Download Micro chpt. 9 notes

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CHAPTER 9
1.
a. The eukaryotic genome, which is contained within the cell nucleus, is the largest and typically a
linear double-stranded DNA divided into separate units, or chromosomes (e.g. human genome is
3 billion base pairs on 23 chromosomes). Replication is by DNA Polymerase. The prokaryotic
genome is loosely organized in the cytoplasm (nucleoid) and is typically a smaller, single, circular,
double-stranded DNA (e.g. S. aureus genome is 3 million base pairs on one chromosome).
Prokaryotes may also have small extrachromosomal DNA called plasmids (a few thousand base
pairs each). Replication is also by DNA Polymerase. Viruses have the smallest but most
variable genomes. Viral genomes are typically measures in thousands of bases and may be
either double- or single-stranded DNA or RNA. Replication of the viral genome relies on host
DNA Polymerase or viral enzymes such as reverse transcriptase.
b. For cells, the basic genetic material is in the form of an elongate strand of DNA that is defined by
several levels of organization. The entire collection of this genetic material (DNA) in a cell is what
constitutes its genome. The genome is organized into one or more individual units of DNA called
chromosomes. Each chromosome contains a series of informational modules--the genes. Each
gene exists as a specific sequence of nitrogen bases that guide the formation of a protein or
serve as a template for an RNA molecule.
2. In eukaryotes, DNA strands are spooled around proteins called histones. These structures undergo
several orders of coiling and supercoiling. For example, human DNA would be approximately six feet
in length if unwound but can be packaged into a small nucleus about 10 micrometers in diameter.
3. DNA strands have a direction called 5’3’, which indicates the orientation of the sugars in the sugarphosphate backbone. In order for two complementary strands of DNA to hybridize or form base
pairs, the strands must be oriented antiparallel, which means that they are oriented side-by-side but
in opposite 5’3’ directions.
4.
a. Assume that the right-hand side of the DNA molecule is where the strands separate, replication
begins, and the replication fork moves from right-to-left. The leading strand would be copied from
right-to-left (5’3’) in the same direction as the movement of the replication fork with use of the
top DNA strand as the template. The lagging strand would be copied from left-to-right (5’3’) in
the opposite direction from the movement of the replication fork with use of the bottom DNA
strand as the template but only when enough of the template is exposed.
b. Semiconservative replication describes the fact that the new double-stranded DNA molecules
produced by replication are composed of one original strand (template) and one new strand
(copy). Because replication follows the base-pairing rules, each daughter DNA molecule is
identical to the original parent.
5. DNA is a very stable molecule. The chemical bases that extend from the sugar-phosphate backbone
of each strand can pair with its complimentary base. Adenine pairs with thymine (2 hydrogen bonds)
and guanine pairs with cytosine (3 hydrogen bonds). Because adenine and guanine are purines
(large bases), there is exactly enough room between two DNA strands to pair with their
complimentary pyrimidines (small bases). Furthermore, complimentary strands of DNA can be easily
separated (breaking of hydrogen bonds) to create template DNA for replication; new hydrogen bonds
can form as the proper complimentary bases are inserted into position.
6. The expression of genes carried in DNA can be described as DNA  mRNA protein. DNA carries
all of the instructions for the cell. Each instruction called a gene is first transcribed into a similar
format, mRNA, and then translated into a protein.
Chapter 9
7. A gene is a recipe for making a protein in the cell. Each triplet of bases encodes an amino acid of the
new polypeptide. The ribosome with some help from tRNA molecules is responsible for translation of
the message.
8. A gene of 9,900 base pairs encodes a protein consisting of 3,300 amino acids. Each amino acid is
encoded by a three-base codon.
9. DNA typically exists in a double-stranded form and contains many genes (the genome). DNA
nucleotides contain the sugar deoxyribose and the bases adenine, cytosine, guanine, and thymine.
RNA typically exists in single-stranded form but may involve some intramolecular base pairing and
typically contains only a single gene, although the RNA in prokaryotes sometimes codes for a few
genes. RNA nucleotides contain the sugar ribose and the bases adenine, cytosine, guanine, and
uracil. A structural component of ribosomes (rRNA), RNA encodes proteins (mRNA) and plays a role
in translation (tRNA).
10.
a. Transcription begins at the promoter, a special sequence of bases in DNA upstream of the
encoded gene, which is recognized by RNA Polymerase.
b. The template strand of DNA is the strand from which the complimentary RNA sequence is
transcribed. The coding strand of DNA is the sequence identical to that of the RNA.
c.
Only one strand of DNA is transcribed because the RNA produced must be single-stranded to
function properly. Either strand of DNA can be transcribed throughout the genome but not for an
individual gene.
11. The start codon (AUG) is the codon that signifies the initiation of translation and encodes methionine,
the first amino acid of every polypeptide. There are three stop codons (UAA, UAG, UGA) that cause
termination of translation. There are no corresponding tRNAs for these codons; consequently, the
polypeptide is not elongated and the translation complex disassembles.
