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Chapter 16: OBJECTIVES
1. Explain why researchers originally thought protein was the genetic material.
Researches originally though protein was the genetic material because biochemists had identified
proteins as a class of macromolecules with great heterogeneity and specificity of function,
essential requirements for the hereditary material. Moreover, little was known about nucleic
acids, whose physical and chemical properties seemed far too uniform to account for the
multitude of specific inherited trait expressed by every organism.
2. Summarize experiments performed by the following scientists, which provided evidence that
DNA is the genetic material:
a. Frederick Griffith: Studied bacteria in animals, producing one smooth bacteria and the other
rough, arriving to the conclusion of transformation, a change in the phenotype due to the
assimilation of external genetic material by a cell.
b. Alfred Hershey and Martha Chase: Hershey and Chase demonstrated that it was DNA that
functioned as the phages’ genetic material. Viral proteins, labeled with radioactive sulfur,
remained outside the host cell during infection.
c. Erwin Chargaff: Chargraff analyzed the base composition of DNA from a number of different
organisms concluding that the amounts of the four nitrogenous bases vary from species to
another. He also found a peculiar regularity in the ratios of the nucleotide bases.
3. List the three components of a nucleotide.
Each nucleotide is composed of three parts: a phosphate group, which is joined to a pentose
(five-carbon sugar), which in turn is bonded to an organic molecule called a nitrogenous base.
4. Distinguish between deoxyribose and ribose.
Deoxyribose, the sugar component of DNA, has one less hydroxyl group than ribose, the sugar
component of RNA.
5. List the nitrogen bases found in DNA, and distinguish between pyrimidine and purine.
The Nitrogen bases found in DNA are: Adenine with Thymine and Guanine with Cytosine.
Purines are adenine with guanine, nitrogenous bases with two organic rings. Purines are twice
as wide as Pyrimidines (Cytosine and Thymine) which contain one single ring.
6. Explain how Watson and Crick deduced the structure of DNA, and describe what evidence
they used.
Watson and Crick discovered the double helix by building models to conform to X-ray data.
Basing their model on data from Franklin’s X-ray diffraction photo of DNA, Watson and Crick
discovered that DNA is a double helix. Two anti-parallel sugar-phosphate chains wind around the
outside of the molecule; the nitrogenous bases project into the interior, where they hydrogenbond in specific pairs.
7. Explain the "base-pairing rule" and describe its significance.
During DNA replication, base pairing enables existing DNA strands to serve as templates for new
complementary strands. A goes with T and G goes with C.
8. Describe the structure of DNA, and explain what kind of chemical bond connects the
nucleotides of each strand and what type of bond holds the two strands together.
The structure of a DNA strand: Each nucleotide unit of the polynucleotide chain consists of a
nitrogenous base (T, A, C, OR G), the sugar deoxiribose, and a phosphate group. The
phosphate group of the nucleotide is attached to the sugar of the next nucleotide in a line. The
result is a "backbone" of alternation phosphates and sugars, from which the bases project. The
two DNA strands are held together by hydrogen bonds between the nitrogenous bases, which are
paired in the interior of the double helix. The base pairs are 0.34 nm apart.
9. Explain, in their own words, semiconservative replication, and describe the Meselson-Stahl
experiment.
Semiconservative replication deals with the two strands of the parental molecule separating and
each functioning as templates for synthesis of a new complimentary strand. The Mesleson-Stahl
experiment tested three hypotheses of DNA replication. Meselson and Sathl cultured E. coli for
several generations on a medium containing a heavy isotope of nitrogen. The bacteria
incorporated the heavy nitrogen into their nucleotides and then into their DNA. The scientists
then transferred the bacteria to a medium containing the lighter more common isotope of
bacteria. Thus, any new DNA that the bacteria synthesized would be lighter than the "old" DNA
made in the heavy Nitrogen medium. Meselson and Stahl could distinguish DNA of different
densities by centrifuging DNA extracted from the bacteria.
