BIOL 23100 Exam 2 Study Guide
BIOL 23100 Exam 2 Study Guide BIOL 23100 - 001
Popular in Biology III: Cell Structure And Function
BIOL 23100 - 001
verified elite notetaker
Popular in Biological Sciences
This 10 page Study Guide was uploaded by Gayatri on Saturday October 17, 2015. The Study Guide belongs to BIOL 23100 - 001 at Purdue University taught by Peter James Hollenbeck in Fall 2015. Since its upload, it has received 280 views. For similar materials see Biology III: Cell Structure And Function in Biological Sciences at Purdue University.
Reviews for BIOL 23100 Exam 2 Study Guide
Report this Material
What is Karma?
Karma is the currency of StudySoup.
You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!
Date Created: 10/17/15
BIOL 23100 Exam 2 Study Guide DNA Replication and Transcription Telomeres Semiconservative replication of DNA each newly made strand of DNA has one original parental strand and one newly synthesized strand and each time one parental strand is always conserved so the original always exists Complications in DNA replication due to properties of DNA polymerase 0 DNA polymerase can only synthesize strands from 5 9 3 and it reads the parental strand 3 9 5 I This causes two different methods of replication for each of the two strands at the replication fork One strand the leading strand is continuously made from the 3 end The other strand the lagging strand is made in shorter fragments Okazaki fragments because since its 5 end is by the replication fork the replication process is repeated over and over from each newly exposed 3 part each time that the strand unwinds to let out more DNA 0 DNA polymerase cannot directly bind to DNA and start making a new strand it needs a free 3 OH end to link with the rst nucleotide it builds called a primer I DNAdependent RNA polymerase primase is an enzyme that can directly attach to DNA and make a copy of it but it produces RNA not DNA and it does this for a small region providing the primer DNA polymerase needs RNA primer a piece of complementary strand of RNA made by RNA polymerase it is required by DNA polymerase as a template to start its replication since DNA polymerase cannot directly attach to the open strand and start building new DNA Due to this mechanism after DNA polymerase does its job the new copy consists of DNA and RNA fragments To get rid of these three enzymes work together I Nuclease digests the RNA primers I Repair polymerase fllls gaps with DNA I Ligase seals gaps between the strands End problem that results from DNA replication of a linear chromosome 0 When RNA primer is cut out of the LAST DNA strand there is nothing at the end a gap that cannot be lled by normal action of polymerase and ligase I This means that the new strand has lost some of the 5 end and is shorter than the parental strand I This problem is solved by telomerase Telomerase a complex of RNA and proteins extends the normal 3 end of the parental strand end of which contains a Grich repeat series which then serves as a template for the elongation of the new strand in the same way as before 0 Primase adds RNA primer DNA pol extends it ligase seals gaps and nuclease eats away RNA primer 0 The extra 3 end of parental ssDNA is degraded so the two are now of equal length RNA dependent DNA polymerase activity Two modi cations made at the ends of mRNA transcripts RNA Capping a guanine nucleotide with a methyl group is added covalently at the 5 end of the new mRNA strand it confers stability on the RNA Polyadenylation A series of adenine nucleotides are added on to the 3 end of the new mRNA referred to as polyA tail 0 O The Genetic Code and Protein Translation Transcription conversion of information from one form to another in the same language Translation conversion of information between two different languages Codon a triplet of nucleotides in mRNA Degeneracy of the genetic code 0 Occurs when one set of elements does not uniquely map into another set 0 Comes from having 64 base triplets coding for only 20 amino acids 0 Multiple base combinations code for the same amino acids The genetic code and properties that make it nonrandom o Codons for the same amino acid tend to be similar with differences existing in the third position 0 Amino acids with similar physical properties are usually encoded by similar codons 0 Some amino acids are encoded by more codons than others Impact of nonrandomness on the effects