IB Biology - Curriculum Notes
7.2 Transcription and Gene Expression
Nature of science: Looking for patterns, trends and discrepancies—there is mounting evidence that the environment can trigger heritable changes in epigenetic factors. (3.1)
The following website is a really good introduction to the topic of gene expression and epigenetics.
Watch the videos at http://learn.genetics.utah.edu/content/epigenetics/and complete both of the interactive explorations on “Gene Control” and “Lick your Rats”. Also read Epigenetics and Inheritance, Nutrition and the Epigenome, and Epigenetics and the Human Brain.
∑ - Transcription occurs in a 5’ to 3’ direction.
β - Application: The promoter as an example of non-coding DNA with a function.
Good Video - https://www.youtube.com/watch?v=9AfBsTAQ8zs
∑ - Nucleosomes help to regulate transcription in eukaryotes.
Good video on methylation and acetylation.
β - Skill: Analysis of changes in the DNA methylation patterns.
Luong, P. Basic Principles of Genetics, Connexions Web site. [http://cnx.org/content/m26565/1.1/] (2009)
*** Complete the data based questions on page 358 of your text book***
∑ - Gene expression is regulated by proteins that bind to specific base sequences in DNA.
∑ - The environment of a cell and of an organism has an impact on gene expression.
© 2013 Nature Education Adapted from Pierce, Benjamin. Genetics: A Conceptual Approach, 2nd ed. All rights reserved.
***Do the data-based questions on page 358 of your textbook***
∑ - Eukaryotic cells modify mRNA after transcription.
∑ - Splicing of mRNA increases the number of different proteins an organism can produce.
•RNA polymerase adds the 5´ end of the free RNA nucleotide to the 3´ end of the growing mRNA molecule.
Theory of knowledge:
•The nature versus nurture debate concerning the relative importance of an individual’s innate qualities versus those acquired through experiences is still under discussion. Is it important for science to attempt to answer this question?
Nature of science: Developments in scientific research follow improvements in computing—the use of computers has enabled scientists to make advances in bioinformatics applications such as locating genes within genomes and identifying conserved sequences.
∑ - Understandings:
∑ - Initiation of translation involves assembly of the components that carry out the process.
∑ - Synthesis of the polypeptide involves a repeated cycle of events.
∑ - Disassembly of the components follows termination of translation.
β - Skill: The use of molecular visualization software to analyse the structure of eukaryotic ribosomes and a tRNA molecule.
Go to the PDB and search for a tRNA molecule. Explore the structure of the tRNA using the 3D molecular visualization software
β – Application - tRNA-activating enzymes illustrate enzyme–substrate specificity and the role of phosphorylation.
∑ - Free ribosomes synthesize proteins for use primarily within the cell.
Free ribosomes in the cytoplasm synthesize proteins that will be used inside the cell in the cytoplasm, mitochondria and chloroplasts (in autotrophs)
∑ - Bound ribosomes synthesize proteins primarily for secretion or for use in lysosomes.
∑ - Translation can occur immediately after transcription in prokaryotes due to the absence of a nuclear membrane.
β - Skill: Identification of polysomes in electron micrographs of prokaryotes and eukaryotes.
∑ - The sequence and number of amino acids in the polypeptide is the primary structure.
∑ - The secondary structure is the formation of alpha helices and beta pleated sheets stabilized by hydrogen bonding.
∑ - The tertiary structure is the further folding of the polypeptide stabilized by interactions between R groups.
∑ - The quaternary structure exists in proteins with more than one polypeptide chain.
*** Do the data-based questions on page 369 and 371 of your textbook***
Nature of science: Developments in scientific research follow improvements in computing—developments in bioinformatics, such as the interrogation of databases, have facilitated research into metabolic pathways. (3.8)
***Read the paragraph on Bioinformatics on page 368 to familiarize yourself with what this means***
•Names of the tRNA binding sites are expected as well as their roles.
•Examples of start and stop codons are not required.
•Polar and non-polar amino acids are relevant to the bonds formed between R groups.
•Quaternary structure may involve the binding of a prosthetic group to form a conjugated protein
7.1 DNA Structure and Replication
Nature of Science: Making careful observations—Rosalind Franklin’s X-ray diffraction provided crucial evidence that DNA is a double helix. (1.8)
β - Skill: Analysis of results of the Hershey and Chase experiment providing evidence that DNA is the genetic material.
Watch the following animation and explanation of the Hershey-Chase experiment http://highered.mheducation.com/sites/9834092339/student_view0/chapter14/hershey_and_chase_experiment.html
Do the data-based questions on page 345 to reinforce your understanding.
β - Application: Rosalind Franklin’s and Maurice Wilkins’ investigation of DNA structure by X-ray diffraction.
Watch the video on
http://www.dnai.org/a/index.html (finding the structure > players > Rosalind Franklin) on Rosalind Franklin and read through the articles on page 345 and 346 of your text.
Describe the deductions Franklin was able to make regarding the structure of DNA.
∑ - Understandings
∑ Nucleosomes help to supercoil the DNA
β - Skill: Utilization of molecular visualization software to analyse the association between protein and DNA within a nucleosome.
Very good molecular visualization of histone proteins and their interaction with DNA. https://www.youtube.com/watch?v=vbueAuw96zA
***Do the data-based questions on page 349 of your textbook***
∑ - DNA structure suggested a mechanism for DNA replication.
The rungs of the ladder contain two nitrogenous bases (one from each strand) that are bonded together by hydrogen bonds.
Since these two strands are anti-parallel replication occurs in different directions on the DNA strand
Purines are two ring nitrogenous bases and pyrimidines are single ring nitrogenous bases.
The nitrogenous bases match up according the Chargaff’s Rules in which adenine (purine) always bonds to thymine (pyrimidine), and guanine (purine) always bonds with cytosine (pyrimidine).
These three understandings are combined to explain the full process of replication.
∑ - DNA replication is continuous on the leading strand and discontinuous on the lagging strand.
∑ - DNA polymerases can only add nucleotides to the 3’ end of a primer.
∑ - DNA replication is carried out by a complex system of enzymes.
∑ - Some regions of DNA do not code for proteins but have other important functions.
Good video on telomerase function http://highered.mheducation.com/sites/9834092339/student_view0/chapter14/telomerase_function.html
β - Application: Tandem repeats are used in DNA profiling.
***Work through the activity and questions on page 352 and 353***
β - Application: Use of nucleotides containing dideoxyribonucleic acid to stop DNA replication in preparation of samples for base sequencing.
Theory of knowledge:
Highly repetitive sequences were once classified as “junk DNA” showing a degree of confidence that it had no role. To what extent do the labels and categories used in the pursuit of knowledge affect the knowledge we obtain?