biochemistry-

Advanced Biochemistry for Bioinformatics

March 31, 2024 Off By admin
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Introduction to Biomolecules

Overview of proteins, carbohydrates, and lipids

Proteins, carbohydrates, and lipids are three major classes of biomolecules essential for various biological processes in living organisms. Here’s an overview of each:

  1. Proteins:
    • Structure: Proteins are macromolecules composed of amino acids linked together by peptide bonds. They have a complex three-dimensional structure determined by the sequence of amino acids.
    • Function: Proteins serve a wide variety of functions in the body, including catalyzing biochemical reactions (enzymes), providing structural support (collagen), aiding in immune responses (antibodies), and facilitating transport of molecules (hemoglobin).
    • Examples: Enzymes, antibodies, hemoglobin, collagen.
  2. Carbohydrates:
    • Structure: Carbohydrates are molecules composed of carbon, hydrogen, and oxygen atoms, with a ratio of hydrogen to oxygen atoms similar to that in water (2:1). They can be simple sugars (monosaccharides), two sugars linked together (disaccharides), or long chains of sugars (polysaccharides).
    • Function: Carbohydrates are a major source of energy for the body. They also play roles in cell structure (cellulose in plants, chitin in fungi), cell recognition, and signaling.
    • Examples: Glucose, sucrose, cellulose, glycogen.
  3. Lipids:
    • Structure: Lipids are diverse molecules that are hydrophobic (“water-fearing”) and include fats, oils, waxes, phospholipids, and steroids. They are composed of hydrocarbon chains and often contain a glycerol backbone.
    • Function: Lipids serve as energy storage molecules, form the lipid bilayer of cell membranes, act as signaling molecules (e.g., prostaglandins), and provide insulation and protection for organs.
    • Examples: Triglycerides (fats and oils), phospholipids, cholesterol.

In summary, proteins are made up of amino acids and are involved in a wide range of functions, carbohydrates are composed of sugars and serve as a major energy source, and lipids are hydrophobic molecules with diverse functions, including energy storage and cell membrane structure.

Structural features and functions in cellular processes

Structural features and functions in cellular processes can vary widely depending on the specific biomolecule or cellular structure being discussed. Here, we’ll focus on some key structural features and their functions in cellular processes:

  1. Cell Membrane:
    • Structure: The cell membrane is composed of a phospholipid bilayer with embedded proteins, cholesterol, and carbohydrates.
    • Function: It acts as a barrier, regulating the passage of substances in and out of the cell. It also plays a role in cell signaling and communication.
  2. Cytoskeleton:
    • Structure: The cytoskeleton is a network of protein filaments (e.g., microtubules, actin filaments, intermediate filaments) that provide structural support and facilitate cell movement.
    • Function: It maintains cell shape, anchors organelles, facilitates cell division, and enables cell motility.
  3. Nucleus:
    • Structure: The nucleus is surrounded by a nuclear envelope composed of two lipid bilayers. It contains chromatin (DNA and proteins) and a nucleolus.
    • Function: It houses the cell’s genetic material (DNA), regulates gene expression, and synthesizes ribosomal RNA (rRNA).
  4. Mitochondria:
    • Structure: Mitochondria have an outer membrane, an inner membrane with folds called cristae, and a matrix.
    • Function: They are the site of aerobic respiration, producing ATP (adenosine triphosphate), which is the cell’s primary energy source.
  5. Endoplasmic Reticulum (ER):
    • Structure: The ER is a network of membranes, including rough ER (with ribosomes) and smooth ER (without ribosomes).
    • Function: Rough ER is involved in protein synthesis and processing, while smooth ER is involved in lipid metabolism and detoxification.
  6. Golgi Apparatus:
    • Structure: The Golgi apparatus consists of flattened membrane-bound sacs called cisternae.
    • Function: It modifies, sorts, and packages proteins and lipids into vesicles for transport to other cellular destinations.
  7. Lysosomes:
    • Structure: Lysosomes are membrane-bound organelles containing digestive enzymes.
    • Function: They break down macromolecules, old organelles, and foreign substances in a process called autophagy.
  8. Ribosomes:
    • Structure: Ribosomes are complexes of RNA and proteins, existing as free ribosomes in the cytoplasm or bound to the ER.
    • Function: They are the site of protein synthesis, translating mRNA into proteins.

These structural features and their functions are essential for maintaining cellular integrity, regulating cellular processes, and ensuring proper cell function and survival.

Enzyme Structure and Function

Enzyme kinetics and mechanisms

Enzyme kinetics is the study of the rates at which enzymes catalyze chemical reactions. Understanding enzyme kinetics is crucial for elucidating enzyme mechanisms and optimizing enzymatic reactions. Here’s an overview of enzyme kinetics and mechanisms:

  1. Enzyme Mechanisms:
    • Lock and Key Model: Enzyme has a specific active site that fits the substrate like a key in a lock.
    • Induced Fit Model: Active site undergoes conformational changes upon substrate binding to achieve a better fit.
    • Catalytic Mechanisms: Enzymes can catalyze reactions through mechanisms such as acid-base catalysis, covalent catalysis, and metal ion catalysis.
  2. Allosteric Regulation:
    • Allosteric Enzymes: Enzymes with multiple subunits where binding of a regulatory molecule at one site affects the activity at the active site.
    • Allosteric Activators/Inhibitors: Modulate enzyme activity by stabilizing different enzyme conformations.
  3. Cooperativity:
    • Positive Cooperativity: Binding of substrate to one active site increases the affinity of other active sites for substrate.
    • Negative Cooperativity: Binding of substrate to one active site decreases the affinity of other active sites for substrate.

Enzyme kinetics and mechanisms provide a framework for understanding how enzymes function and are regulated, which is fundamental to many aspects of biochemistry and molecular biology.

