Lecture 1 Notes - Introduction to CMB
Lecture 1 Notes - Introduction to CMB BIL 255
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This 7 page Class Notes was uploaded by Elizabeth Mompoint on Tuesday September 22, 2015. The Class Notes belongs to BIL 255 at University of Miami taught by Dr. Mallery in Fall 2015. Since its upload, it has received 74 views. For similar materials see Cellular & Molecular Biology in Biology at University of Miami.
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Date Created: 09/22/15
Cell and Molecular Biology Lecture 1 What is Cell and Molecular Biology Cell and Molecular Biology is the study of life amp the living cell through the analysis of the fundamental molecules found within cells The goal is to understand the molecular basis of cell function and the fundamental CELLULAR PROCESSES ranging from cell respiration cell division and protein trafficking to signal transduction and cell migration to photosynthesis and the formation of tissues during development and wound healing It is designed to interpret the properties of the organism by understanding the structure and functions of its basic molecules in cells and their complex interactions It tries to connect molecules not just to reactions of high specificity but to intricate pathways concerned with cellular tissue and organism homeostasis It also provides a natural connection between basic biological research and medicine The science of biology is built upon 3 theories 1 The theory of evolution 2 The cell theory 3 Equilibrium thermodynamics Cell Molec is a compilation of four separate disciplines 1 Cell thsiologv compares how cells answer universal problems 2 Svstemic thsiologv the science of organ systems and whole organism physiology 3 Biochemistry looks at the chemical and physical commonality of mechanisms of cellular reactions 4 Molecular biologv studies the properties of organisms through their basic molecules Molecular biology has established that basic processes such as the genetic code and protein synthesis are similar in all living systems The experimental approaches used in cell regulation and function are multidisciplinary and include biochemical and biophysical experimentation Its primary procedural philosophy has been reductionism or the belief that complex phenomena can be reduced to simpler physical processes or that entities of a given kind are collections or combinations of entities of a simpler more basic kind It must also deal with complexity and complex systems systems that can interact in many different ways so that the whole takes on a realm of its own can adapt and evolve to changing conditions is prone to sudden and seemingly unpredictable changes its collective characteristics cannot easily be predicted from its sole components the WHOLE is greater than and often significantly different from the sum of its PARTS it exhibits Emergent Properties U PP Ni Cells A cell is the smallest entity which can exhibit the characteristic of life Cell biology is the scientific discipline that studies the cell as an individual unit and as a contributing part of a larger organism Cells can differentiate in order to acquire particular functions Cells gt tissues gt organs gt organ systems gt organisms The smallest know cells are a group of tiny bacteria called mycoplasms about 03 micrometer in diameter with a total mass of 1014 gram Human cells are about 400000 times larger about 20 micrometers across A human being may be composed of more than 75000000000000 cells 75 x 10quotl3 cells A Cell Biologist is a scientist who studies the properties of cells the interactions and communication among cells and the biochemical phenomena which are shared by all cells 0 Fundamental Questions Asked via CMB What is the definition of life How do the properties of molecules contribute to life Can we construct a living cell off the shelf if we know its molecular parts 0 CMB is rooted in the 2 major theories of Biology Evolution Darwinian Natural Selection 0 Changes in the allele frequency of a population s gene pool from one generation to the next in uenced by the environment and enhances a population s reproductive fitness leading to better adaptation via Natural Selection Cell