Unit-3-Chemistry-of-Proteins

Intended Learning Outcomes

• Categorize amino acids based on functional group and polarity: Recognizing the differences between various amino acids based on their chemical properties and how they influence protein structure and function.

• Explain the amphoteric property of amino acids due to amino and carboxyl groups: Understanding how amino acids can act both as acids and bases, allowing them to interact in various biological contexts.

• Illustrate the formation of peptides as a reaction between different amino acids: Detailing the process through which amino acids join together via peptide bonds, leading to the formation of dipeptides, tripeptides, and larger polypeptides.

• Determine the sequence of amino acids and names of peptides: Analyzing peptide sequences to understand their nomenclature and significance in biological systems.

• Explain the importance of some small peptides: Discussing the roles of biologically active peptides and their physiological significance, including signaling and regulatory functions in organisms.

• Describe the different levels of protein structure and their interrelationship: Outlining the hierarchical nature of protein structure from primary to quaternary levels and how they affect overall protein function.

• Relate protein structure to its physiological function: Connecting the specific shapes and configurations of proteins to their roles in biological systems, demonstrating structure-function relationships.

• Differentiate hydrolysis and denaturation of proteins: Clarifying these two processes and their implications for protein function and stability, and how they impact biological activities.

• Describe different methods commonly employed for the purification and characterization of proteins: Examining various techniques used in laboratories to isolate proteins for study, including the principles behind each method.

Unit Outline

I. Amino Acids

• General Structural Features of Amino Acids: Exploring the basic structure, including alpha carbon, amino and carboxyl groups, and variable side chains (R groups).

• Classification of Amino Acids: Categorizing amino acids based on their chemical properties, such as polarity, charge, and side-chain characteristics.

• Amphoteric Properties of Amino Acids (See Page 2)

II. Peptides

• Formation and General Structural Features of Peptides: In-depth discussion on how peptide bonds are formed and the different types of peptides (e.g., bioactive peptides) that play important roles in physiology.

• Nomenclature of Peptides: Detailing how peptide names are derived from their constituent amino acids, emphasizing exceptions and special cases.

• Small Peptides of Physiologic Importance (See Page 13)

III. Three-Dimensional Structure of Proteins

• Primary Structures: Understanding linear sequences of amino acids and how they dictate protein folding.

• Secondary Structures: Examining local folding patterns like alpha-helices and beta-sheets, including the forces that stabilize these structures.

• Tertiary Structures: Discussing the overall 3D arrangement of the entire polypeptide chain and influences such as disulfide bonds and hydrophobic interactions.

• Quaternary Structures: Describing how multiple polypeptide chains associate and the significance of these interactions in functional proteins.

• Protein Denaturation and Hydrolysis (See Page 16): Explaining conditions that lead to denaturation and how hydrolysis breaks down proteins into amino acids.

IV. Protein Purification and Characterization Techniques

• Extracting Pure Proteins from Cells (See Page 26): Discussing methods such as homogenization that prepare cellular extracts for further analysis.

• Purification of Extracted Proteins: Outlining various techniques, such as precipitation and chromatography, essential for purifying proteins for research studies.

• Determination of Protein’s Primary Structure and Protein Identification Techniques: Exploring methods used to analyze and confirm protein sequences and structures.

Proteins as Essential Macromolecules

• Discovered as critical nitrogen-containing compounds for animal survival: Historical context of protein research and its evolution over time.

• The term 'protein' coined by Jacob Berzelius in 1839, derived from Greek 'proteios' (first importance): Understanding the historical significance of proteins in biochemistry.

• Proteins account for 15% of total cell mass and 50% of dry weight: Discussing the critical roles that proteins play in biological systems, emphasizing their abundance in cellular structure.

What Makes a Protein a Protein?

• Natural unbranched polymers of amino acids connected by peptide bonds: Description of the fundamental nature of proteins and their composition.

• Early misconceptions: Addressing past myths regarding protein digestion and the subsequent discoveries that clarified the process.

Structure-Function Relationship

• Large molecules (> 50 amino acids) with specific biological functions linked to their unique conformations: Expanding on the relationship between protein size, shape, and biological roles.

• Example: Native conformation of hemoglobin vital for oxygen transport: Providing specific examples of how protein shape influences its functionality.

• Denaturation disrupts native structure leading to loss of function: Highlighting the implications of denaturation in biological systems.