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.
- organic chem (pertains 2 Carbon) vs nonorganic chemistry
- chapter pertains to basics of organic chem
Introduction
Page 32–33
- many adults suffer from lactose intolerant, infants drink 4 proteins, fats, sugars, but adults – digestive discomfort
- lactase: enzyme lactose ⇒ otr sugar, most: dec aft age of 2, 80% African/Native, 90% Asian Americans intol @ teen, Eu not
- chemical interactions: drive all bio, e.g. lactose by lactase (protein) code by DNA, sugar/protein/fat/nucleic acid, nec 4 life
Introduction to Organic Compounds
3.1 Life’s molecular diversity is based on the properties of carbon
Page 34
- why carbon: unparalleled ability 2 form large/complex molecs, called organic compounds, usu contain H as well
- carbon has 4 electrons in valence shell ⇒ valence 4, can connect to 4 diff atoms, diff shapes occur w/ double bonds
- simplest: methane – CH4
- “carbon skeletons:” C chains backbone of most organic molecs, differ in length, some brnchd/rings, some dbl bonds
- butane + isobutane, 1-Butene + 2-Butene: same chem formula but diff structural arrange, pairs called isomers
- isomers also result from diff arrangements of partners 2 carbon, important 4 pharma b/c 2 isomers have diff props
- form <=> func (e.g. L-Dopa reduce Parkinson’s Disease, R-Dopa no effect)
- 3 types: structural, geometric (partner diff – trans: 2 of same on diff sides, cis: 2 of same on 1 side), enatomers (mirror)
- enatomers have to have cent C w/ 4 bound things
- hydrocarbons: only C + H, e.g. methane, most found in fossil fuels, rare in life but chains present in fats
Hydrocarbon Prefixes & Suffixes
| Prefix/Suffix | Meaning |
|---|---|
| meth- | 1C |
| eth- | 2C |
| prop- | 3C |
| but- | 4C |
| pent/hex/etc- | 5+ C |
| -ane | single bonds only |
| iso- | branched |
| -ene | double bonds (e.g. benzene) |
| cyclo- | ring (exception: benzene) |
3.2 A few chemical groups are key to the functioning of biological molecules
Page 35
- props of organic compound dep: on carbon skeleton + other attached elements, f <=> f
- e.g. testosterone vs. estradiol: both steroid hormones, only differ in 2 grps yet cause diff gender features
- chem groups: 5 functional: part in chem react, polar, hydrophil; methyl group affects molec shape/func
- hydroxyl group: OH, bond 2 C skel, e.g. ethanol, all other alcohols
- carbonyl group: O double bond 2 C, aldehyde if @ end of skel, ketone if mid, simple sugar 1 carbonyl + sev hydroxyl
- carboxyl group: C double bond 2 O + bond 2 OH, contributes H+ ⇒ acid, become ionized, carboxylic acids
- amino group: C bond 2 N, N bond to 2H, ionized: N+ w/ 3 H, base b/c abs H+, amino acd = amino + carbox grp, amines
- phosphate group: P bond to 4O, usu ion (1 O is O-), attach 2 Cskel thru O, organic phosphates, NRG trans (e.g. ATP)
- methyl group: CH₃, methylated compound can be part of DNA, affect exp of genes
Important Chemical Groups of Organic Compounds
| Chemical Group | Type | Polar? | Reactive? | Diagram |
|---|---|---|---|---|
| Hydroxyl group | Functional | Yes | Yes (can remove H) | -OH |
| Carbonyl group | Functional | Yes | Yes (can remove 1/2 bonds) | C=O |
| Carboxyl group | Functional | Yes | Yes (can remove H) | -COOH |
| Amino group | Functional | Yes | Yes (can be ionized) | -NH2 |
| Phosphate group | Functional | Yes (actual charge) | Yes (actual charge) | -OPO32- |
| Methyl group | No | No | -CH3 |
