Exam 1 Problem Set
What are the building blocks of a nucleotide? With regard to the 5
positions on a sugar molecule, how are
nucleotides linked together to form a strand of DNA?
The building blocks of a nucleotide are a nitrogenous base, a sugar, and a phosphate.
Nucleotides are linked together through
a phosphodiester bond on the 5’ carbon of one sugar with the 3’ carbon of another sugar.
What parts of a nucleotide (namely, phosphate, sugar, and/or bases) occupy the major and minor grooves of double-
stranded DNA and what parts are found in the DNA backbone? If a DNA-binding protein does not recognize a specific
nucleotide sequence, do you expect that it recognizes the major groove, the minor groove, or the DNA backbone? Explain.
The nitrogenous bases mainly occupy the major and minor grooves of a DNA strand.
The phosphate and sugar mainly occupy
the backbone of a DNA strand.
A DNA binding protein that does not recognize a specific nucleotide sequence would bind to
the DNA backbone because nucleotide sequences mainly occupy a DNA’s grooves.
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
Write out a sequence of an RNA molecule that could form a stem-loop with 24 nucleotides in the stem and 16 nucleotides
in the loop.
5’ AUCGGCAUUCGACCCCCCCCCCCCCCCCUCGAAUGCCGAU 3’
An organism has a G + C content of 64% in its DNA. What are the percentages of A, T, G, and C?
Adenine= 18%, Thymine=18%, Cytosine=32%, Guanine=32%
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?
Based on Chargaff’s rule, we can assume that the RNA is double stranded because of complimentary base pairing.
we cannot know for sure because RNA can have both single stranded and double stranded parts.
In the experiment described in Figure 9.3 on page 224, the DNA extract was treated with DNase, RNase, or protease.
Why was this done? (In other words, what were they trying to demonstrate?)
In the experiment on figure 9.3, although the nucleic acid affected the bacteria, it was still treated with DNase, RNase, and
protease to remove any impurities within the nucleic acid.
When the DNA was treated with DNase, the bacteria remained
the same, proving that DNA was the substance that causes heritable changes.
Experiment 9B on page 233 presents Chargaff’s data from his 1951 paper.
Only in the case of humans does the quantity of adenine actually equal the quantity of thymine. Also in the data from
humans, the quantities of guanine and cytosine are closer than they are for most of the other species. Is there a good
reason for why the paired nucleotide molarities are more equal in humans than they are in any other species