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by: Ezequiel Orn


Ezequiel Orn
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This 40 page Class Notes was uploaded by Ezequiel Orn on Sunday September 6, 2015. The Class Notes belongs to BIO 311C at University of Texas at Austin taught by Staff in Fall. Since its upload, it has received 37 views. For similar materials see /class/181741/bio-311c-university-of-texas-at-austin in Biology at University of Texas at Austin.




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Date Created: 09/06/15
BIO 311C Spring 2009 Exam 1 in this room at this time on Friday Feb 13 next Friday The discussion periods today and tomorrow will be devoted to a review of the subject matter covered on the exam The last 20 minutes of the Wednesday lecture period will be devoted to a review of the subject matter covered through today s lecture More information about the exam will also be provided at that time Lecture 9 Monday 9 Feb 2009 A model of the origin of eukaryotes Textbook Fig 259 p 517 Nuclear envelope E ndoplasmio re t ulum Nucleu 5 Mitochondrion Infolding Ancestral of plasma quot photosynthetic eukaryote membrane Ill 39 PlaaIid En ulfing of photosynthetic gt prokaryute x of aerobic r heterotrophic 3 Ancestral prokaryote prokarvoia Plasma membrane M39wcmndnon Ancestral heterotrophic eukaryote Fig 282 p 577 shows even more extensive incorporation of one cell into another in a process called secondary endocytosis not required reading Chemistry as applied to living cells is especially concerned with A the arrangements of atoms within and between biological molecules chemical structures B changes in the arrangements of atoms amongbiological molecules as they combine and disassociate In various ways chemical reactions In order to appreciate the structures and functions of biomolecules in living cells it is necessary to understand some features of the individual atoms that are components of biomolecules the bonds that hold the atoms of biomolecules together atoms 7 I o bonds H E Ro H H Acetic acid a small organic molecule Levels of Organization within Living Cells Populations of cells tissue 5 Or populations of unicellular organisms 5 x i quot living cells 1 occlusions cellular organelles other cellular structures levels of organization 1 gt considered in most large organic molecules detail in BIO 311C small molecules atoms Major Elements that occur in the Human Body Percentage of From textbook Table 21 p 32 Atomic Number Human Body Symbol Element See p 29 Weight 0 Oxygen 4 s 650 c Cam 4 6 135 Green arrows represent H Hydmgm 4 1 95 elements most abundant in N NJtrogsn lt 7 33 biological molecules Ca Calcium 20 1 s P Ph h lt 15 10 5P quotquot5 Know the chemlcal symbols K Potassium 19 04 for all elements shown In 5 Sulfur 4 16 03 Na Sm um 11 0 2 thIs table and for the trace C Chm 17 02 elements copper Cu Iron Mg Magnesium 12 OJ Fe and manganese Mn Summary of Bond Characteristics of Typical Biological Molecules Bond Tlme Bond Length Bond Angle Bond Strength A deg KJlmol covalent 1 109 109 39 500 typical 400 polar several NA NA hydrogen 3 180 15 39 40 typical 40 electrovalent several NA NA van der waals lt 3 NA NA hydrophobic NA NA NA Covalency of Atoms of Central Importance in Biological Molecules Atom Chemical Symbol Covalency Hydrogen 1 Oxygen Carbon Nitrogen Phosphorous Sulfur D39UZOOI Nonahm These atoms all readily form covalent bonds They each have essential functions in biological molecules R1 X Y R2 covalent bond R1 X Y R2 bond broken One electron remains with each atom R1 X Y The bond strength of a covalent bond may be described as the total amount of energy measured in kilojoules for example required to break a specific covalent bond in each molecule of one mole of molecules The bond length of a covalent bond is the distance generally given in units of A that two covalently bonded atoms are separated from each other A R1 X Y R2 Recall that an angstrom A is a unit of length equal to 110 of a nanometer or one tenmillionth of a millimeter R1 X Y R2 Bond angles not shown accurately R1 X lt Y R2 Bond angles shown more accurately 1 09 an example The bond angle of a covalent bond is the angle formed by 2 bonds that hold 3 adjacent atoms together Chemical Composition of Cells by Weight Active cells are gt50 water Typical animal cells are 60 70 water Many plant cells are gt90 water The nonwater portion of a cell is its quotdry weightquot The dry weight of cells is composed of A B 1 inorganic substance 99 organic molecules Most organic molecules of cells fall into one of 4 four broad categories 1 carbohydrates 2 lipids 3 4 nucleotides and polynucleotides proteins Ways to Express the Formula of