Chapter 2 Notes: Atoms, Bonding, and Biomolecules

Chapter 2 Notes: Atoms, Bonding, and Biomolecules

  • Background context
    • The four major atoms that make up over 95% of the human body are carbon (C), hydrogen (H), nitrogen (N), and oxygen (O).
    • Everything important in biochemistry (proteins, fats, nucleic acids, carbohydrates) is built from combinations of these atoms.
    • The smallest building block is the atom; how atoms combine and bond determines the structure and function of molecules.

Subatomic Particles

  • Subatomic particles and charges
    • Protons: positively charged (+1)
    • Neutrons: neutral (no charge; add mass)
    • Electrons: negatively charged (-1)
    • In chemical bonding, focus is on protons and electrons because of their charge interactions.
  • Basic particle locations
    • Protons and neutrons cluster in the nucleus (the atom’s core).
    • Electrons orbit around the nucleus in regions called orbitals or energy levels.
    • Nucleus analogy: like the sun; electrons orbit around it, with rules governing how many can occupy each shell.

Atomic Structure and the Nucleus

  • Nuclear composition and location
    • Nucleus contains protons and neutrons.
    • Protons + neutrons in the nucleus; electrons orbiting outside.
  • Atomic number (Z)
    • Defined as the number of protons in the atom: Z = \text{# protons}.
    • In a neutral atom, the number of electrons equals the number of protons: \text{#electrons} = Z\,.$
  • Examples of atomic numbers and their basic structure
    • Hydrogen: Z = 1→1proton;neutralatomhas1electron;electronoccupiesthefirstorbital.</li><li>Helium:→ 1 proton; neutral atom has 1 electron; electron occupies the first orbital.</li> <li>Helium:Z = 2→2protons,2electrons;bothelectronsresideinthefirstorbital.</li><li>Neon:→ 2 protons, 2 electrons; both electrons reside in the first orbital.</li> <li>Neon:Z = 10→2inthefirstorbital,8inthesecondorbital;theoutershellisfull.</li></ul></li></ul><h3id="electronorbitalsshellsandtheoctetrule">ElectronOrbitals,Shells,andtheOctetRule</h3><ul><li>Orbitalsandenergylevels<ul><li>Electronsinhabitorbitals/shellsaroundthenucleus,notaliteralplanetarypathbutasimilaridea.</li><li>Thefirstshell(closesttothenucleus)ismoststronglyattractedtothenucleus;electronsherearetightlybound.</li></ul></li><li>Octetrule(capacityofelectronshells)<ul><li>Firstshellcanholdupto→ 2 in the first orbital, 8 in the second orbital; the outer shell is full.</li></ul></li> </ul> <h3 id="electronorbitalsshellsandtheoctetrule">Electron Orbitals, Shells, and the Octet Rule</h3> <ul> <li>Orbitals and energy levels<ul> <li>Electrons inhabit orbitals/shells around the nucleus, not a literal planetary path but a similar idea.</li> <li>The first shell (closest to the nucleus) is most strongly attracted to the nucleus; electrons here are tightly bound.</li></ul></li> <li>Octet rule (capacity of electron shells)<ul> <li>First shell can hold up to2electrons.</li><li>Allshellsbeyondthefirstcanholduptoelectrons.</li> <li>All shells beyond the first can hold up to8electrons(theoctetforstability,thoughinverylargeatomsmorecomplexconfigurationsexist).</li><li>Inthiscourse,wemainlyconsideruptotwoorthreeshellsawayfromthenucleus(largeatomsbeyondchlorinearenotthefocushere).</li></ul></li><li>Valenceelectrons<ul><li>Theelectronsintheoutermostshellarecalledvalenceelectrons.</li><li>Thesedeterminehowatomsbondwithothers.</li><li>Iftheoutermostshellisfull,theatomisusuallyinert(notreactive).</li><li>Ifthereareemptyspotsintheoutermostshell,theatomisreactiveandcanformbondstofillthatshell.</li></ul></li><li>Inertvsreactiveexamples<ul><li>Helium:electrons (the octet for stability, though in very large atoms more complex configurations exist).