Role of enzymes in bioinformatics and molecular biology techniques

Enzymes play a crucial role in bioinformatics and molecular biology techniques, where they are used to manipulate DNA, RNA, and proteins. Here are some key applications of enzymes in these fields:

  1. DNA and RNA Manipulation:
    • Restriction Enzymes: Used to cleave DNA at specific recognition sites. They are fundamental for techniques like restriction fragment length polymorphism (RFLP) analysis, DNA cloning, and gene editing (e.g., CRISPR-Cas9).
    • DNA Ligases: Used to join DNA fragments together by catalyzing the formation of phosphodiester bonds. Essential for DNA cloning and recombinant DNA technology.
    • DNA Polymerases: Catalyze the synthesis of new DNA strands using a DNA template. They are central to techniques like PCR (polymerase chain reaction) and DNA sequencing.
    • RNA Polymerases: Catalyze the synthesis of RNA from a DNA template. Used in techniques like in vitro transcription and RNA interference (RNAi).
  2. Protein Analysis:
    • Proteases: Enzymes that cleave proteins at specific peptide bonds. Used in protein digestion for mass spectrometry analysis and protein sequencing.
    • Kinases and Phosphatases: Enzymes involved in adding or removing phosphate groups from proteins, respectively. Important in signal transduction studies and protein phosphorylation analysis.
    • DNA/RNA-binding Proteins: Enzymes that bind to DNA or RNA molecules to regulate gene expression or aid in DNA/RNA purification and analysis.
  3. Molecular Biology Techniques:
    • PCR Enzymes: DNA polymerases used in PCR to amplify specific DNA sequences. Thermostable polymerases like Taq polymerase are commonly used.
    • Reverse Transcriptase: Enzyme used to convert RNA into complementary DNA (cDNA) in techniques like reverse transcription PCR (RT-PCR) and cDNA library construction.
    • DNA Methyltransferases: Enzymes that add methyl groups to DNA. Used in DNA methylation analysis and epigenetic studies.
  4. Enzyme Engineering:
    • Enzymes are engineered to improve their properties for specific applications, such as increased stability, altered substrate specificity, or enhanced activity under specific conditions. This is crucial for developing new biotechnological tools and processes.

Overall, enzymes are indispensable tools in bioinformatics and molecular biology, enabling researchers to manipulate and study nucleic acids, proteins, and other biomolecules with precision and efficiency.

Metabolism: Basic Concepts and Design

Overview of metabolic pathways and their regulation

Metabolic pathways are interconnected series of chemical reactions that occur within cells to maintain life. These pathways are responsible for the synthesis and breakdown of molecules, such as carbohydrates, proteins, and lipids, and the production of energy. Here’s an overview of some key metabolic pathways and their regulation:

  1. Glycolysis:
    • Overview: Breaks down glucose into pyruvate, producing ATP and NADH.
    • Regulation: Regulated by feedback inhibition, where high levels of ATP and citrate inhibit key enzymes like phosphofructokinase.
  2. Citric Acid Cycle (Krebs Cycle):
    • Overview: Oxidizes acetyl-CoA to produce ATP, NADH, and FADH2.
    • Regulation: Regulated by allosteric inhibitors (e.g., ATP, NADH) and activators (e.g., ADP) of key enzymes.
  3. Gluconeogenesis:
    • Overview: Synthesizes glucose from non-carbohydrate precursors like pyruvate and amino acids.
    • Regulation: Reciprocally regulated with glycolysis to prevent futile cycling, mainly by controlling the activity of key enzymes like fructose-1,6-bisphosphatase and phosphoenolpyruvate carboxykinase.
  4. Glycogen Metabolism:
    • Overview: Synthesizes and breaks down glycogen, a storage form of glucose.
    • Regulation: Regulated by hormones (e.g., insulin, glucagon) and enzymes (e.g., glycogen synthase, glycogen phosphorylase) to maintain blood glucose levels.
  5. Fatty Acid Synthesis:
    • Overview: Synthesizes fatty acids from acetyl-CoA for storage or energy production.
    • Regulation: Regulated by hormonal control (e.g., insulin) and allosteric regulation of key enzymes like acetyl-CoA carboxylase.
  6. Fatty Acid Oxidation (Beta-Oxidation):
    • Overview: Breaks down fatty acids to produce acetyl-CoA and ATP.
    • Regulation: Regulated by substrate availability and hormonal control to match energy demands.
  7. Pentose Phosphate Pathway:
    • Overview: Produces NADPH and ribose-5-phosphate for nucleotide synthesis.
    • Regulation: Regulated by the availability of substrates and the need for NADPH and ribose-5-phosphate.
  8. Amino Acid Metabolism:
    • Overview: Involves the synthesis and breakdown of amino acids for protein synthesis and energy production.
    • Regulation: Regulated by hormonal control, substrate availability, and feedback inhibition of key enzymes.

Regulation of metabolic pathways occurs at multiple levels, including transcriptional regulation of enzyme synthesis, allosteric regulation of enzyme activity, and post-translational modifications. This regulation ensures that metabolic pathways are tightly controlled to meet the cell’s energy and biosynthetic needs.

Application of metabolic pathway analysis in bioinformatics

Metabolic pathway analysis plays a crucial role in bioinformatics by providing insights into the complex interactions and regulation of metabolic pathways within cells. Here are some key applications of metabolic pathway analysis in bioinformatics:

  1. Functional Genomics: Metabolic pathway analysis can be used to interpret high-throughput omics data, such as transcriptomics, proteomics, and metabolomics, to understand how genes, proteins, and metabolites are interconnected in cellular processes.
  2. Disease Mechanisms: By analyzing metabolic pathways, researchers can uncover alterations in metabolic processes associated with various diseases, such as cancer, diabetes, and metabolic disorders, leading to a better understanding of disease mechanisms and potential therapeutic targets.
  3. Drug Discovery: Metabolic pathway analysis can aid in drug discovery by identifying metabolic pathways that are affected by drug treatments and predicting potential drug targets based on their impact on metabolic networks.
  4. Biotechnology and Metabolic Engineering: In biotechnology, metabolic pathway analysis can be used to design and optimize microbial strains for the production of biofuels, pharmaceuticals, and other valuable compounds by manipulating metabolic pathways.
  5. Nutrigenomics: Metabolic pathway analysis can help understand how nutrients and dietary compounds influence metabolic pathways, leading to insights into personalized nutrition and the development of functional foods.
  6. Toxicology: By studying metabolic pathways, researchers can identify metabolic signatures associated with exposure to toxins and environmental pollutants, aiding in toxicological studies and risk assessment.
  7. Evolutionary Biology: Comparative metabolic pathway analysis across species can provide insights into the evolution of metabolic pathways and the adaptation of organisms to different environments.

Overall, metabolic pathway analysis in bioinformatics plays a crucial role in advancing our understanding of cellular metabolism, disease mechanisms, drug discovery, and various other fields, with implications for improving human health, biotechnology, and environmental sustainability.

