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CHAPTER 16

List the three components of a nucleotide.
A phosphate, a sugar and a base.

Distinguish between deoxyribose and ribose.
Deoxyribose and Ribose are both five-carbon sugar components that
alternate with phosphate groups to form the backbone of the polymer and
bind to the nitrogenous bases. However, deoxyribose is present in DNA
whereas ribose is found in RNA.

List the nitrogen bases found in DNA, and distinguish between pyrimidine and
purine.
Adenine, Guanine, Thymine and Cytosine. Purine include Adenine and
Guanine whereas pyrimidine include Thymine and Cytosine.
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
Explain the "base-pairing rule" and describe its significance.
The base-pairing rule says explains that A must pair with T and that G
pairs with C. It is significant because it explains Chargaff’s rule, it
suggests the general mechanisms for DNA replication. If bases of specific
pairs, the information on one strand compliments the other, it dictates the
combination of complementary base pairs, but places restriction on the
linear sequence of nucleotides along the length of a DNA strand. The
sequence of the bases can be highly variable, which makes it suitable for
coding genetic information. Also, though hydrogen bonds between paired
bases are weak bonds, collectively they stabilize the DNA molecule.
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
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.
DNA is a helix with a uniform width of 2 nm. This width suggested that it
had two strands. Purine and pyramidine bases are stacked .34 nm apart.
The helix makes one full turn every 3.4 nm along its length. There are ten
layers of nitrogenous base pairs in each turn of the helix. Enzymes link
the nucleotides together at their sugar-phosphate groups. Hydrogen bonds
hold the bases together.
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
Explain, in your own words, semiconservative replication
Watson and Crick’s model is a semiconservative model for DNA
replication. They predicted that when a double helix replicates, each of
the two daughter molecules would have one old or conserved strand from
the parent molecule and one newly created strand.
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
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 that
have a specific sequence of nucleotides. Specific proteins required to
initiate replication bind to each origin. The DNA double helix opens at
the origin and replication forks spread in both directions away from the
central initiation point creating a replication bubble. Then, new
nucleotides align themselves along the templates of the old DNA strands.
DNA polymerase links the nucleotides to the growing strands. Exergonic
hydrolysis of the phosphate bond drives the endergonic synthess of DNA
and provides the required energy to from the new covalent linkages
between the neucleotides. Helicases are enzymes which catalyze
unwinding fo the parental double helix to expose the template.Ligase and
primase are enzymes that play an important role in the replication of
DNA.
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
Define antiparallel
The sugar phosphate backbones of the two complementary DNA strands
run in opposite directions; that is, they are antiparallel.
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
Distinguish between the leading strand and the lagging strand.
The leading strand is the DNA strand which is synthesized as a single
polymer in the 5’ -> 3’ direction towards the replication fork. The lagging
strand is the DNA strand that is discontinuously synthesized against the
overall direction of replication.
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
Explain how the lagging strand is synthesized when DNA polymerase can add
nucleotides only to the 3’ end.
Lagging strand is produced as a series of short segments called Okazaki
fragments, which are each synthesized in the 5’ -> 3’ direction. Okazaki
fragments are 1000 to 2000 nucleotides long in bacteria and 100 to 200
nucleotides lon in eukaryotes. The many fragments ligated by DNA ligase
, a linking enzyme that catalyzes the formation of a covalent bond between
the 3’ end of each new Okazaki fragment to the 5’ end of the growing
chain.
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
Explain the role of DNA polymerase, ligase, and repair enzymes in DNA
proofreading and repair.
If a segment of DNA becomes damaged, excision repair can help. The
damaged segment is excised by one repair enzyme and the remainding gap
is filled in by base-pairing nucleotides with the undamaged strand. DNA
polymerase and DNA ligase are enzymes that catalyze the filling in
process.
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CHAPTER 17

Explain how RNA differs from DNA.
Ribonucleic acid (RNA) links DNA’s genetic instructions for making
proteins to the process of protein synthesis. It copies or transcribes the
message from DNA and then translates that message into a protein RNA,
like DNA, is a nucleic acid or a polymer of nucleotides. RNA structure
differs from DNA in the following ways: the five carbon sugar in RNA
nucleotides is ribose rather than deoxyribose and the nitrogenous base
uracil is found in place of thymine.

