Genetics Analysis and Principles 5th

Edition Brooker Solutions Manual

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Chapter 9: Molecular Structure of DNA and RNA

Key Terms
A DNA acid) Phosphodiester linkage
Adenine (A) DNase Protease
Antiparallel Double helix Purines
AT/GC rule Grooves Pyrimidines
B DNA Guanine (G) Ribose
Backbone Lysis RNA (ribonucleic acid)
Bacteriophage Major groove RNase
Base pairs (bp) Methylation Strand
Chargaff’s rule Minor groove Thymine (T)
Complementary Molecular genetics Transformation
Cytosine (C) Nucleic acids Triplex DNA
Deoxyribose Nucleoside Uracil (U)
Directionality Nucleotides Z DNA
DNA (deoxyribonucleic Phage

Chapter Outline

1. Molecular genetics is the study of DNA structure and function at the molecular level.
2. Our understanding of genetics comes from our knowledge of the molecular structure
of DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

9.1 Identification of DNA as the Genetic Material

Learning Outcomes:
1. Describe the four criteria that the genetic material must fulfill.
2. Analyze the results of (1) Griffith, (2) Avery, MacLeod, and McCarty, and (3)
Hershey and Chase, and explain how they indicate that DNA is the genetic
material.

1. Genetic material must meet the following criteria:

a. It must contain the information necessary to construct an entire
organism.
b. The genetic material must be transmitted from parent to offspring.
c. The genetic material must be able to be replicated, so it can be passed
from parent to offspring.
d. The genetic material must have variation that can account for the
known phenotypic differences within a species.
2. The chromosome theory of inheritance demonstrated that chromosomes carry
the genetic information. However, chromosomes contain proteins, DNA, and
RNA.

Experiments with Streptococcus Suggested That DNA Is the Genetic Material

1. Griffith’s experiments (1928) involved the study of Streptococcus
 pneumoniae bacteria.
a. These bacteria can produce colonies that have either a smooth or rough
appearance.
b. These strains differ in the chemical characteristics of their capsules.
2. Griffith injected both live and dead bacteria into mice and observed whether
the bacteria caused a lethal infection (Figure 9.1).
a. The type IIIS killed the mouse, but the type IIR did not.
b. If type IIIS was first heat killed, the mouse survived.
c. If type IIR was mixed with dead IIIS, the mouse died. Furthermore,
live type IIIS bacteria were recovered from the mouse.
3. Griffith called the process transformation. The particle responsible was called
the transformation principle.
4. Avery, MacLeod, and McCarty (1940s) designed an experimental system to
test if Griffith’s transforming principle was DNA, RNA, or protein (Figure
9.2).
a. Treated type IIIS extracts with RNase, DNase, or proteases to see
which had the ability to transform type IIR bacteria into type IIIS.
b. Only the sample that was treated with DNase could not transform the
IIR to IIIS, thus DNA was the transforming principle.

Hershey and Chase Provided Evidence That DNA Is the Genetic Material of T2 Phage
1. Conducted an experiment (1952) to test if DNA or proteins were the genetic
material.
2. Used the bacteriophage T2, which infects E. coli, as the experimental system.
T2 contains DNA within a protein coat (Figure 9.3).
a. The T2 lifecycle is diagrammed in Figure 9.4.
b. Their experimental system allowed the T2 phage time to inject its
genetic material into the bacteria. The phage was then sheared from
the surface of the cell using mechanical force (blending).
c. They used radioisotopes to distinguish between the proteins and DNA.
The proteins were labeled with 35S and the DNA was labeled with 32P.
d. Their hypothesis was that only the genetic material of the phage would
be injected into the cell.
e. The experimental system is shown in Figure 9.5.
3. Their results indicated that the majority of the 35S was found in the
supernatant and did not enter the cell. The majority of the DNA, labeled with
32
P, was found in the bacterial cells. DNA was the genetic material.

9.2 Overview of DNA and RNA structure

Learning Outcomes:
1. Define nucleic acid.
2. Describe the four levels of complexity of DNA.

1. DNA and RNA are macromolecules that have the following levels of complexity
(Figure 9.6).
a. Nucleotides that form the repeating structure of nucleic acids.
 b. Strands of nucleotides that are linked together.
c. In DNA (and sometimes RNA), two strands may interact to form a double-
helix.
d. The double-helix folds to form a three-dimensional structure.

9.3 Nucleotide structure

Learning Outcomes:
1. Describe the structure of a nucleotide.
2. Compare and contrast the structure of nucleotides found
in DNA versus RNA.