Carbohydrate Metabolism

Glycolysis, gluconeogenesis, and their regulation

Glycolysis and gluconeogenesis are two interconnected metabolic pathways involved in the synthesis and breakdown of glucose. Here’s an overview of each pathway and their regulation:

  1. Glycolysis:
    • Overview: Glycolysis is the metabolic pathway that converts glucose into pyruvate, producing ATP and NADH.
    • Steps: Glycolysis consists of 10 enzymatic reactions, starting with the phosphorylation of glucose to form glucose-6-phosphate and ending with the production of pyruvate.
    • Regulation: Glycolysis is regulated at key steps to ensure that glucose is efficiently converted to pyruvate. Regulation occurs through allosteric regulation and hormonal control.
      • Allosteric Regulation: Enzymes like phosphofructokinase-1 (PFK-1) and pyruvate kinase are allosterically regulated by metabolites such as ATP, ADP, and citrate. High levels of ATP and citrate inhibit PFK-1, while ADP and AMP activate it.
      • Hormonal Control: Insulin stimulates glycolysis by promoting the dephosphorylation and activation of key enzymes, while glucagon and epinephrine inhibit glycolysis by promoting phosphorylation and inactivation of these enzymes.
  2. Gluconeogenesis:
    • Overview: Gluconeogenesis is the metabolic pathway that synthesizes glucose from non-carbohydrate precursors like pyruvate, lactate, glycerol, and amino acids.
    • Steps: Gluconeogenesis involves a series of enzymatic reactions that bypass or reverse the irreversible steps of glycolysis to convert pyruvate into glucose.
    • Regulation: Gluconeogenesis is regulated to ensure that glucose is synthesized when needed. Regulation occurs mainly through reciprocal regulation with glycolysis and hormonal control.
      • Reciprocal Regulation: Enzymes that catalyze the irreversible steps of glycolysis are inhibited or regulated in the opposite direction in gluconeogenesis. For example, PFK-1 is inhibited, and fructose-1,6-bisphosphatase is activated.
      • Hormonal Control: Glucagon and epinephrine stimulate gluconeogenesis by promoting the phosphorylation and activation of key enzymes, while insulin inhibits gluconeogenesis by promoting the dephosphorylation and inactivation of these enzymes.

Glycolysis and gluconeogenesis are tightly regulated to maintain glucose homeostasis in the body, ensuring that cells have a constant supply of glucose for energy production and other metabolic processes. Their regulation is essential for metabolic flexibility and adaptation to changing energy demands and nutrient availability.

Citric acid cycle and its significance in energy production

The citric acid cycle, also known as the Krebs cycle or tricarboxylic acid (TCA) cycle, is a central metabolic pathway that plays a crucial role in energy production and the metabolism of carbohydrates, fats, and proteins. Here’s an overview of the citric acid cycle and its significance:

  1. Overview of the Citric Acid Cycle:
    • The citric acid cycle takes place in the mitochondrial matrix and consists of a series of enzymatic reactions that oxidize acetyl-CoA, derived from the breakdown of carbohydrates, fats, and proteins, to produce ATP, NADH, and FADH2.
    • The cycle begins with the condensation of acetyl-CoA with oxaloacetate to form citrate, which undergoes a series of reactions to regenerate oxaloacetate and produce ATP, NADH, and FADH2.
  2. Key Steps of the Citric Acid Cycle:
    • Step 1: Acetyl-CoA combines with oxaloacetate to form citrate, catalyzed by citrate synthase.
    • Steps 2-8: Citrate is converted into isocitrate, which undergoes a series of reactions to produce α-ketoglutarate, succinyl-CoA, succinate, fumarate, malate, and finally, oxaloacetate. These reactions result in the production of NADH and FADH2, as well as the substrate-level phosphorylation of GDP to GTP, which can be converted to ATP.
  3. Significance in Energy Production:
    • The citric acid cycle is a major source of ATP production in aerobic organisms, generating high-energy electrons in the form of NADH and FADH2, which are used in oxidative phosphorylation to produce ATP.
    • For every molecule of acetyl-CoA that enters the citric acid cycle, three molecules of NADH, one molecule of FADH2, and one molecule of GTP (or ATP) are produced, which can generate a substantial amount of ATP through oxidative phosphorylation.
  4. Regulation of the Citric Acid Cycle:
    • The citric acid cycle is regulated by feedback inhibition and substrate availability to ensure that it operates efficiently and responds to the energy needs of the cell.
    • High levels of ATP and NADH inhibit key enzymes in the citric acid cycle, such as isocitrate dehydrogenase and α-ketoglutarate dehydrogenase, while ADP and calcium ions can activate these enzymes, promoting the cycle’s activity when ATP levels are low.

In summary, the citric acid cycle is a central metabolic pathway that is vital for energy production in cells, providing the necessary intermediates and reducing equivalents for oxidative phosphorylation to generate ATP. Its regulation ensures that cells can adapt to changing energy demands and maintain metabolic homeostasis.

Pentose phosphate pathway and its role in nucleotide biosynthesis

The pentose phosphate pathway (PPP), also known as the hexose monophosphate shunt, is a metabolic pathway parallel to glycolysis that plays a key role in generating NADPH and pentose sugars. One of its primary functions is to provide the cell with NADPH for biosynthetic reactions and to maintain redox balance. Here’s an overview of the pentose phosphate pathway and its role in nucleotide biosynthesis:

  1. Overview of the Pentose Phosphate Pathway:
    • The PPP consists of two phases: the oxidative phase and the non-oxidative phase.
    • Oxidative Phase: Glucose-6-phosphate is oxidized to ribulose-5-phosphate, generating NADPH and releasing CO2 in a series of reactions catalyzed by glucose-6-phosphate dehydrogenase (G6PD) and 6-phosphogluconate dehydrogenase (6PGD).
    • Non-oxidative Phase: Ribulose-5-phosphate can be converted into other sugars, such as ribose-5-phosphate for nucleotide biosynthesis, or recycled back to glucose-6-phosphate for glycolysis.
  2. Role in Nucleotide Biosynthesis:
    • The PPP is essential for the biosynthesis of nucleotides, which are the building blocks of DNA and RNA.
    • Ribose-5-phosphate, a product of the PPP, is converted into 5-phosphoribosyl-1-pyrophosphate (PRPP), a key intermediate in nucleotide biosynthesis.
    • PRPP is used in the synthesis of purine and pyrimidine nucleotides, which are essential for DNA and RNA synthesis and other cellular processes.
  3. Other Functions of the Pentose Phosphate Pathway:
    • NADPH Production: The PPP is a major source of NADPH, which is required for biosynthetic reactions, such as fatty acid synthesis and the reduction of glutathione to protect against oxidative stress.
    • Redox Balance: The PPP helps maintain redox balance in the cell by generating NADPH, which can act as a reducing agent in various metabolic reactions.

