Chapter 2: The Chemical Basis of Life

Note: My bio notes are in an ultra-condensed format. It may be impossible to understand the strange acronyms I use here. That being said, it may serve as a good review.

Introduction

Pages 16–17

  • coral reef: dvers ecosys, calcium carbonate skels of small coral ani, habitat, CO2 threat, CO2 + H2O = acid, effect l8r in chp
  • why begin w/ chemistry: basis of life, elements combine 2 compounds that make up org, chem reactions underlie cell func
  • water: life/chem tied, life begin in water/evolve for 3 bil yr bf spread 2 land, all life dep on water (e.g. human cell ~75% wt)
  • emergence: chapter make connections, apparent even at lowest levels (atoms, molecules, molecular interactions)

Elements, Atoms, and Compounds

2.1 Organisms are composed of elements, in combinations called compounds

Page 18

  • matter: makes everything, anything space & mass, on Earth: states solid/liquid/gas, water – all 3 in nat env (rare ex)
  • element: subst, can’t be broken down ordinary, matter composed of, 92 in nat, 118 synth, each hs symbol (1/2 ltrs nm)
  • compound: substance w/ 2+ elements in fixed ratio, more common than pure elements (pure form rare)
  • compound ex: often 2 elems, salt (NaCl, pure elms poison,) 2H + O (gas) = water, emergence: compound vs. elms – diff prop
  • compounds in life: most 3+ elms, sugar: C, H, O, proteins: C, H, O, N (small amnt of sulfur,) diff arrange -> unique props
  • hman need 5, plnt 17, O/C/H/N 96% liv mtcalc/phos/pota/sul/Na/Cl/mag mst rest (bone, nerve signal)
  • trace elems: essent but sm, e.g. iron – all life, process/transport O₂, sme e for certan (e.g. iodine – vertbr)

2.2 Trace elements are common additives to food and water

Page 19 – Connection

  • Trace elements are required in very small quantities, but, in some cases, even those small requirements are difficult to fulfill.
  • iod: mk horm, 0.15 mg/day, goiter (thy grow), srs in fetal/childhd, iod salt but 30% no acc, sea/dairy/green nat, mst inlnd
  • flouride: 60yr ADA support into comm drink wtr, form of flourine (sm in all wtr), strng enamel, reduce tooth decay
  • more additives: preserve, nutrients, look better, iron fortification, vitamins – ex. compound, nutritious

2.3 Atoms consist of protons, neutrons, and electrons

Page 20

  • atom: from Greek word “indivisible,” smallest unit of matter that retains props of element, million per dot

Subatomic Particles

  • basics: 100+ subatomic particles but only 3 relevant in bio, proton (+),electron (-), neutron (neutral)
  • anatomy: protons/neutrons tight in nucleus, attract btw +/- keep elect near nuc, electron cloud, nuc as pea in stad ctr
    • neutrons space apart protons (b/c protons repel), electrons attracted to protons

Atomic Number and Mass Number

  • atomic number: per-element # of protons in ea atom (e.g. He have 2), most atoms pro = elec ⇒ net elec charge: 0
  • mass number: # of pro/neut, mass of two parts almost ident = 1 dalton, electron = 1/2000 daltons ⇒ cont very lttl
    • atomic mass: weighted average of all isotopes on earth

Isotopes

  • isotopes: same element but diff # of neut, behvae identically, name w/ mass, Carbon-12 99% of C, C-13/C-14
  • radioactive isotope: nucleus decays, give particles/energy, harm microorganism but help date, e.g. carbon-14
    • decay (somewhat) predictably

2.4 Radioactive isotopes can help or harm us

Page 21 – Connection

  • basis: living cells cannot distinguish btw isotopes but instruments can ⇒ monitor fate of atoms in organisms

Basic Research

  • tracers: follow molecules thru chem changes in org, e.g. trace CO2 in plants to sugar

Medical Diagnosis and Treatment

  • tracers in medicine: tag chemicals that accumulate in specific areas, measure where radiation collects, tiny amnt of iso
  • use for treatment: iodine in thy, radioactive iodine kill thy cancer
  • PET: positron-emission tomography, metabolizd subst (glucose/oxygen) trace ==> 3D images w/ high meta act (e.g. ❤️/🧠)
  • use for Alzheimer’s: PIB radioactive protein bind 2 beta-amyloid, detect w/ PET, help verify therapy efficacy

Dangers

  • harms: uncontrolled expos dam molecules/DNA, chem bonds, 1986: Chernobyl, few doz die, 100k evacuate, thy cancer
  • natural sources: radon (rad gas) <=> lung cancer, accumulate in buildings near uranium, homeowners radon tests/removal

