BIO OUTLINE Essay Research Paper BIOLOGY 220 free essay sample

BIO OUTLINE Essay, Research Paper BIOLOGY 220 OUTLINE SECTION II Text: Essential Cell Biology I. Opening Remarks ( Chapter 3 ) A. Life creates order out of upset through a ceaseless series of chemical reactions B. This is Metabolism and the ability to Metabolize C. Most of the chemical reactions required by the cell would non happen at physiological conditions D. Control of these reactions is achieved by specialised protein, ENZYMES. II. Basic Principles of Energy A. Energy # 8211 ; Basicss Principles 1. Define Energy # 8211 ; ability to make work 2. Define Work # 8211 ; the ability to alter the manner affair is arranged 3. Define Kinetic Energy 4. Define Potential energy # 8211 ; energy of place 5. First Law of THERMODYNAMICS? Energy can be transferred or transformed by neer created or destroyed. 6. Explain transferred or transformed? Different sorts of energy a. Radiant ( solar ) B. Chemical ( e.g. gasolene, saccharides, fats ) c. Mechanical ( involves motion ) d. Atomic. 7. Second Law of THERMODYNAMICS # 8211 ; In any energy transmutation or reassign some energy is lost to the environing environment as heat. a. Define Entropy B. 2nd Law says # 8211 ; ENTROPY IS INCREASING c. ADD HEAT LOSS TO ENERGY DIAGRAM ABOVE. B. The Concept of Free Energy 1. Free energy # 8211 ; the part of a systems energy that can execute work given changeless Thymine throughout system ( e.g. , populating cell ) 2. Entire free energy of a system ( G ) is define by this equation G = H # 8211 ; TS a. H = entire energy of system = ENTHALPY b. T = absolute temp in K ( KELVINS ) ( ? C + 273 ) c. S = information d. Note that T increases value of S since as Heat additions, molecular gesture additions, and upset additions. 3. Spontaneous Procedures a.Definition # 8211 ; occur w/o outside aid ( energy ) # 8211 ; energy of system is sufficient to transport out reaction or procedure b.Is non concerned with rate or clip, so self-generated procedures will non needfully happen in a utile clip frame 4. Determining when a system can undergo self-generated alteration a. Stability B. The alteration in Free Energy is negative for self-generated systems. G = Gfinal province # 8211 ; Ginitial province or.DG = DH # 8211 ; TDS III. Basicss of Chemical Reactions A.All reactions require an input of energy to acquire them started 1. Energy OF ACTIVATION or ACTIVATION ENERGY a. Define Activation Energy with operating expense B. For some reactions the activation energy can be provided by the reacting molecules themselves. c. For others, the activation is really high since the reacting molecules must be brought together in precisely the right orientation in order for the reaction to take topographic point ( ? effectual hit? ) .. B.Enzymes cut down activation energy ( Chap5. p. 167-69 ) 1. Define Catalyst 2. Specify Substrate 3. Random interactions lead to Enzyme-Substrate Complex formation ( effectual hit ) 4. Enzymes cut down activation energy by a. Increasing the figure of effectual hits between substrates 5. Enzymes are proteins a. reappraisal construction of proteins. 6. Define Active Site a. Active Site can work by ( 1 ) form similarities ( 2 ) chemical attractive force ( 3 ) both B. Example: Ribonuclease c. Review stairss of RNAse active site d.Another illustration: Lysozyme: pg.170 Figure 5-28 7. Discourse how enzymes are named a. See Table 5-2 p.169 for list of common enzyme group names and functions.. IV. Factors set uping Reactions ( in general, including enzyme-mediated ) ( Back to Chapter 3 ) A. Free energy considerations ( as discussed earlier ) 1. Free energy alteration must be negative B. Concentration of the molecules in the system besides determines whether a reaction will happen. 1. As the concentration of one molecule increases the reaction will travel toward the production of the other molecule ( Le Chatlier # 8217 ; s Principle ) . C. BIG QUESTION # 8211 ; how much of a concentration difference is required to get the better of a.G that might be unfavourable. 1. Rewrite.G to reflect concentration constituent 2. .G = .G O + 0.616ln [ B ] / [ A ] a. 0.616 is a changeless B. .G O is the Standard Free Energy alteration ( 1M @ pH=7 ) in kcal/mole c. @ 37 O C d. Note that when [ A ] = [ B ] , concentration effects are negated and.G=.G O ( ln 1 = 0 ) . D. For a reversible reaction A? ? B ( see Figure. 