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Exploration Homework

by: Somto Nwogbo

Exploration Homework Biology 230W

Somto Nwogbo
Penn State
GPA 3.6
Biology 230W
Dr. Malcos and Dr. Burpee

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A study of cellular phenomena including molecular genetics and metabolic interactions. (BIOL 220W, 230W, and 240W )
Biology 230W
Dr. Malcos and Dr. Burpee
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This 12 page Bundle was uploaded by Somto Nwogbo on Wednesday October 14, 2015. The Bundle belongs to Biology 230W at Pennsylvania State University taught by Dr. Malcos and Dr. Burpee in Fall 2015. Since its upload, it has received 39 views. For similar materials see Biology 230W in Biology at Pennsylvania State University.

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Date Created: 10/14/15
Name Somto Monique Nwogbo Access ID smn5309 Week 3 Exnloration Homework Genome Organization Use the Epigenetics Intro only article in Wikipedia to answer the following question in one or two sentences 1 What doe the field of epigenetics study and how is it different compared to genetic studies The field of epigenetics focuses on the heritable changes that occur in the chromatin without causing changes in DNA sequence eg DNA methylation Genetics focuses on genes gene variation and heredity but epigenetics focuses on the inherit changes that affect the transcription of a gene Epigenetics does not involve changes to the DNA sequence neither are the processes involved heritable ie the changes are not passed down from generations to generations Use the Gene Intro Structure and Function Gene Expression Genetic Code sections article in Wikipedia to answer the following questions in one or two sentences 2 What is the difference between a gene and a allele A gene is the region of DNA that produces a functional RNA or protein through gene expression Mutations of a specific gene can create variants to a phenotypic trait and variants of a gene are known as alleles 3 What is the actual code of the genetic code It s the specific though redundant language that a ribosome translates to produce a certain protein The code can also be referred to as a codon and these are nucleotide triplets that encode the genetic information of a cell 4 In addition to proteincoding DNA what other regulatory sequences may be present in a gene please be specific The promoter sequence enhancer silencer ribosome binding site and terminator 5 What two types of molecules typically bind to promoter regions to facilitate transcription Enhancer and silencer 6 Enhancers are always located close to the start of a gene True or False Could be located far away but the intermediate DNA sequence can be looped to promote proximity Or enhancer can be located on another chromosome in close proximity 7 activator proteins bind to enhancers to increase the initiation rate of transcription while repressor proteins bind to silencers to decrease the initiation rate of transcription 8 What type of macromolecule are transcription factors Protein 9 Looking at the diagram of a typical eukaryotic proteincoding gene what genetic components not modifications are seen in the mature mRNA the mRNA used for translation Splicing of introns and alternative splicing 10 What is an operon What group of organisms has operons They are a cluster of genes cotranscribed together under a single promoter Prokaryotes eukaryotes in the production of rRNA and bacteriophages 11 What is the process of gene expression Transcription and translation 12 What are the possible products of gene expression Functional RNA products or protein products Use the PostTranscriptional Modification Wikipedia article to answer the following questions in two sentences or less 13 What are the three coposttranscriptional modifications that occur to mRNA and what is their main result A 5 Capping the free triphosphate group at the 5 end of the mRNA is replaced with a cap 7methylguanosine This cap is added onto the 5 end by an enzyme called guanyl transferase The cap protects the 5 end from enzymatic breakdown in the nucleus and helps assist the mRNA to the cytoplasm B Polyadenylation Here a polyAtail is added to the free hydroxyl group on the 3 end The polyAtail can sometimes be up to 250 nucleobases long and is added to the 3 end by an enzyme called polyA polymerase The polAtail also protects the mRNA strand from degradation C RNA splicing the removal of introns noncoding regions of the mRNA and the remaining exons are linked together to form a continuous chain of a protein coding