In your own words, briefly explain how information flows from gene to protein.
Information flows from gene to protein through two major processes,
transcription and translation. Transcription is the synthesis of RNA using
DNA as a template. A gene’s unique nucleotide sequence is transcribed
from DNA to a complementary nucleotide sequence in mRNA. The
resulting mRNA carries this transcript of protein building instructions to
the cell’s protein synthesizing machinery. Translation is the synthesis of a
polypeptide, which occurs under the direction of mRNA.

Distinguish between transcription and translation.
Transcription- The transfer of information from DNA molecule into an
RNA molecule
Translation- The transfer of information from an RNA molecule into a
polypeptide, involving a change of language from nucleic acids to amino
acids.

Describe where transcription and translation occur in prokaryotes and in eukaryotes.
Prokaryotes
Transcription: Cytoplasm
Translation: Cytoplasm
Eurokaryotes
Transcription: Nucleus
Translation: Cytoplasm

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.
Codon- A three-nucleotide sequence of DNA or mRNA that specifies a
particular amino acid or termination signal; the basic unit of the genetic code.
For each 3 letters it equals an amino acid. It consists of three bases coding
for 61 amino acids.
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
Explain the process of transcription including the three major steps of initiation,
elongation, and termination.
Initiation- The RNA polmerses attaches to promoter regions on the DNA
and begins to unzip the DNA into two strands. A promoter region for
mRNA transcriptions contains the sequence T-A-T-A (called TATA Box)
Elongation- Occurs as the RNA polymerase unzips the DNA and
assembles RNA nucleotides using one strand of the DNA as a template. As
in DNA replication, elongation of the RNA molecules occurs in the 5’  3’
direction. In contrast to DNA replication, new nucleotides are RNA
nucleotides (rather than DNA nucleotides), and only one DNA strand is
transcribed.
Termination- Occurs when the RNA polymerase reaches a special sequence
of nucleotides that serve as a termination point. In eukaryotes, the
termination region often contains the DNA sequence AAAAAAA

Describe the general role of RNA polymerase in transcription.
It pry the two strands of DNA apart and hook together the RNA nucleotides
as they base-pair along the DNA template

Distinguish among mRNA, tRNA, and rRNA.
mRNA (Messenger RNA)- Is a single strand of RNA that
provides the template used for sequencing amino acids into a
polypeptide.
tRNA (Transfer RNA)- Is a short RNA molecule (consisting of about 80
nucleotides) that is used for transporting amino acids to their proper place
on the mRNA template.
rRNA (Ribosomal RNA)- Nolecules are the building blocks of ribosomes.
The nucleolus is an assemblage of DNA actively being transcribed into
rRNA

Describe the structure of tRNA and explain how the structure is related to
function.
Interactions among various parts of the tRNA molecules reslt in basepairings between nucleotides, folding the tRNA in such a way that it forms
a three-dementional molecule. (In two dimensions, a tRNA resembles the
three the three-leaflets of a clover leaf.) The 3’ end of the mRNA. Exact
base-paring between the third nucleotides of the tRNA anticodons and the
third nucleotide of the mRNA codon is often not required. This “wobble”
allows the anticodon of some tRNAs to base-pair with more than one kind
of codon. As a result, about 45 different tRNAs base-pair with 64 different
codons.

