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MCB 2050 Midterm Questions With Complete Solutions A dysfunctional P-TEFb protein that has lost its kinase ability is expressed in a eukaryotic cell. Which could be expected to occur?
- NELF remains bound to the DNA
- DSIF is unable to keep RNA polymerase clamped onto the DNA
- Transcriptional elongation no longer proceeds
- NELF remains bound to DSIF
- All of the above could occur Correct Answers 5. all of the above could occur A molecule that is recognized by antibody to produce an immune response is called a/an: Correct Answers Antigen? A southern Blot is used to analyze _______, while a northern blot is used to analyze_______ Correct Answers DNA, RNA According to the reading what particular feature of molecular hybridization makes it a powerful tool in molecular biology? Correct Answers That molecular hybridization is highly specific An antibody generated against the mouse IgG constant domain and produced in rabbits is referred to as:
- Rabbit anti-mouse
- More than one of these responses is correct
- Labeled secondary antibody
- Mouse anti-rabbit
- Primary antibody Correct Answers are Eukaryotic or Prokaryotic polymerases more complex? Correct Answers Eukaryotic (ex. yest) are more complex Define Euchromatin Correct Answers 'eu' = true --> lightly stained chromosome regions --> where most eukaryotic genes are located --> genetically active Define heterochromatin Correct Answers 'hetero' = different --> regions of chromosomes that are more intensely stained --> DNA is more densely packed --> rich in repetitive DNA mostly located in centromeres and telomeres --> generally not accessible to transcriptional machinery --> genetically inactive Describe the RNA polymerase II Clamp Domain... Correct Answers Opens when downstream DNA is inserted into this region, and swings shut when the enzyme is in elongation mode. The shut position makes enzyme very processive (enzymes ability to catalyze = add bases) G-C base pairs contain ____ hydrogen bonds, while A-T pairs contain ____ Correct Answers 3, 2 heavy chains and light chains are different in that: Correct Answers
- providing a docking site for enzymes that modify the RNA being transcribed
- All of the above require phosphorylation of the CTD Correct Answers 2. preventing chromatin condensation Place the following events of RNA splicing in the correct sequence: I. Formation of a 2' 5' phosphodiester bond between the branch point and 5' end of the intron II. The first transesterification reaction, catalyzed by U2 and U III. Recruitment of U3, U4, and U5 to the preRNA IV. Binding of SF1 to the branch point A V. Joining of the two exons via a 3' 5' phosphodiester bond A.IV, III, II, I, V B.III, IV, II, I, V C.IV, III, I, II, V D.III, IV, II, V, I E.II, IV, III, I, V Correct Answers A Place the following steps of transcriptional activation in the correct order: I. binding of the mediator complex to the DNA II. acetylation of histones III. formation of the transcription bubble IV. recruitment of pioneer transcription factors V. phosphorylation of the CTD of RNA polymerase Correct Answers IV, II, I, III, V Put the following steps of a Southern Blot in the correct order.
- The membrane is incubated with radio-labeled probes
- Sample DNA is broken into fragments and run on an electrophoresis gel.
- The membrane is visualized via X-ray and an autoradiogram is generated.
- Sample DNA is transferred from the electrophoresis gel to a solid membrane. Correct Answers 2, 4, 1, 3 The branch point A does not participate in base pairing with the ________ to allow for the first ________ reaction in RNA splicing via the ________ group of the branch point A. A. U1 snRNA; polymerization; 3' OH B. 3' splice site; debranching; 5' PO C. 3' splice site; transesterification; 3' OH D. U2 snRNA; transesterification; 2' OH E. U2 snRNA; debranching; 2' OH Correct Answers D The point at which half of the DNA strands are denatured is called the ______ of a given sequence Correct Answers The spilceosome consists of:
- snRPS
- snRNAs
- U
- U
- all of the above Correct Answers all of the above
What are the positions of the Core Promoter Elements? Correct Answers BRE -37 -> - TATA -31 -> - INR -2 -> + DPE +28 -> + What are the properties of a Promoter Correct Answers 1. functions within a short distance; ~ several hundred bps from transcription initiation site
- immediately upstream from the initiation site (for RNA pol 2)
- position dependent: usually non-functional if moved
- orientation dependent: drive transcription in one direction only What are the properties of an Enhancer? Correct Answers 1. can function over a long distance; maybe over tens of kbps from transcription initiation site
- can be upstream, downstream from the start of within introns
- position independent: usually still functional when moved
- orientation independent: function in either normal or the inverted orientation What are the regions of CTD that most heavily transcribed, and what are they referred to as? Correct Answers regions 74 EF and 75B, they are called PUFFS What are the RNA pol II GTFs that are labeled as TFII Correct Answers TFIIA, TFIIB, TFIID, TFIIE, and TFIID
What are the three elements that direct the positioning of the polymerase? Correct Answers TATA box, Initiator, BRE (TFIIB recognition element) or DPE (downstream promoter element) What are the two largest subunits of RNA polymerase 2 called (eukaryotic) and what are they similar to in bacterial RNA polymerase? Correct Answers RPB1 and RPB2, they are similar to B' and B in bacterial RNA polymerase What are two sub-units that extend from the core portion of yeast RNA polymerase 2? Correct Answers RPB4 and RPB What conditions will cause double stranded DNA to denature? Correct Answers high temp What do cyclins do? Correct Answers activates the transition to the next stage and then gets degraded What does MG 2+ do in RNA pol II? Correct Answers participates in catalysis of phosphodiester bond formation What does RNA polymerase I transcribe and what is its function? Correct Answers it is a ribosome component and it synthesizes only Pre-rRNA What does RNA polymerase II transcribe and what is its function? Correct Answers mRNA -> encodes proteins snRNA -> RNA splicing siRNA-> translation control
