Answered Review Questions
The Recipe of Life
1. Describe the Griffith experiment (1928). What transformed the rough
strain into a smooth strain?
As shown above, Frederick Griffith experimented with two strains of
Streptococcus pneumoniae bacteria. The cells of the “smooth” strain
(S) are encapsulated and cause a lethal case of pneumonia. The
“rough” strain (R) lack a capsule and are harmless. Mice injected with
S cells die. Mice injected with R cells live. Mice injected with S cells
that have been heat-killed also live. However, if you inject the mice
with a mix harmless R cells with dead S cells, the mice die. These
mice when examined post-mortem have both living R and S cells
inside of them. What made the harmless R cells grow capsuies?
Griffith suspected the transformation factor was DNA. DNA from the
dead S cells was picked up by R cells and the new genetic information
allowed them to grow capsules.
2. What was the contribution of Oswald Avery (1944)?
Avery tested Griffith’s prediction by chemically isolating all the organic
compounds in the heat-killed S cells and introducing each one in turn
into R cells to see which compound transformed the cells. Avery
discovered that it was DNA that transformed the cells.
3. Why didn’t the scientific community accept Griffith’s and Avery’s
hypothesis?
Back in 1869, a German bacteriologist explored the chemical make-up
of the nucleus. Friedrich Mieschner discovered that a nucleus contains
two compounds: DNA and Proteins. Thomas Hunt Morgan determined
that something in the nucleus was responsible for inheritance of traits.
Most scientists thought that DNA was too simple a molecule to be the
recipe for life. Most sided with proteins because proteins are
complicated and the there are thousands of different kinds.
4. What changed their mind?
Martha Chase and Alfred Hershey comfirmed that DNA was the
genetic material. By labeling the protein coat of a bacteriophage
with radioactive sulphur (just found in proteins) and the viral DNA
inside the capsid with radioactive phosphorus (in DNA but not in
proteins), they discovered that phages inject their DNA into
bacteria. The phages take over the cellular machinery and make
new viruses. Chase and Hershey found the radioactive DNA in not
only the bacteria plus in the new phages made after the infection.
Their results convinced the scientific community that DNA was the
genetic material.
5. Describe Chargaff’s Rules.
Back in the 1940’s, Edwin Chargaff, an Austrian American biochemist,
examined the relative amounts of adenine, guanine, cytosine, and
thymine in the DNA of a variety of organisms. Chargaff compared the
amounts of these bases in everything from bacteria to humans. What
stood out was that for each species, the amount of adenine always
equaled the amount of thymine. Likewise, the amount of guanine was
the same as cytosine. The pattern is constant regardless of the
species, and so it is known as “Chargaff’s rules”. Later, in the early
1950’s, James Watson and Francis Crick concluded from Chargaff’s
rules that in the DNA molecule every adenine binds to thymine and
every guanine always binds to cytosine forming rungs of the double
helix.
6.
Explain the contributions of Franklin, Wilkins, Crick, and Watson.
Rosalind Franklin and Maurice Wilkins were trying to determine the
structure of DNA. They did an x-ray diffraction on the DNA molecule. In
1953, James Watson and Francis Crick, inferred from the x-ray
diffraction picture and Chargaff’s rules the structure of DNA. In the
1960’s, Crick, Watson, and Wilkins received Nobel prizes for their
work. Unfortunately, Rosalind Franklin had died from cancer a few
years earlier.
7. Describe the structure of DNA
DNA is built of subunits called nucleotides. A nucleotide is composed
of three parts: deoxyribose sugar, a nitrogenous base (A, C, G, T), and
a phosphate group.
DNA is a long chain of nucleotides covalently bonded together forming
a polynucleotide. A polynucleotide is a chain of nucleotides covalently
bonded to each other.
DNA is a double helix composed of two polynucleotides that spiral
around one another. DNA looks like a twisted rope ladder.
