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Exam 4 Study Guide

by: Ifeoma O'Gonuwe

Exam 4 Study Guide BIOL-L

Marketplace > Indiana University > Biology > BIOL-L > Exam 4 Study Guide
Ifeoma O'Gonuwe
Molecular Biology
Melissa Konkol

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Molecular Biology
Melissa Konkol
Study Guide
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This 9 page Study Guide was uploaded by Ifeoma O'Gonuwe on Thursday April 30, 2015. The Study Guide belongs to BIOL-L at Indiana University taught by Melissa Konkol in Fall 2014. Since its upload, it has received 90 views. For similar materials see Molecular Biology in Biology at Indiana University.


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Date Created: 04/30/15
Exam 4 Study Guide is transcribed to 0 DNA mRNA is translated to a 0 mRNA protein What is the template for translation 0 mRNA In eukaryotes where does transcription occurs 0 Nucleus In eukaryotes where does translation occur 0 Cytoplasm In prokaryotes where does transcription occur 0 Cytoplasm In eukaryotes where does translation occur 0 Cytoplasm What is a codon o A set of three bases What is the first codon 0 AUG What are the stop codons o UGA UAA UAG What are features of an amino acid 0 Amino group carboxyl group proton R group How do you define a reading frame 0 Start and stop codon What does an open reading frame specify o A single protein How was the genetic code cracked 2 ways 0 1 Make transcripts consisting of one nucleotide o 2 Make transcripts of alternating nucleotide What transcribes tRNA 0 Pol III What does transfer RNA encode o Noncoding RNA What is the structure of tRNA 0 Cloverleaf secondary structure What does the anticodon consist of what is made of 0 Three bases in tRNA In which orientation do codons and anticodon bind o Antiparallel What does the codon do the anticodon o Complementary base pair What is the wobble effect 0 A charged tRNA can interact with multiple codons What does the 5 nucleotide of the anticodon base pair with o 3 nucleotide of the codon What is the alternative base 0 Inosine What is a silent mutation o A change in the basepair that still makes the desired amino acid What is a missense mutation o A change in the basepair that changes the codon to a different amino acid What is a nonsense mutation o A single base pair change to a premature stop codon What is a frameshift mutation 0 An addition of a basepair that leads to shift in the reading frame What is Google Genomics o In prokaryotes when does translation begin 0 While transcription is still occurring What is uncharged tRNA 0 tRNA without amino acid What is charged tRNA 0 tRNA with an amino acid attached to the acceptor stem How does aminoacyltRNA synthetase charge an amino acid 0 Attach amino acid to tRNA What is monocistronic o It means it has one open reading frame What is polycistronic o It means it has multiple reading frames 0 Happens when the genes are in operon What is the ribosome made of 0 Protein and rRNA What does an aminoacyltRNA synthetase o It charges a tRNA What are the sizes for large and small prolltaryotic subunits o 30 and 50 70s ribosome What are the sizes for large and small eukaryotic subunits o 40 and 60 80s ribosome What is the large subunit also called 0 Peptidyl transferase center What does the peptidyl transferase center do 0 Form peptide bonds between amino acids What does the decoding center do 0 tRNA reads mRNA codons What is the small subunit called 0 Decoding enter What is the target of most antibiotics 0 Bacterial ribosome any thing with a 70s ribosome and 30s and 50s subunit Where does IF1 bind o Binds to the A site Where does IF3 bind o Binds to the E site Where does IF1 bind o Binds to the IF1 which binds to the A site What do IF2 and IF1 do 0 Will contact initiator tRNA and help it bind small subunit Where does the small subunit bind on the mRNA in prokaryotes 0 RES What is the RES 0 A consensus sequence When the small subunit in prokaryotes binds RBS of rRNA what happens to the start codon o It is positioned in P site Once the small subunit in prokaryotes binds the RBS what happens with the start codon 0 Start codon is positioned in the P site When the start codon is positioned in the p site what happens to the initiator tRNA 0 It enters p site In eukaryotes what blocks the A and E sites 0 eiFl eiFlA and eiF5 What is