The Three-Dimensional Structure of Proteins

Protein

Polymers of amino acids linked by peptide bonds.

Native Conformation

3-D shapes of proteins with biological activity.

Random Coil

Proteins lacking a regular repeating structure.

Molecular Mass

Calculated by amino acid residues times 110.

Polypeptide

Chain of amino acids forming a protein.

Amino Acid Residues

Building blocks of proteins, typically 100-1000 per protein.

Monomeric Protein

Protein composed of a single polypeptide chain.

Oligomeric Protein

Protein made of multiple polypeptide chains.

Conjugated Protein

Protein attached to other macromolecules.

Globular Proteins

More soluble proteins with diverse functions.

Fibrous Proteins

Less soluble proteins providing structural support.

Enzymes

Biological catalysts facilitating biochemical reactions.

Amylase

Enzyme that digests carbohydrates in the mouth.

Structural Proteins

Provide mechanical support to cells and organisms.

Collagen

Fibrous protein giving strength to bones and skin.

Immune Proteins

Antibodies that bind and destroy foreign substances.

Transport Proteins

Carry small molecules through the bloodstream.

Lipoproteins

Transport insoluble biomolecules in the blood.

Ferritin

Protein used for nutrient storage.

Hormones

Regulatory proteins like insulin and prolactin.

G Proteins

Transmit hormonal signals inside cells.

Receptor Proteins

Mediates transmission of nerve impulses and signals.

Primary Structure

Sequence of amino acids in a polypeptide chain.

N-terminal End

Start of the polypeptide chain sequence.

C-terminal End

End of the polypeptide chain sequence.

Secondary Structure

Localized 3-D arrangements of polypeptide chain.

Alpha-helix

Common secondary structure formed by hydrogen bonds.

Beta-pleated Sheet

Another secondary structure with hydrogen bonding.

Domains

Clusters of secondary structural motifs in proteins.

Super-secondary Structure

Specific clusters of secondary structures in proteins.

Tertiary structure

3-D arrangement of all atoms in a protein.

Prosthetic groups

Non-amino acid portions of proteins.

Quaternary structure

Arrangement of multiple polypeptide subunits.

Subunits

Individual polypeptide chains in a protein.

Primary structure

Amino acid sequence of a protein.

Sickle-cell anemia

Condition caused by a single amino acid change.

Red blood cells

Cells that transport oxygen in the body.

Site-directed mutagenesis

Technique to replace specific amino acid residues.

Secondary structure

Hydrogen-bonded arrangement of polypeptide chains.

Ramachandran angles

Angles phi and psi for peptide bond rotation.

a-Helix

Right-handed helical structure stabilized by hydrogen bonds.

B-pleated sheet

Secondary structure with parallel or antiparallel strands.

Hydrogen bonds

Attractive forces between hydrogen and electronegative atoms.

Pitch

Linear distance between corresponding points on helix turns.

C-O group

Part of peptide bond involved in hydrogen bonding.

N-H group

Part of amino acid involved in hydrogen bonding.

Proline

Amino acid that disrupts a-helix structure.

Cyclic structure

Proline's structure restricts backbone rotation.

Intrachain hydrogen bonding

Hydrogen bonding within the same polypeptide chain.

Bond strength

Stability of interactions between atoms in proteins.

Amino acid residue

Individual amino acid within a protein sequence.

Conformation

Three-dimensional shape of a protein.

Biological activity

Function of a protein based on its structure.

Helical conformation

Arrangement allowing linear structure in proteins.

Maximum bond strength

Optimal stability in protein folding patterns.

3.6 residues

Number of amino acids per turn in a-helix.

5.4 Å

Distance between turns in an a-helix.

R groups

Side chains of amino acids extending outward.

Electrostatic Repulsion

Repulsion from like-charged side chains proximity.

Steric Repulsion

Crowding from bulky side chains proximity.

𝝰-Helical Conformation

Side chains lie outside the helix structure.

𝝰-Carbon

Carbon atom adjacent to amino acid side chain.

Lysine (Lys)

Positively charged amino acid side chain.

Arginine (Arg)

Positively charged amino acid side chain.

Glutamate (Glu)

Negatively charged amino acid side chain.

Aspartate (Asp)

Negatively charged amino acid side chain.

Valine (Val)

Bulky side chain causing steric repulsion.

Isoleucine (Ile)

Bulky side chain causing steric repulsion.

Threonine (Thr)

Bulky side chain causing steric repulsion.

B-Pleated Sheet

Extended peptide backbone with zigzag structure.

Hydrogen Bonds

Bonds between peptide chains in B-sheets.

Interchain Hydrogen Bonds

Hydrogen bonds between different peptide chains.

Intrachain Hydrogen Bonds

Hydrogen bonds within the same peptide chain.

Parallel B-Sheet

Chains aligned in the same direction.

Antiparallel B-Sheet

Chains aligned in opposite directions.

R Groups

Side chains alternate above and below the plane.

S-Trans Peptide Bond

Planar bond configuration in peptide chains.

310 Helix

Helix with three residues per turn.

B-Bulge

Irregularity in antiparallel B-sheets.

Reverse Turns

Regions where polypeptide chain folds back.

Glycine

Amino acid commonly found in reverse turns.

Proline

Cyclic amino acid found in reverse turns.

Supersecondary Structures

Combination of a and B strands.

BaB Unit

Two parallel B-strands connected by a-helix.

aa Unit

Contains two antiparallel a-helices.

B-Meander

Antiparallel sheet formed by tight reverse turns.

Greek Key

Polypeptide chain doubles back on itself.

Motifs

Repetitive supersecondary structures in proteins.

B-Barrel

Extensive B-sheets folding back on themselves.

Motifs

Patterns in proteins that do not predict function.

Protein Sequences

Similar sequences indicate similar protein functions.

Domains

Structural units associated with specific protein functions.

Collagen

Most abundant protein in vertebrates, found in tissues.

Triple Helix

Structure of collagen formed by three polypeptide chains.

Tropocollagen

Basic unit of collagen, molecular weight 300,000.

Amino Acid Sequence

Collagen has repeating X—Pro—Gly or X—Hyp—Gly.

Hydroxyproline

Modified proline essential for collagen stability.

Glycine

Every third residue in collagen, allows tight packing.

Superhelical Arrangement

Collagen chains twist to form a stiff rod.

Hydrogen Bonds

Stabilize collagen chains via hydroxyproline and hydroxylysine.