3-20 p.92 ) 1. One way is energetically favored ( -.G ) over the other 2. For illustration A to B is favored 3. As A converts to B, the concentration consequence of greater sums of B begins to get the better of the + ? ? ? ? ? ? ? G ( for B A ) , to a point where B? ? A is equal to A? ? B. 4. In Table 3-1 some computations were done to find when.G=0 ( equilibrium ) , that is when.G O = -0.616ln [ B ] / [ A ] ( con # 8217 ; t on following page ) . 5. It is of import to observe that it requires important surplus of the favorite merchandise ( B ) to force the reaction back to unfavored merchandise ( A ) . 6. Enzymes do non alter the equilibrium point.. V.Factors Affecting Enzyme-Mediated Chemical reactions A. Physical Parameters impacting Enzyme Activity ( use graphs ) 1. Temperature 2. pH B. Concentration effects 1. Unlimited substrate in the presence of limited enzyme a. Impregnation dynamicss b. where did we see this before -answer: membrane transporters 2. Unlimited enzyme in the presence of limitless substrate. VI. Regulating Enzyme Chemical reactions A. Competitive suppression 1. Chemical reaction rate is [ substrate ] dependant B. Non-competitive suppression 1. reaction rate is [ substrate concentration ] independent 2. Inhibitor binds at a site other than active site 3. causes conformational alteration in enzyme # 8211 ; makes active site unavailable C. Allosteric Control 1. allo = other steric = construction or province 2. Like noncompetitive # 8211 ; Control Molecule binds at surrogate site 3. alternate site = allosteric site 4. Control Molecule called a REGULATORY SUBSTANCE a. may increase or diminish activity. 5. Allosteric enzymes exist in 2 different provinces a. R ( elaxed ) province = high affinity for substrate b. T ( ense ) province = low affinity for substrate 6. Binding of regulative substance can bring on either province. a. Allosteric Inhibitor # 8211 ; adhering causes T province b. Allosteric activator # 8211 ; adhering causes R province. 7. Allosteric enzymes and Reaction rate a. Regulative substances may hold multiple binding sites. Leads to sigmoidal graph of reaction rate B. For T to R province # 8230 ; enzyme activity is low until sufficient regulator binds to change over enzyme wholly to R province c. For R to T province # 8230 ; enzyme activity is high until sufficient regulator binds to change over enzyme wholly to T province d. Regulator may be substrate or merchandise. D. Allosteric Feedback Inhibition 1. end merchandise Acts of the Apostless as regulator of 1st enzyme in tract 2. Discuss Threonine to Isoleucine tract a. enzyme # 1 = threonine deaminase. E. Regulation by Covalent Modification 1. add-ons may include a. Ca 2+ b. PO4 # 8211 ; phosphorylation ( 1 ) Added by protein kinases ( 2 ) Removed by protein phosphotases c. CH3 # 8211 ; methylation d. COCH3 # 8211 ; acetylation 3. binding can up or down modulate enzyme. F. GTP-binding Proteins 1. Binding of GTP or GDP can do major conformational alterations 2. Phosphorylation of bonded GDP and Dephosphorylation of bonded GTP can besides do alterations 3. Mode of action a. Exchange of GTP and GDP b. Dephosphorylation of edge GTP 4. Exchange and phosphorylation can hold different rates a. Control achieved by different rates for different reactions B. See Figure 5-37 pg. 176. G. Ribozymes 1. RNA based accelerators 2. Self splicing RNA molecules c. besides show activity with some proteins ( 1 ) remotion of proteins from ribosomes ( 2 ) separation of aminic acids from transfer RNA. H. Coenzymes 1. vitamins 2. minerals 3. Carriers a. Discuss coupled reaction diagrams b. Electron Carriers ( 1 ) NAD ( Figure 13-8 ) , A ; NADP ( 2 ) FAD ( Figure 4-12 ) ( 3 ) oxidized and reduced signifiers ( 4 ) show chemical science ( 5 ) Dehydrogenase? oxidising enzymes ( 6 ) Reductase # 8211 ; cut downing enzymes c. Function as cofactors in oxidation-reduction reactions d. required by enzymes that are involved in oxidizations or decreases? negatron givers or receiving systems. I. ATP # 8211 ; cosmopolitan energy currency of the cell 1. Describe molecular construction a. nucleoside triphosphate 2. Describe rhythm ATP? ? ADP + P a. .G 0 = -7.3 kcal/mole b. Phosphorylation and its relationship to Redox 3. Energy required to do ATP or Energy released from ATP hydrolysis depends on.G 0 and the comparative concentrations in the cell a. For some cells the ATP/ADP ratio attacks 1000 B. Under these conditions, the.G for the hydrolysis of ATP to ADP can near 11-13 kcal/mole ( retrieve G equation includes a concentration factor ) . J. Coupling Reactions to the Hydrolysis of ATP 1. The hydrolysis of ATP can be linked to reactions with + ? ? ? ? ? ? ? G o Overall reaction: Glu +NH3? ? Gln.G 0 = +3.4kcal/mole Measure 1: Glu + ATP? ? Glu-P + ADP.G 0 = -7.3kcal/mole Measure 2: Glu-P + NH3? ? Gln.G 0 = +3.4kcal/mole NET.G 0 = # 8211 ; 3.9 kcal/mole. 2. Can besides be coupled to Dehydration reactions or about any synthesis reaction that has a + ? ? ? ? ? ? ? G 0 3. If the coveted merchandise has a.G 0 * +7.3 kcal so the reaction is broken down into steps.. K. ATP Production ( Some coverage in Chap 13 p.409 # 8211 ; 410 ) 1. Substrate-level phosphorylation a. Direct enzymatic transportation of phosphate group A ; energy to ADP from a high energy substrate b. low efficiency. 2. Chemiosmotic Phosphorylation? MITCHELL THEORY a. Transportation indirectly through proton gradient ( 1 ) electrochemical gradient ( 2 ) stored charge = ENERGY ( 3 ) high efficiency achieved through step-wise transportation = ELECTRON TRANSPORT CHAIN B. 3 demands for Chemiosimosis ( 1 ) Selectively Permeable membrane ( 2 ) H+ pumping Enzymes ( Active Transport ) ( 3 ) ATP Synthase c.Introduce ATP synthase # 8211 ; enzyme that captures energy from proton gradient and transportations it to ATP production # 8211 ; Figure 13-3 A ; 13-13. c. Discuss charge separation and release of energy ( 1 ) offprint charges across dielectric # 8211 ; Battery Analogy: Figure 13-11 ( 2 ) Make a charge gradient across an dielectric ( 3 ) CHARGE SEPARATION REPRESENTS STORED ENERGY ( 4 ) Release Energy by leting gradient to disperse ( 5 ) In life cells, charge separation achieved with different ion concentrations across membranes ( ION GRADIENTS ) ( 6 ) ex. H+ gradient ( 7 ) Figure 13-15. 3. Jagendorf experiments -a. Knew of being of pH differences within chloroplast B. Review experiment with operating expense c. Experiment shows connexion between H+ gradient, H+ flow, and phosphorylation of ADP to ATP. 4. Latest information on ATP Synthase a. Still unknowns ( 1 ) how it works so fast ( 2 ) how it couples proton flow to ATP production B. Background information on construction ( 1 ) Figure 13-14 ( 2 ) 3 parts ( 3 ) F0 # 8211 ; subunit # 8211 ; channel for protons ( 4 ) F1 # 8211 ; subunit # 8211 ; catalytic fractional monetary unit? ATP production ( a ) called ATPase ( B ) uses ATP to pump protons ( 5 ) Stalk # 8211 ; connects F0 to F1. c. Latest info on construction of F1 ( 1 ) made of 6 fractional monetary units + ? fractional monetary unit ( a ) 3? fractional monetary units ( B ) 3? fractional monetary units ( degree Celsius ) arranged in jumping manner ( vitamin D ) ? fractional monetary unit contains catalytic activity ( vitamin E ) ? subunit extends into chaff part I ) knife shaped protein. d. Current theory of how it works ( 1 ) H+ traveling through F0 causes? fractional monetary unit to revolve ( 2 ) knife border contacts? fractional monetary unit ( 3 ) ? fractional monetary unit is deformed leting for ADP A ; P binding, individually, to active site ( 4 ) ? fractional monetary unit releases contact ( 5 ) ? subunit reformation brings ADP + P in contact and reaction takes topographic point. VII. PHOTOSYNTHESIS ( Chapter 13 # 8211 ; p.430- 438 ) A. Overview # 8211 ; Use? Energy Flow through Populating Systems? OH to set things in position. B. Overall reaction 1. Radiant Energy + H2 O + CO2? ? O2 + Glucose 2. Balanced equation: a. 6CO2 + 6H2 O + Radiant Energy? ? C6 H12 O6 + 6O2 3. Leaf construction a. Epidermis b. Spongy and Palisade Mesophyll ( 1 ) Where photosynthesis takes topographic point c. Stomates. 4. Chloroplast construction? EMPHASIZE ORGANIZATION a. Outer membrane B. Inner membrane c. Stroma # 8211 ; Glucose production enzymes d. Thylakoid membrane ( 1 ) Light absorbing molecules or Photosystems ( 2 ) Electron conveyance chain/Proton pumps ( 3 ) NADP reductase ( 4 ) ATP synthase e. Thylakoid infinite or lms? proton reservoir. C. Photosynthesis as a REDOX 2-step 1. REVIEW STRUCTURE 2. Energy capturing? LIGHT DEPENDENT REACTIONS a. Capture energy in the signifier of ATP and NADPH B. Use negatrons from oxidization of H2O 3. Energy storage? Light INDEPENDENT REACTIONS a. Take energy from ATP and NADPH and utilize it to cut down C dioxide. D. Light Dependent Reactions 1. Happen on thylakoid membrane 2. Discuss electromagnetic spectrum a. Gamma, X, UV, Visible ( 380nm-750nm ) , IR, Micro, Radio b. Violet, Indigo, Blue, Green, Yellow, Orange, Red c. High energy, Short wavelength, High freq # 8212 ; Low, Long, Low. 3. Pigments a. Imbedded in the thylakoid membrane B. All have hydrophobic dress suits anchored in thylakoid membrane c. Chlorophylls ( a A ; B ) ? Mg 2+ Center? Figure 13-30 d. Carotenes # 8211 ; pure hydrocarbons? aromatics rings linked by polyunsat? vitamin D concatenation e. Xanthophylls # 8211 ; as above w/ intoxicants on rings f. Draw soaking up spectrum on board. 