In summary, the pentose phosphate pathway is a critical metabolic pathway that plays a key role in providing NADPH for biosynthetic reactions and maintaining redox balance in the cell. Its role in nucleotide biosynthesis is essential for cell growth and proliferation, making the PPP a vital pathway for cellular metabolism.

Lipid Metabolism

Overview of fatty acid metabolism and its regulation

Fatty acid metabolism, also known as lipid metabolism, involves the synthesis, breakdown, and modification of fatty acids, which are essential components of cell membranes and a major energy source for the body. Here’s an overview of fatty acid metabolism and its regulation:

  1. Fatty Acid Synthesis (Fatty Acid Biosynthesis):
    • Overview: Fatty acid synthesis occurs in the cytoplasm and involves the conversion of acetyl-CoA into long-chain fatty acids, primarily palmitate (16:0).
    • Steps: The process starts with the carboxylation of acetyl-CoA to form malonyl-CoA, which is then used in a series of enzymatic reactions catalyzed by fatty acid synthase (FAS) to elongate the fatty acid chain.
    • Regulation: Fatty acid synthesis is regulated by the availability of substrates (acetyl-CoA and malonyl-CoA), hormonal control (insulin), and allosteric regulation of key enzymes like acetyl-CoA carboxylase (ACC).
  2. Fatty Acid Degradation (Fatty Acid Oxidation):
    • Overview: Fatty acid oxidation occurs in the mitochondria and involves the breakdown of fatty acids into acetyl-CoA, which enters the citric acid cycle for energy production.
    • Steps: Fatty acid oxidation involves a series of enzymatic reactions, including beta-oxidation, where fatty acids are sequentially shortened by two-carbon units.
    • Regulation: Fatty acid oxidation is regulated by the availability of fatty acids and energy demands of the cell. Hormones like glucagon and epinephrine stimulate fatty acid oxidation, while insulin inhibits it.
  3. Regulation of Fatty Acid Metabolism:
    • Hormonal Regulation: Insulin promotes fatty acid synthesis by activating enzymes like ACC and promoting the synthesis of fatty acids from glucose. Glucagon and epinephrine stimulate fatty acid breakdown by activating hormone-sensitive lipase.
    • Allosteric Regulation: Enzymes involved in fatty acid metabolism are regulated by allosteric effectors. For example, ACC is inhibited by long-chain fatty acyl-CoA, indicating when fatty acid synthesis is not needed.
    • Transcriptional Regulation: The expression of genes encoding enzymes involved in fatty acid metabolism is regulated by transcription factors, such as sterol regulatory element-binding proteins (SREBPs), which respond to cellular lipid levels.
  4. Role of Fatty Acid Metabolism in Health and Disease:
    • Dysregulation of fatty acid metabolism is associated with various metabolic disorders, such as obesity, type 2 diabetes, and cardiovascular disease.
    • Understanding the regulation of fatty acid metabolism is important for developing therapies for these diseases and for studying lipid metabolism in health and disease.

In summary, fatty acid metabolism is a complex process involving the synthesis, breakdown, and modification of fatty acids. Its regulation is tightly controlled to maintain lipid homeostasis and meet the energy needs of the cell.

Significance of lipid metabolism in cellular signaling and disease

Lipid metabolism plays a crucial role in cellular signaling and is implicated in various diseases. Here’s an overview of the significance of lipid metabolism in cellular signaling and disease:

  1. Cellular Signaling:
    • Second Messengers: Lipids such as phosphatidylinositol 4,5-bisphosphate (PIP2), phosphatidylinositol 3,4,5-trisphosphate (PIP3), and diacylglycerol (DAG) act as second messengers in signal transduction pathways.
    • Membrane Fluidity: Lipids affect membrane fluidity, which is crucial for the function of membrane-bound receptors and signaling molecules.
    • Protein Modification: Lipids can post-translationally modify proteins, such as palmitoylation, which affects protein localization and function in signaling pathways.
  2. Role in Disease:
    • Obesity and Metabolic Syndrome: Dysregulation of lipid metabolism can lead to obesity, insulin resistance, and metabolic syndrome, increasing the risk of type 2 diabetes and cardiovascular disease.
    • Cancer: Alterations in lipid metabolism are observed in cancer cells, where increased de novo lipogenesis supports rapid cell proliferation and survival.
    • Neurological Disorders: Lipid metabolism is critical for brain function, and dysregulation has been implicated in neurodegenerative disorders such as Alzheimer’s and Parkinson’s disease.
    • Inflammation: Lipids, particularly eicosanoids derived from arachidonic acid, play a role in inflammation and immune response, and dysregulation can contribute to inflammatory diseases.
  3. Therapeutic Target: Targeting lipid metabolism is a promising approach for treating various diseases. For example, inhibitors of fatty acid synthase are being investigated as potential anticancer agents, and drugs targeting lipid metabolism are used to manage dyslipidemia and cardiovascular disease.

In conclusion, lipid metabolism is integral to cellular signaling and is involved in the pathogenesis of various diseases. Understanding the role of lipid metabolism in health and disease can lead to the development of novel therapeutic strategies for treating these conditions.

