Genetics Ch. 9

If one DNA strand is 5′-GGCATTACACTAGGCCT-3′, what is the sequence of the complementary strand?

3'-CCGTAATGTGATCCGGA-5'

Make a side-by-side drawing of two DNA helices: one with 10 bp per 360° turn and the other with 15 bp per 360° turn.

A drawing of a DNA helix with 10 bp per turn will look like the drawing on the left in Figure 9.12. To have 15 bp per turn, you need to add 5 more base pairs, but the helix should still make only one complete turn.

What chemical group (phosphate group, hydroxyl group, or a nitrogenous base) is found at the 3′ end of a DNA strand? What group is found at the 5′ end?

A hydroxyl group is at the 3' end and a phosphate group is at the 5' end.

Discuss the differences in the structural features of B DNA and Z DNA.

B DNA is a right-handed helix and the backbone is relatively helical, whereas Z DNA is a left-handed helix and the backbone appears to zigzag slightly. Z DNA has the bases tilted relative to the central axis, whereas they are perpendicular in B DNA. There are also minor differences in the number of bases per turn.

In what ways are the structures of an α helix in a protein and the double helix of DNA similar, and in what ways are they different?

Both structures are helical and both are stabilized by hydrogen bonds. An α helix in proteins is a single-stranded structure formed from a single polypeptide. A DNA double helix is formed from the interaction of two separate strands. With regard to the chemistry of the interactions that stabilize an α helix and a DNA double helix, there are some interesting similarities and differences. Hydrogen bonding stabilizes the α helix, but the hydrogen bonding occurs along the backbone, where carbonyl oxygens and amide hydrogens interact with each other. The amino acid side chains, which project from the polypeptide backbone, may also interact favorably, but that is not a consistent feature of an α helix. In a DNA double helix, the hydrogen bonds are between bases (which project from the backbone) that are in separate strands. Base stacking also is a consistent feature that stabilizes the DNA double helix. Stacking of amino acid side chains does not occur within a single α helix.

Discuss the structural significance of complementarity in DNA and in RNA.

Complementarity is important in several ways. First, it is needed to copy genetic information. This occurs during replication, when new DNA strands are made, and during transcription, when RNA strands are made. Complementarity is also important during translation for codon/anticodon recognition. It also allows RNA molecules to form secondary structures and to recognize each other.

Compare the structural features of a double-stranded RNA structure with those of a DNA double helix.

Double-stranded RNA and DNA both form a helical structure due to base pairing. The structures differ in that the number of base pairs per turn is slightly different and RNA follows an AU/GG base-pairing rule, whereas DNA follows the AT/GC rule.

An organism has a G + C content of 64% in its DNA. What are the percentages of A, T, G, and C?

G = 32%, C = 32%, A = 18%, T = 18%.

Write a sequence of an RNA molecule that could form a stem-loop with 24 nucleotides in the stem and 16 nucleotides in the loop.

Here is an example of an RNA molecule that could form a hairpin that contains 24 nucleotides in the stem and 16 nucleotides in the loop. 5'-GAUCCCUAAACGGAUCCCAGGACUCCCACGUUUAGGGAUC-3' The complementary stem regions are underlined.

Within a protein, certain amino acids are positively charged (e.g., lysine and arginine), some are negatively charged (e.g., glutamate and aspartate), some are polar but uncharged, and some are nonpolar. If you knew that a DNA-binding protein was recognizing the DNA backbone rather than a base sequence, which amino acids in the protein would be good candidates for interacting with the DNA?

Lysines and arginines, which are positively charged, and also polar amino acids could be interacting with the negatively charged double helix.

The genetic material found within some viruses is single-stranded DNA. Would this genetic material contain equal amounts of A and T and equal amounts of G and C?

Not necessarily. The AT/GC rule applies only to double-stranded DNA molecules.

On further analysis of the DNA described in conceptual question C21, you discover that the triplex DNA in this alien organism is composed of a double helix with a third strand wound within the major groove (just like the DNA in Figure 9.15). How would you propose that this DNA is able to replicate itself? In your answer, be specific about the base-pairing rules within the double helix and which part of the triplex DNA would be replicated first.

One possibility is a sequential mechanism. First, the double helix could unwind and replicate itself (as described in Chapter 11). This would produce two double helices. Next, the third strand (bound in the major groove) could replicate itself via a semiconservative mechanism. This new strand could be copied to make a copy that is identical to the strand that lies in the major groove. At this point, you would have two double helices and two strands that could lie in the major groove. These could assemble to make two triple helices.

An RNA molecule has the following sequence: 5'-CAUCC [AUCCAUUCCCC] AUCCGAUAA [GGGGAAUGG] AUCC [GAAUGGAU] AAC-3' Parts of region 1 can form a stem-loop with region 2 and with region 3. Can region 1 form a stem-loop with region 2 and region 3 at the same time? Why or why not? Which stem-loop would you predict to be more stable: a region 1/region 2 interaction or a region 1/region 3 interaction? Explain your choice.

