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Principles of Biology

by: Danial Gorczany

Principles of Biology BIO 113

Danial Gorczany

GPA 3.94


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This 35 page Class Notes was uploaded by Danial Gorczany on Sunday October 25, 2015. The Class Notes belongs to BIO 113 at University of Michigan - Flint taught by Staff in Fall. Since its upload, it has received 28 views. For similar materials see /class/228613/bio-113-university-of-michigan-flint in Biology at University of Michigan - Flint.


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Date Created: 10/25/15
Lecture 1 Micrograph Images Light microscopy Lenses Condenser Field Diaphragm http alevelnutescumM agnificatiunlo Eye Fma Image Eyepiece Prujectur Lens quot 7 OhjEEUVE 39 Spemm en Cmndenser Lens http wwwcasmiamiuhedumbirwsmicmscupescumpaundscupehtml Phase contrast micrographs httpmirrn mamaer 39 39 39 39 39 39 39 quot 39 html Transmission v scanning electron microscopy eleclmn quotMorman in Mm beam u backscallered electrons L i SEM mmmm secondar 39electrons S M I 1 i ii H H Lransmmed elemans TEM Inlurmaunn m immui MHKUHL b um and mm iicld imaging Hams in Phase Bantuask and BIG Micms apy httnlmirm magnetf n 39 39 39 39 39 39 39 39 39 hfml Note halos in a b c are artefactual The Scale of the Universe awesome website httphtwinsnetscae2bordercoorwhite Oniahgski h c39ells 200x ht 397 57 quot vkv Lg l Dartmuuth CaHege Cereal black rust Uredospores from wheat black rustas seen through the light microscope httpwww7inrafrhypSpathogene6pucgrahtm 4 u Credit DanmoudwCoHege TopHat Question 1 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NamentausamnnetwarkthhA exaFANNIEmmugatedtavhaHmdm mp www mmsmvvu mm5an gsHerY uarestenctDQKZS mm Binary fission prokaryotic reproduction Piasmid V V Eukaryotic somatic cell cycle mitosis h The cell cycle lm 2012an Eduaaliun Euka ryotic mitosis Slmr chromauds romowmas Oanlramare Mllollc Sliler chromallda Daughmr cull condanalng aylndle sapamlng lormlng I The M mlm c phase muwmamm m The eukaryotic cellular milieu Fl39llJld between the cells lntareelluler Gel or interstitial r r Tembmne Figure 4 5 Cine call and Its Aseeeiatad Fluids BIO 326 Lecture 1 Cells and Tissues 1 Understand the 4 criteria for life and how they relate to cells a All living things have DNA b All living things have a means of taking in energy from the outside world and converting it to energy they can use 9 9 All living things can sense and respond to change All living things can reproduce 2 Understand the three tenets of cell theory a Cell the basic unit of structure in biology b Every organism either consists of cells or is itself a single cell c All cells arise only from preexisting cells cl 12 developed in 1839 by Theodor Schwann and 3 added in 1855 by Rudolf Virchow 3 Understand the basic principles of microscopy 3 Microscopes magnify images b Resolving power the fineness of detail that a microscope can reveal the smallest distance that two objects can approach one another and still be recognized as separate c Resolution is a function of the wavelength of the illumination source employed 4 Understand the basic principles of light microscopy Be able to identify micrographs taken using light microscopy 3 Light microscope Uses visible light sun or artificial source wavelength of around 500nm can distinguish objects as small as about half of this 250nm Can visualize the smallest cells and the major internal structures iquot Uses 3 lenses 1 Condenser lens focuses light on the specimen 2 Objective lens magnifies image 3 Projector lens aka eyepiece to convey magnified image to the eye iv Brightfield microscopy 1 Most living cells are largely transparent to transmitted light 2 Overcome this by staining cells 3 Stains are highly toxic so used when cells don t have to be alive v Phasecontrast microscopy 1 Light travels at different speeds through regions of the cell that differ in composition 2 Converts these differences in refractive index into differences in contrast revealing more detail 5 Understand the basics principles of electron microscopy Be able to identify whether micrographs were taken using light or electron microscopy 3 Transmission electron microscopy TEM i Electron