initiator tRNA charged with in eukaryotes o fMet What does eiF4G do 0 Interact with polyA tail and polyA binding proteins 9 circular DNA structure How is mRNA recruited to small subunit 0 eIF4E binds to the 5 cap Small subunit and associated eIFs align initiator tRNA in P site by 0 Scanning mRNA 5 to 3 What begins termination 0 Stop codon in the A site Are there tRNAs that correspond to a stop codon 0 NO What does Class I release factors bind to the stop codon do 0 Release polypeptide chain from tRNA in P site In prokaryotes are all stop codons recognized by the same class I release factor 0 No In eukaryotes are all stop codons recognized by the same class I release factor 0 Yes What causes class I RFs to dissociate 0 Class II factor GDP exchange to GTP Explain the class I dissociation 0 Class II factor with GDP binds to A site GDP has high affinity to class factor 0 GDP is exchanged for GTP 9 kicks off class I o GTP has a high affinity for ribosome but it is hydrolyzed to GDP which kicks off GDP and class II factors After class II factors is kicked out of the A site are the E and P sites empty 0 No How do you empty the E and P sites 0 RRF inserts in the A site 0 EFG kicks RRF into P site 0 Release of P and E site tRNAs What happens when tRNAs have been released from the P and E site 0 mRNA is released What stimulates ribosome dissociation o IF3 What is ribosome recycling 0 Removal of tRNAs and mRNAs from ribosome which is then dissociated into large and small subunit 0 What is the exon junction complex 0 Proteins 0 Where are EJCs located 0 Approximately 20 nucleotides upstream of EJC o What do EJCs serve as for the advancing ribosome o Guideposts o If the ribosome comes into contact with an EJC what does it do 0 Keep translating 0 How does translation terminate think of EJC 0 Stop codon with no EJC proteins downstream o What is nonsensemediated mRNA decay 0 Degradation of mRNA with a premature stop codon o What does the cell do if it reaches a stop codon without more EJC proteins ahead 0 Terminate translation 0 What does the cell do if it reaches a stop codon and there are more EJC proteins ahead 0 Ribosome is displaced and proteins are recruited to degrade mRNA 0 What do antibiotics target 0 Prolltaryotes or both prolltaryotes amp eulltaryotes o A lot of antibodies target what 0 Ribosomal and translational machinery o What does puromycin do 0 Inserts within A site of ribosome o If puromycin enters the ribosome where is the peptide bond formed 0 On puromycin o If puromycin enters the ribosome where is the polypeptide chain added 0 On puromycin o If the polypeptide chain is added to puromycin what happens to additional amino acids 0 They can t be added 0 If the puromycin is in he ribosome what happens to the resulting protein 0 It is truncated and dissociates from the ribosome Lecture 34 o What is a primary sequence 0 Amino acid sequence in a polypeptide chain 0 What is secondary structure 0 Local structure 0 What is a tertiary structure 0 Folded structure of polypeptide chain 0 What is a quaternary structure 0 Arrangement of multiple subunits in a larger complex 0 What do chaperone proteins do 0 Aid in folding o How does GroELGroES work 1 Partially folded protein binds edge of one GroEL subunit 2 ATP biding allows GroES lid to bind subunit of GroEL 3 Once the GroES lid binds to GroEl the protein moves to the interior of GroEl and is folded 4 ATP hydrolysis releases the folded protein and GroES 0 Where is protein folded in GroELGroES OOOO o GroEL s interior Why does the partially folded protein move to interior of GroEL o GroES binds subunit of GroEL In GroELGroES when the protein is folded what does ATP hydrolysis do 0 Releases the folded protein and GroES What is a protein localization sorting motif 0 Amino acid within a protein that targets that protein to the appropriate location Where is a protein localization located 0 Nterminus Cterminus or both What is the nuclear localization sequence 0 A protein localization sorting motif Nuclear localization sequence targets the protein to which location 0 Nucleus What does the nuclear localization sequence consist of 0 510 basic positively charged amino acid What is the endoplasmic reticulum retention sequence 0 A protein localization sorting motifs What does the endoplasmic reticulum retention sequence consist of o KDEL LysAspGluLeu Can a protein leave the ER