strand for translation in the cytoplasm Name Somto Monique Nwoabo Access ID mn5309 Week 4 Exnloration Homework Transcription and Translation Part Splicing Last week we started into the topic of transcription and we ll finish up this week and then move onto translation Here s a nice animation from McGrawHill giving a general overview of RNA splicing For a more indepth look here s another from NDSU that includes many of the structures we will discuss in class Read the Wikipedia article Splicesome Intro and Composition 1 What is the major role of the splicesome Removes introns form premRNA 2 What are the two major molecules in a spliceosome snRNA and protein complexes 3 What are snRNA What is snRNP How are these two molecules related snRNA small nuclear RNA U1 U2 U4 U5 and U6 snRNP snRNA associated protein factors 4 In terms of posttranscriptional processing what s so important about the nucleotides GU and AG within an intron 0 Signal the action of the spliceosome on an intron GU is the splice site on the 5 end and AG is the splice site for the AG on an intron Part II Protein Translation Use the Wikipedia articles tRNA Intro section and Translation biology Intro Section The Virtual Cell Animation Collection website has several good animations for the overview of translation while this second animation from the DNA Learning Center provides a more realistic view of the process 5 One end of a tRNA contains protein while the other contains an anticodon 6 What is the function of aminoacyltRNA synthetase An enzyme that attaches the appropriate amino acid to its tRNA 7 What are the four major stages of translation Initiation ribosomes assembled and first tRNA is attached to start codon AUG Elongation amino acid is transferred from the tRNA in the Psite to the one in the Asite Translocation ribosome moves on to next mRNA codon an amino acid chain is created 0 Termination translation is complete ribosomal subunits detach from mRNA and a polypeptide is formed 8 The first codon on virtually all mRNAs is AUG Part III Protein Translation Rouah Endonlasmic Reticulum Use the Wikipedia article Endoplasmic reticulum Structure Rough Endoplasmic Reticulum to answer the following questions 9 Ribosomes present in the RER are stable and associate with the RER over a long period of time True or False 10 Under what conditions will a ribosome associate with the RER During translation of mRNA by a free ribosome The polypeptide produced must be en route for secretion Ribosome attaches to the RER at translocon 11 What types of molecules make up the translocon Heterotrimer sec61 Oligossaccharyl transferase complex Membrane protein TRAM 12 What two major function does the translocon complete Facilitate the transportation of proteins through the hydrophobic layer of the RER membrane Facilitates the proper positioning of transmembrane proteins on the RER membrane Part llll Protein Structure Use the Wikipedia article Protein Structure Intro to answer the following questions 13 What interactions contribute to the overall shape folding of a protein lonic interactions hydrogen bonding Van der Waals forces and hydrophobic packing 14 What makes up the primary structure of a protein What bonds contribute to this structure Linear sequence of amino acid chains Covalent bonds called peptide bonds contribute to this structure 15 What are the two main types of secondary structure What bonds contribute to this structure 0 Secondary structures Alpha helix and beta sheets 0 Hydrogen bonds 16 What forces are involved with formation of protein tertiary structure Hydrophobic interactions Salt bridges Hydrogen bonds Tight packaging of Rfunctional groups side chains Disulfide bonds 17 What is quaternary structure of a protein 0 3D model of multiple protein subunits properly packed together 18 What is the definition of a protein structural domain Why are they important 0 A selfstabilized protein structure that folds independently of the other protein chains Importance Due to stability is allowed to exist independently and be used to conform functional protein molecules and predict protein function based on protein domains Name Somto Monique Nwogbo Access ID mn5309 Week 9 Exnloration Homework DNA Replication and Repair Review the process of DNA replication from BIOL11O tutorial DNA Replication posted on ANGEL under the Lessons Tab Week 9 I Origin of Replication Use the Wikipedia article Origins of Replication and prior knowledge from class to answer the following questions 1 What is the major difference in origins of replication between bacteria nonarchea and eukaryotes