Chemical Bonds

2.5 The distribution of electrons determines an atom’s chemical properties

Page 22

  • only electrons directly involved in chemical act of atom
  • electron shells: diff electrons in diff shells, ea have characteristic dist from nucleus, # of shells/atom vary
  • orbitals: volumes of space where electrons most likely, ea have 2 electrons, 1st shell – 1 orb/2 e, 2nd shell – 4 orb/8 e
    • atoms equally distribute electrons among orbitals
  • valence shell: outermost shell, # of elecs here determine chem props, atoms try to complete valence shells
  • ex: main comp of bio mol, react b/c outer shells incomplete, e.g. H only 1 but max 2, He/Ne/Ar full shells ⇒ inert/unreactv
  • chemical bonds: when 2 incomplete atoms react, ea atom share/exchange elecs, usu cause stay close together
  • Periodic table trends: down – # of shells, right – # of valence elecs, reactivity: metals down, nonmentals up

2.6 Covalent bonds join atoms into molecules through electron sharing

Page 23

  • covalent bond: two atoms share pair of electrons, enable valence complete, form molecule (e.g. H2, H2O)
  • valence/bonding capacity: # of covalent bonds an atom can form, dep on # of elecs 2 fill vs/elecs in vs
  • double bond: H₂ – one shared pair, O₂ – two pairs of electrons ⇒ double bond (H-H, O=O)
  • compounds formed: methane (CH₄), water (H₂O), carbon has valence 4
  • electronegativity: how strng atom att shred elecs, H₂/O₂ share eq ⇒ nonpolar covalent bond, CH₄: C/H sim
    • inherent prop of elem – general pattern: inc on top-right of pd tb
    • most to least: O, N, CH
  • polar covalent bonds: elecs closer 2 one atom, atoms part -/+, e.g. H₂O: O more en, elecs spend more time @ O
    • \(\delta\) – indicates partial charge
  • typically nonmetal-nonmetal
  • ways to depict: molecular formula, electron distribution diagram, structural formula, space filling model

2.7 Ionic bonds are attractions between ions of opposite charge

Page 24

  • table salt ex of how transfer elecs bond, Na: 1 elec in outer vs. Cl: 7, Na transf outer elec 2 Cl, both Na/Cl full
  • ion: atom get +/- charge b/c gain/loss elecs, opposites attract ⇒ ionic bond, result comp neutral, – ions: suffix -ide
    • term atom implies neutral charge, ion – new name
    • positively charged ion: cation, negatively charged ion: anion
  • salt: ionic compound, often found as crystals in nature, table salt ust familiar example
  • env affects bond strength: e.g. dry – strong, wet (see 2.13) – bond brk ⇒ drugs as salts b/c stable when dry but dis in wtr
  • typically metal-nonmetal

2.8 Hydrogen bonds are weak bonds important in the chemistry of life

Page 24–25

  • hydrogen bonds: most chem bonds covalent but weaker also crucial to life, H bonds best illu w/ wtr
    • both intramolecular and intermolecular
    • strength: covalent > ionic > hydrogen
    • requires proximity, only polar molecules
    • negative member always H
  • wtr as polar molec: slight – @ O, slight + @ H, allow H to attract 2/“flirt” w/ other slightly – atoms
  • etymology: H always + part in hydrogen bond, e.g. + H attract 2 – O in other H2O atoms
  • uses: create protein shape, hold DNA strands together (Chapter 3), wtr’s polarity/bonds ⇒ life support
  • collective bonds > one bond

2.9 Chemical reactions make and break chemical bonds

Page 25

  • chemical reactions: breakage/formation of bonds, e.g. 2 H₂ + O₂ ⇒ 2 H₂O
  • reactants: starting materials, product: resulting material; only rearrange matter (no +/- matter)
    • Law of Conservation of Mass
  • chem reac in orgs: photosynthesis, sun powers series of chem reac: 6 CO₂ + 6 H₂O ⇒ C₆H₁₂O₆ (glucose) + 6 O₂
  • in cells, many chemical reactions happen in water

General Types of Chemical Reactions

Name Formula
Combination (Synthesis) A + B → AB
Decomposition AB → A + B
Single Displacement A + BC → AC + B
Double Displacement AB + CD → AD + BC
Combustion CₓHy + O₂ → CO₂ + H₂O

Water’s Life-Supporting Properties

2.10 Hydrogen bonds make liquid water cohesive

Page 26

  • reason behind wtr life support: structure/interactions of molecules, polarity ⇒ hydrogen bond
  • cohesion: same kind molec stick, strng 4 wtr b/c H bnd, e.g. trees trans wtr, adhesion: subst cling 2 other, eg 2 wll
    • fact that hydrogen bonds only last for few trillionths of a sec does not matter; too many water molecs
  • cohesion + adhesion = capillary action
  • surface tension: difficulty 2 stretch/break surface, H bonds ⇒ water high (invis film), water strider stride acrss surface

