Chapter 4: A Tour of the Cell

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.


  • cytoskeleton act as travel arteries, both internally and externally, ustand nature hand in hand wot/ invent/refine instruments
  • discov: 1665 Robert Hooke mag cork, saw “ltl rooms” (cellulae), Leeuwenhoek refined lense desc, e.g. teeth “animalcules”
  • improved microscopes vastly expand view of cell, e.g. flourescence 4 cytoskeletons
  • parts in cell moving/interacting

Introduction to the Cell

4.1 Microscopes reveal the world of the cell

Pages 52–53

  • light microscope (LM): glorified magnifying class, light pass thru specimen, before use in 1600s no know about cells
    • ocular lens + objective lens ⇒ compound LM
  • magnification: img vs. act ratio, e.g. 1-cell Paramecium – LM 230x = light micro, 230x mag, act size 0.33mm
    • mangifications multiply when compounded
    • ? – at large manifications, can LMs only provide 2D images?
  • resolution: imp fact, abl 2 distinguish nearby obj, all have limits 2 res, human eye 0.1/0.2mm, LM 0.2 μm (1000x effectively)
    • spatial res – distance required 2 be visualized as 2 separate objects, lesser ⇒ higher resolution
  • cell theory: mid-1800s, all living things composed of cells, all cells from other cells, LM + staining tech only 1665–1900s
  • electron microscope (EM): alt, focus beam of electrons thru spec/on2 surface, res 2nm, explore cell ultrastruct/3D prot
  • scanning EM (SEM): study surf, e-beam scan surf (usu gold coat), detect excite e, Para cilia, oral groove – fd, ~3D
    • no int. struct, ours: res 3.5nm, mag 100,000x
  • transmission EM (TEM): study int, e-beam thru very thin stained sect, stain scatters electrons, artifical colorize, 2D
    • res 0.14nm, mag 1,500,000x
  • caveat: EM only on dead cells b/c prep methods kill cells, LM can still study living cells
  • differential interference contrast microscopy (DIC): amplify density diff, 3D, otr use flourescent stains spec 2 cert struct
  • cell size: most cells 1–100 μm (only micro), certain bacteria 0.2 μm, bird eggs large, nerve cell up2 1m long but thin
    • viruses ~50–100 nm

Basic Sizes

NameAbbreviationSizeOther Notes
millimetermm10⁻³ mSmall ticks on a ruler
micrometerµm10⁻⁶ mAlso called the micron, equivalent to 1% of the thickness of a hair
nanometernm10⁻⁹ mRoughly equivalent to a line of about 10 carbon atoms
Protip: You can type µ (Greek mu) on a Mac by using the shortcut alt + m.

Note about Nanotech

At extremely small scales, materials have completely different properties. Hence, nanotech is the study of materials at the nano-scale. Electron microscopes are very useful tools for this field.

4.2 The small size of cells relates to the need to exchange materials across the plasma membrane

Page 54

  • cell size limits: lower – must be able 2 carry DNA/prot/struct. upper – geometry, need surface area to support volume of cell

Surface-to-Volume Ratio

  • small cube surface-to-volume > large cube surface-to-volume, thin/elongated shapes (neurons) also provide large sa/v ratio

The Plasma Membrane

(more in a later module)

  • plasma membrane: flexible boundary btw cell & surround, amazingly thin, 8k cell membranes/thickness of page, f/f
  • phospholipid bilayer: pls group together to form 2 layers, hydrophobic tails inward, hydrophilic outward expose 2 wtr
  • regulating flow of materials: nonpolar easy move thru bilayer, prot form channels (~ tunnels in memb), pumps (NRG 2 trans)
    • channels have ambiphilic outer coating, polar inner coating

4.3 Prokaryotic cells are structurally simpler than eukaryotic cells

Page 55

Be ready to draw a Venn Diagram comparing and contrasting prokaryotic cells with eukaryotic cells on the upcoming quiz and/or test!
  • prokaryotic cells: Bacteria & Archaea, all others eukaryotic cells
  • differences: eukaryotic cells memb-enclosed nucleus that houses DNA, memb-enclosed organelles, prokar smaller/simpler
  • sim: plasma memb, cytosol thick fluid in cell, 1+ chromosomes, ribosomes make prot, cytoplasm int
  • molec diff: DNA cluster in nucleoid (nuc-like) but no memb, ribosomes smaller/diff, molec diff helps antibiotics target
  • outer prok: rigid cell wall out plasma memb, some have sticky capsule ⇒ stick 2 otrs, flagella projections propel thru liq
    • capsule have fimbriae hairs – important on quiz/test!
  • size: most 10% size of typ euk, require EM