4. Light Energy Absorption a. achieved by pigment molecules b. Excitation event A ; excitement energy ( see Figure 13-32 ) ( 1 ) negatrons at land province ( interior orbital ) ? excited? by photon of visible radiation to excited province ( outer orbital ) ( 2 ) can stay in this province for merely a billionth of a 2nd c. Possible destinies of excitement energy ( 1 ) If excited negatron returns to anchor province? FLUORESCENCE + heat ( 2 ) Excited negatron is picked up by stable acceptor molecules. aroused negatron is transferred to stable orbital of the same energy degree ( Figure 13-32 ) ( a ) Light energy converted to chemical energy. ( 3 ) Inductive transference ( a ) energy is transferred to next pigment molecule I ) quiver of aroused vitamin E # 8211 ; sets up electromagnetic field. two ) adjacent vitamin E # 8211 ; in tantamount orbitals begin to vibrate in resonance three ) energy is transferred. ( B ) little or no loss of energy. 5. Capturing and Converting Light Energy to Chemical Energy a. Photosystems ( see Figure 13-31 for general diagram ) ( 1 ) Photosystem I ( a ) 110 chlorophyll a + 16 # 8211 ; bcarotenes = CORE ANTENNA ( B ) Reaction Center = particular chlorophyll a molecule: P700 ( 700 refers to light absorbing belongingss @ 700nm ) ( degree Celsius ) Energy is absorbed by Core Antenna and passed by inductive resonance to P700 so to 1? acceptor. ( 2 ) Photosystem II ( a ) 40 Chlorophyll a + ** B provitamin As = CORE ANTENNA ( B ) Reaction Center = particular chlorophyll a molecule: P680 ( 3 ) Energy is absorbed by Core Antenna and passed by inductive resonance to P680 so to 1? acceptor B. Light Reaping Complexes ( Not shown in Alberts diagrams ) ( 1 ) One associated with each PS ( 2 ) Designated LHC I and LHC II ( 3 ) Collections of pigment molecules imbedded in thylakoid membrane ( 4 ) In close physical propinquity if non physically attached to PS? s ( 5 ) Funnel excitement energy to reaction centres via inductive resonance. USE PHOTO REVIEW HANDOUT W/ EXPLANATION BELOW 6. Non-Cyclic negatron Photophosphorylation ( Figure13-34 = Z Scheme with electron volt evaluations ) a. The participants ( 1 ) Mn -center # 8211 ; Water Oxidizing Enzyme ( 2 ) LHC II A ; PS II ( 3 ) Plastoquinone? e- bearer? aromatic ring w/ long chair hydrocarbon? non attached to PS II ( 4 ) Cytochrome b6 # 8211 ; e- bearer? Heme ( Fe ) incorporating protein Fe2+ ? Fe 3+ ( 5 ) Cytochrome degree Fahrenheit. ( 6 ) PROTON PUMPING IN PS II ( a ) b6+f complex = H+ pump ( B ) Sets up H+ gradient between Stroma and Thylakoid lms ( degree Celsius ) H+ pumped from stroma into lms ( vitamin D ) Flow out through CF0CF1? ATPase imbedded in thylakoid lms. ( vitamin E ) Make ATP in Stroma ( 7 ) Personal computer = e- bearer # 8211 ; plastocyanin? ( a ) Cu incorporating protein: Cu+ ? Cu2+ ( 8 ) negatrons are passed to PS I ( 9 ) Ferrodoxin # 8211 ; Fe/S centre? nomadic # 8211 ; non attached to PS I ( 10 ) NADP+ Reductase? usage negatrons to cut down NADP+ to NADPH. 7. Cyclic Photophosphorylation a. negatrons pass from Ferrodoxin to cytochrome b6 b. merely produces ATP c. may be used to bring forth the extra ATP needed to drive glucose production ( ~3:2 ATP: NADPH ) . E. LIGHT-INDEPENDENT REACTIONS ( Calvin Cycle ) 1. Occur in stroma 2. Use ATP and NADPH to cut down CO2 to Glucose 3. Review procedure utilizing an operating expense 4. Points to Stress a. Reducing enzyme = Ribulose bisphosphate carboxylase ( rubisco ) b. Ribulose bisphosphate = RuBP c. PGA = Phosphoglycerate d. PGAL = Phosphoglyceraldehyde e. Each bend of the rhythm # 8230 ; REFER TO HANDOUT. f. 1 molecule of glucose requires ( 1 ) 18 ATP? 7.3 kcal/mole ten 18 = 131.4 kcal ( 2 ) 12 NADPH? 