theory All living things are made of cells 0 Small membrane bound compartments filled Cells times The 1839 0 ll My A of 5 memory 39 quot5 Ur Cl39r ndal rs Mainstream Gymnaspen ns quot3 lg j Iquot Eminudonj39ts Wilma Wm sum was thin f Coelonmmles i39 Mnnofm 3 a 3 J 1 S 39 395 1 r Milan hunttnrt Chlomplan ln l Anmmmanuna Granobaciena Puf q a W Nominations 7 7 rs gmm mum ALLe menu IE 39Heprnrlueijon of euruimrs l habitat 3 increasing motions of trails thal E h li Elimination oil inclluI dunls with E rt ll trailE seminal until reproduclhne success with concentrated aqueous solutions of reactive chemicals a collection of catalysts that cause a complicated series of chemical reactions and divides into two sets living today can trace their ancestry back to ancient and all of them have a common descent from a M LUCA Last Universal Common Ancestor two main proponents of the cell theory proposed in were Matthias Jakob Schleiden 18221895 amp Theodor Schwann l 8 10 1882 Schleiden studied plant etiology and cell formation in Berlin Schwann discovered pepsin a digestive enzyme for protein that sugar and starch fermentation are life processes the striated muscles in the upper esophagus and the myelin sheath of peripheral nerves He coined the term metabolism to describe chemical changes that are observed in living tissue and he formulated the basic principle of embryology TABILE 11 HISTORICAL LANDMIR KS iliH DETERMINING CELL STRUCTURE 1965 1963 1974 1994 Table 1v l Essential oil Biology Moi Hind Skiertoe 10101 iloohe uses a primitive microscope to describe small pores In sections of cork that he calls quotcellsquot D Leouwen hoel t reparts his discovery oi protozoa Nine years later he sees bacteria tor the rst time Brown publishes his microscopic observations at orchids clearly describing the cell nucleus Schleiden anti Schwann propose the cell theory stating that the nucleated cell is the universal building block of plant and animal tiswes Kollilter describes mitochondria in muscle cells Flemming describes with 9 rent clerity chromosome behavior during mitosis in animal cells Calal and other hlsto l oglsts develop staining methods that reveal the structure of nerve cells and the organization of neural tissue Golgi first sees anti describes the Golgi apparatus by staining cells with silver nitrate C lboverl links chromosomes end heredity by observing chromosome behavior during sexual reproduction Palade Po rter and Sit5st rand develop methods of electronr microscopy that enable many intracellular structures to be quot seen orthe rst time In one of the rst applications of these techniques Huxley shows that muscle contains arrays of protein larrnentsathe first evidence of a cytoslteleton quot Robertson describes the bilayer structure oi the cell membrane seen for the rst time in the electron microscope crystallography Perm proposes e lowerresolution structure for hemoglobin Christian de Duve and his colleagues use a nil 39 39 39 quot twosome lrom a preparation of rat liver 9 Petran and collaborators make the rst confocal microscope 9 Lazanld es and Weber use Huoroscu nt antibodies to stain theI cytoslteleton 9 39nn r Kener describes the rst detailed protein structure sperm whale mroglobinl to a resolution oi I2 rim using ltrey r L JJ mquot Chal e and oollabo rotors introduce green uorescent protein GFPI as a marker to follow the behavior of proteins in living cells technology III ll 8 Jill al 0 Consequences of Cell Theory Cell theory replaces Vitalism the theory that things cannot be explained only in terms of their physical and chemical nature and that there is something nonmaterial a vital force that makes them different than nonliving things Cell theory led to mechanists who believed that life was a mechanical process that can be explained entirely by the workings of laws of chemistry and physics without a vital force There are no laws of chemistry or physics unique only to the living condition studying the cells in one organism has direct application to other organisms 0 The Tree of Life amp Cell Types All living cellular organisms have been grouped into binomial taxonomic levels as kingdoms based upon morphology The molecular approach of CMB changed this pattern and today