Nuclear membrane disintegrates Centrioles move to opposite poles Spindle apparatus formed by microtubules What happens in telophase? Correct Answers Nuclear membrane reforms Chromosomes decondense What is a CPG island? Correct Answers the promoters for about 70 percent of protein-coding genes in vertebrate, are characteristic of genes transcribed at a low rate. CpG rich DNA contains less nucleosomes and are easier to transcribe. Initiates in both directions, but proceeds only over the ORF What is a transcription factor? Correct Answers a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. What is an enhancer? Correct Answers a short (50-1500 bp) region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur. What is Pax6? Correct Answers an example of complex regulation of a eukaryotic gene
Pax6 protein is required for development of the eye, certain regions of the brain and the spinal cord, and pancreas cells. What is splicing Correct Answers joining of two exons and removal of an intron What is the cell cycle? Correct Answers ordered series of events that lead to cell divisions and the production of two daughter cells What is the chromosome segregation checkpoint? Correct Answers have all chromosomes reached opposite poles? What is the G1 phase cyclin, what does it regulate and how Correct Answers cyclin D, regulates CDK 4/ --> coordinate cell growth with entry into a new cell cycle in response to growth factors --> inactivates CDK inhibitors allowing activation of G1/S cyclins What is the G1 phase? Correct Answers gap phase between birth of new cell (M) and chromosome replication (S)- cell grows in preparation for the next mitosis What is the G1/S phase cyclin, what does it regulate and how Correct Answers cyclin E, regulates CDK --> inactive inhibitor (Rb) that suppresses S-phase CDK activity in G --> allows synthesis of genes controlling S phase progression including cyclin A
What is the spindle assembly checkpoint? Correct Answers are all chromosomes attached to mitotic spindles? What is unique about PAX6 Correct Answers it has three alternative promoters that can produce three similar proteins What molecule does Northern Blot study? Correct Answers What molecule does Southern blot study? Correct Answers What molecule does Western Blot study? Correct Answers What process creates immunoglobulin diversity? Correct Answers What type of bonds are broken when double stranded DNA is denatured? Correct Answers not phosphodiester What would be expected to decreases the melting temperature of double stranded DNA? Correct Answers low G-C content and High A-T content When B cell receptors encounter antigen, the cell will divide rapidly in a process called: Correct Answers When double stranded DNA splits into two single stranded molecules this is called... Correct Answers Denaturation Where is the commitment point, and what does it do? Correct Answers The decisions whether to divide or not is taken in late
G1 phase. This decision is tightly regulated. Cells that will never divide arrest before this start point Which cells of the immune system are responsible for producing secreted antibody? Correct Answers not stem cells Which is considered a negative regulator of transcription?
- NELF
- P-TEFb
- TFIIH
- 5' Cap
- All of the above Correct Answers 1. NELF Which is not involved in transcriptional initiation?
- chromatin decondensation
- acetylation of histones
- DSIF
- mediator complex.
- TATA box Correct Answers 3. DSIF Which of the following best describes a 'probe' as used in molecular hybridization techniques?
- a ds DNA or RNA molecule under analysis
- the specific location of DNA or RNA within living or fixed cells
- a short single stranded labelled DNA or RNA molecule used to detect its complementary sequence within a mixture of DNA or RNA
- Covalent bonds formed between the amino acids within the antigen binding site and the epitope
- Van der Waals forces between amino acids of the antigen binding site and the epitope
- Molecular hybridization that occurs between the antibody and the antigen
- Hydrophobic forces between amino acids of the antigen binding site and the epitope Correct Answers Which of the following statements about antibody structure is correct?
- The antigen binding site is located on the light chain
- The variable regions from both the light and heavy chains form the antigen binding site
- The hyper-variable regions are located on the constant domains of both the heavy and light chains 4.The full antibody molecule is a tetramer comprised of 4 identical polypeptide chains
- The heavy and light chains are held together by hydrogen bonds Correct Answers 2 Which technique could be used to produce a human karyotype? Correct Answers Fluorescence in situ hybridization
You are studying the genes involved in embryo development. Which of the following techniques could be used to visualize the locations with high expression of a particular gene of interest in a whole mounted embryo? Correct Answers In situ? You wish to isolate a specific protein from a mixed sample of proteins. Which of the techniques is best suited for this task? Correct Answers You wish to study the protein-protein interactions of a specific protein. Which of the following techniques is best suited for this task? Correct Answers Co-Immunoprecipitation You wish to visualize the location of a particular protein in fixed cells, what is one method you could use to do this?
- Western Blot
- Immunofluorescence
- Southern Blot
- Fluorescence in situ
- hybridization
- Immunoprecipitation Correct Answers 2
