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by: Ezequiel Orn


Ezequiel Orn
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Jerry Brand

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Date Created: 09/06/15
BIO 311c Spring 2009 Don t forget discussion periods start this week Attendance will be taken during discussion periods Attend the discussion period that you have been assigned Lecture 3 Monday 26 Jan 2009 Categories of Living organisms Historically living organisms have been categorized according to their broad structural characteristics Since the development of electron microscopy in the 19505 living organisms have been divided into broad categories based primarily on the internal structures of their cells Since the development of modern molecular biology during the last 20 years living organisms are increasingly defined according to their genetic information content quotA AT TTG TGAACC TTiI 13 AM 5 TA Al GG TGG TT CCTTGTTTG AB All AAAAAAAC TTTAACCC CTTTT CCAGGC 613 TC iIGGTAATTTCTTAAC C CCCCACTA FLAG TTATCTTG ATTCCIIAGCCAGTATTAGECCAT AG 136 CTCC CCCATTACCTTGTATC TTTA ACCCAA Elli TAAAAAC C AACAACG TG ACATCCAGTC AAC CECCATCACCGCCGG ACAAACG AGGTG TACTTA TTCG ATG AG TTG GTTGE CCCC C CC TATA A way of classifying all living organisms is to separate them into three broad groups called domains Domain Bacteria gt I prokaryotes kingdom Monera Domain Archaea Domain Eukaryota gt Organisms are categorized into these three domains based on differences in the genetic information contained in their cells In this course we will consider the prokaryotes bacteria and Archaea together since their cells structures and many of their functions are very similar The Domain Eukaryota may be divided into 4 Kingdoms Protists gt most are unicellular These will be Fungi they conSIst of a smgle cell considered in most detail in ltPlants gt most are multicellular this course Animals they conSIst of many cells A Fivekingdom System for Classifying all Living organisms Animalia euka ryotes Protista Includes organisms of the Monera prokaryotes domains Bacteria and Archaea This system although considered outdated is a practical conceptual way of categorizing living organisms based on structures and functions of their cells Prokaryote organisms consist of one or more prokaryotic cells while eukaryotes consist of one or more eukaryotic cells A prokaryotic cell Textbook Fig 66 p 98 Also see Concept 271 p 573 electron microscope image diagrammatic illustration based on electron microscope observations Most prokaryotic cells are less than 5 pm in diameter Many are less than 1 pm in diameter Examples of the appearance of prokaryotes at high magni cation See textbook Figure 272 p 557 l l l l i vl 1 inn 2 pm 5 ml a Spherical occi b Rodshaped c Spiral bacilli Prokaryotic cells are very simple in shape Prokaryotes occur as single cells or as simple organizations of cells Prefix diplo Two cells together Prefix strepto Chains of cells Prefix staphylo packets of cells streptobacillus Prokaryotes can be given descriptive names based on the shapes of their cells and how their cells are arranged Examples diplococcus Streptobacillus Staphylococcus staphylococcus Typically there is no differentiation of cells into different cell types within a prokaryotic organism An Exception Some streptobacillustype prokaryotes that are classified as cyanobacteria produce specialized cells called heterocysts which convert atmospheric nitrogen to ammonia Anabaena a photosynthetic prokaryote vegetative cells do photosynthesis a heterocyst does nitrogen fixation Typically there is no communication among cells within a prokaryotic organism Exception Until very recently prokaryotes were not known to communicate with each other Now many kinds of prokaryotes are known to be capable of guorum sensing This is a process whereby a prokaryote senses whether there are a lot of other bacteria of the same species in the vicinity It slows or stops its own growth if the population density is high The genetic information of prokaryotic cells consists of a single circular molecule of DNA The DNA and proteins that are bound to it is called the chromosome A typical length circumference of a prokaryotic cell chromosome is 15 mm That is approximately 1000 times the length of a typical prokaryotic cell Electron microscope photograph electron micrograph of a broken prokaryotic cell with its chromosome released into the surroundings This demonstrates the great length of the chromosome with respect to the length of the cell Also see Textbook Fig 278 p 559 The chromosome occurs in a portion of the cell called the nucleoid The nucleoid occupies over half of the interior of some prokaryote cells The nucleoid is not surrounded by its own membrane chromosome plasmid Some prokaryotic cells contain additional tiny circles of DNA with associated proteins called plasmids Plasmids are typically less than 1 of the length of a prokaryotic chromosome Some kinds of prokaryotic cells contain many identical copies of a plasmid Ribosomes All living cells must make synthesize proteins The structures that contain the chemical machinery for protein synthesis are called ribosomes 20 nm ribosome Sometimes several ribosomes in the process of synthesizing proteins are held together as a unit aligned in a row This entire unit is called a polysome D x f f q 4 protein quot l y 1 l polysome Prokaryotic cells contain slightly smaller ribosomes than do eukaryotic cells Prokaryotietype ribosomes are called 708 ribosomes 70 ribosomes are approximately 20 nm in diameter Most other occlusions in prokaryotic cells are stored sources of food andor energy packets of enzymes viruses or waste products various occlusions polysome q l example of occlusions ribosome In cell biology an occlusion is a structure within a cell that is not surrounded by its own membrane Most kinds of prokaryotic cells are surrounded by an envelope that consists of an inner membrane and an outer membrane along with a liquidfilled space enclosed between them The inner membrane is the plasma membrane The outer membrane is sometimes called the cell wall The space between the two membranes is called the periglasmic space or the intermembrane space plasma membrane illustrated in blue outer membrane illustrated in pink envelope intermembrane space not shown well Cytoplasm the entire space enclosed by the plasma membrane Most prokaryotes fall into one of two categories depending on the structure of their envelope Gram Positive Bacterium Outside of cell Peptidoglycan layer not a typical membrane N porous envelopex Inside of cell Plasma membrane Gram Negative Bacterium Outside of cell A homer membrane lt Peptidoglycan layer envebpex Inside of cell lntermembrane space Plasma membrane Most prokaryotes do not contain internal membranebounded organelles Exceptions prokaryotes that are capable of photosynthesis or respiration From textbook Fig 277 p 559 membranes for membranes for respiration cytOPIasm photosynthesis Pairs of respiratory or photosynthetic membranes separate the cytoplasm from an intermembrane space Many prokaryotes contain structures exterior to their envelope Some have a gelatinous sheath or capsule Some have tiny projections called pili Some have larger projections that spin called bacterial flagella quotflagellaquot lt more accurately called quotbacterial flagellaquot See textbook Fig 66 for view of a gelatinous sheath External sheaths and capsules are considered to be nonliving components of the cell Prokaryotic Flagellum From textbook Fig 276 p 536 cell envelope Prokaryotic flagella function by spinning on an axle that is embedded in the cell envelope axil bacterial flagellum BIO 311C Spring 2009 Lecture 27 Friday 3 Apr 1 General Description of Glycolysis Glycolysis is a metabolic pathway that a cleaves a C6 molecule a hexose typically glucose into two producing two C3 pyruvate molecules b generates two highenergy bonds by the conversion of 2 ADP Pi to 2 ATP for every C6 molecule utilized in the pathway c collects two pairs of hydrogen atoms as 2 NADH for every C6 molecule utilized in the pathway Thus glycolysis is a catabolic pathway Glycolysis showing Initial Reactants and Final Products qucose 2ADP pi ZNAD 2 pyruvate 2ATP H20 2NADH 1 H AG 85 lemole of glucose Thus glycolysis is a highly exergonic metabolic pathway Glycolysis Showing glucose breakdown coupled to ATP production and NAD reduction Glucose C6 C3 glycolysrs 2 pyruvate 2 ADP Pi 2 NAD 2 ATP H20 2 NADH H carbon flow oxidation and reduction energy capture 11 y oxidation l c6H1zo6 2 NAD PM 2 Pyr 2 NADH W i o reduction 2 ADP Pi 2 ATP H20 Glycolysis showing structural and chemical formulas of the initial reactant glucose and the final product pyruvic acid pyruvate OH OH I 2 o H C o H IOH l col sis crif c M y 2 60 c Ha I T on CH3 H OH 2ATP C H 0 c H o 3 4 3 6 12 6 2 NADH pyruvic acid Dglucose Note not all substrates are shown in this representation of glycolysis although the other substrates two each of reactants ADP Pi NAD and product H are easily deduced from the substrates that are shown The ratio of Hatoms to Oatoms in the initial reactant Dglucose is 21 The ratio of Hatoms to Oatoms in the nal product pyruvic acid is 43 less than 21 The chemical formulas demonstrate that 4 hydrogen atoms are lost from each glucose molecule oxidized to pyruvic acid in glycolysis 12 Pyruvic acid vs Pyruvate The names pyruvic acid and pyruvate are often used interchangeably in describing the final product of glycolysis Some textbooks use one term while other textbooks use the other term Yet they describe different molecular species 0 c c I OH I 0 i0 CO CH3 CH3 pyruvic acid Pyruvate The carboxylic acid functional group The carboxylic acid functional group 39 not charged is charged Names of protonated carboxylic acids generally end in quotic acidquot Names of unprotonated carboxylic acids generally end in quotate Consider that glycolysis takes place in the cytoplasmic matrix of cells Then is the nal product of glycolysis best described as quotpyruvic acidquot or is it best described as pyruvate Glycolysis can be divided into 2 phases an quotinvestmentquot phase and a quotpayoffquot phase each of which involves 5 enzymecatalyzed metabolic reactions Phase 1 39 t t h f 39 Glucose Inves men p aseo gyco ysus 20f C3 2 ATP 2 ADP Phase 2 ff h f 39 2 of C3 pay 0 p ase o g yco ys39s 2 of oxudlzed C3 molecules 4 ADP 2 Pi 4 ATP 14 Phase 1 of Glycolysis CH OH 2 39 3 0 H col sis Phase1 H cqu g y y 2 of HCOH C I I T Hzc o H OH 2 of ATP 2 of ADP glucose glyceraldehyde 3 phosphate gly3P Phase 1 of glycolysis does not oxidize substrate nor collect energy as high energy phosphate bonds In fact it uses up 2 highenergy phosphate bonds per glucose Note No Pi is produced during Phase 1 of glycolysis because the phosphate released during ATP hydrolysis is attached to substrate producing glysP The first reaction of Phase 1 of glycolysis is phosphorylation of glucose which activates the glucose in preparation for subsequent reactions 0 THon H2C6 E 1 6 0 H h k39 M 2 C O CJOH H C 9 ma 9 4 A 16 kJmol c HC HO I OH Ho CJ EH H OH I LH H ATP ADP All subsequent reactions in glycolysis involve phosphorylated substrate Only in the last reaction is the substrate dephosphorylated to give a non phosphorylated final product 16 The hexokinasecatalyzed reaction couples an exergonic process with an endergonic process in order to drive the