53 kcal/mole ten 12 = 636 kcal ( a ) Note 53 kcal/mole # 8211 ; ref: Campbell pg. 178 for NADH to O2? H2 O ( 3 ) Takes 767.4 kcal to do 1 molecule of glucose ( 686 kcal ) ( a ) 686/767.4 = 89 % efficiency. F. PHOTORESPIRATION ( Use Study Sheet ) 1. Rubisco prefers O2 to CO2 2. If rubisco binds O2 a. Procedure uses 6 extra ATP b. Regenerates RuBP c. Produces a 2-C compound ( alternatively of 3-C ) d. This compound is sent to peroxisome and chondriosome ( 1 ) converted to Glycerate ( 3C ) ( 2 ) transported back to chloropl ast ( 3 ) Uses ATP to change over to 3-PGAL 3. Net LOSS OF ENERGY 4. Some workss waste every bit much as 50 % of the energy they make on this procedure 5. For workss under ideal conditions? photorespiration poses no jobs 6. Some workss have evolved constructions to cut down photorespiration. G. C4 workss 1. Use spacial ( C4 ) isolation of Rubisco to forestall Photorespiration 2. Fix Carbon into 4-Carbon organic Acids 3. Particulars ( Use Study Sheet ) a. Rubisco sequestered off from O2 in specialised cells? BUNDLE SHEATH CELLS B. Capture CO2 utilizing shuttle molecules c. C4 usage PEP ( phosphoenol pyruvate ) and Pepco ( PEP carboxylase ) to capture CO2 and funnel it into Calvin Cycle. ( 1 ) C4 comes from intermediates ( oxalacetate and malate ) which are 4-C molecules ( 2 ) Other workss called CAM workss. VIII. Oxidative Respiration # 8211 ; Overview A. Review cell organisation and where reactions are taking topographic point B. Emphasize function of ATP made in Photosynthesis IX. Glycolysis # 8211 ; Chapter 4: 110-118 A. Interested merely in the large image ( see Figure 4-3, pg. 111 ) B. Stress 3 major events 1. Energy Investment 2. Cleavage of Glc into 2 3-carbon sugars 3. Energy Generation a. Stored as NADH b. ATP c. FILL OUT ATP SUMMARY TABLE. C. Review Figure 4-3 with pupils 1. If they want to larn the stairss, that? s mulct. 2. Merely be responsible for names in Figure. a. Glucose b. Fructose 1,6 bisphosphate c. Glyceraldehyde 3-Phosphate ( PGAL ) d. Pyruvate D. Other points to stress 1. No engagement of molecular Oxygen 2. Direct dependance on the handiness of NAD+ a. Use this as a lead into Fermentation. X. Fermentation # 8211 ; Regeneration of NAD+ in the absence of Oxygen A. Discuss what is needed to maintain Glycolysis traveling 1. ADP # 8211 ; no job since cell is utilizing ATP quickly 2. Glucose 3. NAD+ # 8211 ; must happen a manner to oxidise NADH to acquire to ATP bring forthing measure. B. Review 2 Fermentation tracts with study sheet. Eleven. Mitochondrial Events # 8211 ; Oxidation of Pyruvate to CO2 A. Review construction of Mitochondrion B. Transition Reactions # 8211 ; Review with Study Sheet 1. Enzyme # 8211 ; Pyruvate Dehydrogenase Complex a. 3 enzymes B. 60 polypeptide ironss 2. See Figure 4-8 # 8211 ; p. 118 3. FILL OUT ATP SUMMARY TABLE C. Kreb? s Cycle ( Citric Acid Cycle ) 1. Good overview # 8211 ; Figure 4-11 pg. 120 2. Review with Study Sheet a. Students responsible for names and events. D. Chemiosmotic Phosphorylation # 8211 ; Chap. 13 # 8211 ; p.410 # 8211 ; 429 1. Conversion of stored energy ( NADH A ; FADH2 ) into ATP 2. Stored Energy used to bring forth an a H+ gradient 3. Review with Study Sheets a. Ubiquinone Structure B. Figure 13-20 c. Figure 13-10 # 8211 ; Summary d. Figure 13-21 # 8211 ; Shows Redox potencies 4. Complete ATP SUMMARY TABLE a. Doesn? t take into history ATP used for conveyance out of the Mitochondria d.See Problem 13-5 pg. 420? Outputs are 2.5 and 1.5 ( for NADH and FADH2 and NADHcytosol. Uses 6 of 36 for conveyance. Twelve. The Metabolic Pool A. Use Study Sheet to cover B. See Figure 4-18 p.127 in text for similar but more elaborate intervention. Thirteen. Deoxyribonucleic acid as the GENETIC MATERIAL? A History Lesson ( ref: Bio 120 Outline ) Fourteen. Features of the Genetic Material and the Central Dogma ( ref: Bio 120 Outline ) Fifteen. Deoxyribonucleic acid STRUCTURE A. Discovery 1. James Watson 2. Francis Crick 3. Maurice Wilkins 4. Rosalind Franklin B. Basic construction 1. Sugar phosphate anchor 2. Nitrogen bases as rounds 3. Double spiral 4. Basic Unit = Nucleotide a. phosphate b. sugar c. N base. C. Backbone 1. Deoxyribose sugar 2. Reason for name 3. Review enumeration 4. Where phosphate bonds 5. 