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by: Ezequiel Orn


Ezequiel Orn
GPA 3.89

Jessica Wandelt

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Jessica Wandelt
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This 27 page Class Notes was uploaded by Ezequiel Orn on Sunday September 6, 2015. The Class Notes belongs to BIO 311C at University of Texas at Austin taught by Jessica Wandelt in Fall. Since its upload, it has received 24 views. For similar materials see /class/181710/bio-311c-university-of-texas-at-austin in Biology at University of Texas at Austin.




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Date Created: 09/06/15
Worksheet 1 The Chemical Context of Life 1 An atom consists of a nucleus and an outer part called the electron cloud The nucleus contains PROTONS and NEUTRONS 2 Fill in the charge for each type of subatomic particle 1 Proton b Neutron 0 c Electron 1 3 The atomic number of an element indicates the number of PROTONS in the nucleus of the atom and also tells us the number of ELECTRONS outside the nucleus This number is unique for each element 4 The mass number of an element can vary This number is the sum of the PROTONS and NEUTRONS of an atom Thus you can determine the number of NEUTRONS by subtracting the atomic number from the mass number 5 Draw the structure of the magnesium atom atomic number 12 amp mass number 24 This was a bit hard to draw on computer but you get the idea 7 just have them show how many protons neutrons and electrons amp where they are in the atom 6 Isotopes of an element differ in the number of neutrons found in the nucleus A One isotope of chlorine has 17 protons and 18 neutrons B while another has 17 protons and 20 neutrons For both isotopes fill in the atomic number mass number and number of electrons outside the nucleus I Isotope I protons I neutrons I Atomic I Mass I electrons I A 17 18 17 35 17 I B I 17 I 20 I 17 I 37 I 17 I 7 Electrons around the nucleus of an atom are found in different energy levels or electron shells The first shell closest to the nucleus can hold up to 2 electrons The second electron shell can hold up to 8 electrons 8 Complete the following electron distribution diagrams Identify each atom My computer is not letting me do this right now but all of the answers are in Figure 29 of the textbook Just draw circles around these nuclei to show the electron shells chlorine sodium 11 Hydrogen carbon 9 Fill in the following chart 10 TF The chemical properties of an atom are primarily determined by the number of electrons present in the valence shell Correct the statement if it is falseTrue The number of electrons needed to complete the valence shell will determine the atoms behavior 11 TF Atoms with a completed full valence shell are highly reactive Correct the statement if it is false False Atoms with a full valence are inert Atoms with incomplete valence shells are chemically reactive 12 A covalent bond is formed when two atoms share a pair of electrons Using electron shell diagrams show how two oxygen atoms atomic 8 participate in a covalent bond with each other See figure 212b 13 Which of the following is a olar covalent bond Due to different electronegativities a H H b C C c 0 H d 0 0 14 An ionic bond is formed by the attraction of an anion to a cation An anion is an ion with a negative charge while a cation has a positive charge 15 An ion is an atom that has acquired an electrical charge by either losing or gaining an electron 16 Using electron shell diagrams show how a lithium atom atomic 3 and a chlorine atom atomic 17 form an ionic bond Basically the same as figure 214 but with one less electron shell for lithium as compared to sodium 17 Below is a water molecule Label the molecule to show partial charges Draw a second water molecule next to this one and indicate with a dashed line where you would expect a hydrogen bond to form H O O is slightly negative H s are slightly positive H bond forms between positive H of one water and H negative 0 of another Worksheet 2 Water 1 Below is a water molecule Label the molecule to show partial charges Draw a second water molecule next to this one and indicate with a dashed line where you would expect a hydrogen bond to form 0 O is slightly negative H s are slightly positive H bond forms between positive H of one water and H negative 0 of another 2 What is the maximum number of hydrogen bonds a water molecule can form 4 3 If the temperature of a body of water increases what happens to the hydrogen bonds between the water molecules Circle one Hydrogen bonds are formed Hydrogen bonds are broken 4 A gram of water at 0 C occupies more or less circle one volume than a gram of water at 4 C Why Water expands as it cools below 4 C 5 When a salt is dissolved in water salt is the solute or solvent and water is the solute or solvent Circle one for each 6 Is table salt NaCI hydrophilic or hydrophobic hyd rophilic What happens to the NaCI when it is added to water Ionic bonds between Na and CI are broken Each ion becomes hydrated surrounded by water molecules 7 In pure water the concentration of H is 101M and the concentration of OH39 is 101 8 What is the formula for calculating the pH of a solution pH og H 9a What is an acid a IIh tanre that inrrea e iHi of solution 9b What is an acidic solution a solution where lHi gt OH i 10a What is a base a substance that reduces H of solution 10b What is a basic solution a solution where lOH i gt iHi 11a If the pH of a solution is 10 then the H is 10 M 11b Is this solution acidic or basic basic 11c What is the CH of the solution 101M 12a If the pH of a solution is 6 then the OH39 is 10iM 12b Is this solution acidic or basic acidic 12c What is the H 10i M 13 How would you make 1 L ofa 1 M solution of MgCIz 94 g MgC2 water up to 1L 14 How would you make 3 L ofa 02 M solution ofglucose C5H1205 108 g C6H126 water up to 3L 1 U39l How would you make 500 ml ofa 3 M solution of H2C03 93 g water up to 500ml Worksheet 3 Biomolecules 1 Draw each of the following chemical groups a carbonyl CO b hydroxyl OH c sulfhydryl 5H d carboxyl COOHe phosphate 0P03239f amino NH3 2 Name of the chemical reaction that breaks a polymer down to its individual monomers Hydrolysis 3 Name of the chemical reaction used to build polymers by joining individual monomers together Dehydration reaction type of condensation reaction 4 Name the monomers used to build each of the following macromolecules Lipids None ipids are not polymers Carbohydrates monosaccharides Proteins amino acids Nucleic Acids nucleotides 00 Um 5 List the major functions of the carbohydrates energy storage structural support cell communication recognition 6 Draw a straight chain aldohexose Which chemical groups are always found in a straight chain sugar 0 OH OH OH OH HC CH CH CH CH CHZOH Carbonyl CO and hyd roxyls OH In aldohexose carbonyl on C1 hydroxyl on each of the five other carbons 7 Draw a straight chain ketohexose a structural isomer of the aldohexose above What are structural isomers OH O OH OH OH HZC C CH CH CH CHZOH In ketohexose carbonyl on CZ hyd roxyl on each of the five other carbons Structural isomers save atoms but with different covalent arrangementpartners 8 What is the name of the covalent bond that links carbohydrate monomers Between which chemical groups does it form Glycosidic linkage between OH on one sugar in ring form and OH on another sugar in ring form 9 Using the figure shown at rig ht as a reference a draw 2 molecules of glucose joined by a 14 El linkage see below b draw 2 molecules of glucose joined by a 1 4 El linkage see below c Write the molecular formula for each disaccharide drawn above El glucose El glucose C12H22011 El glucose El glucose C12H22011 d What is the significance to most animals if carbohydrate monomers are connected by El or Cl linka g e s ONLY HAVE ENZYMES TO HYDROLYZE ALPHA LINKAGES CANNOT DIGEST BETA 14 GLYCOSIDICLIN KAGES e Which linkages are found in starch glycogen WITH 4 AND VII 6 cellulose 10 List the major functions of the different types of lipids triglycerides phospholipids and steroids Triglycerides energy storage cushioning phospholipids membrane structure steroids membrane structure cell communication 11 What characteristic is used to categorize different lipids in the same class of biomolecules why are triglycerides phospholipids and steroids grouped together Hydrophobic water insoluble 12a In the space below draw one saturated fatty acid molecule and one unsaturated fatty acid molecule both containing 12 carbon atoms SATURATED HOOC 7 CH2 7 CH 7 CH2 7 CH2 7 CH2 7 CH2 7 CH2 7 CH2 7 CH2CH2CH3 UNSATURATED HOOC 7 CH2 7 