2-2 Transcription

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Samuel McCabe

Technology

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Essential Biology 3.5 Transcription & Translation (Core)

Stephen Taylor

Chemistry 81 MtSAC Dr. V. Prutyanov Spring 2020 Mechanism of SN2 Reaction Student:______________________ Predicting SN2 reactivity by calculating transition states for RCl + Br - In this exercise you will consider the reactivity of alkyl chlorides towards SN2 reactions. Specifically, you will use Molecular Orbital calculations to explore the relative SN2 reactivity of the following compounds: CH3Cl, EtCl, i-PrCl and PhCH2Cl. The approach you will use is to calculate the energy of the SN2 transition state for the attack of Br - on the alkyl chloride, and subtract the energy of the reactants from it. That should allow to calculate the activation energy, Ea for the following process: RCl + Br- → RBr + Cl- The obtained data analysis should illustrate the impact of the structure of R on the rate of the SN2 reaction as larger activation energy corresponds to a slower reaction. Another variable in this work is the solvent that is going to be introduced later to model the reaction more realistically. Procedure 1. Choose the “5-bonded-carbon” structure from the Inorganic drawing template. This puts the five valences in the desired trigonal bipyramidal geometry, three planar and 120° apart (the equatorial bonds), and the other two at 90° to this plane (called the axial bonds). 2. Add a nucleophile and a LG to the axial valences that are at 180° to each other, and the appropriate groups to the equatorial valences to build each transition structure. Open “Calculations” menu, chose the right charge (-1 for an anion, for example) and run a semi- empirical PM3 “Equilibrium geometry”. This should yield a good starting point for the Transition State search with C-Br distance around 2.2 Å and C-Cl 2.4 Å. If necessary, adjust the bond distances using “Measure distance” option within “Geometry” menu. 3. After the optimization above is complete (you might resubmit “failed” calculations), open the calculations menu and choose “Transition State Geometry”. Check the IR box. Submit the job. 4. If the TS search is successful it should have one and only one negative (or so-called “imaginary”) frequency that could be apparent from the IR spectrum. Click on spectrum icon on the upper panel and chose Calculated IR box in a pop-up window. Clicking on the corresponding frequency on the top of the table will animate the imaginary frequency that leads to collapse of the TS to the products. Hence the name “imaginary” as the common vibrations are reversible and do not collapse a molecule. In this mechanism, the expected movement would be a departure of the leaving group upon an approachment of the nucleophile. 5. Record the energy of the TS in a table below. Safe you file! 6. In a separate file, build the nucleophile and the alkyl chloride together and calculate the energies of the reactants using semi-e.

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Name: __________________________________ Date: ____________________ SERIES AND PARALLEL CIRCUITS Introduction In today’s lab, you are going to investigate the characteristics of circuits with resistors in series and circuits with resistors in parallel. To investigate the characteristics, you are going to apply Ohm’s Law. Voltage (V) = Current (I) x Resistance (R) Purposes 1. To determine the equivalent resistance of resistors in series. 2. To determine the equivalent resistance of resistors in parallel. 3. To apply Ohm’s Law to simple circuits. Materials This lab requires you to create simulated circuits using the PhET Circuit Construction Kit Virtual Lab ( be sure you use the HTML5 version, not the Java version). Part 1: Applying Ohm’s Law to a Simple Circuit Create the following simple circuit using the simulation. The simulation shows electrons flowing from the negative terminal of the battery (black end), through the resistor (light bulb) and the positive terminal (copper colored end). Change the current direction by selecting Conventional Current (in top right box). This shows the direction physicists thought current was flowing before the existence of the electron was discovered. Set the voltage and resistance in your circuit using the values in the table below that correspond to the first letter of your last name: First letter of Last Name Voltage Resistance G-I 7 V 7 Ω Change the setting on the battery and light bulb by clicking on the component and using the arrows and/or slider at the bottom of the simulation screen. Enter the values you are using in the table below: Voltage Resistance Current V Ω A Using your assigned values of voltage (V) and resistance (R), use Ohm’s Law to calculate the current to demonstrate that the ammeter reading is correct. Result of this calculation = A Now double the voltage. Indicate the new values in the circuit in the following table: Voltage Resistance Current V Ω A So when the voltage is doubled, the current is (put an X next to your choice) a ½ of what it was. b ¼ of what it was. c 4 times what it was. d 2 times what it was. Do not change the voltage of the battery from new value (listed above). Double the resistance. Indicate in the following table the values of the circuit after making the change. Voltage Resistance Current V Ω A So when the resistance is doubled, the current is (put an X next to your choice) a ½ of what it was. b ¼ of what it was. c 4 times what it was. d 2 times what it was. For part 2 and 3, keep the voltage the same as the value you were assigned in part 1. Use the following values of resistances in your circuit using the values in the table below that correspond to the first letter of your last name First letter of Last Name Volt ...

