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Chapter 16
Virginia Gil
Period 3
12/3/02
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. At the time,
nucleic acids were believed to be 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:
- 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.
- Alfred Hershey and Martha Chase: Hershey and Chase established that it was DNA
that functioned as the phages’ genetic material. Viral proteins, labeled with radioactive
sulfur, remained outside the host cell during infection.
- 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.
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), and then 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 nitrogenous bases with two organic rings (adenine with guanine)
and are twice as wide as Pyrimidines. Pyrimidines (Cytosine and Thymine) 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 hydrogen bond 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.
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 in turn are paired in the interior of the double helix.
9. Explain, in their own words, semiconservative replication, and describe the MeselsonStahl experiment.
Semiconservative replication has to do 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.
Single-strand binding proteins then attach in chains along the unpaired DNA strands,
holding these templates straight until new complementary strands can be synthesized.
Helicase is the enzyme that works at the crotch of the replication fork, untwisting the
double helix and separating the two "old" strands.
11. Explain what energy source drives endergonic synthesis of DNA.
I learned this concept in my previous biology course.
12. Define antiparallel, and explain why continuous synthesis of both DNA strands is not
possible.
The two DNA strands are antiparallel; to be precise, 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’. The enzyme 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.
Chapter 17
4. Explain how RNA differs from DNA.
DNA differs from RNA by their pentose sugars; deoxyribose in DNA and ribose in
RNA. Also, 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 -to-nucleotide 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 base, 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 given 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 proposes 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 separates 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
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, ribosomes and
small molecules of host cells to synthesize multiple copies of them.
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 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, triggering 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 bacterial 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 Fcell. 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
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. During interpahse, the
chromatin fibers are usually highly extended and tangled. Eukaryotic chromosomes
contain an enormous amount of DNA relative to their length.
2. Describe the current model for progressive levels of DNA packing.
First, 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 experimentally 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 highly compacted that it is visible with a light microscope during interphase.
Chapter 20
1. Explain how advances in recombinant DNA technology have helped scientists study
the eukaryotic genome.
Advances in recombinant DNA technology have helped scientists with
cloning. Since most genes exist in only one copy per genome, something on the order
of one part 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.
In nature, restriction enzymes protect bacteria against intruding DNA from other
organisms, such as viruses or other bacterial cells. They work by cutting up the foreign
DNA, a process called 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. In an 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 sample
digested with a different restriction enzyme.
7. List and describe the two major sources of genes for cloning.
The two major sources of genes for cloning are DNA isolated directly from an
organism and complementary DNA made in the laboratory from mRNA templates.
Scientists isolate DNA directly by starting with the entire 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.