Given a sequence of bases in DNA, predict the corresponding codons transcribed
on mRNA and the corresponding anticodons of tRNA.
AAA GTA
CTC
ATG
GAT
CCC UGC
AGA
CGU
UCG
Proline Cysteine Arginine Leucine Serine

Describe the structure of a ribosome, and explain how this structure relates to
function.
Ribosomes have three binding sites—one for the mRNA, one for a tRNA
that carries a growing polypeptide chain (P site, for “polypeptide), and one
for a second tRNA that delivers that next amino acid that will be inserted
into the growing polypeptide chain (A site, for “amino acid”)

Describe the difference between prokaryotic and eukaryotic mRNA.
Prokaryotic
mRNA is produced by transcription
Eukaryotic
First it produces Pre-mRNA, and then develops mRNA, but it later
has to go from the nucleus to the cytoplasm

Explain how eukaryotic mRNA is processed before it leaves the nucleus.
mRNA must be translocated from nuclus to cytoplasm

Explain why base-pair insertions or deletions usually have a greater effect than basepair substitutions.
N/A
CHAPTER 18

List and describe structural components of viruses.
Viral Genomes- Their genomes may consist of double stranded DNA,
single stranded DNA, double stranded RNA, or single stranded RNA.
Capsids and Envelopes- The protein shell that encloses the viral genome is
called a capsid. They are built from a large number of protein subunits
called capsomeres. Influenza viruses, and many other viruses found in
animals, have viral envelopes, membranes cloaking their capsids. They are
derived from membrane of the host cell.

Explain why viruses are obligate parasites.
Viruses are obligate intracellular parasites; they can only reproduce within
a host cell. An isolated virus is unable to replicate itself- or do anything
else, for that matter, except infect an appropriate host cell.

Explain the role of reverse transcriptase in retroviruses.
Retro viruses are equipped with a unique enzyme called reverse
transcriptase, which can transcribe DNA from an RNA template,
providing an RNA – DNA information flow.

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 molecules on the surface
of the cell.

Distinguish between lytic and lysogenic reproductive cycles using phage T4 and
phage l as examples.
A reproduction cycle of a virus that culminates in death of the host cell is
known as a lytic cycle. It begins when the tail fibers of a T4 virus stick to
specific receptor sites on the outer surface of an E.coli cell. The sheath of
the tail then contracts, thrusting a hollow core through the wall and
membrane of the cell. The phage injects its DNA into the cell, leaving an
empty capsid as a “ghost” outside the cell. Once infected, the E.coli cell
quickly begins to transcribe and translate the viral genes. Nucleotides
salvaged from the cell’s degraded DNA are recycled to make copies of the
phage genome. The phage parts come together, and three separate sets of
proteins assemble to form phage heads, tails, and tail fibers. The phage
then directs production of an enzyme that digests the bacterial cell wall.
With a damaged cell wall, osmosis causes the cell to swell and finally
burst, releasing 100 to 200 phage particles.
In contrast to the lytic cycle, the lysogenic cycle reproduces the viral
genome without destroying the host. Infection of an E.coli cell by lambda
begins when the phage binds to the surface of the cells and injects its
DNA. Within the host, the lambda DNA molecules forms a circle. What
happens next depends on the type of reproductive mode; lytic or
lysogenic. During lysogenic cycle, the lambda DNA molecule is
incorporated into a specific site of the host cell’s chromosomes, and it is
then known as a prophage. Bacteria reproduce normally, copying the
prophage and transmitting it to daughter cells. Then many cell divisions
produce a colony of bacteria infected with prophage.

Explain how viruses may cause disease symptoms, and describe some medical
weapons used to fight viral infections.
Some viruses damage or kill cells by causing the release of hydrolytic
enzymes from lysosomes. Some viruses cause the infected cells to produce
toxins that lead to diseases symptoms, and some have toxic components
themselves, such as envelope proteins. Vaccines are harmless variants or
derivatives of pathogenic microbes that stimulate the immune system to
mount defenses against the actual pathogen. Adenine arabinosideis is an
antiviral drug that interferes with viral nucleic acid synthesis. Another is
acyclovir, which seems to inhibit herpesvirus DNA synthesis.