Water H20 Chemical formula HOH or H OH Structural formulas O Stereo formula 1 H H 05 Polarity of Water 6quot H20 Water is a polar molecule because 1 it39s bond angle isn39t 180 making the molecule asymmetrical 2 its oxygen atom is much more electronegative than the hydrogen atoms so it s covalent bonds are Liar covalent bonds 3 Two lone pairs of electrons negative charges on the oxygen atom project away from the hydrogen atoms Both 0 and N are very electronegative in comparison to H C P and S Atom Chemical Svmbol Covalencv Electroneqative Hydrogen H 1 Oxygen O 2 V V Carbon C 4 Nitrogen N 3 V Phosphorous P 5 Sulfur S 2 O and N form polar covalent bonds when bonded to H C S or P Polar Bonding of Water polar bond polar covalent bond I I negativel I 539 positively charged I 5 0 O charged surface I surface I I 8 39O H H 5 Be sure to know the difference between a golar covalent bond and a golar bond Polar Bonding example aldehyde positively 839 C ar e H shuerac R Polar Bonding example amine negatively S il H H 8 post el charged 39 39 V Y surface N Chffrged N H su ace R R Summary of Bond Characteristics of Polar Bonds Bond Tlme Bond Length Bond Angle Bond Strength A deg KJlmol covalent 1 109 109 39 500 typical 400 polar several NA NA hydrogen 3 180 1 quot 4 0 typical 40 electrovalent several NA NA van der waals lt 3 NA NA hydrophobic NA NA NA Polar Attraction Between two Water Molecules H 6o 8 Electropositive hydrogen atom 6 Electronegative oxygen atom H H H Hydrogen Bond Between Two Water Molecules H 0 Bond Characteristics of a Hydrogen Bond Between Two Water Molecules H O 3 A lt gt hydrogen bond Bond length 3 A Bond angle 180 Bond strength 30 40 KJlmole 5 2 OH b Description of a Hydrogen Bond A hydrogen bond may form within a molecule or between two molecules when a hydrogen atom that is covalently bonded to an oxygen atom or a nitrogen atom approaches another oxygen or nitrogen atom The hydrogen atom comes to lie appr0ximately midway between the two electronegative atoms and is bonded to both BIO 311C Spring 2009 Lecture 6 Monday 2 Feb 2009 Relationship Among Various Organelles of the Endomembrane System of Eukaryotic Cells Ovesicle nuclear envelope 9 quot rough I smooth 0 golgi O er er I bulk molecules for O me transport out foodevnergy of the cell residual food y lysosome 4 bodies vacuole cell Substances leave the lumen spaces of the endomembrane system into the cytoplasmic matrix one molecule at a time through lysosomes Substances are transported into the extracellular space in bulk through the plasma membrane Membranebounded Organelles that are not a part of the Endomembrane System These organelles divide by fission rather like peroxysomes prokaryotic cell division Their membranes are constructed of molecules that are assembled from the cytoplasmic matrix or that are synthesized within the organelle mitOChondrion The contents of their luminal spaces are not mixed with luminal contents of endomembrane organelles chloroplast Also see textbook Figs 617 618 619 p 110 111 A primary function of peroxysomes is destruction of hydrogen peroxide Consider the following twostage process 1 In an organelle such as a mitochondrion adjacent to a peroxysome or in the peroxysome itself Transfer of O 2 H oxrdlzed organic 2 molecule quotn 2quot hydrogen atoms Reduced organic molecule H202 quotnquot hydrogen atoms 2 In the peroxysome to H202 H20 12 02 peroxysome hydrogen peroxide Sum reduced organic oxidized or anic molecule 12 02 g H20 molecule The mitochondrion is the primary site of energy production in most eukaryotic cells From textbook Fig 617 p 110 lntermembrane space Outer membrane The mitochondrial envelope consists of two membranes an inner and an outer membrane The mitochondrial inner membrane separates two compartments the matrix and an intermembrane space Most metabolic activity of the mitochondrion occurs in the matrix and at the inner membrane The primary function of mitochondria is respiration Oxidized oxidation 1 Reduced organic molecule 02 gt 002 H20 Stored energy glucose ATP th 39 2 Stored energy ADP Pi amp ATP H20 Each of these numbered events is a process involving a set of chemical reactions not just a single reaction The names of the processes are written above the arrows Other components of mitochondria include DNA packaged much like DNA occurs in prokaryote cells All machinery necessary for protein synthesis including ribosomes The proteinsynthesis machinery is similar to the proteinsynthesis machinery of prokaryotic cells Enzymes that facilitate synthesis of lipids and various other organic compounds Some of these compounds are used in mitochondria and some are exported for use elsewhere in the cell Components of the Cytoskeleton