of singlebase mutations in the DNA 0 This decreases chances of error because if the third base is changed chances are that it will be replaced with a letter that codes for the same AA Experiments that revealed the genetic code 0 Nirenberg and Mathhaei 1961 I Protein synthesis in vitro cellfree system I Made synthetic mRNAs with speci c bases These were made into proteins and the AA composition of the protein allowed them to determine with AAs were coded by which codons I Uuuuuuu 9 Phephephe I Ccccccc 9 Propropro Outcomes that occur for a protein when a single codon changes in the DNARNA 0 Same amino acid is made in the mutated position Similar amino acid is made in the same position Different amino acid is made in the same position A start codon is changed into a normal codon A normal codon is changed into a start codon A normal codon is changed into a stop codon A stop codon is changed into a normal codon OOOOOO Protein Translation Ribosomes Structure and function of a tRNA 0 The shape is in the form of a threeleaf clover with four stems on which the tRNA folds itself and forms base pairs I 3 of the stems have loops D anticodon and TpsiC in which 8 bases form a circle I 4th stem is attached to the appropriate amino acid at the 3 end 0 tRNA works to match up codons with their amino acids at the ribosome General structure of a ribosome 0 Two subunits I Small 30 proteins one rRNA I Large 50 proteins 3 rRNAs 0 Has 3 active sites A P E Steps in the Translation Cycle 0 Initiation initiator tRNA carrying MET comes in to P site and the mRNA is scanned until the AUG codon is reached This initiates the joining of the large ribosomal subunit with the small one o Continuation elongation factor Tu f1ts aminoacyl tRNA in the A site and if correct it forms base pairs with the mRNA codon GTP is hydrolyzed Then peptidyl transferase breaks the covalent bond between the COOH end of the polypeptide chain and the tRNA in site and transfers the chain to the free NH3 group of the amino acid in the A site forming a peptide bond During this the large subunit slides over and with the use of GTP hydrolysis so does the small subunit The empty tRNA is thus moved to the E site and is removed 0 Termination when either UAA UAG or UGA reach the A site peptidyl transferase adds water to the COOH terminus instead of an amino acid which releases the polypeptide from the peptidyl tRNA and also the ribosome The polypeptide diffuses away and the ribosome dissociates Maj or components of this machinery and their roles o Initiator tRNA a charged aminoacyl tRNA with met the start codon amino acid I Responsible for bringing the start codon amino acid to the P site of the small subunit so that the ribosome can assemble and begin translation 0 Translation initiation factors accessory proteins I Are loaded into the P site when the tRNA with met binds I They dissociate right before the large subunit joins the small one to form the ribosome o Elongation factor Tu a protein I Fits the aminoacyl tRNA into the A site during elongation I Hydrolyzes GTP when the aminoacyl tRNA in the A site base pairs with the mRNA codon o Peptidyl transferase ribosomal enzyme I Breaks the covalent bond between COOH of growing peptide chain and tRNA in the P site I Transfers the chain to the free NH3 group of the amino acid in the A site forming a peptide bond I When stop codons are reached it binds water 0 the COOH terminus causing the polypeptide to be released from the peptidyl tRNA and away from the ribosome o Elongation factor g protein I Uses the energy of GTP hydrolysis to move the small subunit over to line up with the large subunit Polysome a circular assembly of mRNA and ribosomes that allows for multiple ribosomes to be working on a single strand of RNA at the same time to translate it into proteins more ef cient than one ribosome having to go through the whole protein Structure and Function of Cellular Membranes Maj or lipids found in cell membranes 0 Phospholipids glycerol backbone with ester linkages to two long chain fatty acids hydrophobic tail and phosphoester linkage to polar head usually choline and ethanolamine hydrophilic head 0 Sphingolipids serine backbone onetwo acyl tails and various head groups 0 Glycolipids lipids with head groups that include one or more linked sugars Lipid mobility within the bilayer o FleXion of acyl chains 109sec o Rotation within lea et 107 sec 0 Lateral diffusion