Structure of Proteins PPT: Proteins are complex biomolecules made up of amino acids linked by peptide bonds, and their structure is organized into four levels. The primary structure is the unique sequence of amino acids in a polypeptide chain. This sequence determines the protein’s characteristics and function. The secondary structure refers to localized folding patterns such as alpha-helices and beta-pleated sheets, stabilized by hydrogen bonds. The tertiary structure is the overall three-dimensional shape of a single polypeptide, formed by interactions among R groups, including hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges. The quaternary structure exists in proteins with multiple polypeptide chains, where these subunits assemble into a functional protein. Hemoglobin is a classic example. Proper folding is essential for a protein’s biological activity, and misfolding can lead to diseases like Alzheimer’s. Understanding protein structure is key in fields like molecular biology, biochemistry, and drug design, as it underpins how proteins work in living systems.
Biochemistry Notes | Biochemistry PPT
Structure of Proteins PPT
Structure of Proteins (Handouts)
Protein Structure
- Proteins have four levels of structural organization: primary, secondary, tertiary, and quaternary.
- All functional proteins have at least up to the tertiary level of structure.
- Some proteins have all four levels (up to quaternary structure)
Primary Structure
- The primary structure is the amino acid sequence of a protein.
- It includes the number and order of amino acids.
- The primary structure determines all other levels of protein structure.
- Primary structure is stabilized by peptide bonds (covalent bonds).
- Insulin was the first protein to have its sequence determined (by Frederick Sanger).
Importance of Primary Structure
- Provides insights into a protein’s 3D structure, function, cellular location, and evolution.
- Primary structure data is used for sequence searching in databases (BLAST).
Three-Dimensional Structure of Proteins
- Protein backbones have many bonds with potential for free rotation, allowing numerous conformations.
- Each protein has a unique 3D structural conformation.
- Conformation: The spatial arrangement of atoms in a protein.
- Functional, folded proteins are called native proteins.
- Protein conformations are mainly stabilized by weak interactions.
- These weak interactions can be easily distorted.
- Proteins have three levels of 3D organization: secondary, tertiary, and quaternary.
Secondary Structure
- Secondary structure is the local conformation of a polypeptide chain.
- It’s the folding pattern of the polypeptide backbone.
- Secondary structures are stabilized mainly by hydrogen bonds.
- The two most important secondary structures are α-helices and β-conformations (β-sheets).
(A). α-Helix
- The α-helix is a common secondary structure, repeating every 5.4 Å.
- The polypeptide backbone is tightly wound around an imaginary axis, with R groups protruding outward.
- Pitch of helix: A single turn of the helix, about 5.4 Å.
- Each helical turn includes 3.6 amino acids.
- The α-helix twist is right-handed in all proteins.
- α-helices are stabilized by hydrogen bonds between the hydrogen attached to the electronegative nitrogen atom of the peptide linkage and the electronegative carbonyl oxygen atom of the fourth amino acid on the amino-terminal side of the peptide bond.
- Every peptide bond participates in hydrogen bonding within the α-helix.
- Interactions between amino acid side chains can stabilize or destabilize α-helices.
- For example, a long block of glutamic acid residues will not form an α-helix due to the repulsion of negatively charged carboxyl groups.
- Proline residues also destabilize α-helices because the nitrogen atom is part of a rigid ring, preventing rotation.
(B). β-Conformations (β-Plates)
- β-conformations organize polypeptide chains into sheets.
- The polypeptide backbone is extended into a zigzag structure.
- Zigzag chains arranged side-by-side form β-sheets.
- β-sheets are also stabilized by hydrogen bonds between adjacent chain segments.
- R-groups of adjacent amino acids protrude in opposite directions from the zigzag structure.
- β-sheets can be arranged in two ways: anti-parallel and parallel.
Tertiary Structure
- Tertiary structure is the overall 3D arrangement of all atoms in a protein.
- It involves a single polypeptide chain with one or more secondary structures.
- Tertiary structure is defined by atomic coordinates.
- It is stabilized by covalent bonds (e.g., disulfide bonds between cysteine residues) and other interactions.
- Proteins with a single subunit have up to tertiary structure.
Quaternary Structure
- Many functional proteins contain more than one polypeptide chain (subunit).
- Quaternary structure is the arrangement of subunits in 3D complexes in a multi-subunit protein.
- For a protein to have quaternary structure:
- It must have more than one polypeptide subunit.
- Subunits should not have permanent (covalent) interactions (like disulfide bonds) between them.
- Insulin does not have quaternary structure because its two polypeptides are covalently linked by disulfide bonds. Thus, insulin has up to tertiary structure.
Native Conformation of Proteins
- Native proteins are in their folded/assembled, fully functional form.
- They are in an unaltered form, not changed by denaturing agents.
- Native proteins possess all levels of structural organization (up to quaternary, if applicable).
- Some enzymes have multiple native states and transition between them for regulation.
- Native PAGE is a separation technique used for purifying native proteins.
- SDS-PAGE disrupts the native conformation of proteins.
Denaturation of Protein
- Denaturation is the disruption of secondary and tertiary structures.
- It disrupts bonds stabilizing these structures but does not break peptide bonds (primary structure).
- Denaturation is observed as coagulation.
- Denaturing agents include heat, alcohol, acids, bases, and heavy metals.
Characteristics of Denatured Proteins
- Loss of native structure and biological activity.
- Primary structure remains intact.
- Denatured proteins are often insoluble in water and more easily digested.
- Denaturation is usually irreversible but can be reversible in some cases.
Renaturation of Protein
- Renaturation is the process of a denatured protein returning to its native conformation.
- Careful denaturation can sometimes be reversed.
- Example: Hemoglobin denatures in salicylate but can renature upon its removal.
References
- Berg, J.M. and Tymoczko, J.L., 2018. Stryer biochemie (Vol. 8). Heidelberg: Springer Spektrum.
- Nelson, D.L., Lehninger, A.L. and Cox, M.M., 2008. Lehninger principles of biochemistry. Macmillan.
- Voet, D. and Voet, J.G., 2010. Biochemistry. John Wiley & Sons.
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