4.4 Eukaryotic cells are partitioned into functional components

Pages 56–57

  • all euk fundamentally sim, profoundly diff from prok
  • cells have multiple copies of structures (e.g. 100s mito, mils ribo, 30 chloroplasts), diff shapes/proportions dep on func
  • organelles: “ltl organs,” perform specific funcs in cell, each organelle ounded by memb that suits func
  • (see table in Functional Groups of Organelles)
  • cellu metab: chem act of cells, most in oelles, many enz in oelle memb, oelle chem env vary, H-perox only peroxisomes
    • metab: sum of all chem reac in body (e.g. build stuff)
  • ani-exclusive oelles: lyso, centrosomes, flagel/cil (ani: some, in plnt: sperm/pollen of a few species)
  • plant-exc: cell wall (diff from prok), plasmodesmata (sing: plasmodesma) channels connect cells, chloroplast, cent vacuole
  • euk non-memb struct: cytoskel – prot fibers that extend thru cell ⇒ support/move, ribosomes occur thruout & on memb

Functional Groups of Organelles

genetically control cellnucleus, ribosome
manufacture, distribute, break down moleculesendoplasmic reticulum, golgi apparatus, lysosomes, vacuoles, peroxisomes
be the powerhouse of the cellmitochondria, chloroplasts (plants only)
support structure, movement, and communicationcytoskeleton, plasma membrane, plant cell wall

The Nucleus and Ribosomes

4.5 The nucleus contains the cell’s genetic instructions

Page 58

  • nucleus is ctrl ctr
  • nuc: ctrl prot synth, DNA+prot, org chrm (hman 2+ mtr), prot help coil, not div: contents diffuse in chromatin
  • prep 2 divide: DNA copied ⇒ each daughter gets ident genes, chromatin coils further into fam chrmsmes (visible 2 LM)
  • nuc envelope: dbl nuc memb, 2 pl bilayer + prot layers, ~ plasma memb, prot-lined nuc pores, connect 2 endo ret
  • nucleolus: prom struct in nuc, ribosomal RNA (rRNA) synth ac2 DNA inst & form subunits of ribosomes, join out of nuc
  • messenger RNA: mRNA, direct prot synth, transcription of DNA, moves 2 cytoplasm & translate 2 prot @ ribo
    • transcription + translation = central dogma
A quick and wholly unnecessary note regarding mutations.
They happen. Most of them are silent or negative.

4.6 Ribosomes make proteins for use in the cell and for export

Page 59

  • ribo: carry out nuc cmds, use mRNA 2 build prot, cells that make lots of prot req lots of ribo/prom nucleolus
  • loc: free ribo in cytosol, bound ribo attach 2 out of endo retic or nuc env, struct ident, move?, func in either loc
  • diff func: most free ribo make prot 4 cytosol (e.g. sug brk enz), bound make prot for memb/oelle or ext use (see 4.8)
  • proc: mRNA ⇒ ribo ⇒ polypeptide chain

The Endomembrane System

4.7 Many organelles are connected in the endomembrane system

Page 59

  • endomemb sys: many memb part of sys, some memb phys connect (e.g. nuc + ER), others linked via vesicles (~ car)
  • members: nuc env, endo retic, golgi app, lysosomes, vacuoules, plasma memb, synth/dist/store/exp molec
  • endo retic (ER): lgst comp, extensive nw of flat sacs/tubules (“little net”), both direct + indirect interact w/ rest of sys
  • role of ER: enclose space separate from cytosol, divide cell into functional comp (each w/ pot diff conditions)

4.8 The endoplasmic reticulum is a biosynthetic workshop

Page 60–61

  • smooth vs. rough ER: ER one of major manufact sites in cell, rough has bound ribosomes, smooth none, membs interconn

Smooth ER

  • func in metab proc: contains enz, synth lipids, sex hormones (ovaries/testes cells rich in sER), detox (see liver usage)
  • liver usage: lg amnt of sER, enz proc drugs/harm subst, as expose 2: amnt of detox enz inc ⇒ tolerance/inc eff of otr drugs
  • func as calcium ion store: e.g. muscle, sER memb pump calc ions in2 ER, when nerve stim: calc from sER 2 cytosol, contract

Rough ER

  • secretory prot: many cells secrete prot from rER ribo, e.g. pancreas insulin, gluc metab, Type 1 diabetes when destroyed
  • prod proc: polypep in2 rER cavity, fold, short sug chain link 2 polypep ⇒ glycoprot, transport vesicle pack/ship
  • next steps: golgi apparatus further process, another transport vesicle releases from plasma memb
  • func as memb maker: grows in place by adding prot/plip, portions transf 2 otr comp of endomemb sys via trans vesicles