past each other 106diameters sec 0 Flipping between lea ets without ippase once per day 0 Temperaturedependent phase transitions vary based on lipid s properties Maintenance of lipid asymmetry through sorting is done by two phospholipidtranslocating enzymes 0 Scramblase in the ER membrane work to shift phospholipids between the lumenal and cytoplasmic lea ets done randomly o Flippase sorts speci cally makes sure phospholipids with amine head groups are located in the intracellular lea et Membrane component mobility experiments l Frye and Edidin a Mouse cell fused with human cell 9 hybrid heterocaryon b Found that over time membrane proteins were mobile and could diffuse laterally in the plane took 40 min to mix 2 FRAPing Fluorescence recovery after photo bleaching a Membrane proteins uorescently labeled in live cells and a spot was bleached on cell surface b Recovery brightness was not completely recovered at once but slowly came back and told us that membrane proteins diffused laterally into bleached region to increase the brightness but different proteins diffused differently 3 Single Particle tracking a Individual membrane proteins were labeled with antibody that had gold on it individual movement was followed b Found that lateral diffusion does occur confirmed that different proteins diffuse differently Structure and Function of Integral Membrane Proteins Membranespanning portions of integral membrane proteins 0 Usually alpha helices with hydrophobic amino acid side chains R groups and phospholipids on either side 0 Sometimes can be beta strands arranged in a barrel shape Functions of integral membrane proteins 0 Receptors bind stuff outside the cell and convey information to the inside without conveying molecules Transporters active needing energy and passive using gradient energy Enzymes speed up reactions Regulators proteins that sendrespond to signal change activity of other proteins Junctions important for cellcell interactions most proteins serve more than one of these functions Maj or membrane proteins examples 1 Nerve Growth Factor NGF Receptor a membranespanning receptor tyrosine kinase a Outside is the receptor inside has enzyme activity single alphahelix span b Dimerization function brings two NGF receptors together to dimerize c Enzyme function causes two receptors to phosphorylate each other phosphorylation creates binding sites for other proteins that also become phosphorylated on tyrosine residues d Result signaling complex pathways of signaling are activated through activation and phosphorylation of target proteins 2 Ion Channels diffusion down a gradient passive transport no external energy used a Made of multiple alpha helices that have hydrophobic and hydrophilic faces b NaCa superfamilies of channels exist as ionspecific pores in the membrane c 24 membranespanning domains per channel 4 separate subunits that span 6 times each Some are leaky but still selective always open e Some are gated only open under specific conditions changes in transmembrane voltage ligand binding mechanical force etc Important for nerve impulse conduction 0000 3 Sodium Glucose Symporter active transporters use energy a Present where Na outside concentration is high and Glucose inside concentration is high b Symporter uses favorable ow f 2Na into the cell to drive unfavorable transport of glucose into the cell coupled transport c Two kinds of binding sites i 2 for Na ii 1 for glucose When Na binds makes glucose binding more likely d Two states i One site faces outside one inside ability to ip between them ii When Na binds makes glucose binding more likely e Process when both are facing outside Na and glucose binds molecule ips and both and released inside cell 2Na glucose 4 Sodium Potassium ATPase N aK pump a Na is higher outside K is higher inside this disequilibrium is maintained by the pump through a threestep mechanism i The pump binds 3 Na inside ATP phosphorylation causes it to ip and face the outside and Na diffuses away ii 2 K bind from outside it ips again due to ATP phosphorylation and faces inside 2K diffuses away into cytosol iii Electrogenic function the pump generates an electrical and a chemical gradient 1 3 2 NaK ratio moved by each cycle 2 Conversion of ATP into potential energy rest is stored Disequilibrium across the membrane Na is lO20x higher outside than inside K is lO20x higher inside than outside 0 This disequilibrium is