Nucleic Acids

Unit 1 · Topic 1.6 end-of-topic test

Answer every question. Check each multiple-choice answer as you go; the feedback tells you what a wrong choice assumed. For the two free-response questions, write your answer in full, then open the scoring guide and mark your own work against it.

Question 1

One nucleotide, drawn as three joined shapes marked 1, 2 and 3.

The figure shows one nucleotide drawn as three joined shapes, marked 1, 2 and 3. Part 2, the five-sided ring, is the five-carbon sugar. Part 1 is a small circle attached to one side of the sugar; part 3 is a six-sided ring attached to the other side.

What are parts 1 and 3?

A. 1 is a nitrogenous base; 3 is a phosphate group B. 1 is a fatty acid; 3 is a nitrogenous base C. 1 is a phosphate group; 3 is a nitrogenous base D. 1 is a phosphate group; 3 is an amino acid

Question 2

Two nucleotides are taken from different places along the same DNA strand and compared side by side.

Which part of the two nucleotides might be different?

A. The phosphate group B. The nitrogenous base C. The five-carbon sugar D. All three parts

Question 3

A chemical treatment cuts a single strand of DNA into two shorter pieces. Each piece is still an unbroken chain of nucleotides.

Which bond did the treatment break?

A. A covalent bond between a sugar and the next phosphate B. A hydrogen bond between two neighboring bases C. The bond that holds a base onto its own sugar D. The attraction between the strand and the surrounding water

Question 4

One end of a short single strand of RNA is examined. That end carries a free phosphate group.

What can be said about that end?

A. It is the 3' end B. Either end could carry the phosphate C. It is an end where a sugar has broken off D. It is the 5' end

Question 5

A single strand of four nucleotides. X and Y mark its two ends.

The figure shows a single strand of four nucleotides. Phosphate groups are drawn as circles and five-carbon sugars as pentagons. The two ends are marked X and Y.

Which end is the 3' end?

A. Y, because its sugar carries a free hydroxyl group B. X, because its sugar carries a free hydroxyl group C. X, because it carries the free phosphate group D. Y, because a strand is read from left to right

Question 6

A researcher tags the very first nucleotide laid down in a new DNA strand, then lets the strand grow to 500 nucleotides long.

Where is the tagged nucleotide now?

A. At the 3' end, where the new nucleotides are added B. In the middle, because both ends grow equally C. At the 5' end, which never gains new nucleotides D. Outside the strand, pushed off as it grew

Question 7

A drug binds tightly to the free hydroxyl group at the 3' end of a growing DNA strand and blocks it.

What happens to that strand?

A. It keeps growing, but from the 5' end instead B. It stops growing; no new nucleotide can be joined on C. It grows faster, because the blocked end holds units in place D. It falls apart into separate nucleotides

Question 8

A student copies the sequence of a short DNA strand as C-T-T-A-G but forgets to mark which end is the 5' end. A classmate says the same five bases are there either way, so the mark can be skipped.

Does the missing mark matter, and why?

A. It does not matter; the same bases in the same amounts carry the same information B. It does not matter; a strand can be read from either end and means the same C. It matters only because the 5' end is the end that carries the free phosphate D. It matters; the order read 5' to 3' is the information, and read the other way the order differs

Question 9

Two DNA strands are made from the same pool of nucleotides. One reads 5'-G-A-T-T-C-3'. The other reads 5'-C-T-T-A-G-3'.

How do the two strands compare?

A. Different; the bases sit in a different order read 5' to 3' B. The same; they are built from the same bases in the same amounts C. The same; one is just the other read backwards D. Different; only one of the two strands has a 3' end

Question 10

A DNA sample is warmed to about 90 °C. The two strands come apart, but each separated strand is still a complete, unbroken chain of nucleotides.

Which bonds did the heat break?

A. The covalent bonds along each backbone B. The hydrogen bonds between paired bases C. Covalent bonds joining the bases of the two strands D. Both the covalent bonds and the hydrogen bonds

Question 11

A single strand of RNA folds back on itself so that two stretches of its bases pair up, held by hydrogen bonds. One base lies opposite an adenine.

Which base is it?

