2.3 Organic Compounds in Living Systems

Organic compounds are the building blocks of life, forming the basis of all living systems. Carbohydrates, lipids, proteins, and nucleic acids play crucial roles in energy storage, cell structure, and genetic information transfer.

These compounds are essential for cellular processes and are synthesized through various metabolic pathways. Understanding their structure and function is key to grasping how living organisms maintain life and adapt to their environments.

Organic Compounds in Living Systems

Major Classes and Composition

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• The four major classes of organic compounds in living systems are carbohydrates, lipids, proteins, and nucleic acids
  • Each class has distinct structures and functions that contribute to cellular processes
• Organic compounds are primarily composed of carbon, hydrogen, oxygen, and nitrogen atoms
  • The arrangement and bonding of these atoms determine the unique properties of each class of organic compounds
• Living organisms synthesize organic compounds through various metabolic pathways (photosynthesis, cellular respiration)
  • These compounds are essential for growth, development, and maintenance of life

Synthesis and Importance in Living Systems

• Carbohydrates, lipids, proteins, and nucleic acids are synthesized by living organisms
  • Carbohydrates are produced through photosynthesis in plants and serve as energy storage and structural components
  • Lipids are synthesized from fatty acids and glycerol and function as energy storage, cell membrane components, and signaling molecules
  • Proteins are synthesized from amino acids and have diverse roles (enzymes, structural components, signaling molecules, transport)
  • Nucleic acids (DNA and RNA) are synthesized from nucleotides and store and transmit genetic information
• These organic compounds are crucial for the proper functioning and survival of living organisms
  • They participate in various cellular processes (energy production, cell signaling, cell structure, genetic information storage and transfer)
  • Deficiencies or imbalances in these compounds can lead to health issues and diseases (malnutrition, metabolic disorders, genetic disorders)

Structure and Function of Macromolecules

Carbohydrates

• Carbohydrates are composed of carbon, hydrogen, and oxygen atoms in a 1:2:1 ratio
  • They serve as the primary energy source for cells
  • Classified as monosaccharides, disaccharides, or polysaccharides based on their complexity
• Monosaccharides (glucose, fructose) are simple sugars that serve as building blocks for more complex carbohydrates
  • They can be linked together to form disaccharides and polysaccharides
• Disaccharides (sucrose, lactose) are formed by the joining of two monosaccharides through a glycosidic bond
  • Commonly found in foods and serve as energy sources
• Polysaccharides (starch, glycogen, cellulose) are long chains of monosaccharides
  • Starch and glycogen serve as energy storage molecules
  • Cellulose provides structural support in plant cell walls

Lipids

• Lipids are a diverse group of hydrophobic organic compounds
  • Include fats, oils, waxes, and steroids
  • Serve as energy storage molecules, structural components of cell membranes, and signaling molecules
• Triglycerides are the most common type of lipid
  • Consist of three fatty acid molecules attached to a glycerol backbone
  • Saturated fatty acids have single bonds between carbon atoms, while unsaturated fatty acids have one or more double bonds
• Phospholipids are a major component of cell membranes
  • Consist of two fatty acid tails attached to a glycerol backbone with a phosphate group and a polar head
  • This structure creates a hydrophobic and hydrophilic region, allowing for the formation of lipid bilayers
• Steroids (cholesterol, hormones like testosterone and estrogen) have a characteristic four-ring structure
  • Play important roles in cell membrane structure and serve as signaling molecules

Proteins

• Proteins are polymers of amino acids linked together by peptide bonds
  • Have diverse functions (catalyzing reactions, providing structural support, facilitating cell signaling and transport)
• The primary structure of a protein is determined by the sequence of amino acids, encoded by the genetic code
  • This sequence determines the protein's unique three-dimensional shape and function
• The secondary structure refers to local folding patterns (alpha helices, beta sheets) stabilized by hydrogen bonding between amino acid residues
• The tertiary structure is the overall three-dimensional shape, determined by interactions between amino acid side chains (hydrogen bonding, ionic bonding, disulfide bridges)
• Quaternary structure refers to the arrangement of multiple polypeptide subunits in a multi-subunit protein (hemoglobin)