maintained by NaK ATPase through a 2part cycle binding conformational change and release 0 3 kinds of disequilibrium I Na gradient I K gradient I Electrogenic makes inside of cell negative Membrane Function the Nerve Impulse Vm membrane potential sum of all contributions to voltage across the membrane 0 Maj or contributing ions are Na and K Na is lO20x higher outside than inside K is 10 20x higher inside than outside Vx equilibrium potential of a speci c ion X value that would be reached if that ion and only that ion were allowed to ow across the membrane until it reached its electrochemical equilibrium Four characteristics of nerve conduction 1 Rapid rates are 50100 msec accomplished via electrical impulses carried by long processes 2 All or none no partial signals either a 100 signal is propagated or none at all 3 Unidirectional an impulse is conveyed along an axon in one direction only no feedback 4 Undiminished no matter the axon length the signal arrives at the synapse with same amplitude axons in our bodies are up to a meter long these properties make signal transduction a quick reliable and ef cient process Membrane protein complexes responsible for the axon s resting membrane potential 0 NaK ATPase generates the electrochemical disequilibrium o K leak channel responsible for Vm 70mV Membrane protein complexes responsible for the axon s action potential and how they behave o Voltagegated ion channels closed at rest but open at threshold voltage when the membrane depolarizes due to a stimulus 50 mV I Na channels open quickly and close quickly initial in ux of Na ions 9 further depolarization I K channels open slowly and close slowly ef ux of K ions 9 repolarization Action potential propagation along the axon o Depolarization in one region affects adjacent regions due to the diffusion of ions current ow I Flow of charge causes depolarization in adjacent regions which triggers action potentials there and keeps going all the way down the axon o Unidirectionality caused by the refractory period I Once channels have opened and closed they cannot open again for a few milliseconds so the action potential can only move in one direction and cannot bounce back to the direction it came from Energetics of Solute Movement Across Membranes Charged solutes move based on 1 charge gradient and 2 concentration gradient 0 As for Na the charge gradient ows in because negative outside 9 positive inside and concentration gradient ows in also because high concentration outside 9 low concentration inside so we know that Na ows in 0 But in certain cases such as K the charge gradient ows in but the concentration gradient ows out because high concentration inside 9 low concentration outside so the data must be quantitatively measured to find true direction of ion ow Gibbs free energy of solute gradients equation AG RTlnXinXOut zFVm o RTlnXinXOut accounts for concentration difference I Converted to 57 kJmol x logXinXOut o zFVm accounts for charge difference I z charge of species I F Faraday s constant 100 kJNmol I Vm membrane potential Using Gibbs free energy 0 If AG 0 X is at equilibrium 0 If AG lt 0 then ow of X into cytoplasm is favorable Nemst equation VX RTzF x ln X out X in 0 Used to find equilibrium potential for a specific ion X 0 Convert to VX 59mVz x logX0utXin o If Vm VX then ion X is at equilibrium Bioenergetics Overview and Glycolysis Four stages of metabolism glucose breakdown l Glycolysis I Occurs in cytosol I Chemical energy 9 chemical energy enzymatic coupled reactions I Energy harvested in the form of ATP high energy electrons I C6leO6 9 10 steps 9 2 pyruvates C3 9 Stage 2 2 TCA Cycle Krebs I Occurs in mitochondrial matrix I Chemical energy 9 chemical energy enzymatic coupled reactions I Energy harvested in the form of GTP high energy electrons I 2 pyruvates C3 9 release of C02 and CoA 9 acetyl CoA C2 9 cycle of C4 9 C5 9 C6 C02 released each time 3 Electron transport chain I Occurs in inner mitochondrial membrane I Proton pumping redox energy 9 potential energy in gradient I Energy harvested in the form of potential energy of the protein gradient across the membrane I Crossing over of high energy electrons form one to another protons released 02 released at end and turned into H20 4 Mitochondrial ATP Synthesis I Occurs across inner mitochondrial membrane intermembrane space and matrix I Proton ow down its gradient coupled with ATP synthase I Energy