3.3 Cells make large molecules from a limited set of small molecules
Page 36
- 4 main molec lacsses: carbo, proteins, nucleic acids, lipids, carbo/prot/nucl acids gigantic macromolecules
- polymers: cells make macromolecs by joining small molecs, chain w/ ident/sim building blocks (monomers)
Making Polymers
- dehydration reaction: link by remove H₂O as 2 molecs bonded, one monom lose hydroxyl, other loses 1H, common
Breaking Polymers
- hydrolysis: break w/ wtr, cells sometimes break down polymers (eg. digestion), reverse of dehyd react, add wtr 2 break
- enzymes: specialized macrom that speed up chem react, help dehyd react/hydrolysis, e.g. lactase brk lactose
The Diversity of Polymers
- ingredients: only 40–50 common comps (few rare), e.g. prot 20 amino acids, DNA 4 nucleotides, arrangement cause vary
- monomers universal to nearly all life but arrangements vary from species to species
- large bio molecs have unique props from arrangement of atoms, form = function
Carbohydrates
3.4 Monosaccharides are the simplest carbohydrates
Page 37
- carbohydrates: range from small sugars to large polysaccharides (starch in pasta, potatoes)
- monosacharides: monomers of carbohydrates, e.g. honey: glucose & fructose, hook together form cmplx sug, polysach
- general mult of CH₂O, sug have hydroxyl groups + 1 carbonyl, aldehyde/ketone, e.g. glucose: comm, import, C₆H₁₂O₆
- glucose vs. fructose: same chem formula but diff shape (fructose ketone, glucose aldehyde), diff props, fructose sweeter
- C skels of monosa: glu/fruc 6-C long, others 3–7, -ose suffix for sug, most comm – 5-C: pentoses, 6-C: hexoses
- rings: in aq sol, most pent/hex rings, e.g. gluc: 1st C bind to O attached to 5th C
- ring diagrams: abb by rm C, vary line thick 2 indicate ring flat but atom extend, simp ring w/ only O rep gluc
- use: NRG (part. gluc) (e.g. dextrose – aq sol gluc inject 2 provide rpair NRG), raw mat (e.g. amino, fatty acids), mk di/polysa
3.5 Two monosaccharides are linked to form a disaccharide
Page 38
- disaccharides: 2 monosa, dehy reac, e.g. maltose: gluc+gluc ⇒ O link, malt sug in seeds, beer/whisk/malt milk cand
- sucrose: most comm, gluc+fruc, in plnt sap, provide NRG + mat 2 plnt, from sugarcane stem/sug beets root ⇒ table sug
3.6 What is high-fructose corn syrup, and is it to blame for obesity?
Page 38 – Connection
- reg sug disaccharide sucrose, most processed foods have HFCS – contain monosaccharides of sucrose
- ing: starch main carb in corn (from gluc), industry hydrolyzes, 1970s: enzyme gluc 2 fruc (55% fruc, not much diff from sug)
- effects: clear liq cheaper, easier to mix, circumstantial ev 1980–2000: 2x obesity, 3x HFCS, 0.79x reg sug
- co/co: does correlation btw HFCS/obesity indicate cause, alarming but no sci ev of effect, some obese countries low HFC
- implication: HFCS not entire but ev that over sug/low physical act contribute to weight gain, health/varied nutrition tips
3.7 Polysaccharides are long chains of sugar units
Page 39
- polysaccharides: macromolecules, polymers 100–1ks monosaccharides, storage molecs or struct comp
- starch: gluc storage in plnts, long gluc chains, helical shape, (un)branch variants, animals starch ⇒ gluc enz, potato/grain
- glycogen: animals store gluc, more heavily branched than starch, most in granules in liver/muscle
- cellulose: tough plnt cell walls, monomers link in diff orient ⇒ H bonds if align, form cable-like microfibrils, lumber
