Questions on DNA and RNA structure

Question 1

Compare the structure of a DNA molecule with the structure of a messenger RNA molecule.

Accepted Answer

B1 DNA contains the pentose sugar deoxyribose, whereas mRNA contains ribose B1 DNA contains thymine, whereas mRNA carries uracil in its place B1 DNA is two antiparallel strands wound into a helix, whereas mRNA is a single strand B1 DNA can be hundreds of millions of nucleotides long, whereas an mRNA molecule is far shorter, usually hundreds to tens of thousands of nucleotides long

Question 2

A nucleic acid extracted from a virus contains adenine 31%, guanine 19%, cytosine 27% and thymine 23%. Suggest what these figures tell you about the structure of the molecule, and suggest one further measurement that would test your conclusion.

Accepted Answer

B1 in a double-stranded molecule adenine would equal thymine and guanine would equal cytosine, because each base has a fixed partner opposite it B1 here adenine at 31% does not equal thymine at 23%, and guanine at 19% does not equal cytosine at 27% B1 the molecule cannot therefore be double-stranded; it is single-stranded DNA, since thymine rather than uracil is present B1 any one workable further measurement: heat the sample and look for a temperature at which strands separate, since a single-stranded molecule has no paired bases to separate

Question 3

Describe the double helix formed by DNA, and describe how DNA is packaged to fit inside a eukaryotic nucleus about 6 μm across.

Accepted Answer

B1 the two antiparallel polynucleotide strands are wound around each other into a right-handed spiral, with roughly ten base pairs per complete turn B1 the bases lie on the inside of the helix, shielded from the surrounding water, while the charged sugar-phosphate backbones lie on the outside B1 in a eukaryotic cell the DNA is wound around histone proteins B1 that DNA-histone complex is then coiled repeatedly, so that about two metres of DNA is compacted to fit inside a nucleus only a few micrometres across

Question 4

Compare the organisation of DNA in a eukaryotic cell with its organisation in a bacterial cell.

Accepted Answer

B1 eukaryotic DNA is linear and organised into several separate molecules, chromosomes, whereas a bacterium's DNA is usually one circular molecule B1 eukaryotic DNA is wound around histone proteins, whereas bacterial DNA is not wound around histones, though it is still supercoiled to fit inside the cell B1 eukaryotic DNA is held within a membrane-bound nucleus, whereas bacterial DNA lies free in the cytoplasm, in a region called the nucleoid B1 eukaryotic DNA is very much longer in total than bacterial DNA, so eukaryotic packaging must condense a far greater length into a comparable or larger volume

Question 5

Explain how the length of a DNA molecule and the sequence of its bases together allow it to store a very large amount of information.

Accepted Answer

B1 there is no limit to how many nucleotides can be joined into a polynucleotide, so an extremely long molecule, such as human chromosome 1 at about 249 million base pairs, can exist B1 the backbone is identical at every position along the molecule and carries no information itself; it is the order of the four bases that is free to vary B1 a short stretch of only ten bases can already be arranged in 4¹⁰ ways, a little over a million, so the number of possible sequences grows enormously with length B1 combining a very long molecule with a base sequence that can vary at every position gives a capacity for information that is, for practical purposes, unlimited

Question 6

A student says that the two strands of a DNA molecule are identical, so either one is simply a spare copy of the other. Discuss whether this is an accurate description of the relationship between the two strands.

Accepted Answer

B1 what is right in the claim: each strand does carry the full information needed to rebuild the other, since the identity of every base on one strand fixes the identity of the base opposite it B1 against: the two strands are not identical in sequence; adenine on one strand is paired with thymine on the other, and guanine with cytosine, so the base at a given position on one strand is not the same base as the one at the corresponding position on the other B1 against: the two strands also run in opposite, antiparallel directions, so even where the base sequences are complementary they are not read in the same direction, and are not copied in the same way when the molecule is replicated B1 judgement: 'complementary' and 'identical' are not synonyms; the strands carry the same information in complementary rather than identical form, which is what makes accurate copying and repair possible

Question 7

Explain why every base pair in a DNA molecule is the same width, and explain what this means for the shape of the molecule as a whole.