harvested in the form of ATP High energy electrons in the cell 0 Hydride ions H 39 H 2e39 0 Carrier molecules move hydride ions form harvest sites to sites of use NAD H 39 9 NADH FADH H 39 9 FADHz oxidized form 9 reduced form Nature and role of the electron carrier NAD in glycolysis o Dinucleotide adenine a nonbase nicotanimide 0 When hydride charge is accepted its bonds are rearranged in a nicotine ring 0 Its role is to carry the high energy electrons from where they were generated in the cytosol or the mitochondrial matrix to the site where they will be used to synthesize ATP on the inner mitochondrial membrane Glycolysis o Occurs in 10 total steps each with its own enzymes I lSt three steps involve input of energy 2 ATP per glucose for phosphorylation I Next three steps work to split 6C 9 2 x 3C rearranging of bonds I Last few steps give us 4 ATP 2NADH but only 2 net ATP gained I Inputs 2 ATP in steps I done by hexokinase and 3 done by phosphofructokinase I Outputs 4 ATP 2 each at 7 and 10 2 NADH at 6 Anaerobic followup to glycolysis Fermentation 0 C3 pyruvate 9 C3 lactate reducing power is used up 0 This is necessary for glycolysis to continue because NAD is reduced through oxidation of NADH and this NAD is needed for catalysis of step 6 in glycolysis Bioenergetics Mitochondria Properties of the different membranes 0 Inner mitochondrial membrane I High protein content 75 I Very impermeable I Large surface area bc highly folded 0 Outer mitochondrial membrane I Very permeable leaky I Has porins integral membrane proteins made of parallel beta sheets I Ionic composition is same on both sides of OMM TCA cycle 0 Occurs in the mitochondrial matrix 0 A high energy C3 compound enters matrix a C2 acetyl groups goes in and the carbon compounds are systematically oxidized giving out low energy COzs 0 Changes in free energy are captured as NADFADH 4 NADH and l FADH2or GTP synthesis 1 GTP o 9 total steps 8 in cycle 6 of 8 are coupled to energy harvesting Inputs Pyruvate 2 NAD GDP Pi FADH coA o Outputs 4 NADH l FADHz 3 CO2 l GTP per pyruvate molecule 0 Energy from carbohydrate oxidation electrons is harvested by NAD 9 NADH and FADH 9 FADHz Nature and function of NAD and FADH in the TCA cycle 0 NAD and FADH are electron acceptors that use energy and harvest it by reducing themselves to NADH and FADH2 o NADH is a product of glycolysis and the TCA cycle 0 FADH2 is only produced in the Krebs cycle Electron transport chain 0 Made up on protein complexes that can accept electrons from molecules with lower electron affinity and donate them to molecules with higher electron affinity Four complexes exist 1 Complex 1 NADH dehydrogenase 2 Complex II Succinate dehydrogenase 3 Complex 111 Cytochrome BCl 4 Complex IV Cytochrome C oxidase o NADH and FADH2 transfer electrons to parts of the electron transport chains that have higher affinity for electrons These electrons move down the chain going to those with higher and higher aff1nities these electron transfers are spontaneous AG lt 0 0 At three steps in the ETC the free energy from electron transfer is coupled to unfavorable proton pumping from mitochondrial matrix 9 across inner mitochondrial membrane 9 intermembrane space I This creates a pH and charge gradient across IMM ApH 12 pH units AV gt lOOmV 0 At end of ETC the final electron transfer process is from Cytochrome C 9 Oxygen Without Oxygen the whole chain backs up with everything in its reduced form and stops functioning 0 Inputs NADH FADH2 ADP H 02 o Outputs NAD FADH ATP HzO Energy of carbohydrate oxidation harvested by the ETC is stored as potential energy in the proton gradient across the membrane established by the proton pumping done by the protein complexes This energy is then used by ATP synthase to make ATP ATP Synthase a multisubunit protein which has a shiftable transmembrane channel that allows protons to ow through from IMS 9 across IMM 9 matrix down gradient favorable transport and couples this process to the making of ATP from ADP and Pi 0 F0 A rotary mechanism takes in H in ux of H causes it to rotate generating a conformational change in the other part of the molecule F1 and energy of movement helps make the ADP Pi bond to make ATP 0 12 H make a full rotation each rotation makes 3 ATP 9 4 H ow through per ATP molecule Forms of energy that are interconverted by this complex 0 Potential energy 9 kinetic energy energy from the gradient is used to