CH 7 C C 7 CH2 7 CH2 7 CH2 7 CH2 7 CHzCHzCHg cis 12b Write the molecular formula for each molecule you have drawn below Saturated fatty acid molecular formula C12H2402 Unsaturated fatty acid molecular formula C12H2202 12cWhat is the difference between a saturated and unsaturated fatty acid SATURATED FA HAVE NO DOUBLE BONDS EACH CARBON IS SATURATED WITH HYDROGENS UNSATURATED FA HAVE DOUBLE BONDS FEWER HYDROGENS PER CARBON ATOM 12d In the space below draw a geometric isomer of the unsaturated fatty acid you drew in 12a What are geometric isomers Label each of your isomers cis and trans H UNSATURATED HOOC 7 CH2 7 CHz 7 C C 7 CH2 7 CH2 7 CH2 7 CH2 7 CHzCHzCH3 trans H Geometric isomers have same atoms with same covalent arrangementspartners but differ in orientation about CC cis groups on same side of CC trans groups on opposite sides of CC 13 In the space below draw glycerol OH OH OH HZC CH CH2 14 What is the name of the bond that links fatty acids to glycerol Between which chemical groups do these bonds form Ester linkage between OH on glycerol and COOH on fatty acid 15 What determines whether a triglyceride is solid or liquid at room temperature The structure and packing of the fatty acids Straightlong fatty acids pack tightly together 9 triglyceride more solid at RT with saturated or TRANS unsaturated fatty acids Kinkedshorter fatty acids pack ess tightly 9 triglyceride less solid at RT with CIS unsaturated fatty acids 16a How does the chemical composition of a phospholipid differ from that of a fat FAT GLYCEROL 3 FATTY ACIDS PHOSPHOLIPIDS GLYCEROL 2 FATTY ACIDS PHOSPHATE GROUP 16b How does the behavior properties of a phospholipid differ from that of a fat hint think about what you just answered above FATS HYDROPHOBIC ALL HYDROPHILIC PARTS ARE COVERED BY HYDROPHOBIC PHOSPHOLIPIDS AMPHIPATHIC HYDROPHILIC HEAD HYDROPHOBIC TAIL 17 List the major functions of proteins in cellsorganisms Catalysts enzymes structural support storage of amino acids defense transport communication chemical messengers amp receptors regulation 18 Draw a generic amino acid with the side chain labeled R Draw an enantiomer of your amino acid What are enantiomers R R H3N C COO OOC C NH3 H H Enantiomers have the same atoms with same covalent arrangementspartners but differ in orientation about asymmetric carbon a carbon with 4 different groups attached like the alpha carbon of amino acid due to tetrahedral arrangement of 4 groups around central carbon 19 Draw two generic amino acids joined by a peptide bond Circle the peptide bond Between which chemical groups did the peptide bond form 0 R H3N cc039 H I n W 0 32 2 Amino NH2 and carboxyl COOH 20 What is the difference between a polypeptide and a protein POLYPEPTIDE IS NONFUNCTIONAL LINEAR SEQUENCE OF AMINO ACIDS PROTEIN IS POLYPEPTIDE THAT IS FOLDEDCOILED INTO FUNCTIONAL CONFORMATION 21 For each of the following amino acids state whether its R group is polar polar ampcharged or nonpolar Would each be hydrophobic or hydrophilic a Leucine NONPOLAR b Cysteine NONPOLAR SPECIAL c Glutamic acid CHARGED d Tyrosine POLAR e Serine POLAR f Histidine CHARGED 22 Would you expect an amino acid with a nonpolar amino acid to be found on the external surface of a water soluble protein or buried internally Explain your answer BURIED INTERNALLY HYDROPHOBIC EFFECT 23a What type of bonds are important for primay structure of proteins Covalent peptide bond 23b Which atoms from which chemical groups are involved in the primary structure of proteins H from NH2 and OH from COOH 23c List two amino acids you might nd involved in primary structure Anyall 24a what type of bonds are important for secondary structure of promins Hydrogen Which atoms from which chemical groups are involved in the secondary structure of proteins H from NH and O from cO leftovers of NH2 and COOH of polypeptide backbOnd 24c List two amino acids you might nd involved in secondary structure Anyall 24d List the two regular patmms of secondary structure seen in promins Alpha helix and beta pleated sheet 25a Bonds important for the tertiary structure of proteins occur between which parts of the amino acids in a polypeptide Rgroups 25b Fill in the chart below describing the types of inmrac ons involved in the tertiary structure of proteins In the third and f L 39 39 2 examples of 39 39 39 involved in each type of bond TYPE OF INTERACTION STRONG OR WEAK 2 AMINO ACIDS INVOLVED 1HYDROGEN BOND WEAK SERINE GLUTAMINE ZVAN DER WAALS WEAK 3 IONIC BOND WEAK LYSINE 4 DISULFIDE BRIDGE STRONG CYSTEINE CYSTEINE 26 what types of bonds are important in determining quaternary structure of promins HYDROGEN BONDS VAN DER WAALS IONIC BONDS DISULFIDE BRIDGES hat is denaturation Which levels of promin structure are usually disrupted by denaturation WHEN A PROTEIN UNRAVELS AND LOSES rrs NATIVE A DENATURED PROTEIN IS IOLOGICALLY INACTIVE 28 List the major functions of the nucleic acids smre transmit and use39 express the genetic information PHOSPHATE 29a Label the three Components of the nucleotide 29b Does this nucleotide oontain a purine or Purine adenine 7 don t need to know specific 29c TO which ZOther nucleotides might this Pyrimidines 7 either cymsine or thymine in this case thymine 29d Is this a DNA nucleotide or an RNA nucleotide How can you tell DNA 7 No 70H on 2c of sugal deoxyribose 30 Name of the covalent bond that joins neighboring nucleotides in a polynucleotide chain Between which chemical groups does it form PhOsphOditer between hydroxyl and phospham 31a What type of bonds hold the two strands of a DNA molecule together Hydrogen 31b Between which components of the nucleotides are these bonds formed Nitrogenous bases 31c The two strands in a DNA molecule are antiparallel Explain what this means THE 2 STRANDS RUN IN OPPOSITE DIRECTIONS 32 Which functional group is found at the 5 end of an RNA molecule At the 3 end of an RNA molecule 5 phosphate 3 hydroxyl 33 List three different types of RNA used by the cell Give a brief description of the function of each mRNA messenger RNA copy of a gene used to specify primam structure of a proteinI carries message to ribosome rRNA ribosomal RNA used to make ribosome along with protens tRNA transfer RNA that translates nucleotide language of mRNA into amino acid language of polypeptide transfers amino acids to ribosome 34 List two differences between DNA and RNA 1 DEOXYRIBOSE SUGAR IN DNA RIBOSE SUGAR IN RNA 2 A T C G BASES IN DNA A U G C BASES IN RNA 3 DNA USUALLY DOUBLE STRANDED39 RNA USUALLY 9 Metabolism 1 What distinguishes reversible inhibition from irreversible inhibition Attachment of the inhibitor to the enzyme Covalent bonding usually irreversible Weak bonding reversible 2 What distinguishes competitive inhibition from noncompetitive inhibition Where the inhibitor binds to the enzyme Active site competitive Elsewhere noncompetitive regulatory site a on and 3 glucose ring CHZO CH20 3 Compare kinetic energy and potential H H energy Kinetic the energy of motion Potential the energy stored by matter as a result of its location or arrangement 0 39 H H 4 What 395 free energy b Starch 1 4 lirtikage of or glucose The portion of a system 5 energy that is available to perform work CI39ILZO 5 How does knowing the DG of a reaction F 9 allow us to predict if it is spontaneous or not H DG spontaneous O llG nonspontaneous H H c Celluld39sle 1 4 linkage of 3 glucose monomers 6 Describe the differences between an endergonic reaction and an exergonic reaction Exergonic energy out release of free energy negative DG spontaneous Endergonic energy in absorb free energy positive DG nonspontaneous 7 What is the activation energy of a reaction Initial investment of energy required to start a reaction get it up to the transition state Energy needed to get over energy barrier 8 What is a catalyst Describe how enzymes work as catalysts How do enzymes affect DG Catalyst chemical agent that speeds up a reaction without being consumed by the reaction Enzymes speed up chemical reactions by lowering the activation energy barrier decreasing the amount of energy needed to get over energy barrier and they don t affect DG 9 Explain how an enzyme can be inhibited or stimulated by an allosteric regulatory molecule Binding of an allosteric inhibitor to one regulatory site will stabilize the inactive conformation Binding of an allosteric activator to one regulatory site will stabilize the active conformation 10 Give an example of a catabolic reaction and an anabolic reaction Catabolic cell respiration fermentation Anabolic biosynthesis of polypeptides polysaccharides nucleic acids fats 11 How does ATP hydrolysis power cellular