6.3 Amino acid biosynthesis and protein metabolism
3 min read•august 7, 2024
Plants are master chemists, creating amino acids from scratch. They use simple molecules like oxaloacetate and α-ketoglutarate to build complex amino acids, grouping them into families based on their origins.
Proteins, the workhorses of cells, are constantly made and broken down. Plants recycle amino acids during senescence, moving nitrogen from old leaves to growing parts. This process is key to efficient nutrient use.
Amino Acid Biosynthesis
Amino Acid Families and Biosynthetic Pathways
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- Amino acids are grouped into families based on their biosynthetic pathways and precursor molecules
- Amino acid biosynthesis involves a series of enzymatic reactions that convert precursor molecules into specific amino acids
- The biosynthetic pathways for amino acids are tightly regulated to maintain optimal levels of each amino acid in the cell
- Key enzymes in amino acid biosynthesis are often subject to by the end product amino acid to prevent excessive accumulation
Aspartate and Glutamate Families
- The aspartate family includes aspartate, asparagine, lysine, methionine, and threonine which are derived from aspartate as a precursor
- Aspartate is synthesized from oxaloacetate, an intermediate of the citric acid cycle, by the enzyme aspartate aminotransferase
- The glutamate family includes glutamate, glutamine, proline, and arginine which are derived from glutamate as a precursor
- Glutamate is synthesized from α-ketoglutarate, an intermediate of the citric acid cycle, by the enzyme glutamate dehydrogenase (using NADPH and NH4+)
Aromatic and Branched-Chain Amino Acids
- Aromatic amino acids include phenylalanine, tyrosine, and tryptophan which are derived from the shikimate pathway
- The shikimate pathway begins with the condensation of phosphoenolpyruvate (from glycolysis) and erythrose 4-phosphate (from the pentose phosphate pathway) to form chorismate, the precursor for aromatic amino acids
- Branched-chain amino acids include leucine, isoleucine, and valine which are derived from pyruvate and α-ketobutyrate as precursors
- The biosynthesis of branched-chain amino acids involves a series of parallel reactions catalyzed by enzymes with broad substrate specificity (can act on multiple substrates)
Protein Metabolism
Protein Synthesis and Degradation
- Protein synthesis () occurs on ribosomes and involves the assembly of amino acids into polypeptide chains based on the genetic code
- The process of protein synthesis includes initiation, elongation, and termination steps which are regulated by various factors (initiation factors, elongation factors, release factors)
- Proteolysis is the breakdown of proteins into smaller peptides or individual amino acids by proteolytic enzymes (proteases)
- Proteolysis plays a crucial role in protein turnover, regulation of cellular processes, and recycling of amino acids for new protein synthesis
Nitrogen Remobilization and Senescence
- Nitrogen remobilization involves the redistribution of nitrogen from source tissues (older leaves) to sink tissues (developing leaves, fruits, seeds) during plant growth and development
- During leaf senescence, proteins are degraded and the released amino acids are transported to sink tissues for reuse in new protein synthesis
- Senescence is a highly regulated process that involves the coordinated expression of genes related to protein degradation, nutrient remobilization, and cell death
- Key enzymes involved in nitrogen remobilization during senescence include proteases, glutamine synthetase, and asparagine synthetase which convert amino acids into transportable forms (glutamine, asparagine)
Key Terms to Review (18)
Allosteric Regulation: Allosteric regulation is a process by which an enzyme's activity is modified through the binding of an effector molecule at a site other than the enzyme's active site. This mechanism allows for the fine-tuning of metabolic pathways, particularly in amino acid biosynthesis and protein metabolism, ensuring that the cells can efficiently respond to changes in their environment and maintain homeostasis.
Aspartate pathway: The aspartate pathway is a metabolic route involved in the biosynthesis of several amino acids, primarily aspartate and its derivatives. This pathway plays a critical role in the synthesis of important amino acids such as asparagine, methionine, threonine, and lysine, which are essential for protein synthesis and overall cellular function.
ATP consumption: ATP consumption refers to the process by which adenosine triphosphate (ATP) is utilized by cells to perform various biochemical functions essential for life. This energy currency is vital for processes such as amino acid biosynthesis and protein metabolism, where ATP provides the necessary energy for the synthesis of proteins and the modification of amino acids. Understanding ATP consumption is crucial for grasping how cells manage energy and carry out metabolic reactions effectively.
Auxins: Auxins are a class of plant hormones that play a crucial role in coordinating various growth and behavioral processes in plants, including cell elongation, apical dominance, and responses to light and gravity. They influence several physiological functions, connecting processes like nutrient uptake, transport, and growth regulation throughout the plant.
Decarboxylase: Decarboxylase is an enzyme that catalyzes the removal of a carboxyl group from a substrate, resulting in the release of carbon dioxide (COâ‚‚). This process is essential in amino acid metabolism, as it helps convert amino acids into biologically active compounds, impacting protein synthesis and overall cellular functions.