Deoxyribose is a five-carbon monosaccharide. Biochemists have
mapped the molecule by numbering each carbon in the sugar. Next to
the number, there is also what looks like an apostrophe. For example,
the first carbon in ribose is called the 1’ (one prime) carbon. The term
“prime” refers to the apostrophe. The apostrophe represents that the
carbon is part of a carbohydrate. For every kind of nucleotide, the
nitrogenous base is always attached to the 1’ carbon, the phosphate
group is always attached to the 5’ carbon, and the 3’ carbon always
holds a hydroxyl group (–OH).
The DNA molecule looks like a twisted rope ladder. The sides of the
ladder are called the sugar-phosphate backbone. Each nucleotide is
attached to the one above by means of a covalent bond between the
phosphate group and the 3’ carbon. The repeating pattern of sugar
hooked to phosphate hooked to sugar gives the backbone its name.
Just like other organic compounds, the sugar-phosphate backbone is
built by dehydration synthesis.
A DNA molecule is described as “anti-parallel” because one
polynucleotide is oriented in the opposite direction to the other. A DNA
molecule kind of resembles a divided highway with traffic moving in
opposite directions.
Since DNA is anti-parallel, one polynucleotide is oriented with the 5’
end of the ribose sugars pointing up and the 3’ end pointing down. This
is the 5’ strand. The other polynucleotide is oriented in the opposite
direction with the 3’ end pointing up and the 5’ end pointed down. This
is called the 3’ strand.
5’ strand
3’ strand
A synonym of the 5’ strand is the leading strand. The 3’ strand is also
known as the lagging strand.
8. Where is DNA located in a cell?
Within the cells of animals, plants, fungi, and protists, DNA is stored in
the nucleus. Bacteria lack a nucleus and so store their DNA in a
portion of the cytoplasm called the nucleoid region.
9. What is a chromosome?
A chromosome is a very long piece of DNA. A typical chromosome
contains hundreds of genes.
10. What is a gene?
Technically, a gene is a length of DNA that codes for a polypeptide.
Later in the semester, we will slightly modify this definition.
11. What is the function of DNA?
DNA carries the information for building proteins. The sequence of
nucleotides in a DNA molecule determines the sequence of amino
acids in a polypeptide of a protein. A DNA molecule is a collection of
recipes for making proteins. Since proteins are the machinery of life,
DNA is the recipe for making an organism.
12. Explain semi-conservative replication.
In 1954, Crick and Watson proposed a mechanism for DNA replication.
This hypothesis was later confirmed by Meselson and Stahl in 1958.
See a diagram of their experiment below.
Prior to cell division, a cell must make a copy of its DNA to pass along
to the next generation. Copying DNA is called “replication”. Rather than
build a DNA molecule from scratch, the new DNA is composed of one
old DNA strand (used as the template) and one brand new strand.
“Semi-conservative” means that half of the new DNA molecule is old
DNA.
13. How can the speed of DNA replication increase while the rate of
replication remains constant?
The conundrum of DNA replication is that in humans the replication
enzymes can copy at a rate of 50 base pairs per second. That may
seem like a fast rate but there are 3.1 billion base pairs in the human
genome. At that rate, if the machinery started at one end of the DNA
and replicated all the way down to the other end, it would take ~ 2
years to copy one DNA molecule. Replication occurs much faster than
that. How? Well, the answer is that DNA replication starts at many
places along the molecule. These separate “origins of replication” form
“replication bubbles”. Once a bubble forms, replication moves in both
directions. These expanding bubbles of replication will eventually meet
and the whole genome will be copied in a matter of hours rather than
years.
14. Describe DNA replication.
Replication begins with an enzyme called helicase. Helicase moves
along the double helix unwinding and unzipping the double helix
breaking the hydrogen bonds between the nitrogenous bases. Next, a
group of enzymes, called DNA Polymerase, attach complementary
nucleotides to the DNA strands and build the sugar phosphate
backbone.