- “insoluble fiber:” animals no enz to hydrolyze cellulose, not nutrient for hman (but 4 digest health), fruit/veg/whole grain
- some microorganisms digest cellulose: e.g. cows/termites have in digest, fungi recycle
- chitin: struct polysach, use by insects/crustaceans, build exoskeletons, fungi cell walls
- hydrophillic: almost all carbs are b/c hydroxyl groups, cotton bath towels absorb due to hydrophillic nature of cellulose
Lipids
3.8 Fats are lipids that are mostly energy-storage molecules
Page 40
- lipids: diverse molec rpg, diff b/c hydrophobic (~ oil, vinegar in salad dressing)
- not huge macromolecs, not polymers from monomers, 3 types: fats, phospholipids, steroids
- fat: lg lipids from glycerol (3 Cs each w/ hydroxyl), fatty acids (carboxyl group + 16–18 CH₂ chain), nonpolar CH hydphb
- fatty acid link 2 glycerol via dehydration reaction ⇒ fat produed, 3 fatty acids ⇒ triglyceride synonym for fat
- unsaturated fatty acid: chain contains 1+ dbl bonds, (CH₂-CH=CH-CH₂), bends, w/o is saturated (C saturate w/ H)
- most anim fats sat, pack closely, solid @ room temp; most plant/fish unsat, liq, oils, hydrogenate make sat but trans fat
- func: l-t NRG storage, 1g fat = 2x in 1g polysac, plnts: starch nbd vs. mobile anims: get arnd easy by carry fat, have to burn
- reasonable body fat normal/healthy, stock l-t fuel in adipose cells, swell/shrink as deposit/withdraw, fat cushion/insulate
3.9 Scientific studies document the health risks of trans fats
Page 41 – Scientific Thinking
- hydrogenate: 1890s, unsat ⇒ sat fats by add H, shelf life/frying ability, 50s/60s sat fat w/ heart disease ⇒ inc hydro veg oil
- new research: 1990s, trans fat risk > sat, one study: eliminate prevent 1/5 hrt att, 2006 FDA req label, laws restrict
- experimental studies est risk of trans fats: hard 2 measure risk/restricted in timeframe
- observational studies: many sci studies, longer time period, retrospective but unreliable self-report, survivorship bias
- Nurses’ Health Study: 1976, 120k fm nurse, 80k 4 fat, 5% inc sat fat NRG ⇒ 17% inc risk coronary heart dis, 2% trans/93
- policy changes: promoting hydrogenated veg oils ⇒ regulating/banning trans fats, policy changes reflect sci understanding
3.10 Phospholipids and steroids are important lipids with a variety of functions
Page 42
- phospholipids: major comp cell membranes, sim 2 fats but 2 fatty acids, neg chrg phosphate grp attach third C in skel
- f <=> f: hydrophobic tails of fatty acids cluster in ctr, hydrophilic phosphate heads face wet env on either side of membrane
- steroids: lipids w/ 4 fused rings in Cskel, eg. cholesterol – membs, precur other ster (sex horm), too- atherosclerosis
3.11 Anabolic steroids pose health risks
Page 42 – Connection
- anabolic steroids: synthetic var of testosterone, test cause muscle/bone mass buildup in puberty, maintain masc traits
- uses: treat anemia/dis that dest bone muscle, some ath enhance performance but bad effs
- abuse: despite risk, US Congress/professional sports authorities/college athletic programs ban, test drugs, penalize violator
Proteins
3.12 Proteins have a wide range of functions and structures
Page 43
- protein: polymer of amino acids, struct/func most elaborate/varied, nearly every dyn func dep
- enzymes: catalysts speed/regulate most chem reac, e.g. lactase
- other types: transport (move sugar, etc into cells), defensive (e.g. antibodies), signal (e.g. hormones) ⇒ receptors in membs
