Molecular Biology of Bacteria

LECTURE PRESENTATIONS
For BROCK BIOLOGY OF MICROORGANISMS, THIRTEENTH EDITION

Michael T. Madigan, John M. Martinko, David A. Stahl, David P. Clark
Chapter 6
Lectures by
John Zamora
Middle Tennessee State University
2012 Pearson Education, Inc.
Molecular Biology
of Bacteria
I. DNA Structure and Genetic Information
6.1 Macromolecules and Genes

6.2 The Double Helix
6.3 Supercoiling
6.4 Chromosomes and Other Genetic Elements

Functional unit of genetic information is the gene
Genes are in cells, and are composed of DNA

Three informational macromolecules in cell
DNA
RNA
Protein

Genetic information flow can be divided into three
stages
Replication: DNA is duplicated (Figure 6.3)
Transcription: information from DNA is transferred
to RNA
mRNA (messenger RNA): encodes polypeptides
tRNA (transfer RNA): plays role in protein synthesis
rRNA (ribosomal RNA): plays role in protein
synthesis
Translation: information in RNA is used to build

polypeptides
Figure 6.3
DNA
REPLICATION
TRANSCRIPTION OF
BOTTOM STRAND
RNA
TRANSLATION
Protein

Central dogma of molecular biology
DNA to RNA to protein
Eukaryotes: each gene is transcribed

individually
Prokaryotes: multiple genes may be
transcribed together

Four nucelotides found in DNA (Figure 6.1):
Adenine (A)
Guanine (G)
Cytosine (C)
Thymine (T)
Backbone of DNA chain is alternating phosphates

and the pentose sugar deoxyribose
Phosphates connect 3-carbon of one sugar to
5-carbon of the adjacent sugar
Figure 6.1
Pyrimidine bases
Cytosine
(C)
Thymine
(T)
Uracil
(U)
Purine bases
Adenine
(A)
Guanine
(G)
5 position
Nitrogen base
attached to
1 position
3 position
Phosphodiester
bond
Phosphate
Ribose
H only
in DNA
Deoxyribose

All cells and some viruses have DNA in
double- stranded molecule (Figure 6.4)
Two strands are antiparallel
Two strands have complementary base
sequences
Adenine always pairs with Thymine
Guanine always pairs with Cytosine
Two strands form a double helix (Figure 6.5)
Figure 6.4
3-Hydroxyl
5-Phosphate
Hydrogen
bonds
Phosphodiester
bond
5-Phosphate
3-Hydroxyl
Figure 6.5
One helical turn

(10 base
pairs)
Minor
groove
Sugar
phosphate
backbone
3.4
nm
Major
groove

Size of DNA molecule is expressed in base
pairs
1,000 base pairs = 1 kilobase pairs = 1 kbp
1,000,000 base pairs = 1 megabase pairs =
1Mbp
E. coli genome = 4.64 Mbp
Each base pair takes up 0.34 nm of length
along the helix
10 base pairs make up 1 turn of the helix

Inverted Repeats (Figure 6.6)
Repeated sequence that is arranged in an
inverse orientation
Stem Loops (Figure 6.6)

Short double-helical regions caused by
nearby inverted repeats
Common in RNA, but not DNA
Figure 6.6
Inverted repeats
Loop
Stemloop
structure
Stem

Hydrogen bonds between DNA strands hold two
strands together
AdenineThymine pair has two hydrogen bonds
and GuanineCytosine pair has three hydrogen
bonds
GC pairs are stronger than AT pairs
High heat breaks hydrogen bonds, causing

denaturation (melting; Figure 6.7)
GC-rich DNA melts at higher temperatures than
AT-rich DNA
Figure 6.7
Single strands
1.2
A260
Melting
1.0
Tm 85.0
Double
strand
0.8
72
76
80
84
C
88
92
96
6.3 Supercoiling
Supercoiled DNA: DNA is further twisted to
save space (Figure 6.8)
Negative supercoiling: double helix is
underwound
Positive supercoiling: double helix is
overwound
Relaxed DNA: DNA has number of turns

predicted by number of base pairs
Negative supercoiling is predominantly found
in nature
DNA Gyrase: introduces supercoils into DNA
(Figure 6.9)
Figure 6.8
Break one strand
Rotate one end of broken

strand around helix and seal
Supercoiled circular DNA

Relaxed, covalently closed
circular DNA
Proteins
Break one strand
Supercoiled
domain
Seal
Nick
Relaxed, nicked circular DNA