Nitrogen Fixation and Amino Acid Biosynthesis

Mechanisms of nitrogen fixation

Nitrogen fixation is the process by which atmospheric nitrogen (N2) is converted into ammonia (NH3) or related nitrogenous compounds by certain microorganisms, primarily bacteria and archaea. There are two main mechanisms of nitrogen fixation:

  1. Biological Nitrogen Fixation (BNF): This process is carried out by nitrogen-fixing microorganisms, mainly diazotrophic bacteria and some archaea. BNF occurs in the following steps:
    • Nitrogenase Complex: Nitrogen fixation is catalyzed by the nitrogenase enzyme complex, which consists of two key proteins: dinitrogenase reductase (Fe protein) and dinitrogenase (MoFe protein).
    • Reduction of Nitrogen: Atmospheric nitrogen (N2) is reduced to ammonia (NH3) in a series of enzymatic reactions catalyzed by nitrogenase. This process requires energy in the form of ATP and electrons from a reducing agent like ferredoxin.
    • Regulation: BNF is a highly regulated process, as nitrogenase is sensitive to oxygen and requires an anaerobic environment. Nitrogen-fixing bacteria have developed various strategies to protect nitrogenase from oxygen, such as forming specialized structures called heterocysts (in cyanobacteria) or living in symbiosis with plants (e.g., rhizobia in legumes).
  2. Industrial Nitrogen Fixation: In addition to biological nitrogen fixation, nitrogen can also be fixed industrially through the Haber-Bosch process. This process involves the high-temperature and high-pressure catalytic reduction of nitrogen and hydrogen gases to produce ammonia. The ammonia produced through the Haber-Bosch process is a key component of fertilizers and plays a crucial role in modern agriculture.

In summary, nitrogen fixation is a vital process that converts atmospheric nitrogen into a form that can be used by plants and other organisms. Biological nitrogen fixation, carried out by nitrogen-fixing microorganisms, and industrial nitrogen fixation, through the Haber-Bosch process, are two key mechanisms by which nitrogen is fixed in nature.

Biosynthesis pathways of amino acids and their relevance in bioinformatics

The biosynthesis of amino acids is a complex process that involves multiple interconnected pathways. These pathways are crucial for synthesizing the building blocks of proteins and play a significant role in various cellular processes. Understanding these pathways is essential in bioinformatics for studying protein structure and function, metabolic modeling, and designing therapeutic interventions. Here’s an overview of the biosynthesis pathways of amino acids and their relevance in bioinformatics:

  1. Overview of Amino Acid Biosynthesis Pathways:
    • Essential vs. Non-essential Amino Acids: Amino acids are classified into essential (must be obtained from the diet) and non-essential (can be synthesized by the body) based on their biosynthetic pathways.
    • Transamination and Deamination: A key step in amino acid metabolism is the transfer of amino groups between amino acids and α-keto acids, catalyzed by aminotransferases. Deamination removes amino groups, leading to the formation of ammonia, which is toxic and must be eliminated through the urea cycle.
  2. Relevance in Bioinformatics:
    • Protein Structure Prediction: Knowledge of amino acid biosynthesis pathways is essential for accurately predicting protein structure and function. Understanding the properties of different amino acids helps in modeling protein folding and interactions.
    • Metabolic Modeling: Amino acid biosynthesis pathways are important components of metabolic models used in bioinformatics. These models help in understanding cellular metabolism, identifying metabolic pathways, and predicting the effects of genetic and environmental perturbations.
    • Drug Design: Amino acid biosynthesis pathways are potential targets for drug design. Inhibitors of enzymes involved in these pathways can be developed as antimicrobial or anticancer agents.
  3. Regulation of Amino Acid Biosynthesis:
    • Feedback Inhibition: Amino acid biosynthesis pathways are regulated by feedback inhibition, where the end product of a pathway inhibits the activity of an enzyme earlier in the pathway. This ensures that amino acids are synthesized only when needed.
    • Transcriptional Regulation: Gene expression of enzymes involved in amino acid biosynthesis is regulated at the transcriptional level by transcription factors. These factors respond to cellular signals and environmental cues to regulate amino acid synthesis in response to changing conditions.

In conclusion, the biosynthesis pathways of amino acids are fundamental to cellular metabolism and have broad relevance in bioinformatics. Understanding these pathways helps in studying protein structure and function, metabolic modeling, and drug design, making them crucial in various bioinformatics applications.

Nucleotide Biosynthesis

Biosynthesis pathways of nucleotides and their regulation

The biosynthesis of nucleotides involves complex pathways that are essential for DNA and RNA synthesis, energy metabolism, and cell signaling. These pathways are tightly regulated to ensure the cell has an adequate supply of nucleotides for various cellular processes. Here’s an overview of the biosynthesis pathways of nucleotides and their regulation:

  1. De Novo Synthesis of Purine Nucleotides:
    • Overview: Purine nucleotides (adenosine and guanosine) are synthesized from simpler precursors through a series of enzymatic reactions.
    • Steps: The pathway starts with the synthesis of inosine monophosphate (IMP) from phosphoribosyl pyrophosphate (PRPP) and glutamine. IMP is then converted to adenosine monophosphate (AMP) or guanosine monophosphate (GMP) through additional enzymatic steps.
    • Regulation: The rate-limiting step in purine nucleotide biosynthesis is catalyzed by the enzyme amidophosphoribosyltransferase (ATase), which is feedback inhibited by AMP, GMP, and their nucleotide derivatives (ADP, GDP).
  2. De Novo Synthesis of Pyrimidine Nucleotides:
    • Overview: Pyrimidine nucleotides (cytidine, uridine, and thymidine) are synthesized from aspartate and carbamoyl phosphate.
    • Steps: The pathway involves the synthesis of uridine monophosphate (UMP) from carbamoyl phosphate, aspartate, and PRPP, followed by conversion to cytidine monophosphate (CMP) and thymidine monophosphate (TMP).
    • Regulation: The rate-limiting step in pyrimidine nucleotide biosynthesis is catalyzed by the enzyme carbamoyl phosphate synthetase II (CPS II), which is regulated by feedback inhibition by UTP.
  3. Salvage Pathways:
    • In addition to de novo synthesis, cells can also salvage nucleotides by reclaiming bases and nucleosides from degraded RNA and DNA.
    • Salvage pathways are energetically favorable compared to de novo synthesis and are important for maintaining nucleotide pools in rapidly dividing cells.
  4. Regulation of Nucleotide Biosynthesis:
    • Transcriptional Regulation: The expression of genes encoding enzymes involved in nucleotide biosynthesis is regulated by transcription factors that respond to cellular nucleotide levels and growth signals.
    • Feedback Inhibition: Key enzymes in nucleotide biosynthesis pathways are subject to feedback inhibition by end products of the pathway. This ensures that nucleotide synthesis is tightly regulated and adapted to the cell’s needs.

In summary, the biosynthesis pathways of nucleotides are essential for cellular function and are tightly regulated to maintain nucleotide pools and meet the cell’s metabolic demands. Understanding the regulation of these pathways is important for studying nucleotide metabolism and developing therapeutic interventions for diseases related to nucleotide imbalance.

