Proteins and Enzymes: The Proteome

1. Introduction to Proteins

• Proteins are a diverse group of organic molecules that are essential for life.
• They are polymers made up of amino acid monomers.
• Proteins perform a vast array of functions within cells and organisms.

KEY TAKEAWAY: Proteins are the workhorses of the cell, carrying out a wide variety of functions essential for life.

2. The Proteome

• The proteome is the entire set of proteins expressed by a cell, tissue, or organism at a certain time under defined conditions.
• Unlike the genome (which is relatively constant), the proteome is dynamic and varies depending on factors such as:
  • Cell type
  • Developmental stage
  • Environmental conditions
• Proteomics is the study of the proteome, including protein identification, quantification, and function.

APPLICATION: Proteomics is used in drug discovery, diagnostics, and personalized medicine.

3. Amino Acids: The Building Blocks of Proteins

• Amino acids are the monomers that make up proteins.
• Each amino acid has a central carbon atom bonded to:
  • An amino group (\(-NH_2\))
  • A carboxyl group (\(-COOH\))
  • A hydrogen atom (\(-H\))
  • A variable R-group
• The R-group distinguishes one amino acid from another and determines its chemical properties.
• There are 20 common amino acids found in proteins.
• Amino acids are linked together by peptide bonds to form polypeptides.

3.1 Peptide Bond Formation

• A peptide bond is formed through a dehydration reaction (removal of water) between the carboxyl group of one amino acid and the amino group of another.
• The resulting chain of amino acids is called a polypeptide.

STUDY HINT: Draw out the structure of a peptide bond to understand how it forms.

4. Protein Structure

Proteins have four levels of structural organization:

4.1 Primary Structure

• The primary structure is the linear sequence of amino acids in a polypeptide chain.
• It is determined by the genetic code.

4.2 Secondary Structure

• The secondary structure refers to local folding patterns within a polypeptide chain.
• Common secondary structures include:
  • α-helix: A coiled structure stabilized by hydrogen bonds between amino acids.
  • β-pleated sheet: A sheet-like structure formed by hydrogen bonds between adjacent polypeptide strands.

4.3 Tertiary Structure

• The tertiary structure is the overall three-dimensional shape of a single polypeptide chain.
• It is determined by interactions between R-groups, including:
  • Hydrogen bonds
  • Ionic bonds
  • Hydrophobic interactions
  • Disulfide bridges

4.4 Quaternary Structure

• The quaternary structure is the arrangement of multiple polypeptide chains (subunits) in a multi-subunit protein.
• Not all proteins have quaternary structure.

REMEMBER: Primary = sequence, Secondary = local folding, Tertiary = overall shape, Quaternary = subunit arrangement.

5. Protein Diversity and Function

Proteins perform a wide variety of functions in living organisms:

VCAA FOCUS: Be able to link specific protein functions to their structure.

6. Enzymes: Biological Catalysts

• Enzymes are proteins that act as biological catalysts.
• They speed up biochemical reactions by lowering the activation energy.
• Enzymes are highly specific for their substrates (the molecules they act on).
• Enzymes are not consumed in the reactions they catalyze.

6.1 Enzyme-Substrate Interaction

• The active site is the region of an enzyme where the substrate binds.
• The enzyme and substrate interact to form an enzyme-substrate complex.
• The enzyme catalyzes the conversion of the substrate into products.
• The products are released, and the enzyme is free to catalyze another reaction.

6.2 Models of Enzyme-Substrate Binding

• Lock-and-key model: The active site has a rigid shape that perfectly complements the substrate.
• Induced-fit model: The active site changes shape to better fit the substrate. This is now the accepted model.

6.3 Factors Affecting Enzyme Activity

• Temperature: Enzymes have an optimal temperature range for activity. High temperatures can denature the enzyme.
• pH: Enzymes have an optimal pH range for activity. Extremes of pH can denature the enzyme.
• Substrate concentration: Increasing substrate concentration increases the rate of reaction until the enzyme is saturated.
• Enzyme concentration: Increasing enzyme concentration increases the rate of reaction (assuming sufficient substrate).
• Inhibitors: Substances that reduce enzyme activity.

6.4 Enzyme Inhibitors

• Competitive inhibitors: Bind to the active site, blocking the substrate from binding.
• Noncompetitive inhibitors: Bind to another part of the enzyme, changing its shape and reducing its activity.

6.5 Coenzymes and Cofactors

• Cofactors: Inorganic ions (e.g., \(Zn^{2+}\), \(Fe^{2+}\)) required for enzyme activity.
• Coenzymes: Organic molecules (e.g., vitamins) required for enzyme activity.

EXAM TIP: Understand the difference between competitive and noncompetitive inhibitors and how they affect enzyme activity. Be prepared to interpret graphs showing enzyme activity under different conditions.