gun produces beams which are focused onto the specimen Some electrons are absorbed and these areas appear darker clearer areas are where electrons have passed through mU EEu ES hesmdhdh er n 1hrh much baterthan Scanmng E Ectmn rhrcrdscdpe w r SmaH regrdh men 270 as dppdsedm 37 x v r CDmp ExprEp prucEss magEmuSl be verythrhrdrexectrdhsm passthmugh r Pmehuax fur anerads r thmgs that appEartD be thErE dde m Errnrs m prEp rathEr than actuaHy berhg pan dr spedrheh o b Scanmng E E mn mmrDSEDpy and r back andfnnh weru H Axsdrhdstdccdr Hvacuum m Wrde dEpVLh foncus aHDWS EXEEHEHI rrhpressrdh hESrD shape er nbje s hesmdud IrZEInm r CDmp EX prEp prucEss r Pmehuawdr anerads main images a b F uDrESEEnt dyas r SDmE dyes spEm caW slam pamcu ar stru urEs Examp E hdechsxDm brhdughthm DNA and Wm dhh ddresce when bDund H used c ceheucahyehcdded ddrescehtrhdwecdwes r creerr ddrescehtprmerhcwrscxassrcexarhpxeyddwrudserhthexab H CEHSmducEdtDmakEpmtEmstDWhmhthEGFPtaghasbEEnattachEd hr Usedmmudwdcaudhdnhrsprmerhrhahhhgceh indirectlmmunohistochemistry conned oe mum on Immuno umescence HRPO DAB 5970 Sngnzw Labeled Secondary Fhmrescem Tag Amway ana ymmmi HEN Laheed Mary many Pmteins mews CellTISSUE CellTISSUE Diagram 1 llluslranon ofndrrect lmmunahrstochemvstry and meuno uarescenoe methods mp NMWeme mhnhhdhahrmhm sw 7 Be able to describe what prokaryotes and eukaryotes are and how they differ Table 41 a b c d e Prokaryotes No membrane bound organelles including nuclei Eukaryotes Membranebound organelles including a nucleus 3 domains i Bacteria ii Archaea iii Eukaryotes Where do viruses fit in If you were a scientist who was given some samples of unknown organisms and you wanted to identify the domain of those organisms how would you do it 8 Understand the basics of prokaryotic cell reproduction binary ssion 3 4 5 6 239 Image Source Ecoddingtonl4 Creative Commons AttributionShare Alike 30 Unported License 1 DNA tightly coiled in bacterium 2 DNA replicates 3 DNA is pulled to separate poes as bacterium increases size to prepare for splitting Diagram is not completely correct as DNA attaches itselfto the inner cell wall 4 The growth ofa new cell wall begins the separation into 2 cells 5 The new cell wall fully develops resulting in the complete split of the bacterium 6 The new daughter cells have tightly coiled DNA ribosomes and plasmids 9 Understand the basics ofthe eukaryotic cell cycle and the functions of its 4 phases 5 DNA synthesis Restriction point b The cell cycle 5 2012 Fearsan Eaucanon Inc The cell cycle is a carefully coordinated set of events that ensures successful cell division into two identical daughter cells 61 gap 1 cell grows and checks that it has necessary energy and materials to proceed to the next phase assures that DNA is undamaged before replication in the S phase 5 Synthesis DNA replication GZ Gap 2 cell checks that DNA is fully replicated before M phase chromosomes condense M Mitosis chromosomal segregation occurs lt 25 Slslev chromnlids CI IIDHIDSDMB Canllumsm Milo condensing spindle Sisllr Izhrwmnlid Daughlal culli separating forming a quotis M mitolic Phase 1 Prophase breakdown of nuclear envelope chromosomal condensation doubling and movement of centrioles aka microtubule organizing centers to poles 2 Metaphase microtubules attach at centromere of sister chromatids resulting tension aligns them in the center of the cell 3 Anaphase cohesin binding sister chromatids together dissolves allowing microtubules to pull one half of each chromatid to each pole Telophase new nuclear envelope forms Cytokinesis establishment of plasma membrane producing 2 individual daughter 91 cells 10 Understand the terminology of eukaryotic cellular microenvironment a Extracellular matrix the meshwork of filaments and fibers that surrounds and supports mammalian cells b Interstitial fluid the aqueous medium outside cells BIO 326 Lecture 2 Chemistry review water carbon and macromolecules 1 Be able to describe how ionic bonds form Be able to identify functional groups which can form ionic bonds in larger molecules and describe the characteristics charged functional groups give that portion of the molecule a Common charged functional groups When a molecule contains one or more ofthese functional groups this portion ofthe