Role of nucleotides in DNA and RNA synthesis

Nucleotides are the building blocks of DNA and RNA, playing essential roles in the synthesis and function of these macromolecules. Here’s an overview of the role of nucleotides in DNA and RNA synthesis:

  1. DNA Synthesis (Replication):
    • Building Blocks: DNA is composed of four types of nucleotides: adenine (A), thymine (T), guanine (G), and cytosine (C).
    • Complementary Base Pairing: During DNA replication, nucleotides are added to the growing DNA strand in a complementary fashion, guided by the base pairing rules (A with T, G with C).
    • Phosphodiester Bond Formation: The sugar-phosphate backbone of DNA is formed by linking the 3′ carbon of one nucleotide to the 5′ carbon of the next nucleotide through phosphodiester bonds.
  2. RNA Synthesis (Transcription):
    • Building Blocks: RNA is composed of four types of nucleotides: adenine (A), uracil (U), guanine (G), and cytosine (C).
    • Template Directed: RNA synthesis is also template-directed, with the RNA polymerase enzyme synthesizing an RNA strand complementary to a DNA template.
    • RNA Processing: Newly synthesized RNA molecules undergo processing steps, such as capping, splicing, and polyadenylation, before becoming functional RNA molecules.
  3. Energy Source: The addition of nucleotides to the growing DNA or RNA strand requires energy, which is provided by the hydrolysis of nucleoside triphosphates (e.g., ATP, GTP) to nucleoside diphosphates (e.g., ADP, GDP) and inorganic phosphate (Pi).
  4. Role of Nucleotide Triphosphates:
    • ATP as a Universal Energy Carrier: Adenosine triphosphate (ATP) is a crucial energy carrier in cells, providing the energy required for various cellular processes, including DNA and RNA synthesis.
    • GTP in Protein Synthesis: Guanosine triphosphate (GTP) is essential for protein synthesis, serving as the energy source for the elongation phase of translation.

In summary, nucleotides are essential for DNA and RNA synthesis, serving as the building blocks for these macromolecules and providing the energy required for their synthesis. Understanding the roles of nucleotides in DNA and RNA synthesis is fundamental to understanding the processes of replication and transcription and their regulation.

Integration of Metabolic Pathways

Cross-talk between different metabolic pathways

Cross-talk between different metabolic pathways refers to the interconnectedness and coordination of various metabolic pathways in cells. This cross-talk allows cells to respond to changing environmental conditions, regulate metabolic flux, and maintain homeostasis. Here are some examples of cross-talk between different metabolic pathways:

  1. Glycolysis and Gluconeogenesis:
    • These two pathways are reciprocally regulated to maintain glucose homeostasis in the body.
    • During fasting or low glucose conditions, gluconeogenesis is upregulated to synthesize glucose from non-carbohydrate precursors, while glycolysis is downregulated.
    • During high glucose conditions, glycolysis is upregulated to catabolize glucose for energy, while gluconeogenesis is downregulated.
  2. Glycolysis and Pentose Phosphate Pathway (PPP):
    • The PPP branches off from glycolysis and produces NADPH and pentose sugars.
    • NADPH produced by the PPP is used in biosynthetic processes and is essential for maintaining cellular redox balance.
    • The intermediates of the PPP can also feed back into glycolysis to generate ATP.
  3. Glycolysis and Citric Acid Cycle (TCA Cycle):
    • The end product of glycolysis, pyruvate, can enter the TCA cycle to generate ATP through oxidative phosphorylation.
    • In aerobic conditions, pyruvate is converted to acetyl-CoA, which enters the TCA cycle to generate reducing equivalents (NADH, FADH2) for ATP production.
  4. Amino Acid Metabolism and the TCA Cycle:
    • Amino acids can be converted into intermediates of the TCA cycle, such as α-ketoglutarate, oxaloacetate, and succinyl-CoA.
    • These intermediates can then enter the TCA cycle to generate ATP or be used for the synthesis of other molecules.
  5. Lipid Metabolism and Glucose Metabolism:
    • Lipids can be broken down into fatty acids and glycerol, which can enter glycolysis or the TCA cycle for energy production.
    • Conversely, excess glucose can be converted into fatty acids through lipogenesis for storage.
  6. Regulation of Metabolic Pathways:
    • Metabolic pathways are regulated by various mechanisms, including allosteric regulation, covalent modification, and gene expression.
    • For example, the TCA cycle is regulated by feedback inhibition and substrate availability to maintain metabolic homeostasis.

Overall, cross-talk between different metabolic pathways allows cells to adapt to changing nutrient availability and energy demands, ensuring the efficient utilization of nutrients and the maintenance of cellular functions.

Systems biology approaches to study metabolic networks

Systems biology approaches to study metabolic networks involve the integration of computational, experimental, and theoretical methods to understand the complex interactions within metabolic pathways and networks. These approaches aim to model and analyze the behavior of metabolic systems at a holistic level, considering the interactions between genes, proteins, metabolites, and environmental factors. Here are some key approaches in systems biology for studying metabolic networks:

  1. Metabolic Network Reconstruction:
    • Genome-Scale Metabolic Models (GEMs): GEMs are computational models that integrate genomic, biochemical, and physiological data to describe the metabolic capabilities of an organism.
    • Constraint-Based Modeling: Constraint-based modeling techniques, such as flux balance analysis (FBA), use mathematical optimization to predict metabolic fluxes in a network based on constraints such as stoichiometry, thermodynamics, and nutrient availability.
  2. Dynamic Modeling:
    • Ordinary Differential Equations (ODEs): ODE-based models describe the dynamic behavior of metabolic networks over time, taking into account the rates of biochemical reactions and the concentrations of metabolites.
    • Stochastic Modeling: Stochastic models simulate the random fluctuations in metabolic processes, which can be important for understanding noise in biological systems.
  3. Network Analysis:
    • Topological Analysis: Network analysis techniques, such as centrality measures and clustering algorithms, are used to identify important nodes (metabolites, enzymes) and modules within metabolic networks.
    • Graph Theory: Graph theory is applied to represent and analyze metabolic networks, revealing patterns of connectivity and identifying key pathways and regulatory nodes.
  4. Integration of Omics Data:
    • Metabolomics: Metabolomics data can be integrated with metabolic models to refine model predictions and identify metabolic phenotypes associated with specific conditions or perturbations.
    • Transcriptomics and Proteomics: Data from transcriptomics and proteomics studies can be integrated with metabolic models to study the regulation of metabolic pathways and the impact of gene expression on metabolic fluxes.
  5. Machine Learning and Data Mining:
    • Machine Learning: Machine learning algorithms can be used to analyze large-scale omics data and identify patterns that are predictive of metabolic behavior.
    • Data Mining: Data mining techniques can uncover hidden relationships within metabolic networks and guide the discovery of novel metabolic pathways or regulatory mechanisms.
  6. Applications in Biotechnology and Medicine:
    • Systems biology approaches to metabolic networks have applications in biotechnology for metabolic engineering and the design of microbial cell factories for biofuel production, pharmaceuticals, and other industrial applications.
    • In medicine, these approaches can be used to study metabolic diseases, identify biomarkers, and develop personalized therapies based on an individual’s metabolic profile.

