Section 1: Nucleic acids, proteins and DNA tools

Follow the information: DNA template, mRNA, tRNA and ribosome, then the protein. On a gel, small fragments travel furthest.

A lesson for this section

Multiple choice, Section A style

Question 1

Which feature is found in an RNA nucleotide but never in a DNA nucleotide?

Question 2

In a sample of double-stranded DNA from a hypothetical bacterium, 18% of the bases are adenine. What percentage of the bases are cytosine?

Question 3

The bases in one strand of a hypothetical DNA molecule are 20% adenine, 30% thymine, 15% guanine and 35% cytosine. What percentage of all the bases in the double-stranded molecule are adenine?

Question 4

Which bonds join the nucleotides of one strand of DNA to each other?

Question 5

Which statement correctly describes ribosomal RNA (rRNA)?

Question 6

In a human liver cell, where does transcription of a gene take place?

Question 7

Part of the template strand of a gene reads 3' TACGGA 5'. Which sequence is the mRNA transcribed from this part?

Question 8

A codon on an mRNA molecule is 5' GCA 3'. Which anticodon on a tRNA molecule pairs with this codon?

Question 9

A hypothetical eukaryotic gene has three exons of 210, 345 and 351 nucleotides, separated by two introns of 402 and 249 nucleotides. The start codon is the first three nucleotides of the first exon and the stop codon is the last three nucleotides of the third exon. How many amino acids are in the polypeptide as it is first made by the ribosome?

Question 10

Which change happens to pre mRNA during RNA processing in a eukaryotic cell?

Question 11

What happens when a ribosome translating an mRNA molecule reaches a stop codon?

Question 12

Which region of a gene is the site where RNA polymerase binds to begin transcription?

Question 13

Which statement about the exons and introns of a eukaryotic gene is correct?

Question 14

An E. coli cell is growing in a medium that contains no tryptophan. Which statement describes its trp operon?

Question 15

A mutant strain of E. coli has a change in the base sequence of the trp operator, so the repressor can no longer bind to it. The repressor protein itself is normal. What is expected when this strain grows in a medium with plenty of tryptophan?

Question 16

A hypothetical mutant strain of E. coli makes a repressor protein that binds the trp operator whether or not tryptophan is present. Its operator, promoter and structural genes are normal. Which prediction is correct?

Question 17

Alpha helices and beta pleated sheets in a polypeptide are examples of which level of protein structure?

Question 18

Haemoglobin is made of four polypeptide chains held together. Which level of structure does this describe?

Question 19

A substitution in a gene replaces one amino acid in an enzyme with an amino acid that has a very different R group. The enzyme no longer catalyses its reaction. Which explanation is best?

Question 20

Which statement about the proteome is correct?

Question 21

Humans have about 20 000 protein coding genes, yet the human proteome contains many more different proteins than this. Which process helps explain the difference?

Question 22

Which sequence shows the path of a protein that is made for export from a cell?

Question 23

Enzymes are proteins that act as catalysts in biochemical pathways. How do they speed up reactions?

Question 24

Percentage of radioactive protein in each location at four times after labelling (hypothetical).
Time / minutes	Rough endoplasmic reticulum / %	Golgi apparatus / %	Secretory vesicles / %	Outside the cell / %
5	85	10	5	0
20	30	60	10	0
60	10	25	60	5
120	5	10	30	55

Hypothetical pancreatic cells are given radioactive amino acids for 3 minutes, then unlabelled amino acids. The table shows where the radioactive protein is found at four times. A second batch of the same cells is treated with compound Q, which stops vesicles from budding off the Golgi apparatus but has no other effect. Where is most of the radioactive protein expected in the treated cells at 120 minutes?

Question 25

A gene has been cut out and placed next to a cut plasmid with matching sticky ends. Which enzyme forms the bonds that seal the gene into the plasmid?

Question 26

When making a recombinant plasmid, why are the plasmid and the DNA containing the gene cut with the same restriction endonuclease?

Question 27

A linear DNA molecule has three recognition sites for endonuclease X. A circular plasmid also has three recognition sites for X. Each is digested completely with X. How many fragments does each produce?

Question 28

What is the function of the CRISPR-Cas9 system in bacteria?

Question 29

Cas9 is used to cut both strands of a gene near the start of its coding sequence. The cell repairs the break by joining the ends, and this often adds or removes one or two nucleotides. Why does this usually knock out the gene's function?

Question 30

During one cycle of the polymerase chain reaction, the mixture is cooled to about 55 °C. What happens at this temperature?

Question 31

A sample contains 200 copies of a target DNA sequence. Assuming the number of copies doubles in every cycle of PCR, what is the smallest number of cycles that gives at least 100 000 copies?

Question 32

In gel electrophoresis, why do DNA fragments move towards the positive electrode?

