CHAPTER 10_DNA Structure and Analysis Flashcards
According to the Watson–Crick model, DNA exists in the form of a (right-handed or left-handed?) double helix
right-handed
what is the bonding between complementary nitrogenous bases?
Hydrogen bonding
For a molecule to serve as the genetic material, it must exhibit four crucial characteristics:
- replication
- storage of information
- expression of information
- variation by mutation
Characteristic of a genetic material that requires the molecule to act as a repository of genetic information that may or may not be expressed by the cell in which it resides
Storage of information
transcription of DNA, in which three main types of RNA molecules are synthesized:
- messenger RNA (mRNA)
- transfer RNA (tRNA)
- ribosomal RNA (rRNA)
chain of amino acids
polypeptide
central dogma of molecular genetics:
“DNA makes RNA, which makes proteins.”
a change in the chemical composition of DNA
mutation
Levene postulated incorrectly that identical groups of these four components were repeated over and over, which was the basis of his _________
tetranucleotide hypothesis for DNA structure
Frederick Griffith, a medical officer in the British Ministry of Health. He performed experiments with several differentstrains of the bacterium __________
Diplococcus pneumoniae.* (now named Streptococcus pneumoniae)
what does virulent mean?
infectious
what does avirulent mean?
noninfectious
virulence depends on the presence of
a polysaccharide capsule; which strain has this capsule, virulent or avirulent?
Virulent
Encapsulated bacteria form smooth, shiny surfaced colonies (S) when grown on an agar culture plate; non-encapsulated strains produce rough colonies (R).
Each strain of Diplococcus may be one of dozens of different types called ______ that differ in the precise chemical structure of the polysaccharide constituent of the thick, slimy capsule.
serotypes
Griffith concluded that the heat-killed IIIS bacteria somehow converted live avirulent IIR cells into virulent IIIS cells. Calling the phenomenon _______, he suggested that the transforming principle might be some part of the polysaccharide capsule or a compound required for capsule synthesis, although the capsule alone did not cause pneumonia.
transformation
To use Griffith’s term, the transforming principle from the dead IIIS cells served as a _______— that is, a nutrient source—for the IIR cells.
“pabulum”
chemical name then used to describe DNA
“sodium desoxyribonucleate”
Further testing clearly established that the transforming principle was ____
DNA
In a reasonably short time, many new phages are constructed and the bacterial cell is lysed, releasing the progeny viruses. This process is referred to as the _____
lytic cycle
Because DNA contains phosphorus (P) but not sulfur, 32P effectively labels DNA; because proteins contain sulfur (S) but not phosphorus, 35S labels protein.
if E. coli is treated with the enzyme lysozyme, the outer wall of the cell can be removed without destroying the bacterium. Enzymatically treated cells are naked, so to speak, and contain only the cell membrane as their outer boundary. Such structures are called ________
protoplasts (or spheroplasts)
When added to E. coli protoplasts, the purified DNA resulted in the production of complete fX174 bacteriophages. This process of infection by only the viral nucleic acid, called _______
transfection
Indirect evidences that supports the concept that DNA is the genetic material in eukaryotes
- Distribution of DNA (Diploid; haploid)
- Mutagenesis
The molecule serving as the genetic material is expected to absorb at the wavelength(s) found to be mutagenic.
UV light is most mutagenic at the wavelength of _______, and both DNA and RNA absorb UV
light most strongly at —— nm. On the other hand, protein absorbs most strongly at _______, yet no significant mutagenic effects are observed at that wavelength.
260 nanometers (nm)
280 nm
Direct evidence that supports the concept that DNA is the genetic material in eukaryotes
Recombinant DNA studies
involves splicing together DNA sequences from different organisms
recombinant DNA technology
can provide the full set of DNA sequences of organisms
Genomics
Their RNA serves as a template for the synthesis of the complementary DNA molecule
Retroviruses
The process, _______, occurs under the direction of an RNA-dependent DNA polymerase enzyme called _________
reverse transcription
reverse transcriptase
Building blocks of nucleic acids
Nucleotides (sometimes called mononucleotides)
3 essential components of a nucleotide:
- nitrogenous base
- pentose sugar (a 5-carbon sugar)
- phosphate group
two kinds of nitrogenous bases:
- nine-member double-ring purines and the
- six-member single-ring pyrimidines.
The two purines are…
Adenine
Guanine
Some viruses contain an RNA core rather than a DNA core. In these viruses, it appears that RNA serves as the genetic material—an exception to the general rule that DNA performs this function
tobacco mosaic virus (TMV)
_______ is a molecule composed of a purine or pyrimidine base and a ribose or deoxyribose sugar. If a phosphate group is added to the nucleoside, the molecule is now called a ______
nucleoside
nucleotide
_______ are important in cell bioenergetics because of the large amount of energy involved in adding or removing the terminal phosphate group.
adenosine triphosphate (ATP) and guanosine triphosphate (GTP)
The linkage between two mononucleotides consists of a phosphate group linked to two sugars. It is called…
phosphodiester bond
–includes alterations of chromosome number and rearrangements within and between chromosomes
–provides the raw material for the process of evolution
Genetic Variation
Hershey and Chase knew from existing
data that:
1. T2 phages consist of approximately 50
percent protein and 50 percent DNA
2. Infection is initiated by adsorption of the
phage by its tail fibers to the bacterial cell.
