Delve AP Biology Lecture 3: 10/2/11 Melissa Ko and Anne Huang

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1 Delve AP Bilgy Lecture 3: 10/2/11 Melissa K and Anne Huang Tday s Agenda: I. Review f Previus Lecture II. Regulatin f Enzymes III. Diversity f Life and the Rle f Evlutin IV. Cells as a Unit f Life and Hw We Study Cells V. Eukarytic vs. Prkarytic Cells VI. Animal vs. Plant Cells VII. Parts f the Cell VIII. What are Viruses? Diseases and Pathgens I. Review f Previus Lecture Energy and Entrpy Gibbs Free-Energy and Chemical Reactins ATP as an Energy Surce Enzymes and their Rle in Bilgy II. Regulatin f Enzymes The envirnment that affects flding als affects enzyme functin. Temperature, ph, and the type f slvent [plar, nnplar, etc.] can all change enzyme structure by interrupting prtein flding and amin acid interactins. Cfactrs - nnprtein helpers fr catalytic activity Cenzyme - rganic cfactr [vitamins] Cmpetitive inhibitr: binds at same site as the substrate, cmpetes fr binding and leads t lack f activity nncmpetitive inhibitr: binds at anther site, which smehw affects the substrate s ability t bind [usually when a nncmpetitive inhibitr binds, it changes the cnfrmatin f the entire enzyme and desn t allw the substrate t bind] Reversible vs. irreversible [pisns]: whether the inhibitr s effect can be undne. Is the enzyme dead r can it be used again? Allsteric regulatin: any case where a prtein s functin at ne site is affected by the binding f a regulatry mlecule at anther site [can be inhibitrs r activatrs] Cperativity: activatin f ne binding site affects binding at anther site, can be psitive r negative [Psitive cperativity wuld mean that when ne site is bund, it is easier fr the ther site t be bund. Negative cperativity is the ppsite.] Feedback: negative if utput causes decrease in enzyme/pathway activity, psitive if utput causes increase in enzyme/pathway activity Lcalizatin f enzymes: leads t different effects depending n where enzymes are fund. Accessibility t different substrates, can be in different envirnments which affects structure. 1

2 Remember systems bilgy where we cnsider nt just ne piece in a system, but hw they all interact. There are s many wrking prteins in a cell s we cnsider enzymes as a system III. Diversity f Life and the Rle f Evlutin Great diversity in life, many different species. Taxnmy is the classificatin f species New taxnmy scheme rganizes life int three dmains: Bacteria, Archaea, Eukarya. This is based n cmparisn f DNA sequences f rganisms. Bacteria are diverse, cmmn prkarytes Archaea are prkarytes like bacteria, but they have a different evlutinary path Sme are extremphiles [ex: thermphiles]. They have different bichemistry and structures that allw them t live under extreme cnditins Eukarya are eukarytes, include prtists, plants, animals, fungi Prtists are single-celled animals, sme simple multicellular animals Plants are multicellular, use phtsynthesis t make their wn fd Fungi are multicellular, decmpsers, get fd frm dead things Animals are multicellular, eat ther rganisms fr fd Despite the wide differences/variety in species, there is unity in many things like the use f energy, DNA inheritance, cell structures, etc. The thery f evlutin is based n adaptatin [a prperty f life]. The diversity f life can be explained frm adaptatins f rganisms t different circumstances. These changes accumulate and are heritable, leading t separate species. Why d adaptatins ccur? They depend n variatin between rganisms in terms f traits. The traits must be heritable, and they can cme frm sexual reprductin r frm mutatins. It depends n cmpetitin [due t limited resurces and t many rganisms]. Nt all rganisms survive and variatin leads t sme being mre likely t survive than thers. This leads t the reprductin f the mst fit r successful rganisms. Organisms wh are mst suited fr the circumstances t survive and reprduce are mre likely t reprduce mre. Less successful rganisms d nt reprduce as much. The fllwing generatins inherit the traits f the fit rganisms that cntributed t their reprductive success. Overall, mre rganisms live and reprduce with favrable traits. This leads t a change ver time in the frequent traits amng the species: adaptatin. Tree f life: evlutin prpses that all living things have a shared ancestr. Evlutin has led t rganisms diverging int separate species. This is als called descent with mdificatin, as rganisms change and mve away frm ancestr. The rganisms adapt t new situatins and species becme mre diverse. Lking at the dmains, we can suppse that there were evlutinary situatins and pressures fr eukarytes and multicellular life t arise. Descent with mdificatin als can explain why we see s many species all ver the wrld. Hwever, the similarities between living rganisms is apparent if life cmes frm a shared ancestr. Thus, studying the basic unit f life [the cell] helps us understand all living things. IV. Cells as a Unit f Life and Hw We Study Cells Cells are basic unit f life [they are the smallest unit that perfrms all activities f life]. 2

