🧬AP Biology Unit 1 – Chemistry of Life

Key Concepts and Definitions

• Matter consists of atoms, the fundamental building blocks of all substances
• Elements are pure substances that cannot be broken down into simpler substances by chemical means and are composed of only one type of atom
• Compounds are substances made up of two or more elements that are chemically combined in a specific ratio
• Molecules are groups of atoms held together by chemical bonds and can be composed of the same or different elements
• Ions are atoms or molecules that have gained or lost electrons, resulting in a net positive or negative charge
• pH is a measure of the concentration of hydrogen ions in a solution, indicating its acidity or alkalinity on a scale from 0 to 14
• Buffers are substances that help maintain a relatively stable pH in a solution by absorbing excess hydrogen or hydroxide ions
• Metabolism refers to the sum of all chemical reactions that occur within an organism, including both catabolic and anabolic processes

Atomic Structure and Chemical Bonds

• Atoms consist of protons, neutrons, and electrons
  • Protons have a positive charge and are located in the nucleus
  • Neutrons have no charge and are also located in the nucleus
  • Electrons have a negative charge and orbit the nucleus in shells
• The atomic number of an element is equal to the number of protons in its nucleus, which determines its identity
• Isotopes are atoms of the same element that have different numbers of neutrons, resulting in different atomic masses
• Chemical bonds form when atoms share or transfer electrons to achieve a more stable electronic configuration
• Covalent bonds involve the sharing of electrons between atoms, resulting in the formation of molecules
  • Single, double, and triple covalent bonds involve the sharing of one, two, or three pairs of electrons, respectively
• Ionic bonds involve the transfer of electrons from one atom to another, resulting in the formation of positively and negatively charged ions that attract each other
• Hydrogen bonds are weak electrostatic attractions between a hydrogen atom bonded to a highly electronegative atom and another electronegative atom, such as oxygen or nitrogen

Water and Its Properties

• Water is a polar molecule due to the uneven distribution of electrons between the oxygen and hydrogen atoms, resulting in a slightly positive charge on the hydrogen atoms and a slightly negative charge on the oxygen atom
• 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, meaning it can absorb or release a large amount of heat energy without significantly changing its temperature, which helps regulate the temperature of living organisms
• Water's high heat of vaporization allows it to absorb a large amount of heat energy during evaporation, which helps cool surfaces and regulate body temperature through sweating
• As a universal solvent, water can dissolve a wide variety of polar and ionic substances, facilitating chemical reactions and the transport of nutrients and waste products in living organisms
• The density of water is highest at 4°C, which allows ice to float on the surface of bodies of water, insulating the liquid water below and enabling aquatic life to survive in cold environments

Carbon and Organic Molecules

• Carbon is the basis for all organic molecules due to its ability to form four stable covalent bonds and create a wide variety of complex structures
• Hydrocarbons are organic molecules composed entirely of carbon and hydrogen atoms, such as methane (CH4) and benzene (C6H6)
• Functional groups are specific arrangements of atoms within organic molecules that give them distinct chemical properties
  • Examples of functional groups include hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), and phosphate (-PO4)
• Isomers are compounds that have the same molecular formula but different structural arrangements, resulting in different properties
  • Structural isomers have the same atoms arranged in different bonding patterns (butane and isobutane)
  • Stereoisomers have the same bonding patterns but different spatial arrangements (cis and trans isomers)
• Polymers are large molecules composed of repeating subunits called monomers, which are covalently bonded together
  • Examples of natural polymers include cellulose, starch, and proteins
  • Synthetic polymers include plastics like polyethylene and nylon

Macromolecules: Structure and Function

• Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen atoms, typically in a 1:2:1 ratio
  • Monosaccharides are simple sugars that serve as the building blocks of more complex carbohydrates (glucose, fructose)
  • Disaccharides are formed when two monosaccharides are joined together by a glycosidic bond (sucrose, lactose)
  • Polysaccharides are long chains of monosaccharides that serve as energy storage or structural components (starch, cellulose)
• Lipids are a diverse group of hydrophobic organic molecules that include fats, oils, waxes, and steroids
  • Triglycerides are the main form of energy storage in animals and consist of three fatty acid molecules bonded to a glycerol molecule
  • Phospholipids are the primary components of cell membranes and have a hydrophilic head and two hydrophobic tails
• Proteins are large, complex molecules composed of amino acids linked together by peptide bonds
  • The sequence of amino acids in a protein determines its unique three-dimensional structure and function
  • Enzymes are specialized proteins that catalyze biochemical reactions by lowering the activation energy
• Nucleic acids are organic molecules that store and transmit genetic information in living organisms
  • DNA (deoxyribonucleic acid) is a double-stranded molecule that carries the genetic instructions for an organism's development and function
  • RNA (ribonucleic acid) is a single-stranded molecule that plays various roles in gene expression, including serving as a template for protein synthesis

Enzymes and Biochemical Reactions

• Enzymes are biological catalysts that speed up chemical reactions in living organisms without being consumed in the process
• The active site of an enzyme is a specific region where the substrate binds and the reaction takes place
  • The shape and chemical properties of the active site determine the enzyme's specificity for its substrate
• Enzymes lower the activation energy of a reaction by stabilizing the transition state, allowing the reaction to proceed more quickly
• Factors that affect enzyme activity include temperature, pH, substrate concentration, and the presence of inhibitors or activators
  • Enzymes typically have an optimal temperature and pH range at which they function most efficiently
• Competitive inhibitors are molecules that bind to the active site of an enzyme, preventing the substrate from binding and slowing down the reaction
• Non-competitive inhibitors bind to a site other than the active site, causing a conformational change that reduces the enzyme's activity
• Allosteric regulation involves the binding of a molecule at a site other than the active site, which can either enhance (allosteric activator) or inhibit (allosteric inhibitor) the enzyme's activity

