Group 4 Gene Expression Group Members Kenneth van Golen, University of Delaware Nike Olabisi, University of Delaware Amy Warenda Czura, Suffolk County Community College Vladimir Jurukovski, Suffolk County Community College Jacqueline Washington, Nyack College Peter Park, Nyack College Facilitators Ross Nehm, Stony Brook University Casey Roehrig, Harvard University

Gene Expression: A Basic Overview Context: Intended for Introductory Biology (first course of a two semester series). The topic should be covered within one class week; 3 lecture hours. The teachable unit will be taught in the middle of the course after introduction to chemistry, proteins, and enzymes.

Learning Goals The students should be able to: Demonstrate knowledge of the relationships among DNA, genes, RNA and proteins. Know the detailed mechanisms of the processes of transcription and translation. Learning Outcomes The students should be able to: Define and illustrate the basic structure of a gene. Outline the basic steps of the central dogma. Define and explain the process of transcription. Compare and contrast prokaryotic and eukaryotic transcription. Apply genetic code to translation. Define and explain the process of translation.

Learning Goals The students should be able to: Demonstrate knowledge of the relationships among DNA, genes, RNA and proteins. Know the detailed mechanisms of the processes of transcription and translation. Understand how genetic mutations impact protein function. Learning Outcomes The students should be able to: Define and illustrate the basic structure of a gene. Outline the basic steps of the central dogma. Define and explain the process of transcription. Compare and contrast prokaryotic and eukaryotic transcription. Apply genetic code to translation. Define and explain the process of translation. Describe the various types of genetic mutations. Predict the effect of mutations on protein structure and function.

Let’s assess your knowledge of the basic concepts of transcription and translation from the previous lesson that applies to today’s topic.

Let’s start with a piece of DNA Coding strand 5’ …ATGCGTTTAGAATGA… 3’ 3’ …TACGCAAATCTTACT… 5’ Template strand

Writing Activity: Given the following sequence on your handout, transcribe the sequence of the mRNA (1 minute) Template strand of DNA 3’ …TACGCAAATCTTACT… 5’ mRNA ?

CLICKER Question: Choose your answer Template Strand of DNA 3’ …TACGCAAATCTTACT… 5’ mRNA ? A.5’ UACGCAAAUCUUACU 3’ B.3’ UACGCAAAUCUUACU 5’ C.3’ AUGCGUUUAGAAUGA 5’ D.5’ ATGCGTTTAGAATGA 3’ E.5’ AUGCGUUUAGAAUGA 3’

3’ …TACGCAAATCTTACT… 5’ Key concepts nucleic acids have polarity mRNA transcript is complementary and antiparallel to the DNA template strand. DNA  RNA C – G G – C T – A A – U

CLICKER Answer 3’ …TACGCAAATCTTACT… 5’ A.5’ UACGCAAAUCUUACU 3’ B.3’ UACGCAAAUCUUACU 5’ C.3’ AUGCGUUUAGAAUGA 5’ D.5’ ATGCGTTTAGAATGA 3’ E.5’ AUGCGUUUAGAAUGA 3’

CLICKER Answer Explanation 3’ …TACGCAAATCTTACT… 5’ A.5’ UACGCAAAUCUUACU 3’ Misconception: RNA is just DNA with U instead of T

CLICKER Answer Explanation 3’ …TACGCAAATCTTACT… 5’ A.5’ UACGCAAAUCUUACU 3’ Misconception: RNA is just DNA with U instead of T B. 3’ UACGCAAAUCUUACU 5’ Misconception: Same as A, but also polarity is reversed

CLICKER Answer Explanation 3’ …TACGCAAATCTTACT… 5’ A.5’ UACGCAAAUCUUACU 3’ Misconception: RNA is just DNA with U instead of T B. 3’ UACGCAAAUCUUACU 5’ Misconception: Same as A, but also polarity is reversed C. 3’ AUGCGUUUAGAAUGA 5’ Misconception: Sequence correct but polarity is reversed

CLICKER Answer Explanation 3’ …TACGCAAATCTTACT… 5’ A.5’ UACGCAAAUCUUACU 3’ Misconception: RNA is just DNA with U instead of T B. 3’ UACGCAAAUCUUACU 5’ Misconception: Same as A, but also polarity is reversed C. 3’ AUGCGUUUAGAAUGA 5’ Misconception: Sequence correct but polarity is reversed D. 5’ ATGCGTTTAGAATGA 3’ Misconception: RNA is the exact complement of DNA

CLICKER Answer Explanation 3’ …TACGCAAATCTTACT… 5’ A.5’ UACGCAAAUCUUACU 3’ Misconception: RNA is just DNA with U instead of T B. 3’ UACGCAAAUCUUACU 5’ Misconception: Same as A, but also polarity is reversed C. 3’ AUGCGUUUAGAAUGA 5’ Misconception: Sequence correct but polarity is reversed D. 5’ ATGCGTTTAGAATGA 3’ Misconception: RNA is the exact complement of DNA E. 5’ AUGCGUUUAGAAUGA 3’ Correct!