A. Thymine B. Guanine C. Adenine D. Uracil

Question 12

One stretch of a DNA strand reads G–C–A–T–T. The partner strand lies directly beneath it, base for base.

Written position by position beneath the given strand, what does the partner strand read?

A. G–C–A–T–T B. C–G–U–A–A C. C–G–T–A–A D. T–A–G–C–C

Question 13

The percentage of each base was measured in three nucleic-acid samples. Sample W: adenine 31%, thymine 31%, guanine 19%, cytosine 19%. Sample X: adenine 28%, thymine 22%, guanine 24%, cytosine 26%. Sample Y: adenine 22%, uracil 28%, guanine 27%, cytosine 23%.

Which sample or samples could be double-stranded, with every base paired with its partner?

A. X only B. W only C. W and X D. W and Y

Question 14

A double-stranded DNA sample from a lake microbe is analyzed. Adenine makes up 32% of the bases and cytosine 18%.

What percentage of the bases is thymine?

A. 32% B. 18% C. 50% D. It cannot be worked out from this

Question 15

A student builds a model of a DNA double helix: two strands twisted around each other.

Which arrangement matches DNA?

A. Backbones outside, bases inside, strands run the same way B. Backbones inside, bases outside, strands run opposite ways C. Backbones inside, bases outside, strands run the same way D. Backbones outside, bases inside, strands run opposite ways

Question 16

A drawing of a piece of double-stranded DNA, copied from a student's notes.

The figure is copied from a student's notes. It shows a piece of double-stranded DNA with the ends of both strands labeled and the paired bases joined by dashed lines. The left strand is labeled correctly.

What, if anything, is wrong with the drawing?

A. Nothing; both strands of DNA run the same way B. The right strand should have its 3' end at the top C. Both strands should be turned over so their 3' ends are at the top D. The dashed lines should be solid; covalent bonds join the two strands

Question 17

One strand of a short piece of DNA reads 5'-T-T-G-C-A-3'.

Read from its own 5' end, what does the partner strand read?

A. 5'-A-A-C-G-T-3' B. 5'-A-C-G-T-T-3' C. 5'-T-G-C-A-A-3' D. 5'-U-G-C-A-A-3'

Question 18

An unknown nucleic acid is broken down, and the five-carbon sugar released is ribose.

What else should be true of this nucleic acid?

A. It contains uracil and is typically single-stranded B. It contains thymine and is typically double-stranded C. It contains uracil and is typically double-stranded D. It contains thymine and is typically single-stranded

How to tackle the free-response questions. Read the verb first: describe asks what you see or know; explain asks why or how, so name the mechanism; predict asks what will happen and why; justify asks for the evidence that supports a claim. Each point is earned by one idea, stated in a sentence that names the thing and the mechanism. Extra words earn nothing; a wrong extra can lose the point. If there is a figure or table, use what it shows. When you finish, check the box for each point your answer earns and compare your sentences with the full-credit answer.

Free response 1 · Analyze Model or Visual Representation · 4 points

The figure is a schematic of a piece of double-stranded DNA, six nucleotides long. Each nucleotide is drawn as three joined shapes: a small circle, a five-sided shape and a rectangle. Along each strand the circles and five-sided shapes alternate to form the backbone, and each rectangle hangs off a five-sided shape and points toward the other strand. In the boxed nucleotide the three shapes are marked: 1 is the circle, 2 is the five-sided shape, and 3 is the rectangle. The bases of the top strand are written as letters, and the top strand's ends are labeled: it reads 5'-A-T-G-C-C-A-3'. The bottom strand's ends are marked X (beneath the top strand's 5' end) and Y (beneath the top strand's 3' end), and its bases are left blank. Dashed lines between the rectangles mark where the two strands are held together.

A piece of double-stranded DNA, six nucleotides long. The top strand reads 5'-A-T-G-C-C-A-3'. The bottom strand's ends are marked X (left) and Y (right) and its bases are left blank. One nucleotide is boxed, with its three parts marked 1, 2 and 3.

(a) Describe the boxed nucleotide by identifying the parts marked 1, 2 and 3. (1 point)

A full-credit answer: 1 is the phosphate group, 2 is the five-carbon sugar (deoxyribose), and 3 is the nitrogenous base, here guanine.

