Biochemistry Foundations - Summary Notes

Life's Origins & Basic Principles

• Life arose approximately 4 billion years ago, with the early Earth providing an environment conducive to the formation of organic molecules. Microorganisms were the earliest forms of life, obtaining energy from chemicals (chemoautotrophs) or sunlight (photoautotrophs) to synthesize essential biomolecules.

• Principle 1: Cells are the fundamental units of life, sharing remarkable similarities in their basic structures and functions, despite the vast diversity in their complexity and specific roles. All known living organisms are composed of one or more cells, and these cells are responsible for carrying out all life processes.

• Principle 2: Cells utilize carbon-based metabolites as the primary building blocks to construct complex structures and to store genetic information essential for self-replication and inheritance. These metabolites include sugars, amino acids, nucleotides, and lipids, all of which are based on the versatile chemistry of carbon.

• Principle 3: Living organisms exist in a dynamic steady state, constantly extracting energy from their environment to maintain homeostasis and counteract the natural tendency towards entropy. This energy is used to power various cellular processes, including biosynthesis, transport, and mechanical work.

• Principle 4: Cells possess the remarkable ability to replicate and self-assemble, accurately copying and transmitting genetic information from one generation to the next. This process involves the precise orchestration of DNA replication, RNA transcription, and protein synthesis, ensuring the continuity of life.

• Principle 5: Organisms undergo evolution over time, driven by mechanisms such as natural selection, genetic drift, and mutation, leading to the stunning diversity of life forms observed today, all sharing a common ancestry and fundamental biochemical principles.

• Biochemistry is the field that seeks to describe the intricate structures, complex mechanisms, and diverse chemical processes that occur within living organisms, providing insights into the molecular basis of life.

Cellular Foundations

• Cells: are the fundamental structural and functional units of life, responsible for all biological processes.

• Plasma membrane: defines the cell periphery, acting as a selective hydrophobic barrier that separates the internal cellular environment from the external surroundings, and contains various proteins involved in transport, signaling, and cell-cell interactions.

• Cytoplasm: the internal volume of the cell, consisting of the cytosol and various suspended particles, including organelles and ribosomes.

• Cytosol: an aqueous solution that contains a complex mixture of enzymes, RNA molecules, metabolites, ions, and other essential components required for cellular function.

• Genome: the complete set of genes (DNA) that encodes all the information necessary to build and maintain an organism, stored in the nucleoid region in prokaryotes or within the nucleus in eukaryotes.

• Cell size is limited by diffusion rates, which affect the efficiency of nutrient uptake and waste removal; cells typically range in size from 1 to 100 μm.

• All cells have a plasma membrane, which is essential for maintaining cell integrity and regulating the passage of substances into and out of the cell.

Domains of Life

• Three domains: Bacteria, Archaea, and Eukarya, representing the major divisions of life based on fundamental differences in cellular structure, biochemistry, and genetics.

• Archaea are more closely related to Eukarya than to Bacteria, as revealed by comparative genomics and molecular phylogenetic analyses.

• Aerobic organisms utilize O2 as the terminal electron acceptor in respiration, while anaerobic organisms utilize other electron acceptors such as nitrate, sulfate, or CO2.

• Obligate anaerobes are unable to survive in the presence of O2, as they lack the necessary protective mechanisms to detoxify reactive oxygen species; facultative anaerobes can thrive in either aerobic or anaerobic conditions, depending on the availability of O2.

Energy and Biosynthesis

• Phototrophs harness sunlight as their primary energy source, converting light energy into chemical energy through photosynthesis; chemotrophs obtain energy through the oxidation of chemical compounds, either organic or inorganic.

• Autotrophs are capable of synthesizing complex biomolecules from simple inorganic precursors such as CO2, utilizing either light energy or chemical energy; heterotrophs rely on preformed organic nutrients as their source of carbon and energy.

Cell Structure

• Bacterial/Archaeal cell envelope: a complex structure that includes the plasma membrane, an outer membrane (in Gram-negative bacteria), and a peptidoglycan layer (in most bacteria), providing structural support and protection to the cell.

• Gram-positive bacteria: characterized by a thick peptidoglycan layer that lies outside the plasma membrane, but lack an outer membrane.

• Gram-negative bacteria: possess a more complex cell wall structure, with an outer membrane containing lipopolysaccharide (LPS) and a thin peptidoglycan layer in the periplasmic space.

