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