we have a higher order of 3 domains Eubacteria true bacteria Archaea ancient prokaryotes and Eukarya modern eukaryotes 0 By comparing similar amp divergent sequences this new RNA phylogeny tree produced a tree with only 3 distinct 39 1 1 branches or Domain ME HREA Eu Sulfatebus thgmx human L Acmpyrum V yeesb cyanobacteria Methanofhenrmbaswte Bv 39 39lls Methanocosrus Trypwosome 39i39ordia39 cummarl Thermal 390 1 if 9 a mmr 1 changeil nuclealid Irishmanan Aquifer cell gurFH lmlialWWrxilhedLWEs mdeenw Hi i Iquot Monera bacteriyi onera Archaea 7 Flrotista 5 kingdoms formerly the higlhest rank of biological taxonomy Animalia Plantae Fungi Carl Woese compared nucleotide sequences of the small subunit I A p rRNA from many species and found that ribosomes and rRNA I 1 quot m h p are found in all cells 39 39 g 221 rRN A 49 ribosomal proteins 3 rRNA mDlecules 33 rihvosurnal proteins 1 rRNA molecule I I law We subunit 9 small subunit 5 39 now 13001000 mw 2000000 liarg e s uillJurnit r 39 32 Kli 39eremt proteinstr 4 di erertt t l39lh molecules small 5 ulburnit complete eu lsarwtic iriibosorne MW 2142000001 iFiigluire 13 Essential Ce ll Eiallogqr4l ed arland Science In Within the 3 domains there are only 2 successful Plans of Cellular Organization which are distinguished primarily by size amp type of internal structures the organelles they possess 1 Prokaryote before the nucleus a Includes archaea bacteria and eubacteria as well as members of the original Kingdom Monera now Domains Archaea and Eubacteria b 3 main cellular shapes in prokaryotic cells cocci bacilli and spirochetes spiral cells 99 Treponema paliidum rodshaped cells eg Escherichia coli Saimonella spherical cellsi 29 Strepto caccus Flannel9 Essential Eellliir mr d lluedJ39EEnrlaud sch de bacillus rad sillaped A white Blaine ceill purple engulls Staphylococcus aureus bacteria yellow 0 always pathogenic a a corner cs39ise oi elxin Mouton cg boils respiratory disgage in g sinuczisi and fcl ICIIZUI39IlI39IJ Spherical cocci MESA methicilin resistant Staph aureuis causes 5 c Size range from 01 10 um diameter no nucleus no significant internal membrane bound organelles compared to eukaryotes d Medical classification via differential Gram Staining of cell walls Nucleus Higherorder chromatin I Interphase chromosome r folding Loops cullquot lal Prokawotlc l 30nrn lber L W associated with quot P39Bi39Plasml c El lt Cl llFDl l l DSOme and cell wall f scaffold quotBeads an a stringquot nlucleasornes 39 Sim39lp e is d histone I Gene sequent 1 subunits 39 Egggrlgene families MWquot J mm HEB HH H4 0mm I riohlle 13 sequence convened membrane fl V E Ements N I DNA lntrons Spacer DNA uc sesame I I 2 membrane areas Gram stain crystal violet rinsed with iodine counterstained with safraniniso Carnal1w rate parlinrn purpleblack stain quot i r 39 5 ol39 l ipapalysacehaliua I mammalcut lipids1 noiyaac s 39139 I 7 r k 39 Gm l cm Peptldogllycau 139 ME a cells membrane 1 7 quot llerquot llL39u39r39rllIIlxm39 39 r perplidogw ani f if wall mm my 7 m I ii wall WM r H j r Plasma membrarneq V Plasma membrane l 39 5 it Isl l 7 i 39 Wquot 7 V 7 5 r r Protein 39 I l quot 395 Ilquot 39 a i 1 1 H I p Gramsquot 39 Gram u l positive I v39 V negative 7 bacterial I hiagiigrm 20 vim la Gm positive peptldoglyean lraps In Gralmneglaliver crystal violet is pin kaish stain crystal Violet easnly rinsedl away revealing red dye 39 10 am Bacillus anthraeis is anthrax E tell a intestinal bacteria is food palsielnlng MM mmwmn mmm mmmmwm Sta phylacnccus and palsloning Salmonella typhoid fever andl puisulning Streptococcus e strep throat Hellieebatter pylori e peptic ulcers 8i gastritis Enterocuc cus end ucarditis E meningitis ILeglanellla Ieginnailres pneumonia Clust ridiuam hntullsm 8x colitis Cyanobaeterla a blue green algae 2 Eukaryote true nucleus a Includes algae amp protozoa fungi amp slime molds and all plants amp animals b Cell plan of multicellular organisms c Characteristics include a nucleus genes in chromosomes an endomembrane system nuclear membrane ER Golgi vesicles presence of more exible cell walls allows endocytosisphagocytosis presence of organelles presence of a cytoskeleton provides framework to be larger amp provide formshape sexual reproduction