endergonic process in the forward direction Also see Lecture 24 ATPase Not ATP 526 ADP Pi AG 30 kJmol tightly cose6 phosphatase 39e 39 glucose glu6 Jal 6 AG 14 kJmol Tightly coupled reaction hexokinase ATP glucose T39ADP glu6 AG 16 kJmol 17 Phase 2 of Glycolysis 4 ADP 2 Pi 4 ATP 2 NADquot 2 NADH H o co glycolysis Phase 2 2 0f Hc payoff phase Hzc O CH3 glyceraldehyde3phosphate Pyruvate Pyr gly3P More oxidized substrate More reduced substrate Two molecules of substrate are considered instead of one since two gly3P are produced for every glucose molecule that enters glycolysis Example of a branched metabolic pathway 7 1 5 E3 R A gtB gtC E6 X RY Depending on the context any or all of the following may be considered a metabolic pathway E8 Z A gtC A gtT A gtZ C gtT 21 Glycolysis as a part of a branched pyr metabolic pathway hexokinase glucose B gtCVA phosphofructokinase an allosteric enzyme X an allosteric enzyme Y a final product other than QIYCOIysis glucose gt pyr pyruvate a different lucose metabolic pathway a nal product other 9 than pyruvate 22 See textbook Fig 921 p 181 BIO 311C Spring 2009 In general you are responsible for all reading assignments even when the reading material goes beyond the lecture information Lecture 5 Friday 30 Jan 2009 Rough Endoplasmic reticulum rer From textbook Fig 612 p 105 The membrane of endoplasmic reticulum is continuous with the outer membrane of the nuclear envelope and the lumen of the endoplasmic reticulum is continuous with the intermembrane space of the nuclear envelope ribosomes cisternae tubules lumen Definitions A vesicle is a spherical cellular organelle surrounded by a single membrane that contains enzymes and performs metabolic functions A lumen is separated from the vesicle cytoplasmic matrix by the vesicle membrane active metabolism A vacuole is a spherical cellular organelle surrounded by a single membrane that contains few if any enzymes and does not perform many metabolic functions A lumen is separated from the cytoplasmic matrix by the vacuolar membrane vacuole storage A cisternae is somewhat like a flattened vesicle so the lumen space is very narrow Cisleruae ul Endoplasmic Uuman reliculum The Ribosome is the Site of Synthesis of Polypeptide Chains Proteins are polypeptide chains that have coiled and folded into a functional unit Large subunit Small subunit Ribosome mRNA contains coded information Polypeptide chain 39b ring each bead represent an amino acid i Polypeptide chain being produced on a ribosome The polypeptide chain grows in length one amino acid at a time as the mRNA slides along the ribosome Insertion of Polypeptide Chains into the Endoplasmic Reticulum From textbook Fig 1721 p 343 Ribosome D membrane of cytoplasmic rough er matrix Endoplasmic reticulum er Ribosomes that are attached to the endoplasmic reticulum and the outer surface of the plasma membrane are used to synthesize some watersoluble proteins that are deposited in the intermembrane space some waterinsoluble proteins that become integral components of the membrane Compartmentalization of Proteins by Eukaryotic Cells proteins that were synthesized by ribosomes attached to endoplasmic reticulum or the outer nuclear membrane transmembrane water soluble protein protein l water soluble protein protein that was synthesized by a non attached ribosome Slice through a piece of the t endoplasmic reticulum Cytoplach matrix k V Portion of a eukaryotic cell Functions of the Rough Endoplasmic Reticulum Insertion of proteins into the fabric of the er membrane or into the lumen for constructing new membrane processing chemical modification transport to other membranebounded organelles transport out of the cell Synthesis of lipids and their insertion into the er membrane Attachment of small carbohydrates called oligosaccharides to the lumen surface of the er membrane ngosaccha de a kind of carbohydrate I Ptquot 13943 Oligosaccharides are attached to only the inner luminal face of the endoplasmic reticulum Smooth Endoplasmic reticulum ser Ser tUbUIGS vesicle being formed from endoplasmic reticulum transitional er The ser in some cells occurs only as slight extensions of the rer that are in the process of forming vesicles Those small extensions are then called transitional endoplasmic reticulum Functions of the Smooth Endoplasmic Reticulum Processing of previously synthesized membrane and lumen proteins Continued synthesis and incorporation of lipids into the er membrane Detoxification of some kinds of toxic organic molecules such as those with benzene rings by chemically modifying them Continued attachment of oligosaccharides small carbohydrates to the lumen surface of membrane proteins and lipids Processing of the carbohydrates that were previously attached to the lumen surface of membrane proteins and lipids A Golgi Body arrows represent the direction vesicle from smooth endoplasmic reticulum of membrane migration to the forming face 0f 9 9i cis forming face J vesicle cycled back to nuclear J envelope endoplasmic reticulum or cis face of golgi trans maturing face vesicle from maturing Modified from textbook Fig 613 p 106 face to other organelles Functions of the Golgi Modification of carbohydrates that were previously attached to proteins and lipids on the lumen surface of the cisternae Packaging of luminal proteins into forms suitable for their final destination eg to another membranebounded organelle or exported from the cell Sorting of components within the membrane and in the lumen so that each component can be a part of the right vesicle and targeted to its correct final destination Lysosomes lipm l They are vesicles approximately 05 pm in diameter The inner surface of their membrane is lined with protective carbohydrate acid hydrolysis The lumen is acidic and is filled with hydrolytic enzymes that function at acid pH values acid hydrolases The acid hydrolases are capable of hydrolyzing practically all large molecules found in living cells including those from which cells are constructed covalent bond hydrolysis 0 0 rquot eoH Ha large molecule equotquot quotmequott two smaller molecules water The acid hydrolysis enzymes in lysosomes are so diverse in function that together they can destroy virtually all kinds of large organic molecules that occur within the cell which contains the lysosome Thus they are capable of destroying every structure of the cell including membranes Questions for consideration 1 Why don39t the hydrolytic enzymes contained in lysosomes destroy the lysosome membrane and escape into the cytoplasmic matrix then destroy cell components 2 Why would a cell produce an organelle of such destructive power that it could destroy the cell that contains it Illustration of the Protective Coating of Carbohydrate on the Inner Surface of a Lysosome inp r 39 protective oligosaccharides 5 k I 39 v hydrolytic enzyme 9 9 V A Lysosome Examples of Lysosome Functions From textbook Fig 614 p 107 primary lysosome gt quot7 v Ingestion of food for 9 Intracellular digestion food vacuole plasma membrane secondary lysosome Inside cell primary lysosome gt I g Autopl 39agy ce lular organelle In vacuole a plasma membrane Functions of Lysosomes Intracellular digestion Destruction of bacteria other pathogens and toxins Recycling of wornout organelles and occlusions Tissue development in complex multicellular organisms Autolysis breakdown of cellular components after the cell dies Review Lysosomes and plasma membrane are formed from vesicles that are derived from golgi bodies plasma membrane Some vesicles leaving the golgi fuse with the plasma membrane Some vesicles leaving the golgi become functional as lysosomes Transport vesicles from the golgi that fuse with the plasma membrane are capable of a expanding the plasma membrane allowing the cell to become larger b exporting substances from the cell without releasing any contents of the cytoplasmic matrix trans Golgi Functions of the Plasma Membrane It keeps the cytoplasmic contents of the cell separated physically and chemically from the environment It regulates the movement of substances into and out of the cell It provides specific surface receptors for communication with other cells viruses and chemical substances in the surrounding environment It provides attachment sites for intracellular and extracellular component of the cell membrane of an animal cell plasma Textbook Fig 77 membrane p 128 BIO 311C Spring 2009 Lecture 29 Wednesday 8 Apr 1 Illustration of Proton Transport Across the Mitochondrial Inner Membrane During Mitochondrial Electron Transport Also textbook Fig 916 p 175 mitochondrial inner rane becomes basic 4 slum Irl iwrl chain ls mitochondrial electron transport a metabolic pathwaw Function of ATP Synthase in the Mitochondrial Inner Membrane Mitochondrial electron transport causes a higher concentration of H on th ide of the membrane The resulting difference in pH and electric charge across the membrane is a form of stored energy he only path available for protons to travel back acr the membrane to neutralize the pH and electric charge on both sides of the membrane is through an enzme complex that captures as ATP some of the energy released during proton flow matrix An en me complex may be defined as a structure composed of several or many polypeptide chains that a ach together in order to perform one or more enzymatic reactions eg Pyr dehydrogenase is sometimes called enzyme complex Structure amp Functions of ATP Synthase a transmembrane Enzyme Complex Containing a Transmembrane component and a Peripheral component From textbook Fig 914 p 174 r MITOCHDNDRIAL MATRIX Chemiosmosis is the name of the process that synthesizes ATP from the dissipation of a proton gradient across a biological membrane From textbook Fig 916 p 175 lnlommnilnno space Inner mltochomtrill mamhrlnl Mllaohundrill Electron Iraniwrl chllu cumiu39mosis matrix minum phospnarylallan Oxidative phosphoryation is the sum of 1 39 39 melmuane 39 39 39 during electron transport and 5 gradient chemiosmosis Metabolic Pathways and Processes that Participate in Respiration note difference in terminology from that given In previously lectures Gycoysis Occurs in the cytoplasmic matrix Pyruvate dehydrogenase 39 Krebs cyde Occur in mitochondria Mitochondrial electron transport chain f eUKa ymes Gcholysis Occurs in the cytoplasmic matrix Pyruvate dehydrogenase KFEbS CVCIE Occur in mitochondria oxidative Mitochondrial electron transport chain f eUKanes phosphorylation Chemiosmosis 6a Summary of the Metabolic Pathways and Processes of Respiration to from atmosphere atmosphere in Mitochondrial Krebs cycle 2 c2 4 602 2 ATP 2 NADH 6 NVADH 2 FADH2 6102 eleciron transport and chemismo sis 6ATP 61ATP 3918 ATP 394ATP Approximately 38 molecules of ATP are synthesized per glucose molecule respired However in eukaryotes 2 ATP per glucose are required to move respiratory substrates NADH ADP and Pi into the mitochondrion and substrates NAD and ATP out of the mitochondrion by active transport so in eukaryotes there is a net production of 36 ATP per glucose Some kinds of microorganisms are capable of doing respiraton in the absence of 02 That process is called anaerobic respiration summary of metabolic processes in aerobic respiration Citric acid e39ectmquot 12 02 glycolysis pyr dehyd cycle transport chain V V 39 chemiosmosis 7 H20 summary of metabolic processes in anaerobic respiration OXIdized small organic