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Saul Olaf Loaiza Meléndez

Lab 15: DNA Model Discovery Kit Answer sheet (For use with DNA Model Kit with instructions based on those by KD Blographics) DNA and RNA - Compounds and Structure: DNA the genetic material found in the nucleus of eukaryotic cells, is a very complex molocule formed using six compounds, PHOSPHATE, a SUGAR (deoxyribose), and four BASES (adenine, guanine, cylosine, and trymine), Lkewise, the complex RNA molecule found in cells is formed using six compounds, PHOSPHATE, a SUGAR (ribose), and four BASES (adenine, guanine, cytosine, and uracil). Foliow the instructions found with the DNA puzzie kit to categorize puzzfe pieces, and ibontify the specific compound name for each puzzle piece labeled 1 - 8 . You will not be able to fill out the entire chart at once, but list the name of each pioce when you can identily it and whether it is found in DNA, RNA, or BOTH. a. Write the inltial of the bases in the order found in your DNA ladder, below. DNA iop strand: C G A A I G A S Q. Briefly describe the pairing of bases in the "rungs" of your DNA ladder. Is there a pattern to the base pairing (use base names), and is there a pattern to the base types (purines and pyrimldines) found in the pairs? Why do you think they pair up in this manner? Kes) Guantie and Cu Mosine, Adiec and Thamire. DNA REPLICATION: Before cells car divide inso new cells, they must make components for the new cels. Duplicating DNA called DNA replication, is part of thil process. Foliow DNA wit instructions to make new DNA using the original double strand, then answer the following. Q. Describe the role hydrogen bonding plays in the process of replication, and the compesition of the resulting DNA strands including whether or not they are identical using key words like "original" and "eopy". Higlvogen ponding heivs to kec an ins shuchere of plda stroid TRANSCRIPTION - DNA to RNA: Although DNA carries the code to make proteins, it cannot leave the nucleus and travel to the ribosomes where protein synthesis occurs. Something else must take the message. Follow the instructions with your DNA kit to explore transcription, and then answer the questions, below. Describe the base sequence of the mRNA you have formed showing which bases pair up with the bases of the oriainal DNA. Briefly describe how the results of transcription differ from the process of DNA replication. Tronsciption differs from DNp repicatiop, making RNA COpy TRANSLATION - RNA to PROTEINS: The genetic code is carried in linear sequence of bases. A protein is made of a linear sequence of amino acids. The languages are different, but if translated, the codes are the same. Follow the instructions in your DNA kit to study translation. When you've completed the puzzle activity, fill in the answers, below. Fill in each three bese sequence in the mRNA and the tRNA that you used in this lab activily. Look at the table of amino acids on the last page. Each column represents the base sequences from DNA. mRNA and TRNA that transiate to an .

Lab 15- DNA Model Discovery Kit Answer sheet (For use with DNA Model K.pdf

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DNA Nucleotide Template Synopsis: Find someone who needs computer support and solve their problem. Identify someone who is having a problem with technology. The problem should not be simple or simplistic in nature. The person you assist cannot be yourself or someone who is currently living with you. While you may choose who to help and the problem to solve, the problem needs to be real and of sufficient depth for a IT graduate student. After you have solved the problem, create a document which will clearly, completely, and accurately describe the problem and the solution you discovered. Ensure the user understands what the problem was and how you solved it. Include the user’s (the person you helped) name and email address within the document. Submit your document after you solve the user’s problem. RNA Nucleotide Template tRNA Template DNA and Protein Synthesis Hands-On Labs, Inc. Version 42-0051-00-02 Review the safety materials and wear goggles when working with chemicals. Read the entire exercise before you begin. Take time to organize the materials you will need and set aside a safe work space in which to complete the exercise. Experiment Summary: You will learn the structure and function of DNA and RNA. You will learn the similarities and differences between DNA and RNA. You will learn the process of protein synthesis and create and use models to demonstrate both transcription and translation. © Hands-On Labs, Inc. www.HOLscience.com 1 EXPERIMENT Learning Objectives Upon completion of this laboratory, you will be able to: ● Review the structure and function of DNA. ● Identify the codons that code for amino acids in DNA and RNA. ● Explain the purpose of start and stop codons in protein synthesis. ● Summarize the steps involved in protein synthesis and define a ribosome and its three sites. ● Summarize the steps of transcription, including: initiation, elongation, and termination. ● Summarize the steps of translation, including; initiation, elongation, and termination. ● Illustrate and model the processes of transcription and translation. ● Construct a series of tRNA molecules and write the anti-codons and amino acids each tRNA carries. ● Explain the difference in the number of amino acids that were present at the start and at the end of the translation model. Time Allocation: 3 hours www.HOLscience.com 2 ©Hands-On Labs, Inc. Experiment DNA and Protein Synthesis Materials Student Supplied Materials Quantity Item Description 1 Camera, digital or Smartphone 1 Pair of scissors 1 Printer 10 Sheets of printer paper 1 Pen or pencil 1 Tape HOL Supplied Materials Quantity Item Description 1 DNA Nucleotide Template 1 RNA Nucleotide Template 1 tRNA Template Note: To fully and accurately complete all lab exercises, you will need access to: 1. A computer to upload digital camera images. 2. Basic photo editing software such as Microsoft Word® or PowerPoint®, t.

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