work The transfer of the terminal phosphate group to another molecule phosphorylation creates a reactive phosphorylated intermediate that undergoes a change that performs work 12 What is a spontaneous reaction A reaction that does not require the input of energy Worksheet 4 Cell amp Cell Structure Match each term below to the following descriptions Terms may be used once more than once or not at all a Mitochondria b Rough ER c Smooth ER d Nucleus e Vacuole f Ribosome g Lysosome h Golgi apparatus i Chloroplast j Pilifimbriae k Nucleoid l Capsule m Flagella n Cell wall 0 Plasma membrane 1 7 iThe region where DNA is found in prokaryotic cells K 2 Site of protein synthesis in both prokaryotic and eukaryotic cells F 3 Involved in genetic control of eukaryotic cells DF 4 These organellesstructures are found in plant cells and not animal cells I N V 5 In prokaryotic cells these are naked and composed of the protein flagellin M 6 Contains phospholipids A B C D E G H I O 7 Energy transforming organelles A I 8 Hair like appendages on prokaryotic cells that aid in attachment J 9 Components of the endomembrane system B C E G H O 10 Site of cellular respiration in nearly all eukaryotic cells A 11 Sticky outer layer that aids in protection and attachment of some prokaryotic cells L 12 if Site of photosynthesis in eukaryotic cells I 13 Found in eukaryotic cells not prokaryotic cells A B C D G H I 14 DNA found here D K 15 Found in prokaryotic cells not eukaryotic cells J K L 16 These organellesstructures are found in animal cells and not plant cells G For each of the following statements decide if it applies to the Archaea A Bacteria B Prokaryotes P Eukarya E or all 17 7 Contain circular chromosomes P 18 7 Contain membrane bound organelles E 19 7 Flagella made from microtubules E 20 7 Peptidoglycan present in cell walls B 21 7 Cellulose present in cell walls E 22 7 Contain 7OS ribosomes P AND E IN MITOCHONDRIA AND CHLOROPLASTS 23 7 Contain DNA A 24 7 Ribosomes contain two subunits All 25 7 DNA 9 RNA 9 protein All 26 Contain linear chromosomes E 27 Contain SOS ribosomes E 28 Contain cytoplasm Al Worksheet 5 Cell Membrane Structure amp Function H Describe the Fluid Mosaic Model of membrane structure Membrane is fluid not static due to the phospholipid bilayer fluidity depends on hydrocarbon tails of phospholipids Membrane is a mosaic of different components The variety of proteins in the membrane adds most to the mosaic nature N What factors affect membrane fluidity How do they affect fluidity increase or decrease Temperature increase T increase fluidity decrease T decrease fluidity Fatty acid saturation saturated FA decrease fluidity unsaturated cis FA increase fluidity Fatty acid length increased length decreased fluidity decreased length increased fluidity Cholesterol increased cholesterol decreased fluidity generally 5 Compare integral membrane proteins and peripheral membrane proteins Integral membrane proteins penetrate the hydrophobic core of the lipid bilayer break the surface They are amphipathic Peripheral membrane proteins are attached to the surface of the membrane not embedded within it They are general hydrophilic 4 What is the main function of membrane glycoproteins and glycolipids On which side of the plasma membrane are you most likely to find such molecules Cell cell recognition Typically found on the extracellular side of the plasma membrane 4b Outline the events involved in the production amp targeting of a membrane glycoprotein How does the cell ensure that the sugars are on the proper side of the membrane The polypeptide is built by a bound ribosome into RER membrane Completed protein in RER membrane Sugars added to protein on side facing lumen of RER RER membrane with glycoprotein pinched into a vesicle carried by motor protein on microtubule to cis golgi Glycoprotein modified as it moves from cis trans golgi Glycoprotein in membrane of trans golgi packaged into vesicle and carried by motor proteins on microtubules to plasma membrane Vesicle fuses with plasma membrane such that glycoprotein is now part of plasma membrane Sugars that were facing the interior of the RER vesicle golgi vesicle 9 faces outside of cell Ensure proper orientation by building with correct orientation in RER build facing lumen if it will end up facing extracellular fluid 5a What does it mean for a substance to diffuse down its concentration gradient Substance moves from region of higher concentration to region of lower concentration 5b Can a substance diffuse against its concentration gradient Explain No Diffusion is defined as movement down a gradient 5c Molecules diffuse down their concentration gradient until they are equally distributed Describe what happens to molecule movement at this point DYNAMIC EQUILIBRIUM MOLECULES CONTINUE MOVING BUT THERE IS NO NEI39 DIRECTION OF MOVEMENT MOVEMENT IN ONE DIRECTION EQUALS MOVEMENT IN OPPOSITE DIRECTION 6 What is osmosis Why is it important for cells The diffusion of water across a selectively permeable membrane Water diffuses from the region of lower solute concentration high concentration of free water to the region of higher solute concentration low concentration of free water Water movement can affect cell volumestructure 7a What will happen to a plant cell placed in a hypotonic environment Hypertonic environment Isotonic environment Hyptotonic cell becomes turgid best scenario for plant Hypertonic ce becomes plasmolyze Isotonic cell is flaccid limp or wilted 7b What will happen to an animal cell placed in a hypotonic environment Hypertonic environment Isotonic environment Hyptotonic expands may burst Hypertonic shrivels Isotonic proper volume 8 What is facilitated diffusion Is it active or passive Why must some solutes cross membranes by facilitated diffusion rather than by simple diffusion Passive transport with the help of membrane transport proteins It is passive thus passive transport Some substances that are large andor polarhydrophilic cannot easily cross the hydrophobic core of the membrane by themselves 9 What is the difference between a carrier protein and a channel protein Which type of transport protein would you expect to be used in facilitated diffusion Active transport A channel protein are simply hydrophilic passageways through the membrane while carrier proteins grab their cargo and change shape to shuttle to get it across the membrane Facilitated diffusion both types used Active transport only carrier proteins used 10 Why does the Na KT pump require energy and what is the energy source This is an example of which type of active transport Pumping ions against their gradient active transport ATP Primary active transport using ATP directly 11 What are the two components of an electrochemical gradient Concentration gradient Membrane potential voltage across membrane 12 What is secondary active transport co transport How could a cell use the gradients of Na and K to move a substance into the cytoplasm against its gradient What is required for this to occur Coupling the active transport of one substance B with the diffusion of another substance A Use the energy stored in the gradient of the substance moving down hill A Use ATP to build the gradient of A Diffusion of Na into cell could power movement of another substance into cell against gradient Requires a co transport protein gradient of Na ATP to build Na gradient Na K pump to build Na gradient 13 Compare exocytosis and endocytosis Give an example of whywhen a cell might use each for what purpose Exocytosis bulllt movement out of cell via fusion of vesicle with membrane secretion of hormones or other molecules Endocytosis bulk movement into cell via formation of vesicle from membrane phagocytosis of bacterium by white blood cell lots of others 14 Assume the following gradients across a cell membrane high 02 outside low 02 inside high COZ inside low COZ outside high glucose inside low glucose outside high Hl outside ow Hl inside For each of the following describe the mechanism of transport any energy required and any protein required a Movement of Oz into cell Simple diffusion no E required gradient is E source no protein required b Movement of glucose into cell Primary active transport ATP glucose pump Secondary active transport H gradient co transport protein that moves both in Movement of H out of cell Primary active transport ATP H pump some type of secondary active transport d Movement of C02 out of cell Simple diffusion no E required gradient is E source no protein required Worksheet 6 Cytoskeleton and Cell junctions 1 List the three components of the eukaryotic cytoskeleton What