BIOL 112 Unit 2 Practice Questions Spring 2024 PDF

BIOL 112: Unit 2 Practice Questions =================================== **Updated Spring 2024** This document contains some questions for you to practice. The questions are grouped by topic. We encourage you to use the learning objectives to guide your studying; ask yourself if you could answer ea...

BIOL 112: Unit 2 Practice Questions =================================== **Updated Spring 2024** This document contains some questions for you to practice. The questions are grouped by topic. We encourage you to use the learning objectives to guide your studying; ask yourself if you could answer each objective if it was in the form of a question. There are different levels of questions provided: 1. 2. **\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_** Unit 2-1: Nucleic Acids - Structure, DNA assembly and organization ------------------------------------------------------------------ ### Unit 2-1: Study questions: 1. 2. 3. 4. A. B. C. D. 5. A. B. C. D. E. ### Unit 2-1: Exam Style Questions: 6. A. B. C. D. E. 7. A. B. C. D. E. 8. A. B. C. D. E. 9. A. B. C. 10. A. B. C. D. ### Unit 2-1: Open Response (ORQ) Style Questions 11. Unit 2-2: Biological information flow ------------------------------------- ### Unit 2-2 Study Questions: 1. Transcription is the process of copying [ DNA] to [RNA] 2. [Translation] is the synthesis of [protein] from mRNA. 3. Describe the general difference between DNA replication and Protein synthesis. When does the cell use either of these processes? Are there similarities? Unit 2-3 Transcription *-* Gene structure ----------------------------------------- ### Unit 2-3 Study Questions: 1. +-----------------------+-----------------------+-----------------------+ | **Compare/contrast... | **Eukaryotes** | **Bacteria** | | ** | | | +=======================+=======================+=======================+ | Chromosome structure | Contains histones | Does not contain | | | (nucleosomes) | histones | +-----------------------+-----------------------+-----------------------+ | Site of transcription | Nucleus | Cytoplasm | +-----------------------+-----------------------+-----------------------+ | What is the promoter | TATA box, 25 bp | -35 box and -10 box | | structure? | upstream | | +-----------------------+-----------------------+-----------------------+ | What are the proteins | General transcription | Sigma | | involved contacting | factors | | | the promoter? | | | | | Tata Binding Protein | | | | (TBP) | | +-----------------------+-----------------------+-----------------------+ | Is splicing (removal | Yes | No | | of introns) required? | | | +-----------------------+-----------------------+-----------------------+ | Capping and tailing | Yes | No | | of mRNA? | | | +-----------------------+-----------------------+-----------------------+ | Site of translation | Cytoplasm | Cytoplasm | +-----------------------+-----------------------+-----------------------+ | Can translation occur | No | Yes | | while transcription | | | | is still occurring? | | | +-----------------------+-----------------------+-----------------------+ 2. +-----------------+-----------------+-----------------+-----------------+ | **Gene | **Bacterial | **Eukaryotic | **Description | | structure** | Gene? √** | Gene? √** | and Function** | +=================+=================+=================+=================+ | Promoter | √ | √ | Binds the RNA | | | | | Polymerase | +-----------------+-----------------+-----------------+-----------------+ | Introns | | √ | Sequence that | | | | | are cut out in | | | | | RNA | | | | | processing/spli | | | | | cing | +-----------------+-----------------+-----------------+-----------------+ | Stop codon | | | Does not | | | | | function in | | | | | transcription, | | | | | only | | | | | TRANSLATION! | | | | | Codes for the | | | | | end of protein | | | | | synthesis. | +-----------------+-----------------+-----------------+-----------------+ | 5' CAP | | √ | Added to mRNA | | | | | once the 5' end | | | | | is synthesized | | | | |. | +-----------------+-----------------+-----------------+-----------------+ | TATA box | | √ | sequence on Euk | | | | | promoter, | | | | | TBP/general | | | | | transcription | | | | | factors bind | | | | | here | +-----------------+-----------------+-----------------+-----------------+ | -10 and -35 box | √ | | sequence on Bac | | | | | promoter, sigma | | | | | binds here | +-----------------+-----------------+-----------------+-----------------+ | Template strand | √ | √ | DNA strand that | | | | | Codes for the | | | | | mRNA | +-----------------+-----------------+-----------------+-----------------+ | Transcription | √ (+1 site) | √ | First base that | | start site | | | is transcribed | | | | | into mRNA | | | | | | | | | | Bac = \~10 | | | | | bases from -10 | | | | | box | | | | | | | | | | Euk = \~25 | | | | | bases from TATA | | | | | box | +-----------------+-----------------+-----------------+-----------------+ | Terminator | √ (hairpin) | √ | Terminates | | | | | transcription | | | | | -- | | | | | | | | | | Bac = hairpin | | | | | loop, Euk -- | | | | | multiple repeat | | | | | sequences | +-----------------+-----------------+-----------------+-----------------+ | +1 site | √ | √ | First base that | | | | | is transcribed | | | | | into mRNA | +-----------------+-----------------+-----------------+-----------------+ | Start codon | | | Does not | | | | | function in | | | | | transcription, | | | | | only | | | | | TRANSLATION! | +-----------------+-----------------+-----------------+-----------------+ | Exons | | √ | Coding regions | | | | | that may be | | | | | spliced out or | | | | | kept in a mRNA | | | | | transcript. | +-----------------+-----------------+-----------------+-----------------+ | Ribosomal | | | Does not | | binding site | | | function in | | | | | transcription, | | | | | only | | | | | TRANSLATION! | +-----------------+-----------------+-----------------+-----------------+ | Non-template | √ | √ | Opposite strand | | /coding | | | of the template | | | | | but often used | | | | | to read the | | | | | code! (Same | | | | | sequence as the | | | | | mRNA except | | | | | with T's | | | | | instead of U's. | +-----------------+-----------------+-----------------+-----------------+ | Poly A tail | | √ | Added after | | | | | mRNA made in | | | | | Euk. | +-----------------+-----------------+-----------------+-----------------+ ### Unit 2-3 Exam Style Questions: See the Mastery Learning Modules Activities for Practice Problems on this unit. This can be found on the BIOL 112 Tutorial Canvas site under Mastery Learning Modules Unit 2-4: Transcription*-Mechanism of transcription* ---------------------------------------------------- ### Unit 2-4 Study Questions: 1. **Compare and contrast** **Eukaryotes** **Bacteria** ----------------------------------------------------------- ---------------- ----------------- Splicing (yes or no) Yes No Site of initiation for transcription (promoter structure) TATA box -35 and -10 box RNA has 5'cap (yes or no) yes no RNA has 3' poly A tail (yes or no) yes no ### Unit 2-4 Exam Style Questions: 2. A. B. C. D. A. B. C. D. E. 1. 2. 3. A. B. C. D. E. 3. A. B. C. D. E. 4. A. B. C. D. E. 5. 1. 2. 3. 4. A. B. C. D. E. 6. 1. 2. 3. 4. A. B. C. D. E. 7. A. B. C. D. E. 8. A. B. C. D. E. ### Unit 2-4 Open Response Style (ORQ) Questions: 9. If Arginine were replaced with by Serine in the protein (both shown below) **predict** what would be the effect on the protein-DNA binding. See next page...  Could this replacement have an effect on transcription of this gene? **Explain** your reasoning for your prediction. If Serine were in the protein there would be a substantial decrease in R-group size, and there would be no possibility for ionic bonds, decreasing the strength and frequency of protein-DNA binding. This would likely result in less frequent transcription. Compared to the original situation: In the DNA sequence, if guanine were replaced by thymine (shown at right), **predict** what would be the effect on the protein-DNA binding. Could this replacement have an effect on transcription of this gene? **Explain** your reasoning for your prediction. With a base substitution, different non-covalent interactions will be possible between the protein and the side of the base. i.e. from purine to pyrimidine structures This could also perturb the regular structure of the DNA. For both of these reasons, it is likely that the frequency of protein-DNA binding will decrease. This would likely result in less frequent transcription 10. Unit 2-5: Translation --------------------- ### Unit 2-5 Study Questions: 1. How is translation initiated in bacteria? What part of the mRNA transcript does the ribosome bind to? How does this differ in Eukaryotes? 