</li> <li>In this course, we mainly consider up to two or three shells away from the nucleus (large atoms beyond chlorine are not the focus here).</li></ul></li> <li>Valence electrons<ul> <li>The electrons in the outermost shell are called valence electrons.</li> <li>These determine how atoms bond with others.</li> <li>If the outermost shell is full, the atom is usually inert (not reactive).</li> <li>If there are empty spots in the outermost shell, the atom is reactive and can form bonds to fill that shell.</li></ul></li> <li>Inert vs reactive examples<ul> <li>Helium:Z = 2;firstshellfull(2electrons)→inert;tendsnottoreact.</li><li>Neon:; first shell full (2 electrons) → inert; tends not to react.</li> <li>Neon:Z = 10;firstshellfull(2),secondshellfull(8)→inert.</li></ul></li><li>Carbonexampletoillustratedistribution<ul><li>Carbon:; first shell full (2), second shell full (8) → inert.</li></ul></li> <li>Carbon example to illustrate distribution<ul> <li>Carbon:Z = 6;distribution:2electronsinthefirstshell,4inthesecondshell.</li><li>Thisplacescarbonwith4valenceelectrons,whichstronglyinfluencesitsbondingversatility.</li></ul></li></ul><h3id="buildingmoleculescovalentandionicbonds">BuildingMolecules:CovalentandIonicBonds</h3><ul><li>Covalentbonds(sharingelectrons)<ul><li>Covalentbondsinvolvesharingelectronsbetweenatoms.</li><li>Bondingleadstomoleculescomposedofmultipleatoms.</li><li>Indrawings,asinglecovalentbondisrepresentedbyasinglelineandcorrespondstoonepairofelectrons(i.e.,2electronstotal).</li></ul></li><li>Ionicbonds(transferofelectrons)<ul><li>Ionicbondsarisewhenelectronsaretransferredfromoneatomtoanother.</li><li>Thistransfercreateschargedspecies:acation(positivelycharged)andananion(negativelycharged).</li><li>Oppositechargesattractandholdtheionstogether.</li><li>Examplesequence(sodiumandchlorine)</li><li>Sodium(Na):; distribution: 2 electrons in the first shell, 4 in the second shell.</li> <li>This places carbon with 4 valence electrons, which strongly influences its bonding versatility.</li></ul></li> </ul> <h3 id="buildingmoleculescovalentandionicbonds">Building Molecules: Covalent and Ionic Bonds</h3> <ul> <li>Covalent bonds (sharing electrons)<ul> <li>Covalent bonds involve sharing electrons between atoms.</li> <li>Bonding leads to molecules composed of multiple atoms.</li> <li>In drawings, a single covalent bond is represented by a single line and corresponds to one pair of electrons (i.e., 2 electrons total).</li></ul></li> <li>Ionic bonds (transfer of electrons)<ul> <li>Ionic bonds arise when electrons are transferred from one atom to another.</li> <li>This transfer creates charged species: a cation (positively charged) and an anion (negatively charged).</li> <li>Opposite charges attract and hold the ions together.</li> <li>Example sequence (sodium and chlorine)</li> <li>Sodium (Na):Z = 11;losesoneelectronfromtheoutershelltoachieveastableconfiguration(outershellbecomesfilledupto2inthefirstshelland8inthesecond,withtheremainingelectronmovedtothethirdshell).</li><li>Chlorine(Cl):; loses one electron from the outer shell to achieve a stable configuration (outer shell becomes filled up to 2 in the first shell and 8 in the second, with the remaining electron moved to the third shell).</li> <li>Chlorine (Cl):Z = 17;gainsoneelectrontocompleteitsoutershell(nowithasafulloutershellinthethirdlevel).</li><li>Resultingcharges:Nabecomes; gains one electron to complete its outer shell (now it has a full outer shell in the third level).</li> <li>Resulting charges: Na becomes\text{Na}^+;Clbecomes; Cl becomes\text{Cl}^-.</li><li>TheelectrostaticattractionbetweenNa+andCl−formstheionicbond,producingNaCl.</li></ul></li><li>Sharingvstransferincontext<ul><li>Covalentbondscanbenonpolarorpolardependingonelectronsharingsymmetry(seebelow).</li><li>Ionicbondsinvolvecompleteelectrontransferandformationofionswithchargesthatattract.