is the subunit used to build each Microtubules tubulin heterodimer Micrfilaments actin monomer Intermediate filaments subunit varies different proteins used to build 2a Describe the structure common to both cilia and flagella Both have 92 arrangement of microtubules covered in plasma membrane 9 microtubule doublets surrounding 2 single microtubules Microtubules connected by cross linking proteins and dynein 2b Describe two major differences between cilia and flagella Cilia shorter and more numerous move in whip like motion Flagella longer and fewer move in undulating snake like motion 3 Compare eukaryotic and prokaryotic flagella Eukaryotic covered by plasma membrane composed of microtubules and motor proteins and cross linking proteins undulate Prokaryotic naked not covered by PM composed of flagellin protein no microtubules rotate from motor 4 List two processes that might be disrupted if cells are treated with atruncuin a toxin that causes microfilaments to depolymerize fall apart Cell crawlingmovement cell shape changes muscle contraction cytoplasmic streaming cytokinesis in animal cells 5 List two processes that might be disrupted if cells are treated with colchicine a toxin that causes microtubules to depolymerize fall apart Mitosis vesicle movement secretion cell movement via ciliaflagella cytokinesis in plant cells 6 What is a motor protein List one motor protein associated with microtubules and one associated with microfilaments Protein protein complex that is capable of ATP dependent movement on cytoskeleton Microtubule kinesin and dynein Microfilament myosin 7 For each of the following name the correct type of cell junction Desmosomes Joins cells together to strengthen tissues but still permits passage of material between the cells Tight junctions Functions as a barrier blocking passage of material between cells from one side of epithelial cell layer to the other Gap junctions Protein channels that connect cells and permit the rapid passage of small materials between the cells Plasmodesmata Connects plant cells which are otherwise isolated by their surrounding cell walls 8 How are gap junctions and plasmodesmata similar How are they different Both channels that connect cytoplasms of neighboring cells allow small substances to pass between cells Plasmodesmata are lined by plasma membrane gap junctions are lined by proteins 9 What are the main components of the extracellular matrix Where are they made and how do they come to be in their final location Collagen glycoprotein embedded in a proteoglycan matrix Made by bound ribosomes secreted out of cell via vesicles passing through golgi to plasma membrane 10 How is the extracellular matrix attached to a cell List the molecules involved Integrins in the plasma membrane connect to glycoproteins in the extra cellular matrix 11 Describe the basic structure of a plant cell wall Cellulose fibers embedded in a polysaccharideprotein matrix Can be flexible or rigid 12 What is the function of the middle lamella It is sticky holds neighboring cell walls cells together Worksheet 7 Energy Harvesting Pathways 1 What is oxidation Reduction Oxidation loss of electrons OIL Reduction gain of electrons RIG 2 What is a reducing agent An oxidizing agent Reducing agent electron donor reduces another substance Oxidizing agent electron acceptor oxidizes another substance 3 What is NAD What is its function in aerobic energy harvesting cellular respiration What is the generic name of the enzyme that catalyzes the reduction of NAD During which stages is it reduced During which stages is it oxidized Which of these reactions is exergonic Endergonic NAD is a coenzyme that carries electrons in the cell nicotinamide adenine dinucleotide In cellular respiration it carries high energy electrons from organic fuels to the electron transport chain Dehydrogenases transfer electrons from organic fuels to NAD 9 NADH NAD is reduced during glycolysis pyruvate oxidation and the citric acid cycle NADH is oxidized during oxidative phosphorylation ETC Oxidation of NADH is exergonic reduction of NAD is endergonic 4 What is substrate level phosphorylation During which phases of cellular respiration does substrate level phosphorylation occur Mode of ATP synthesis where an enzyme transfers a phosphate group from a substrate molecule organic molecule to ADP Occurs in glycolysis and the citric acid cycle 5 4 molecules of ATP are made during glycolysis Why is the net yield for glycolysis only 2 molecules of ATP 2 molecules of ATP are used during the energy investment phase of glycolysis 6 Glycolysis occurs in the cytosol while the final three stages of cellular respiration occur in the mitochondrion Where in the mitochond rion do the final three stages occur How do the products of glycolysis get into the mitochond rion Pyruvate oxidation and citric acid cycle occur in the mitochondrial matrix oxidative phosphorylation takes place in the inner mitochondrial membrane Pyruvate from glycolysis enters mitochondria by active transport via a transport protein NADH from glycolysis cannot enter mitochondria rather the electrons it carries are shuttled into the mitochond rion and are then used to reduce other molecules of NAD or FAD already inside 7 During glycolysis 1 molecule of glucose is broken down to 2 molecules of what Pyruvate 3C 8 What determines if the product of glycolysis will be used for fermentation or cellular respiration The presence cellular respiration or absence fermentation of oxygen 9 Before the citric acid cycle can begin the 3C product of glycolysis must first be converted to what What is released as a waste product Acetyl CoA C02 is released as a waste product This reaction also generates NADH 10 The complete oxidation of 1 molecule of pyruvate results in the formation of how many NADH How many FADH2 Includes conversion of pyruvate to acetyl CoA one cycle of citric acid cycle NADH H 4 FADH2 1 11 The complete oxidation of 1 molecule of glucose results in the formation of how many NADH How many FADH2 Includes glycolysis conversion of pyruvate to acetyl CoA citric acid cycle NADHH 22610 FADH2 2 12 NADH and FADH2 both transfer electrons to the electron transport chain Why does the release of electrons from NADH to the ETC result in the production of more ATP than the release of electrons from FADH2 Electrons from NADH are passed directly to the first protein complex of the ETC allowing H to be pumped out of the mitochondrial matrix by all 3 H pumps add more to the gradient Electrons from FADHZ are passed to the second protein complex of the ETC so they only contribute to the pumping of H by the last two H pumps 3amp4 Thus FADH2 contributes less to the H gradient and results in the production of fewer ATP 13 What is chemiosmosis What is the name of the enzyme involved in making ATP Why can t chemiosmosis make ATP without the ETC why do we need both the ETC and chemiosmosis in oxidative phosphorylation Chemiosmosis using H gradient to do work make ATP ATP synthase is the enzyme that uses the H gradient to make ATP The cell needs the ETC to make the H gradient as electrons are passed down the ETC energy is released that is used to pump H 9 build H gradient across inner mitochondrial membrane Without the H gradient there is no energy source for making ATP 9 need both ETC to make H gradient and chemiosmosis to use H gradient to make ATP 14 The complete oxidation of one molecule of glucose results in the formation of how many molecules of ATP via oxidative phosphorylation Why is this number not exact 8 ATP 10 NADH lead to the production of 25 ATP each and 2 FADH2 lead to the production of 15 ATP each 1 ETC and production of ATP are not directly linked ETC creates gradient that is used to make ATP 2 Depends on how electrons from NADH made in glycolysis get into mitochondria 3 Some energy of gradient is used to get pyruvate into mitochondria and do other work 15 What is fermentation Anaerobic catabolism of organic molecules It is an extension of glycolysis necessary to regenerate the NAD used in glycolysis 16 What are the two main types of fermentation How are they similar How do they differ Alcohol fermentation and lactic acid fermentation Similar both regenerate NAD by reducing pyruvate or a derivative of pyruvate Differ in alcohol fermentation a derivative of pyruvate acetaldehyde is reduced by NADH C02 madeIn lactic acid fermentation pyruvate is directly reduced by NADH no C02 made 17 Explain how the cell can use feed back inhibition to regulate the rate of cellular respiration End product of process ATP can feedback and allosterically inhibit an enzyme early in the