• Archaea: exhibit diverse cell wall compositions, with some species possessing a peptidoglycan-like layer, while others have a proteinaceous S-layer for rigidity and protection.

• E. coli cytoplasm: a crowded environment containing ribosomes, enzymes, metabolites, DNA (organized in the nucleoid region), plasmids, and other essential components required for bacterial cell function.

• Eukaryotic cells: distinguished by the presence of membrane-bound organelles, such as mitochondria (involved in cellular respiration), endoplasmic reticulum (ER, involved in protein synthesis and lipid metabolism), Golgi apparatus (involved in protein processing and trafficking), lysosomes (involved in intracellular digestion), and peroxisomes (involved in detoxification).

• Plant cells: contain unique organelles such as vacuoles (involved in storage and waste removal) and chloroplasts (the sites of photosynthesis).

• Ribosomes are not membrane-bound organelles, but rather macromolecular complexes responsible for protein synthesis, found in both prokaryotic and eukaryotic cells.

• Cytoskeleton: a dynamic network of protein filaments, including actin filaments, microtubules, and intermediate filaments, that provides structural support to the cell, facilitates cell movement, and mediates intracellular transport.

• Endomembrane system: a network of interconnected membranes that segregates metabolic processes, facilitating the efficient execution of diverse biochemical reactions within the cell.

• Exocytosis/endocytosis: transport mechanisms involving membrane fusion and fission, allowing cells to secrete substances into the extracellular environment and to internalize extracellular materials, respectively.

Supramolecular Assemblies & Biochemicals

• Supramolecular structures are complex arrangements of molecules held together by noncovalent interactions, such as hydrogen bonds, van der Waals forces, and hydrophobic interactions, which play crucial roles in biological systems.

• In vitro (in glass) studies are conducted in a controlled laboratory setting, while in vivo (in living) studies are performed within living organisms, and may yield different results due to the complexity of biological systems.

• Essential elements for life include bulk elements (e.g., carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur) and trace elements (e.g., iron, zinc, copper, iodine), all of which are required for various biological functions.

• Biomolecules: carbon compounds with various functional groups that can form single, double, or triple bonds, providing the structural diversity and chemical reactivity necessary for life.

Biomolecule Functional Groups

• Common functional groups: methyl, ethyl, phenyl, carbonyl, carboxyl, amino, hydroxyl, phosphoryl, sulfhydryl, and others, each contributing unique chemical properties to biomolecules.

• Central metabolites: amino acids, nucleotides, sugars, fatty acids, and other small molecules that are essential for core metabolic pathways and cellular functions.

• Secondary metabolites: specialized compounds produced by certain organisms, often with unique biological activities (e.g., antibiotics, toxins, pigments).

• Metabolome: the complete set of small molecules present in a cell, tissue, or organism; metabolomics is the comprehensive characterization of the metabolome, providing insights into metabolic pathways and cellular physiology.

• Macromolecules: large polymers with molecular weights greater than 5,000 Da, including proteins, nucleic acids, and polysaccharides, that are essential for cellular structure and function, and exhibit specific orientations and three-dimensional structures.

• Oligomers: shorter polymers composed of a few repeating units.

• Proteome: the entire collection of proteins in a cell or organism; proteomics involves the large-scale study of protein expression, structure, and function.

• Genome: the complete DNA or RNA sequence that contains the genetic instructions for an organism; genomics focuses on the structure, function, and evolution of genomes.

• Glycome: all carbohydrate-containing molecules in a biological system, including glycoproteins, glycolipids, and polysaccharides.

• Lipidome: the complete set of lipids in a cell or organism, encompassing a diverse range of molecules with roles in membrane structure, energy storage, and signaling.

Molecular Geometry

• Configuration: the fixed spatial arrangement of atoms in a molecule, which cannot be altered without breaking covalent bonds, giving rise to isomers with distinct properties.

• $geometric_isomers$: arise from the restricted rotation around double bonds, resulting in different arrangements of substituents on the same side or opposite sides of the double bond.

• Chiral centers: asymmetric carbons that are bonded to four different substituents, giving rise to stereoisomers that are non-superimposable mirror images of each other. A molecule with $n$ chiral centers can have a maximum of $2^n$ stereoisomers.

