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1.E: Overview, DNA, and Genes (Exercises)

These are homework exercises to accompany Nickle and Barrette-Ng's "Online Open Genetics" TextMap. Genetics is the scientific study of heredity and the variation of inherited characteristics. It includes the study of genes, themselves, how they function, interact, and produce the visible and measurable characteristics we see in individuals and populations of species as they change from one generation to the next, over time, and in different environments.

1.1   How would the results of the cross in Figure 1.11 have been different if heredity worked through blending inheritance rather than particulate inheritance?

1.2  Imagine that astronauts provide you with living samples of multicellular organisms discovered on another planet. These organisms reproduce with a short generation time, but nothing else is known about their genetics.

a) How could you define laws of heredity for these organisms?

b) How could you determine what molecules within these organisms contained genetic information?

c) Would the mechanisms of genetic inheritance likely be similar for all organisms from this planet?

d) Would the mechanisms of genetic inheritance likely be similar to organisms from earth? 

1.3 It is relatively easy to extract DNA and protein from cells; biochemists had been doing this since at least the 1800’s.  Why then did Hershey and Chase need to use radioactivity to label DNA and proteins in their experiments?

1.4  Compare Watson and Crick’s discovery with Avery, MacLeod and McCarty’s discovery.

a) What did each discover, and what was the impact of these discoveries on biology?

b) How did Watson and Crick’s approach generally differ from Avery, MacLeod and McCarty’s?

c) Briefly research Rosalind Franklin on the internet. Why is her contribution to the structure of DNA controversial?

1.5  Starting with mice and R and S strains of S. pneumoniae, what experiments in additional to those shown in Figure 1.3 to demonstrate that DNA is the genetic material?

1.6 List the information that Watson and Crick used to deduce the structure of DNA.

1.7   Refer to Watson and Crick’

a) List the defining characteristics of the structure of a DNA molecule. 

b) Which of these characteristics are most important to replication? 

c) Which characteristics are most important to the Central Dogma?

1.8 Compare Figure 1.13 and Table 1.1. Which of the mutants (#1, #2, #3) shown in Figure 1.13 matches each of the phenotypes expected for mutations in genes A, B,C?

1.9  Refer to Table 1.2

a) What is the relationship between DNA content of a genome, number of genes, gene density, and chromosome number?

b)  What feature of genomes explains the c-value paradox?

c)  Do any of the numbers in Table 1.2 show a correlation with organismal complexity?

1.10 a) List the characteristics of an ideal model organism. 

b) Which model organism can be used most efficiently to identify genes related to:

          i)       eye development

          ii)     skeletal development

          iii)    photosynthesis

          iii)    cell division

          iv)    cell differentiation

          v)     cancer

1.11 Refer to Figure 1.8

a) Identify the part of the DNA molecule that would be radioactively labeled in the manner used by Hershey & Chase

b) DNA helices that are rich in G-C base pairs are harder to separate (e.g. by heating) than A-T rich helices.  Why?

Chapter 1 - Answers

1.1 If genetic factors blended together like paint then they could not be separated again.  The white flowered phenotype would therefore not reappear in the F2 generation, and all the flowers would be purple or maybe light purple.

1.2 a) Identify pure breeding lines of the individuals that differed in some detectable trait, then cross the lines with the different traits and see how the traits were inherited over several generations.

     b) Purify different biochemical components, then see if any of the components were sufficient to transfer traits from one individual to another.

     c) It depends in part whether the organisms all evolved from the same ancestor.  If so, then it seems likely.

    d) The extraterrestrials would not necessarily (and perhaps would be unlikely) to have the same types of reductional divisions of chromosome-like material prior to sexual reproduction.  In other words, there are many conceivable ways to accomplish what sex, meiosis, and chromosomes accomplish on earth.

1.3 Hershey and Chase wanted to be able to track DNA and protein molecules from a specific source, within a mixture of other protein and DNA molecules.  Radioactivity is a good way to label molecules, since detection is quite sensitive and the labeling does not interfere with biological function.

1.4 a) Avery and colleagues demonstrated that DNA was likely the genetic material, while Watson and Crick demonstrated the structure of the molecule.  By knowing the structure, it was possible to understand how DNA replicated, and how it encoded proteins, etc.

      b) Avery and colleagues performed experiments, while Watson and Crick mostly analyzed the data of others and used that to build models.

       c) Watson and Crick relied on Franklin’s data in building their model.  It is controversial whether Watson and Crick should have been given access to these data.

1.5 The experiments shown in Figure 1.3 show that DNA is necessary for transformation, (since removing the DNA by nuclease treatment removes the competency for transformation).  However, this does not demonstrate that DNA is sufficient to transfer genetic information; you could therefore try to purify S strain DNA and see if injecting that DNA alone could transform R strains into S strains.

1.6 Chargaff’s Rules, X-ray crystallography data, and Avery, MacLeod & McCarty and Hershey & Chase’s data, as well as other information (e.g. specific details about the structure of the bases).

1.7  a) Right-handed, anti-parallel double helix with a major and minor groove.  Each strand is composed of sugar-nucleotide bases linked together by covalent phosphodiester bonds. Specific bases on opposite strands of the helix pair together through hydrogen bonding, so that each strand contains the same information in a complementary structure. 

         b) The complimentarity of the bases and the redundant nature of the strands.

         c) The order of the bases.

1.8 Mutant strain #1 has a mutation in gene B (but genes A and C are functional).

Mutant strain #2 has a mutation in gene A (but genes B and C are functional).

Mutant strain #3 has a mutation in gene C (but genes A and B are functional).

1.9  a) There is little correlation between any of these.

        b) Genomes have different amounts of non-coding DNA between genes.

        c)  No.

1.10     a) Fast and simple to grow in high density, diploid,

             b) i)             zebrafish (for vertebrate eyes); flies for eyes in general

       ii)           zebrafish

       iii)          Arabidopsis

       iii)          yeast

       iv)          C. elegans

       v)           arguably, any of the organisms, but the vertebrates would be most relevant

1.11 a) Hershey & Chase labeled the phosphate groups that join the bases

        b) G-C pairs have more hydrogen bonds, so more energy is required to break the larger number of bonds in a G-C rich region as compared to an A-T rich region.