</li></ul></li></ul><h3id="covalentbondingnonpolarvspolar">CovalentBonding:NonpolarvsPolar</h3><ul><li>Nonpolarcovalentbonds<ul><li>Electronsaresharedequallybetweenatoms.</li><li>Example:carbondioxide,.</li> <li>The electrostatic attraction between Na+ and Cl− forms the ionic bond, producing NaCl.</li></ul></li> <li>Sharing vs transfer in context<ul> <li>Covalent bonds can be nonpolar or polar depending on electron sharing symmetry (see below).</li> <li>Ionic bonds involve complete electron transfer and formation of ions with charges that attract.</li></ul></li> </ul> <h3 id="covalentbondingnonpolarvspolar">Covalent Bonding: Nonpolar vs Polar</h3> <ul> <li>Nonpolar covalent bonds<ul> <li>Electrons are shared equally between atoms.</li> <li>Example: carbon dioxide,\mathrm{CO_2},whereelectronsaresharedtoformbondsthatareeffectivelyequalalongastraightline;thisresultsinanonpolarmolecule.</li></ul></li><li>Polarcovalentbonds<ul><li>Electronsaresharedbutnotequally;electrondensityisdrawntowardoneatommorethantheother.</li><li>Example:water,, where electrons are shared to form bonds that are effectively equal along a straight line; this results in a nonpolar molecule.</li></ul></li> <li>Polar covalent bonds<ul> <li>Electrons are shared but not equally; electron density is drawn toward one atom more than the other.</li> <li>Example: water,\mathrm{H_2O},whereoxygenattractselectrondensitymorethanhydrogen.</li><li>Partialchargesareindicatedwithdeltanotation:, where oxygen attracts electron density more than hydrogen.</li> <li>Partial charges are indicated with delta notation:\delta^-onthemoreelectronegativeatom(oxygen)andon the more electronegative atom (oxygen) and\delta^+ontheothers(hydrogens).</li><li>Resultingpartialchargescreatedipolesandcaninfluenceintermolecularinteractions.</li></ul></li></ul><h3id="hydrogenbondsandtheirsignificance">HydrogenBondsandTheirSignificance</h3><ul><li>Whatisahydrogenbond?<ul><li>Ahydrogenbondisaweakattractionbetweenthepartialnegativechargeononemolecule(e.g.,alonepaironoxygen)andthepartialpositivechargeonahydrogenatombondedtoahighlyelectronegativeatominanothermolecule.</li><li>Althoughweakerthancovalentorionicbonds,hydrogenbondsarecumulativelystrongandcrucialinbiology.</li></ul></li><li>Whytheymatter<ul><li>Water’sproperties(e.g.,surfacetension,cohesion)aregreatlyinfluencedbyhydrogenbondingamongH2Omolecules,enoughtosupportsmallorganisms(e.g.,waterstriders)onthesurface.</li><li>HydrogenbondsstabilizetheDNAdoublehelixbylinkingcomplementarybasesacrossstrands,enablingthestructureessentialforgeneticinformationstorageandreplication.</li></ul></li></ul><h3id="connectionstobiomoleculesandrealworldrelevance">ConnectionstoBiomoleculesandReal−WorldRelevance</h3><ul><li>Howbondingshapesbiomolecules<ul><li>Thefourmajoratoms(C,H,N,O)formthebackboneandfunctionalityofproteins,fats,nucleicacids,andcarbohydratesthroughcovalentandnoncovalentinteractions.</li><li>Bondingpatternsdeterminethethree−dimensionalshapes,reactivity,andinteractionsofbiomolecules.</li></ul></li><li>Foundationalprinciplestiedtobroaderchemistryandbiology<ul><li>Atomicnumberandneutralitygoverntheelectronconfigurationandpotentialforbonding.</li><li>Theoutermostelectrons(valenceelectrons)guidechemicalreactivityandcompoundformation.</li><li>Electronegativitydifferencesdrivecovalentbondpolarityandtheformationofhydrogenbonds,whichunderpinmanyphysiologicalprocesses.</li></ul></li></ul><h3id="quickreferencekeyformulasandconcepts">QuickReference:KeyFormulasandConcepts</h3><ul><li>Atomicnumber:on the others (hydrogens).</li> <li>Resulting partial charges create dipoles and can influence intermolecular interactions.</li></ul></li> </ul> <h3 id="hydrogenbondsandtheirsignificance">Hydrogen Bonds and Their Significance</h3> <ul> <li>What is a hydrogen bond?