Proteins and Their Functions in Biology

Basic Structures of Protein and Protein Metabolism

• Proteins are organic compounds made of amino acids arranged in a linear chain and joined by peptide bonds.
• Amino acids differ based on the chemical structure of the side chain.
• Proteins have various functions, including building materials, enzymes, hormones, and antibodies.
• Protein structure dictates its function.
• Proteins are categorized into globular and fibrous types, each with their unique characteristics.
• Globular proteins are spherical, soluble in water, and carry out specific functions.
• Fibrous proteins are long and narrow, insoluble in water, and primarily support structure.
• Hemoglobin serves as an example of a globular protein. Its structure is important for oxygen transport.
• Protein breakdown and synthesis are essential biological processes involving amino acids.
• Excess nitrogen from amino acid breakdown is excreted from the body.
• Nitrogen balance (negative/positive) describes the relationship between protein degradation and synthesis.

Learning Outcomes

• List various protein functions.
• Describe amino acids and their role in protein structure.
• Differentiate between globular and fibrous proteins.
• Explain the importance of protein structure, using hemoglobin as an example.
• Describe amino acid breakdown and synthesis.
• Explain how excess nitrogen is excreted.

Protein Structure

• Protein structure is crucial for function.
• Aberrant protein structure can lead to various disorders, such as sickle cell anemia.
• Sickle cell anemia arises from a point mutation that substitutes a nonpolar amino acid (Valine) for a polar one (Glutamate), creating a rigid hemoglobin polymer
• Studying protein structure aids in the development of therapeutics.
• Disruption of structure disrupts function.

Amino Acids

• Amino acids are the fundamental units of proteins.
• All amino acids have an amino group and a carboxyl group connected to a central carbon atom.
• The 20 amino acids differ in their side chains (R groups), leading to their distinct properties.
• These properties are crucial for protein folding into specific 3D structures.

Amino Acids (Chemical Structure)

• Amino acids are grouped based on their chemical structures:
  • Aliphatic
  • Aromatic
  • Polar
  • Sulfur-containing
  • Charged (positive or negative)

Peptide Formation and Structure

• Amino acids are linked together through peptide bonds.
• The sequence of amino acids (primary structure) is essential for protein function.
• Secondary, tertiary, and quaternary structures emerge from interactions between amino acid residues.

Protein Structure Levels

• Primary structure: The sequence of amino acids.
• Secondary structure: Repetitive, local structures like alpha-helices and beta-sheets.
• Tertiary structure: The three-dimensional folding pattern of the entire polypeptide chain.
• Quaternary structure: The arrangement of multiple polypeptide chains in a protein.

Sickle Cell Anemia

• Sickle cell anemia is a disease caused by an abnormal hemoglobin variant (HbS).
• The substitution of Valine for Glutamate in the β-globin chain leads to polymerization of hemoglobin, leading to deformed red blood cells (RBCs), causing various health problems.

Knowledge Check - 1

• Actin is the protein involved in muscle contraction.

Knowledge Check - 2

• Hydrogen bonds stabilize the secondary structure of proteins.

Overview of Protein & Nitrogen Metabolism

• Dietary protein is broken down into amino acids.
• Amino acids are used for protein synthesis and other metabolic pathways.
• Nitrogen from amino acids is converted to urea and excreted from the body.

Protein Turnover Rate

• Protein turnover rates vary greatly among proteins.
• Short-lived proteins are rapidly degraded.
• Long-lived proteins such as collagen have slower turnover rates.
• Nitrogen balance reflects the state of protein synthesis and degradation in the human body.

Catabolism of Amino Acids

• Amino acids are broken down into their component parts, including amino groups and carbon skeletons.
• The carbon skeletons are often integrated into other metabolic pathways.
• The amino groups are processed through transamination, oxidative deamination, and the urea cycle.

Step 1: Transamination

• An amino group is transferred from an amino acid to a-ketoglutarate, forming glutamate and a keto acid.
• Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) are key enzymes.
• Pyridoxal phosphate (vitamin B6) is a crucial coenzyme.

Step 2: Oxidative Deamination

• The amino group is removed from glutamate, forming ammonia and a-ketoglutarate.
• Glutamate dehydrogenase catalyzes this reaction.
• Ammonia is then transported and converted to urea.

Step 3: Ammonia Transport to the Liver

• Ammonia is toxic and must be transported to the liver for detoxification.
• The glutamate-glutamine cycle and the glucose-alanine cycle are important mechanisms for transporting ammonia.

Step 4: Urea Cycle

• Urea is the major nitrogenous waste product.
• The urea cycle occurs in the liver to convert ammonia into urea.
• Two nitrogen atoms are derived from ammonia and aspartate.
• The urea is then excreted in urine.

Integration of Amino Acid, Carbohydrate, and Fat Metabolism

• Amino acids are crucial for various metabolic processes, including energy production.
• The carbon skeletons of amino acids can be used to synthesize glucose or be converted into keto acids or fatty acids.

Glucogenic/Ketogenic Amino Acids

• Amino acids are categorized as glucogenic, ketogenic, or both, depending on the metabolic fates of their carbon skeletons.
• Some amino acids can be used to produce glucose, while others yield energy in the form of ketone bodies.
• Leucine and lysine are exclusively ketogenic.

Conversion of Amino Acids to Specialized Products

• Various amino acids are precursors for the synthesis of specialized products such as neurotransmitters, hormones, and other molecules.

Summary of Protein Structure

• Protein structure is specific.
• Protein structure dictates its function.
• Loss of structure leads to a loss of function.

Knowledge Check – 3

• Hemoglobin's heme groups containing iron are crucial for its oxygen-carrying function.

Knowledge Check – Flash Card 2

• A deficiency in the urea cycle enzyme ornithine transcarbamylase (OTC) is the likely cause of the symptoms and lab results.

References

• Note: This section provides a summary of referenced materials, and the full texts or details are not included here.