10. Describe the process of DNA replication, and explain the role of helicase, single strand
binding protein, DNA polymerase, ligase, and primase.
DNA Replication begins at special sites called origins of replication. Y-shaped replication forks
form at opposite ends of a replication bubble, where the two DNA strands separate.
DNA polymerases catalyze the synthesis of the new DNA strand working in the 5’ ----->3’
direction.
Simultaneous 5’ ----> 3’ synthesis of anti-parallel strands at a replication fork yields a continuous
leading strand and short, discontinuous segments of lagging strand. The fragments are later
joined together with the help of DNA ligase.
DNA synthesis must start on the end of a primer, (primase, joins RNA nucleotides to make the
primer).
Helicase is the enzyme that works at the crotch of the replication fork, untwisting the double helix
and separating the two "old" strands.
Single-strand binding proteins then attach in chains along the unpaired DNA strands, holding
these templates straight until new complementary strands can be synthesized.
11. Explain what energy source drives endergonic synthesis of DNA.
I comprehend what energy source drives endergonic synthesis of DNA for I learned it previous in
the year, and in my previous Biology honors course.
12. Define antiparallel, and explain why continuous synthesis of both DNA strands is not possible.
The two DNA strands are antiparallel; that is, their sugar-phosphate backbones run in opposite
directions. Continuous synthesis of both DNA strands is not possible. DNA Polymerase
elongated strands only in the 5’---->3’ direction. One new strand, called the leading strand, can
therefore elongate continually in the 5’ ----->3’ direction as the replication fork progresses. But
the other new strand, the lagging strand, must grow in an overall 3’----> 5’ direction by the
addition of short segments, Okazaki fragments, that individually grow 5’ -----> 3’. An enzyme
called ligase connects the fragments.
13. Distinguish between the leading strand and the lagging strand.
The leading strand is the new continuous complementary DNA strand synthesized along the
template strand in the mandatory 5’--->3’ direction.
The lagging strand is a discontinuously synthesized DNA strand that elongates in a direction
away from the replication fork.
14. Explain how the lagging strand is synthesized when DNA polymerase can add nucleotides
only to the 3¢ end.
DNA polymerase cannot initiate a polynucleotide strand; it can only add to the 3’ end of an
already started strand. The primer is a short segment of RNA synthesized by the enzyme
primase.
15. Explain the role of DNA polymerase, ligase, and repair enzymes in DNA proofreading and
repair. Enzymes proofread DNA during its replication and repair damage to existing DNA. In
mismatch repair, proteins proofread replication DNA and correct errors in base pairing. In
bacteria, DNA polymerase itself functions in mismatch repair, proofreading each nucleotide
against its template as soon as it is added to the strand. Upon finding an incorrectly paired a
nucleotide, the polymerase backs up, removes the incorrect nucleotide, and replaces it before
continuing synthesis.
In excision repair, a segment of the strand containing the damage is cutout by one repair enzyme,
and the result gap is filled in with nucleotides in the undamaged strand. The enzymes involved in
filling in the gap are DNA polymerase and DNA ligase.
DNA repair enzymes, for example in our skin cells is to repair genetic damage caused by the
ultraviolet rays of sunlight.
Chapter 17 - OBJECTIVES
4. Explain how RNA differs from DNA. DNA differs from RNA by their pentose sugars;
deoxyribose in DNA and ribose in RNA. A second difference is that RNA has the nitrogenous
base uracil in place of thymine.
5. In your own words, briefly explain how information flows from gene to protein. DNA controls
metabolism by commanding cells to make specific enzymes and other proteins. Information flows
from gene to protein by transcription and translation. Both nucleic acids and proteins are
informational polymers with linear sequences of monomers - nucleotides and amino acids,
respectfully.
6. Distinguish between transcription and translation. Transcription is the nucleotide -tonucleotide transfer of information from DNA to RNA. Translation is the informational transfer from
nucleotide sequence in RNA to amino acid sequence in a polypeptide.