molecule or inorganic Citric acid e39ectmquot glycolysis pyr dehyd cycle transport chain SUbStance sum as S V V 39 chemiosmosis 7 reduced small organic molecule or inorganic substance such as HZS Aerobic and anaerobic respiration are identical except that in anaerobic respiration a substance other than 02 serves as the final terminal 8 accepter of reducing units in the electron transport chain Catabolism of various fuel molecules I T ese substances serve as u h m energysupplying 323 5Wquot G39V m 139 molecules rather than as food acids construction molecules when th y e are used in respiration Glyqolysls Gilliam Textbook Fig 920 p 180 oxi miva WWW The location of photosynthesis in a plant Lou cross union Imer oum rma he mmbrlna In Thyhkoid s nac membrane space mbv From textbook Fig 103 p 187 The interior spaces of leaves are mostly allow the evaporative loss of water vapor Photosynthesis occurs in chloroplasts Since chloro lasts typically are green the tissues that do photosynthesis are generally green in color Photosynthesis in plants from a physiological perspective light a 6 H 0 from 6 002 2 soilroots diffusion through holes individua vascular system stomata in leaves ce atmospher 6 O2 C6H1206 j to various plant tissues net reaction light energy 6 co2 6 H20 C6H1206 6 02 photosynthesis Chloroplast Structure From textbook Fig 103 p 187 Chloroplasts are a kind of large plastid found in green plant cells often 5 pm or larger in diameter The chloroplast envelope consists of two membranes an outer membrane and an inner membrane along with an intermembrane space Internal to the envelope is a watery space called the stroma within which is imbedded an interconnected system of membranes called thylakoids Thylakoids enclose internal spaces called the lumen Thus the chloroplast contains three different membrane systems the outer membrane the inner membrane and thylakoid membranes separating three distinct aqueous spaces the intermembrane space the stroma and the lumen from the cytoplasmic matrix The reactions of photosynthesis take place in the stroma and within the thylakoid membranes 13 Why leaves are green From textbook Fig 107 p 190 Light from the sun contains a Reflected mixture of all colors Colored quot9 molecules pigments in the chloroplasts absorb all colors except green quite efficiently Ch39 39 P39 5t Thus mostly green light passes on throu h the chloroplast or is reflected from it The overall chemical equation for photosynthesis is very similar to the reverse of the chemical equation for respiration light energy 6 C02 6 H20 photosynthesis C5H1206 6 02 respiration CGH1206 6 02 6 C02 6 H20 A metabolic pathway or process must be exergonic spontaneous in order to go in the forward direction regardless of whether it is anabolic or catabolic metabolic pathway Reactants Ar Products AG lt 0 heat 16 Both photosynthesis and respiration are exergonic processes light energy 6 co2 6 H20 P 5yquot es s CSH1206 6 02 AG 9000 kJmole heat CSH1206 6 02 respira i 6 co2 6 H20 AG 1700 kJmole ATP heat Photosynthesis is an anabolic process Respiration is a catabolic process 18 Carbon flow in Photosynthesis 6 of c1 1 of 06 Carbon flow in Respiration 1 of C6 6 of C1 The 06 of both photosynthesis and respiration is hexose typically glucose The C1 of both photosynthesis and respiration is 002 Summary of Energy flow in photosynthesis light energy energy input 12000 kJmole of C6 6 C02 6 H20 C6H1206 6 02 Energy required AG 2880 lemoe of ca heat 2880 lemole 0 0 effICIency W X 100 A 24 A The remaining 76 of the energy introduced by light is given off as heat assuring that photosynthesis is an exergonic process Overview of Oxidation and Reduction in Photosynthesis light energy 12 H20 6 02 12 of 2H oxidation of water 6 Co2 CSH1206 reduction of C02 6 H20 reduction of co2 6 co2 6 H20 CSH1206 6 02 oxidation of water 20 2 Metabolic Pathways and Processes that Participate in Photosynthesis Light harvesting and energy trapping Photosynthetic electron transport Chemiosmosis light reactions of photosynthesis Calvin Cycle dark reactions of photosynthesis Photophosphorylation BIO 311C Spring 2009 Although we learn in textbooks that the cytoskeleton is a feature only of eukaryotic cells in fact prokaryotic cells have components that are very similar to components of a eukaryotic cytoskeleton The following article is from the January 23 2009 issue of Science Magazine Protein Filaments Caught in the Act wwwsciencemagorg gt Previous issues gt Volume 323 page 472 Lecture 7 Wednesday 4 Feb 2009 The microtubule doublets of each flagellum or cilium extend into the cell for a short distance where they become microtubule triplets in a structure called a basal body In cells that contain flagella separate microtubules or bundles of several microtubules often start at the region of the basal bodies and extend into various regions of the cell They are called flagellar roots nucleus flagellated unicellular eukaryote Basal bodies differ from flagella or cilia in that that they are composed of 9 triplets instead of doublets of microtubules do not contain a central pair of microtubules do not contain dynein and are not surrounded by plasma membrane 025 pm See textbook Fig 622 p 114 3 Cb QDQ oc g diagram of a cross section of a basal body electron microscope picture of a cross section of a basal body diagram of a side view of a basal body blue represents associated proteins that hold the triplets together In the cytoplasmic matrix of eukaryotic cells there is a region called the centrosome or microtubule organizing center MTOC Microtubules radiate from this region In animal cells there are two structures called centrioles in the centrosome From textbook Fig 69 p 100 v centrosome The MTOC provides a reference point for organizing the locations of various structures animal cell within the cell with respect to a framework of microtubules The two centrioles in a centrosome lie at right angles to each other Each centriole in the centrosome appears identical to a basal body See textbook Fig 622 p 114 Although all eukaryotes contain a microtubule organizing center MTOC plant cells do not contain centrioles in this center Many individual microtubules radiate from the MTOC in various directions within the cytoplasmic matrix The contents of the cell are organized with respect to this center and its radiating microtubules Because of their location near the center of the cell and their role in organizing the positions of other components of the cell the MTOC is sometimes called the quotcell centerquot Microtiupule Electron microscope picture of H gg gf39ng microtubules radiating from the MTOC of a plant cell See textbook Fig 69 p 101 for a diagrammatic illustration of a plant cell MTOC centrosome The centrosome MTOC plays acentral role in mitosis and other events associated with eukaryotic cell division duplicated pair of centrioles pairs of centrioles stages of mitosis nucleus The animal cell illustrated here is just beginning the The cell is now in a later stage of process of mitosis The pair mitOSiS One Centrosom39e has of centrioles has recently migratEd t0 the OPPOSite Side Of been dupiicated and there the cell forming a second MTOC are now two centrosomes in the MTOC Relationship Between Basal Bodies and Centrioles in a Unicellular Flagellated Eukaryote flagella basal bodies centrosome containing centrioles flagellar roots nucleus These illustrations represent two stages in the life cycle of the same cell 1 During most of its lifetime the cell has flagella with basal bodies as well as flagellar roots that radiate deep into the cell interior helping to organize the cell contents 2 The cell loses it39s flagella when it prepares to undergo mitosis and divide The basal bodies then move to a site near the center of the cell where they become centrioles as a centrosome forms Microtubules are produced by the cell and radiate from the centrosome where they provide a framework for reorganizing cellular components in preparation for mitosis and cell division After the cell divides the centrioles of each new cell will again migrate to the front part of the cell to become basal bodies and provide a framework for the formation of new flagella Micro laments form a framework of thin lamentous structures within the cytoplasm of eukaryotic cells F t to kal 61 113 mm ex a e quot Microfilamentsvaryinlengthandmaybe in hundreds of nm long They are always7 nm H actin filaments in diameter Micronlaments are dynamic structures dis assembled into protein monomers single proteins called g actin when no longer needed then reassembled into new microrilaments as needed elsewhere in the c ll AG bun Micronlaments are also sometimes called quotthin filamentsquot or quotactin filamentsquot T 7 m r v Microfilaments are important for maintaining the shapes of animal cells microvilli small protrusions on the surface of these epithelial cells used to increase surface area epithelial cell Specific shapes are often maintained in eukaryotic cells that don39t contain external walls by microfilaments that are distributed within the cytoplasm to produce a gellike E 39th I39 I II th 1 39 P39 e39a ce 5 a con5stency the cytogel line the small intestine Some eukaryotic cells have highly irregular cell surfaces to increase their surfacevolume ratio or to facilitate their movement along a surface These irregular shapes are maintained in many kinds of cells without an external wall by microfilaments extending into the cell projections Examples of Microfilament Function See textbook Fig 627 p 117 Myosin lament yosin arm a Myosin motors in muscle cell contraction filaments p 4 Parallel actin 1 K c Cytoplasmic streaming in plant cells Nonmovin cytoplasm gel r a cyclosis Ilt cmomplast Musc39ece Streaming Cr gt TNY Actlnlllament cy oplasm 439 r sol 1 Vacuole l quot Cell wall J I 39 if Anlmal muscle cell Plant cequot Gel with actin network Sol with actln subunits 14 4x I Extending 39 lt pseudopodium 4 gA quot 1 gt t 139 r b Amoeboid movement Protist cell Intermediate filaments form a framework of thin filamentous structures within the cytoplasm of most eukaryotic cells green microfilaments orange nucleus Protem subunits 39l fibrous subunits 10 mm Intermediate filaments vary in length and may be several of pm long Many different kinds of intermediate filaments occur in eukaryotic cells depending on the organism and the type of tissue They vary in diameter depending on the kind of intermediate filament within the range of 8 to 12 nm Intermediate filaments are not dynamic structures Most kinds remain intact for the life of the cell after they are assembled From textbook Table 61 p 113 A Few of the Many Types of Intermediate Filaments that Occur in Higher Animal Cells Keratin is the major component of skin cell cytoplasmic matrix is the major component of hair and nails is the main component of bird feathers Neurofilaments occur in the cytoplasmic matrix of nerve cells Lamins occur in nucleoplasm Keratin intermediate filaments align in parallel within the cytoplasmic matrix of skin cells They are concentrated at points where the cell is connected tightly to adjacent cells through anchoring junctions called desmosomes Skin cells continuously die and are replaced by new cells The dead cells are completely destroyed except for the keratin microfilaments which remain as a surface coating on the outer layer of skin Keratin is highly protective