Question 33

Distance travelled by each band of a DNA ladder.
Fragment size / bp	Distance from well / mm
1000	12
800	18
600	25
400	34
200	46

A DNA ladder and an unknown fragment were run on the same gel. The table gives the distance each ladder band travelled from the well. The unknown fragment travelled 30 mm. What is the best estimate of its size?

Question 34

Numbers of repeats at three STR loci (hypothetical).
Person	Locus 1	Locus 2	Locus 3
Mother	12, 14	8, 9	20, 22
Child	12, 16	9, 11	20, 20
Man P	16, 17	10, 11	20, 23
Man Q	13, 16	11, 11	21, 24
Man R	12, 15	8, 9	20, 21

The table shows hypothetical DNA profiles, as the numbers of repeats at three short tandem repeat (STR) loci, for a mother, her child and three men. Assuming one of the men is the child's biological father, which man is he?

Question 35

Why are two different primers added to a PCR mixture?

Question 36

To make human insulin in E. coli, the inserted DNA is made from mature mRNA (or synthesised from the known sequence) rather than cut from a human chromosome. Why?

Question 37

A plasmid carries a gene for ampicillin resistance and a gene for tetracycline resistance. A human gene is inserted into a site inside the tetracycline resistance gene, which inactivates it. The plasmids are mixed with bacteria that are sensitive to both antibiotics. Which bacteria contain a recombinant plasmid?

Question 38

Which organism is transgenic?

Question 39

Bacteria and plasmids are chilled with calcium chloride and then briefly warmed to 42 °C. What is the purpose of this step?

Question 40

In a hypothetical field trial, a genetically modified wheat line resistant to a fungal disease yields 4.2 tonnes per hectare where the unmodified line yields 3.5 tonnes per hectare. What is the percentage increase in yield?

Question 41

Some mRNA codons and the amino acids they code for.
mRNA codon	Amino acid
UUU	Phe
UUC	Phe
CUU	Leu
UUA	Leu
UAU	Tyr

A triplet on the template strand of a gene reads 3' AAA 5'. Using the codon table, which single base substitution in this triplet would leave the amino acid unchanged?

Question 42

In a mutant strain of E. coli, a codon near the start of the coding sequence of the gene for the trp repressor protein has changed to a stop codon. The trp operon itself is unchanged. What happens to transcription of the trp structural genes when tryptophan is abundant?

Question 43

trpE mRNA and enzyme activity in four strains (hypothetical, arbitrary units).
Strain	mRNA without tryptophan	mRNA with tryptophan	Enzyme activity without tryptophan	Enzyme activity with tryptophan
Wild type	100	5	100	5
Strain J	100	100	100	100
Strain K	100	5	0	0
Strain L	2	2	2	2

The table shows hypothetical measurements for wild type E. coli and three mutant strains: the amount of trpE mRNA, and the activity of the enzyme trpE codes for, in a medium without tryptophan and in one with plenty of tryptophan. Which conclusion is best supported by the data?

Question 44

A circular plasmid of 8.0 kb is digested completely with different endonucleases (hypothetical results). EcoRI alone gives one band of 8.0 kb. BamHI alone gives bands of 3.0 kb and 5.0 kb. EcoRI and BamHI together give bands of 1.0 kb, 2.0 kb and 5.0 kb. Which statement about the recognition sites is supported?

Question 45

At a hypothetical STR locus, each repeat is 4 bp long, and every PCR product also includes 60 bp of flanking DNA. A mother's PCR products at this locus are 108 bp and 124 bp. Her child's products are 116 bp and 124 bp. How many repeats must the child's biological father have in at least one of his alleles at this locus?

Section B questions

A secreted digestive enzymeSection B · 8 marks

Cells lining the small intestine of a hypothetical mammal make enzyme L, a protein that they secrete into the gut. The gene for L has four exons and three introns. In the mature mRNA, the sequence from the first nucleotide of the start codon to the last nucleotide of the stop codon is 1512 nucleotides long.

(a) Name the enzyme that transcribes the gene for L. [1]

0 words · a sentence

(b) Calculate the number of amino acids in enzyme L as it is first made by the ribosome. [2]

amino acids

0 words · one point a mark

(d) A mutation inserts one extra nucleotide near the start of exon 1. Explain why the enzyme L made from this gene is likely to be non-functional. [2]

0 words · one point a mark

Regulation of the trp operonSection B · 8 marks

A researcher measures the amount of mRNA transcribed from trpE, the first structural gene of the trp operon, in three strains of E. coli. Each strain is grown in a medium without tryptophan and in a medium with plenty of tryptophan. The table shows the hypothetical results.