Region 1 cannot form a stem-loop with region 2 and region 3 at the same time. Complementary regions of RNA form base pairs, not base triplets. The region 1/region 2 interaction would be slightly more stable than the region 1/region 3 interaction because it is one nucleotide longer, and it has a higher amount of GC base pairs. Remember that GC base pairs form three hydrogen bonds compared to AU base pairs, which form two hydrogen bonds. Therefore, helices with a higher GC content are more stable.

What is meant by the term DNA sequence?

The DNA sequence refers to the sequence of nucleotide bases.

Describe how bases interact with each other in the double helix. This description should include the concepts of complementarity, hydrogen bonding, and base stacking.

The bases conform to the AT/GC rule of complementarity. There are two hydrogen bonds between the A and T bases, and three hydrogen bonds between the G and C bases. The planar structures of the bases stack on top of each other within the helical structure to provide even more stability.

What are the building blocks of a nucleotide? With regard to the 5′ and 3′ positions on a sugar molecule, how are nucleotides linked together to form a strand of DNA?

The building blocks of a nucleotide are a sugar (ribose or deoxyribose), a nitrogenous base, and a phosphate group. In a nucleotide, the phosphate is already linked to the 5 position on the sugar. When two nucleotides are linked together, a phosphate on one nucleotide forms a covalent bond with the 3 hyrdroxyl group on another nucleotide.

A double-stranded DNA molecule is 1 cm long, and the percentage of adenine in it is 15%. How many cytosines does this DNA molecule contain?

The first thing we need to do is to determine how many base pairs are in this DNA molecule. The length of one base pair is 0.34 nm, which equals 0.3410-9 m. One centimeter equals 10-2 meters. There are approximately 2.9107 bp in this DNA molecule, which equals 5.8107 nucleotides. If 15% are adenine, then 15% must also be thymine. This leaves 70% for cytosine and guanine. Because cytosine and guanine bind to each other, there must be 35% cytosine and 35% guanine. If we multiply 5.8107 times 0.35, we get (5.8 107 )(0.35) = 2.0 107 cytosines (about 20 million cytosines)

Let's suppose you have recently identified an organism that was scraped from an asteroid that hit the earth. (Fortunately, no one was injured.) When you analyze this organism, you discover that its DNA is a triple helix, composed of six different nucleotides: A, T, G, C, X, and Y. You analyze the composition of the DNA and find the following amounts of the six bases: A = 24%, T = 23%, G = 11%, C = 12%, X = 21%, Y = 9%. What rules would you propose that govern triplex-DNA formation in this organism? Note: There is more than one possibility.

The key issue in the answer is that there are base pairing rules. Otherwise, it would not be possible to replicate the genetic material. One answer would be that the DNA is composed of a double helix obeying the AT/GC rule and the third strand binds to the major groove so that X binds next to AT pairs and Y binds next to GC pairs. This would explain why the amounts of X, A, and T are approximately equal, as are the amounts of Y, G, and C. You could propose other correct scenarios.

As described in Chapter 15, the methylation of cytosine bases can have an important effect on gene expression. For example, the methylation of cytosines may inhibit the transcription of genes. A methylated cytosine base has the following structure: Would you expect the methylation of cytosine to affect the hydrogen bonding between cytosine and guanine in a DNA double helix? Why or why not? (Hint: See Figure 9.12 for help.) Look back at question 2 in More Genetic TIPS and speculate as to how methylation could affect gene expression.

The methyl group is not attached to one of the atoms that hydrogen bonds with guanine, so methylation would not directly affect hydrogen bonding. It could indirectly affect hydrogen bonding if it perturbed the structure of DNA. Methylation may affect gene expression because it can alter the ability of proteins to recognize DNA sequences. For example, a protein might bind into the major groove by interacting with a sequence of bases that includes one or more cytosines. If the cytosines are methylated, this may prevent a protein from binding into the major groove properly. Alternatively, methylation could enhance protein binding.

What structural feature allows DNA to store information?

The nucleotide base sequence is the means by which DNA stores information.

What part(s) of a nucleotide (namely, phosphate, sugar, and/or base) is(are) found in the major and minor grooves of double-stranded DNA, and what part(s) is(are) found in the DNA backbone? If a DNA-binding protein does not recognize a specific nucleotide sequence, do you expect that it binds to the major groove, the minor groove, or the DNA backbone? Explain.

The nucleotide bases occupy the major and minor grooves. Phosphate and sugar are found in the backbone. If a DNA-binding protein does not recognize a nucleotide sequence, it probably is not binding in the grooves, but instead is binding to the sugar-phosphate backbone. DNA-binding proteins that recognize a base sequence must bind into a major or minor groove of DNA, which is where the bases are accessible to such proteins. Most DNA-binding proteins that recognize a base sequence fit into the major groove. By comparison, other DNA-binding proteins such as histones, which do not recognize a base sequence, bind to the DNA backbone.