Nucleic Acids

• Nucleic acids (DNA and RNA) are polymers of nucleotides that store and transmit genetic information
  • Essential for the processes of replication, transcription, and translation
• DNA (deoxyribonucleic acid) is a double-stranded molecule composed of four nucleotide bases
  • Adenine (A), thymine (T), guanine (G), and cytosine (C)
  • Bases form complementary base pairs (A-T and G-C) through hydrogen bonding, creating the characteristic double helix structure
• RNA (ribonucleic acid) is typically single-stranded and contains the nucleotide uracil (U) instead of thymine
  • Three main types: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)
  • Each type has specific functions in protein synthesis

Role of Organic Compounds in Cells

Energy Production and Storage

• Carbohydrates, primarily glucose, are oxidized during cellular respiration to produce ATP
  • ATP is the primary energy currency of the cell
  • Process occurs in the cytoplasm and mitochondria and involves glycolysis, the Krebs cycle, and the electron transport chain
• Lipids, particularly triglycerides in adipose tissue, serve as energy storage molecules
  • Can be oxidized for energy production when needed

Cell Structure and Function

• Lipids, especially phospholipids, are the main components of cell membranes
  • Regulate the passage of molecules in and out of the cell
• Proteins serve as structural components (cytoskeletal elements) and are involved in cell signaling pathways and transport processes

Genetic Information Storage and Transfer

• Nucleic acids (DNA and RNA) are essential for the storage, transmission, and expression of genetic information
  • DNA serves as the blueprint for protein synthesis
  • RNA acts as an intermediary in the process
• During replication, DNA is copied to produce identical daughter strands
  • Ensures genetic information is passed on to the next generation of cells
• In transcription, genetic information in DNA is used to synthesize complementary RNA strands (primarily mRNA)
  • mRNA carries the genetic code to the ribosomes for protein synthesis
• Translation is the process by which the genetic code carried by mRNA is used to synthesize proteins at the ribosomes
  • tRNA molecules transport specific amino acids to the ribosomes for incorporation into the growing polypeptide chain

Importance of Enzymes in Reactions

Enzymes as Biological Catalysts

• Enzymes are biological catalysts that speed up chemical reactions in living systems
  • They lower the activation energy required for the reaction to occur
  • Crucial for maintaining life, as most cellular processes would occur too slowly without enzymes
• Enzymes are typically proteins with specific three-dimensional structures
  • Create an active site where the substrate (reactant) binds
  • Active site has a unique shape and chemical properties that allow it to interact with the substrate through various intermolecular forces (hydrogen bonding, van der Waals interactions)

Enzyme-Substrate Interactions and Efficiency

• The induced-fit model describes how the binding of the substrate to the active site causes a conformational change in the enzyme
  • Brings the substrate into proper alignment for the reaction to occur
  • Helps explain the high specificity of enzymes for their substrates
• Enzymes are not consumed during the reaction and can be used repeatedly
  • Makes them highly efficient catalysts
• Enzymes can catalyze reactions in both directions, depending on the concentrations of substrates and products

Factors Influencing Enzyme Activity

• Enzyme activity is influenced by various factors
  • Temperature, pH, and the concentration of substrates, products, and cofactors
  • Each enzyme has an optimal temperature and pH range at which it functions most efficiently
• Some enzymes require cofactors, which are non-protein molecules that assist in the catalytic process
  • Cofactors can be inorganic ions (iron, magnesium) or organic molecules called coenzymes (NAD+, FAD)
• Enzyme inhibitors are molecules that decrease or stop enzyme activity by binding to the enzyme and interfering with its function
  • Competitive inhibitors resemble the substrate and compete for binding to the active site
  • Non-competitive inhibitors bind to other sites on the enzyme, altering its conformation and decreasing its activity

Regulation of Metabolic Pathways

• Enzymes play a vital role in regulating metabolic pathways by controlling the rate of specific reactions
• Allosteric enzymes have regulatory sites distinct from their active sites
  • Particularly important in metabolic regulation
  • Allow for the modulation of enzyme activity in response to cellular conditions
• Feedback inhibition is a common regulatory mechanism in metabolic pathways
  • The end product of a pathway inhibits the activity of an enzyme earlier in the pathway
  • Helps maintain homeostasis by preventing the excessive accumulation of the end product