and larger cell volume 10X gt than bacteria size 50 to 20 um diameter CHRE MDSC WE quot p r quot e39 l lil lll i l ilfl d The actin filaments in four different structures immuomnttags i Microvilli ii Contractile bundles in the cytoplasm r iii Fingerlike filopodia protruding from the leading edge 8 x 12 15 5 m ofamoving cell ll l 12 iv Contractile ring during cell division 39 39 39 g nu clear 7 nucleus envelope 1 o Hm Chromosomes occupy differentberrito ies within a nucleus Flluo nascent markers were used to paint individual chromosomes in a human cell Ea l39l chromosme occupies a discrete territory Note the tum homologs efchromclsome 9 are located in dli erentlpositions Charmer a BJm le EDIng muted that uumlles mi genes cluster an edge alrinuc leus in rlnctullal rah and resrue leaner inside in ch iipmumlts which are active mimic the den diurnal SiLOci 2M9 p20 Universal Characteristics of all Cells T L y 139 4 3 t r P T microtubu Ie l 39E39ti d cltfrosrs E vacuole endueurne lemme uid lled quot quota oK K x n A 51 39 o g fill p arutniplhagusume 1quot quot 0quot 4 39 K FIEI DNISOME munM lumillflii39vll l1IIIPRLIIHI R rrrrrr 1quot plasma ll11 embra me no leus Golgi apparatu s chromatin a DNA nuclear pore 7 wl u cell wall ea rly Endusnme chilloropllast if rilbosomes in cytosoll acti I I till a orients PLANT CELL vacuole mem brane Iona pla st All cells store their hereditary info in DNA All cells replicate their hereditary in for via template polymerization All cells transcribe hereditary info into intermediate RNA via template transcription All cells translate RNA in that same mechanistic way via codonzanticodon Chargaft pairing using the same universal genetic code All cells use protein catalysts enzymes to makebreak covalent bonds All cells regulate the rate of gene transcription translation so only a portion of possible RNAproteins are copied thus hereditary info not only dictates the nature of a cell s proteins but also whenwhere they are to be made in a process know as differential gene activity nucleolus lyst Ferrel HI Eteeotial Cell Iliolegy more Garland Etienne guru endoplasmic reticulum miitocho ndrton ANIMAL CEth actin laments peroxisome ribomme Golgi apparatus PtanrlIIrr wrrtirrl Coll ebqt39 l r Irrl 9 Garland Srimoe BillI 1quot let 39 39 intermediate fillarrnerrts m it mtubulle cantrrnsorrrr e with a pair of centrioles Eh mma mum extra celllular matrix nucl ea r pore slurp 39 539 V 7quot 7 39 nuclealr envel pe 7 39 i le i lysoeome i 7 u nucleolus pllasma membrane A nucleus endoplasmrc mrtochond rror reticulum Three advantages of Using hydrophobic molecule5 39in cells all Hydrophoble molecules eponlaneuuslyclueter in water quot it one vigorously millee water and hydrophobic o l I I 360311 2 3qu molecules such as lipids 9 003 Fe it 9 the lipids wili disperse O Once the liquid oomee to rest lhe lipids Spontaneously form a layer at the top oi the liquid thereby minimizing interaction with the polar water meter u lee Long hydopholblo molecules such as lipids spontaneously form a highly organized arrangement without any additional energy added all Phospholipid membranes spontaneously repel large hydrophlllo molecules While large charged moleculesoannot penetrate the phoephollpld bileyer small neutral mean ditluee freely molecules such as 02 across the membrane bl Phoepholipicl membranes spontaneously reeeel When submerged in water p hospholioide form a bilayer membrane with their lipid 39tailsquot oriented away from th e wete r39 If the biloyer is dieruptd 3 for any reason too a change in pressure on one side of the membrane thie could form a quotisar39 in Ihe mem trans The hydrophobic nature at the phoepholipio tells 1altotire them to spontaneously reassemble into a bllayer oeoauee this is the lowest enveerr oomiguration lor lipids submerged in water Spontaneous reformation allows the membrane to fullyr recover its blleyer arrangement without the l input of any energy All cells metabolize or consume free energy which creates covalent bonds to stay away from chemical equilibrium 0 The processes that cells have evolved to obtain free energy include 0 Heterotrophy oxidation of foods via oxidation of covalent bonds 0 Lithotrophy chemical electron donors provide