A DNA-binding protein recognizes the following double-stranded sequence: 5′-GCCCGGGC-3′ 3′-CGGGCCCG-5′ This type of double-stranded structure could also occur within the stem region of an RNA stem-loop. Discuss the structural differences between RNA and DNA that might prevent the DNA-binding protein from recognizing a double-stranded RNA molecule.

The number of bases per turn is different in an RNA double helix and a DNA double helix. Also, protein binding may be affected by the structure of the sugar, which is ribose in RNA, but deoxyribose in DNA.

Which of the following DNA double helices would be more difficult to separate into single-stranded molecules by treatment with heat, which breaks hydrogen bonds? GGCGTACCAGCGCAT CCGCATGGTCGCGTA ATACGATTTACGAGA TATGCTAAATGCTCT Explain your choice.Page 227

The sequence in part A would be more difficult to separate because it has a higher percentage of GC base pairs compared to the one in part B. GC base pairs have three hydrogen bonds compared with AT base pairs, which only have two hydrogen bonds.

Draw the structure of a phosphodiester linkage.

The structure is a phosphate group connecting two sugars at the 3 and 5 positions, as shown in Figure 9.7.

Draw the structure of deoxyribose and number the carbon atoms. Describe the numbering of the carbon atoms in deoxyribose with regard to the directionality of a DNA strand. In a DNA double helix, what does the term antiparallel mean?

The structure of deoxyribose is shown in Figure 9.4. You begin numbering at the carbon that is to the right of the ring oxygen and continue to number the carbon atoms in a clockwise direction. Antiparallel means that the backbones are running in the opposite directions. In one strand, the sugar carbons are oriented in a 3 to 5 direction, while in the other strand, they are oriented in a 5 to 3 direction.

Draw the structures of guanine, guanosine, and deoxyguanosine triphosphate.

The structures can be deduced from Figures 9.4 and 9.6. Guanine is the base by itself. Guanosine is the base attached to a ribose sugar. Deoxyguanosine triphosphate is a base attached to a deoxyribose sugar with three phosphates.

List the structural differences between DNA and RNA.

The sugar in DNA is deoxyribose; in RNA it is ribose. DNA contains the base thymine, while RNA has uracil. DNA is a double helical structure. RNA is single stranded, although parts of it may form double-stranded regions.

What is the meaning of the term genetic material?

The term genetic material refers to the actual substance that contains genetic information. It is usually DNA, but in some viruses it can be RNA.

After the DNA from type S bacteria is exposed to type R bacteria, list all of the steps that you think must occur for the type R bacteria to start making a capsule.

The transformation process is described in Chapter 7. 1. A fragment of DNA binds to the cell surface. 2. It penetrates the cell membrane. 3. It enters the cytoplasm. 4. It recombines with the chromosome. 5. The genes within the DNA are expressed (i.e., transcription and translation). 6. The gene products create a capsule. That is, they are enzymes that synthesize a capsule using cellular molecules as building blocks.

A medium-sized human chromosome contains about 100 million bp. If the DNA were stretched out in a linear manner, how long would it be?

There are 108 base pairs in this chromosome. In a double helix, a single base pair traverses about 0.34 nm, which equals 0.3410-9 meters. If we multiply the two values together: 108 (0.34 10-9) = 0.34 10-1 m, or 0.034 m, or 3.4 cm. The answer is 3.4 cm, which equals 1.3 inches! That is enormously long considering that a typical human cell is only 10 to 100 µm in diameter. As described in Chapter 10, the DNA has to be greatly compacted to fit into a living cell.

As the minor and major grooves wind around a DNA double helix, do they ever intersect each other, or do they always run parallel to each other?

They always run parallel.

A double-stranded DNA molecule contains 560 nucleotides. How many complete turns occur in this double helix?

This DNA molecule contains 280 bp. There are 10 base pairs per turn, so there are 28 complete turns.

Look up the meaning of the word transformation in a dictionary and explain whether it is an appropriate word to describe the transfer of genetic material from one organism to another.

Transformation means changing from one form to another. In bacterial genetics, transformation involves the uptake of DNA into another bacterium. This may change the form (i.e., phenotype) of the bacterium. For example, transformation may change a rough bacterial strain into a smooth strain. The form or phenotype of the strain has been changed.

Could single-stranded DNA form a stem-loop structure? Why or why not?

Yes, as long as there are sequences that are complementary and antiparallel to each other. It would be similar to the complementary double-stranded regions observed in RNA molecules (e.g., see Figures 9.17 and 9.18).

The base composition of an RNA virus was analyzed and found to be 14.1% A, 14.0% U, 36.2% G, and 35.7% C. Would you conclude that the viral genetic material is single-stranded RNA or double-stranded RNA?

You would conclude that it is probably double-stranded RNA because the amount of A equals U and the amount of G equals C. Therefore, this molecule could be double stranded and obey the AU/GC rule. However, it is also possible that it is merely a coincidence that A happens to equal U and G happens to equal C, and the genetic material is really single stranded.