3 Prperties f life: rder, adaptatin, respnse t envirnment, energy use, regulatin, grwth/develpment, reprductin Cells exhibit structure, they are nt randm and mixed up Cells have DNA r heritable infrmatin that allws adaptatins Cells can sense and respnd t envirnmental cues Cells have metablism: eat glucse, make ATP, use energy t d things Cells are regulated t have a certain behavir and can maintain their internal envirnment [hmestasis] Cells grw in size, cmplexity Cells can make new cells, new cells nly cme frm pre-existing cells Heritable infrmatin = dexyribnucleic acid r DNA. DNA is rganized int genes [units f inheritance]. A chrmsme is a lng DNA mlecule with many genes n it. The genes/heritable infrmatin is usually cnverted t prteins, which are the tls/wrkhrses f the cell. The cllectin f all heritable infrmatin in a cell is its genme. Prkarytic cells are smaller and simpler. Their size generally ranges frm 1-10 µm, thugh they can be up t 100 nm. They have n internal membrane-bund rganelles and n nucleus. They have ne circular strand f DNA [plasmid]. Eukarytic cells are larger and mre cmplex. Their size generally abut µm, s they are abut 10 times larger than prkarytes. Eukarytes have subcellular rganizatin and rganelles. They have many DNA mlecules [chrmsmes] in a nucleus. They can be rganized int multicellular rganisms. Organelles [ little rgans ] are subcellular structures which may r may nt be separated by a membrane. Each rganelle has a special structure and functin. Hw d we knw what we knw abut cells and bilgy? Mstly relies n bservatin at first. Micrscpy is the primary tl fr lking at bilgical structures. It has a certain magnificatin r ability t enlarge an image. It has limits n reslutin r ability t distinguish bjects in image. Light micrscpy uses visible light passing thrugh a specimen and lenses t magnify the image Brightfield (stained r unstained) is mst cmmn. Stained images require fixing r killing the specimen. Unstained has n cntrast and is hard t distinguish Phase-cntrast tries t fix cntrast prblems, keeps cells alive, relies n variatin f density f specimen Differential-interference-cntrast (DIC) tries t fix cntrast, als relies n density and tries t make image 3D Flurescence lks fr tagged mlecules, uses dyes r antibdies, use UV radiatin t excite mlecules which then emit visible light Cnfcal kind f flurescence micrscpy, tries t get thin sectin f specimen Electrn micrscpy uses beams f electrns instead f visible light, requires fixing r killing specimen and taking thin samples, usually requires freezing r cating specimen in metal Scanning electrn micrscpe (SEM) lks at the surface f the specimen, gives 3D image fr utside structures 3