energy H2 HZS S Fe O Autotrophy capture of light energy in via pigments photosynthesis mmMWWm4mMWWWW lipid molecule 7 Cl molecule protein molecules All cells are enclosed in a spontaneously Q Jpoelmgm hml mi39iilemg aggregating amphiphilic phospholipid will bilayer membranes regulate nutrientwater filial 39 1 El transfer concentrate molecules internally through embedded protein transport molecules a M Bl Figure lI15 Essential ell Mallow IITl39l ed ED anann Stienoe IBM hydrocarbon 1 til Cholesterol stiffenis memeblra es by filling in gaps between P Iipicls Basic Properties of Cells Life Have an evolutionary origin via chemical evolution from a LUCA Highly complex mix of biomolecules C O H N which yields cellular structural complexity Can selfreplicate themselves mitosis amp meiosis Acquire a utilize energy via metabolic pathways glycolysis Krebs etc cells obey laws of chemistry and physics Cells metabolize are capable of 1000 s of reactions via enzyme proteins Capable of selfregulation series of ordered reactions that are selfadjusted division growth amp differentiation leads to cellular form and function Osmoregulate control what gets inout of membranes organelle or plasma Are motile involved in numerous mechanical activities including assembly disassembly movement of organelles and motor proteins Respond to stimuli via cell surface receptors paracrine vs endocrine Cells die absence of life is a defining characteristic of living Viruses exhibit some of the characteristics of cells but they don t have the ability to reproduce themselves on their own What types of cells does CMB study Model Organisms cheap plentiful prolific reproducers with simple genomes amp unique properties for practical research analysis CMB s research model organisms have often used to study gene expression 0 Bacteriophages viruses that infect bacteria today used as cloning vectors 0 Escheriichia coli bacteria common to the human colon molecular work horse Eukaryotic models include l DNA RNA protein synthesis ii Gene regulation cancer and control of cell proliferation transport of proteins and organelles inside cells infection and immunity Possible gene therapy approaches Yeast iSaccharomyces cerevisiael Control of cell cycle and cell division Protein secretion and membrane biogenesis Function of the cytoskeleton Cell differentiation Aging Gene regulation and chromosome structure Fruit fly iDrosopliiia meiarrogasteri Development of the body plan Generation of differentiated cell Hneages Formation oi the nervous system heart and musculature Programmed celli death Genetic control of behavior Cancer genes and control of cell proliferation Control of cell polarization Effects of drugs alcohol pesticides Mice including cultured cells Models of cancers and other human diseases Gene regulation and inheritance infectious disease Development of body tissues Function of mammalian immune system Formation and function of39 brain and nervous system Figure 1i13 Molecular Cell Biology Seventh Edition 2013 Will Freeman and Company Bacteria DNA RNAfprotein synthesis Metabolism Gene regulation Targets for new antibiotics Cell cycle Signaling Fluundlworm l Caenorhabditis elegansl Development of the body plan Cell lineage Formation and function of the nervous system Control of programmed cell death Cell proliferation and cancer genes Aging Behavior Gene regulation and chromosome structure Zebralish Development of vertebrate body tissues Formation and function of brain and nervous system Birth detects Cancer Plant Arahidopsis thalianal Development and patterning of dssues Genetics of cell biology Agricultural applications Physiology Gene regulation immunity infectious disease 0 Zebrafish help scientists answer big questions about genetics and how diseases emerge 0 Their embryos are clear and grow outside of the mother s body allowing researchers to observe their development from the moment an egg is fertilized Additional model systems for generic amp embryonic development research include 0 Hcla cells an immortal cell line of human cervical cancer cells that grow prolifically in culture 0 Fibroblast cells connective tissue cells easily grown in tissue culture
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