Unit Questions

At the start of each new unit of the course, unit questions are posted on the course web site. Students are encouraged to consider how the material presented throughout the unit relates to the unit questions.


Molecular Biology

BioGeoChemical Cycles


Recombinant DNA


  • Why do we study microorganisms?
  • How do we know the things we know in biology?
  • What is the basis of biological interactions on the molecular level?
1 Introduction

You are given a microscope slide that contains both living cells and empty membrane vesicles. When observed in a microscope, the two are indistinguishable. What is so special about the cell?

At what level does MIT focus its study of biology? Why?

What are the characteristics required for something to be considered alive?

What is the relationship between organisms and the environment in which they live?

2 Biochemistry I

What is a molecule? How many different kinds of molecules are present in each cell?

What do we mean when we say "structure of a molecule?" How does a molecule's structure enable its function?

What forces govern/enable molecular interations in a cell?

What are the fundamental types of biological macromolecules? What are the functions of each type of macromolecule in a cell?

3 Biochemistry II

We have learned that biological macromolecules are made from a small number of simple subunits. For example, proteins are made of only 20 different amino acids. Yet each cell needs to manufacture different protein molecules that serve wide range of functions. (a) Estimate the number of types of protein molecules each cell needs to make simultaneously. Is it on the order of 10s? 100s? 1000s? 10,000s? 100,000s? or millions? (b) These proteins assume a wide variety of shapes that allow them to perform their different functions. How is this variability achieved?

What functions do sidechains of amino acids serve in a protein?

4 Biochemistry III

What is the function of the membrane in a cell?

Why are certain elements of human diet designated as "essential?" Do yeast have "essential" diet elements?

5 Biochemistry IV

What is the significance of a delta G of a given reaction?

Why is ATP a common intermediate in many reactions in a cell?

Where in the ATP molecule is the energy stored? Why does this particular way of storing energy allow ATP to serve as an "energy storage" molecule for the cell?

What other molecules do you imagine could perform this role?

Why are catalysts needed for energetically favorable reactions in a cell?

What do catalysts do to speed up reactions?

How do catalysts accomplish their functions?

6 Biochemistry V

In what way is the cell's use of ATP and NADH similar?

Why was it advantageous for a cell to develop glycolysis?

Why are the enzymes that catalyze the steps of glycolysis so similar in yeast and in humans?

7 Biochemistry VI

Why couldn't organisms develop oxidative respiration before photosynthesis arose?

What was the effect of advent of noncyclic photophosphorylation on the environment on Earth?

Molecular Biology

  • How is the heritable information encoded in the cell?
  • How does that information direct cellular function?
  • How does a cell know which genes to express?
8 DNA as Genetic Material

Even before the discovery of what genetic material is, scientists knew that it has three characteristics. What are they?

Explain why Griffith isolated live SIII and not live SII from the mouse that died after the injection of RII + heat-killed SIII.

Avery's results were published in 1944. Nevertheless, acceptance of DNA as transforming principle didn't come until 1950s. Was the experiment not convincing, or was there another reason for this delay?

9 Molecular Biology I

What is the key feature of DNA that allows it to
-encode information?
-pass information from one generation to the next?
mutate (change its information)?

Near the bottom of Watson and Crick's 1953 paper on the discovery of the structure of DNA is the following sentence:
"It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material."
How does the structure of DNA suggest a copying mechanism?


Molecular Biology II

Process of Science

Why is the ability to copy DNA so important?

DNA replication is remarkably accurate. Do you think it would have been possible to evolve a more accurate polymerase? If so, would it have been evolutionarily advantageous? Why or why not?

If there existed a 3'-->5' DNA polymerase, where would the energy for catalyzing the bond formation come in that reaction?

Would a scheme in the question above be more or less energetically favorable for an organism to employ?

11 Molecular Biology III

Why is it important for the cell to be able to distinguish parental (old) DNA strands from their daughter (new) DNA strands?

What led scientists to investigate the relationship between DNA and proteins?