if it has the endoplasmic reticulum retention sequence 0 How How can a protein with the KDEL endoplasmic reticulum retention sequence leave the ER 0 KDEL sequence must be cleaved off SRP signal sequence is an example of what 0 Protein localization sorting motif Where does a protein enter the endomembrane system 0 Endoplasmic reticulum What allows proteins to be targeted to specific locations within the endomembrane system 0 Sorting motifs List the different parts of the endomembrane system 0 Nuclear envelope endoplasmic reticulum Golgi apparatus lysosomes vacuoles vesicles and the cell membrane How is the endomembrane system connected 2 ways 0 Directly or via vesicles What is the endoplasmic reticulum continuous with 0 Nuclear envelop What is cisternae 0 System of connected sacs and tubules What is the area inside the cistarna called 0 Lumen How many types of ER are there 0 Two What is smooth ER 0 ER without any attacked ribosomes What is smooth ER involved in o Lipid synthesis What is rough ER 0 ER with ribosomes attached on the cytoplasmic side What is rough ER involved in 0 Protein synthesis and folding Where do rough ER synthesized proteins go 2 places 0 1 secreted from the cell 0 2 remain within endomembrane SRP sequence targets proteins to which location 0 Endomembrane system To what does the signal recognition particle SRP bind 0 Signal sequence Where is the signal sequence located 0 Protein translated by ribosome What happens once the signal sequence and signal recognition particle bind 0 Translation is halted Once translation is halted SRP brings and to receptor in ER membrane 0 Ribosome polypeptide What happens after SRP leaves 0 Translation resumes Once translation resumes how does the polypeptide enter ER 0 Through translocation complex Once the protein polypeptide is in ER what happens 0 The signal sequence is removed because protein is now part of the endomembrane system What does the golgi apparatus do 0 Modifies sorts and packages proteins for export Where do transport vesicles dock on the Golgi apparatus 0 Cis face of Golgi apparatus What happens after proteins reach trans face of Golgi 0 Proteins are placed into membrane vesicles Once proteins from Golgi are placed in membrane vesicles where do they go 2 places 0 1 Different parts of the cell 0 2 Secretory vesicles 9 secretion outside of the cell What is signal transduction o Cascade of biochemical reactions that eventually reaches a target What interacts with a cellsurface receptor 0 Signal Give an example of a signal 0 A hormone Signal transduction cascade refers to 0 Signal after binding to cellsurface receptor being transferred to intermediate proteins or molecules What elicits a cellular response in signal transduction 0 Most downstream member of a cascade What is the typical response of signal transduction cascade 0 Activation or repression of a particular gene What is another name for a signal 0 A ligand What detects a ligandsignal 0 Cell surface receptor What are the two domains of a cell surface receptor 0 Extracellular and intracellular domains What part of the cell surface receptor binds to the ligand o Extracellular domain What part of the cell surface receptor relays the signal through signal transduction cascade o Intracellular domain When the ligand binds to the extracellular domain of the cell surface receptor how does the intracellular domain know this happens 2 things 0 Binding of ligand to extracellular domain of the cell surface receptor changes shape of receptor 0 Binding of ligand to extracellular domain of the cell surface receptor brings two or more receptors into contact What is a kinase 0 An enzyme that adds a phosphate group to a protein What happens when RTK is bound by its ligand 0 Receptors dimerize Once RTK receptors dimerize what happens to kinase domains 0 They are activated in the intracellular domains and activity is turned on What happens after RTK dimerizes 0 Trans phosphorylation occurs What is trans phosphorylation o RTKs phosphorylated each other tyrosine What does trans phosphorylation do to the signal pathway 0 Make it active Where does paracrine act on 0 Local target cells What are paracrines o Signals released by cells into the extracellular medium Where does juxtracrine act on 0 Target cells in direct contact with the signaling cell What are juxtacrines o Signals tethered to the membrane not