Chapter 11

Mechanisms of
Microbial Genetics
 Terminology
• Genetics: the study of what genes are, how
they carry information, how information is
expressed, and how genes are replicated
• Gene: a segment of ________that encodes a
functional product, usually a ____________
• Chromosome: structure containing DNA that
physically carries hereditary information; the
chromosomes contain the genes
• Genome: ___ the genetic information in a cell
 Terminology
• Genomics: the molecular study of genomes
• Genotype: the genes of an organism p 431
• Phenotype: _______________ of the genes
 DNA p 422-3
• Polymer of nucleotides: adenine, thymine,
cytosine, and guanine p 423
• Double helix associated with ___________
• “Backbone” is deoxyribose-phosphate
• Strands are held together by ________ bonds
between AT and CG
• Strands are antiparallel
• __________________________
Figure 8.3a _____ replication. P 420
5′ end 3′ end
Parental
strand Parental
strand

1
1 The double helix of the parental
DNA separates as weak hydrogen Replication
bonds between the nucleotides on fork

opposite strands break in response

to the action of replication
Insert Fig 8.3a
2 enzymes.

2 Hydrogen bonds form

between new complementary 2
nucleotides and each strand
of the parental template to
form new base pairs.
3
3 Enzymes catalyze the formation
of sugar-phosphate bonds Daughter
5′ end 3′ end
between sequential strand
Parental
Parental
nucleotides on each resulting daughter strand strand
Daughter
strand. strand
forming

The replication fork

 New Template
Strand Strand

Sugar

Phosphate
1

Insert Fig 8.4

2

Hydrolysis of the phosphate

bonds provides the energy
for the reaction.
When a nucleoside
triphosphate bonds to
the sugar, it loses two
phosphates.
 DNA Synthesis
• DNA is copied by DNA polymerase
– In the __'  __' direction
– Initiated by an RNA ____________________
– Leading strand is synthesized continuously
– Lagging strand is synthesized discontinuously
– ____________________ fragments
– RNA primers are removed and Okazaki fragments
joined by a DNA polymerase and DNA ligase
Figure 8.5 A summary of events at the DNA replication ____________ 1:40

DNA polymerase

Replication
fork
Inser Fig 8.5
RNA primer
Primase

DNA polymerase

Okazaki fragment DNA ligase

DNA
polymerase
Table 8.1 Important ________ in DNA Replication, Expression, and Repair

Insert Table 8.1

Figure 8.6 Replication of _________________________ DNA.
Replication forks

REPLICATION

An E. coli chromosome
1 in the process of replicating
Origin of replication

Parental strand Daughter strand

Replication fork
Replication fork

Termination of
replication

Bidirectional replication of a circular bacterial DNA molecule

 Transcription
• DNA is transcribed to make RNA (mRNA,
tRNA, and __________________)
• Transcription begins when RNA polymerase
binds to the ________________ sequence
• Transcription proceeds in the 5'  3' direction
• Transcription stops when it reaches the
terminator sequence
Figure 8.7 The process of transcription.

RNA polymerase

DNA

TRANSCRIPTION

DNA

mRNA

1 Protein RNA polymerase bound to DNA

Promoter (gene begins)

Template
RNA polymerase strand of DNA
1 RNA polymerase binds to the
promoter, and DNA unwinds at
the beginning of a gene.
Insert Fig 8.7

2 RNA is synthesized by complementary base

pairing of free nucleotides with the
nucleotide bases on the template strand of RNA
DNA. RNA
nucleotides
3 The site of synthesis moves
along DNA; DNA that has been RNA synthesis
transcribed rewinds.

4 Transcription reaches the

terminator.

Terminator
5 RNA and RNA polymerase are released, and
(gene ends)
the DNA helix re-forms.
Figure 8.11 RNA processing in ________________ cells. P 460

Exon Intron Exon RNA polymerase

Intron Exon
DNA
Met
Met
1 In the nucleus, a geneDNA
composed
Met
of exons and introns
is transcribed to RNA by RNA polymerase.

RNA
transcript

1
2 Processing involves snRNPs in the nucleus to remove
the intron-derived RNA and splice together the exon-
derived RNA into mRNA.