Chromosomal DNA
with supercoiled domains
Figure 6.9
DNA gyrase makes

double-strand break
One part
of circle
is laid
over the
other
Relaxed
circle
Helix
makes
contact
in two
places
Unbroken
helix is
passed
through
the break
Double-strand
break resealed
Following
DNA gyrase
activity, two
negative
supercoils
result
Supercoiled
DNA
6.4 Chromosomes and Other Genetic

Elements
Genome: entire complement of genes in cell
or virus
Chromosome: main genetic element in
prokaryotes
Other genetic elements include virus
genomes, plasmids, organellar genomes, and
transposable elements

Elements
Viruses contain either RNA or DNA genomes
Can be linear or circular
Can be single or double stranded
Plasmids: replicate separately from chromosome

Great majority are double stranded
Most are circular
Generally beneficial for the cell (e.g., antibiotic
resistance)
NOT extracellular, unlike viruses

Elements
Chromosome is a genetic element with
housekeeping genes
Presence of essential genes is necessary for
a genetic element to be called a chromosome
Plasmid is a genetic element that is

expendable and rarely contains genes for
growth under all conditions

Elements
Transposable Elements
Segment of DNA that can move from one site to
another site on the same or a different DNA
molecule
Inserted into other DNA molecules
Three main types:
Insertion sequences
Transposons
Special viruses
II. Chromosomes and Plasmids

6.5 The Escherichia coli Chromosome
6.6 Plasmids: General Principles
6.7 The Biology of Plasmids

Escherichia coli is a useful model organism
for the study of biochemistry, genetics, and
bacterial physiology
The E. coli chromosome from strain MG1655
has been mapped using conjugation,
transduction, molecular cloning, and
sequencing (Figure 6.10)
Figure 6.10
lac operon
(lactose
degradation)
100/0
Origin of
replication
HfrH
P804
10
90
HfrC
20
Not1 restriction
sites, in kbp
80
Escherichia coli K-12

30
70
KL14
trp operon
60
Hfr44
40
(tryptophan
biosynthesis
50
his operon
(histidine
biosynthesis)

Some features of the E. coli chromosome
Many genes encoding enzymes of a single
biochemical pathway are clustered into operons
Operons equally distributed on both strands
~5 Mbp in size
~40% of predicted proteins are of unknown
function
Average protein contains ~300 amino acids
Insertion sequences (IS elements)

Plasmids: genetic elements that replicate
independently of the host chromosome
(Figure 6.11)
Small circular or linear DNA molecules
Range in size from 1 kbp to >1 Mbp; typically
less than 5% of the size of the chromosome
Carry a variety of nonessential, but often very
helpful, genes
Abundance (copy number) is variable
Figure 6.11

A cell can contain more than one plasmid, but
it cannot be closely related genetically due to
plasmid incompatibility
Many incompatibility (Inc) groups recognized
Plasmids belonging to same Inc group
exclude each other from replicating in the
same cell but can coexist with plasmids from
other groups

Some plasmids (episomes) can integrate into
the cell chromosome; similar to situation seen
with prophages
Removal (curing) plasmids from host cells
can result from various treatments
Conjugative plasmids can be transferred
between suitable organisms via cell-to-cell
contact
Conjugal transfer controlled by tra genes on
plasmid

Genetic information encoded on plasmids is
not essential for cell function under all
conditions but may confer a selective growth
advantage under certain conditions