4.9 The Golgi apparatus modifies, sorts, and ships cell products

Page 61

  • golgi apparatus: 1898 It sci Camillo Golgi disc, conf 50yr ltr by EM, stack of flat sacs, pot 100s/cell, correl w/ secrete
  • func: molec warehouse/proc station 4 ER prod, sacs no conn (unlike ER), one side rec, modify as progress thru stack, ship
  • ex of modify: enz modify carbs in glycoproteins, molec ident tags (e.g. phosphate grp) add 2 help sort 4 ship
  • finished products: release from plasma memb or become part of otr organelle (e.g. plasma memb, lysosome)

4.10 Lysosomes are digestive compartments within a cell

Page 62

  • lysosome: sac of digest enz, Grk “breakdown body,” made from rER + golgi app, provides acidic env, isolate digest enz
  • func: food in food vacuole ⇒ fuse2 lyso, digest nutrients, white blood destroy bacteria via lyso, recycle (e.g. damage oelle)
  • inherited lysosomal storage dis: lack 1+ lyso enz, undigest mat interfere, oft erly child fatal, e.g. Tay-Sachs: brain no lipid dig

4.11 Vacuoles function in the general maintenance of the cell

Page 62

  • vacuoles: large vesicles, variety func, e.g. food vacuole, contractile vacuoles (expel excess wtr)
  • more func: digest func (~ lyso), flower pigments, poisons/unpalatables deter eat, e.g. nicotine/caffeine/var pharm chem
  • central vacuole: plnt cell, helps cell grow in size by abs wtr, stockpiles vital chem, act as trash can (store toxic waste)

4.12 A review of the structures involved in manufacturing and breakdown

Page 6

  • structural conn: nuc env, rER, sER; functional conn: ER ⇒ trans vesi ⇒ golgi app ⇒ lyso/vac/secrete out of plasma memb
  • peroxisome: metab not in endomemb (relate unknow), brk fatty ac/detox, transf H in comp 2 O ⇒ H-per (H₂O₂) ⇒ wtr

Energy-Converting Organelles

4.13 Mitochondria harvest chemical energy from food

Page 63

  • mito/mitochondrion: cell resp in near all euk, food chem NRG ⇒ ATP chem NRG, ATP main NRG source
  • anat: 2 memb, intermemb space (active) enclose mitochondrinal matrix: DNA/ribo, enz, inner cristae folds inc sa

4.14 Chloroplasts convert solar energy to chemical energy

Page 64

  • chloroplasts: mst of lv wld runs on NRG from photosynth (sun light ⇒ sug chem), psynth, plnts/algae/some plankton
  • compart: complex, 2 memb, stroma: int fluid, DNA/ribo, enz, thylakoids: interconn sacs, granum stack, thy sp
    • NO CRISTAE!!1
  • thylakoids: solar power packs, sites where chlorophyll molec in thylakoid memb trap solar NRG

4.15 Mitochondria and chloroplasts evolved by endosynthesis

Page 64 – Evolution Connection

  • endosymbiont theo: mito & cp each 1 circ DNA molec (~ prok chrom), theo: mito/cp formerly small prok live in lg cells
  • how beneficial: host get ability 4 use increasing O ⇒ NRG, endosymb get protect, over time merge

The Cytoskeleton and Cell Surfaces

4.16 The cell’s internal skeleton helps organize its structure and activities

Page 65

  • cytoskeleton: protein fibers extend thruout cell, major role in org struct/act of cell, allow 4 int/ext movement
  • 3 fiber types: microtubules/mt (thickest), microfilaments/actin filaments/mf (thinnest), intermediate filaments/intf
  • mt: hollow tubes, comp: globular prot tubulins (reusable), ani: ext from centrosome (near nuc, 2 centrioles – mt rings)
    • diameter: 25 nm
  • mt role: shape cell, tracks 4 oelles w/ motor prot 2 move (e.g. 2 food vac), guide chrm move when cell divide, cilia/flagella
  • intf: cells of most ani, coil fibrous prot, reinfor cl, anchor some oelles (e.g. nuc intf cage), mr perm, out skin: dead cells intf
    • diameter: 10 nm
  • mf: aka actin filaments, solid rods, globular prot actin twist dbl chain, form nw just in pmemb 2 sup cell shape, ani cells imp
    • diameter: 7 nm
  • mf cl move: mf + filaments mysoin (motor prot) interact ⇒ muscle cl contract, amoeboid (crawl) – Amoeba protist, wht bld
    • when cl mv, mf projection made in dir

4.17 Scientists discovered the cytoskeleton using the tools of biochemistry and microscopy

Page 66 – Scientific Thinking

  • bf discovery: biologists thought oelles float freely in cell
  • 1940s isolate musc cells actin & myosin, 1954 microscop observe in muscle contrct, next decade: stain mf, EM find in all cls
  • immunoflourescence microscopy: 1974, antibody prot bind 2 actin & attach flourescent molec, 1st time visualize cytoskel
  • molecular cytochemistry: inject flourescent actin into living cells, enable visualize dynamic behavior of cytoskel prot
  • 1980s video camera + microscope
  • sci new tech ⇒ understand cytoskel grow

