Chemistry of Life — Comprehensive Study Notes Flashcards

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Matter

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Matter has mass and occupies space, and it is affected by gravity. It consists of elements and compounds and is distinct from energy, which can move matter and perform work.

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Element

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An element is a pure substance that cannot be broken down by ordinary chemical means into another substance. Examples include hydrogen ($H$) and nitrogen ($N$).

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Compound

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A compound consists of two or more different elements combined in a fixed ratio, such as $H_2O$ or $CO_2$. Compounds have properties distinct from the elements that compose them.

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CHNOPS

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CHNOPS refers to the six major elements of life: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur. These elements make up about 96% of living matter, with others like Ca and K present in smaller amounts.

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Subatomic Particles

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Atoms consist of neutrons (mass ~1, no charge) and protons (mass ~1, +1 charge) in the nucleus, and electrons (negligible mass, -1 charge) in shells. These particles determine atomic mass, atomic number, and chemical behavior.

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Isotope

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Isotopes are atoms of the same element that differ in the number of neutrons but have the same number of protons. Radioactive isotopes are useful as tracers and in medical diagnosis but can be harmful with uncontrolled exposure.

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Valence Electrons

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Valence electrons are the electrons in the outermost shell of an atom and determine its chemical reactivity and bonding patterns. Atoms form bonds to achieve a full valence shell, often resembling the nearest noble gas configuration.

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Covalent Bond

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A covalent bond forms when two atoms share one or more pairs of electrons. Covalent bonds can be polar if electrons are shared unequally (e.g., $H_2O$) or nonpolar if shared equally (e.g., $O_2$).

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Ionic Bond

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Ionic bonds form when one atom donates electrons to another, producing oppositely charged ions that attract each other, such as $Na^+$ and $Cl^-$. Ionic interactions are strongly influenced by the surrounding environment, especially water.

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Hydrogen Bond

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A hydrogen bond is a weak attraction between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom. Hydrogen bonds are crucial for the structure and properties of water and biological molecules.

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Van der Waals

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Van der Waals interactions are slight, fleeting attractions that occur when molecules are very close, due to transient charge fluctuations. They are the weakest intermolecular forces but can be significant in large numbers, such as enabling gecko adhesion.

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Molecular Shape

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A molecule's three-dimensional structure determines its function because shape affects how molecules interact with others. Similar shapes can allow synthetic drugs to mimic natural molecules, for example opiates mimicking endorphins.

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Chemical Reaction

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A chemical reaction transforms reactants into products, and some reactions are reversible, reaching chemical equilibrium when forward and reverse rates balance. At equilibrium reactions continue but there is no net change in concentrations.

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Polarity

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Polarity in a molecule arises from unequal sharing of electrons between atoms of different electronegativities, creating partial charges. Water is a polar molecule with a slightly negative oxygen and slightly positive hydrogens, enabling hydrogen bonding.

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Cohesion

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Cohesion is the tendency of like molecules to stick together due to hydrogen bonding, which contributes to surface tension. Cohesion helps transport water in plants by allowing water molecules to cling to each other in the xylem.

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Adhesion

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Adhesion is the attraction between unlike molecules, such as water clinging to vessel walls, which helps counteract gravity during water transport. Adhesion works with cohesion to move water upward in plant xylem during transpiration.

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Surface Tension

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Surface tension measures how difficult it is to stretch or break the surface of a liquid, arising from cohesive hydrogen bonds at the surface. High surface tension allows insects to walk on water and influences droplet formation.

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Specific Heat

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Water has a high specific heat, meaning it requires a large amount of energy to change its temperature, which moderates climate and helps organisms maintain stable internal temperatures. Large bodies of water thus absorb and release heat slowly.

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Heat Vaporization

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Water's high heat of vaporization means evaporating water absorbs substantial energy, providing cooling via evaporative cooling like sweating. Molecules with the highest kinetic energy escape as gas, lowering the temperature of the remaining liquid.

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Ice Expansion

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When water freezes it expands and becomes less dense than liquid water, so ice floats and insulates the liquid below. This property allows life to persist under frozen surfaces in ponds and lakes during cold seasons.

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Universal Solvent

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Water is a versatile solvent because its polarity and ability to hydrogen-bond allow it to dissolve many ionic and polar substances. Hydrophilic substances interact with water, whereas hydrophobic substances like oils are excluded.

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pH Scale

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The pH scale measures hydrogen ion concentration using $pH=-\log[H^+]$, ranging from 0 (very acidic) to 14 (very basic) with 7 neutral. Most biological fluids fall between pH 6 and 8, and small deviations can disrupt biological function.

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Acid

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An acid increases the hydrogen ion concentration in a solution, for example $HCl$ dissociating to release $H^+$. Acids lower pH and can alter macromolecular structure and enzyme activity in biological systems.

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Base

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A base reduces hydrogen ion concentration by accepting $H^+$ or releasing $OH^-$, such as $NaOH$. Bases raise pH and can likewise impact biomolecules and cellular processes.

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Buffer

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Buffers minimize changes in $[H^+]$ and $[OH^-]$ by reversible reactions of weak acids and bases, maintaining stable pH in biological fluids. The carbonic acid–bicarbonate system is a key buffer that helps keep blood around pH $\sim 7.4$.

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Ocean Acidification

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Ocean acidification occurs when atmospheric $CO_2$ dissolves in seawater to form carbonic acid, lowering ocean pH. This process threatens coral reefs and organisms that rely on carbonate for shells and skeletons.

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Carbon

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Carbon is tetravalent with four valence electrons, allowing it to form up to four covalent bonds and create large, complex molecules. Its bonding versatility underlies the diversity of organic compounds essential to life.