since it is impenetrable to most solvents and inert to most chemical agents keratin lament desmosome See textbook Fig 632 p 121 skin cells Some ways that intermediate filaments are different from microfilaments and microtubules Microtubules and microfilaments are made of globular proteins while intermediate filaments are made of fibrous proteins Microtubules and microfilaments are dynamic structures that can be quickly disassembled and reassembled from their subunits by the cell Intermediate filaments are very stable and most of them are not disassembled after they are formed Microfilaments and microtubules perform a large variety of functions many of which involve movement Each kind of intermediate filament has a very narrow range of functions and intermediate filaments generally do not facilitate movement Microtubules as well as microfilaments are virtually identical in all eukaryotic cells while intermediate filaments are quite specialized and each different type of cell has its own specific intermediate filaments with its own functions Diameters of different kinds of microfilaments are also somewhat different from each other Globular vs Fibrous Polypeptide Chains Globular POMPeptide Fibrous polypeptide c alns proteins chains proteins Molecular models of Molecular models of a an actin ilament kerati intermediate a microfllament filament External Coatings of Cells Nearly all kinds of cells prokaryotic and eukaryotic have a coating external to the plasma of membrane Depending on the kind of cell and its location this coating may be used to shield the cell from physical andor chemical agents in its environment protect the cell from being eaten by other cells or organisms make the cell stronger andlor more rigid protect the cell from drying out anchor the cell to a surface or to another cell allow the cell to swim andlor float in water serve as an array of sensors allowing the cell to detect and react to its environment andlor allowing other cells in the environment to detect and react to it BIO 311C Spring 2009 Lecture 25 Monday 30 Mar 1 Oxidation of a Hydrocarbon Pathway 1 0H 2H O R CH CHi 4 R C CH3 hydmlySis alcohol ket ne H OH 2H R CHz CH3 4 R CHCH2 saturated unsaturated hydrocarbon hydrocarbon H OH H o o 2 O h drol sis quot R CH quot2 y y R CHz CHZOH T R CHz CH 2 OH a39 h 39 2H 1 aldehyde 2H ca39b y39c acu Pathway 2 With respect to a saturated hydrocarbon hydrocarbons with a single double bond and alcohols are 2 units more oxidized aldehydes and ketones are 4 units more oxidized carboxylic acids are 6 units more oxidized More details of some of the individual reactions of these pathways are 3 shown in the following four presentation slides Reaction 6 Unsaturation of a Saturated Hydrocarbon 2H R CHZ CH3 4 R CH CH2 saturated unsaturated hydrocarbon hydrocarbon This halfreaction could be written to show more detail as 2H unsaturation R C H 2C H 3 dehydrogenase enzyme R C H C H 2 satu rated wrung unsaturated hydrocarbon 2H hydrocarbon Reaction Hydrolysis of an Unsaturated Hydrocarbon IDH R CH CH3 alcohol Note this reaction produces R CH CH2 a secondary alcohol unsaturated hydrocarbon This reaction may be written to show more detail as H OH OH 5 hydrolysis I enz me unsaturated dehydration alcohol hydrocarbon HOH Reaction Hydrolysis of an Unsaturated Hydrocarbon R CH CH2 unsaturated hydrocarbon Note this reaction produces a primary alcohol R CHZ CHZOH alcohol This reaction may be written to show more detail as HOH hydrolysis R CHCH2 enz me R CHZ CHZOH unsaturated aesqyaratw alcohol hydrocarbon H0H Oxidation of an Alcohol Oxidation of a secondary alcohol Reaction CH 2H R CH CH3 439 R C CH3 alcohol ketone Oxidation of a primary alcohol Reaction II alcohol 2H aldehyde Oxidation of Two Sulfhydryl Functional Groups to Form a Disulfide oxidation R1sH H SR2 2H R1SSR2 Illustration 2H reduced SH T oxidized S Disulfide bonds are important for stabilizing the tertiary structures of many proteins A Redox Reaction Involving both Hydrogen Atoms and Lone Electrons alcohol H aldehyde 0 R C OH R C H H 2H1 Oxidation of an alcohol a halfreaction 2 H 2 e39 2 ferric ions 2 Fe 2 Fe Reduction of ferric ions 2 ferrous ions a halfreaction net reaction RCHZOH 2 Fe3 RCHO 2 Fe 2 H Protons are often reactants or products of metabolic redox reactions Acidication of the medium by a redox reaction T o R C OH R Clt H H 2H 1 2 H20 2 e39 2 H3O 2 H 2 Fe 2 Fe 9 RCHZOH 2 Fe3 2 H20 RCHO 2 Fe 2 H3O RX 10 Metabolic redox reactions often affect the acidity of a cell compartment Abbreviated Structure of NAD a dinucleotide that is an important hydrogenatom carrier in cells These are nitrogen bases Adenine note the positive charge on the OCH2 nitrogen base 039 O39 J J Y Y Nucleotide 1 Nucleotide 2 AMP NMP Nicotinamideadeninedinucleotide NAD Reduction of NAD Net halfreaction NAD 2H OXIdIzed NAD H2co J L 2HTgtH e39 H NADH H Reduced NAD Typical Reaction Involving the Reduction of NAD alcohol H aldehyde 0 h If t R f OH madam R cH oxidgtiZngefaacnlztlwgohol H 2H1 enzyme H H 939 NAD reduction NADH re gala5613 ISZU39 Net reaction as usually shown dehydrogenase RCHZOH NAD RCHO NADH H In practice the H product would combine with water to produce H30 NAD acts as a carrier of reducing units in living cells Example H alcohol I aldehyde 0 Reaction 1 Rg IC OH R3 CH oxidation of H 1 enzyme H an alcohol 3 NAD NADH NADH NAD Reaction 2 W reduction of a enzymez disulfide R1SSR2 RFSH R2 SH disulfide sulfhydryls NAD acquires two reducing units in Reaction 1 NADH donates two reducing units in Reaction 2 Sum of the Reactions 1 and 2 R3CH20H R1SSR2 gt R3CHO R1SH RZSH Reactions 1 and 2 from the Previous Presentation Slide Shown in a Slightly Different Way NAD if alcohol idation of alcohol aldehyde an alcohol NADH Reaction 2 reSFCtll g f a R1 S s R2 reduction of disu ide R39I SH RZ SH ISU I e NAD Reactions 1 and 2 from the Previous Presentation Slide Shown as One Continuous Process NAD alcohol mamquot 0f mom aldehyde Two separate metabollc reactlons can be shown as one continuous process when both reactions occur in one compartment and a product of one NAMJ mmmmbammwmmeMMdebn enzyme 2 8H R SH R1 3 3 R2 reduction of disu ide R1 2 NAD enz 1 enz 2 net alcohol R1SSR2 aldehyde R1SH RzSH An alcohol is oxidized and a disulfide is reduced Other Important Hydrogenatom Carriers in Cells 2H H NADP 2H gtNADPH H 2H FAD FADH2 FAD 2H FADH2 Structure of NADP Adenine V Nucleotide 1 Nucleotide 2 AMP with an extra phosphate NMP The extra phosphate on NADP allows each enzyme that catalyzes a redox reaction to distinguish NADP from NADwhich doesn t carry the extra phosphate Thus NAD and NADP can function in distinct metabolic reactions even though they may occur in the same cellular compartment and function by the same mechanism Review Components of a Typical Metabolic Reaction Substrates An enzyme Cofactors not required for all reactions In showing a metabolic reaction the name of the enzyme and any cofactors are usually written above or below the arrows Exam ple Enzyme name ABWCD Review Requirements of Metabolic Reactions Each reaction must proceed in the right direction ie the reaction must have a negative AG value in order to proceed in the forward direction Each reaction must have an available pathway for most metabolic reactions a mechanism that uses an enzyme in order to proceed at all The rate and extent of each reaction must be carefully controlled Four levels of organization of the metabolism of a living cell Individual metabolic reactions Metabolic pathways Metabolic systems thA Metabolism collectively within the cell Cellular metabolism is regulated at each of these levels of organization A metabolic system is a set of two or more metabolic pathways in a cell that have some relationship to each other Definitions A metabolic pathway is a set of sequentially connected metabolic reactions that all occur within the same compartment of a cell A quotset of sequentially connected reactionsquot is two or more reactions such that a product of the first reaction serves as a reactant of the second reaction a product of the second reaction serves as a reactant of the third reaction etc Two sequentially connected reactions that occur in the same compartment are said to be coupled together Thus a metabolic pathway consists of a series of coupled reactions A enzyme1 B Example B is a product on one reaction and a reactant of the other B enzymeZ C BIO 311C Spring 2009 Lecture 12 Wednesday 18 Feb Some General Functions of Water in Cells It is a solvent for most biological molecules It is a powerful orienting force for those molecules and parts of molecules that don39t dissolve in it It provides a medium for effective intracellular movement of molecules and cell components It provides an appropriate environment for the chemical reactions that occur in cells metabolic reactions lt participates directly as a reactant or product in many metabolic reactions It is a source and sink for H3O and OH39 ions These ions also participate in many biological reactions and they stabilize the 3dimensional shapes of many biological molecules It provides stability in a constantly changing environment Inorganic Ions of Importance in Living Cells Some inorganic ions that occur at high concentrations in cells Mg2 K H2P04IHPO42 Some inorganic ions that occur at low concentrations in cells Ca2 Na H3O OH39 Fe2lFe3 Cations often neutralize anions on the surfaces of biological membranes and macromolecules iva ent ca ians especia y Mg often serve as gawk br dges wi chin a Mama awe M c e a m U C m 0 m m b O m n e e m e b V 0 Inorganic phosphate serves as a good buffer in cellular compartments that are maintained at pH values between 6 and 8 OH from H20 039 pH lt6 pH gt8 At 10393 M concentration inorganic phosphate is present in the cytosol at a higher concentration than are most other inorganic ions Iron Fe2 is a component of the blood protein hemoglobin lt binds covalently to 02 thus transporting oxygen throughout the body From Textbook Fig 521 p 83 Some general Functions Performed by Inorganic Ions in Cells They balance electrical charges on biological molecules thereby stabilizing their structures especially K and Mg They serve as structural components by acting as an electrical bridge between two charged functional groups within a single molecule or else between two separate molecules primarily Mg2 They help buffer cell components at desired pH values especially phosphate They bond covalently electrovalently or in other ways to some biological molecules eg Fe2 They act as coenzymes cooperating with enzymes in many enzyme catalyzed reactions especially Mgz They participate directly in reductionoxidation reactions especially Fe2IFe3 and CulCu2 Their concentration in cells is carefully regulated in order to regulate the rates of major metabolic processes especially Ca2 Each living cell contains thousands of different kinds of organic molecules biomolecules Nearly all of them are synthesized within the cell by the cell Some Questions of Profound Importance in Cell Biology How do cells make so many different kinds of specific biomolecules How do cells make each kind of biomolecule at just the right time How do cells make just the right amount of each kind of biomolecule How do cells place each kind of biomolecule in just the right location How do cells keep each kind of biomolecule for just the right length of time before eliminating