12.
a. mRNA codons
UAC CAG AUA CAC UCC CCU GCG ACU
tRNA anticodons
AUG GUC UAU GUG AGG GGA CGC UGA
Amino acids
Tyr Gln Ile His Ser Pro Ala Thr
b. mRNA codons
UAU CAA AUU CAU UCG CCC GCA ACA
The third base of the codon can typically be changed because the genetic code is redundant.
c.
The type and order of amino acids is shown in 13a.
13.
a. Bacterial genes are often organized in operons, a collection of genes transcribed as one mRNA
and whose expression is jointly controlled. The first codon, AUG, encodes formyl methionine.
Eukaryotic genes are each carried on their own mRNA molecule. The pre-mRNA contains exons
(coding regions) and introns (intervening non-coding sequences) that must be processed by
spicing out the introns and producing a mature mRNA for translation. The mRNA is also modified
with a polyA tail and a 5’ cap. The first codon, AUG, encodes a different form of methionine.
b. The pre-mRNA contains exons (coding regions) and introns (intervening non-coding sequences)
that must be processed by splicing out the introns and producing a mature mRNA for translation.
14.
a. An operon is a group of genes in prokaryotic DNA that is transcribed as a single unit and whose
expression is jointly controlled. The promoter is the site of transcriptional initiation and RNA
Polymerase binding. The operator sequence lies downstream of the promoter and serves to bind
regulator proteins (e.g. repressor) that impede progress of RNA Polymerase.
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Chapter 9
b. The lac operon is an inducible operon system. The binding of the lac repressor to the operator
sequence normally inhibits expression. When lactose is present, it binds to the lac repressor and
removes it from the operator. Expression is induced. In contrast, a repressible operon system
would normally be expressed until a substrate bound to a repressor protein, which then bound to
the operator to inhibit expression.
c.
For figure 9.18-- the lac operon--there are two events which would reverse the actions of the
operon:
1. If the bacterium has used up available lactose or encounters a new environment where
lactose is absent, this causes the repressor molecule to change configuration, becomes
functional, and insers at the operator gene, thereby blocking transcription and translation of
the structural genes and generally shutting down the operon and synthesis of enzymes.
2. If glucose is present , a second regulatory system inactivates the operon, even if lactose is
present. This is because the metabolic pathways are adapted to using glucose as the
preferred energy source.
For figure 9.19--a repressible operon--the operon is reversed when its product (the corepressor)
is present in very low concentrations. This could happen in a cell that was nutrient deprived or
not growing. The product is thus no longer available to bind the repressor, changing its shape.
The repressor is no longer able to fit its usual site on the operator gene, it falls away, and the
structural genes become open for transcription and translation. The enzymes that are needed to
synthesize product are now available, and new product is formed.
15. The Ames test screens chemicals for their carcinogenic potential. Auxotrophic mutant bacteria that
lack DNA repair mechanisms are exposed to the chemical and the rate of reversion to the wild type is
determined. If the rate is higher than the low spontaneous rate of reversion, then the chemical is
considered to be a mutagen.
16. Mutations occur in the following types: 1) a silent mutation, which is a single base change that does
not alter the encoded amino acid; 2) a missense mutation, which is a single base change that
changes the encoded amino acid; 3) a nonsense mutation, which is a single base change that
changes the amino acid codon to a stop codon; and 4) a frameshift mutation, which can arise from
insertions or deletions of bases in multiples of one or two. A missense mutation, which can be
beneficial because it might confer drug resistance without altering protein function. Nonsense and
frameshift mutations are often harmful because they alter the size and/or sequence of the protein,
typically rendering it nonfunctional.
17.
a. Conjugation is the transfer of replicated plasmid DNA through a sex pilus that is attached to a
recipient without pili. The donor retains a copy of the plasmid. Sometimes a segment of
chromosomal DNA is transferred during the process. Transformation is the acquisition of naked
DNA (plasmid or chromosomal fragments) from the external environment. Only competent cells
have this ability, induced either naturally (e.g. S. pneumoniae), chemically, or electrically (e.g.
calcium chloride or electroporation). Transduction is the transfer of DNA by a bacteriophage.
When a bacterial cell is infected, chromosomal fragments or plasmid DNA can become packaged
into bacteriophage particles. These particles transfer DNA but do not cause lytic infection.
Recipient cells are phage specific.
b. Generalized transduction (see Fig. 9.24) occurs during phage infection, in which random bacterial
chromosomal fragments become packaged as phage particles. These phage particles, while
much less numerous than normal phage, can transfer to new bacterial cells and the DNA can
become integrated into the host chromosome. Specialized transduction (see Fig. 9.25) occurs
when a prophage, which is integrated into a specific site in the chromosome, is excised;
occasionally it picks up a neighboring segment of chromosomal DNA. Every phage particle
produced contains the chromosomal DNA, and, when it is transferred to a new host cell, the
donated bacterial DNA becomes integrated into the host chromosome.
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Chapter 9
18. Transposons are “jumping genes,” or segments of DNA that encode their own excision and
integration (see Fig. 9.26). They can enter the cell on a plasmid, excise from the plasmid, and
integrate into the host chromosome. Transposons can then change position within the host
chromosome and eventually be inserted into a new plasmid for transfer to another host cell.
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