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Transcription - extras for HL

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  • Transcription - extras for HL

Making mRNA in the nucleus

This lesson begins with a review of the process of transcription and the role of RNA polymerase but quickly turns to the control of gene expression using nucleosomes and methylation. Experiments with Drosophila on board the International Space station serve as examples. The final short activity shows how the splicing of mRNA can also affect the proteins produced.

Lesson Description

Guiding Questions

Why does RNA synthesis progress in just one direction?

What characteristic of the nucleoside-triphosphate molecule helps the 5' carbon of the ribose bind to the 3' carbon in the RNA polymer?

Why can't the 3' carbon of the nucleoside triphosphate bind the 5' carbon of the growing RNA molecule?

Compare this reaction with the hydrolysis of ATP to form ADP and Pi

Activity 1 - Transcription & Gene expression HL extras

Read the seven slides in this HL transcription and gene expression presentation which summarise the main concepts which HL students need to know about transcription and gene expression.

Make brief notes from each of the slides

Activity 2 - Regulation of transcription (Gene expression)

Complete the following methylation data analysis questions which investigate the control of gene expression in a recent cancer study, "SHOX2 DNA Methylation Is a Biomarker for the Diagnosis of Lung Cancer" by Kneip, Schmidt et al.

(The full text can also be accessed in the Journal of Thoracic Oncology Volume 6, ISSUE 10, P1632-1638, October 01, 2011)

Activity 3 - Control of transcription - Animation

Watch the following shot video about the   Control of transcription and discuss the questions below.

Questions

  1. Give an examples of genes which are transcribed in all cells.

    e.g. genes for processes like glycolysis

  2. What are transcription factors?

    Proteins which migrate into the nucleus and activate gene transcription.

  3. Where does transcription occur in the cell?

    The nucleus

  4. The transcription protein complex is made up of a group of proteins attached to DNA. What do they do?

    These proteins ensure that transcription of genes in the cell occurs appropriately,

    They indicate the beginning of genes which are being expressed,
    (Note: RNA polymerase cannot bind to a promoter by itself.
    It requires these protein factors added to the promoter to help it bind, and then transcribe the mRNA )

    This gene expression depends on signalling within the cell or  environmental factors.

These questions can be completed on this  Control of transcription student worksheet

Teachers notes

This lesson covers some of the extra details about transcription which are required for HL.

The presentation in activity one can be used for a teacher exposition of these points or students could make notes from the slides independently. The concepts of gene regulation may seem complicated to some students, but the details have been kept a simple as possible.

In activity two data from a medical study of lung cancer cells is presented very simply. The study is aiming to find biomarkers for diagnosis of lung cancer through identification of methylation of a specific gene on chromosome 3. The first part of the worksheet is an uncomplicated data analysis.

As the gene, SHOX2, in the study is thought to code for a gene regulator protein the later questions on the worksheet test students' understanding of this more difficult concept of gene transcription regulator proteins. The students are finally asked to suggest a possible mechanism for methylation of the SHOX2 gene causing lung cancer. This required a link to regulation of oncogenes which were introduced in the cells topic Control of cell cycle & cancer (Topic 1)

The third activity is designed as a plenary activity where students and teacher discuss a video showing some concepts in gene expression. This will give the teach an opportunity to clarify any points of confusion which students have about this topic.

This Methylation data question - model answers page shows suggested answers to the questions in activity two. There are many more points than marks suggested on the question.

Further information on methylation - extra to the IB guide

DNA methylation typically occurs at "CpG sites" (cytosine-phosphate-guanine sites)
These are places where a base cytosine is directly followed by a guanine base in the DNA sequence.
A methyl group ( - CH3) is added to the cytosine by methylation.
Human DNA has about 80–90% of CpG sites methylated
Areas in the DNA which are GC-rich have been found where none of the CpG sites are methylated.
These areas are associated with the promoters of many mammalian genes and 'housekeeping genes' - those genes which are expressed in all cells and control the everyday functioning of cells.