process PFK in glycolysis Worksheet 8 Photosynthesis 1 Where does the O that is released during photosynthesis come from How do we know H20 Experiment C02 2H2099 CHZO H20 02 C02 2H20 99 CHZO H20 02 2 Name the two stages of photosynthesis Where does each occur Light reactions thylakoid membrane amp across thylakoid membrane Calvin cycle stroma 3 What is a pigment What is the main pigment involved in photosynthesis Substance that absorbs visible light Chlorphyll a accessory pigments chlorophyll b and carotenoids 4 What are the two components of a photosystem What is the function of each component Light harvesting complexes absorb light and pass energy to reaction center Reaction center transfer excited electron from special chlorophyll a molecule to primary electron acceptor start PS 5 Outline the pathway of noncyclic electron flow during photosynthesis What is the source of electrons What are the products of noncyclic electron flow PS 11 H20 9 ETC leads to production of ATP 9 PS I 9 ETC 9 NADP reductase 9 NADPH Source of electrons splitting of water Products 02 ATP chemiosmosis NADPH 6 Outline the pathway of cyclic electron flow during photosynthesis What is the source of electrons What are the products of cyclic electron flow PS I 9 EI39C leads to production of ATP 9 PS I Source of electrons P700 chlorophyll a of PS 1 Products ATP 7 Contrast chemiosmosis in cellular respiration and photosynthesis Cellular respiration oxidative phosphorylation oxidation of food as source of energy H gradient across inner mitochondrial membrane high in intermembrane space Hs diffuse down gradient into matrix to make ATP ATP synthase KNOB on matrix face of inner mito Membrane Photosynthesis photophosphorylation light as source of energy H gradient across thylakoid membrane high in thylakoid space Hs diffuse down gradient out to stroma to make ATP ATP synthase KNOB on stroma face of thylakoid membrane 8 What is carbon fixation What is the name of the enzyme that fixes carbon during the Calvin cycle Carbon fixation the incorporation of inorganic carbon C02 into organic compounds Rubisco 9 How many ATP and NADPH are necessary to make one molecule of glyceraldehyde 3 phosphate G3P What is the source of these ATP and NADPH ATP 9 NADPH 6 Light reactions extra ATP from cyclic electron flow Worksheet 9 DNA Structure amp Replication 1 Name the three components of a DNA nucleotide What is a dNTP PHOSPHATE GROUP ON 5 C OF SUGAR NITROGENOUS BASE ATC G PENTOSE SUGAR DEOXYRIBOSE dNTP deoxyribonucleotides with 3 phosphate groups deoxyribonucleoside triphosphate 2 What are the base pairing rules in a DNA double helix which bases pair together across double helix How many hydrogen bonds form between each base pair A T 2 H BONDS G C 3 H BONDS 3 How would the results of Avery McCarty and MacLeod have differed if protein was the genetic material Hershey and Chase AMM would only see transformation R 9 5 when protein present never when proteases added HampC 35S Iabelled proteins would be in the pellet with the bacteria 32P Iabelled DNA would be in supernatant 4 Briefly explain the semi conservative model of DNA replication EACH STRAND OF PARENT MOLECULE SERVES AS TEMPLATE FOR THE SYNTHESIS OF NEW DAUGHTER DNA MOLECULES EACH DAUGHTER DNA MOLECULE IS CONSTRUCTED OF ONE OLD PARENT STRAND AND ONE NEW DAUGHTER STRAND 5 Draw the results expected from the famous Meselson and Stahl experiment if the bacterial cells were allowed to replicate three times 3 rounds of DNA replication in the medium containing 14N assuming CONSERVATIVE ON TOP SEMICONSERVATIVE IN MIDDLE DARK BLUE WOULD BE N 15 LIGHT BLUE Nl4 Need to nish 3rd round Conservative 1 dark double helix 7 light double helices Semi 2 hybrids 6 light helices 1 YOU CAN DRAW THE RESULTING BANDS OF THE 39 DENSITY GRADIENT AS WELL IF YOU WANT Conservative thin heavy band thick light band Semi thin hybrid band thick light band 6 What is the site of DNA replication initiation called How many of these sites are typically found in a prokaryotic chromosome How many in a eu karyotic chromosome Why a difference ORIGIN OF REPLICATION 1 IN PROKARYOTIC CIRCULAR CHROMOSOME MANY 100 S 1000 S IN EUKARYOTIC CHROMOSOMES Prokaryotic much smaller than eukaryotic 7 What is the specific reaction catalyzed by DNA polymerase ADDS A dNTP nucleoside triphosphate to the 3 end of a growing DNA strand Forms the phosphodiester bond between the 3 OH of last nt on strand and the 5 phosphate group of the incoming nt 8 To which end of the leading strand does DNA polymerase add dNTPs To which end of the lagging strand 3 for both Always adds dNTPs to the 3 end Can only add dNTPs to a 3 OH 9 What is an Okazaki fragment Where do we find Okazaki fragments Segments of the lagging strand produced serially as the replication fork opens up allowing backwards DNA replication Found on lagging strand 10 What is the function of primase Why does DNA replication require this enzyme To start the production of a new DNA strand DNA polymerase is NOT able to initiate the production of a DNA strand DNA polymerase can ONLY add to the 3 end of an existing nt strand Primase starts replication by adding a short stretch of linked complementary RNA nucleotides primer DNA polymerase can then add DNA nucleotides to the 3 end of this RNA primer 11 Many other enzymes and proteins are involved in DNA replication briefly describe the function of each of the following in replication a Helicase separates the two strands of the DNA at the replication forks b Topoisomerase relieves the strain ahead of the replication fork caused by action of helicase c Single stranded binding protein bind and stabilize the separated DNA strands so they can serve as templates d DNA ligase completes the phosphodiester backbone between neighboring Okazaki fragments forms last phosphodiester bond 12 What is the importance of the 339 to 5 exonuclease activity of DNA Pol Proofreading by DNA polymerase If wrong nt added it can back up and remove the wrong nt and the add the correct one Increases the accuracy of DNA replicatin 13 What is a telomere What is the function of a telomere The ends of linear chromosomes made up of nt repeats contain no genes They function as buffers to protect the genes found in the chromosomes The ends of the chromosomes get shorter with each division so the telomeres are shortened without the loss of genetic info Worksheet 10 Cytoskeleton and Cell Division 1 Describe the basic events of binary fission What is the result of this process Copy DNA DNA replication grow split cell contents End with 2 identical cells clones 2 The cell cycle consists of mitosis and interphase Interphase is further divided into three parts Next to each cell cycle phase or subphase give a brief description of its function GI first gap cell growth make proteins amp organelles 5 synthesis cell growth make proteins amp organelles amp DNA replication 62 second gap cell growth make proteins amporganeles M Mitosis division of nucleus and cytokinesis division of cytoplasmcell 3 What is a sister chromatid A centromere A kinetochore Sister chromatids are the identical copies of the original DNA double helix that result from DNA replication They are held together at the centromere Centromeres are the specialized regions of the duplicated chromosome where the sister chromatids are held together The kinetochore is the protein structure on the condensed chromosomes where the microtubules will attach The kinetochore wi associate with the centromere region 4 What is the goal of mitotic cell division To generate 2 genetically identical cells each with an exact copy of all chromosomes 5 Give a brief overview of chromosome condensation What is the function of the histone proteins When do chromosomes condense Hierarchical folding of chromosome The histones are the proteins that help to fold spool the chromosomes The nucleosome is the basic structure of chromatin folding It is made up of DNA wrapped twice around 8 histones Chromosomes start condensing in prophase and they reach the most compact form by metaphase 6 List the 5 phases of mitosis as discussed in class For each give a brief description of the location amp structure of the chromosomes the location of centrosomes MTOCs and the structure of the spindle 1 Prophase chromosomes consist of 2 sister chromatids starting to condense found in nucleus Duplicated centrosomes starting to move apart from one another as spindle begins to form between 2 Prometaphase replicated chromosomes fully condensed with kinetochores at centrosomes Nuclear envelope fragmented so chromosomes in cytoplasmDupicated centrosomes at opposite ends of cell spindle