- muscle proteins: contractile proteins, struct proteins in tendon/ligament fibers, e.g. collagen = 40% of prot in hman
- storage proteins: supply amino acids 2 dev embryo, e.g. eggs/seeds
- shape: most globular, chain, sulfur stablize, e.g. lysozyme (swt/tear/sal), struct prot typ fibrous (long/thin), slk fb strn > stl
- more spec shape: e.g. coils/twists, 3D shape, nearly all prot bind 2 otr molec, e.g. lysozyme shape allow 2 bind 2 bact target
- denaturation: protein unravels, lose shape ⇒ lose func, excessive heat (e.g. frying an egg), wrong pH/salt concent
- cold temps also imp prot func but do not denature
- improper folding: Alzheimer’s/Parkinson’s accum misfold proteins, prions infect srs degen brain dis (e.g. mad cow dis), f/f
3.13 Proteins are made from amino acids linked by peptide bonds
Page 44
- amino acids: amino group + carboxyl group + H + R-group (var, glycine H, all otrs C + func grps), all bind 2 central C
- hydrophobic/hydrophillic: dep on wtr R groups r polar, if contain acids/bases ⇒ charged @ cell pH
- linking: dehyd reac, carboxyl group + amino group, peptide bond result, dipeptide and polypeptide
- variety from sequences of 20 amino acids, most polypeptide 100/1000+ amino acids in length
- folding: R groups influence (e.g. hydrophobic amino acids cluster in ctr), H bonds/ionic bonds/disulfide bridges det shape
3.14 A protein’s functional shape results from four levels of structure
Page 45 – Visualizing the Concept
Primary Structure
- precise sequence of a-acids, e.g. transthyretin (vt A + hormone trans): peptide bonds connect 127 amino acids, 3-ltr abb
- only group not affected by denaturation, all other groups are
Secondary Structure
- segments of chain coil/fold in2 local patterns, H bonds, e.g. alpha helix, beta pleated sheet (arrow 2 carboxyl end of chain)
Tertiary Structure
- overall 3D shape, R grps interact (e.g. hydrophob), H/ionic/disulfide, e.g. tthyretin: 1 a-Helix, sev b-sheets ⇒ globular shape
Quaternary Structure
- only in some prot, mult polypeptides into one protein, e.g. 4 subunits of transthyretin
Nucleic Acids
3.15 DNA and RNA are the two types of nucleic acids
Page 46
- DNA: deoxyribonucleic acid, 1/2 nucleic acids, nucleic, contain genes ⇒ code for amino acid sequences, inherit dt
- RNA: ribonucleic acid, intermed btw DNA/prot, in nucleus: DNA transcribe 2 RNA, move out of nuc, translate 2 prot
- recent research has found many other unknown uses for DNA/RNA
3.16 Nucleic acids are polymers of nucleotides
Pages 46–47
- nucleotide: monomers of nucleic acids, – chrg phosphate group link 2 5-C sug link 2 nitrogenous base (green) – N + C
- bases: Adenine-Thymine (RNA: Uracil not Thymine), Cytosine-Guanine
- polynucleotide linking: dehyd reac, sugar binds 2 phosphate grp, sugar-phosphate backbone, inc. nitrogenous bases
- double helix: DNA only, 2 wrap/pair, hold tgthr via H bonds, zip into stable dbl helix, most DNA molecs ks/ms of pairs
- complementary: each polynucleotide predictable counterpart of other, key to DNA replication/transcription, f/f
3.17 Lactose tolerance is a recent event in human evolution
Page 47 – Evolution Connection
- lact intol study: 2002, group of sci study genes of 196 lactose-intolerant adults (Afr/Asi/Eur), lact intol actual hman norm
- concent in NEur: lact tol surv adv, cold ⇒ 1 harvest/yr, ani main food src, cattle domest 9k yrs ago NEur, year-rnd dairy
- other mutations: 2006 study, 43 ethnic EAfr grps, 3 more diff mutations from 7k yrs ago ~ EAfr cattle domest time