12 Molecular Biology IV

How is information transfered from a nucleic acid to a protein?

Why was the need for a transitional molecule postulated?

13 Gene Regulation I

Why can't a patient infected with HIV ever be cured?

Why are there loops when a human DNA is hybridized w mRNA for the same gene?

How is it possible that your skin cells and liver cells contain the same genes but perform different functions?

What types of mutants in the lac operon would lead to constant expression of the lacZ, lacY, and lacA genes?

BioGeoChemical Cycles

  • What is all the biomass created from?
  • What three things do all organisms need in order to live?
  • Why are the biogeochemical cycles important?
16 The Biosphere

Why do we say that Ecology is a strict natural science?

What are "emergent properties" and why are they important?

In the early stages of life on Earth, Photosynthesis greatly outweighed Respiration. What was the result of this phenomenon?

What is the relationship between organisms and their environment?

Why is it fair to say that many processes operate in similar way at all scales?

Why is it legitimate to view the biosphere as a network of genes?

Most organisms in the world are __________.

17 Carbon and Energy Metabolism

Why does metabolic diversity exist?

What type of organisms are responsible for most of that diversity?

Why is it important to look at the interaction of organisms in the environment, rather than just at each organism separately?

18 Productivity and Food Webs

What do food webs represent in terms of biogeochemical cycles? Why?

Why are the various efficiencies defined for the food web diagrams important?

How is it possible that, collectively, terrestrial and aquatic ecosystems have approximately equal contributions to total global photosynthesis, despite great differences in the biomass of their primary producers?

19 Regulation of Productivity

What factors determine variability in terrestrial ecosystem productivity?

What factors determine variability in aquatic ecosystem productivity?

How does the mode of regeneration of nutrients in the soil determine the character of the ecosystem?

Why is there a need for a number of mechanisms of nutrient transport from the deep ocean to the sunlit surface waters in the oceans?

Is it possible that in the same environment two different things would be limiting for two different organisms? Why or why not?

20 Limiting Factors and BioGeoChemical Cycles

Why is it important that the nutrients cycle through the biosphere?

The flux of CO2 to the atmosphere due to human activities is only a small fraction of the flux due to global respiration. Why, then, is it causing a significant increase in the reservoir of CO2 in the atmosphere?


  • Why do geneticists look for organisms lacking a trait?
  • What is the general method by which genetic experiments are performed?
15 Bacterial Genetics

What is a gene?

How are genes responsible for traits?

A complementation test involves crossing strains that display what kinds of phenotypes with respect to each other?

Recombination frequency indicates what about the genes affected in the mutants being considered?

21 Mendelian Genetics

What was remarkable about Mendel's research at the time it was conducted?

Why were Mendel’s findings ignored at the time of publication?

22 Mitosis and Meiosis

What are chromosomes made up of?

Why isn't mitosis an adequate process for forming gametes?

What is the advantage of sexual reproduction?

How does Chromosomal Theory of Inheritance mesh with Mendel’s postulated inheritance principles?

23 Diploid Genetics

Why were Mendel's model and Chromosomal Theory of Inheritance at odds over the predicted results of a dihybrid cross?

Why does recombination of genes occur?

What factors should be considered when trying to determine a mode of inheritance of a particular phenotype from pedigrees?

Recombinant DNA

  • What does recombinant DNA technology allow scientists to do that they were not able to do before?
  • Recombinant DNA is a set of tools. What are those tools used for?
  • Where did these tools come from?
24 Recombinant DNA I

What does it mean to clone a DNA fragment?

What are restriction enzymes? Why are they important?

What are plasmids?

25 Recombinant DNA II

What is a library?

How do you find a piece of DNA or RNA in a library?

26 Recombinant DNA III

How can we determine the sequence of a specific segment of DNA?

What important feature of gene regulation needs to be adjusted when cloning a gene for expression in a new species?

How is the process of homologous recombination used in the recombinant DNA toolbox?

Why is PCR a powerful technique in the recombinant DNA toolbox?

What is DNA fingerprinting?