the 20 different amino acids unique.
Both polar and electrically charged R-groups interact readily with water and are hydrophilic.
Nonpolar R-groups lack charged or highly electronegative atoms capable of forming hydrogen bonds with water. These R-groups are hydrophobic, meaning that they do not interact with water. Instead of dissolving, hydrophobic R-groups tend to coalesce in aqueous solution.
If the R-group in your amino acid does not have a negative charge, a positive charge, or an oxygen atom, then you are looking at a nonpolar amino acid, such as methionine.
The C-N covalent bond that results from this condensation reaction is called a peptide bond.
There are three key points to note about the peptide-bonded backbone:
- R-group orientαfion: The side chains of each residue extend out from the backbone, making it possible for them to interact with each other and with water.
- Directionαnal: There is an amino group (-NH3 +) on one end of the backbone and a carboxyl group (-Coo-) on the other.
- Flexibility: Although the peptide bond itself cannot rotate because of its double-bond nature, the single bonds on either side of the peptide bond can rotate. As a result, the structure as a whole is flexible
Generally, when fewer than 50 amino acids are linked together in this way, the resulting polymer is called an oligopeptide (“few-peptides”) or simply a peptide.
Polymers that contain 50 or more amino acids are called polypeptides (“many-peptides”).
The term protein is often used to describe any chain of amino acid residues.

3.2 What Do Proteins Look Like?

Biochemists refer to the unique sequence of amino acids in a protein as its primary structure.
The next level of organization in proteins-secondary structure-is generated in part by interactions between functional groups in the peptide bonded backbone.
In most proteins, these polar groups are aligned and form hydrogen bonds with one another when the backbone bends to form one of two possible structures:
- an a-helix (alpha-helix), in which the polypeptide’s backbone is coiled
- a B-pleated sheet (beta-pleated sheet), in which segments of a peptide chain bend 180° and then fold in the same plane
A protein’s distinctive overall three-dimensional shape, or tertiary structure, results from interactions between residues that are brought together as the backbone bends and folds in space.
There are five types of interactions involving R-groups that are important:
- Hydrogen bonding
- Hydrophobic interactions
- Van de Waals interactions
- Covalent bonding
- Ionic bonding
These disulfide (“two-sulfur”) bonds are frequently referred to as bridges, because they create strong links between distinct regions of 1e same polypeptide or two separate polypeptides.
The combination of polypeptides, referred to as subunits, gives some proteins quaternary structure.
In addition, cells contain macromolecular machines: complexes of multiple proteins that assemble to carηr out a particular function.

3.3 Folding and Function

More recent work has shown that cells contain special proteins called molecular chaperones that can facilitate protein folding.
Certain normal proteins can be induced to fold into infectious, disease-causing agents which are called prions.

3.4 Protein Functions Are as Diverse as Protein Structures

Proteins are crucial to most tasks required for cells and organisms to exist:
- Cαtαlysis Many proteins are specialized to catalyze, or speed up, chemical reactions. A protein that functions as a catalyst is called an enzyme.
- Structure
- Movement
- Signaling
- Transport
- Defense
Catalyzed reactions involve one or more reactants, called substrates.
As researchers began to test Fischer's model, the location where substrates bind and react became known as the enzyme’s active site.

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Chapter 3- Protein Structure and Function

3.1 Amino Acids and Their Polymerization

Most of these molecules are composed of just 20 different building blocks, called amino acids.
In all 20 amino acids, a central carbon atom (referred to as the carbon) bonds covalently to four different atoms or groups of atoms:
- H-a hydrogen atom
- NH2-an amino functional group
- COOH-a carboxyl functional group
- a distinctive R-group”
The combination of amino and carboxyl functional groups is key to how these molecules behave.
The R-group, or side chain, represents the part of the amino acid core structure that makes each of the 20 different amino acids unique.
Both polar and electrically charged R-groups interact readily with water and are hydrophilic.
Nonpolar R-groups lack charged or highly electronegative atoms capable of forming hydrogen bonds with water. These R-groups are hydrophobic, meaning that they do not interact with water. Instead of dissolving, hydrophobic R-groups tend to coalesce in aqueous solution.
If the R-group in your amino acid does not have a negative charge, a positive charge, or an oxygen atom, then you are looking at a nonpolar amino acid, such as methionine.
The C-N covalent bond that results from this condensation reaction is called a peptide bond.
There are three key points to note about the peptide-bonded backbone:
- R-group orientαfion: The side chains of each residue extend out from the backbone, making it possible for them to interact with each other and with water.
- Directionαnal: There is an amino group (-NH3 +) on one end of the backbone and a carboxyl group (-Coo-) on the other.
- Flexibility: Although the peptide bond itself cannot rotate because of its double-bond nature, the single bonds on either side of the peptide bond can rotate. As a result, the structure as a whole is flexible
Generally, when fewer than 50 amino acids are linked together in this way, the resulting polymer is called an oligopeptide (“few-peptides”) or simply a peptide.
Polymers that contain 50 or more amino acids are called polypeptides (“many-peptides”).
The term protein is often used to describe any chain of amino acid residues.

3.2 What Do Proteins Look Like?

Biochemists refer to the unique sequence of amino acids in a protein as its primary structure.
The next level of organization in proteins-secondary structure-is generated in part by interactions between functional groups in the peptide bonded backbone.
In most proteins, these polar groups are aligned and form hydrogen bonds with one another when the backbone bends to form one of two possible structures:
- an a-helix (alpha-helix), in which the polypeptide’s backbone is coiled
- a B-pleated sheet (beta-pleated sheet), in which segments of a peptide chain bend 180° and then fold in the same plane
A protein’s distinctive overall three-dimensional shape, or tertiary structure, results from interactions between residues that are brought together as the backbone bends and folds in space.
There are five types of interactions involving R-groups that are important:
- Hydrogen bonding
- Hydrophobic interactions
- Van de Waals interactions
- Covalent bonding
- Ionic bonding
These disulfide (“two-sulfur”) bonds are frequently referred to as bridges, because they create strong links between distinct regions of 1e same polypeptide or two separate polypeptides.
The combination of polypeptides, referred to as subunits, gives some proteins quaternary structure.
In addition, cells contain macromolecular machines: complexes of multiple proteins that assemble to carηr out a particular function.

3.3 Folding and Function

More recent work has shown that cells contain special proteins called molecular chaperones that can facilitate protein folding.
Certain normal proteins can be induced to fold into infectious, disease-causing agents which are called prions.

3.4 Protein Functions Are as Diverse as Protein Structures

Proteins are crucial to most tasks required for cells and organisms to exist:
- Cαtαlysis Many proteins are specialized to catalyze, or speed up, chemical reactions. A protein that functions as a catalyst is called an enzyme.
- Structure
- Movement
- Signaling
- Transport
- Defense
Catalyzed reactions involve one or more reactants, called substrates.
As researchers began to test Fischer's model, the location where substrates bind and react became known as the enzyme’s active site.