Insert Fig 8.11

mRNA
Met

3 After further modification, the mature mRNAMet

travels to the cytoplasm, where it
directs protein synthesis.

Nucleus

Cytoplasm
 Translation
• mRNA is translated in _______ (three nucleotides)
• Translation of mRNA begins at the start codon: AUG
• Translation ends at _____ codons: UAA, UAG, UGA
Figure 8.9.1-2 The process of ____________________.

RNA polymerase
TRANSLATION Ribosome
Met
DNA
Leu
mRNA
DNAMet
Ribosomal P Site
subunit tRNA
Protein

Anticodon
1
Ribosomal Start Second mRNA
mRNA
subunit codon codon

1 Components needed to begin
Insert
translation come together.
2 On the assembled ribosome, a tRNA carrying the first
Fig 8.9 (1) and
amino acid (2)
is paired with the start codon on the mRNA.
The place where this first tRNA sits is called the P site.
A tRNA carrying the second amino acid approaches.
Figure 8.9.3-4 The process of translation.

Peptide bond forms

Met
Met Phe

Met Leu
A site DNAMet Leu Gly

E site

1 mRNA
mRNA Ribosome moves
along mRNA

3 The second codon of the mRNA pairs with a tRNA carrying 4 The ribosome moves along the mRNA until the second tRNA is
the second amino acid at the A site. The first amino acid in the P site. The next codon to be translated is brought into the
Insert Fig 8.9 (3) and (4)
joins to the second by a peptide bond. This attaches the A site. The first tRNA now occupies the E site.
polypeptide to the tRNA in the P site.
Figure 8.9.5-6 The process of translation.

tRNA released Met Growing

Met Leu
Gly
polypeptide chain
Leu Phe
Gly Met
Phe

mRNA

Insert Fig 8.9 (5) and (6) mRNA

5 The second amino acid joins to the third by another peptide 6 The ribosome continues to move along the mRNA,
bond, and the first tRNA is released from the E site. and new amino acids are added to the polypeptide.
The process of translation.

Polypeptide
Met Gly Met
Arg
released
Gly
Met
Met
Phe

Phe
Gly
Arg
mRNA
New protein

mRNA
Insert Fig 8.9 (7) and (8)
Stop codon

7 When the ribosome reaches a stop codon, 8 Finally, the last tRNA is released, and the ribosome comes
the polypeptide is released. apart. The released polypeptide forms a new protein.
Figure 8.10 Simultaneous transcription and translation in ____________.
TRANSLATION RNA polymerase

DNA
Met
Met

mRNA
Met DNAMet

Protein

RNA Ribosome Peptide

Insert Fig 8.10

Met Met

Met
Met

Direction of transcription RNA DNA

polymerase

5′

Peptide
Polyribosome

Ribosome

mRNA
Direction of translation
 Regulation
• Constitutive genes are expressed at a ______
rate
• Other genes are expressed only as needed
– _____________________ genes
– Repressible genes
– Catabolite repression
The Lactose Operon (_________)

Figure 7.18
The Tryptophan Operon (_______)

Figure 7.19
 Attenuation in the Tryp Operon

• When tryptophan is __________, translation of the short leader

peptide encoded by trpL proceeds, the terminator loop between
regions 3 and 4 forms, and transcription terminates. When tryptophan
levels are depleted, translation of the short leader peptide stalls at
region 1, allowing regions 2 and 3 to form an antiterminator loop, and
RNA polymerase can transcribe the structural genes of the trp operon.
Figure 8.14 The growth rate of E. coli on glucose and __________________.

Bacteria growing on glucose

as the sole carbon source
grow faster than on lactose.

Log10 of number of cells

Glucose

Lactose

Time

Bacteria growing in a medium

All glucose
consumed
containing glucose and lactose
first consume the glucose and
then, after a short lag time, the
Log10 of number of cells

lactose. During the lag time,

intracellular cAMP increases,
Lactose used
the lac operon is transcribed,
Glucose Lag more lactose is transported
used time
into the cell, and
β-galactosidase is synthesized
to break down lactose.