Amount of trpE mRNA in three strains (hypothetical, arbitrary units).
Strain	Without tryptophan	With plenty of tryptophan
Wild type	100	8
Strain X	100	100
Strain Y	3	3

(a) Calculate the percentage decrease in trpE mRNA in the wild type when tryptophan is added. [1]

(b) Explain the result for the wild type grown with plenty of tryptophan. [2]

0 words · one point a mark

(d) Strain Y makes almost no trpE mRNA in either medium. Suggest one change in strain Y that would explain this, and explain how it has this effect. [2]

0 words · one point a mark

(e) Predict whether strain Y could grow well on a medium that contains no tryptophan. Give a reason. [2]

0 words · one point a mark

Knocking out a gene with CRISPR-Cas9Section B · 9 marks

Researchers want to knock out gene G in a hypothetical rice variety. They give rice cells Cas9 and two guide RNAs that target sites 140 base pairs apart within an exon of gene G, so that the DNA between the two cuts can be lost. From each regenerated plant they amplify the region of gene G with PCR, using primers on either side of the target sites, and run the products on a gel. Without an edit, the PCR product is 620 base pairs (bp). The table shows the bands seen for four plants. Rice is diploid.

Bands seen after PCR of gene G and gel electrophoresis (hypothetical).
Plant	Band size / bp
Plant 1	620
Plant 2	480
Plant 3	620 and 480
Plant 4	no band

(a) Describe the function of CRISPR-Cas9 in bacteria. [3]

0 words · one point a mark

(b) Explain how a guide RNA directs Cas9 to gene G rather than to other genes. [2]

0 words · one point a mark

(d) Calculate how many base pairs were removed from gene G in Plant 2. [1]

(e) Explain why the deletion in Plant 2 is likely to stop gene G from producing a functional protein. [2]

0 words · one point a mark

Finding bacteria with a recombinant plasmidSection B · 8 marks

Plasmid pX (hypothetical) is a 5.0 kb circle with a gene for ampicillin resistance and a gene for tetracycline resistance. Its only BamHI site lies inside the tetracycline resistance gene, and it has one EcoRI site elsewhere. A 1.2 kb DNA copy of a human gene, made from its mRNA, is cut out with BamHI and ligated into the BamHI site of pX. The human DNA has one EcoRI site of its own. The plasmids are mixed with bacteria that are sensitive to both antibiotics.

(a) Calculate the size of a recombinant plasmid. [1]

(b) One recombinant plasmid is digested completely with EcoRI and gives two fragments. One is 2.3 kb. Calculate the size of the other fragment. [1]

(c) The bacteria are grown on agar with ampicillin, and each colony is then transferred to agar with tetracycline. Which colonies contain a recombinant plasmid? [1]

(d) Explain why bacteria that contain a recombinant plasmid grow on ampicillin agar but not on tetracycline agar. [3]

0 words · one point a mark

(e) The bacteria make the correct human protein from the inserted DNA. Explain why the DNA copy is made from mRNA, and why bacteria can read a human gene. [2]

0 words · one point a mark

One gene, two proteinsSection B · 8 marks

Gene M of a hypothetical mammal has four exons. In muscle cells its mature mRNA contains exons 1, 2 and 4; in liver cells it contains exons 1, 3 and 4. The exons are 300, 159, 210 and 255 nucleotides long (exons 1 to 4). The start codon is the first three nucleotides of exon 1 and the stop codon is the last three nucleotides of exon 4; there are no other untranslated nucleotides.

(a) Calculate the number of amino acids in the muscle protein as it is first made by the ribosome. [2]

amino acids

(b) How many more amino acids does the liver protein have than the muscle protein? [1]

amino acids

0 words · one point a mark

(d) A substitution in exon 2 of gene M changes one codon into a stop codon. Predict the effect on the muscle protein and on the liver protein, and explain your predictions. [3]

0 words · one point a mark

Agarose concentration and fragment movementSection B, investigation · 9 marks

A student investigates how the concentration of agarose in a gel affects the distance travelled by a 500 bp DNA fragment. She makes gels of four concentrations, runs three gels of each, and measures the distance from the well to the band. The table shows her results.

Distance travelled by a 500 bp fragment in gels of four agarose concentrations.
Agarose concentration / %	Gel 1 / mm	Gel 2 / mm	Gel 3 / mm	Mean / mm
0.5	41	43	42	42
1	29	31	30	30
1.5	22	20	21	21
2	15	16	14	15

(a) State the independent variable in this investigation. [1]

0 words · a sentence

(b) Suggest two variables that the student should keep the same. [2]

0 words · one point a mark

(c) Calculate the percentage decrease in the mean distance travelled when the agarose concentration rises from 0.5% to 2.0%. [2]

(d) Explain the trend shown by the results. [2]

0 words · one point a mark

(e) Explain why the student ran three gels at each concentration. [2]

0 words · one point a mark