Check the box for each point your answer earns

identifying all three: 1 = phosphate group; 2 = five-carbon sugar (deoxyribose); 3 = nitrogenous base (guanine).

Accept: 'sugar' without naming deoxyribose; 'base' or 'G' for part 3. Working the parts out from their places (the shape that hangs off toward the other strand is the base; the backbone alternates phosphate and sugar; the shape joined to both is the sugar) is the intended route.

Do not award the point if any part is misidentified (for example, 1 as a base or 3 as an amino acid).

Common slip: Reading the three parts in the wrong order, or calling the base an amino acid. Phosphate, then sugar, then base.

(b) Describe the two different kinds of bond in the model: the bonds that join one nucleotide to the next along a strand, and the bonds shown by the dashed lines. (1 point)

A full-credit answer: Along a strand, the sugar of one nucleotide is joined to the phosphate of the next by covalent bonds, forming the sugar-phosphate backbone. The dashed lines are hydrogen bonds between paired bases, and they hold the two strands together.

Check the box for each point your answer earns

stating BOTH: nucleotides along a strand are joined by covalent bonds (sugar of one nucleotide to phosphate of the next, forming the sugar-phosphate backbone), AND the dashed lines are hydrogen bonds between paired bases that hold the two strands together.

Accept: "weak attractions like those between water molecules" for hydrogen bonds if named as hydrogen bonds somewhere in the answer.

Do not award the point for saying the two strands are joined by covalent bonds, or for naming only one kind of bond.

Common slip: Joining the two strands with covalent bonds. Between the strands there are only hydrogen bonds; the covalent bonds run along each backbone.

(c) Represent the bottom strand: write the sequence of its bases reading from its own 5' end, and mark which of X and Y is that 5' end. (1 point)

A full-credit answer: Y is the bottom strand’s 5' end, because the strands are antiparallel. Read from Y, the bottom strand is 5'-T-G-G-C-A-T-3'.

Check the box for each point your answer earns

the bottom strand written 5'-T-G-G-C-A-T-3' with Y marked as its 5' end (so X is the 3' end; the strands are antiparallel). The end labels and the sequence are one representation: the point is earned when the sequence runs in the direction the labels give.

Accept: the bottom strand written position by position beneath the top strand as 3'-T-A-C-G-G-T-5', with its ends labeled to match.

Do not award the point for 5'-T-A-C-G-G-T-3' (right bases, wrong direction), for any uracil, or for X marked as the 5' end.

Common slip: Writing the partner bases in the same left-to-right order as the top strand, 5'-T-A-C-G-G-T-3'. The bottom strand runs the other way, so its own 5' to 3' reading is reversed.

(d) Explain how this model shows that the sequence of one strand carries all the information needed to build the other strand. (1 point)

A full-credit answer: Each base pairs with only one partner, A with T and G with C, so the order of bases on one strand fixes the order on the other. The bottom strand can be filled in from the top strand alone, base by base; the information is held in that order.

Check the box for each point your answer earns

explaining that each base pairs with only one partner (A with T, G with C), so the order of bases on one strand fixes the order of bases on the other; the information is held in that order of bases.

Accept: "the bottom strand could be filled in from the top strand alone, base by base" together with a reference to the pairing rules.

Do not award the point for statements about copying or how a cell makes a new strand; the point is for the pairing argument.

Common slip: Describing how a cell copies its DNA. The point is the pairing argument: one partner per base, so one strand fixes the other.

Free-response score: 0 of 4

Free response 2 · Conceptual Analysis · 4 points

A laboratory isolates the nucleic acid from a virus. Tests show that it is a single strand, that its sugar is ribose, and that its bases are adenine, uracil, guanine and cytosine, present as adenine 27%, uracil 21%, guanine 29%, cytosine 23%. The DNA of the cells the virus infects is double-stranded, with adenine 30%, thymine 30%, guanine 20%, cytosine 20%.

(a) Identify the kind of nucleic acid the virus carries. Then describe two structural differences between it and the cells' DNA, naming what each of the two has. (1 point)

A full-credit answer: The viral nucleic acid is RNA. It has ribose as its sugar where DNA has deoxyribose, and it has the base uracil where DNA has thymine. It is also a single strand, where the cells' DNA is two strands paired together.