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Tetravalence

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Tetravalence refers to carbon's four valence electrons, enabling the formation of four covalent bonds in various configurations. This property allows carbon to form chains, rings, and branched structures seen in biomolecules.

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Bond Types

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Carbon forms single, double, and triple covalent bonds, each affecting molecular geometry and reactivity. The type of bond influences molecule rigidity and biological function.

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Isomer

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Isomers are molecules with the same molecular formula but different arrangements of atoms, leading to distinct properties. Types include structural isomers, cis–trans isomers, and enantiomers which are mirror images.

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Enantiomer

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Enantiomers are mirror-image isomers that can have dramatically different biological effects because receptors are chiral. A historical example is thalidomide, where one enantiomer caused birth defects while the other had therapeutic effects.

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Functional Groups

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Functional groups are specific atom groupings that confer characteristic chemical behaviors to organic molecules. Common groups include hydroxyl ($-OH$), carbonyl ($>C=O$), carboxyl ($-COOH$), amino ($-NH_2$), sulfhydryl ($-SH$), phosphate ($-OPO_3^{2-}$), and methyl ($-CH_3$).

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Hydroxyl

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The hydroxyl group ($-OH$) defines alcohols and increases molecule polarity and solubility in water. Hydroxyl-containing molecules like ethanol participate readily in hydrogen bonding.

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Carboxyl

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The carboxyl group ($-COOH$) characterizes carboxylic acids and can donate a proton, acting as an acid in aqueous solutions. Its ionized form ($-COO^-$) is common in amino acids and metabolic intermediates.

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Monomer

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A monomer is a small organic molecule that serves as a building block for polymers by covalent bonding. Examples include amino acids for proteins and nucleotides for nucleic acids.

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Polymer

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A polymer is a long molecule composed of repeating monomer units linked by covalent bonds, formed by dehydration synthesis. Polymers can be broken down into monomers via hydrolysis.

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Dehydration Synthesis

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Dehydration synthesis (condensation) joins monomers by removing a water molecule, forming a new covalent bond such as peptide bonds between amino acids. This reaction builds polymers from smaller units.

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Hydrolysis

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Hydrolysis breaks polymer bonds by adding water, yielding monomers and releasing energy. This reaction is essential for digestion and recycling of biological macromolecules.

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Amino Acid

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Amino acids are the monomers of proteins, each containing an amino group ($-NH_2$), a carboxyl group ($-COOH$), and a variable R group that determines properties. There are 20 standard amino acids with diverse side-chain chemistries.

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Protein Levels

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Protein structure is described in four levels: primary (amino acid sequence), secondary (alpha helices and beta sheets via hydrogen bonds), tertiary (3-D folding from side-chain interactions), and quaternary (assembly of multiple polypeptides). Each level is crucial for final function.

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Chaperonin

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Chaperonins are protein complexes that assist other proteins in folding properly by providing an isolated environment. They help prevent misfolding and aggregation that could impair function.

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Denaturation

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Denaturation is the loss of a protein's native conformation due to changes in pH, temperature, or chemical environment, causing loss of function. If conditions are extreme, denaturation can be irreversible.

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Nucleotide

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A nucleotide, the monomer of nucleic acids, consists of a five-carbon sugar, a phosphate group, and a nitrogenous base. Nucleotides assemble into DNA and RNA polymers that store and transmit genetic information.

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DNA vs RNA

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DNA is typically double-stranded with deoxyribose sugar and thymine, storing hereditary information, while RNA is usually single-stranded with ribose sugar and uracil, involved in protein synthesis and regulation. Both are composed of nucleotide sequences that encode information.

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Information Flow

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Genetic information flows from DNA to RNA to protein, where DNA is transcribed into RNA and RNA is translated into polypeptides. This central dogma underlies gene expression and cellular function.

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Carbohydrate

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Carbohydrates serve as fuel and structural material, ranging from monosaccharides like glucose to polysaccharides like starch and cellulose. Their general formula often approximates $CH_2O$, and glycosidic linkages determine structure and digestibility.

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Alpha Glucose

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Alpha ($\alpha$) glucose is a form of glucose where the hydroxyl on carbon-1 is oriented down in the ring; it is the monomer of starch and glycogen. $\alpha$ linkages produce helical polymers that are readily digestible by enzymes.

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Beta Glucose

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Beta ($\beta$) glucose has the hydroxyl on carbon-1 oriented up in the ring and is the monomer of cellulose. $\beta$ linkages create straight, fibrous chains that form strong structural materials resistant to enzymatic digestion in many animals.

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Lipid

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Lipids are hydrophobic macromolecules including fats, phospholipids, and steroids; they function in energy storage, membrane structure, and signaling. Triglycerides consist of glycerol bonded to three fatty acids and vary in saturation.

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Saturated Fat

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Saturated fatty acids have no double bonds between carbons and are saturated with hydrogen, typically solid at room temperature and common in animal fats. Their straight chains pack tightly, affecting membrane fluidity and health when consumed in excess.

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Unsaturated Fat

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Unsaturated fatty acids contain one or more C=C double bonds that create kinks in the chain, preventing tight packing and usually remaining liquid at room temperature. Cis double bonds, common in nature, influence membrane fluidity and metabolic properties.

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Phospholipid

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Phospholipids have a hydrophilic phosphate-containing head and two hydrophobic fatty-acid tails, enabling them to form bilayers that make up cell membranes. Their amphipathic nature drives membrane formation and function.

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Cholesterol

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Cholesterol is a steroid lipid that modulates membrane fluidity and serves as a precursor for steroid hormones. It is integral to animal cell membranes and has important physiological roles, though excess levels are linked to health risks.