7. Describe where transcription and translation occur in prokaryotes and in eukaryotes; explain
why it is significant that in eukaryotes, transcription and translation are separated in space and
time. In a prokaryotic cell, which lacks a nucleus, mRNA produced by transcription is immediately
translated without additional processing. In a eukaryotic cell, the two main steps of protein
synthesis occur in seperate compartments: transcription in the nucleus and translation in the
cytoplasm. Thus, mRNA must be translocated from the nuclear envelope. The RNA is first
synthesized as pre-mRNA, which is processed by enzymes before leaving the nucleus as
mRNA. This compartmentalization in eukaryotes provides an opportunity to modify mRNA in
various ways before it leaves the nucleus.
8. Define codon, and explain what relationship exists between the linear sequence of codons on
mRNA and the linear sequence of amino acids in a polypeptide. Codons are the mRNA base
triplets. For each gene, one of the two strands of DNA functions as a template for transcription.
The same base-pairing rules that apply to DNA synthesis also guide transcription, but the base
uracil takes place of thymine in RNA. During translation, the genetic message is read as a
sequence of base triplets, analogous to three-letter code words. Each of these triplets specifies
the amino acid to be added to the corresponding position along a growing protein chain.
9. List the three stop codons and the one start codon.
Stop codons: UAA; UAG; UGA
Start codon: AUG
10. Explain in what way the genetic code is redundant and unmistakable.
The genetic code is redundant in that codons may repeat themselves when growing into the
polypeptide chain. Genetic information is encoded as a sequence of non-overlapping base
triplets, each of which is translated into a specific amino acid during protein synthesis.
11. Explain the evolutionary significance of a nearly universal genetic code.
The near universality of the genetic code suggests that the code had already evolved in
ancestors common to all kingdoms in life.
12. Explain the process of transcription including the three major steps of initiation, elongation,
and termination.
Transcription begins at the initiation site when the polymerase separates the two DNA
strands and exposes the template strand for base pairing with RNA nucleotides. The RNA
polymerase works its way "downward" from the initiation site, prying apart the two strands of DNA
and elongation the mRNA in the 5’--->3’ direction. In the elongation stage, the participation of
protein factors occur in the cycle of 1) codon recognition 2) peptide bond formation 3)
translocation. In the wake of transcription, the two DNA strands re-form the double helix. The
RNA polymerase continues to elongate the RNA molecule until it reaches the termination site, a
specific sequence of nucleotides along the DNA that signals the end of the transciption unit. The
mRNA, a transcript of the gene is release, and the polymerase subsequently dissociates from the
DNA.
16. Distinguish among mRNA, tRNA, and rRNA. mRNA is messenger RNA functioning as a
genetic messenger from DNA to protein synthesizing machinery of the cell.
tRNA is transfer RNA, whose function is to transfer amino acids from the cytoplasm’s amino acid
pool to a ribosome.
rRNA is ribosomal RNA is formed by ribosomal subunits who are aggregates of numerous
proteins. rRNA is the most abundant type of rRNA.
26. Describe the difference between prokaryotic and eukaryotic mRNA.
In a prokaryotic cell, mRNA is produced by translation while transcription is in process. In
eukaryotic cells, mRNA is produced in the nucleus and must be translocated from nucleus to
cytoplasm. The RNA is first synthesized as pre-mRNA, which is processed by enzymes before
leaving the nucleus as mRNA. The nuclear envelope in eukaryotic cells separate transcription
and translation
28. Describe some biological functions of introns and gene splicing.
In RNA splicing, introns are removed and exons joined.
29. Explain why base-pair insertions or deletions usually have a greater effect than base-pair
substitutions.
Base-pair insertions are always disastrous, often resulting in frameshift mutations that disrupt
the codon messages downstream of the mutation. Base-pair substitutions within a gene have a
variable effect. Many substitutions are detrimental, causing missense or nonsense mutations.