Check the box for each point your answer earns

RNA, together with any two of: ribose where DNA has deoxyribose; uracil where DNA has thymine; a single strand where DNA is double-stranded; each difference stated for both molecules.

Accept: 'the sugar differs (ribose in RNA, deoxyribose in DNA)' and 'the base differs (uracil in RNA, thymine in DNA)' in any wording that names both sides.

Do not award the point for RNA alone, for differences in base percentages (those are amounts, not structure), or for two differences with the DNA side missing.

Common slip: Listing the viral features from the description with nothing on the DNA side, or giving the percentage differences. Name the nucleic acid and, for each difference, what DNA has instead.

(b) Explain why the cells' DNA has equal amounts of adenine and thymine and equal amounts of guanine and cytosine, but the viral nucleic acid shows no such matching. (1 point)

A full-credit answer: In double-stranded DNA every adenine is paired across the two strands with a thymine and every guanine with a cytosine, held by hydrogen bonds, so the paired bases must be present in equal amounts. The viral strand is single, so its bases have no partners and no such matching is required.

Check the box for each point your answer earns

explaining that in double-stranded DNA every adenine is paired with a thymine and every guanine with a cytosine across the two strands (held by hydrogen bonds), so the paired bases must be present in equal amounts, whereas the viral strand is single and its bases are not paired with a partner strand, so no such constraint applies.

Accept: "one-to-one pairing" or "every A has a T opposite it" as the mechanism.

Do not award the point for restating the percentages without the pairing argument.

Common slip: Restating the percentages. The point is the one-to-one pairing across two strands, and its absence in a single strand.

(c) Suppose a second strand of RNA were built alongside the viral strand so that every base on the viral strand is paired with a base on the new strand. Predict the percentage of each base in the new strand. (1 point)

A full-credit answer: Adenine 21%, uracil 27%, guanine 23%, cytosine 29%: each base in the new strand takes the percentage of its partner in the viral strand.

Check the box for each point your answer earns

adenine 21%, uracil 27%, guanine 23%, cytosine 29%.

Accept: the same values described in words (uracil takes adenine's 27%, adenine takes uracil's 21%, cytosine takes guanine's 29%, guanine takes cytosine's 23%).

Do not award the point for any answer containing thymine, or for repeating the viral strand's own percentages.

Common slip: Repeating the viral strand’s own percentages, or bringing in thymine. The new strand is RNA, and each of its bases is the partner of the base opposite.

(d) A student says the new strand in part (c) would be an exact copy of the viral strand, because the two carry the same information. State whether the student is right about the sequence, and whether the student is right about the information, and justify both answers. (1 point)

A full-credit answer: The student is wrong about the sequence: the new strand is complementary, not identical, because each position holds the partner base (U opposite A, A opposite U, C opposite G, G opposite C). On information, each base has only one partner, so either strand fixes the other: the two carry the same information in complementary form. Their orders of bases differ, so the new strand’s sequence is not the viral sequence, but the viral sequence can be worked out from it.

Check the box for each point your answer earns

a response that does BOTH of the following: (1) states that the sequence is NOT identical, because each position on the new strand holds the partner base (U opposite A, A opposite U, C opposite G, G opposite C); AND (2) takes a reasoned position on the information using the pairing rules, either that the two strands carry the same information in complementary form (because each base has only one partner, so either strand fixes the other), or that the new strand carries different information (a different order of bases) from which the viral sequence can nevertheless be worked out.

Accept: 'complementary, not identical' together with either position on information, provided the reasoning rests on one base pairing with only one partner.

Accept as an addition, not required: the two strands would run in opposite 5' to 3' directions (antiparallel).

Do not award the point for agreeing that the two sequences are identical, or for a yes or no about the information with no reasoning from base pairing.

Common slip: Agreeing that the two strands are identical, or giving a yes or no about the information with no reason. The reasoning rests on each base pairing with only one partner.

Free-response score: 0 of 4

Multiple choice checked: 0 of 18 correct.

Next: Inside one amino acid