secreted Where does endocrine act on o Distant target cells What are endocrines o Signals released into the bloodstream What does autocrine act on 0 Cell surface receptors of the same cell What autocrines o Signals secreted by cell Step one of MAPK pathway 0 Ligand binding RTK 9 dimerize 9 trans phosphorylate Step two of MAPK pathways 0 Grb2 binds phosphorylated RTK and SOS 9 binds Ras o RTKSOSRas 9 GDP exchange for GTP 9 activates Ras Step three of MAPK pathways 0 Ras activates MAPKKK Step four of MAPK pathways 0 MAPKKK phosphorylates and activates another kinase Step five of MAPK pathways 0 MAPKK phosphorylates and activates another kinase Step six of MAPK pathways o MAPK phosphorylates transcriptional activators active enough to enter nucleus and activate transcription Two things that must happen before electrophoresis of proteins 0 Treat with SDS 0 Treat with BME What two things does SDS do 0 Gives protein uniform negative effect 0 Denatures proteins What is sodium doecyl sulfate 0 A strong ionic detergent What does treatment with BME do 0 Reduces disulfide bonds between cysteine and amino acid Why does SDSPAGE add a stain 0 To allow for visualization What does SDSPAGE use to separate proteins by size on a polyacrylamide gel 0 Electrical current What is western blot 0 Technique used to visualize individual proteins In western blot what is SDS PAGE used for 0 To separate proteins In western blot what happens after SDS page 0 Transfer SDS page results to a filtermembrane that nonspecifically binds proteins In western blot what position are the proteins on the filter paper 0 Same position as in the polyacrylamide gel In western blot how are nonspecific binding sites blocked 0 Covering filter with powdered milk solution In western blot how is a specific protein highlighted 2 steps 0 Filter paper is incubated with an antibody specific to protein 0 An enzyme attaches to antibody and emits light Why would you use protein purification 0 To study a particular protein How do you make a cell extract 0 Bursting open cells By making a cell extract what happens to the proteins 0 They escape What is a lysate 0 Product of lysed cells containing a mixture of protein What is the most common method for protein purification 0 Column chromatography In ionexchange chromatography proteins are separated based on 0 Surface charge In ionexchange chromatography if beads are negatively charged charged proteins will bind to them 0 Positively charged In ionexchange chromatography if beads are negatively charged charged proteins will remain in the column 0 Positively charged In ionexchange chromatography if beads are negatively charged charged proteins will pass through column o Negatively charged What is elution 0 Proteins to be released from beads in a buffer solution In gelfiltration chromatography proteins are separated based on 0 Size and shape In gelfiltration chromatography which proteins are in the column 0 Smaller proteins get stuck In gelfiltration chromatography which proteins elute more rapidly 0 Larger proteins After each column ionexchange or gelfiltration are collected at different salt concentrations or different elution times 0 Fractions What do you do to the fractions from column exchange 0 Assay fractions for protein of interest What does coimmunoprecipitation test 0 If two proteins interact In coimmunoprecipitation what is the bait 0 Antibodies specific to the first protein bound to the beads In coimmunoprecipitation what is the prey o The second protein In coimmunoprecipitation if the prey binds to the bait where will it end up 0 In the column In coimmunoprecipitation if the prey does bind to the bait where will it end up 0 Flow out of the column In coimmunoprecipitation what is performed no the eluted antibodyprotein complex 0 SDS Page and Western blot using antibodies specific to both proteins bait and prey In coimmunoprecipitation how many bands would you expect on the Western blot if there is NO interaction between the bait and prey 0 One I Why 0 The prey would have flowed out of the column and would not be in the antibodyprotein complex therefore antibodies would not have bound to it because it wouldn t have been present In coimmunoprecipitation how many bands would you expect on the Western blot if there IS an interaction between the bait and prey 0 Two


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