molecule is water soluble hydrophilic able to be transported in bloodstream Jun Amino bl Positively charged group 2 Be able to describe how the 2 types of covalent bonds form Be able to identify these bonds in larger molecules and describe the characteristics they give that portion of the molecule a Covalent bonds sharing of electrons a Nonpolar equal sharing of electrons 1 Common functional groups containing nonpolar bonds hydrocarbons When a molecule contains one or more ofthese functional groups this portion ofthe molecule is hydrophobic lipid soluble not able to be transported in bloodstream without a hydrophilic carrier m cHa cH crgtr cns Ethane Propane crrzcn2 an E on Ethylene Acetylene Kcltr WWQ c c H H Benzene b Polar unequal sharing of electrons 1 Common functional groups containing polar bonds When a molecule contains one or more ofthese functional groups this portion ofthe molecule is water soluble hydrophilic able to be transported in bloodstream 3 Be able to describe how these weak bondsinteractions work Be able to recognize hydrogen bonds in macromolecule structures a Hydrogen bonds b Van der Waals interactions c Hydrophobic interactions 4 Understand the properties of water which impact cellular processes Extracellular fluid ECF a Water is present both inside and outside ofthe cells b Water is made up of2 polar covalent bonds c These polar bonds unequal sharing of electrons allow water molecules to hydrogen bond with other water molecules cl This hydrogen bonding accounts for water s cohesiveness which accounts for its a high surface tension b high boiling point c high specific heat giving it high temperature stabilization ability important because large amounts of heat are given off during metabolism prevents cells from having a serious overheating problem 9 high heat of vaporization amount of energy required to convert 1 gram of liquid into vapor makes water an excellent coolant e Water is an excellent solvent many molecules inside cells have polar or charged regions and therefore form hydrogen or ionic bonds with water molecules forming a shell of hydration around the ionmolecule v a Hydration of sodium ion b Hydration of chloride ion Similar spheres of hydration form around charged functional groups increasing their solubility 5 Understand that acids are molecules that give H to water Be able to recognize the functional group carboxylic acid in a molecule a Acidic solutions contain a high concentration of hydrogen ions b In water protons hydrogen ions never exist alone but associate with another molecule forming H30 c Example functionalgroupcarboxylic acid COOH HO O C Cl l HCOH gtH C H H l H c H CH3 I H actually H302 but Lactic Awquot Lactate for convenience we just write H 6 Understand that bases are molecules that take H from water Define the word quotprotonatedquot H20 gt OH H eg NH2 H gt NH3 7 Be able to define the word quotmacromoleculequot Be able to describe each of the 4 classes of macromolecules a A large complex molecule with relatively large molecular weight Macromolecules usually refers to large biological polymers which are made up of small monomers linked together true of all classes except lipids 5339 4 classes of macromolecules 39 Carbohydrates Nucleic acids iquot Proteins iv Lipids 2 Be able to define the general characteristics of a carbohydrate saccharide and to list sample functions a Simple sugars make up monomers called monosaccharides which can form long chain polymers CnHZnOn b Produced by photosynthesis c Not informational molecules but examples of function include Glucose metabolic energy building block for complex molecules such as starch cellulose major component of plant cell walls and chitin exoskeleton of arthropods Ribose backbone of nucleic acids Oligosaccharides attach to cellular proteins and lipids help determine shape function identification ofthese molecules may serve as binding site for proteins Polysaccharides typically have a storage or structural role in cells longterm storage of food sugars reinforcing plant cell walls important components of the extracellular matrix 3 Be able to draw the Fischer projection of glucose Be able to identify the a and 3D forms of glucose in its Haworth projection a Monosaccharides are the repeating units