R plasmids
Resistance plasmids; confer resistance to
antibiotics and other growth inhibitors
(Figure 6.12)
Widespread and well-studied group of
plasmids
Many are conjugative
Figure 6.12
mer
Replication
functions
sul
str
IS1
94.3/0 kbp
IS1
25 kbp
75 kbp
tra
cat
50 kbp
IS10
IS10
oriT
tet
Tn10

In several pathogenic bacteria, virulence
characteristics are encoded by plasmid genes
Virulence factors
Enables pathogen to colonize

Enables pathogen to cause host damage
Hemolysin
Enterotoxin

Bacteriocins
Proteins produced by bacteria that inhibit or
kill closely related species or even different
strains of the same species
Colicin, nisin
Genes encoding bacteriocins are often

carried on plasmids
III. DNA Replication

6.8 Templates and Enzymes
6.9 The Replication Fork
6.10 Bidirectional Replication and the
Replisome
6.11 The Polymerase Chain Reaction (PCR)

DNA replication is semiconservative (Figure 6.13)
Each of the two progeny double helices have one
parental and one new strand
Precursor of each nucleotide is a

deoxynucleoside 5-triphosphate (dNTP;
Figure 6.14)
Replication ALWAYS proceeds from the 5 end to
the 3 end
Animation: DNA Replication: Synthesis

Figure 6.13
Semiconservative
replication
Parental
strand
New
strand
Figure 6.14
Base
Base
Growing
point
DNA
polymerase
activity
Deoxyribonucleoside
triphosphate
Base

DNA polymerases catalyze the addition of
dNTPs
Five different DNA polymerases in E. coli
DNA polymerase III is primary enzyme
replicating chromosomal DNA
DNA polymerases require a primer

Primer made from RNA by primase
6.9 The Replication Fork

DNA synthesis begins at the origin of replication
in prokaryotes
Replication fork: zone of unwound DNA where
replication occurs (Figure 6.16)
DNA helicase unwinds the DNA
Extension of DNA
Occurs continuously on the leading strand
Discontinuously on the lagging strand
Okazaki fragments are on lagging strand
Figure 6.16
RNA primer
Lagging
strand
Primase
Helicase
Free 3-OH
Single-strand
binding protein
DNA polymerase III
Leading
strand
RNA primer

Replisome
DNA synthesis is bidirectional in prokaryotes
Two replication forks moving in opposite
directions (Figure 6.20)
DNA Pol III adds 1,000 nucleotides per

second
Replisome: complex of multiple proteins
involved in replication (Figure 6.22)
DNA pulled through the replisome
Figure 6.20
Movement
of fork
Origin (DnaA
binding site)
Replication
fork
Lagging
Leading
Leading
Lagging
Replication
fork
Origin
Figure 6.22
Direction of
new synthesis
Newly synthesized
strand
RNA primer
DNA polymerase III
DNA helicase
Leading strand
template
Tau
Parental DNA
RNA primer
DNA polymerase III
DNA primase
Newly synthesized strand

Direction of
new synthesis
Lagging
strand
template
Single-strand
DNA-binding
proteins
DNA gyrase

Replisome
DNA replication is extremely accurate
Proofreading helps to ensure high fidelity
Mutation rates in cells are 1081011 errors per

base inserted
Polymerase can detect mismatch through
incorrect hydrogen bonding
Proofreading occurs in prokaryotes, eukaryotes,
and viral DNA replication systems
6.11 The Polymerase Chain Reaction

The polymerase chain reaction (PCR) is
basically DNA replication in a test tube
Conceived by Kary Mullis
Also called DNA amplification

Steps in PCR (Figure 6.24)
Add DNA
Add primer
Add DNA polymerase
Taq polymerase or Pfu polymerase
Heat and cool

Heat and cool
Figure 6.24
Target sequence
DNA
polymerase
Heat
PCR
cycle
Copies of
target
sequence
Primers
Repeat cycle
Repeat cycle
Copies of target sequence
Primer extension
108
107
106
105
104
103
102
10
2 4 6 8 10 12 14 16 18 20
Number of PCR cycles