4 Transmissin electrn micrscpe (TEM) lks as crss-sectin f specimen, can see the inside structure Besides bserving cells, hw d we knw hw they wrk r what they d? Hw d we study cell functin? We can apply reductinism by studying what the individual parts f a cell d. Cell fractinatin is a methd f separating the parts f the cell. It requires breaking pen the cell t frm a hmgenate. It then uses a centrifuge t separate the different pieces in the hmgenate by size Centrifuges and ultracentrifuges are machines that spin samples very fast and apply a lt f frce n the sample. This leads t the separatin f samples by size since larger bjects feel mre frce and sink t the bttm faster than smaller bjects Cell fractinatin separates cells int rganelles, which allws us t islate parts s we can study them V. Structure f Eukarytic vs. Prkarytic Cells Basic structure f cells: separated frm their envirnment by a membrane called the plasma membrane. They cntain heritable genetic infrmatin [DNA]. They have stuff r fluid inside called cytsl. The cytplasm als describes the interir f cell, includes stuff in cytsl. All cells have ribsmes, which make prteins frm genes. Prkarytic cells have a nucleid, which is the center regin where DNA mstly stays. There is n membrane physically separating the nucleid frm the cytplasm. They have a cell wall, a rigid structure arund the plasma membrane. Prkarytes als can have a capsule, which is an extra cating arund the cell wall. They use pili fr cmmunicatin [an example f cmmunicatin wuld be the exchange f DNA between prkarytic cells]. Sme prkarytes als use flagella fr mvement. Eukarytic cells have a nucleus, which is a membrane bund structure surrunding the DNA. It is a physical barrier between the DNA and the cytplasm. Eukarytes have ther membrane bund rganelles. They generally d nt have a capsule. The presence f a cell wall depends n whether it is an animal r plant cell. VI. Animal vs. Plant Cells Bth are eukarytes [have a nucleus and membrane-bund rganelles]. They have cmmn rganelles, but there are sme rganelles that are fund exclusively in animal r plant cells. When studying rganelles, it is imprtant t remember their specific structure and functin. VII. Organelles Organelles Fund in Bth Animal and Plant Cells [p.100] Nucleus: cntains DNA Ribsmes: make prteins [nt membrane-bund, als fund in prkarytes] ribsmes can be free in the cytplasm r attached t the rugh ER ER: rugh [help synthesize prteins that will be secreted r attached t the cell membrane] vs. smth [synthesize lipids, metablize carbhydrates, detxificatin] Glgi: help mdify and ship prteins t where they need t g Mitchndria: cellular respiratin, prduce ATP 4

5 Perxisme: cntains xidizing enzymes which break dwn txins int hydrgen perxide Cytskeletn: rganizes the structure f the cell, made f 3 main fibers (micrtubules, micrfilaments, and intermediate filaments) Organelles Only Fund in Animal Cells Lyssmes: help the cell digest macrmlecules Centriles [part f the cytskeletn]: their functin is still unknwn. Current research says that centriles may be invlved in cell divisin, but they are nt necessary Organelles Only Fund in Plant Cells Chlrplasts: phtsynthesis, cnverts sunlight int chemical energy [glucse] Central vacule and tnplast: a vacule is a cmpartment surrunded by a plasma membrane [tnplast]. The plant s central vacule stres many imprtant rganic and inrganic [ptassium, chlride ins] cmpunds. It als helps the plant cell grw [can increase the size f the cell easily by increasing the size f the central vacule] Cell wall: uter-mst layer that maintains the cell s shape, made f cellulse Plasmdesmata: channels/pres in the cell wall that cnnects the cytplasms f surrunding cells Extracellular cmpnents f cells Cell wall [plant cells nly!] Functins: Prtectin, maintenance f cell shape, prevents excessive uptake f water Sme prkarytes, fungi, and prtists have cell walls as well Grwth f cell wall Primary cell wall- first the yung plant cell secretes a relatively thin and flexible cell wall Middle lamella- between the cell walls f neighbring plants, there is a thin layer that has a lt f sticky plysaccharides called pectins When the cell stps grwing, it strengthens its cell wall. It will either harden its primary cell wall, r it will add a secndary cell wall between the plasma membrane and the primary cell wall Extracellular matrix [animal cells nly!] Functins: Structural supprt, regulatin f cell behavir, current research shws that the ECM can als regulate gene expressin Structure: Integrins are prteins within the cell s plasma membrane. They are bund t the ECM n the utside f the cell and bund t ther prteins and micrfilaments n the inside. This linkage can transmit stimuli between the utside and inside f the cell, regulating the cell s behavir Fibrnectin are glycprteins that cnnect the ECM t the integrins Mst abundant cmpnent f ECM: cllagen [glycprtein, >50% f ttal prtein in human bdy! when yu get ld, the cllagen fibers break dwn and yu get saggy and wrinkly...] The cllagen fibers are embedded in a netwrk f prteglycans 5