Given the mRNA we transcribed on the handout, assume the sequence is in frame and translate the amino acid sequence. 5’ …AUGCGUUUAGAAUGA… 3’ Think-Pair-Share (1 min think, 1 min share) Compare with neighboring groups (1 minute) Is there anything else you need to do this?

Genetic Code located in the middle of the table: share with your neighbor!

Given the following mRNA, translate the amino acid sequence. 5’AUG CGU UUA GAA UGA 3’ What did you get?

Given the following mRNA, translate the amino acid sequence. 5’AUG CGU UUA GAA UGA 3’ Did you get this? Met Arg Leu Glu Stop Methionine Arginine Leucine Glutamic Acid Stop codon

Group Activity Directions: Form three groups at your table and have each group work on one of the following base changes to the original DNA sequence on your handout. After making the DNA change transcribe and translate the new sequence. (2 minutes) Group #1: Change the 8 th base from A to C #2: Change the 9 th base from T to C #3: Change the 11 th base from T to A

Template DNA 3’ TAC GCA AAT CTT ACT 5’ Change the 8th base to C Group 1

Template DNA 3’ TAC GCA ACT CTT ACT 5’ mRNA Base changed from A to C Group 1 outcome

Template DNA 3’ TAC GCA ACT CTT ACT 5’ mRNA 5’ AUG CGU UGA GAA UGA 3’ Base changed from A to C This base becomes G Group 1 outcome

Template DNA 3’ TAC GCA ACT CTT ACT 5’ mRNA 5’ AUG CGU UGA GAA UGA 3’ Protein Met Arg Stop Base changed from A to C This base becomes G The new codon is a stop codon Original Protein Met Arg Leu Glu Stop Group 1 outcome

Template DNA 3’ TAC GCA AAT CTT ACT 5’ Change the 9th base to C Group 2

Template DNA 3’ TAC GCA AAC CTT ACT 5’ mRNA Base changed from T to CGroup 2 outcome

Template DNA 3’ TAC GCA AAC CTT ACT 5’ mRNA 5’ AUG CGU UUG GAA UGA 3’ Base changed from T to C This base becomes G Group 2 outcome

Template DNA 3’ TAC GCA AAC CTT ACT 5’ mRNA 5’ AUG CGU UUG GAA UGA 3’ Protein Met Arg Leu Glu Stop Base changed from T to C This base becomes G The new codon does not change the amino acid Original Protein Met Arg Leu Glu Stop Group 2 outcome

Template DNA 3’ TAC GCA AAT CTT ACT 5’ Change the 11th base to A Group 3

Template DNA 3’ TAC GCA AAC CAT ACT 5’ mRNA Base changed from T to A Group 3 outcome

Template DNA 3’ TAC GCA AAC CAT ACT 5’ mRNA 5’ AUG CGU UUG GUA UGA 3’ Base changed from T to A This base becomes U Group 3 outcome

Template DNA 3’ TAC GCA AAC CAT ACT 5’ mRNA 5’ AUG CGU UUG GUA UGA 3’ Protein Met Arg Leu Val Stop Base changed from T to A This base becomes U The new codon changes the amino acid from Glutamic Acid to Valine Original Protein Met Arg Leu Glu Stop Group 3 outcome

CLICKER Activity (30 seconds): All sequence changes in DNA genes are deleterious (harmful) to protein structure. A. True B. False

Nonsense Mutation Silent Mutation Missense Mutation Original DNAAAT CTT MutationACTACTAACCATCAT mRNAUGAUUGGUA ProteinLeu  StopLeu  LeuGlu  Val A change in the DNA is called a mutation. Summary

Example of a missense mutation with a significant biological consequence Sickle-cell disease is the result of a single amino acid substitution

Homework Due Next Class: 1. Use the DNA sequence on your handout and make as many single base mutations that you can that will result in the creation of: A. Nonsense mutations B. Silent mutations 2. Predict what would happen during translation if the third base was deleted from the DNA sequence? Next topic: Mutations - Altered Genes

Conclusions of Instructional Tidbit Strategy Students have been introduced to genetic mutations though different forms of active learning activities; clicker questions, group activities and homework to account for diversity in learning styles Formative assessment; post test of transcription and translation built on prior instruction was incorporated into the learning experience, with guidance and feedback from instructors addressing misconceptions After these learning activities, students should now be able to describe various types of genetic mutations We will transition to the next topic to complete the learning goals and outcomes of this unit, after which the students should be able to predict the effect of mutations on protein structure and function