it A very general way to identify an organic molecule is to indicate the number of carbon atoms it contains For example an organic molecule containing a total of 7 carbon atoms could be described as a C7 molecule This designation by itself tells almost nothing about the chemical physical or biological properties of the molecule and doesn t even indicate which functional groups are present But it is still sometimes useful Example from the to Exam 1 H S A C5 molecule I H H C H H Th I t I I eco ors are no HCC0CC Significant for this I H illustration H o Definition A carbohydrate is a simple sugar a modified sugar or a polymer of a sugar Thus in order to understand carbohydrates it is necessary to understand sugars Description of a simple sugar A simple sugar consists of a chain usually unbranched with 3 7 carbon atoms with the following characteristics 1 One of the carbon atoms occurs as an aldehyde or else a ketone functional group 2 Each of the other carbon atoms occurs as an alcohol functional group 3 Hydrogen atoms are attached to all other positions on the carbon atoms in order to satisfy their covalencies aldehyde ketone representation functional group functional group 0 standard R C R1 C Rz representation H O o more descriptive CC C CC H The carbon atom that forms the aldehyde or ketone functional group must also be covalently bonded to another carbon atom or to a hydrogen atom Aldehyde and ketone functional groups are very similar to each other in their chemical properties and in their biological functions Structural Formula of a 6carbon Sugar formula with all an acceptable slightly abbreviated structure covalent bonds shown with not all covalent bonds shown H c o H HOH H o c H HO39CH H OH HCOH H c o H H0H H 0H CHZOH IL Dglucose It is standard practice to show a sugar with the carbon atoms oriented vertically and with the aldehyde or ketone functional group at or near to the top of the molecule Formulas that represent sugars C3H03 chemical formula I3 H H c o c o H H H structural formula A 3carbon sugar also called a C3 sugar C6H1206 chemical formula structural formula A 6carbon sugar also called a C6 sugar note that C H and 0 occur in a 121 ratio CnHZnOn or CHZOn in sugars The name carbohydrate indicates quotcarbon waterquot suggested by the ratios of the atoms that occur in sugars Chemical formulas are generally not sufficient to represent the chemical nature of sugars Example Two compounds each with the chemical formula C3H603 but with very different structural formulas and even different functional groups aldehyde H H 0 o o carboxyllc acud c functional group C functional group H I H alcohol lt HCo alCOhOI HCo functional group functional groups I Hco H C H I methyl H I functional group H H a C3 sugar a C3 compound that is not a su ar C3H603 g C3H03 Carbon atoms of sugars are numbered from the top down I I I I a I I I I 5 0 ID 3 I JlJ Ntlg z m f w 1 quot0 I J o I I I 0 I lt2 Generic names of sugars 1 indicate the number of carbon atoms in the sugar 2 indicate whether the sugar contains an aldehyde or a ketone functional group 3 indicate that it is a carbohydrate by giving it a suffix of quotosequot i HISOH C0 I H 0 HOiI H C H Cf39O H H C OH HOH CHZOH HCOH IL A Idehgde sugartaldosa car on sugar nose A ketone suQar ketose A more complete name is aldotriose A 6carbon sugar hexose A more complete name is ketohexose BIO 311C Spring 2009 Lecture 15 Wednesday 25 Feb Review Lipids are biological molecules that 1 are not water soluble ie they are hydrophobic and 2 do not fit into any other major category of biological molecules Nonpolar lipids are typically mostly carbon and hydrogen atoms They do not contain a high proportion of oxygen or nitrogen atoms Polar lipids generally contain a high proportion of oxygen andor nitrogen atoms At least one end of the molecule is hydrophilic although the hydrpphobic portion keeps it from dissolving in aqueous solutions In this course we distinguish several rather similar terms polar covalent bond polar bond polar bonding polar molecule polar lipid Formation of a triglyceride from a glycerol and three fatty acids In three separate dehydration reactions H C OH HlOH glycerol 3 fatty acids H Z OH l Three glyceride bonds formed Seegigggtlon 3 H20 H H L OSC H c o c triglyceride 3 H20 H T o c H A kind of reaction that is important in cells deh dration reaction acid alcohol y ester H20 diglyceride phosphate dehydration reaction H20 H kiwi cg phosphatIdIc acrd H20 H C O C a H C O T OH l o acid alcohol dehydratlon rx39 ester water phosphatidic acid contains 3 ester bonds two carboxylic acid ester bonds and one phosphate ester bond phosphatidic acid is a polar lipid phosphatidic acid R polar dehydration reaction phospholipid H20 Phospholipids are very polar lipids H phosphodiester bond The Steroid Ring Structure Each line represents a single covalent bond between two carbon atoms Each point where two or more lines intersect represent a carbon atom There are sufficient hydrogen or other atoms attached to each carbon atom to satisfy the covalency of each carbon atom Abbreviated Structure of Cholesterol HO Cholesterol is a nonpolar lipid although the alcohol functional group gives it slight polarity and is very important for its functions lsoprene units Very abbreviated structure where carbon atoms represent ends of straight lines structure showing all atoms but not all covalent bonds lsoprene units are C5 hydrocarbon portions of molecules with the chemical structure shown here Some General Functions Performed by Lipids in Cells They are a major form of stored energy in cells especially as triglycerides They are a major component of biological membranes especially phospholipids and steroids Some hormones are lipids usually modified fatty acids and some steroids Many plant quotnatural productsquot are lipids isoprenoid lipids Illustration of a Polypeptide amino acids peptide bonds Polypeptide chain Folding and other modifications g F r E E a E E a E Ell 5quot a 3 E g 3 3 3 IE E 3 a E 3 iii 2 a h E a i 2 3 5 illq a A quotH m E a g r 392 E m in E E 1quot quot 39 m u i 539 E E 339 5i If E E Functional Protein Structural Formula of an Amino Acid H A single amino acid that is not chemically attached to anything else is called a quotfree amino acidquot HaN IC COO R central carbon atom Characteristics of Free Amino Acids A central carbon atom is attached to four chemical groups The central carbon is an asymmetric carbon atom unless R is identical to one of the other three chemical groups Both the amino and the carboxylic acid functional group are ionized except at extreme pH values Ways of Showing the Structural Formula of an Amino Acid H T o N C H I cOH R H H Detailed structure H H2N C COOH R H3N C COO Abbreviated Structure Uncharged form does not occur in aqueous solutions at neutral pH Charged form that occurs in aqueous solutions at near neutral pH Amino Acids Used to Construct Proteins central carbon atom H Twenty different kinds of amino acids are C COO used for constructing proteins each with a different quotRquot group Since the central carbon atom of an amino acid is asymmetrical there are 2 enantiomers of each kind of amino acid Cells use only the quotLquot enantiomer of each kind of amino acid to construct proteins The Rgroup of a few kinds of amino acids carry an amino or a carboxylic acid functional group These free amino acids carry three electrical charges Aspartic Acid shown without its functional groups ionized H H I 0 HgtN lt cltOH 7H2 0 CltOH How many electric charges would this free amino acid have in the cytoplasmic matrix of a living cell How many asymmetric carbon atoms does this free amino acid contain Glycine shown without its functional groups ionized H l HN clz cltOH H How many electric charges would this free amino acid have in the cytoplasmic matrix of a living cell How many asymmetric carbon atoms does this free amino acid contain Formation of a Peptide Bond from Two Amino Acids These atoms are lost as a molecule of water during the formation of a peptide bond H These atoms are covalently bonded together during formation of a peptide band In general R1 and R2 will not be the same chemical structures Dipeptide Formation From Two Amino Acids O 0 H HN2C H H o R1 coo39 aa1 aaz 1 U N dehydration reaction dipeptide H20 Atoms of peptide bond A Peptide Bond Between Two Amino Acids A peptide bond between two amino acids consists of O the four atoms shown at right All 6 atoms shaded in grey above lie in the same rigid plane with the C N doublebonded oxygen projecting in the opposite I direction as the hydrogen atom that is bonded to the H nitrogen atom The carboxylic acid and amino functional groups can no longer ionize after they have become incorporated into a peptide bond Oligopeptides and Polypeptides Dipeptide Two amino acids covalently bonded together by a peptide bOnd Tripeptide Three amino acids covalently bonded Oligopeptide together by two peptide bonds 3 20 amino acids covalently bonded Tetrapeptide Four amino acids covalently bonded together by peptide together by three peptide bonds bonds i Polypeptide also called a polypeptide chain More than twenty amino acids covalently bonded together by peptide bonds BIO 311C Spring 2009 Lecture 36 Monday 27 Apr 1 Textbook Fig 167 Overview Origin of replication Lagging strand P 317 Lea ing strand Leading strand Overall directions Singlestrand of replication binding protein Hell 856 Leading strand Lagging strand DNA pol I DNA pol 111 DNA ligase N 991 M 7 l l I u39L39ir39 4 Fl 4 11qu 339 ELJD LJ Also be familiar with information in Table 161 p317 14a The length of eukaryotic DNA decreases with each round or replication End at parental Leading strand DNA strands rPLagging silent Pol I doesn t Lasl lragmenl Previous fragment Work here r r Removal cl primers and replacement with DNA where a 339 end is available lur DNA pelymemse Second round of replicalion 5 3 Further unds m replicatlon halter and shorter daughter molecules Textbook Fig 1619 p 319 O A sequence of nucleotides at each end of each molecule of eukaryotic nuclear DNA is called a telomere The telomere DNA does not contain code for useful genetic information Each time the DNA replicates the new polynucleotide chains ge somewhat shorter at each end thus decreasing the length of the telomere After replicating many times the telomere is completely lost Subsequent replications then begin to lose useful genetic information at the ends of the DNA eventually causing the cell to die Many kinds of eukaryotic cells can only replicate a certain number of times before they die perhaps due to the loss oftelomeres DNA Proofreading During Replication rim Dramnsohhcv phcanon mxvml xlmmamalelyexd rhemmvrcnlmxa The gure illustrates a replication fork with red lines representing nucleotides of the new growing polynucleotide chains um polymerase and thermal basaand yephmuml proceeds r 39 39 39 inserting new growing 39 chain L 39 a 39 39 approximately1 in 105 nucleotides inserted is incorrect DNA polymerase is actually part of a larger aggregation of proteins called a replic tion complex A si e on this comp ex is able to detect that an incorrect nucleotIde has been inserted and remove the incorrectly inserted nucleotide The replication complex then inserts the correct nucleotide A mechanism for repair of damaged DNA Damaged DNA I nuclease m 7 l L DNA polymerase W DNA I39Jl w r Hgase From Textbook