30. Describe how mutagenesis can occur.
Errors in DNA replication, repair, or recombination can lead to base-pair substitutions,
insertions, or deletions. Mutations from such errors may spur. Mutagens, physical or chemical
agents, later interact with DNA to cause mutations, or mutagenesis.
Chapter 18 OBJECTIVES
2. List and describe structural components of viruses.
Most viruses consist of a genome enclosed in a protein shell. Viruses are not cells but generally
consist of nucleic acid enclosed in a protein shell called a capsid. The viral genome may be
single or double stranded DNA or single or double stranded RNA.
3. Explain why viruses are obligate parasites. Viruses are obligate intracellular parasites that use
the enzymes, ribosome’s and small molecules of host cells to synthesize multiple copies of
themselves.
5. Explain the role of reverse transcriptase in retroviruses.
Retroviruses are equipped with a unique enzyme called a reverse transcriptase, which can
transcribe DNA from an RNA template, providing an RNA ----->DNA information flow.
6. Describe how viruses recognize host cells.
Viruses identify their host cells by a "lock-and-key" fit between proteins on the outside of the virus
and specific receptor proteins on the outside of the virus and specific receptor molecules on the
surface of the cell.
7. Distinguish between lytic and lysogenic reproductive cycles using phage T4 and phage l as
examples. In the lytic cycle of phage replication, injection of a phage genome into a bacterium
programs the destruction of host DNA, the production of new viruses, and digestion of the
bacterial cell wall, which bursts and releases the new virus.
In a lysogenic cycle, temperate viruses insert their genome into the bacterial chromosome as a
prophage. In this innocuous form, the virus can be passed on to host daughter cells until it is
stimulated to leave the bacterial chromosome and initiate a lytic cycle.
11. Explain how viruses may cause disease symptoms, and describe some medical weapons
used to fight viral infections.
Emerging viruses may cause disease symptoms by infection of the body as the body makes
efforts at defending itself against the infection. The immune system is the basis for the major
medical weapon for preventing viral infections - vaccines. Vaccines are harmless variants or
derivatives of pathogenic microbes that stimulate the immune system to mount defenses against
the actual pathogen.
12. List some viruses that have been implicated in human cancers, and explain how tumor
viruses transform cells.
Tumor viruses insert viral DNA into host cell DNA, trigerring subsequent cancerous changes
through their own or host cell oncogones.
14. List some characteristics that viruses share with living organisms, and explain why viruses do
not fit our usual definition of life.
Viruses share the characteristic that they can be double stranded DNA or RNA. It is
however, very different from eukaryotic chromosome, which have linear DNA molecules
associated with a considerable amount of protein. Viruses do not fir our definition of life as they
lack in structures and most metabolic machinery found in cells. Most viruses are little more than
aggregates of nucleic acids and proteins - genes packed in protein coats.
16. Describe the structure of a bacterial chromosome.
The bacterial chromosome is a circular DNA molecule with few associated proteins.
Accessory genes are carried on smaller rings of DNA called plasmids.
18. List and describe the three natural processes of genetic recombination in bacteria.
Three natural processes of genetic recombination in bacteria are transformation, - the
alteration of a bacterial cell’s genotype by the uptake of naked, foreign DNA from the surrounding
environment - transduction - a recombination mechanisms in which phages transfer beacterial
genes from one hose cell to another - and conjugation - the direct transfer of genetic material
between two bacterial cells that are temporarily joined.
20. Explain how the F plasmid controls conjugation in bacteria.
In conjugation, a primitive kind of mating, an F+ cell transfers DNA to an F- cell. The transfer
is brought by the plasmid called the F plasmid, which carries genes for the sex pili and other
functions needed for mating. In an F+ cell, the F episome in integrated into the bacterial
chromosome, and the F+ cell will transfer chromosomal DNA along with the F episome DNA in
conjugation.