Energy yield: Energy yield refers to the amount of energy produced from a biochemical process, particularly in relation to the synthesis and breakdown of biomolecules. In the context of amino acid biosynthesis and protein metabolism, energy yield is essential for understanding how organisms generate and utilize energy to support growth, repair, and various metabolic functions. This concept is crucial because it highlights the efficiency and productivity of metabolic pathways, influencing how organisms balance energy intake with energy expenditure.
Essential Amino Acids: Essential amino acids are the amino acids that cannot be synthesized by the body and must be obtained through diet. They play a crucial role in protein metabolism and amino acid biosynthesis, as they are the building blocks for proteins that are vital for growth, repair, and overall bodily function.
Feedback inhibition: Feedback inhibition is a regulatory mechanism in biological systems where the end product of a metabolic pathway inhibits an earlier step in the pathway, effectively controlling the production of that product. This process helps maintain homeostasis by preventing the overproduction of substances, ensuring that resources are used efficiently within the cell. It plays a crucial role in pathways such as nitrogen assimilation and amino acid biosynthesis, where balancing the availability of nutrients is vital for plant growth and development.
Gibberellins: Gibberellins are a group of plant hormones that play critical roles in regulating growth and development. They influence processes such as stem elongation, seed germination, and flowering, making them essential for various stages of a plant's life cycle. Their interactions with other hormones highlight their importance in the complex signaling networks that control plant physiology.
Nitrate assimilation: Nitrate assimilation is the process by which plants and some microorganisms convert nitrate (NO3-) into organic compounds, primarily amino acids. This process is crucial for the synthesis of proteins and other nitrogen-containing molecules essential for plant growth and development. Nitrate assimilation plays a key role in nutrient cycling and impacts overall plant metabolism, linking inorganic nitrogen sources to biological function.
Nitrogen fixation: Nitrogen fixation is the process by which atmospheric nitrogen (N₂) is converted into a form that plants can use, typically ammonia (NH₃), through the action of certain bacteria. This process is crucial for plant growth because nitrogen is an essential component of amino acids, proteins, and nucleic acids. By facilitating the conversion of inert atmospheric nitrogen into biologically available forms, nitrogen fixation plays a significant role in both amino acid biosynthesis and the establishment of beneficial associations between plants and microbes.
Non-essential amino acids: Non-essential amino acids are amino acids that the body can synthesize on its own, meaning they do not need to be obtained directly through the diet. These amino acids play vital roles in protein synthesis and other metabolic processes, contributing to the body's overall health and functionality.
Peptide bond: A peptide bond is a covalent chemical bond that links amino acids together in proteins. This bond forms when the carboxyl group of one amino acid reacts with the amino group of another, resulting in the release of a water molecule in a dehydration synthesis reaction. Peptide bonds are fundamental for protein structure and function, as they determine the sequence and arrangement of amino acids, which ultimately influences the protein's 3D conformation and biological activity.
Protein folding: Protein folding is the process by which a linear chain of amino acids acquires its functional three-dimensional structure. This intricate process is essential for proper protein function and involves various interactions such as hydrogen bonds, ionic interactions, and hydrophobic effects. Understanding protein folding is crucial because misfolding can lead to various diseases and impacts amino acid biosynthesis and protein metabolism.
Shikimic acid pathway: The shikimic acid pathway is a metabolic route found in plants, fungi, and some bacteria that leads to the biosynthesis of aromatic amino acids such as phenylalanine, tyrosine, and tryptophan. This pathway is crucial for the production of not only these amino acids but also various secondary metabolites like flavonoids and alkaloids, which play essential roles in plant metabolism and defense mechanisms.
Side chain: A side chain refers to the specific group of atoms that are attached to the backbone of an amino acid. This part of the amino acid plays a crucial role in determining the chemical properties and function of the amino acid, influencing how proteins fold and interact with each other. Different side chains can vary significantly in size, shape, charge, and polarity, which impacts the overall structure and function of proteins.
Transaminase: Transaminases are enzymes that catalyze the transfer of an amino group from an amino acid to a keto acid, forming new amino acids and enabling the interconversion of amino acids and their corresponding carbon skeletons. These enzymes play a critical role in amino acid biosynthesis and protein metabolism by facilitating the synthesis and degradation of amino acids, which are vital for various cellular functions and overall metabolism.
Translation: Translation is the biological process in which messenger RNA (mRNA) is decoded by ribosomes to synthesize proteins. This crucial step occurs after transcription and involves the assembly of amino acids into polypeptide chains, which ultimately fold into functional proteins. Understanding translation is vital for grasping how genetic information is expressed and how proteins are synthesized in plants, impacting their growth, development, and response to environmental changes.