Topic 3b: Additional Higher Level Transcription and Translation
Campbell Chapters 16,17 and 18
*It is strongly recommended that you read and take column notes on all of chapters 16,17 and 18 in addition to answering the “Understandings” and “Sample Questions and Assessment Statements” below. For all other chapters, simply reading the suggested pages and doing any more work that you deem necessary will be enough.
DNA Structure and Replication : Chapter 16
Essential Idea: The structure of DNA is ideally suited to its function.
Nature of Science:
•Making careful observations—Rosalind Franklin’s X-ray diffraction provided crucial evidence that DNA is a double helix.
Understandings:
- Nucleosomes help to supercoil the DNA. 320-323
- DNA structure suggested a mechanism for DNA replication. 311-312
- DNA polymerases can only add nucleotides to the 3’ end of a primer. 312-319
- DNA replication is continuous on the leading strand and discontinuous on the lagging strand. 314-318
- DNA replication is carried out by a complex system of enzymes. 316-318
- Some regions of DNA do not code for proteins. 334-336
Application and Skills:
•Application: Rosalind Franklin’s and Maurice Wilkins’ investigation of DNA structure by X-ray diffraction. 308-310
•Application: Use of nucleotides containing dideoxyribonucleic acid to stop replication in preparation of samples for base sequencing. 408-409
•Application: Tandem repeats are used in DNA profiling. 405-407; Online
•Skill: Analysis of results of the Hershey and Chase experiment providing evidence that DNA is the genetic material. 306-308; Activity
•Skill: Utilization of molecular visualization software to analyze the association between protein and DNA within a nucleosome. 320-323; Online
Sample Questions and Assessment Statements:
•Describe the structure of DNA, including the antiparallel strands, 3’–5’ linkages and hydrogen bonding between purines and pyrimidines. 309-310; 314-319
•State that DNA replication occurs in a 5’ to 3’ direction. 315-316
•Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase, DNA polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates. 311-318
•State that DNA replication is initiated at many points in eukaryotic chromosomes. 313-314
Guidance:
•Details of DNA replication differ between prokaryotes and eukaryotes. Only the prokaryotic system is expected.
•The proteins and enzymes involved in DNA replication should include helicase, DNA gyrase, single strand binding proteins, DNA primase and DNA polymerases I and III.
•The regions of DNA that do not code for proteins should be limited to regulators of gene expression, introns, telomeres and genes for tRNAs.
TOK:
•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?
AIMS:
•Aim 6: Students could design models to illustrate the stages of DNA replication.
Transcription and Gene Expression: Chapters 17 and 18
Essential Idea: Information stored as a code in DNA is copied onto mRNA.
Nature of Science:
•Looking for patterns, trends and discrepancies—there is mounting evidence that the environment can trigger heritable changes in epigenetic factors.
Understandings:
- Transcription occurs in a 5’ to 3’ direction. 328
- Nucleosomes help to regulate transcription in eukaryotes. 320; 356-357
- Eukaryotic cells modify mRNA after transcription. 334-336
- Splicing of mRNA increases the number of different proteins an organism can produce. 334-336
- Gene expression is regulated by proteins that bind to specific base sequences in DNA. 356-364
- The environment of a cell and of an organism has an impact on gene expression. 351-356; 358
Application and Skills:
•Application: The promoter as an example of non-coding DNA with a function. 331-334; 351-356; 358-364
•Skill: Analysis of changes in the DNA methylation patterns. 358
Sample Questions and Assessment Statements:
•Outline the structure of nucleosomes. 320-323
•State that nucleosomes help to supercoil chromosomes and help to regulate transcription. 320-323
•Distinguish between unique or single-copy genes and highly repetitive sequences in nuclear DNA. 548-549
•State that eukaryotic genes can contain exons and introns. 334-335
•State that transcription is carried out in a 5’ to 3’ direction. 332
•Distinguish between the sense and antisense strands of DNA. 330; Online; Handout
•Explain the process of transcription in prokaryotes, including the role of the promoter region, RNA polymerase, nucleoside triphosphates and the terminator. 331-334
•State that eukaryotic RNA needs the removal of introns to form mature mRNA. 334-336
Guidance:
•RNA polymerase adds the 5’ end of the free RNA nucleotide to the 3’ end of the growing mRNA molecule.
TOK:
•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?
Translation: Chapter 17
Essential Idea: Information transferred from DNA to mRNA is translated into an amino acid sequence.
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. 351-361
- Synthesis of the polypeptide involves a repeated cycle of events. 337-344
- Disassembly of the components follows termination of translation. 337-344
- Free ribosomes synthesize proteins for use primarily within the cell. 102-104; 343
- Bound ribosomes synthesize proteins primarily for secretion or use in lysosomes. 102-104; 343
- Translation can occur immediately after transcription in prokaryotes due to the absence of a nuclear membrane. 346-347
- The sequence and number of amino acids in the polypeptide is the primary structure. 81-86
- The secondary structure is the formation of -helices and -pleated sheets stabilized by hydrogen bonding. 81-86
- The tertiary structure is the further folding of the polypeptide stabilized by interactions between R-groups. 81-86
- The quaternary structure exists in proteins with more than one polypeptide chain. 81-86
Application and Skills:
•Application: tRNA-activating enzymes illustrate enzyme-substrate specificity and the role of phosphorylation. 337-339
•Skill: Identification of polysomes in electron micrographs of prokaryotes and eukaryotes. 342-343; 346-347; Online
•Skill: The use of molecular visualization software to analyze the structure of eukaryotic ribosomes and a tRNA molecule. Online
Sample Questions and Assessment Statements:
•Explain that each tRNA molecule is recognized by a tRNA-activating enzyme that binds a specific amino acid to the tRNA, using ATP for energy. 337-339
•Outline the structure of ribosomes, including protein and RNA composition, large and small subunits, three tRNA binding sites and mRNA binding sites. 337-344
•State that translation consists of initiation, elongation, translocation and termination. 340-341
•State that translation occurs in a 5’ to 3’ direction. 337-344
•Draw and label a diagram showing the structure of a peptide bond between two amino acids. 80
•Explain the process of translation, including ribosomes, polysomes, start codons and stop codons. 337-340
•State that free ribosomes synthesize proteins for use primarily within the cell, and that bound ribosomes synthesize proteins primarily for secretion or for lysosomes. 343
Guidance:
•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.