2. What specific sequence or region leads to transcription termination and translation termination? The terminator sequence mediates transcription termination. Translation is terminated by the stop codon. 3. If a given tRNA has an anticodon of 5'-ACU-3', what is the mRNA codon, what is the template strand DNA sequence, and which amino acid does it carry? (3points) **tRNA 3' UCA 5' or 5' ACU 3'** mRNA: 5'- AGU-3' or 3'-UGA-5' template strand: 5'-ACT-3' or 3'-TCA-5' Amino acid: Ser ### Unit 2-5 Exam Style Questions: 4. Given that there are 61 codons for the 20 amino acids, which of the following is good evidence for the wobble hypothesis? A. B. C. D. E. 5. The DNA sequence below (the template strand) is part of the coding region of a gene. What would be the sequence of amino acids for this portion of DNA? (the reading frame is indicated by the vertical lines) 3\' -- ACG\|ATT\|CTT\|TGC - 5 5' - UGC UAA (stop) A. B. C. D. E. 6. A region of DNA is transcribed and the mRNA is translated into a sequence of amino acids. The sequence of amino acids that is encoded by this strand is: What is/are the possible sequence(s) of the corresponding template DNA? 1. 2. 3. 4. 5. 6. A. B. C. D. E. 7. Shown below is a portion of an mRNA stretch, starting at the start codon: The DNA encoding this region would be correctly written as: A. 5' TACCCCTCATTTAAA 3' B. 3' TACCCCTCATTTAAA 5' C. 3' AAATTTACTCCCCTA 5' D. 5' AAATTTACTCCCCTA 3' 8. What is the function of aminoacyl-tRNA synthetases? A. B. C. D. E. 9. Which of the following statements about translation in bacteria are TRUE? 1. 2. 3. 4. 5. A. B. C. D. E. 10. Cells use a two-step process (transcription and translation) to synthesize proteins from the information carried in the DNA, instead of directly translating information in the DNA to proteins. Which of the following statements could explain why this two-step process might benefit the cell? 1. 2. 3. 4. A. B. C. D. E. ### Unit 2-5 Open Response Style (ORQ) Questions: 11. Not all mutations in a [protein coding region] cause a change in phenotype. Explain giving 2 examples. Example: If say a silent mutation will result in no change in phenotype then you must add that there is no change in the polypeptide and/or no change in the shape and function of the protein. If you use base-substitution mutations for both examples then you must explain 2 [different] ways this can result in no change in phenotype. Some examples...The genetic code is degenerate -- some amino acids have more than one codon and a mutation in a codon can result in the same amino acid and no change in the protein. Amino acid substitutions of similar types might not lead to a change in protein function or the substitution is present in the polypeptide chain that does not change the protein shape (folding) or function. 12. Each of the statements below is false.  Re-write the statements to make them factually correct. You must re-write the statements for full points. Examples of changes we were looking for: A. The nitrogenous base thymine is present in DNA while uracil is present in RNA in place of thymine. B. C. Ribosomes translate RNA and RNA polymerase transcribes DNA into RNA. 13. The antibiotic called streptomycin is known to bind to the ribosome. Streptomycin distorts the ribosome structure so the ribosome does not stabilize the correct codon-anticodon base pairs. Instead, the ribosome stabilizes incorrect codon-anticodon base pairs. 14. The following DNA sequence is part of a transcribed region of a gene, and has a start codon in one of the strands only: A. B. C. D. E. F. Unit 2-6: DNA mutations ----------------------- ### Unit 2-6 Study Questions: 1. Practice the effects of a point mutation by using an example of a DNA coding region (any shown in these practice questions). a. b. c. ### Unit 2-6 Exam Style Questions: 2. One of the DNA replication proteins/enzymes is altered in a way that it results in an increased rate of mismatched bases in the newly synthesized DNA strand. Which function is most likely to be disrupted? A. B. C. D. E. 3\. The following nucleotide sequence encodes the C terminus region of a wild type (also called "native" or "normal" or wildtype) protein. The stop codon is underlined. The highlighted bases are mutated to the form below: *Mutant:* 5\'-GCCTCT**T**AAATCAGGAGAACACACTAA-3\' A. B. C. D. E. ### Unit 2-6 Open Response Style (ORQ) Questions: 5\. Explain what the difference is between an error in DNA replication and a mutation. 