5 # 8242 ; to 3 # 8242 ; orientation 6. Antiparallel spiral D. Nitrogen Bases 1. Purines a. Adenine and Guanine 2. Pyrimidines a. Thymine and Cytosine 3. AT brace and GC brace a. Complementary base coupling. E. Chromosomal organisation 1. Aim a. packaging b. organisation c. entree and control 2. Genome size a. E. coli = 4.3 x 106 nucleotide pairs/genome B. Humans = 2 ten 108 nucleotide pairs/chromosome ( 3 x 109 genome ) ( 1 ) stretched out = 6cm. F. Boxing the Eukaryotic Chromosome ( p.250-255 ) 1. Degree 1 ( Figure 8-9 ) a. utilizes proteins called HISTONES b. sum of DNA? ? sum of histones c. really basic ( 1 ) high proportion of positively charged amino acids ( a ) allows for tight binding to negatively charged Deoxyribonucleic acid ( 2 ) lysine and arginine d. DNA + Histone = Chromatin e. Five types of histones ( 1 ) really similar from species to species ( a ) ex. some cow and pea histones differ by 2 aa ) ( 2 ) extremely conserved cistrons. f. DNA + Histone nucleus signifier NUCLEOSOMES ( Figure 8-9 ) ( 1 ) Beadss on a String visual aspect ( 2 ) basic unit of DNA packing ( 3 ) Histone nucleus = 8 # 8220 ; nucleosomal # 8221 ; histone molecules ( a ) nucleosomal histones = H2A, H2B, H3, H4 I ) 2 molecules each compose nucleus ( B ) little proteins ( 102-135 aa ) ( degree Celsius ) Core = HISTONE OCTAMER. 2. Level 2 # 8211 ; 30nm fibre = SOLENOID ( Figure 8-10 ) a. look to be mediated by 5th histone = histone H1 3. Higher degrees of packaging a. refer to overhead of Figure 8-10 b. non clearly understood. 4. Heterochromatin vs. Euchromatin a. hetero = chromosomes in condensed province during interphase b. Eu = chromosomes in less condensed province c. merely euchromatin is actively canned d. may be a harsh signifier of cistron control e. most widely known illustration ( 1 ) Barr Body in females ( a ) one of two X chromosomes is ever in most condensed signifier ( during interphase ) ( B ) Merely cistrons on other chromosome are expressed ( degree Celsius ) females are a Mosaic since different X-chromosomes can be condensed in different cells.. XVI.DNA REPLICATION A. Replication Models 1. Watson-Crick theoretical account implied Semi-Conservative 2. Conservative # 8211 ; possible theoretical account 3. Meselsohn A ; Stahl experiments a. Use 15 N labeled DNA ( 14 N = normal ) B. Basic Stairss 1. Must take into history dual coiling construction 2. Step 1 # 8211 ; separate strands to entree information 3. Step 2 # 8211 ; Make transcripts utilizing old as theoretical account 4. Step 3 # 8211 ; Reform old and new as dual spiral. C. Step 1 # 8211 ; Separating Strands 1. unwind spiral at specific get downing point ( s ) a. ORI = beginnings of reproduction b. DNA HELICASE 2. stabilize unwound spiral so it doesn? t reanneal a. SINGLE STRAND BINDING PROTEINS ( SSB ) 3. prevent supercoiling a. DNA TOPOISOMERASE. D. Step 2 # 8211 ; Making transcripts 1. Use template synthesis 2. Complementary base coupling 3. Necessitate enzyme that can do new DNA polymer. 4. Deoxyribonucleic acid POLYMERASE ( Figure 6-21 A ; 22 ) a. 5 # 8242 ; to 3 # 8242 ; polymerase B. Skiding clinch protein? moderates fond regard of DNA pol to template. c. uses 5 # 8242 ; -nucleotide triphosphates ( ATP, GTP, CTP, TTP ) ( 1 ) supply energy for bond formation d. Review antiparallel construction ( 1 ) requires bidirectional synthesis ( 2 ) Deoxyribonucleic acid pol can merely synthesis unidirectionally ( eg. 5 # 8242 ; to 3 # 8242 ; ) ( 3 ) Synthesis occurs continuously on 3 # 8242 ; to 5 # 8242 ; strand = taking strand ( 4 ) Synthesis occurs discontinuously on 5 # 8242 ; to 3 # 8242 ; strand = lagging strand ( a ) Deoxyribonucleic acid LIGASE connects pieces. e. Requires a primer ( 1 ) de novo synthesis non possible ( 2 ) Primase enzyme lays down RNA primer ( 3 ) Primer must be removed ( a ) see below f. Retroflexing the terminals of dawdling strands ( p.249-250 ) ( 1 ) requires particular enzyme to add dress suits onto templet strand ( a ) dress suits are called # 8211 ; TELOMERES ( 2 ) Enzyme that duplicates them? TELOMERASE ( Figure 8-6 ) ( a ) Contains a short piece of RNA ( B ) in worlds = CCCCAAU ( degree Celsius ) Creates tandem repetitions on terminals of dawdling strand ( GGGGTTA ) ( vitamin D ) allows the terminal of the chromosome to be replicated ( 3 ) leaves a 3 # 8242 ; tail on templet strand. g. Accuracy ( 1 ) 3 # 8242 ; to 5 # 8242 ; exonuclease activity Acts of the Apostless as proofreader ( 2 ) ? senses? mismatch, backs up, removes mismatch, and corrects ( 3 ) methylation of parent strand. Seventeen. DNA REPAIR ( pg. 198-205 ) A. Define Mutation 1. Permanent alteration in DNA codification B. Mismatch Repair system catches mistakes Replication Machinery girls 1. Rpn machinery mistake rate 1 in 10 7 bases transcripts 2. Approximately 10 mistakes/chromosome/rpn rhythm 3. Mismatch = mispaired nucleotide ( Figure 6-25A p.201 ) 4. Mismatch fix enzymes