• Stereospecificity: the ability of a biological system to distinguish between stereoisomers, often crucial for enzyme-substrate interactions and receptor-ligand binding.

• Enantiomers: stereoisomers that are mirror images of each other and are non-superimposable.

• Diastereomers: stereoisomers that are not mirror images of each other.

• Racemic mixture: an equimolar solution of enantiomers, resulting in no net optical rotation.

• Conformation: the spatial arrangement of groups in a molecule that can change position through rotation around single bonds, allowing for flexibility and adaptability.

Thermodynamics

• Living organisms exist in a dynamic steady state, maintaining constant internal conditions, rather than at equilibrium, which would imply death.

• System: the specific part of the universe under consideration, including reactants, products, solvent, and atmosphere.

• Universe: system + surroundings, encompassing everything outside the system.

• Types of systems: isolated (no exchange of matter or energy), closed (exchange of energy but not matter), open (living organisms, exchange of both matter and energy with the surroundings).

• First law of thermodynamics: energy is conserved; it cannot be created or destroyed, only converted from one form to another.

• Second law of thermodynamics: the total entropy ($S$, randomness or disorder) of an isolated system always increases over time.

• Enthalpy ($H$): the heat content of a system, reflecting the number and kinds of chemical bonds present.

• Free energy ($G$) = $H - TS$, represents the amount of energy in a system available to do useful work.

• Spontaneous reactions: reactions that occur without the input of external energy, characterized by a negative change in free energy (\Delta G < 0).

• Endergonic reactions require energy input to proceed, while exergonic reactions release energy.

Energetics & Equilibrium

• Energy coupling links thermodynamically unfavorable reactions with favorable ones, often involving ATP hydrolysis, to drive biological processes.

• Equilibrium constant ($K_{eq}$) = $[C]^c[D]^d/[A]^a[B]^b$ at equilibrium, for the reversible reaction $aA + bB \rightleftharpoons cC + dD$, indicating the ratio of products to reactants at equilibrium.

• Mass-action ratio ($Q$): the ratio of products to reactants at any given time, reflecting the current state of the reaction relative to equilibrium.

• Standard free-energy change: $\Delta G = \Delta G^\circ + RTln([C][D]/[A][B])$, where $\Delta G^\circ$ is the standard free-energy change under standard conditions, $R$ is the gas constant, and $T$ is the absolute temperature.

• At equilibrium, $\Delta G = 0$, indicating that the forward and reverse reaction rates are equal.

• Enzymes enhance reaction rates by lowering the activation energy, without being consumed in the process.

• Activation energy ($\Delta G^\ddagger$): the energy difference between the reactants and the transition state, representing the energy barrier that must be overcome for the reaction to occur.

• Catabolism: the degradative phase of metabolism, breaking down complex molecules into simpler ones, yielding energy in the form of ATP and reducing equivalents (NAD(P)H).

• Anabolism: the synthetic phase of metabolism, utilizing energy to build complex biomolecules from simpler precursors.

• Metabolism: the overall network of enzyme-catalyzed pathways in a cell or organism, encompassing catabolism and anabolism.

• Feedback inhibition: a regulatory mechanism in which the product of a metabolic pathway inhibits an enzyme earlier in the pathway, preventing overproduction of the product.

Genetics

• DNA: encodes the complete set of instructions for the synthesis of cellular components and provides the template for self-replication, ensuring inheritance of genetic information.

• DNA of E. coli: a single circular molecule of approximately 4.64 million nucleotide pairs, encoding thousands of genes.

• DNA structure: deoxyribonucleotides pair specifically (A-T, G-C) via hydrogen bonds, forming a stable double helix structure that carries genetic information.

Evolution

• Mutation: changes in the DNA sequence, which can arise spontaneously or be induced by external factors, and can lead to variations in traits.

• Wild type: the normal, unmutated form of a cell or organism.

• RNA can act as a catalyst, demonstrating enzymatic activity in certain biological reactions.

• Protocells: self-organized, spherical lipid vesicles that may have been precursors to the first living cells, capable of encapsulating and protecting self-replicating RNA molecules.

• First cells likely used inorganic fuels, such as iron sulfide, as energy sources in the early Earth environment.

• Eukaryotic cell evolution: involved key events such as the development of a chromosome, the formation of a nucleus, and endosymbiosis with bacteria, leading to the origin of mitochondria and chloroplasts.

• Homologs: proteins with sequence similarities