Energy in Living Systems

• Energy is the capacity to do work or cause change and is required for all life processes
• The first law of thermodynamics states that energy cannot be created or destroyed, only converted from one form to another
• The second law of thermodynamics states that every energy transfer or transformation increases the entropy (disorder) of the universe
• Adenosine triphosphate (ATP) is the primary energy currency in living organisms, used to power cellular processes such as metabolism, transport, and movement
  • ATP consists of an adenosine molecule bonded to three phosphate groups, with high-energy bonds between the phosphates
  • The hydrolysis of ATP to ADP (adenosine diphosphate) and inorganic phosphate releases energy that can be used to drive cellular processes
• Photosynthesis is the process by which plants and other autotrophs convert light energy into chemical energy stored in glucose
  • The light-dependent reactions occur in the thylakoid membranes of chloroplasts and involve the absorption of light energy by chlorophyll to generate ATP and NADPH
  • The light-independent reactions (Calvin cycle) occur in the stroma of chloroplasts and use the ATP and NADPH from the light-dependent reactions to fix carbon dioxide into glucose
• Cellular respiration is the process by which cells break down glucose to release energy in the form of ATP
  • Glycolysis occurs in the cytoplasm and involves the breakdown of glucose into two pyruvate molecules, generating a small amount of ATP and NADH
  • The Krebs cycle (citric acid cycle) occurs in the mitochondrial matrix and involves the oxidation of acetyl-CoA derived from pyruvate, generating CO2, ATP, NADH, and FADH2
  • Oxidative phosphorylation occurs in the inner mitochondrial membrane and involves the transfer of electrons from NADH and FADH2 through the electron transport chain, creating a proton gradient that powers ATP synthase to generate a large amount of ATP

Practical Applications and Lab Techniques

• Spectrophotometry is a technique used to measure the absorption of light by a sample at different wavelengths, which can be used to determine the concentration of a substance or monitor the progress of a reaction
• Chromatography is a method used to separate mixtures of compounds based on their differential affinities for a stationary phase and a mobile phase
  • Paper chromatography and thin-layer chromatography (TLC) are simple techniques that can be used to separate and identify pigments or amino acids
  • Column chromatography and high-performance liquid chromatography (HPLC) are more advanced techniques used for purifying proteins or analyzing complex mixtures
• Electrophoresis is a technique used to separate charged molecules (such as proteins or nucleic acids) based on their size and charge when subjected to an electric field
  • Gel electrophoresis uses a porous gel matrix (such as agarose or polyacrylamide) to separate molecules as they migrate through the gel
  • SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) is a common method for separating proteins based on their molecular weight
• Enzyme assays are used to measure the activity of an enzyme by monitoring the rate at which it catalyzes a specific reaction
  • Colorimetric assays involve the use of a substrate that changes color when acted upon by the enzyme, allowing the reaction rate to be measured using a spectrophotometer
  • Coupled assays involve linking the enzyme-catalyzed reaction to a second reaction that produces a measurable product, such as NADH or ATP
• Recombinant DNA technology involves the manipulation of DNA molecules to create new genetic combinations or express foreign genes in host organisms
  • Restriction enzymes are used to cut DNA at specific sequences, allowing DNA fragments to be isolated and combined with other DNA molecules
  • Plasmids are small, circular DNA molecules that can be used as vectors to introduce foreign DNA into bacterial cells for cloning or expression purposes

Common Misconceptions and FAQs

• Misconception: Atoms are the smallest particles of matter.
  • Reality: Atoms are composed of even smaller subatomic particles, such as protons, neutrons, and electrons. Quarks and leptons are considered the smallest known particles.
• Misconception: All bonds involve the sharing of electrons.
  • Reality: While covalent bonds involve the sharing of electrons, ionic bonds involve the transfer of electrons from one atom to another, resulting in the formation of ions.
• Misconception: Water is a universal solvent because it can dissolve anything.
  • Reality: While water is an excellent solvent for many substances, it cannot dissolve non-polar molecules like oils and fats. The term "universal solvent" refers to its ability to dissolve more substances than any other liquid.
• Misconception: All organic molecules contain carbon and hydrogen.
  • Reality: While most organic molecules contain carbon and hydrogen, some (like carbon dioxide and carbon monoxide) do not contain hydrogen. The defining characteristic of organic molecules is the presence of carbon.
• Misconception: Enzymes are living organisms.
  • Reality: Enzymes are not living organisms; they are proteins that catalyze chemical reactions. They are produced by living cells but are not alive themselves.
• Misconception: Energy is lost during chemical reactions in living systems.
  • Reality: Energy is not lost but rather converted from one form to another, in accordance with the first law of thermodynamics. However, some energy is released as heat during these conversions, which cannot be used to perform work (second law of thermodynamics).
• FAQ: What is the difference between an atom and a molecule?
  • An atom is the smallest unit of an element that retains its chemical properties, while a molecule is a group of atoms held together by chemical bonds. Molecules can be composed of the same or different elements.
• FAQ: How do enzymes speed up chemical reactions?
  • Enzymes lower the activation energy of a reaction by providing an alternative pathway for the reaction to occur. They do this by binding to the substrate(s) and stabilizing the transition state, making it easier for the reaction to proceed.