<ul> <li>A hydrogen bond is a weak attraction between the partial negative charge on one molecule (e.g., a lone pair on oxygen) and the partial positive charge on a hydrogen atom bonded to a highly electronegative atom in another molecule.</li> <li>Although weaker than covalent or ionic bonds, hydrogen bonds are cumulatively strong and crucial in biology.</li></ul></li> <li>Why they matter<ul> <li>Water’s properties (e.g., surface tension, cohesion) are greatly influenced by hydrogen bonding among H2O molecules, enough to support small organisms (e.g., water striders) on the surface.</li> <li>Hydrogen bonds stabilize the DNA double helix by linking complementary bases across strands, enabling the structure essential for genetic information storage and replication.</li></ul></li> </ul> <h3 id="connectionstobiomoleculesandrealworldrelevance">Connections to Biomolecules and Real-World Relevance</h3> <ul> <li>How bonding shapes biomolecules<ul> <li>The four major atoms (C, H, N, O) form the backbone and functionality of proteins, fats, nucleic acids, and carbohydrates through covalent and noncovalent interactions.</li> <li>Bonding patterns determine the three-dimensional shapes, reactivity, and interactions of biomolecules.</li></ul></li> <li>Foundational principles tied to broader chemistry and biology<ul> <li>Atomic number and neutrality govern the electron configuration and potential for bonding.</li> <li>The outermost electrons (valence electrons) guide chemical reactivity and compound formation.</li> <li>Electronegativity differences drive covalent bond polarity and the formation of hydrogen bonds, which underpin many physiological processes.</li></ul></li> </ul> <h3 id="quickreferencekeyformulasandconcepts">Quick Reference: Key Formulas and Concepts</h3> <ul> <li>Atomic number:Z = \text{# protons}</li><li>Neutralatomelectroncount:</li> <li>Neutral atom electron count:\text{#electrons} = Z</li><li>Firstshellcapacity:</li> <li>First shell capacity:2electrons</li><li>Othershellscapacity(octetrule):uptoelectrons</li> <li>Other shells capacity (octet rule): up to8electrons</li><li>Covalentbond(single):twoelectronssharedbetweentwoatoms⇒representedbyoneline</li><li>Ionicbond:transferofelectronscreatesions;oppositechargesattract</li><li>Nonpolarcovalentbond:equalsharingofelectrons</li><li>Polarcovalentbond:unequalsharing;partialchargeselectrons</li> <li>Covalent bond (single): two electrons shared between two atoms ⇒ represented by one line</li> <li>Ionic bond: transfer of electrons creates ions; opposite charges attract</li> <li>Nonpolar covalent bond: equal sharing of electrons</li> <li>Polar covalent bond: unequal sharing; partial charges\delta^-onthemoreelectronegativeatomandon the more electronegative atom and\delta^+ontheother</li><li>Hydrogenbond:interactionbetweenpartialchargesacrossmolecules;importantforwaterpropertiesandDNAstructure</li></ul><h3id="carbonexamplerecap">Carbonexamplerecap</h3><ul><li>Carbonwithon the other</li> <li>Hydrogen bond: interaction between partial charges across molecules; important for water properties and DNA structure</li> </ul> <h3 id="carbonexamplerecap">Carbon example recap</h3> <ul> <li>Carbon withZ = 6$$: distribution 2 in the first shell, and 4 in the second shell; this outer-shell configuration contributes to carbon’s versatile bonding patterns (forming diverse molecules essential for life)

    Practice observations to prepare for class

    • Identify whether a bond is covalent or ionic based on electron transfer vs sharing
    • Determine whether a molecule is polar or nonpolar based on electron sharing and electronegativity differences
    • Recognize the role of hydrogen bonds in biological structures (e.g., DNA, proteins, water-dependent processes)