The cytoskeleton of eukaryotic cells consists of 1 rodlike structures 2 proteins that are associated with these structures Rodlike structures of the cytoskeleton include a microtubules b microfilaments c intermediate filaments The associated proteins are utilized to a attach various components of the cytoskeleton together b attach components of the cytoskeleton to other cellular structures such as membranebounded organelles c allow movement of components of the cytoskeleton with respect to each other or with respect to other components of the cell These quotmovementquot proteins are called quotmotorquot molecules Motor molecules are components of the cytoskeleton Motor molecule Microtubule ATP powered of cytoskeleton Some motor molecules cause microtubules or microfilaments to slide past each other in order to facilitate movement Organelle Receptor for motor molecule Motor molecule Microtubule ATP powered of cytoskeleton Other motor molecules cause cellular structures which are not a part of the cytoskeleton to slide along microtubules or microfilaments in order to facilitate movement See also textbook Figs 621 Micrntubules farm a framework nftubular structures within the cytoplasm of eukaryntic cells ntubulin ltubulin length 39 variable Tubulin is a kind of protein Microtubules vary in length and may be several pm long They are always 25 nm in diameter Microtubules are dynamic structures dl assembled into tubuli dimers when no longer needed then re assembled from the dimers into new microtubules as needed elsewhere A dimer is a molecule that consists of two often identical or very similar molecules chemically bonded together Microtubules along with their motor molecules and other MAPs guide the movements of chromosomes during mitosis blue microtubules green and intermediate filaments of microtubules called a spindle red of the ce MAP microtubuleassociated protein Diagram of Some Features of a Typical Singlecelled Eukaryotic Organism which Contains Flagella ageHa plasma membrane microtubules nucleus Flagella are components of many kinds of eukaryotic cells They are flexible rodlike structures projecting from the cell and surrounded by plasma membrane A parallel array of microtubules runs longitudinally along them External Appearance of Flagella Cells that contain flagella generally have only one or a very few flagella Flagella are typically very long sometimes much longer than the length of the cell Flagella generally move with a whiplike motion to propel the cell through water or to move water past the cell A singlecelled unicellular eukaryotic organism that contains two anterior agella External Appearance of Cilia Cells that contain cllia usually have many cilia C a are typically much shorter than the length of the cell 39 39 1 z r r through water or to move water past the cell The heating of all cilia 1 From textbook Fig 2311 p 534 Qs A singlecelled unicellular organism at is covered with cilia Many kinds ofhuman cells contain a single cilium projecting from the cell in most kinds of cells it does not eat and its function in most kinds ofcells is not well unders ood Crosssectional View ofa Flagellum or Cilium From textbook Fig 624 p 115 9 microtubule doublets 2 central microtubules dynein a motor molecule plasma membrane electron microscope picture digramatic representation a and flagella appear dent cal ec nal ew cros Mechanism of movement of Flagella and Cilia a Energy in the form of ATP is directed to a motor molecule called dynein b Energized 39 39 uuumel c Since all microtubule doublets are anchored together at their base dynein movement causes the entire structure to hen ss Ilnk n5 Mlcmmbule Cm V i moiems inside doublets i ll Dumvdnuhlals l From textbook Fig 625 l p 116 Dynein arm i This illustration shows that T stration shows the movemen would occur without bending that occurs since the bending if the doublets were doublets are all anchored at not all anchored at their bases their bases Bending of a microtubule doublet causes the entire flagellum or cilium to bend since all of the doublets and other components of the flagellum are anchored together Sequential energization of dynein on different microtubule doublets causes the flagellum to bend in different directions at different periods of time From textbook Fig 625 p 116 Numbered arrows show different directions of flagellar bending at different periods of flagellum or cilium showing time plasma membrane covering An elaborate cellular control mechanism regulates exactly which dynein molecule is energized at each interval of time thereby controlling the direction of bending of the doublets at each interval of time


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