4.18 Cilia and flagella move when microtubules bend

Page 66–67

  • cilia: sing cilium, short/many appendages, propel protists, otr protists may use flagella (longer, only few), cytoskel role
  • c/f on otr: cil trachea (mucus, smok impair), most ani/some plnt flagell sperm, flagel undulate whiplike move, cilia ~ row oars
  • sim: comm struct/mech, pmemb wrap, mst euk: “9 + 2” – 9 dbl-mt arnd cent mt pair, anchor: basal body ~ centri (sprm: bc)
  • dyneins: motor prot along outer, 2 “feet” “walk” along adjacent mt dbl, coordinate 2 bend mt, mt held tgthr by x-link prt
    • each feet exerts sliding force, uses ATP, ex of cellular work
  • cil sig-rec “antenna”: nonmotile (lack cent pair), 1/cl, in vert: mst cls primary cil, disc cent ago, imp: embry, sens recep, cl fn

4.19 The extracellular matrix of animal cells function in support and regulation

Page 67

  • extracellular (ec) structures: most cells synthesize/secrete mat ext of pmemb, essent 2 many cell fn, can span mult cls
  • ec matrix: bind in tiss, pro/sup pm, glycprt collagen strng fibers (40% b p), otr gp on cent plysch, integrins 2 pm/mf
  • integrin fn: integrate, signals btw ECM & cytoskel, ECM can regulate cell (embry path, gene act), cancer ⇒ ECM chnge, sprd

4.20 Three types of cell junctions are found in animal tissues

Page 68

  • cell jct: adhere, interact, comm neighboring cells in ani tiss (e.g. digest tract), 3 types
  • tight jct: 2 cells knit tight by prot, prevent fluid leakage across cell layers (e.g. digest tract)
  • anchoring jct: ~ rivets, fasten cls in2 strng sheets, sturdy intf anch in cytoplasm, comm in mech stress tiss (e.g. skin/musc)
    • aka desmosomes, can contain keratin
  • gap jct: aka communicating jct, allow small molec 2 flow thru prot-lined pores btw cls, e.g. heart/embry coordination

Diagram with improper keming illustrating gap junctions, adherens junctions, tight junctions, and desmosomes (anchoring junctions). This diagram shows a gap junction, adherens junction (not covered), tight junction, and desmosome (anchoring junction).

4.21 Cell walls enclose and support plant cells

Page 68

  • cell wall: plnt, protects cls, keep plnts upright, cellulose in matrix of otr polysac/prot, ~ steel-reinforce concrete
  • layers (ex>in): pectins (plysch) adh cls, thin/flex primary wl 2 enab grwth (strng when stop grw), some cls: 2ndary wl (wood)
  • plasmodesmata: ~ gap jct, line w/ pm, cytosol passing thru allow wtr/otr molec freely move btw cells
    • fn: wtr, food, chem msg

4.22 Review: Eukaryotic cell structures can be grouped on the basis of four main functions

Page 69

Cell structures in eukaryotes can be grouped into four major categories, each of which contain organelles with similar structures:

1. Genetic Control
NucleusDNA replication, RNA synthesis, assembly of ribosomal subunits in nucleolus
RibosomesPolypeptide/protein synthesis
2. The Endomembrane System – Manufacturing, Distribution, and Breakdown
Rough ERSynthesis of membrane lipids and proteins, secretory proteins, and hydrolytic enzymes; formation of transport vesicles
Smooth ERLipid synthesis; detoxification in liver cells; calcium ion storage
Golgi apparatusModification and sorting of macromolecules; formation of lysosomes and transport veicles
Lysosomes (in animal cells and some protists)Digestion of ingested food or bacteria and recycling of a cell’s damaged organelles and macromolecules
VacuolesDigestion; storage of chemicals and cell enlargement; water balance
Peroxisomes (not part of endomembrane system)Diverse metabolic processes (e.g. breaking down compounds in fatty acids and harmful compounds), with breakdown of toxic hydrogen proxide by-product
3. Energy Processing
MitochondriaConversion of chemical energy in food to chemical energy of ATP
Chloroplasts (in plants and algae)Conversion of light energy to chemical energy of sugars
4. Structural Support, Movement, and Communication Between Cells
CytoskeletonMaintenance of cell shape; anchorage for organelles; movement of organelles within cells; cell movement (crawling, muscle contaction, bending of cilia and flagella)
Plasma membraneRegulate traffic in and out of cell
Extracellular matrix (in animals)Support; regulation of cellular activities
Cell junctionsCommunication between cells; binding of cells in tissues; sealing organs (e.g. digestive tract)
Cell walls (in plants)Support and protection; binding of cells in tissues

All these organelles work together to fulfill the properties of life, which are emergent at the cell.

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