almost fully formed microtubules begin interacting with free chromsomes 3 Metaphase replicated chromosomes each attached to microtubules from both centrosomes are found on metaphase plate midway between centrosomesCentrosomes at opposite ends of cell spindle fully formed between them Kinetochore microtubules attached to kinetochores nonkinetochore microtubules are overlapping 4 Anaphase Sister chromatids separated are now individual chromosomes still attached via kinetochores to spindle microtubules are being moved to centrosomesCentrosomes at opposite ends of cell are moving away from one another due to the action of overlapping nonkinetochore microtubules 5 Telophase Individual chromosomes are now becoming less condensed as a nuclear envelope reforms around each complete set Each set found in the newly forming daughter cellsOne centrosome found in each of the newly forming daughter cells next to newly forming nuclei The spindle has broken down 7 Explain the basic structure of the spindle What are the basic functions of the spindle When does each occur Made up of microtubules and associated proteins motors built between 2 microtubule organizing centers centrosomes Microtubules from the two centrosomes grow to the middle of the cell There are 2 classes of spindle microtubules kinetochore and nonkinetochore The kinetochore microtubules attach to the chromosomes and are responsible for separating the chromosomes during anaphase The nonkinetochore microtubules from the two centrosomes overlap in the middle of the cell and are responsible for elongating the cell during anaphase 8 Compare cytokinesis in animal cells and plant cells Animal cytokinesis via cleavage A cleavage furrow forms due to the action of actin amp myosin in the contractile ring results in the pinching of the cell into 2 Plant cytokinesis via cell plate formation Golgi vesicles at the equator old metaphase plate fuse together to form cell plate that will mature into cell wall and plasma membrane between 2 daughter cells Microtubules required for transport of golgi vesicles to equator No microfilaments 9 What is a checkpoint What are the three major checkpoints in the cell cycle Control point in the cell cycle where the cell requires a go ahead signal to progress Give the cell an opportunity to check that everything is OK before moving on Three checkpoints 61 10 Cyclins and Cd ks work together to regulate progress through the cell cycle a What is a cyclin A regulatory protein Concentration fluctuates cyclically b What is a Cdk A kinase regulated by cyclins Activity fluctuates with concentration of cyclin c Explain how these two components fluctuate during the cell cycle Cyclin concentration fluctuates Cdk activity fluctuates with cyclin concentration 11 What is the goal of meiotic cell division To generate four haploid cells that are genetically distinct from one another 12 For each stage of meiosis list the major events that occur P1 chromosomes condense spindle starts to form homologs pair up crossing over NEBD microtubules capture chromosomes M1 homologous chromosomes line up at metaphase plate A1 homologous chromosomes separate and entire duplicated chromosomes move to opposite ends of cell T1 and cytokinesis 2 haploid cells created each contains one set of duplicated chromosomes spindles break down chromosomes may elongate nuclear envelope may reform P2 spindles form in both cells microtubules capture chromatids chromosomes may condense NEBD may occur M2 duplicated chromosomes line up at metaphase plate A2 sister chromatids separate and the individual chromosomes move to opposite ends T2 and cytokinesis 4 haploid daughter cells form nuclear envelopes reform chromosomes elongate spindles break down 13 Compare metaphase and anaphase of mitosis meiosis I and meiosis 11 What lines up at the metaphase plate in each What separates in each Metaphase duplicated chromosomes sister chromatids Metaphase I homologous chromosomes homologs Metaphase II duplicated chromosomes sister chromatids 14 What are homologous chromosomes What happens to homologous chromosomes in mitotic cell division In meiotic cell division Homologous chromosomes are pairs of chromosomes of same size with information for same genes One of each pair is maternal one is paternal In mitosis the homologs function independently of one another it doesn t matter that there are homologs In meiosis the homologs pair up swap parts and separate the goal of meiosis is to separate the homologous pairs so that there is only one of each type of chromosome in each daughter cell 15 What is crossing over What is the result of crossing over What is independent assortment How do crossing over and independent assortment increase genetic diversity Crossing over reciprocal exchange of genetic material between non sister chromatids sister chromatids of a homologous pair swap DNA Crossing over results in chromosomes that contain some maternal DNA and some paternal DNA new combinations of DNA GENETIC diversity Independent assortment each pair of homologous chromosomes lines up independently of the others during metaphase 1 either maternal chromosome or paternal chromosome of each pair can line up on the left This allows for many possible combinations of maternal and paternal chromosomes in the daughter cells a daughter cell could inherit all paternal chromosomes or all maternal chromosomes half and half or anything in between These help to explain why siblings may look alike but generally are not identical 16 Fill in the following chart comparing meiotic and mitotic cell division Starting of pairs Division of of chromatids Number of Chromosome cell of chromosomes metaphase daughter cells of daughter homologs metaphase I amp II if end cells I amp II if applicable annlir ahle 2n 16 8 Mitosis 16 32 2 2n 16 2n 16 8 Meiosis I 16 I 32 4 n 8 H 8 in each II 16 in each cell n 4 0 Mitosis 4 8 2 n 4 N 4 0 Meiosis NA NA Can t happen NA Worksheet 11 Gene Expression 1 What is gene expression The process by which DNA directs the synthesis of an RNA or protein product Includes transcription or transcription amptranslation 2 What is transcription What is translation Transcription synthesis of RNA any under the direction of DNA Translation synthesis of a polypeptide under the direction of an mRNA 3 In a eukaryotic cell where does transcription occur Translation Where do these processes occur in a bacterial cell Eukaryotic Transcription nucleus Translation cytosol Bacterial Transcription amptranslation cytosol or nucleoid 4 What is a codon Where do we typically find codons Codon is a three nucleotide sequence nt triplet that specifies an amino acid or stop signal found in mRNA or DNA 5 What is a promoter The DNA sequence that marks where transcription should begin The site where RNA polymerase will bind by itself or via transcription factors to start transcribing 6 Compare transcription initiation in bacteria and eukaryotes Bacteria RNA Pol binds promoter separates 2 strands of double helix and begins copying Eukaryotes Transcription factors bind promoter amp allow RNA Pol 2 to bind Then separate the 2 strands amp begin copying 7 In which direction does RNA polymerase elongate an mRNA RNA Pol adds bases only in the 5 9 3 direction 8 How does elongation of the polynucleotide differ between DNA replication and transcription In DNA replication both strands of the parent DNA molecule are copied and the daughter strands stay with the parent template strand In Transcription only one strand of the parent DNA molecule is copied and the transcript mRNA leaves the parent template shortly after being made 9 How does transcription end in bacteria In eukaryotes Bacteria transcribe terminator sequence which causes RNA Pol to detach and release completed mRNA Eukaryotes transcribe polyadenylation signal sequence PASS which causes the pre mRNA to be released 10 Briefly describe the three events that occur during pre mRNA processing in the eu karyotic nucleus What is the function of each 1 Addition ofa 5 cap a modified guanine nucleotide is added in reverse to the 5 end of the transcript Functions export from nucleus protection from nucleases translation initiation 2 3 poly A tail They polyadenylation sequence near the 3 of the transcript causes the addition of 200 AMPs to the 3 end of the transcript Functions export from nucleus protection from nucleases translation initiation 3 Splicing spliceosome cuts out introns and joins together the exons to create the mature mRNA Functions necessary to get coding information into one continuous stretch 11 What is the function of a tRNA Describe the structure of a generic