🧬Molecular Biology Unit 2 – Chemical Foundations of Molecular Biology

Key Concepts and Terminology

• Molecular biology studies the structure, function, and interactions of molecules essential to life, particularly DNA, RNA, and proteins
• Atoms are the basic units of matter consisting of protons, neutrons, and electrons
• Chemical bonds, including covalent, ionic, and hydrogen bonds, hold molecules together and determine their properties
• Water is a crucial solvent in biological systems due to its polarity and ability to form hydrogen bonds
• pH is a measure of the acidity or alkalinity of a solution, with a scale ranging from 0 to 14
  • Acidic solutions have a pH below 7, while basic solutions have a pH above 7
• Buffers are solutions that resist changes in pH when small amounts of acid or base are added
• Organic compounds, such as carbohydrates, lipids, proteins, and nucleic acids, are the building blocks of life
• Macromolecules are large, complex molecules formed by the polymerization of smaller subunits (monomers)
• Energy is required for biochemical reactions and is often stored in the form of ATP (adenosine triphosphate)

Atomic Structure and Chemical Bonds

• Atoms consist of a positively charged nucleus containing protons and neutrons, surrounded by negatively charged electrons
• The number of protons in an atom determines its element, while the number of neutrons can vary, resulting in different isotopes
• Electrons occupy specific energy levels (shells) around the nucleus, with the outermost shell being the valence shell
• Chemical bonds form when atoms share, gain, or lose electrons to achieve a stable electronic configuration
• Covalent bonds involve the sharing of electrons between atoms, resulting in the formation of molecules
  • Single, double, and triple covalent bonds can form depending on the number of electrons shared
• Ionic bonds form when electrons are transferred from one atom to another, creating positively and negatively charged ions that attract each other
• Hydrogen bonds are weak electrostatic attractions between a hydrogen atom bonded to an electronegative atom (such as oxygen or nitrogen) and another electronegative atom
• Van der Waals forces are weak intermolecular attractions that result from temporary dipoles induced by the movement of electrons

Water and Its Properties in Biology

• Water is a polar molecule due to the uneven distribution of charge between the oxygen and hydrogen atoms
• Hydrogen bonding between water molecules gives rise to many of water's unique properties, such as high surface tension, cohesion, and adhesion
• Water has a high specific heat capacity, allowing it to absorb and release large amounts of heat without significant temperature changes, which helps regulate body temperature in living organisms
• The high heat of vaporization of water allows for effective evaporative cooling in organisms (sweating)
• Water's ability to dissolve a wide range of substances makes it an excellent solvent for biochemical reactions
  • Hydrophilic substances readily dissolve in water, while hydrophobic substances do not
• The cohesive and adhesive properties of water enable capillary action, which is important for water transport in plants and blood vessels
• Ice is less dense than liquid water due to the arrangement of hydrogen bonds, allowing aquatic life to survive in frozen water bodies

pH and Buffers

• pH is a logarithmic scale that measures the concentration of hydrogen ions $(\ce{H+})$ in a solution
• The pH scale ranges from 0 to 14, with 7 being neutral, values below 7 being acidic, and values above 7 being basic (alkaline)
• The pH of a solution can be calculated using the equation: $pH = -\log_{10}[\ce{H+}]$
• Acids are proton donors that increase the concentration of $\ce{H+}$ in a solution, while bases are proton acceptors that decrease the concentration of $\ce{H+}$
• Buffers are solutions that minimize changes in pH when small amounts of acid or base are added
  • Buffers typically consist of a weak acid and its conjugate base, or a weak base and its conjugate acid
• The Henderson-Hasselbalch equation relates the pH of a buffer system to the concentrations of its components: $pH = pK_a + \log_{10}\frac{[A^-]}{[HA]}$
• Biological systems rely on buffers to maintain a stable pH, which is essential for the proper function of enzymes and other cellular processes
  • Examples of biological buffers include the bicarbonate buffer system in blood and the phosphate buffer system in cells

