Proteins: Structure, Function, and Building Blocks

Introduction to Protein Functions
- Proteins are fundamental for nearly every cellular process.
- They serve many important functions, including:
  - Forming structures: Such as cytoskeletal elements of an animal cell.
  - Mediating biochemical reactions: For example, the breakdown of glucose.
  - Transporting materials.
  - Supporting cell structure.
  - Helping cells move.
  - Regulating cell identity, communication, and internal signaling.
Amino Acids: The Building Blocks of Proteins
- Proteins are constructed from repeating monomeric units called amino acids.
- Amino acids are linked together by covalent bonds to form a chain.
- \text{Basic Structure of an Amino Acid} :
  - Each amino acid features a central carbon atom (also known as the alpha-carbon, often shaded in diagrams).
  - Bonded to this central carbon are four distinct groups:
    1. An amino group (nitrogen-containing) on the left.
    2. A carboxyl group (carbon and oxygen-containing) on the right.
    3. A hydrogen atom.
    4. A unique R-group (or side chain).
- \text{Chemical Behavior in Aqueous Environments (like a cell)} :
  - Amino groups act as bases; they tend to pick up a proton (\text{H}^+) in water, becoming positively charged (\text{N} ext{H}_3^+).
  - Carboxyl groups act as acids; they tend to drop a proton (\text{H}^+) in water, becoming negatively charged (\text{C} ext{O} ext{O}^-).
  - Consequently, in a cellular environment, amino acids exist in a charged state with a positive amino group and a negative carboxyl group.
- \text{The R-Group} :
  - The R-group (or side chain) is the distinguishing feature of each amino acid, determining its unique chemical properties and identity.
  - The letter 'R' is a symbolic placeholder for various atoms or groups of atoms; it is not an element symbol.
  - Based on the chemistry of its R-group, an amino acid can be classified as:
    - Fully charged
    - Partially charged
    - Not charged at all
  - The diversity of these R-groups underpins the incredible diversity of protein structures and functions.
Levels of Protein Structure
- Proteins must fold into specific three-dimensional shapes to be functional.
- \text{1. Primary Structure} :
  - This is the fundamental, linear sequence of amino acids in a polypeptide chain.
  - Amino acids are connected by covalent peptide bonds, formed between the carboxyl group of one amino acid and the amino group of the next.
  - By convention, the sequence is always written from the N-terminus (amino end, on the left) to the C-terminus (carboxyl end, on the right).
  - Proteins range in size from small (e.g., 100 amino acids) to very large (more than 30,000 amino acids), with most being a few hundred to a few thousand amino acids long.
  - Unique primary structures lead to unique folded structures and diverse functions.
- \text{2. Secondary Structure} :
  - Refers to common, local folding patterns within segments of the polypeptide chain.
  - These structures are stabilized primarily by hydrogen bonds formed between atoms of the polypeptide backbone (not the R-groups).
  - The two most common types are:
    - Alpha helices (\alpha-helices): Twisting patterns in the chain.
    - Beta sheets (\beta-sheets): Zigzag, pleated patterns.
  - Secondary structures contribute to stabilizing the overall protein fold.
- \text{3. Tertiary Structure} :
  - This represents the overall, unique three-dimensional shape of a single polypeptide chain.
  - It is the fully folded, functional state of the protein.
  - The folding process is entirely determined by the primary amino acid sequence and the chemistry of the R-groups.
  - Various types of bonds and interactions between R-groups stabilize the tertiary structure:
    - Hydrogen bonds
    - Electrostatic bonds
    - Ionic bonds
    - Covalent bonds
  - Crucially, proteins are not functional until they have achieved their unique tertiary structure.
- \text{4. Quaternary Structure} :
  - This level of structure exists only in some proteins.
  - It describes the arrangement and association of multiple polypeptide chains (subunits) to form a larger, functional protein complex.
Conclusion
- The immense diversity observed in protein functions is directly linked to the incredible diversity and complexity of their structures.
- Specific examples of proteins and their roles in cellular processes will be continually explored throughout the course.