6 Intercellular Junctins Plant cells: plasmdesmata Hles in the cell wall, cnnects the cytplasm f adjacent cells Water, small mlecules can pass freely frm cell t cell Unifies mst f the plant int ne living cntinuum Animal cells: 3 different types f junctins Tight junctins: the membranes f neighbring cells are tightly pressed against each ther and bund tgether by prteins. This frms a seal arund the cell, preventing leakage [fr ex: urine is held in ur bladder, tight junctins prevent leakage] Desmsmes/anchring junctins: fasten 2 cells tgether like a rivet [fund in skin] Gap junctins/cmmunicating junctins: cytplasmic channels b/w adjacent cells [analgus t plant s plasmdesmata]. There is a pre surrunded f special membrane prteins, and ins/sugars/amin acids/small mlecules can pass thrugh. Necessary fr quick cmmunicatin between cells [ex: heart muscle cells: electrical signals passed thrugh gap junctins because it is faster] VIII. Viruses Are viruses prkarytes r eukarytes? They are actually neither! Structure: Very simple and small [even smaller than a ribsme] Nucleic acid enclsed in a prtein cat [capsid], smetimes a membranus envelpe [stlen frm the hst cell] Viral genme: can be single stranded r duble stranded DNA r RNA Reprductive cycle f viruses: Obligate intracellular parasites : can nly reprduce in a hst cell First, the virus inserts its genme int the hst cell [there are many ways that viruses d this. One example is bacteriphage, which injects its genme int the hst cell] Once the viral genme is inside, the hst cell replicates and transcribes the viral genes, replicating the viral genme and prducing viral prteins fr the capsid The viral genmes and prteins self-assemble int new baby viruses, which exit the cell [smetimes burst ut f hst cell and kill it] Specific reprductive cycles [lytic vs. lysgenic] depend n the class f virus Are viruses alive? Yes: evlutinary adaptatin, sme rder N: cannt reprduce n their wn, cannt prcess energy cannt d anything withut a hst cell Viral Diseases Viruses cause many diseases [ex: smallpx, pli, SARS, influenza, AIDS]. Why are viral diseases s deadly? They are difficult t eradicate, and new viruses appear very quickly [emerging viruses] Why are viral diseases s difficult t eradicate? Vaccines cntain a weakened versin f the virus, which stimulates the immune system t develp immunity t the virus. When the actual virus infects yu, yur immune system will remember the virus and fight ff the viral infectin faster and strnger 6

7 Unfrtunately, vaccines d nt always wrk [ex: flu vaccine: need a new ne every year, have ~75% effectiveness rate]. Why are vaccines nt very effective? Viruses reprduce quickly, viral genmes evlve quickly Viruses have few enzymes f their wn, s we can t target viruses by inhibiting their enzymatic functins [this is hw antibitics wrk] Why d new viral diseases appear s quickly? High mutatin rate f viral genmes + fast reprductin => evlve quickly Spread f existing viruses t ther hst species [ex: SARS came frm a flu virus previusly seen nly in birds] Viruses are able t travel faster and farther nw, thanks t technlgy that allws fd/prducts/peple t travel arund the wrld 7