Fig 1618 P 318 Although DNA is replicated almost perfectly on rare occasion an incorrect base is inserted Also DNA is occasionally damaged after it is synthesized Cells have elaborate repair mechanisms for correcting various kinds of errors Damagedetecting proteins scan the DNA for errors then recruit repair enzymes to sites of damage The example shown here nucleoside excision repair of damage due to the fusion of two adjacent thymine bases is only one of many kinds of repair mechanisms DNA as a Series of Functional Units A molecule of DNA can be thought of as a linear sequence of thousands of specific functional units functional unit interspersed with stretches of DNA with no known of DNA function Individual functional units vary in length l from just a few nucleotidepairs to many thousands of nucleotidepairs The character of each functional unit is determined by the sequence of its nucleotides These units of function are called genes when their function is known Genes along a molecule of DNA can be divided into three main categories a structural genes whose information content is used to synthesize RNA during transcription 039 regulatory genes whose function is to control the rate of transcription O genes that are not directly involved in transcription Some stretches of DNA have no know function and are often called junk DNA That is almost certainly a misleading term Structural and Regulatory Genes proteincoding structural gene regulatory nonproteincoding gene structural gene DNA transcription f m RNA used as an g RNA used as information a StruCtural molecule molecu e translation protein A structural gene is a gene whose information content is used to synthesize a complementary molecule of RNA during transcription ie It generates a product The term quotstructural moleculequot means something different than does quotstructural genequot A structural molecule in a cell is a molecule that is a component of some structure within the cell Illustration of Information Flow in Prokaryotic and Eukaryotic Cells prokaryotic cell 39 1 I wmscalmnm I M fv39 I mm Ribasamn wmmnm J x K Palypepride All information ow in prokaryotic cells occurs in the cytoplasmic matrix Relatively little processing of information molecules occurs in prokaryotic cells Information flow and processing in eukaryotic cells is partitioned between the nucleoplasm and the cytoplasmic matrix Additional systems of information ow in eukaryotes occur within the matrix of mitochondria and in the stroma of plastids not shown in these illustrations Th organellar systems of information flow are very similar to information ow systems in prokaryotic cells Textbook Fig 173 p 329 eukaryotic cell Nuclear envolono 39 39 fl quotfai s i ima 1W JVV 4 PmmRNA RNA PROCESSING W N r W Rlbusome I TRANSLATION x v quot Pulypeplldr Flow of Information in Cells information read in the 339 gt 539 direction The strand of DNA that is transcribed is called the template strand or more commonly the pigs strand or still more commonly the sense strand From textbook Fig 174 p 329 Strand of DNA containing coded 5 Strand of mRNA containing coded information written from DNA and read to polypeptide chain in the 539 gt 339 direction The three nucleotide units of RNA are called codons Polypeptide chain written from RNA starting from the amino carboxyllc terminal end aminoK 1 004 7 39 J acid end end Use of the Genetic Code 339 portion of a molecule of mRNA codon 1 codon 2 codon 3 00010quot 4 Second mRNA hm Key to the genetic code c I A G Use of the genetic code makes it possible to determine the sequence of amino acids in a polypeptide chain by knowing the sequence of nucleotides in a molecule of mRNA codon 1 codes for the amino acid quottrpquot Can you use the code to determine the amino acids generated by codons 2 3 and 4 First mRNA base 539 end Third mRNA base 339 end Textbook Fig 175 p 330 By knowing the information content of a portion of any one information molecule it is possible to deduce the information content of the corresponding portion of any of the other information molecules 539 339 minusstrand I C A A G C T A C T DNA 339 539 plusstrand l l l l l l l l l G T T C G A T G A 539 339 mRNA C A A G C U A C U Vhcodon N jr39gn len Na W 933quot polypeptide chain In order to deduce the information content of all other information molecules corresponding to the content of any one molecule it is necessary to know a the genetic code b the nucleotide basepairing rules Often when the sequence of a gene that codes for a protein is presented only the sequence of the minus strand is displayed shown lefttoright from the 539 end to the 339 end of the gene That sequence corresponds to the sequence of nucleotides in transcribed RNA only with T substituted for U unit of coded information Example 39 39 DNA 5 3939393939 u C T A T T A G A C 3939393939 u 3 minus strand seCIuence plus strand not shown RNA synthesized 5 CUAUUAGAC 3 from plusstrand Can you deduce the amino acid sequence that would be derived from this minus strand sequence of nucleotides if this region of DNA codes for a portion of a polypeptide chain Methods are currently available to determine the sequences of large expanses of DNA form any organism in a very short time The complete DNA sequences of many organisms including humans have been determined Proteins are the central molecules of cell and by extension organism functions Thus it appears that it might be possible to determine functions of a cell simply by knowing the DNA content of the cell Since all body cells of a living organism contain the same content of DNA it appears that it might be possible to know the functions of an entire living organism by knowing the DNA content of any one of its cells Yet only a small proportion of cell functions and an even smaller proportion of wholeorganism functions have been accurately predicted by DNA sequences alone Illustration of a transcription unit within a DNA polynucleotide chain 539 339 strand 3 A Ir DNA 539 strand transcr39pr39on transcription start pomt stop point transcription unit quotupstreamquot of quotdownstreamquot of transcription unit transcription unit direction of transcription A transcription unit is a stretch of nucleotides in a molecule of DNA that is used as a template to produce a molecule of RNA with a complementary sequence of nucleotides Most transcription units are somewhere between a few hundred and a few thousand nucleotides long Requirements for the Start of Transcription RNA polymerase DNA 339 strand A i 539 strand promoter transcription unit The enzyme that catalyzes the synthesis of a new molecule of RNA from a DNA template is called RNA polymerase A specific sequence of DNA immediately upstream of the transcription unit on the strand of DNA is called a promoter The promoters for most transcription units are a few dozen nucleotides long RNA polymerase a large enzymatic protein must bind to this site before transcription can begin Note The transcription unit is a structural gene while the promoter is a regulatory gene Regulation of Transcription RNA transcription unit promoter polymerase 539 I DNA 339 strand 539 strand operon Inducer OI39 repressor A unit of regulated synthesis of RNA includes a promoter and a transcription unit of DNA In prokaryotes this entire unit is called an operon In eukaryotes other proteins called transcription factors also bind to the promoter site and influence the ability of RNA polymerase to bind to the promoter site and begin to synthesize RNA Still other proteins in eukaryotes can influence the effectiveness of RNA polymerase in less direct ways in order to serve as transcription inducers or repressors They enhance or suppress respectively the function of RNA polymerase BIO 311C Spring 2009 Graded exams will be returned during discussion periods today and tomorrow A Key to Exam 1 will be placed on the course web site on Wednesday If you believe your Exam 1 has been scored inaccurately take your exam to Jingjie and explain your concern to her on or before this Friday Feb 20 If you still have a concern then please see me We will not consider any changes after noon on Monday Feb 23 The average for Exam 1 was 72 The high grade was 94 Approximately 13 of the class received a grade higher than 80 Lecture 11 Monday 16 Feb Review amp Summary Reversible Ionization of Water Ionization H20 H20 L H3O OH39 Deionization Note reversible arrows for the reaction show that the reaction goes in both directions A longer arrow pointing toward H20 shows that at equilibrium there is more H20 than H3O or OH39 ln pure water at any instant of time H3O OH39 1 X 10397 M Definition pH log10 H30quotmolalr Thus in pure water pH log10 1 x 107 70 Review Deprotonation of a Phosphate in Water 0 fl fl 39 de rotonation RolloH de rotonation Rolo P ROTo 0 o O H H H proton transfer H proton transfer H 0 H20 protonation H30 H20 protonation 3 net half reaction reversible Note the acceptance of protons by water is not shown H H R o 439 R 0 4 R l abbreviated structures The name of an ionizable functional group is slightly different depending on its ionization state The ionized and nonionized forms of functional groups have very different chemical properties R C ONH carboxylic acid carboxylate H H R N R NH amine H ammonium ion 0 H H II R O P O R O IID O R0Po o O O H h I llIt phosphate p osp a e phosphoric acud monobasic dibasic DefWhen one or more substances is dissolved in water the result is an aqueous solution A teaspoon of sugar dissolved in a glass of water produces an aqueous soln The cytoplasmic matrix of cells is an aqueous soln Although the pH of pure water is 70 some substances change the pH when they are dissolved in water 0 deprotonation of 0 Example When a molecule with R Clt W R Cf carboxylic acid functional group is 0H 039 dissolved in water the resulting aqueous H Proton transfer solution has an increased concentration of H3O This can be expressed as a H20 H30 protonation decrease in the pH of the solution of water Def An aqueous solution with a pH of or very near to 7 is said to be neutral An aqueous solution with a pH lower than 7 is said to be acidic An aqueous solution with a pH higher than 7 is said to be alkaline or basic Question If a molecule containing an ionizable functional group is placed into an aqueous solution then what will be the ionization state of the functional group Answer It depends on the pH of the environment of the functional group neljtral pH 2 lt acidic pHggm basic gt pH 12 acidic pH 5 ne ltral pH and basic pH RCOOH RCOO39 Carboxylic acid Carboxylate ion acidic pH and neutra pH f basic pH RNH3 R39NHz Ammonium ion Amine acidic pH fl basic pH R O P O39 RO p 039 Phosphate 0H Phosphate 0 ion ion Not all compartments in a living cell are at the same pH value Textbook Fig 69 The Mitochondrial matrix p 100 is at a alkaline H 8 The cytoplasmic matrix and most compartments are near Lysosomes neutral pH 74 are at an acidic pH 2 Effect of pH of a Cellular Compartment on the Ionization State of a Carboxyl Functional Group Carboxylic acid acidic compartment of a cell such as a lysosome R C O Carboxylate ion neutral or basic compartment of a cell such as the cytoplasmic matrix Effect of pH of a Cellular Compartment on the Ionization State of an Amine Functional Group H R NH H ammonium ion acidic or neutral compartment of a cell such as the cytoplasmic matrix basic compartment of a cell such at