tRNA How does the structure of a tRNA fit its function Bring amino acids to the mRNA bound in a ribosome to build polypeptide Approximately 80 nts long Complementary base pairing within the tRNA causes a specific 3D structure that looks like an L Has an anticodon on one end that binds mRNA amp a binding site for a specific amino acid on other end Its structure allows it to bring the correct amino acid to the correct codon in the mRNA 12 What is the name of the enzyme responsible for attaching the appropriate amino acid to a tRNA How many different forms of this enzyme are present in a cell Aminoacyl tRNA synthetase 20 different forms 13 There are fewer than 50 different tRNAs in a typical cell and yet there are more than 60 different amino acid coding codons Give a brief explanation for this discrepancy 3rd base wobble Only the first 2 bases involved in codon anticodon recognition have to match exactly In some cases the third base does not have to match Thus one tRNA can complementary base pair at least the first 2 bases with more than one mRNA codon Accounts for some of the redundancy in the genetic code 14 Describe the structure of a typical ribosome Of what macromolecules is it composed Where are these macromolecules synthesized Where is the ribosome made Made from 2 subunits the small subunit ampthe large subunit Both subunits are made from rRNA amp proteins The rRNA is transcribed in the nucleolus of the nucleus The proteins are translated on ribosomes in the cytosol They come together in the nucleolus which is where the ribosomal subunits are made The 2 subunits do not come together until translation initiation in the cytosol 15 Within a ribosome there are four binding sites for various components of the translation machinery Name these sites and describe what binds to each mRNA binding site binds the mRNA E site the exit site empty tRNAs leave the ribosome through this site P site the peptidyl tRNA site peptidyI tRNAs bind this site A site the aminoacyl tRNA site aminoacyl tRNAs bind this site during codon anticodon recognition 16 Outline the events involved in translation initiation that lead to the formation of the translation initation complex 1 Initiator tRNA amp small ribosomal subunit bind to mRNA and scan from 5 end until the first AUG codon is found and recognized by tRNA 2 Large ribosomal subunit binds and forms the translation initiation complex with initiator tRNA in P site 17 What is the reading frame What ensures that mRNAs are read in the correct reading frame Reading the nucleotides in the correct groupings of 3 The start codon AUG sets the correct reading frame 18 In which direction is the mRNA read during translation In which direction is the polypeptide synthesized during translation mRNA is read 5 9 3 The polypeptide is made from the N terminus to the C terminus 19 Translation elongation involves three steps a During codon recognition a tRNA anticodons binds to a complementary codon In which site of the ribosome does this step occur What is present in the other ribosome binding sites A site P site peptidyl tRNA E site nothing mRNA site mRNA b During peptide bond formation a peptide bond forms between two amino acids What part of the ribosome is responsible for catalyzing this reaction Where in the ribosome is the growing peptide located after the peptide bond forms Large ribosomal subunit rRNAs A site the growing polypeptide moves from P to A c Describe the events involved in translocation that reset the ribosome so the next codon is available for recognition Ribosome moves the peptidyl tRNA in A site to P site Empty tRNA in P site is moved to E site and exits mRNA moves with tRNA so that there is a free codon in A site 20 Release factors are responsible for terminating translation What is the signal for a release factor to bind the ribosome How does the release factor stop the synthesis of a polypeptide Stop codons UAG UAA UGA Release factor causes addition of a water to the end of the polypeptide chain which hydrolyzes the polypeptide from the tRNA allowing it to be released 21 What is a polyribosome Are polyribosomes found in bacterial cells or eukaryotic cells Multiple ribosomes translating the same mRNA Found in both bacterial amp eukaryotic cells 22 Where does all polypeptide synthesis begin in eukaryotic cells What determines where polypeptide synthesis will be completed On free ribosomes in the cytosol A signal peptide near the N terminal end of the polypeptide determines location 23 Outline the events involved in the translation amp targeting of the following types of proteins a A cytoplasmic protein Translation starts and ends at a free ribosome in cytosol Completed polypeptide is released into cytoplasm and folds b A mitochondrial protein Translation starts and ends at a free ribosome in cytosol Completed polypeptide is released into cytoplasm folds into final shape and then binds to receptor on mitochond rion allowing it to enter its final target the mitochond rion c A plasma membrane protein Translation starts on a free ribosome A signal peptide at beginning of polypeptide is recognized by an SRP Translation stops as SRP carries ribosome to RER Translation continues on bound ribosome with polypeptide built into RER membrane Completed protein in RER membrane RER membrane with protein pinched into a vesicle carried by motor protein on microtubule to cis golgi Protein modified as it moves from cis9 trans golgi Protein in membrane of trans golgi packaged into vesicle and carried by motor proteins on microtubules to plasma membrane Vesicle fuses with plasma membrane such that protein is now part of plasma membrane Whichever part of the protein was facing the interior of the RER vesicle golgi vesicle 9 faces outside of cell d A lysosomal protein Translation starts on a free ribosome A signal peptide at beginning of polypeptide is recognized by an SRP Translation stops as SRP carries ribosome to RER Translation continues on bound ribosome with polypeptide built into RER lumen Completed protein released into RER lumen Part of RER with protein pinched into a vesicle carried by motor protein on microtubule to cis golgi Protein modified as it moves from cis trans golgi Protein in lumen of trans golgi packaged into new vesicle that becomes lysosome 24 What is a base pair substitution How does a base pair substitution cause a silent mutation A nonsense mutation A missense mutation Replacement of one base pair with another incorrect base pair Silent the mutation results in a codon for the same amino acid or the changed amino acid has no affect on protein structurefunction Missense substitution results in a codon that codes for a different amino acid that causes changes in protein structurefunction Nonsense substitution results in a premature stop codon results in a shortincomplete usually nonfunctional protein 25 What is a frameshift mutation What types of point mutations are likely to result in a frameshift Mutation that disrupts the reading frame switches which nts are read as codons Caused by insertions and deletions of nts whenever the number inserteddeleted is not a multiple of 3 26 The wildtype normal mRNA sequence for a certain gene is given UAC GAA CAC UUA GGG CCC 5 AUG CUU GUG AAU CCC 666 3 a Show the tRNA anticodon sequences that would recognize these codons A in red b What polypeptide sequence is coded for by this mRNA Met Leu Val Asn Pro Gly 27 A point mutation in this same gene results in the following mRNA sequence 5 AUG CUG UGA AUC CCG GG 3 What type of point mutation caused this change Base pair deletion What is the resulting polypeptide sequence Met Leu STOP Worksheet 12 Gene Regulation 1 Transcription and translation are typically coupled in prokaryotes Explain what this means Why is this possible in prokaryotes and not eukaryotes Translation of an mRNA can begin while the mRNA is still being transcribed as soon as 5 end amp start codon are released from RNA Pol simultaneous transcription amptranslation of same gene Prokaryotes lack a nucleus Eukaryotes have a nucleus so that transcription and translation are temporally amp spatially separated 2 Describe the structure of a typical operon How many genes are found in an operon An operon contains an operator a promoter and the genes controlled by this operator amp promoter The number of genes found in an operon can vary 3 What is an inducible operon A repressible operon Inducible usually off transcription but can be induced transcription turned on lac operon Repressible usually on transcription but can be repressed transcription turned off trp operon 4 What is the function of the trp operon