Proteins: Structure, Function, and Classification in Biochemistry

What are proteins primarily composed of?

High molecular weight polypeptides made up of amino acids.

What distinguishes simple proteins from complex proteins?

Simple proteins contain only amino acids, while complex proteins contain additional non-amino acid materials.

What is the axial ratio of globular proteins?

Less than 10, usually around 3 to 4.

Give an example of a globular protein.

Insulin, albumin, or globulin.

What is the axial ratio of fibrous proteins?

Greater than 10.

What are some examples of fibrous proteins?

Keratin, collagen, and fibrin.

What role do disulfide bonds play in proteins?

They stabilize protein structure by linking polypeptide chains through cystine residues.

What are the main types of bonds that stabilize proteins?

Covalent bonds (peptide and disulfide bonds) and non-covalent bonds (hydrogen bonds, hydrophobic interactions, electrostatic bonds, and van der Waals interactions).

What is a peptide bond?

A bond that connects the carbonyl carbon and the amino nitrogen of amino acids.

What is the significance of the phi (φ) and psi (ψ) angles in proteins?

They determine the rotation and conformation of the peptide backbone.

What are the four levels of protein structure?

Primary, secondary, tertiary, and quaternary structures.

What defines the primary structure of a protein?

The sequence of amino acids in the polypeptide chain.

What characterizes the secondary structure of proteins?

Regular arrangements of amino acids, such as alpha-helices and beta-pleated sheets.

What is an alpha-helix?

A coiled structure formed by a series of amino acids adopting similar phi and psi angles.

What is a beta-pleated sheet?

A secondary structure formed by adjacent polypeptide chains running in parallel or anti-parallel directions.

What are random coils in protein structure?

Disordered conformations of denatured proteins that do not represent a secondary structure.

What is the role of hydrogen bonds in protein structure?

They stabilize the structure by forming interactions between the side chains of amino acids and between peptide bonds.

What is the function of electrostatic bonds in proteins?

They form between oppositely charged groups in the side chains of amino acids.

What is the significance of hydrophobic interactions in proteins?

They contribute to the stability of the protein's interior by clustering non-polar side chains.

What is mass spectrometry used for in protein analysis?

To determine amino acid sequences and identify post-translational modifications.

What is the purpose of Sanger sequencing?

To determine the primary structure of proteins, such as insulin.

What are supersecondary structures?

Structural motifs that are combinations of several secondary structures.

What is the role of proteases in protein analysis?

They cleave polypeptides at specific amino acid residues to help determine protein structure.

What amino acids are known to disrupt alpha-helices?

Proline and amino acids with charged or bulky R groups.

What are the five ways tertiary structures are stabilized?

Covalent Bonds, Hydrogen Bonds, Salt Bridges, Hydrophobic Interactions, Metal Ion Coordination.

What is a 'molten globule' in protein folding?

An entity that has extensive secondary structure but disordered tertiary structure.

What role do molecular chaperones play in protein folding?

They accelerate the folding process by providing a protected environment and inhibiting inappropriate interactions.

What is the function of Protein Disulfide Isomerase?

It catalyzes the random cleavage and reformation of disulfide bonds during protein folding.

What is denaturation in the context of proteins?

The disruption of native conformation and weak forces maintaining secondary, tertiary, and quaternary structures, leading to loss of biological activity.

What are common denaturing agents?

Strong acids and bases, heat, ionic detergents, urea, guanidine, heavy metals, and organic solvents.

What is the significance of the primary structure of a protein?

It dictates how proteins spontaneously fold into their native conformation under physiological conditions.

What is the role of prolyl cis-trans isomerase in protein folding?

It catalyzes the inter-conversion of X-Pro peptide bonds between cis and trans conformations, facilitating the folding process.

What are chaperonins?

Cage-like proteins that assist in protein folding, found in bacteria, mitochondria, chloroplasts, and eukaryotes.

What is the structure of collagen?

It consists of a Gly-X-Y sequence, where Y is usually proline or hydroxyproline, forming a triple helix stabilized by hydrogen bonds.

What is the fundamental unit of collagen called?

Tropocollagen, which consists of three polypeptide chains in a right-handed triple helix.

What characterizes fibrous proteins?

They have elongated structures and repeating structural motifs, such as a-keratin and collagen.

What distinguishes globular proteins from fibrous proteins?

Globular proteins have a spherical structure, while fibrous proteins have elongated structures.

What is a key feature of silk fibroin (b-keratin)?

It is composed of stacked anti-parallel beta-sheets, largely consisting of glycine, serine, and alanine.

How does keratin contribute to the structure of hair and wool?

a-helical cables untwist when stretched and spring back when force is removed, providing springiness.

What happens during the folding of proteins?

Proteins undergo a series of conformational adjustments to achieve their native structure, which is optimal for function.

What is the impact of temperature on heat shock proteins?

The rate of synthesis increases at elevated temperatures, helping to reverse denaturation and aggregation of proteins.

What is the significance of hydrophobic amino acids in protein structure?

They contribute to the stability of protein structures by promoting interactions between non-polar side chains.

What is the relationship between protein structure and function?

Proteins have unique conformations that are specifically suited for their biological functions.

What is the typical conformation of a-keratin?

It consists of two right-handed a-helices that aggregate side by side to form long cables with a left-handed twist.

What is the role of salt bridges in protein stability?

Salt bridges are ionic interactions that help stabilize the tertiary and quaternary structures of proteins.