| Date | November 2017 | Marks available | 3 | Reference code | 17N.3.HL.TZ0.10 |
| Level | Higher level | Paper | Paper 3 | Time zone | TZ0 |
| Command term | Suggest | Question number | 10 | Adapted from | N/A |
Question
The table shows a comparison of DNA base sequences in several yeast (Saccharomyces) genomes.
[Source: P. F. Cliften et al. (2001) ‘Surveying Saccharomyces Genomes to Identify Functional Elements by Comparative DNA Sequence Analysis’, Genome Research, 11, pp. 1175–1186. © Cold Spring Harbor Laboratory Press. Reproduced with permission.]
Identify the species that has the lowest percentage of coding sequences.
State how similar nucleotide sequences can be identified.
The yeast Saccharomyces cerevisiae was the first eukaryotic organism to have its entire genome sequenced. Suggest reasons for the choice of yeast as a study organism.
Outline possible medical applications of the polymerase chain reaction (PCR).
Markscheme
S. unisporus
BLASTn/sequence alignment software
“n” required in BLASTn
a. easy to grow
OR
easy/cheap to produce large amounts
OR
fast generation time
b. genomes are small/easy to manipulate
c. metabolically diverse
d. industrial applications/biopharming
e. no ethical issues «with yeast»
[Max 3 Marks]
a. identify different viral/influenza strains
b. genetic testing/testing for genetic disease mutations
c. tissue typing
d. vaccine development
[Max 1 Mark]
| Date | May 2017 | Marks available | 1 | Reference code | 17M.3.HL.TZ1.9 |
| Level | Higher level | Paper | Paper 3 | Time zone | Time zone 1 |
| Command term | Explain | Question number | 9 | Adapted from | N/A |
Question
The cladogram is based on a comparison of open reading frames in DNA taken from fungi. It is an example of how open reading frames can be used in phylogenetic studies.
Outline how open reading frames are identified in DNA.
Explain what the branching off points represent in the cladogram of these fungi.
There are several methods of introducing DNA into a cell in the laboratory. Outline the introduction of recombinant DNA in plant cell protoplasts.
Markscheme
a. identify a start codon and stop codon
b. identify base sequences for a gene/that could code for a polypeptide
c. possible correlation with existing open reading frames in databases
a. represent common ancestors shared by the organisms that emanate from the point
b. indicates time since divergence
c. indicates number of differences in DNA
a. plant cells made into protoplasts by removing their cell wall / use cellulase to produce protoplasts
b. physical methods such as electroporation /microinjection/biolistics
c. chemical methods such as liposomes/calcium chloride/polyethylene glycol «PEG»
d. vectors such as Agrobacterium/tobacco mosaic virus
| Date | May 2017 | Marks available | 6 | Reference code | 17M.3.HL.TZ1.12 |
| Level | Higher level | Paper | Paper 3 | Time zone | Time zone 1 |
| Command term | Explain | Question number | 12 | Adapted from | N/A |
Question
Explain how BLAST searches are carried out and the applications of different types of these searches.
Markscheme
Process (max [5]):
a. BLAST «Basic Local Alignment Search Tool» search enables comparison of an unknown sequence with databases of sequences
b. «software» finds similar sequences / aligns sequences by locating matches between two sequences
c. carries out statistical calculations «to find matches with other sequences»
d. BLASTn used to align/show similarities in nucleotide sequences in nucleic acids
e. BLASTp used to align/show similarities in amino acid sequences in proteins
f. used to identify the gene of a protein
Application (max [2]):
g. one application of BLAST
h. second application of BLAST
eg BLAST can be used for identifying species / locating domains / establishing phylogeny / DNA mapping / other verifiable examples
| Date | November 2016 | Marks available | 1 | Reference code | 16N.3.HL.TZ0.12 |
| Level | Higher level | Paper | Paper 3 | Time zone | TZ0 |
| Command term | Determine | Question number | 12 | Adapted from | N/A |
Question
The genetic code is the information encoded within the mRNA sequence that is translated into proteins by living cells. The codon table is shown.
The alignment was used to obtain a cladogram of these organisms.
State the bioinformatics tool used to obtain the alignment.
State the meaning of the dash (–) in the alignment.
(i) Identify the longest amino acid sequence where there are no differences amongst the five genera.
(ii) Suggest, with a reason, whether the DNA coding for the amino acid sequence identified in (c)(i) must be identical for the five genera.
Describe briefly how the cladogram was obtained.
Determine which two genera are most closely related according to their cytochrome c protein sequence.
Markscheme
BLASTp
Do not allow “BLAST” alone but accept BLASTx.
gap/no amino acid present «for cytochrome c in that organism in that position»
OR
protein is shorter
(i) GLFGR
Can be shown directly on the alignment.
(ii) no, because more than one codon can code for an amino acid/degeneration of the genetic code
ALTERNATIVE 1
a. alignment used to quantify differences and similarities
b. algorithms for cladograms
OR
named algorithms
Named algorithms: least squares, neighbour-joining, parsimony, maximum likelihood or Bayesian inference.
Allow other verifiable algorithms.
c. selection of best model
ALTERNATIVE 2
d. comparing amino acid sequences between organisms
e. more similar sequences correspond to closer evolutionary links/OWTTE
OR
number of differences indicate number of mutations accumulated «over time»
OR
«if mutation rate is assumed to be constant», more mutations imply further evolutionary distance
f. length of lines/position of nodes established by the number of differences/mutations between organisms
Marks should be awarded for statements from only one alternative, not both.
Zea «corn» and Oryza «rice»
Both required.
| Date | May 2016 | Marks available | 2 | Reference code | 16M.3.HL.TZ0.12 |
| Level | Higher level | Paper | Paper 3 | Time zone | TZ0 |
| Command term | Explain | Question number | 12 | Adapted from | N/A |
Question
International agreement limits the hunting of whales. Only the meat of the Minke, Fin and Humpback whales from Southern Hemisphere populations is allowed to be sold on the domestic market in Japan. Scientists obtained five samples of food that were being sold as “whale meat” in a Japanese market place. They identified the species and probable geographic origin of the meat using genetic analysis. The results were used to construct the cladogram.
Using the data in the cladogram, state the reason for sale of Sample 1 meat being illegal in Japan.
Using the data in the cladogram, state the reason for sale of Sample 4 meat being illegal in Japan.
Outline how the polymerase chain reaction (PCR) might have been used in this study.
Explain how sequence alignment software might have been used in this study.
Markscheme
It is from a North Atlantic population
It is from dolphin/species that is not on the list
Collected DNA sample is small/too minute to study
DNA from tissue sample amplified «by PCR»
OR
Obtain increased yields/quantities of specific DNA sequences
Test primers «from legal species» are used
Example of genes used «to construct test primers» eg: 18S ribosome, cytochrome C oxidase
If no amplification occurs, then test is negative
Sequence a sample of DNA/protein from the tissue
Run a BLAST/sequences alignment software search for similar sequences «of DNA/protein»
A match can be used for species identification
OR
Percentage similarity of sequences used to build up cladogram
BLASTp is used if protein sequenced AND BLASTn if DNA sequenced (Both needed)