Organic Compounds in Living Systems

• Organic compounds are carbon-based molecules that are essential for life
• The four main classes of organic compounds in living systems are carbohydrates, lipids, proteins, and nucleic acids
• Carbohydrates are composed of carbon, hydrogen, and oxygen atoms in a 1:2:1 ratio
  • Monosaccharides (simple sugars) are the building blocks of carbohydrates (glucose, fructose)
  • Disaccharides are formed by the joining of two monosaccharides (sucrose, lactose)
  • Polysaccharides are long chains of monosaccharides (starch, cellulose, glycogen)
• Lipids are hydrophobic molecules that include fats, oils, waxes, and steroids
  • Triglycerides are the main form of energy storage in living organisms
  • Phospholipids are the primary components of cell membranes
• Proteins are polymers of amino acids that perform a wide range of functions in living systems (enzymes, antibodies, transport proteins)
• Nucleic acids, DNA and RNA, store and transmit genetic information
  • DNA is a double-stranded helix composed of nucleotides containing the bases adenine (A), thymine (T), guanine (G), and cytosine (C)
  • RNA is single-stranded and contains the base uracil (U) instead of thymine

Macromolecules: Structure and Function

• Macromolecules are large, complex molecules formed by the polymerization of smaller subunits called monomers
• The four main classes of biological macromolecules are carbohydrates, lipids, proteins, and nucleic acids
• Carbohydrates serve as energy sources (glucose), structural components (cellulose), and cell signaling molecules (glycoproteins)
  • Monosaccharides are linked by glycosidic bonds to form disaccharides and polysaccharides
• Lipids have diverse functions, including energy storage (triglycerides), cell membrane structure (phospholipids), and signaling (steroids)
• Proteins have a wide range of functions, such as catalyzing reactions (enzymes), providing structural support (collagen), and transporting molecules (hemoglobin)
  • The primary structure of a protein is its amino acid sequence
  • Secondary structure refers to local folding patterns (α-helices and β-sheets)
  • Tertiary structure is the overall three-dimensional shape of a protein
  • Quaternary structure involves the interaction of multiple protein subunits
• Nucleic acids store and transmit genetic information
  • DNA is a double-stranded helix with complementary base pairing (A-T and G-C)
  • RNA is single-stranded and has various functions, including coding for proteins (mRNA), translating genetic information (tRNA), and catalyzing reactions (ribozymes)

Energy in Biochemical Reactions

• Energy is the capacity to do work or cause change
• In biological systems, energy is often stored in the chemical bonds of molecules, such as ATP (adenosine triphosphate)
• ATP is the primary energy currency of the cell, consisting of an adenosine molecule and three phosphate groups
  • Hydrolysis of ATP to ADP (adenosine diphosphate) and inorganic phosphate releases energy for cellular processes
• Enzymes are biological catalysts that lower the activation energy of chemical reactions, allowing them to proceed more quickly and efficiently
  • Enzymes are highly specific to their substrates and can be regulated by various factors (pH, temperature, inhibitors, activators)
• Metabolism refers to the set of chemical reactions that occur within a living organism to maintain life
  • Catabolic reactions break down complex molecules to release energy (cellular respiration)
  • Anabolic reactions use energy to build complex molecules from simpler ones (photosynthesis, protein synthesis)
• Redox reactions involve the transfer of electrons between molecules
  • Oxidation is the loss of electrons, while reduction is the gain of electrons
  • Redox reactions are crucial in many biological processes, such as cellular respiration and photosynthesis

Techniques and Tools in Molecular Biology

• Polymerase chain reaction (PCR) is a technique used to amplify specific DNA sequences
  • PCR involves the use of primers, DNA polymerase, and thermal cycling to exponentially increase the number of target DNA copies
• Gel electrophoresis is a method used to separate DNA, RNA, or proteins based on their size and charge
  • Agarose gel electrophoresis is commonly used for DNA and RNA, while polyacrylamide gel electrophoresis (PAGE) is used for proteins
• DNA sequencing determines the precise order of nucleotides in a DNA molecule
  • Sanger sequencing and next-generation sequencing (NGS) are widely used methods
• Cloning involves the insertion of a DNA fragment into a vector (plasmid, virus, or artificial chromosome) for propagation in a host cell
• Recombinant DNA technology allows the creation of new DNA molecules by combining DNA from different sources
  • Restriction enzymes are used to cut DNA at specific sequences, while DNA ligase joins DNA fragments together
• Blotting techniques, such as Southern (DNA), Northern (RNA), and Western (protein) blots, are used to detect specific molecules in a sample
• Microarrays and RNA-seq are used to study gene expression patterns by measuring the levels of mRNA in a sample
• CRISPR-Cas9 is a powerful genome editing tool that allows precise modification of DNA sequences in living cells