that make up polysaccharides b A sugar is an aldehyde or ketone that has two or more hydroxyl groups Aldosugars have a terminal carbonyl group Ketosugars have an internal carbonyl group Ketone Ketose Aldehyde Aldose CHZOH 90 ljo Hitlerl l HoiciH 9 o Htlz0H 0 film JL I ll H 3 CH R R39 CHZOH RCH 0404 Number of carbons can vary from 37 c Glucose is the most common monosaccharide in the biological world CHZOH CHZOH c 70 l o o H 2 OH r l r Ho 7c 7 H OH DH H 7c 70H 0 a o l H 9 0H OH OH cHon aDGlucose BDGlucose DGluCOSE Fischer projection depicts glucose as a linear molecule however the ring form is the predominant structure biologically because it is energetically more stable aDglucose Dglucose open BDglucose most stable 36 64 Haworth projection shows spatial relationship of different parts ofthe molecule trace Carbons are numbered beginning with the most oxidized end of the molecule the carbonyl group Formation of the ring structure results in two possible forms depending on the spatial orientation ofthe hydroxyl group on C1 i OH points downward in aDglucose and upward in BDglucose ii The polysaccharide storage molecules starch and glycogen use ot D glucose as their repeating unit iii Storage molecule cellulose uses B D glucose 4 Be able to identify the specific type of glycosidic bond which links carbohydrate monomers a Monosaccharides can be linked covalently to form disaccharides These are formed by a condensation reaction which eliminates water forming a glycosidic bond b Example of ot glycosidic linkage Maltose ot D glucose ot D glucose ADglucose uADaglucosc MALTOSE The glycosidic bond is between carbon 1 of one glucose and carbon 4 ofthe other This is called an ot glycosidic bond because it involves a carbon 1 in the or configuration iquot ot linkages are easily digested by the human body c Example of B glycosidic linkage Lactose B D galactose B D glucose cugoH 112le i 0H 1 1de H OH i Glucose ii on quotIla tose l5 Cquot t Lactose Linkage is between carbon 1 of galactose and carbon 4 ofglucose Carbon 1 ofthe galactose is in the 3 configuration so bond is called a B 14 glycosidic bond B linkages are not easily digested by the human body as we usually lack the enzymes necessary quotlactose intolerant 5 Be able to give the definition and properties of a polysaccharide a Monosaccharides can undergo a series of condensation reactions adding one D glucose unit after another to the chain until very large molecules polysaccharides are formed b The properties of a polysaccharide molecule depend on its length they are usually very long the extent of any branching addition of units to the side ofthe chain rather than one of its ends iquot any folding which results in a more compact molecule iv whether the chain is straight or coiled c There are three basic types of polysaccharides Food storage polysaccharides 1 Plants starches amylose and amylopectin 2 Animals glycogen Structural polysaccharides 1 Plants Cellulose Be able to describe how different glycosidic linkages impact the structure and function of the polysaccharides they form a Amylose plant energy storage is an unbranched straight chain polymer of aglucose with all 114 bonds The molecules coil into a helical structure It forms a colloidal suspension in hot water CHZOH CHQOH CH20H CH20H 0 o o l 0 OH OH OH 0H 0 o o 0 OH 0H OH OH b Amylopectin plant energy storage and glycogen animal energy storage are branched polymers of aglucose a Glucoses are linked together linearly by 1194 glycosidic bonds b Branches are linked to the chains they are branching off from by 1196 glycosidic bonds c Amylopectin and glycogen molecules coil into loose helices which are not highly ordered due to numerous side chains Highly branched I glycogen molecule H I 0 H Glucose 1 11 monomer 1 l Branchmg I H on 9 occurs here 11011 01011 11011 H M o H N o H M o H H o H H H H H 1 o on H 0 on H 0 on H 0 OH H 0 l u on gt4 ow gt4 on n on c Cellulose is a linear chain of several hundred to over ten thousand 3194 linked Dglucose units 5 111011 5 6 11 O390H CIIZOH H 5 0 OH H H H 0 H 39 4 H H 39 H 0211 110 s 2 1120 11 11 011 H 0 leDeglucosc eDvglucosc CELLOBIOSE 1 Cellulose forms rigid linear rods which aggregate into microfibrils


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