Bacteria has a single origin of replication per chromosome while eukaryotes have multiple on each linear chromosome 2 In eukaryotes origins of replication occur at specific stretches of DNA with a high percentage AT base pairs Why would this pattern of base pairing facilitated formation of a replication fork AT base pairing facilitates the initiation of replication because the interaction that takes place within the pairing is weaker only has 2 Hbonds compared to GG with 3 than the CG base pairs thus making it easier to separate 3 What four major proteins complexes or factors are part of the eukaryotic prereplication complex 6 ORC proteins ORC16 Cch Cdt1 Heterohexamer of 6 mini chromosome maintenance MCM proteins 4 Click on the minichromosome maintenance link Why is the MCM complex required to initiate DNA replication at an origin of replication 0 It is a DNA helicase complex that separates the double helix strand of DNA in order to form and elongate the replication fork This process initiates DNA replication ll Replication Fork Use the Wikipedia article DNA Replication and prior knowledge from class to answer the following questions DNA polymerase section 5 What end of a DNA strand does DNA polymerase add nucleotides o 3 end 6 Why are RNA primers required to initiate DNA replication 0 Because the lagging strand of a replication fork makes nucleotides available in a 3 to 5 end the synthesis of short complementary RNA primers are necessary for DNA polymerase to create a complementary strand in this direction 7 What additional function can some polymerases have that affects the accuracy at which is works 0 DNA polymerases also proofreads and makes error corrections to the base pairing nucleotides Replication Process section Initiation 8 What is the end result of the initiation stage of replication 0 The formation of the prereplication complex Replication Process section ElongationReplication ForkDNA replication proteins 9 What is chemical structure is required for the addition of new nucleotides to DNA 0 A free 3 end hydroxyl group 10 There are multiple proteins required for the extension stage of replication What is the major function of each of the following proteins in one sentence each the BIOL11O tutorial may help A Primase an enzyme that helps initiate replication by the addition RNA primers B Ligase the enzyme that joins Okazaki fragments along the lagging strand C DNA Topoisomerase enzyme that temporarily breaks the DNA strand to relieve tension created by the unwinding of the DNA strands by helicase D Singlestrand DNA binding proteins helps hold the ssDNA apart to prevent re annealing of the DNA strand till replication E Clamp proteins helps DNA polymerase maintain contact with DNA template by forming a sliding clamp around DNA 11 Prokaryotes and eukaryotes have multiple polymerase proteins that complete distinct functions What are the major roles of the listed polymerases details found in sections titled Leading strand and Lagging strand Prokaryotes A DNA Polymerase I performs the base pairing of nucleotides between the Okazaki fragments B DNA Polymerase lll primary holoenzyme involved in DNA replication and is found at the replication fork It also performs proofreading and corrects replication errors Eukaryotes A Pol X involved in DNA replication initiation but is not well suited for correcting base pairing mistakes Found at the origins of replications B Pol 5 plays a small role in DNA replication but is mostly involved in correcting mistakes by Pol 6 along the leading strand C Pol 6 involved in replication and repair of both leading and lagging strands Replication Process section Termination 11 What is a teleomere Long repetitive region of nucleotides sequences at each end of a chromatid to prevent deteriorationdegradation or fusion with a close by chromosome Name Access ID Exploration Homeworl Weel 10 Energv Tr sducti Part I The majority of life uses some combination of glycolysis the Krebs Cycle and oxidative phosphorylation to transfer energy in the cell This week we will explore how these processes are regulated some of the molecular underpinnings governing these important energy events and how cells especially the eukaryotes use compartmentalization to facilitate the ow of energy Be sure you understand these processes to the level presented in Biol 110 Tutorials 2527 Tutorials are available under the LESSONS tab in the Week 9 folder Tutorial 25 Thermodynamics Please highlight the correct answer from the choice in the parentheses 1 Spontaneous reactions have negativepositive AG Negative 2 Spontaneous reactions