3. The production of new viruses occurs
within the bacterial cell.
- process of infection by only the viral nucleic acid
transfection
Short chains consisting of up to approximately 30 nucleotides linked together are called ________; longer chains are called
_______
oligonucleotides
polynucleotides
The data available to Watson and Crick, crucial to the development of their proposal, came primarily from two sources:
(1) base composition analysis of hydrolyzed samples of DNA
(2) X-ray diffraction studies of DNA.
X rays scatter (diffract) in a pattern that depends on the molecule’s atomic structure. The pattern of diffraction can be captured as spots on photographic film and analyzed for clues to the overall shape of and regularities within the molecule. This process is called…
X-ray diffraction analysis
Major features of the double helix model by Watson and Crick:
- Two long polynucleotide chains are coiled around a central axis, forming a right-handed double helix.
- The two chains are antiparallel; that is, their C-5′ to C-3′ orientations run in opposite directions.
- The bases of both chains are flat structures lying perpendicular to the axis; they are “stacked” on one another,
- The nitrogenous bases of opposite chains are paired as the result of the formation of hydrogen bonds
- Each complete turn of the helix is 34 Å (3.4 nm) long; thus, each turn of the helix is the length of a series of 10 base pairs.
- A larger major groove alternating with a smaller minor groove winds along the length of the molecule.
- The double helix has a diameter of 20 Å (2.0 nm).
alternative form of DNA ______ does exist as a left-handed helix
(Z-DNA)
The specific A-T and C-G base pairing is described as _______ and results from the chemical affinity that produces the hydrogen bonds in each pair of bases.
complementarity
why is purine-purine and pyrimidine-pyrimidine discounted by Watson and Crick?
Such pairings would lead to aberrant diameters of, in one case, more than and, in the other case, less than 20 Å because of the respective sizes of the purine and pyrimidine rings.
In addition, the three-dimensional configurations that would be formed by such pairings would not produce an alignment that allows sufficient hydrogen-bond formation.
a very weak electrostatic attraction between a covalently bonded hydrogen atom and an atom with an unshared electron pair.
hydrogen bond
The hydrogen atom assumes a partial positive charge, while the unshared electron pair—characteristic of covalently bonded oxygen and nitrogen atoms—assumes a partial negative charge.
the hydrophobic nitrogenous bases are stacked almost horizontally on the interior of the axis and are thus shielded from the watery environment that surrounds the molecule within the cell.
The hydrophilic sugar-phosphate backbones are on the outside of the axis, where both components may interact with water.
These molecular arrangements provide significant chemical stabilization to the helix.
other form of DNA right-handed helices that have been discovered and is found under even greater dehydration conditions than those observed during the isolation of A- and B-DNA
C-DNA
other form of DNA right-handed helices that have been discovered and occur in helices lacking guanine in their base composition
D-DNA and E-DNA
other form of DNA right-handed helices that have been discovered that if DNA is artificially stretched, still another conformation is assumed, called…
P-DNA (named for Linus Pauling)
when a small synthetic DNA oligonucleotide containing only G-C base pairs was studied. ______ takes on the rather remarkable configuration of a left-handed double helix.
Z-DNA
estimate of the periodicity of nitrogenous bases =
3.4 Angstroms apart
strong arcs on periphery of an X-ray diffraction of DNA means that
- closely spaced aspects of the molecule
form of DNA right-handed helices where the base pairs are perpendicular to the helix
B-DNA
form of DNA right-handed helices where they are tilted and pulled away from the helix
A-DNA
RNAs are distinguished according to their sedimentation behavior in a centrifugal field and by their size (the number of nucleotides each contains).
Sedimentation behavior depends on a molecule’s density, mass, and shape, and its measure is called the _______
Svedberg coefficient (S)
The molecule with a melting point (Tm) of 83 degree Celcius has a greater triple-bond GC content than the molecule with a Tm equal to 77 degree Celcius
The red fluorescence is produced by ________ counterstaining of chromosomal DNA
propidium iodide
a unit of measurement for the rate at which a particle sediments in a centrifuge
Svedberg coefficient (S)
function as nonspecific workbenches where proteins are synthesized during translation
Ribosomes
During unwinding, the viscosity of DNA decreases and UV absorption increases (called the _____).
hyperchromic shift
The molecule with a higher Tm has a higher percentage of G-C base pairs than A-T base pairs since G-C pairs share three hydrogen bonds compared to the two bonds between A-T pairs
The denaturation/renaturation of nucleic acids is the basis for one of the most useful techniques in molecular genetics—_____________
molecular hybridization
Because fluorescence is used, the technique is known by the acronym FISH ________.
fluorescent in situ hybridization
This technique may be adapted to separate different-sized fragments of DNA and RNA chains
electrophoresis
What do you call the bond between nitrogenous base and sugar
Glycosidic bond