Overall, systems biology approaches provide a powerful framework for studying metabolic networks, offering insights into the complexity and robustness of biological systems and facilitating the design and optimization of metabolic processes for various applications.

Hormones and Signal Transduction

Overview of hormone signaling pathways

Hormone signaling pathways are complex communication networks that enable cells to respond to hormonal signals in a coordinated manner. These pathways regulate a wide range of physiological processes, including growth, metabolism, development, and homeostasis. Here’s an overview of hormone signaling pathways:

  1. Hormone Reception:
    • Hormones are signaling molecules produced by endocrine glands or tissues that travel through the bloodstream to target cells.
    • Hormones can be classified based on their chemical structure (e.g., peptide, steroid, amine) and mode of action (e.g., nuclear receptors, cell surface receptors).
  2. Types of Hormone Signaling Pathways:
    • Endocrine Signaling: Hormones are released into the bloodstream and travel to distant target cells to elicit a response.
    • Paracrine Signaling: Hormones act locally on nearby target cells.
    • Autocrine Signaling: Hormones act on the same cell that produced them.
  3. Mechanisms of Hormone Action:
    • Cell Surface Receptors: Peptide hormones and some amine hormones bind to cell surface receptors, leading to the activation of intracellular signaling cascades (e.g., cAMP, IP3/DAG pathways).
    • Nuclear Receptors: Steroid hormones and thyroid hormones diffuse across the cell membrane and bind to intracellular nuclear receptors, which then regulate gene expression.
  4. Major Hormone Signaling Pathways:
    • cAMP Signaling Pathway: Activation of G protein-coupled receptors (GPCRs) leads to the production of cyclic adenosine monophosphate (cAMP), which activates protein kinase A (PKA) and regulates various cellular processes.
    • IP3/DAG Signaling Pathway: Activation of GPCRs leads to the production of inositol triphosphate (IP3) and diacylglycerol (DAG), which regulate intracellular calcium levels and activate protein kinase C (PKC).
    • JAK-STAT Signaling Pathway: Activation of cytokine receptors leads to the activation of Janus kinases (JAKs) and signal transducers and activators of transcription (STATs), which regulate gene expression.
    • MAPK/ERK Signaling Pathway: Activation of receptor tyrosine kinases (RTKs) leads to the activation of mitogen-activated protein kinases (MAPKs), which regulate cell proliferation, differentiation, and survival.
  5. Regulation of Hormone Signaling Pathways:
    • Hormone signaling pathways are tightly regulated to ensure proper cellular responses and maintain homeostasis.
    • Regulation can occur at multiple levels, including receptor activation, signal transduction, and gene expression.
  6. Integration of Hormone Signaling Pathways:
    • Hormone signaling pathways are interconnected and often cross-talk with each other to integrate and coordinate cellular responses.
    • Cross-talk between pathways allows for fine-tuning of cellular responses and adaptation to changing environmental conditions.

In summary, hormone signaling pathways play a critical role in regulating various physiological processes in the body. Understanding these pathways is essential for elucidating the mechanisms of hormone action, as well as for developing therapeutic interventions for hormone-related disorders.

Application of signal transduction in bioinformatics

Signal transduction plays a crucial role in bioinformatics, especially in the analysis of cellular signaling pathways and their integration with omics data. Here are some key applications of signal transduction in bioinformatics:

  1. Modeling and Simulation of Signaling Pathways:
    • Bioinformaticians use computational models to simulate signal transduction pathways and understand how signals are transmitted within cells.
    • Mathematical modeling approaches, such as ordinary differential equations (ODEs) and stochastic modeling, are used to describe the dynamics of signaling pathways and predict their behavior under different conditions.
  2. Network Analysis and Integration:
    • Signal transduction pathways are often represented as networks, where nodes represent signaling molecules and edges represent interactions between them.
    • Network analysis techniques, such as centrality analysis and module identification, are used to identify key components of signaling pathways and understand their organization and function.
    • Integration of signaling networks with other omics data, such as gene expression and protein-protein interaction data, helps in elucidating the crosstalk between signaling pathways and other cellular processes.
  3. Disease Mechanisms and Drug Discovery:
  4. Systems Biology Studies:
    • Signal transduction is a key component of systems biology, which aims to understand biological systems as integrated networks of molecules and interactions.
    • Systems biology approaches integrate experimental data with computational models to gain insights into the dynamics and regulation of signaling pathways in a holistic manner.
  5. Personalized Medicine:
    • Understanding the variability in signaling pathway activity among individuals is crucial for personalized medicine.
    • Bioinformatics tools are used to analyze omics data from individual patients and identify signaling pathway signatures that can guide personalized treatment strategies.

In conclusion, signal transduction is a central theme in bioinformatics, with applications ranging from understanding basic cellular processes to developing targeted therapies for disease. Integrating signal transduction data with other omics data and computational models enhances our understanding of complex biological systems and facilitates the development of precision medicine approaches.