the matrix of a mitochondrion Effect of pH of a Cellular Compartment on the Ionization State of a phosphate Functional Group 0 ll R O T O39 O H monobasic phosphate acidic compartment of a cell Note in a very acidic environment more acidic than shown R O P O39 dibasic phosphate neutral compartment of a cell w basic compartment of a cell here phosphate would not carry any net negative charge and should be called phosphoric acid Many Biological molecules have positive and negative charges simultaneously Consider a molecule in the cytoplasmic matrix of a cell pH 7 that contains three ionizable functional groups C C 039 039 H H quot39NH lt 39 quot39NH H H 0 O ll F o o H a 0 Note This molecule would have 3 electric charges about half of the time and 4 electric charges about half of the time Effects of Adding Molecules with an Ionizable Functional Group to a Compartment of a Cell If only one or a very few molecules with an ionizable functional group are placed into a compartment of a cell then the pH the relative amounts of H3O and OH39 of the compartment will determine the ionization state of the functional group If a large number of molecules with an ionizable functional group are placed into a compartment of a cell large enough to make its concentration of the functional group as high or higher than the concentration of H3O or CH then the pH of the compartment will be affected by the ionization state of the functional group Definitions Buffer an agent that prevents or retards a change in the state of a chemical or physical system Chemical Buffer a chemical substance agent resists a change in concentration of some other chemical substance in a solution pH Buffer A chemical buffer that resists a change in the concentration of H3O in an aqueous solution note In molecular biology quotbufferquot always means quotpH buffer unless stated otherwise note quotThe concentration of H30 quot is sometimes written in more abbreviated form as quotthe concentration of H quot or as H note in order to act as an effective pH buffer the concentration of the functional group must be as high or higher than the concentration of H30 or 0H Ionizable functional groups serve as buffers at pH values near where they are half in one ionization state and half in another ionization state Examples neutral basic 8 pH 12 pH 2 lt acidic pH 7 pH 4 acidic pH 5 neutral pH and basic pH RCOOH RCOO39 a Carboxylate ion Carboxylic acid pH 9 acidic pH and neutral p 3 basic pH R NH2 RNH3 n Ammonium ion Amine pH 7 acidic pH 0 basic pH R O P O39 R O P O39 Phosphate 0H f Phosphate 0 39 ion IOn A population of ionizable functional groups can serve as a buffer at pH values near where half are in one ionization state and half in another ionization state Example Typical carboxylic acid O 1 R C 2 o H solution at a pH of 30 O 12 R cf O Definition Consider a population of identical organic molecules with an ionizable functional group at a specific location on the molecule The pK value for that functional group is the pH at which at any instant of time the functional group on half of the molecules is in one ionization state and in the other half of the molecules is in the other ionization state The carboxylic acid functional group shown here has a pK value of 30 It could serve as an effective buffer at pH values ranging from 2 to 4 The exact pK value of a specific functional group dependents on the nature of the Rgroup to which it is attached o 12 R1c OH ThIs carboxyllc acrd With a pK value of rt H 25 would serve as a good buffer in any compa men compartment with a pH somewhere 0 pH 25 1 between approxrmately 15 35 2 R1 Co 1 R c 3 2 2 o ThlS carboxyllc acrd wrth a pK value of H 55 would serve as a good buffer in any compilrggent 2 compartment with a pH somewhere 0 p 39 between approximately 45 65 1 2 R2 Co The effectiveness of a functional group as a pH buffer depends on 1 the pK value of the functional group and 2 the pH of compartment within which it resides Inorganic and organic phosphates serve as good buffers at near neutral pH values Example Typical organic phosphate H solution at a pH of 70 Phosphate functional groups serve as good buffers in the cytoplasmic matrix and in most other compartments of cells Electrovalent Ionic Bonding of an Organic Ammonium Ion to a Negatively Charged Surface electrovalent bond negatively charged 39 surface 39 BIO 311C Spring 2009 Lecture 23 Wednesday 25 Mar 1 Consider the formation of ADP NH2 NH2 N N i r lt N o o lt N 39O E OH HO E O H2 N ll N OH OH OH OH ACICI anhydrIde bond formation Dehydration rx AMP Pi ADP H20 A 30 kJmole The formation of a acid anhydride bond from two phosphoric acid functional groups in a dehydration reaction under standard conditions requires an input of approximately 30 lemole of energy twice the amount of energy that is required in the formation of an ester bond The formation of ATP from ADP Pi also requires approx 30 lemole of energy under standard conditions Now consider some hydrolysis reactions the reverse of dehydration reactions 1 Glu6 Hzowelu pl AG 14kJmole 2 AMP H20 M i A pi AG 15kJmole 3 ADP H20 i f i mmp Pl AG 3o kJmole 4 ATP H20 y i39 sis ADP Pi AG 30 lemole 5 ATP H20 V imlsi AMP A 3o kJmole 6 H20 M AMP 2 PI AG 30 kJmole Hydrolysis of an acid anhydride bond releases about twice as much energy as does the hydrolysis of an ester bond Hydrolyses of each of the acid anhydride bonds of ATP releases about twice as much energy as does hydrolyses of the ester bond O CH2 NH2 ltN 2 J J J O OH OH acid anhydride bonds ester quothighenergyquot bonds bond The Energy Currency of Cells Reactions which release more than approximately 20 lemole of energy produce a large enough amount of energy that some of the energy released during the reaction may be captured to perform useful work in a cell The reverse of these reactions requires special mechanisms since they require the input of over 20 lemole of energy ATP is sometimes called the quotenergy currencyquot of cells since its hydrolysis to ADP or AMP is used extensively to provide energy for cellular processes NH NH2 lg NIK ReVIew N N H20 N N o cnz ltN M N o cu ltN w quotJ Pi A 30 lemole 0 0 OH OH OH OH NH NH2 N N Gquot lt36 N N o cuz ltN M oicuz N W J AG 30 lemole 0 0 OH OH 0H 0H L avg 07m2 OH OH NH2 NH2 lt55quot 6quot oiCH N N N mquot Pi AG 15kJmoe D HO CHZ 0 OH OH OH OH H20 494 2 Pi AG 30 lemole A 30 lemole NH NH lt quot2 lt N o 10 Practice Problems Suppose a large number of molecules X are placed into solution and a pathway exists to convert X into Y The reaction is allowed to come to equilibrium under standard conditions after which there are 1000 times as many molecules Y as molecules X in the solutions Then What is Keq for the reaction X Y What is Keq for the reaction Y X What is AG for the reaction X Y Is the reaction XY endergonic or exergonic mungm What is the AG for the reaction xY when a steadystate equal concentration of X and Y are maintained as the reaction proceeds f What is the AG for the reactiOn XltY if other reactions are coupled to the reaction to maintain 10000 times higher concentration of Y than X as the reaction proceeds 12 Consider the reaction hydrolysis glu6P H20 7 glu Pi AG z 14 lemole Do the following experiment Place 1 mole of glu6P into a glass of water and stir it to fully dissolve Then leave the solution set under a standard set of conditions and wait for the reaction to proceed According to the value of AG the equilibrium constant for this reaction is 428 so when the reaction comes to equilibrium there should be over 400 times as much glucose and inorganic phosphate present as there is glucose6P To determine K eq recall that A 57 kJmole log10 Keq 13 dissolve glu into water wait for equilibrium amounts of glu and Pi to be produced Even after several weeks the glucose6phosphate concentration remains virtually unchanged and almost no glucose or inorganic phosphate appear in the container of water Why Answer Because the reaction has no pathway to proceed and still hasn39t reached equilibrium 14 glu6P H20 Tgt9u Pi This reaction cannot proceed in either direction because no pathway ie no mechanism exists Energetic changes during progress of the reaction glu6P H20 glu Pi 4 high energy intermediate glu Pi glu6P AG G 2 G 1 14 kJmol 4 Progress of the reaction gt Most reactions involving making and breaking covalent bonds do not occur at normal temperatures without the aid of an appropriate catalyst because the substrates cannot obtain enough energy to overcome the energy barrier of the reaction Most metabolic reactions involve breaking two covalent bonds and forming two new covalent bonds Generic example A BC D Specific example glu H OH 1 QIU H IquotD F39i Another way of writing this specific example glu 939quot gt I H H OH H stable molecules stable molecules relatively low energy relatively low energy 939quot G H OH Hypothetical intermediate unstable molecules 15 high energy The addition of a catalyst to a chemical reaction changes the energy of activation but not the AG of the reaction ie Catalysts change the kinetics but not the overall energetics of the reaction Enzymes are catalysts Example glu6P H20 Tgt glu Pi glu6P 939 quot39 Pi no catalyst A with catalyst O G 1 AG 14 kJImDI O G 2 4 Progress of the reaction gt 18 Comparison of the Mechanism of the Same Reaction When Catalyzed by an Enzyme or Not Catalyzed glu H OH 1 glU H Example glu glu 939quot not l catalyzed H OH H OH H OH stable very unstable stable relatively low energy high energy relatively low energy Catalyzed by the glu glu glu enz me called T y H H glucose6 h t t bl phosphatase stable 5 meW a Uquot5 a e stable relatively low energy only Sl39ght39y relat39Ve39y IOW enerQY higher energy old bonds partially broken new bonds partially formed tranSition State Differences in transitionstate intermediates depending on whether or not a reaction is catalyzed by an enzyme A B C D AC B D From textbook Fig 815 p 152 reaction without an me zy E A WIth enzyme is iower Heactants Course of reaction with enzyme AG is unaffected V Products gt m x a r n O n I I1 Progress of the reaction gt Components of an Enzyme Catalyzed Reaction Reactants Can be written as Enzyme Reactants Prod ucts Cofactors A cofactor is a portion of the enzyme other than polypeptide chains The polypeptide chains portion of an enzyme is called an apoenzyme Some cofactors are tightly bound to an apoenzyme as a prosthetic group other cofactors are loosely bound and easily removed from an enzyme and are called coenzymes Many but not all enzymecatalyzed reactions require a cofactor The enzyme and cofactors are the same at the end of the reaction as they were at the beginning of the reaction although they may be transiently altered while the reaction is in progress Some Unique Aspects of Enzymes as Catalysts 1 They are proteins All are globular Many are conjugated Some are monomeric others are oligomeric 2 Each one is very specific for the substrates it recognizes and acts on for the functional groups it modifies or moves for the kind of reaction it catalyzes 3 They function in a rather narrow environmental range at a narrow temperature range at a narrow pH range 4 Some are regulatory and are subject to sensitive control of their rate of catalysis 5 Some are able to couple two reactions together Illustration of a substrate aligned in its active site of an enzyme Proper alignment Improper alignment all functional groups