List some viruses that have been implicated in human cancers, and explain how
tumor viruses transform cells.
Some viruses that have been implicated in human cancers are hepatitis B,
Epstein-Barr, papilloma and HTLV-1. All tumor viruses transform cells
through the integration of viral nucleic acid into host cell DNA.

List some characteristics that viruses share with living organisms, and explain
why viruses do not fit our usual definition of life.
An isolated virus is biologically inert, unable to replicated its genes or
regenerate its own supply of ATP. Yet it has a genetic program written in
the universal language of life. Although viruses are obligate intracellular
parasites that cannot reproduce independently, it is hard to deny their
evolutionary connection to the living world.

Describe the structure of a bacterial chromosome.
The major component of the bacterial genome is one double stranded
DNA molecule arranged in a circle. It has a dense region of DNA called
nucleoid. Many bacteria also have plasmids, which have a small number
of genes.

List and describe the three natural processes of genetic recombination in bacteria.
Transformation- the alteration of a bacterial cell’s genotype by the uptake
of naked, foreign DNA from the surrounding environment. Transductionphages transfer bacterial genes from one host cell to another. Conjugationthe direct transfer of genetic material between two bacterial cells that are
temporarily joined.

Explain how the F plasmid controls conjugation in bacteria.
The F plasmid is required for the production of sex pili. It can convert an
F- cell to F+.

Briefly describe two main strategies cells use to control metabolism.
Metabolic control occurs on two levels. First, cells can vary the numbers
of specific enzyme molecules; that is. They can regulate the _expression
of a gene. Second, cells can vary the activities of enzymes already present.

Distinguish between structural and regulatory genes.
Structural genes are genes that code for polypeptides. Regulatory genes
regulate the operation of the genes.
CHAPTER 1 9

Compare the organization of prokaryotic and eukaryotic genomes.
Although both prokaryotic and eukaryotic cells contain hereditary in the
form of double-stranded DNA, their genomes are organized differently.
Prokaryotic DNA is usually circular, and the nucleoid it forms is so small
that it can be seen only with an electron microscope. In contrast,
eukaryotic chromatin consists of DNA precisely complexed with a large
amount of protein.

Describe the current model for progressive levels of DNA packing.
Nucleosomes- DNA, in association with histone, forms ‘beads on a
string”, consisting of nucleosomes in an extended configuration. 30-nm
chromatin fiber- is tightly wound coil with six nucleosomes per turn.
Looped domains- of 30-nm fibers are visible here because a compact
chromosome has been experimentally unraveled. Metaphase
chromosome- theses multiple levels of chromatin packing form the
compact chromosome, visible at metaphase.

Distinguish between heterochromatin and euchromatin.
Heterochromatin is nontranscribed eukaryotic chromatin that is so highly
compacted that it is visible with a light microscope during interphase.
Euchromatin is the more open, unraveled form of eukaryotic chromatin,
which is available for transcription.
CHAPTER 20

Explain how advances in recombinant DNA technology have helped scientists
study the eukaryotic genome.
Recombinant DNA technology refers to the set of techniques for
recombining genes from different sources in vitro and transferring this
recombinant DNA into a cell where it may be expressed. The use of
recombinant DNA techniques allows modern biotechnology to be a more
precise and systematic process than earlier research methods.

Describe the natural function of restriction enzymes.
Restriction enzymes occur naturally in bacteria where they protect the
bacterium against intruding DNA from other organisms.

Describe how restriction enzymes and gel electrophoresis are used to isolate DNA
fragments.
Restriction enzymes cut the DNA and through gel electrophoresis, the
DNA travels a distance according to its size.

List and describe the two major sources of genes for cloning.
DNA isolated directly from an organism and complementary DNA made
in the laboratory from mRNA templates.
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
Describe how "genes of interest" can be identified with the use of a probe.
Through a process called hybridization
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
Explain the importance of DNA synthesis and sequencing to modern studies of
eukaryotic genomes.
N/A