recognize the mismatches a. Excise wrong base B. Repair c. Must be able to acknowledge the freshly synthesized strand ( 1 ) Nick system # 8211 ; new strands have transient dents ( 2 ) Methylation system # 8211 ; Parent is methylated 5. Reduces error rate to 1 in 10 9. C. DNA Damage outside of Rpn 1. Types of Damage ( Figure 6-27 p.202 ) a. Depurination # 8211 ; self-generated loss of A or G ( 1 ) Leaves a depurinated sugar b. Deamination # 8211 ; loss of amine group on Cytosine ( 1 ) Converted to Uracil c. Thymine Dimer formation due to UV visible radiation exposure d. Many other types caused by reactive metabolic byproducts 2. Effectss can do a. Single base brace alterations ( deaminization ) ( Figure 6-29A ) b. Single-base brace omissions ( depurination ) ( Figure 6-29B ) c. Stalled or uncomplete rpn ( thymine dimers ) . D. DNA Repair Mechanism ( Figure 6-30 p204 ) 1. Deletion of Defect a. Requires specialised nucleases for each type of harm 2. Repair a. Uses DNA pol other than rpn DNA pol 3. Ligation a. Uses DNA Ligase. Eighteen. TRANSCRIPTION # 8211 ; ACCESSING THE CODE A. Central Dogma # 8211 ; From DNA to Protein? Figure 7-1 B.Discuss this as the first measure in Gene Expression PROCESSES INVOLVED IN GENE EXPRESSION ? Using Genetic Information to do the molecules necessary for cellular maps. ? Ultimately, every procedure within a life being is controlled by theavailability of specific cistron merchandises C. Definition of a Gene # 8211 ; Stage # 1 1. Region of DNA contains some information that needs to be accessed. D. The Players 1. The information # 8211 ; Deoxyribonucleic acid a. dual spiral B. 5 # 8242 ; to 3 # 8242 ; and 3 # 8242 ; to 5 # 8242 ; strands 2. The enzyme # 8211 ; RNA Polymerase a. 5 # 8242 ; to 3 # 8242 ; polymerase activity b. substrate ( 1 ) ribonucleoside triphosphates c. local unwinding capablenesss d. DNA binding belongingss e. 3 in Eukaryotes ( 1 ) I # 8211 ; rRNA ( 2 ) II # 8211 ; mRNA + others ( 3 ) III # 8211 ; tRNA + rRNA. 3. The courier # 8211 ; messenger RNA a. Structure # 8211 ; Use Figure 7-3 to compare and contrast with Deoxyribonucleic acid ( 1 ) individual strand ( 2 ) U for T ( 3 ) ribose for deoxyribose E. The Basic Steps ( Figure 7-9 ) 1. Find the part to be copied a. which strand b. where to get down 2. Attach enzyme 3. Transcript 4. Stop. F. Finding the part to be copied 1. Which strand a. Discuss sense vs. non-sense ( 1 ) cistron is ever read 5 # 8242 ; to 3 # 8242 ; regardless of which strand its on ( 2 ) templet is ever 3 # 8242 ; to 5 # 8242 ; regardless of which strand its on ( 3 ) Genes on different strands: Fig 7-10 b. upstream vs. downstream ( 1 ) up = toward 5 # 8242 ; ( 2 ) down # 8211 ; toward 3 # 8242 ; 2. Where to Get down a. Promoters # 8211 ; consensus sequences ( 1 ) TATA box: @ ~ -25 ( a ) RNA pol adhering site ( 2 ) CAAT box: @ ~ -80 ( a ) bind regulative proteins ( B ) consequence rate of induction B. More on this when we cover cistron ordinance. G. Attaching the enzyme 1. Transcription factors A ; RNA Pol bind at booster part a. More inside informations when we cover cistron ordinance 2. Transcription Begins H. Elongation 1. Uses anti-sense as templet 2. transcripts in 3 # 8242 ; to 5 # 8242 ; way bring forthing 5 # 8242 ; to 3 # 8242 ; transcript ( messenger RNA ) I. Termination 1. Probably requires expiration factors 2. Specific DNA sequence signals expiration a. in eucaryotes # 8211 ; most common = AATAAA. J. Compare Eukaryotic and Prokaryotic Transcripts 1. Use Figure 7-13. K. The Eukayotic mRNA # 8211 ; usage Study Sheet 1. Structure a. Use Figure 7-12 B. 5 # 8242 ; cap ( 1 ) 5 # 8242 ; to 5 # 8242 ; linkage to # 8230 ; ( 2 ) ..GTP ( 3 ) fxn ( a ) in interlingual rendition ( subsequently ) ( B ) conveyance out of karyon I ) pores recognize cap ( degree Celsius ) prevent RNAse debasement c. 5 # 8242 ; UTR ( 10-200 bases ) d. coding sequence e. 3 # 8242 ; UTR ( 1 ) extremely conserved ( 2 ) holes length of UTR and site for 3 # 8242 ; tail fond regard f. 3 # 8242 ; poly A ( 30-200+ ) ( 1 ) likely fxn # 8211 ; stableness ( 2 ) messenger RNA w/o poly A debauched rapidly. 