fuel energy of movement in the rotator of the ATP synthase molecule 0 Kinetic energy 9 chemical energy energy of movement is used to create a bond between ADP and Pi making ATP ATP Synthase makes ATP in the matrix but it is actually needed in the cytoplasm o ATPADP Translocator antiporter Swaps ADP 3 in for ATP 4 out I Energy for this to run comes from AV charge gradient across IMM Mitochondria 11 Transport Functions and Evolution Transport across the inner mitochondrial membrane is done in two ways 0 It can be coupled directly to the H owing down the electrochemical gradient I Pyruvate transport done by a symporter in the IMM to move pyruvate from intermembrane space and the cytoplasm 9 matrix along with H ow driven by pH gradient I Phosphate transport done by a symporter which moves Pi from intermembrane space and the cytoplasm 9 matrix along with H ow driven by pH gradient 0 It can be driven indirectly by the electrochemical gradient I ATP and ADP transport done by an antiporter which moves one ATP439 molecule out of the matrix and one ADP339 molecule into the matrix so one net charge is removed from matrix IMM has voltage on inside so the electrical gradient drives this process Stages in bacterial evolution metabolism 35 billion years ago 1 ATP driven proton pump HATPase I Early prokaryotes used abiotic carbs as an energy source and released organic acids I This led to transmembrane pumps that could use ATP to pump protons out of the cell 2 Electron transport chain HATPase I Something needed to be changed so that too much ATP wasn t used to pump protons out I This led to electron transport chains that could use redox as a source of energy for proton pumping 3 Combination Electron transport chain and ATP synthesis I As ef ciency increased ATP dependent proton pump could be reversed and used 0 to synthesize ATP Bacterial evolution 9 mitochondria o Photosynthetic bacteria used sunlight 9 reducing power carbon xation o Bacteria could use water as a source of electrons for C02 reduction 9 9 9 water splitting enzyme led to 02 production and release in large quantities 0 Presence of 02 9 9 9 electron transport chains that could break down molecules to C02 and H20 getting out maximum energy 0 Bacteria that lost photosynthetic capacity became respiratory bacterium similar to mitochondria 0 Origin of mitochondria engulfment phagocytosis of respiratory bacterium by a protoeukaryotic cell Plant Photosynthesis Chloroplast membrane properties 0 Outer envelope membrane I Leaky due to porins 0 Inner envelope membrane I Impermeable due to proteins I Contains a variety of transporters o Thylakoid membrane I Contains membranous sacs called thylakoids stacks of thylakoids are called grana I Continuous all sacs are connected forming an inner compartment called thylakoid lumen Light Dependent Reactions 0 2H20 2NADP 9 02 2NADPH also H gradient 9 ATP formation 0 Water is split electrons are stripped and energized twice 0 Electrons move down ETC coupled to H pumping across thylakoid membrane stroma 9 thylakoid lumen Electrons are nally used to reduce NADP 9 NADPH H ow through ATP synthase to make ATP Occur in membrane and lumen of thylakoids Components photons chloroplasts chlorophyll 9 organized into photosystems antenna complex reaction center 0 Inputs ADP NADP H20 light energy 0 0utputs ATP NADPH 0xygen Light Independent Reactions 0000 0 C02 NADPH reducing power ATP to generate phosphorylated intermediates 9 CH20 carbs ADP NADP Calvin Cycle opposite of TCA cycle takes place Where Carbon is systematically reduced reverse of steps 6 and 7 in glycolysis CH20 exits the cycle 1 out of 6 GAP peels out 5 go on to further synthesis Rubisco an enzyme reduces C02 9 sugar very slow but very abundant in body Occur in stroma Inputs C02 NADPH ATP 0utputs C6H1206 H20 NADP l ADP Products that are available for the plant cell to use in the light independent reactions I ATP I NADPH Both accumulate in stroma during light dependent reaction provide energy for light independent reaction Final photosynthetic products that are made by the plant cell the nal yield that leaves the Calvin cycle is glyceraldehyde3phosphate which then goes on to the pathway for synthesis of larger sugars such as glucose and fructose still occurring in stroma and cytoplasm 0 000000
Are you sure you want to buy this material for
You're already Subscribed!
Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'