functional groups fit correctly don39t fit correctly Effect pH on an Enzyme mo nega ve charges denatured active site active site acidic pH neutral or basic pH Shape of enzyme is altered by electrical repulsion between adjacent functional groups BIO 311C Spring 2009 Lecture 28 Monday 6 Apr 1 Some Alternative Possible Fates of the Pyruvate Generated During Glycolysis food 2ATP 2NADH t39 ucose j 2 r 39e i39t l fquot fermentation g glycolysis 39 py products respiration products Pyruvate may serve a a food source for making bigger and more complex molecules using anabolic pathways Pyruvate may be reduced by fermentation in one of more reactions that regenerate NAD from NADH Pyruvate may serve as a fuel by continuing respiration using catabolic pathways 2 An Example of Pyruvate Used as a Food Building Material NH o 4 2H c c3 l o l 039 co H NCH pmnem synthesis to I 3 I protein CH3 CH3 H20 ala pyruvate nine an amino acid Comparison of Chemical Equations for Fermentation and Glycolysis Fermentation written as a single equation 2 ADP Pi 2 ATP H20 I final 9 ucose products Glycolysis written as a single equation 2 ADP Pi 2 ATP H20 final glucose products 2 pyr 2 NAD 2 NADH W The equations for fermentation and glycolysis look similar except that in fermentation no hydrogen atoms are released ie there is no net oxidation of substrate 4 Definition Fermentation An extended metabolic pathway that includes glycolysis plus one or more additional metabolic reaction that results in the chemical reduction of pyruvate or a substrate derived from it GI col sis ZATP y y 2 NADH reduced oxidized glucose glycolysis 2 pyr Extending Reactions oxidized reduced 2 pyr additiontabollc reactions fermentation product 2 NADH Fermentation shown as a single metabolic pathway 2 ATP 2 NADH fermentation 2 Pquot 2 0f products glucose extending rx glycolysis The final fermentation product is often excreted from cells as waste Question Is fermentation a catabolic process or is it an anabolic process Lactate Fermentation temporary storage or excretion as waste 2 ATP 2 NADH glucose 2 pyr p 2 lactate yr reduction a single reaction glycolysis Lactate fermentation occurs in muscle cells when they cannot get enough oxygen to do complete respiration The Final Reaction in Lactate Fermentation o O C o Co co lactate dehydrogequotase Hc OH CH3 H3 lactate pyruvate N ADH H NAD Note we would multiply this chemical equation by two in order to show the number of lactate molecules generated from one molecule of glucose Some Details of Ethanolic Fermentation excreted as waste 2NADH 2 ATP glucose glycolysis 2 per 2 C2 2 CH3CH20H ethyl alcohol 2 C02 excreted as waste Ethanolic fermentation includes two metabolic reactions in addition to glycolysis Balanced equation of ethanolic fermentation glucose 2 ADP Pi gt2 ethanol 2 CO2 2 ATP H20 Abbreviated Equation of Ethanolic Fermentation 2 ATP 939quot Ethanolic fermentation Ethanolic fermentation occurs in many kinds of cells during times that they are deprived of oxygen It occurs in some kinds of yeast even in the presence of oxygen Note In fermentation all products of glucose metabolism may be discarded except ATP 10 By far the most common fate of products of glycolysis in most kinds of cells is to proceed through respiration In eukaryotic cells the remainder of respiration takes place in mitochondria Cytoplasmic matrix I col sis glucose gy y 2 pyr to mitochondrial matrix 2 ATP 2 NADH to use for cellular metabolism Both pyruvate and NADH bind to mitochondrial transmembrane proteins and are transported across the membranes by active transport 11 The fate of the pyruvate produced during glycolysis is determined by the relative activities of various allosteric proteins that can act on pyruvate regulation by biosynthetic allosteric enzymed PrOduct bind to mitochondria glycolysis t transmembrane glucose 39 pyruva 6 transport protein 016 01 fermentation product 12 Pyruvate is metabolized in a metabolic enzyme called pyruvate dehydrogenase 20f waste to atmosphere 2 2 602 IOH pyruvate III dehydrogenase i0 2 of C CH3 Pyr 2 NAD 2 NADH H Acetyl COA Pyruvate dehydrogenase is actually a cluster of several enzymes bound together and acting as a unit in the mitochondrial matrix Thus it may be thought of as a metabolic pathway rather than a single metabolic reaction Abbreviated illustration of the Pyr dehydrogenase pathway 20f 2002 P rdeh dro enasej 2 of c3 k1 r 20f C2 2 of NADH CoA can be described as a C2 carrier molecule Its full name is Coenzyme A Would the pyruvate dehydrogenase pathway best be described as anabolic or catabolic Balanced equation of pyr dehydrogenase 2 Pyr CoA NAD gt 2 CZCOA 002 NADH H All substrates are multiplied by 2 when considering the number of substrates generated from one glucose molecule since during 15 glycolysis each glucose produces two pyruvates The Citric Acid Cycle also called the TCA Cycle and the Krebs Cycle Showing Important Products waste to atmosphere 2 of 2 ATP Krebs Cycle j 6 of NADH 2 of FADH2 Is the Krebs cycle a catabolic pathway or is it an anabolic pathway Balanced equation of the TCA cycle 2C2CoA 3 NAD FAD ADP Pi Webs C C 9 2CoA 2 CO2 3 NADH H FADH2 ATP H20 17 An Overview of pyr dehydrogenase and the TCA Cycle Fyruvm Textbook Fig 911 p 170 iron glycolysis 2 molecules Derglucnse 000 O 202 quotAV r CoA quot39 Amyl Gun 00 CoA The number of each substrate shown must be multiplied by 2 in order to account for the total number produced from each molecule of glucose reduced C4 molecule Some Intermediate and Final Products of Respiration From Glycolysis 2 ATPglucose 2 NADHIglucose From Pyr Dehydrogenase 1 NADHIpyruvate 2 NADHIglucose 1 COzlpyruvate 2 COzlglucose From the Krebs Cycle 3 NADHCzCOA 6 NADHIqucose 1 FADHZICzCoA 2 FADHzlglucose 1 ATPCzCoA 2 ATPglucose 2 COZICZCoA 4 COzlglucose Sum each molecule of glucose metabolized through glycolysis pyr dehydrogenase and the Krebs cycle produces 6 co2 10NADH 2 FADH2 4 ATP 20 Definition Oxidative Phosphorylation The production of ATP using energy derived from oxidationreduction redox reactions of an electron transport chain Oxidative phosphorylation requires that the redox reactions occur within a membrane that separates two distinct compartments Compartments of the Mitochondrion Essential for Oxidative Phosphorylation matrix inner membrane mitochond rion intermembrane space 22 An Electron Transport Chain Within a Biological Membrane e39 or H atoms from a donor Compartment 1 membrane Compartment 2 e39 or H atoms to an acceptor electron transport chain Reducing units are carried sequentially from one transmembrane protein to another The transfer is oneway only since the AG value for each electron transfer is negative The mitochondrion inner membrane contains an electron transport chain 23 Principle of Operation of an Electron Transport Chain to Generate a Proton Gradient Across a Membrane Compartment1 2 2H 2H 1 39d39 2H 39lt ecumes acl Ic I 1 2e39 2e39 membrane Compartment 2 2H 2e39 2H 2e39 k P4 becomes alkaline 39I39L ALA L4 39 cing quot 39 carriers and electron carriers Whenever protons are needed they are withdrawn from one side of the membrane whenever protons are produced they are released to the other side of the membrane 24 the membrane Initial Components of the Electrontransport Chain of the Mitochondrial Inner Membrane H compartment NAD becomes ac c NADH intermembrane space 2H 2e39 4 inner membrane 2e39 Matrix 2H compartment 2H becomes alkaline Component A is an electron carrier Component B is a hydrogenatom carrier A proton is released into the intermembrane space when the electrons from NADH are transferred to Component A Protons are withdrawn 25 from the matrix when hydrogen atoms are tr nsferred to Component B FADH also donates electrons to an electron transport chain of the mitochondrial inner membrane 2H FAD compartment becomes acidic FADH2 Intermembrane space 4 cont inner membrane Matrix ompartment c becomes alkaline Reducing units from FADH2 that are used in the electron transport cause the H concentration in intermembrane space to increase and the H concentration in the matrix to decrease Electrons entering the mitochondrial electron transport chain from either NADH or FADH2 are ultimately transferred to 02 which along with protons drawn from the matrix reduce the 02 to water From NADH or FADHZ intermembrane space compartment becomes acidic inner membrane matrix 2e compartment H20 becomes alkaline 2H 1202 Protons are removed from the matrix during electron transport to water making the matrix more alkaline with respect to the intermembrane space BIO 311C Spring 2009 Lecture 16 Friday 27 Feb Review H Important characteristics HaN c COO of amino acids R they all contain at least one carboxylic acid functional group and at least one amine functional group Combinations of 20 different amino acids each with a different R group occur in polypeptide chains All but one of these 20 amino acids contain at least one asymmetric carbon atom Oligopeptides and polypeptides have two distinct ends an Nterminal end also called an aminoterminal end a Cterminal end also called a carboxyterminal end example Nterminal end Cterminal end H o T HN lt ltIl T lt coo39 R1 H R2 A dipeptide Hydrogen Bonding Between Two Peptide Groups Direction of polypeptide chain iquot 39 quot2 R1 0 R2 0 E E I II I II Ntermlnal N c c N C Cquotquotquotquotquot end I I l I 39z H H I H no I I I l I H 393 H iquot II I II Ctermina C TT c T Tillll 0 end R3 H R4 H A Direction of polypeptide chain The structure imposed on portions of a polypeptide chain due to hydrogen bonding between different peptide bonds is called the secondam structure of the polypeptide chain Categories of R Groups that Occur in Amino Acids I No Rgroup glycine contains only H W ll With Rgroup A Nonpolar RGroup B Polar RGroup 1 nonionized 2 ionized a cationic H H3N c coo gtlt R generalized amino acid b anionic How many asymmetric carbon atoms does glycine have Leucine an amino acid with a nonpolar Rgroup Se ne an amino acid with a polar noncharged Rgroup Lysine an amino acid with a cationic Rgroup Aspartic acid an amino acid with an anionic Rgroup H H HsN C COO H3N I3 COO CH2 CH2 CH2 lt3o lt3H2 39339 42 The Amino Acid Sequence of a Polypeptide Chain HJN llmlnnmd Each living cell produces V r several thousands of different kinds of polypeptide chains Each kind of polypeptide chain aquot has an exact number of amino acids The sequence of amino acids is exactly the same for each copy of the same kind of polypeptide chain The amino acids of a polypeptide chain are numbered sequentially starting from the Nterminal amino terminal end From textbook Fig 521 p 82 Some Features of This Specific Polypeptide Chain It consists of 127 amino acids lts Nterminal amino acid is Gly lts Cterminal amino acid is Glu Amino acid number 25 is Ala O 7 Cnrhuxyl and Representation of the primary structure of a Specific Polypeptide Chain amino acids peptide bonds l HIM coo Ala Asp Gly Phe Leu Lys Ser Cys A D G F L K S C mumnuma 39 39 39 one a r 39 39 39 39 a r Ir r39 l 39 Sta ingatthe Secondary Structures Contribute to the Overall Size and Shape of a Polypeptide Chain From Textbook Fig 519 p 81 An alphahelix secondary structure A betasheet secondary structure Each alpha helix and beta pleated sheet secondary structure contributes to only a portion of the overall threedimensional shape of the molecule


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