2. Processing # 8211 ; Use Study Sheet a. Intron/Exon construction b. mediated by a group of snRNA? s and proteins c. snRNA + Proteins = snRNP # 8217 ; s d. Several snRNP # 8217 ; s take portion in each splice event e. A composite of working snRNP ; # 8217 ; s is sometimes referred to as a Spliceosome f. Can be cis or trans ( 1 ) Commonwealth of Independent States = linking coding DNAs in same messenger RNA ( 2 ) trans = connectiong coding DNAs from different messenger RNA? s g. Same messenger RNA can be spliced into different cistrons = ALTERNATIVE Splice L. Summarize # 8211 ; Use Figure 7-19. M. Revision of Gene Definition 1. Includes booster and expiration parts 2. Possibly other control sequences XIX.TRANSLATION A. Machinery 1. The codification a. minimal figure to cover all AA = 64 b. degeneration c. Advantage # 8211 ; can absorb some sum of mutant 2. Ribosomes # 8211 ; Use Figure 7-25 a.rRNA # 8211 ; serves to aline ribosome with message and *new evidence* showsit carries out the enzymatic reactionneeded for peptide bond formation ( ref: Science, 11Aug00, p.878 ) . B. Protein # 8211 ; Structural ( Figure 7-26 ) c. Small and big fractional monetary units ( 1 ) little # 8211 ; acknowledgment and alliance ( a ) A A ; P binding sites I ) lower part of these sites two ) involved in adhering transfer RNA to Codon ( messenger RNA ) ( 2 ) big # 8211 ; adhering transfer RNA and doing peptide bond ( a ) peptidyl-transferase activity ( rRNA ) ( B ) GTP hydrolysis activity ( proofreading ) ( degree Celsius ) A A ; P binding sites I ) Major part of these sites two ) binds bulk of transfer RNA with AA attached ( vitamin D ) E ( Exit ) Site. 3. transfer RNA a. transportation RNA b. construction ( 1 ) anticodon part c. Amino Acyl-tRNA synthetase ( 1 ) one for each amino acid ( 20 ) ( 2 ) attach AA to rectify transfer RNA in 2 measure procedure ( a ) AA + ATP AA-AMP + PP ( B ) AA-AMP + tRNA AA-tRNA + AMP ( 3 ) proofreading measure ( a ) truth 1,2 per 40,000 ( B ) done at 2nd measure ( 4 ) merely procedure that ensures the right codon/a.a. coupling. ( 5 ) Active site of enzyme screens Amino Acids based on size. ( a ) Coarse sieve removes AA excessively big for active site. ( B ) Fine sieve removes those little plenty to suit but non rectify ( degree Celsius ) See article: Sieves in Sequence d. Joins 3 # 8242 ; -OH of transfer RNA to carboxyl group of Amino Acid. B. Basic stairss 1. Start # 8211 ; connect message with ribosome a. INTIATION 2. Construct protein a. ELONGATION 3. Termination C. INITIATION # 8211 ; mention to Figure 7-28 1.Binding of little ribosomal fractional monetary unit + instigator transfer RNA ( tRNA met ) + induction factors ( non shown in diagram ) a. Initiator transfer RNA is merely tRNA that can adhere to little fractional monetary unit entirely b. Binds at P site 2. Complex binds to 5 # 8242 ; terminal of messenger RNA a. 5 # 8242 ; cap is critical 3. Complex? scans? mRNA 5 # 8242 ; to 3 # 8242 ; for start codon a. When found, some IFs dissociate to let for subsequent stairss. 4. Large Ribosomal subuint binds? Translation begins D. Elongation 1. assisted by elongation factors 2. EF-tRNANEXT-GTP binds at A site? Use operating expense in binder a. Proofreading measure b. involves GTP hydrolysis c. holds peptide bond formation d. licenses incorrect transfer RNA to spread out of ribosome 3. Peptide Bond Formation # 8211 ; usage operating expense in binder a. Catalyzed by peptidyl transferase b. Aminoacyl ( 3 # 8242 ; -OH # 8211 ; carboxyl ) bond between tRNAP-AAP c. AAP-Carboxyl attaches to AAA-NH2 ( 1 ) transportations concatenation from tRNAP to tRNAA ( 2 ) PEPTIDE BOND FORMATION d. empty tRNAP is released. 4. Small Ribosomal Subunit shifts down one codon ( use Figure 7-27 ) a. TRANSLOCATION B. Shifts transfer RNA attached to nascent concatenation to from A to P site c. Empty transfer RNA displacements to E site -dissociated d. Small subunit displacements back 1 codon to realine with Large fractional monetary unit e. Next transfer RNA binds at A site? procedure continues f. Specific elongation factors ( EF ) have been identified for this procedure 5. A -site is now empty # 8211 ; following transfer RNA binds? rhythm repetitions. E. Termination ( refer to Figure 7-30 ) 1. A-site is occupied by on of the expiration codons 2. Release factor protein binds at A-site 3. Peptidyl transferase hydrolyses last amino-acyl bond 4. New protein is released -Ribosome/ messenger RNA composite dissociates F. Final Gene Definition 1. A part of DNA incorporating the codification for a specific protein or RNA ( e.g. transfer RNA A ; rRNA, snRNA ) plus all the bordering DNA sequences that act as accountants. G. Final Review of Process ( use Figure 7- 33 ) H. READING ASSIGNMENT # 8211 ; PG. 234-240? RNA AND THE ORIGINS OF LIFE