MBOC7_lectureppt_Ch03+-+S24

Chapter 3: Proteins

Overview of Proteins

• Proteins are complex macromolecules essential for various biological functions.

• They are formed from smaller organic building blocks (amino acids) and can possess different structures and functions.

Focused Chapter Contents

• Atomic Structure of Proteins:

  • Amino acids

  • Peptide bonds

  • Levels of protein structure (Primary to Quaternary)

• Shape Dictates Function: The conformation of a protein directly influences its role.

• Protein Functions:

  • Enzymes and catalysts

  • Immune functions (immunoglobulins)

  • Kinase activity and phosphorylation

  • Other key modifications affecting function.

Building Blocks of Proteins

Small Organic Building Blocks of the Cell

• Amino Acids

  • Architectural units for protein synthesis.

Amino Acids

General Structure of Amino Acids

• Fundamental structure includes:

  • An amino group (H₂N)

  • A carboxyl group (COOH)

  • An α-carbon atom

  • A side chain (R), which varies among the 20 standard amino acids.

Families of Amino Acids

• Amino acids categorized by side chain properties:

  • Acidic: Aspartic acid (Asp, D), Glutamic acid (Glu, E)

  • Basic: Lysine (Lys, K), Arginine (Arg, R), Histidine (His, H)

  • Uncharged Polar: Asparagine (Asn, N), Glutamine (Gln, Q), Serine (Ser, S)

  • Nonpolar: Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Glycine (Gly, G), Methionine (Met, M), Proline (Pro, P), Phenylalanine (Phe, F), Tryptophan (Trp, W), Cysteine (Cys, C)

Peptide Bonds

• Formation of peptide bonds occurs through dehydration synthesis:

  • Involves the amino group of one amino acid and the carboxyl group of another, releasing water.

• Peptide bonds link amino acids into polypeptides.

Protein Structure

Levels of Protein Structure

• Primary Structure: Linear sequence of amino acids in a polypeptide chain.

• Secondary Structure: Local folding, including alpha helices and beta sheets, stabilized by hydrogen bonds.

• Tertiary Structure: 3D configuration resulting from interactions between R groups, including hydrophobic interactions and disulfide bonds.

• Quaternary Structure: Assembly of multiple polypeptide chains into a functional protein.

Structural Dynamics

• Proteins fold into their lowest energy conformation, crucial for their function.

• Specific examples of protein structures:

  • Alpha Helix:

    • Coiled structures stabilized by hydrogen bonds.

o - Beta Sheets: - Flat, sheet-like structures, also stabilized by hydrogen bonds.

Protein Domains and Functionality

• Proteins may have multiple functional domains, each with distinct roles.

• Domains: Functional units within proteins, influencing overall function and interactions with other molecules.

Enzyme Function

General Enzyme Characteristics

• Enzymes are biological catalysts that accelerate chemical reactions.

• They work by selectively stabilizing transition states and lowering activation energy.

• Examples of Enzyme Classes:

  • Hydrolases: Catalyze hydrolytic reactions.

  • Kinases: Add phosphate groups to proteins, altering function.

  • Ligases: Join two molecules in reactions requiring energy (e.g., DNA ligase).

Protein Modifications

Regulation through Phosphorylation

• Protein phosphorylation is a major regulatory mechanism in cells, modulating activity and function.

• Ubiquitination: A process signaling for protein degradation or altering cellular location.

Types of Covalent Modifications

• A variety of covalent modifications influence protein function and localization:

  • Phosphorylation, acetylation, and ubiquitination are common examples impacting function.

Conclusion

• Proteins showcase a tremendous diversity in structure and function, determined by their amino acid sequences, conformations, and post-translational modifications.