Time
Figure 8.15 Positive regulation
Promoter
of the ___________ operon.

lacI lacZ
DNA
CAP-binding site RNA Operator
polymerase
can bind
and transcribe
cAMP

Active
CAP Inactive lac
repressor
Inactive
CAP
Lactose present, glucose scarce (cAMP level high). If glucose is scarce, the
high level of cAMP activates CAP, and the lac operon produces large amounts of mRNA for
lactose digestion.
Promoter
lacI lacZ
DNA

CAP-binding site RNA Operator

polymerase
can't bind

Inactive lac
Inactive
repressor
CAP
Lactose present, glucose present (cAMP level low). When glucose is present,
cAMP is scarce, and CAP is unable to stimulate transcription.
Types of _____________________
 The Frequency of Mutation
• Spontaneous mutation rate = 1 in ___ replicated
base pairs or 1 in 106 replicated genes
• Mutagens increase to 10–5 or 10–3 per replicated
gene
Nitrous acid

Adenine ->

ANIMATION Mutations: Types

 Mutagens
• Radiation
– Ionizing radiation – induces breaks in chromosomes
– Nonionizing radiation – induces ________ dimers
• Chemical Mutagens
– Nucleotide analogs – disrupt DNA and RNA
replication and cause point mutations
– Nucleotide-altering chemicals – result in base-pair
substitution mutations and missense mutations
– Frameshift mutagens – result in _______ mutations
DNA Repair

Figure 7.24
Figure 8.25 Griffith’s experiment demonstrating genetic ______________.
P 413-414
RECOMBINATION

Living encapsulated bacteria Living nonencapsulated Heat-killed encapsulated Living nonencapsulated and heat-killed
injected into mouse. bacteria injected into mouse. bacteria injected into mouse. encapsulated bacteria injected into
mouse.

Mouse died. Mouse remained healthy. Mouse remained healthy. Mouse died.

Colonies of encapsulated
bacteria were isolated from
dead mouse.
A few colonies of non-
encapsulated bacteria were
isolated from mouse; phagocytes
destroyed nonencapsulated
bacteria.
No colonies were isolated Colonies of encapsulated
from mouse. bacteria were isolated from
dead mouse.
Figure 8.26 The mechanism of genetic transformation
Recipient cell
in bacteria.

Chromosomal DNA

DNA fragments
from donor cells
Recipient cell takes
up donor DNA.

Donor DNA aligns

with complementary
bases.

Recombination occurs
between donor DNA
and recipient DNA.

Degraded
unrecombined
DNA

Genetically transformed cell

Bacterial Transformation

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Figure 8.27 Bacterial ____________________________.

Mating
Bacterial ________________

Figure 7.31
Bacterial Conjugation

Figure 7.32
 Transposons and Transposition
• Segments of DNA that move from one location to
another in the same or different molecule
• Result is a kind of frameshift insertion
• Transposons all contain palindromic sequences at
each end
• Simplest transposons are insertion sequences
which have no more than two ________ repeats
and gene for transposase
• ______ transposons contain one or more genes not
connected with transposition (e.g. antibiotic
resistance)
Figure 8.31a-b Transposons and insertion.
IS1

Transposase gene

Inverted repeat Inverted repeat

(a) An insertion sequence (IS), the simplest transposon, contains a gene for
transposase, the enzyme that catalyzes transposition. The tranposase gene is bounded
at each end by inverted repeat sequences that function as recognition sites for the
transposon. IS1 is one example of an insertion sequence, shown here with simplified IR
sequences.

Tn5

Kanamycin resistance

IS1 IS1
(b) Complex transposons carry other genetic material in addition to transposase genes.
The example shown here, Tn5, carries the gene for kanamycin resistance and has
complete copies of the insertion sequence IS1 at each end.
Figure 8.31c Transposons and insertion.

Transposase gene

_________________ cuts DNA, leaving sticky ends.

IS1

IS1
Sticky ends of transposon and target DNA anneal.
(c) Insertion of the transposon Tn5 into R100 plasmid
Transposons: Shifting Segments of the Genome

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Transduction

Figure 7.30
Generalized Transduction

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Specialized Transduction

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