are exergonicendergonic Exergonic 3 Hydrolysis of ATP can allow an exergonicendergonic reaction to occur Exergonic Tutorial 26 Glycolysis 4 What are the products of glycolysis and what is the net yield of each product per molecule of glucose A net yield production of 2 molecules of pyruvate 2 molecules of ATP and 2 molecules of NADH per molecule of glucose 3 When considering the reaction C6 H1206 6 02 gt 6 C02 6 H20 energy which molecule is oxidized and which molecule is reduced Glucose is oxidized Oxygen is reduced 4 What is substratelevel phosphorylation Production of ATP from the enzymespecific catalytic transfer of a phosphate molecule from a phosphorylated substrate PEP to ADP during glycolysis Tutorial 27 5 What are the major products of the Krebs cycle you can list them 6 Are NADH and FADH2 oxidized or reduced by the electron transport chain Why NADH and FADH2 are oxidized by the electron transport chain in order to release its bond energy to be stored in ATP molecules The oxidized byproducts are to be reused as energy storing molecules in glycolysis thus providing a continuous cycle of energycoupling ractions The protons H ions from this reaction is used to reduce oxygen to water 7 What molecule is the final electron acceptor of the electron transport chain Oxygen 8 What is the energy released from the transfer of electrons used to complete in the electron transport chain How does it relate to ATP It is used to produce ATP from ADP in the electron transport chain Adding a phosphate group to an adenine diphosphate is a high energy required reaction and so is the removal of that same phosphate group from ATP The energy is stored in the bonds and can be used to provide energy for other important metabolic activities Part II Glycolysis is a regulated process Go to the Wikipedia article Glycolysis REGULATION section only to answer the following questions 9 What does the free energy change tell us about the steps that are regulated or unregulated during glycolysis 0 An unregulated reaction by enzymes is denoted by a delta G zero because the system is in equilibrium and so catalytic enzymes involved have no directionality effect on the progression of the reaction 0 A regulated reaction on the other hand is denoted by a delta G negative then the enzymes catalyzing the reaction have made it spontaneous in a certain direction more favourable 10 There are ten steps to glycolysis Looking at the Change of free energy chart which steps have AG last column values more than 3kJmole away from zero you can just list the numbers of each step 34 19 and 23 kJmol 11 Are these steps reversible Why or why not Irreversible because they are spontaneous regulated reactions In simple words the reactions do not occur at or near equilibrium and one reaction pathway is always preferred compared to the reverse 12 What are the three glycolytic enzymes that are regulated Hexokinase phosphofructokinase and pyruvate kinase 13 How does allosteric control regulation alter a protein s function By binding an effector allosteric inhibitor or allosteric activator to the proteins allosteric site By doing this the proteins activity can either be enhanced or reduced due to the rsulting conformational change of that protein Part III In addition to catabolizing breaking down glucose most organisms can also synthesize glucose from nonsugar molecules through the metabolic process of gluconeogenesis Go the Wikipedia article Gluconeogenesis Introduction and Regulation to answer the following questions 14 Is gluconeogenesis the exact reverse of glycolysis Why or why not 0 Not the exact reverse because rather than the action of 3 regulated enzymes of exergonic reactions in glycolysis hexokinaseglucokinase phosphofructokinase and pyruvate kinase They are replaced with glucose6phosphatase fructose16bisphosphatase and PEP carboxykinasepyruvate carboxylase for gluconeogenesis because they facilitate very strong endergonic reactions 15 What is a biochemical futile cycle 0 When two opposite reaction pathways happens simultaneously and produce no overall effect on the system except using up energy and increasing entropy for the system 16 Under normal condition why does glycolysis and gluconeogenesis NOT form a futile cycle 0 Because the enzymes involved in glycolysis inhibit those involved in gluconeogenesis and vice versa 0 By doing this gluconeogenesis cannot take place at the same time or at least at a very decreased rate therefore preventing the oscillatory property between the two evident in a futile cycle


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