2.11 Water’s hydrogen bonds moderate temperature

Page 26

  • thermal enr: random molec move, heat: transf therm NRG, temperature: intens/avg spd, wtr heat slow thn mtl
  • ht + H bnd: absorb ⇒ break, relese when form, wtr H bonds brk bf ht up ⇒ abs mst heat, cool: molec slow, bnd form, ht rel
    • means: lots of energy needed to heat up water, water holds on to heat, heat released when water cools
  • eff Earth: giant wtr supply mod temp, store heat from Sun + release, stable temp, marine env, 66% body wt ⇒ md body tmp
  • evaporative cooling: when subst evap, remain liq cools b/c molecs w/ grtst NRG leave, no overht, plnt/sweat/trop sea

2.12 Ice floats because it is less dense than liquid water

Page 27

  • sensible density: gas < liquid < solid; for water: gas < solid < liquid b/c wtr H-bonds the most
    • solids best for H-bonds (almost all molecs bonded), liquids only ˜50%, gas basically none
  • water on Earth: 3 states of matter, liquid denser than solid (unusual) due to H bonds
  • reason: as water freezes, H bonds become more stable/spaced apart, water molecs spaced apart ⇒ less dense
  • impact on marine life: prevent all water from freezing solid, blanket of floating ice insulates water below
    • serves as hunting ground for polar bears, climate change problem
    • cold ⇒ hibernate
    • “You’re not dead until you’re warm and dead”

2.13 Water is the solvent of life

Page 27

  • solution: lqd uniform mix, solvent: dissolver (e.g. wtr), solute: dissolved, aqueous sltn: wtr = slv
  • water as solvent: polar, wtr molecs attract 2 solute b/c opp charge (O-Na⁺, H-Cl⁻), eventually srnd/separate ions
  • use for life: any polar compound (e.g. sugar) can be solute, use in cells/blood/plant sap, wtr dislv slutes nec 4 life

2.14 The chemisty of life is sensitive to acidic and basic conditions

Page 28

  • dissociation: small % of wtr mlcs brk into H ions H⁺/hydroxide ions OH⁻, very react, affect complex molecs
  • acids: compounds that contribute H⁺ to solution, e.g. HCl (gastric juice), higher concentration of H⁺ than OH⁻
  • bases: reduce H⁺ concent, some donate OH⁻ 2 combine w/ H⁺ (e.g. sodium hydroxide), others accept H⁺ ions
  • pH scale: acidic/basic, 0–14, each unit: 10-fold change in H⁺, e.g. lmn juice (2) = 10x H⁺ in cola (3), 100x in 4
    • relative – does not take into account other substances, only relative H⁺/OH⁻ ratio
  • neutral solutions: equal concentration of H⁺/OH⁻, neither acid nor base, pH 7, e.g. pure water/inside most cells
  • buffers: subst minimize pH change (accept/donate H⁺ dep on pH), blood pH 7.4, cannot survive if 7.0 or 7.8
    • common in hman: CO₂ + H₂O ⇔ CH₂O₃ (carbonic acid) ⇔ CHO₃ (bicarbonate) + H⁺ (acid)

2.15 Scientists study the effects of rising atmospheric CO₂ on coral reef ecosystems

Pages 28–29 – Scientific Thinking

  • 25% CO₂ released absorb by oceans, expect 2 change ocean chem, harm marine life
  • ocean acidification: CO₂ lower pH of ocean, est 0.1 pH lower than oast 420k yrs, may 8.1 ⇒ 7.8 by cent end
  • calcification: coral ani – calc + carbonate ion = skeletons, H⁺ + CO₃²⁻ ⇒ bicarb (HCO₃⁻, rdce carb ions 40% 2100)
  • one ctrld exp: effect of carbonate ion on rate of reef calcium dispose, lower concentrtn⇒ lower calcification rate
  • more ev: 2011 study volcanoes in Papua New Guinea release CO₂ ⇒ lower pH, less divers/juvenile ⇒ harm
  • controlled experiments + observations = pH ⇒ implications for health of coral reefs and supported diversity

2.16 The search for extraterrestrial life centers on the search for water

Page 29 – Evolution Connection

  • role of wtr in searches for extrat life: water props support life on Earth, other planets maybe same
  • Mars: 2008 Phoenix land, show ice, 2011 MRO liq wtr below, season strms, could rethink evolution

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