Chapter 3: The Molecules of Cells

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/SuffixMeaning
meth-1C
eth-2C
prop-3C
but-4C
pent/hex/etc-5+ C
-anesingle bonds only
iso-branched
-enedouble 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 GroupTypePolar?Reactive?Diagram
Hydroxyl groupFunctionalYesYes (can remove H)-OH
Carbonyl groupFunctionalYesYes (can remove 1/2 bonds)C=O
Carboxyl groupFunctionalYesYes (can remove H)-COOH
Amino groupFunctionalYesYes (can be ionized)-NH2
Phosphate groupFunctionalYes (actual charge)Yes (actual charge)-OPO32-
Methyl groupNoNo-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

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