Nucleotides Are the Building Blocks of Nucleic Acids

1. Nucleotides have three components: a phosphate group, a pentose sugar, and a
nitrogenous base (Figure 9.7 and 9.8).
2. The nitrogenous bases may be divided into two major groups.
a. The purines consist of adenine and guanine.
b. The pyrimidines consist of thymine, cytosine, and uracil.
3. In DNA, the pentose sugar is deoxyribose. In RNA, the pentose sugar is ribose.
4. When a base is attached only to a sugar (no phosphates) it is called a nucleoside.
a. If the base is attached to ribose, they are called adenosine, guanosine,
thymidine, cytidine, and uridine.
b. If the base is attached to a deoxyribose sugar, they are called deoxyadenosine,
deoxyguanosine, deoxythymidine, deoxycytidine, and deoxyuridine.
5. A nitrogenous base that is attached to three phosphate groups is called adenosine
triphosphate (ATP). Two phosphate groups would be ADP (diphosphate) and one
phosphate group would be AMP (monophosphate). This is shown graphically in
Figure 9.9.
6. The numbering of the carbons in the pentose sugar is important to the
understanding of DNA structure (Figures 9.9 and 9.10).

9.4 Structure of a DNA strand

Learning Outcome:
1. Describe the structural features of a DNA strand.

Nucleotides Are Linked Together to Form a Strand

1. DNA and RNA contain nucleotides in a linear arrangement (Figure 9.10).
a. The phosphate groups connect the sugar groups to form a phosphodiester
linkage.
b. The phosphates and sugars form the backbone of the sugar molecule.
2. A phosphodiester linkage has an attachment between the 5’ carbon in one sugar,
and the 3’ sugar in the other. This gives the DNA strand directionality.
3. The sequence of the bases is specific and carries genetic information.

9.5 Discovery of the Double Helix

Learning Outcome:
1. Outline the key experiments that led to the discovery of the DNA double helix.
A Few Key Events Led to the Discovery of the Double-Helix Structure
1. Pauling (1950s) studied the folding patterns of proteins using ball and stick
models. He was actively studying the structure of DNA in the early 1950s (Figure
9.11).
2. Franklin used X-ray diffraction to determine that DNA had a helical structure and
that its diameter was too wide to be a single helix. She also determined that the
helix contains about 10 base pairs per complete turn (Figure 9.12).

Chargaff Found That DNA Has a Biochemical Composition in Which the Amount of A
Equals T and the Amount of G Equals C
1. Chargaff experimentally determined that the amount of adenine in a cell roughly
equals the amount of thymine, and the amount of cytosine roughly equals the
amount of guanine. This is called the AT/GC rule, or Chargaff’s rule.
2. His experimental system is outlined in Figure 9.13.

Watson and Crick Deduced the Double-Helical Structure of DNA

1. The contributions of Chargaff, Pauling, and Franklin provided useful information
for the discovery of DNA structure by Watson and Crick.
2. Watson and Crick experimented with many models of DNA structure, including
one that had magnesium ions holding the two strands together (Figure 9.14),
before developing the double-helix model that paired A with T and C with C
(Figure 9.14).

9.6 Structure of the DNA Double Helix

The Molecular Structure of the DNA Double Helix Has Several Key Features
1. The double-helix structure of DNA has some important features (Figure 9.15).
a. There are 10 base pairs in a complete twist of the helix.
b. The strands are held together by hydrogen bonds between the bases.
c. The adenine in one strand binds with a thymine in the other strand. Cytosine
binds with guanine, according to the AT/GC rule.
d. Adenine and thymine have two hydrogen bonds between them, while guanine
and cytosine have three.
e. The two strands are complementary. If you know the sequence of one strand,
you know the sequence of the opposite strand.
f. The strands of DNA are orientated in opposite directions, and thus are said to
be antiparallel.
g. DNA is a right-handed molecule.
h. DNA has a major groove and minor groove (Figure 9.16).

DNA Can Form Alternative Types of Double Helices

1. DNA may form several different types of secondary structures (Figure 9.17).
a. B DNA is the predominant form in living organisms.
b. Z DNA has a left-handed structure and forms under high ionic conditions.
Cytosine methylation favors this configuration.
c. A DNA is a right-handed molecule that exists under low humidity.
DNA Can Form a Triple Helix, Called Triplex DNA
1. DNA may sometimes form a triple-helix structure (Figure 9.18).
a. Triplex DNA is involved in recombination and to inhibit gene expression.
b. Current research is examining the use of triplex DNA to silence the expression
of target genes, including genes involved in cancer.

9.7 RNA Structure

Learning Outcome:
1. Outline the key structural features of RNA.

RNA Molecules Are Composed of Strands That Fold into Specific Structures
1. RNA has a primary structure that is similar to DNA, but it consists of a single
helix (Figure 9.19).
2. The secondary structure of RNA (Figure 9.20) is due to complementary regions in
the RNA that form base pairs between A and U and G and C. Short regions of the
RNA then form a double-helix, creating many possible secondary structures
including
a. bulge loops.
b. internal loops.
c. multibranched loops and junctions.
d. stem-loops.
3. RNA structure can also be influenced by
a. ion interactions.
b. small molecule interactions.
c. large protein interactions.
4. An example of a three-dimensional RNA molecule that has important biological
functions is tRNA (Figure 9.21).