Freeman Chapter 3 Protein Presentation

Chapter 3

_Protein

Key Concepts

• _{Proteins are made of amino acids. Amino acids vary in structure}

and function.

• _{The structure of a protein can be analyzed at four levels:}

(1) Amino acid sequence

(2) Substructures called -helices and -pleated sheets

(3) Interactions between amino acids that dictate a protein’s overall shape

(4) Combinations of individual proteins that make up larger, multiunit molecules

What Do Proteins Do?

• _{The diverse functions of proteins include: defense, movement,}

Early Origin-of-Life Experiments

Could the first steps of chemical evolution have occurred on ancient Earth?

• To find out, Stanley Miller combined methane (CH₄), ammonia (NH₃), and hydrogen (H₂) in a closed system with water, and applied heat and electricity as an energy source.

• The products included hydrogen cyanide (HCN) and

formaldehyde (H₂CO), important precursors for more-complex organic molecules and amino acids.

The Structure of Amino Acids

• _{All proteins are made from just 21 amino acids.}

• All amino acids have a central carbon atom that bonds to NH₂,

COOH, H, and a variable side chain.

• _{In water (pH7), the amino and carboxyl groups ionize to NH}3+ and

COO–, respectively—this helps amino acids stay in solution and

The Nature of Side Chains

• _{The 21 amino acids differ only in the variable side chain or}

R-group attached to the central carbon

• _{R-groups differ in their size, shape, reactivity, and interactions}

with water.

(1) Nonpolar R-groups: Do not form hydrogen bonds; coalesce in water

(2) Polar R-groups: Form hydrogen bonds; readily dissolve in water

• _{Amino acids with hydroxyl, amino, carboxyl, or sulfhydryl}

functional groups in their side chains are more chemically

What Are Isomers?

Isomers are molecules with the same molecular formula but

different structures. Isomers include the following:

• _{Structural isomers: Differ in the order which their atoms are}

attached

• _{Geometric isomers: Differ in the arrangement of atoms around a}

double bond

• _{Optical isomers: Differ in the arrangement of atoms, or groups,}

Condensation and Hydrolysis Reactions

• Amino acids polymerize to form proteins. Polymerization reactions require energy and are not spontaneous.

• Monomers polymerize through condensation reactions, which release a water molecule. In the reverse reaction, hydrolysis, water reacts with a polymer to release a monomer.

• In the prebiotic soup, hydrolysis would predominate over

condensation because it is energetically favorable. However,

The Peptide Bond

• _{Condensation reactions bond the carboxyl group of one amino}

acid to the amino group of another to form a peptide bond.

• _{A polypeptide is flexible and has directionality (the N-terminus}

Peptide Bond Formation

Carboxyl group

Amino group

Peptide bond

What Do Proteins Look Like?

• _{Proteins are diverse in size and shape, as well as in the chemical}

properties of their amino acids.

• _{Proteins have four basic levels of structure: primary, secondary,}

Primary Structure

• _{A protein’s primary structure is its unique sequence of amino}

acids.

• Because the amino acid R-groups affect a polypeptide’s

Secondary Structure

• _{Secondary structure results in part from hydrogen bonding}

between the carboxyl oxygen of one amino acid residue and the amino hydrogen of another. A polypeptide must bend to allow this hydrogen bonding—thus, -helices or -pleated sheets are formed.

• _{Secondary structure depends on the primary structure—some}

amino acids are more likely to be involved in α-helices; while others, in β-pleated sheets.

Secondary Structures of Proteins

Hydrogen bonds form between peptide chains.

Secondary structures of proteins result.

-helix _-pleated sheet

Ribbon diagrams of secondary structure.

Hydrogen bonds

Secondary Structures of Proteins

Hydrogen bonds form between peptide chains.

Secondary Structures of Proteins

Secondary structures of proteins result.

Secondary Structures of Proteins

Ribbon diagrams of secondary structure.

-helix _-pleated

Arrowheads are at the

Tertiary Structure

• _{The tertiary structure of a polypeptide results from interactions}

between R-groups or between R-groups and the peptide

backbone. These contacts cause the backbone to bend and fold, and contribute to the 3D shape of the polypeptide.

• R-group interactions include hydrogen bonds, van der Waals

interactions, covalent disulfide bonds, and ionic bonds.

Tertiary Structures of Proteins

Tertiary structures are diverse.

Interactions that determine the tertiary structure of proteins

Ionic bond

Disulfide bond Hydrophobic

interactions (van der Waals interactions) Hydrogen bond between

Tertiary Structures of Proteins

Interactions that determine the tertiary structure of proteins

Hydrogen bond between side chain and carboxyl oxygen

Hydrogen bond between two side chains

Hydrophobic interactions (van der Waals interactions)

Ionic bond

Tertiary Structures of Proteins

Tertiary structures are diverse.

A tertiary structure composed mostly of -helices

A tertiary structure composed mostly of -pleated sheets

Van der Waals Interactions

• _{van der Waals interactions are electrical interactions between}

hydrophobic side chains. Although these interactions are weak, the large number of van der Waals interactions in a polypeptide significantly increases stability.

• Covalent disulfide bonds form between sulfur-containing R-groups.

Quaternary Structure

• _{Some proteins contain several distinct polypeptide subunits that}

interact to form a single structure; the bonding of two or more subunits produces quaternary structure.

• _{The combined effects of primary, secondary, tertiary, and}

Quaternary Structures of Proteins

Folding and Function

• _{Protein folding is often spontaneous, because the hydrogen bonds}

and van der Waals interactions make the folded molecule more stable energetically than the unfolded molecule.

• _{A denatured (unfolded) protein is unable to function normally.}

• _{Proteins called molecular chaperones help proteins fold}

Was the First Living Entity a Protein?

• _{Several observations argue that the first self-replicating molecule}

on Earth was a protein:

(1) Amino acids were abundant in the prebiotic soup. (2) Proteins are the most efficient catalysts known.

(3) Self-replicating molecule had to act as a catalyst for the assembly and polymerization of its copy.