6\. Not all mutations in a [protein coding region] cause a change in phenotype. Explain giving 2 examples. Unit 2-7: Regulating gene expression: *the bacterial mal* and *lac* operons as examples --------------------------------------------------------------------------------------- ### OPERON MUTATION QUESTION are part of Mastery Learning Module 3 -see your B112 Tutorial Canvas site for Mastery Activity Worksheets and Mastery Enrichment Worksheets. ### Unit 2-7 Study Questions: 1. MalT is a \_\_\_\_\_\_ regulator of the *malPQ* operon A. Positive B. Negative 2. Compare these two gene expression systems.   *lac* operon *mal* operon ------------------------------------------------------------ -------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------------- Regulates breaking down of: lactose maltose What binds to the operator & when does this occur? The LacI repressor protein binds to the operator when lactose levels in the cells are low. The MalT-maltose activator complex binds to the operator when maltose levels in the cells are high. High levels of what substance affects the operon, and how? High levels of lactose induce the operon, by binding to LacI and removing its repression. High levels of maltose induce the operon, by binding to MalT and enabling its activation function of the operon. Is this positive regulation or negative regulation? Why? This is [negative] regulation because the repressor protein, LacI, inhibits the gene expression. This is [positive] regulation because the activator protein, MalT, enhances/promotes gene expression. ### ### Unit 2-7 Exam Style Questions: 3. Consider the basic structure of an operon. Each protein coding sequence within that operon would have:   4. The genes for the arginine operon are located on a bacterial chromosome. The proteins produced by the operon are used to **synthesize** the amino acid arginine. If the operon is controlled negatively by a regulatory protein ArgR, what would be the role of [arginine]? 5. 6. 7. ### ### Unit 2-7 Open Response Style (ORQ) Questions: 8. Which statements about this operon are true or false (T or F)? T or F Statement -------- ------------------------------------------------------------------------------------------------------------------------------------------------ T The template strand for this operon is the bottom strand. F Each protein coding region within the operon will have its own +1 site. T Each protein coding region within the operon will have its own start codon. F The terminator sequence will stop translation for all 4 proteins. F One ribosomal binding site is shared by all 4 protein coding regions. F Four different RNA polymerases are required to transcribe the operon. F Translation of the proteins further downstream (e.g. proteins 3 and 4) depends on the successful translation of the upstream proteins 1 and 2. T All four proteins can be translated simultaneously as each have their own ribosomal binding site. 9. 4 Lactose from the environment enters the cell and binds to LacI, which leads to a conformational change in LacI. --- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 3 When RNA polymerase tries to bind to the promoter, it cannot get past the LacI repressor protein, therefore RNA polymerase is mostly blocked from transcribing the genes for the lactose metabolizing enzymes. 1 The enzymes β-galactosidase and permease, coded for by *lacZ* and *lacY*, are not required by the cell at low levels of lactose, hence they are transcribed at low levels. 6 Without LacI bound to the operator, RNA polymerase is able to bind to the promoter and transcribe the lac operon. 5 LacI bound to lactose is no longer able to bind to the operator with high affinity. 2 The LacI protein binds to the operator with high affinity.  1 and 2 can be reversed as well. 10. 3 "MalT-maltose" complex-- binds the operator with a greater affinity. --- ----------------------------------------------------------------------------------------------------------------- 2 Maltose binds to MalT and this changes the conformation of MalT. 4 RNA polymerase binds more effectively to the *malPQ* promoter, leading to high levels of *malPQ* transcription. 1 Maltose is transported into the cell from the environment. ### OPERON MUTATION QUESTION are part of Mastery Learning Module 3 -see your B112 Tutorial Canvas site for Mastery Activity Worksheets and Mastery Enrichment Worksheets. ***See also Chocolate Operon Worksheet***