Advanced Topics

Protein synthesis, targeting, and turnover

Protein synthesis, targeting, and turnover are essential processes in cells that regulate the production, localization, and degradation of proteins. Here’s an overview of these processes:

  1. Protein Synthesis (Translation):
    • Protein synthesis is the process by which ribosomes synthesize proteins from messenger RNA (mRNA) molecules.
    • The process involves three main steps: initiation, elongation, and termination.
    • During initiation, the ribosome assembles on the mRNA and begins scanning for the start codon (AUG).
    • During elongation, aminoacyl-tRNA molecules bring amino acids to the ribosome, where they are added to the growing polypeptide chain.
    • During termination, a stop codon is reached, and the ribosome releases the completed protein.
  2. Protein Targeting and Localization:
    • After synthesis, proteins must be targeted to their correct cellular location to perform their functions.
    • Targeting signals, such as signal peptides or localization sequences, direct proteins to specific organelles or compartments within the cell.
    • Proteins destined for the endoplasmic reticulum (ER), Golgi apparatus, lysosomes, or secretion are targeted by signal peptides and undergo cotranslational translocation.
    • Proteins targeted to mitochondria, chloroplasts, peroxisomes, and the nucleus are directed by specific targeting sequences and are imported post-translationally.
  3. Protein Turnover (Degradation):
    • Protein turnover refers to the balance between protein synthesis and degradation in cells.
    • Proteins are degraded by the ubiquitin-proteasome system or by lysosomes through autophagy.
    • Ubiquitin is a small protein that is covalently attached to target proteins, marking them for degradation by the proteasome.
    • Autophagy involves the engulfment of cytoplasmic components, including proteins, into autophagosomes, which then fuse with lysosomes for degradation.
  4. Regulation of Protein Synthesis and Turnover:
    • Protein synthesis and turnover are tightly regulated processes that respond to cellular signals and environmental cues.
    • Regulation can occur at multiple levels, including transcriptional, translational, and post-translational regulation.
    • For example, the mTOR pathway regulates protein synthesis in response to nutrient availability and growth factors, while the unfolded protein response (UPR) regulates protein folding and degradation in the ER.

In summary, protein synthesis, targeting, and turnover are essential processes that ensure the proper production, localization, and degradation of proteins in cells. Understanding these processes is crucial for elucidating cellular functions and mechanisms of disease, as well as for developing therapeutic strategies targeting protein synthesis and degradation pathways.

Photosynthesis and its molecular mechanisms

Photosynthesis is the process by which green plants, algae, and some bacteria convert light energy into chemical energy stored in glucose and other organic molecules. It involves a series of complex molecular mechanisms that take place in specialized cellular structures called chloroplasts. Here’s an overview of photosynthesis and its molecular mechanisms:

  1. Overall Reaction: The overall equation for photosynthesis is:

    6CO2+6H2O+light energy→C6H12O6+6O2

    This equation represents the conversion of carbon dioxide (CO2) and water (H2O) into glucose (C6H12O6) and oxygen (O2) using light energy.

  2. Light-dependent Reactions (Light Reactions):
    • Location: Occur in the thylakoid membranes of chloroplasts.
    • Process:
      1. Light is absorbed by chlorophyll and other pigments in photosystems I and II (PSI and PSII).
      2. Photons excite electrons in chlorophyll, causing them to move to a higher energy state.
      3. The excited electrons are passed along an electron transport chain (ETC), generating ATP and reducing equivalents (NADPH).
      4. Water is split by PSII, releasing electrons, protons, and oxygen (O2) as byproducts.
  3. Calvin Cycle (Light-independent Reactions or Dark Reactions):
    • Location: Occur in the stroma of chloroplasts.
    • Process:
      1. Carbon fixation: CO2 from the atmosphere is fixed into a 5-carbon compound, ribulose-1,5-bisphosphate (RuBP), by the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO).
      2. Reduction phase: ATP and NADPH generated in the light reactions are used to convert the fixed carbon into glyceraldehyde-3-phosphate (G3P), a 3-carbon sugar.
      3. Regeneration of RuBP: Some G3P molecules are used to regenerate RuBP, while others are used to synthesize glucose and other carbohydrates.
  4. Factors Affecting Photosynthesis:
    • Light intensity: Higher light intensity increases the rate of photosynthesis, up to a certain point.
    • Carbon dioxide concentration: Higher CO2 levels increase the rate of photosynthesis, up to a certain point.
    • Temperature: Photosynthesis is optimal at moderate temperatures; extremes can inhibit the process.
    • Water availability: Water is necessary for photosynthesis, and water stress can reduce the rate of photosynthesis.
  5. Role of Photosynthesis in the Environment:
    • Photosynthesis is the primary source of oxygen in the atmosphere, crucial for aerobic respiration in plants and animals.
    • It is the basis of the food chain, as plants convert light energy into chemical energy, which is then passed on to consumers.
    • Photosynthesis plays a crucial role in the carbon cycle, as it removes CO2 from the atmosphere and stores it in organic molecules.

In conclusion, photosynthesis is a vital process that sustains life on Earth by converting light energy into chemical energy and providing oxygen and organic molecules for growth and metabolism. Its molecular mechanisms are highly complex and finely regulated, making it one of the most fundamental processes in biology.

Recent advancements in biochemistry and their implications in bioinformatics

Recent advancements in biochemistry have led to a deeper understanding of molecular processes at the cellular level, providing valuable insights for bioinformatics. Some key advancements and their implications in bioinformatics include:

  1. Structural Biology and Protein Folding:
  2. High-throughput Omics Technologies:
  3. Metabolomics and Metabolic Pathway Analysis:
    • Advances in metabolomics technologies have facilitated the comprehensive analysis of metabolites in biological systems.
    • Integration of metabolomics data with other omics data allows for a systems-level understanding of metabolic pathways and their regulation, aiding in the study of diseases and drug metabolism.
  4. Structural Bioinformatics and Drug Design:
  5. Systems Biology and Network Analysis:
    • Systems biology approaches, integrating data from multiple omics levels, have led to a better understanding of complex biological systems.
    • Network analysis tools in bioinformatics help in studying molecular interactions, signaling pathways, and regulatory networks, providing insights into disease mechanisms and therapeutic targets.
  6. Artificial Intelligence and Machine Learning:

Overall, recent advancements in biochemistry have significantly impacted bioinformatics, enabling researchers to analyze complex biological systems, predict molecular interactions, and develop novel therapeutics with greater precision and efficiency.

Textbooks:

  1. D.L. Nelson and M.M. Cox, Lehninger Principles of Biochemistry, 6th Ed., Macmillan Worth, 2012.
  2. J.L. Tymoczko, J.M. Berg, and L. Stryer, Biochemistry, 8th Ed., W.H. Freeman, 2015.

References:

  1. W.W. Parson, D.E. Vance, and G.L. Zubay, Principles of Biochemistry, Wm. C. Brown Publishers, 1995.
  2. R.K. Murray, D.K. Granner, P.A. Mayes, and V.W. Rodwell, Harper’s Biochemistry, 30th Ed., McGraw Hill, 2015.

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