The trp operon contains the genes that code for the enzymes involved in the production of tryptophan When the trp operon is on these genes are expressed and tryptophan is produced 5 Describe the regulation of the trp operon a in the presence of tryptophan and b the absence of tryptophan Name all components involved and tell where they bind a tryptophan tryptophan corepressor binds to and activates the trpR repressor The active trpR repressor can then bind the operator and block RNA polymerase from transcribing Operon transcription is off b tryptophan trpR repressor is present but in the inactive conformation TrpR repressor cannot bind the operator RNA polymerase binds to the promoter and transcribes the trp genes because not blocked by trpR repressor on operator Operon transcription is on 6 What is the function of the lac operon The lac operon contains the genes that code for enzymes involved in the metabolism of lactose When the lac operon is on these genes are expressed and lactose can be metabolized broken down and used as a source of energy 7 Describe how the lac operon is regulated by both lactose levels and glucose levels Name all components involved and tell where they bind Lactose levels affect activity of lacI repressor turn operon on or off When lactose is absent the lad repressor is active and can bind to the operator When the lad repressor is bound to the operator it block RNA polymerase from transcribing thus shutting the operon off When lactose is present it functions as an inducer It binds to and inactivates the lad repressor The inactive lacI repressor cannot bind to the operator and transcription is on Glucose levels affect levels of cAMP which controls activity of CAP determines highlow level of operon transcription When glucose is absent there are high levels of cAMP cAMP binds to CAP activating it Active CAP binds to CAP binding site and recruits RNA Pol to promoter turns transcription up activates assuming there is lactose present When glucose is present there are low levels of cAMP No cAMP CAP is off cannot bind to operon and transcription levels are low assuming there is lactose present If both lactose and glucose are present the cell prefers to use glucose so the level of lac operon transcription will be low If lactose is present but not glucose the cell needs to use the lactose so the level of lac operon transcription will be high If no lactose present lac operon will be off because there is no lactose to use doesn t matter about glucose levels 8 List the stages of gene expression in a eukaryotic cell At which points can gene expression be regulated Chromatin remodeling Transcription pre mRNA processing mRNA export to cytoplasm Translation Post translational modification Protein targeting Gene expression can be regulated at any of these points The lifespan of the mature mRNA and the mature protein can also be regulated imgngmaawi n 9 How does histone acetylation regulate gene expression Deacetylation Acetylation of histone tails causes chromatin to become less compact amp more accessible for transcription Deacetylation of histone tails leads to the compaction of chromatin and a decrease in accessibility amp transcription 10 What is DNA methylation How does it regulate gene expression Methylation of DNA addition of methyl groups CH3 to bases in the DNA Typically decreases gene expression leads to gene silencing no transcription The methyl groups attract enzymes that deacetylate histones as well see 10 11 Compare general transcription factors and specific transcription factors General essential for transcription of all eukaryotic protein coding genes help RNA Pol H begin transcription sufficient for low levels of transcription Bind to promoter necessary for RNA Pol II to bind to promoter Specific determine transcription of specific genes interact with regulatory DNA sequences enhancers and silencers Can turn up expression of a specific gene or group of genes or turn down off a specific gene or group of genes 12 Describe how multiple genes involved in a common process can be expressed at the same time in a eukaryotic cell Genes to be expressed at the same time in response to the same signal typically contain the same regulatory sequences that bind the same activators 13 What is alternative RNA splicing The production of different alternative mRNAs from the same pre mRNA due to the splicing of different combinations of introns amp exons Leads to the production of different polypeptides 14 Describe a few ways that an eukaryotic cell can regulate the expression of a gene how much functional protein is present in the cell after the mature mRNA is exported to the cytoplasm 1 Regulate lifespane of mRNA mRNA breakdowndeg radation remove poly A tail and 5 cap and nucleases degrade the mRNA miRNAsiRNA bind to complementary sequences in an mRNA and lead to its destruction by nucleases 2 Regulate translation initiation via miRNAs regulatory proteins or 5 cap 3 Regulate protein processing turn off protein by removing phosphate group 4 Regulate lifespan of protein tag with ubiquitin to mark for destruction in proteasome Worksheet 12 Cell Communication 1 What determines which ces will be bound by a ligand LIGAND WILL ONLY BIND CELLS THAT HAVE THE CORRECTSPECIFIC RECEPTOR FOR THAT LIGAND 2 Describe one difference between a ligand for an intracellular receptor and a ligand for an extracellular receptor INTRACELLULAR SMALL amp HYDROPHOBIC MUST PASS THROUGH MEMBRANE EXTRACELLULAR CAN BE LARGE ampWATER SOLUBLE DONquot39 HAVE TO PASS THROUGH 3 In general what happens to a receptor protein when it binds a ligand UNDERGOES SOME SORT OF CHANGE OR ACTIVATION TYPICALLY A CONFORMATIONAL CHANGE 4 List one similarity and one difference between paracrine signaling and endocrine signaling BOTH REQUIRE THE SECRETION OF SIGNAL THAT CAN BE RECEIVED BY MULTIPLE TARGET CELLS Paracrine signals diffuse short distance to target cells Endocrine signals hormones can travel long distances in the blood 5a What is a second messenger SMALL NON PROTEIN DIFFUSIBLE MOLECULE OR ION RESPONSIBLE FOR RELAYING SIGNALS INSIDE THE CELL 5b List the two most widely used second messengers and briefly describe how each is producedreleased CYCLIC AMP THE ENZYME ADENYLYL CYCLASE MAKES CAMP FROM ATP IN RESPONSE TO SIGNALING OUR EXAMPLE SHOWED A G PROTEIN ACTIVATING ADENYLYL CYCLASE CALCIUM IONS STORED IN ERMITOCHONDRIA IN RESPONSE TO SIGNAL LIGAND GATED CALCIUM CHANNELS ON ERMITOCHONDRIA OPEN AND RELEASE CALCIUM INTO CYTOSOL IN OUR EXAMPLE G PROTEIN ACTIVATES PLC WHICH PRODUCES IP3 THE LIGAND FOR THE LIGAND GATED CALCIUM CHANNEL 6 What does it mean that signal transduction cascades amplify signals Give an example of how transduction can amplify a signal AMPLIFICATION SOME STEPS IN THE STP ACTIVATE MORE OF THE NEXT STEP SO THAT THE RESPONSE IS BIGGER THAN THE SIGNAL PHOSPHORYLATION CASCADE EACH KINASE IN THE CASCADE CAN ACTIVATE MORE THAN ONE OF THE NEXT KINASE IN THE CASCADE l What is a protein kinase A protein phosphatase KINASE ENZYME THAT PHOSPHORYLATES ANOTHER MOLECULE TRANSFERS PHOSPHATE GROUP FROM ATP TO ANOTHER MOLECULE PHOSPHATATASE ENZYMES THAT DEPHOSPHORYLATE OTHER MOLECULES REMOVE PHOSPHATE GROUPS FROM PROTEINS 8 Outline the major events involved in the reception of a signal by a a GPCR and b RTK b a G Protein Coupled Receptor Receptor Tyrosine Kinase 1 Ligand binds extracellular side of receptor 1 Ligand binds extracellular side of receptor 2 LIGAND BINDING INDUCES 2 LIGAND BINDING INDUCES CONFORMATIONAL CHANGE IN RECEPTOR CONFORMATIONAL CHANGE IN RECEPTOR RECEPTOR ACTIVATED WHICH CAUSES kinase activation 3 ACTIVATED RECEPTOR INTERACTS WITH AND 3 Phosphorylation of RTK ACTIVATES G PROTEIN GDP LEAVES GTP BINDS 4 ACTIVATED G PROTEIN GTP BOUND LEAVES 4 PHOSPHORYLATED RTK NOW ACTIVE AND CAN RECEPTOR AND GOES TO ACTIVATE ENZYME INTERACT WITH DOWNSTREAM SIGNALING LIGAND LEAVES RECEPTOR MOLECULES THAT WILL CONTINUE THE TRANSDUCTION CASCADE 5 ACTIVATED ENZYME THEN ACTIVATES DOWNSTREAM MOLECULES TO CAUSE RESPONSE 6 G PROTEIN HYDROLYZES GTP BACK TO GDP AND IS ONCE AGAIN INACTIVE DUE TO GTPASE ACTIVITY 9 Why does signaling through an intracellular receptor typically not include the transduction step THE RECEPTORampLIGAND DIRECTLY CAUSE THE RESPONSE THERE IS NO RELAY OF INFORMATION THROUGH DIFFERENT MOLECULESPROTEINS 10 How can two cells bind the same ligand but generate distinct responses 2 CELLS WITH THE SAME RECEPTOR Y CAN BIND THE SAME LIGAND X BUT GENERATE DISTINCE RESPONSES DUE TO THE COLLECTION OF SIGNAL TRANSDUCTION PROTEINSampMOLECULES PRESENT IN THE CELL


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