Genetics Chapter 9 Textbook Questions
BIOL 300 DNA and RNA Practice Problems Exam 1
Terms in this set (13)
C4. What are the components of a nucleotide? With regard to the 5' and 3' positions on a sugar molecule, how are nucleotides linked together in a phosphodiester bond 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 hooked together, a phosphate on one nucleotide forms a covalent bond with the 3' hydroxyl group on another nucleotide.
C7. Describe how bases interact with each other in the double helix. Make sure you address complementarity (complementary base pairs) and hydrogen bonding.
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.
C8. If one DNA strand is 5'-GGCATTACACTAGGCCT-3', what is the sequence of the complementary strand?
C11. Discuss the differences in the structural features of the different forms of DNA: A form, B form, and Z form.
A and B DNA are right-handed helices and the backbones are relatively helical, whereas Z DNA is a left-handed helix and the backbone appears to zigzag slightly.
A DNA and Z DNA have 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.
C12. What parts of a nucleotide (namely, phosphate, sugar, and/or bases) occupy the space within the major and minor grooves of a double-stranded DNA, and what parts are found in the DNA backbone? If a DNA-binding protein (like a histone) is NOT designed to recognize a specific nucleotide sequence, do you expect that it recognizes 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 DNA backbone (i.e., sugar-phosphate sequence).
DNA-binding proteins that recognize a base sequence must bind into a major or minor groove of the DNA, which is where the bases would be accessible to a DNA-binding protein.
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.
C13. 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.
C14. 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?
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 direction.
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.
C17. 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 (like during PCR)? Explain your answer.
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.
C20. If an organism has a G+C content of 64%, what are the percentages of A, T, G, and C? Explain your answer.
C24. 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 base sequences, which amino acids in the protein would be good candidates for interacting with the DNA? Explain your reasoning.
Lysines and arginines, and also polar amino acids.
C27. As the minor and major grooves of the DNA 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.
C28. 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.
C29. 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.
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