Accepted Answer

B1 adenine and guanine are purines, built from two fused rings, while thymine and cytosine are pyrimidines, built from one B1 the pairing rule puts a purine opposite a pyrimidine in every pair, so each rung spans the same distance B1 the two sugar-phosphate backbones therefore stay a constant distance apart along the whole molecule, whereas two purines would bulge and two pyrimidines would pinch

Question 8

A sample of double-stranded DNA contains 3200 bases in total, of which 960 are guanine. Calculate the number of adenine bases in the sample.

Accepted Answer

M1 cytosine equals guanine, so there are 960 cytosine bases, giving 1920 bases in the two of them together M1 subtracts from the total to leave the adenine and thymine: 3200 − 1920 = 1280 A1 adenine equals thymine, so 1280 ÷ 2 gives 640 adenine bases

Question 9

Two double-stranded DNA samples of the same length are heated slowly. Sample X separates into single strands at 68 °C and sample Y at 83 °C. Explain what this difference tells you about the base composition of the two samples.

Accepted Answer

B1 heating separates the strands by breaking the hydrogen bonds between paired bases B1 each G–C pair is held by three hydrogen bonds while each A–T pair is held by only two B1 sample Y needs more energy, and so a higher temperature, before its strands come apart, so it has the higher proportion of guanine and cytosine

Question 10

Describe how two nucleotides are joined together during the synthesis of a polynucleotide, naming the reaction, the bond formed and the parts of each nucleotide involved.

Accepted Answer

B1 the phosphate group of one nucleotide reacts with a hydroxyl group on the pentose sugar of the next B1 the reaction is a condensation, in which a molecule of water is released B1 the bond formed is a covalent phosphodiester bond, giving a backbone that strictly alternates sugar and phosphate

Question 11

Explain what is meant by describing the two strands of a DNA molecule as antiparallel, and explain what this means for the direction in which each strand is copied during replication.

Accepted Answer

B1 antiparallel means the two strands run in opposite directions, so wherever one strand has its 5′ end, the other strand has its 3′ end at that same position B1 running in opposite directions is what lines each base up opposite its complementary partner, so hydrogen bonds form between the pairs along the whole length B1 DNA polymerase can only build a new strand in one direction, so the antiparallel arrangement of the two template strands is why the two new strands cannot be synthesised in the same way as each other

Question 12

Describe the role of ribosomal RNA (rRNA) in a ribosome, and describe how its role differs from that of messenger RNA.

Accepted Answer

B1 rRNA, together with protein, forms the two subunits of a ribosome, giving the ribosome its structure B1 rRNA also catalyses the formation of peptide bonds between adjacent amino acids during translation B1 unlike messenger RNA, rRNA does not carry a coding sequence read as codons; its role is structural and catalytic rather than carrying genetic information from gene to ribosome

Question 13

Name the three components of a single DNA nucleotide, and name the bond that joins one nucleotide to the next along a strand.

Accepted Answer

B1 a phosphate group, a pentose sugar (deoxyribose) and a nitrogenous base B1 a phosphodiester bond, formed by condensation between the phosphate of one nucleotide and the sugar of the next

Question 14

State two ways in which a molecule of transfer RNA differs from a molecule of messenger RNA.

Accepted Answer

B1 any one of: tRNA is short, at about 80 nucleotides; it folds into a clover leaf held by hydrogen bonds between complementary stretches of its own sequence; it carries an anticodon; it has a binding site for a specific amino acid B1 any second, different point from the same list, or the matching contrast that mRNA is a run of codons with no clover-leaf fold and no amino acid binding site

Question 15

State what is meant by the 5′ end of a DNA strand, and state what is meant by the 3′ end.

Accepted Answer

B1 the 5′ end is the end at which carbon 5 of the terminal sugar faces outward, usually carrying a phosphate group B1 the 3′ end is the end at which carbon 3 of the terminal sugar faces outward, usually carrying a free hydroxyl group