27. Briefly describe two main strategies cells use to control metabolism.
Cells control metabolism by regulating enzyme activity or by regulating enzyme synthesis
through the activation or inactivation of selected genes.
30. Distinguish between structural and regulatory genes.
A structural gene is a gene that codes for a polypeptide. A regulatory gene is the product of
a repressor. Transcription for the regulatory gene produces an mRNA molecule that is translated
into repressor protein. Regulatory genes are transcribed continuously.
Chapter 19 OBJECTIVES
1. Compare the organization of prokaryotic and eukaryotic genomes.
Prokaryotic DNA is usually circular, and the nucleoid it forms is so small that it can be seen
only with an elkectrion microscope. However, eukaryotic chromatin concists of DNA precisely
complezed with a large amount of protein.
2. Describe the current model for progressive levels of DNA packing.
DNA in association with histone, forms "beads on a string, " consisting of nucleosomes in an
extended configuration. each nucleosome has two molecules each of four types of histone. The
fifth histone may be present on DNA adjacent to the "bead". The 30-nm chromatin fiber is a tightly
wound coil with six nucleosomes per turn. Looped domains of 30-nm fibers are visible here
because compact chromosomes have been experimently unraveled. These multiple levels of
chromatin packing form the compact chromosome visible at metaphase.
4. Distinguish between heterochromatin and euchromatin.
Euchromatin is the more open, unraveled form of eukaryotic chromatin, which is available for
transcription. Heterochromatin is nontranscribed eukaryotic chromatin that is so highyl compacted
that it is visible with a light microscope during interphase.
Chapter 20 OBJECTIVES
1. Explain how advances in recombinant DNA technology have helped scientists study the
eukaryotic genome.
Advances in recombinant DNA technology have helped scientists study the eukaryotic
genome with cloning. Since most genes exist in only one copy per genome, the ability to clone
such rare DNA fragments has become a valuable tool in biological research.
2. Describe the natural function of restriction enzymes.
Restriction enzymes protect bacteria against intruding DNA from other organisms, such as
viruses or other bacterial cells as they work by cutting up the foreign DNA - restriction.
3. Describe how restriction enzymes and gel electrophoresis are used to isolate DNA fragments.
Gel electrophoresis separates macromolecules on the basic of the rate of movement through
a gel under the influence of an electric field. For example, the larger molecules move more slowly
through the gel and are located toward the bottom. The bands contain DNA restriction fragments.
Each fragment is a DNA cample digested with a different restriction enzyme. In every day life, we
use electrophoresis when looking at fingerprints.
7. List and describe the two major sources of genes for cloning.
The two major sources of genes for cloning include:
-DNA isolated directly from an organism
-complementary DNA made in the laboratory from mRNA templates. Scientists isolate DNA
directly by starting with all the DNA from cells of an organism with the gene they want and
constructing recombinant DNA molecules. The population of recombinant molecules formed is
then introduced into bacterial cells. The resulting set of thousands of plasmid clones is referred to
as a genomic library. Complementary DNA is DNA made in the laboratory using mRNA as a
template and the enzyme reverse transcpritase. Complementary DNA lacks introns and is
therefore smaller than the original gene and easier to clone. It is also much more likely to be
functional in bacterial cells, which lack the machinery for removing introns from RNA transcripts.
However, to be transcribed, the cDNA will have to be joined to an appropriate bacterial promoter
because no promoter will be present in the cDNA copy of the gene.
9. Describe how "genes of interest" can be identified with the use of a probe.
The selection of a desired gene in a recombinant DNA can be accomplished using
radioactively labeled nucleic acid segments of complementary sequence called probes.
10. Explain the importance of DNA synthesis and sequencing to modern studies of eukaryotic
genomes.
Recombinant DNA technology has enabled investigators to answer questions about
molecular evolution, probe details of gene organization and control, and produce and catalog
proteins of interest. Medical applications of recombinant DNA technology include the
development of diagnostic tests for detecting mutations that cause genetic disease.