Applications of PCR
Phylogenetic studies
Surveying different groups of environmental
organisms
Amplifying small amounts of DNA
Identifying a specific bacteria
Looking for a specific gene
IV. RNA Synthesis: Transcription
6.12 Overview of Transcription

6.13 Sigma Factors and Consensus Sequences
6.14 Termination of Transcription
6.15 The Unit of Transcription

Transcription (DNA to RNA) is carried out by
RNA polymerase
RNA polymerase uses DNA as template
RNA precursors are ATP, GTP, CTP, and UTP
Chain growth is 5 to 3 just like DNA replication

Only one of the two strands of DNA are
transcribed by RNA polymerase for any gene
Genes are present on both strands of DNA,
but at different locations
RNA polymerase has five different subunits
RNA polymerase recognizes DNA sites called
promoters

Promoters: site of initiation of transcription
Recognized by sigma factor of RNA polymerase
Transcription stops at specific sites called

transcription terminators
Unlike DNA replication, transcription involves
smaller units of DNA
Often as small as a single gene
Allows cell to transcribe different genes at
different rates
Figure 6.25
RNA
polymerase
(core
enzyme)
Promoter
region
Sigma recognizes
promoter and
initiation site
Sigma
factor
Gene(s) to be transcribed
light green strand)
Transcription begins;
sigma released. RNA
chain grows
Sigma
RNA
Termination site
reached; chain
growth stops
DNA Short transcripts

Polymerase
and RNA
released
Longer transcripts
Transcription: The Process
Animation: The Process of Transcription
6.13 Sigma Factors and Consensus

Sequences
Sigma factors recognize two highly conserved
regions of promoter (Figure 6.26)
Two regions within promoters that are highly
conserved:
Pribnow box: located 10 bases before the start of
transcription (10 region)
35 region: located ~35 bases upstream of
transcription
Figure 6.26
RNA polymerase
(core enzyme)
Transcription
Sigma
mRNA start
1.
2.
3.
4.
5.
6.
35 sequence
Pribnow box
Consensus
Promoter sequence
6.14 Termination of Transcription

Termination of RNA synthesis is governed by
a specific DNA sequence
Intrinsic terminators: transcription is
terminated without any additional factors
Rho-dependent termination: Rho protein
recognizes specific DNA sequences and
causes a pause in the RNA polymerase

Unit of transcription: unit of chromosome
bounded by sites where transcription of DNA to
RNA is initiated and terminated
Most genes encode proteins, but some RNAs
are not translated (i.e., rRNA, tRNA)
Three types of rRNA: 16S, 23S, and 5S
rRNA and tRNA are very stable
tRNA cotranscribed with rRNA or other tRNA
mRNAs have short half-lives (a few minutes)

Prokaryotes often have genes clustered together
These genes are transcribed all at once as a
single mRNA
An mRNA encoding a group of cotranscribed

genes is called a polycistronic mRNA
Operon: a group of related genes cotranscribed
on a polycistronic mRNA
Allows for expression of multiple genes to be
coordinated
V. Protein Structure and Synthesis

6.16 Polypeptides, Amino Acids, and the
Peptide Bond
6.17 Translation and the Genetic Code
6.18 Transfer RNA
6.19 Steps in Protein Synthesis
6.20 The Incorporation of Selenocysteine and
Pyrrolysine
6.21 Folding and Secreting Proteins

Peptide Bond
Proteins play a major role in cell function
Catalytic proteins (enzymes)
Structural proteins
Proteins are polymers of amino acids

Amino acids are linked by peptide bonds to
form a polypeptide (Figure 6.30)
Figure 6.30
C-terminus
N-terminus
Peptide
bond

Peptide Bond
The linear array of amino acids in a
polypeptide is called its primary structure
The chemical properties of the amino acid are
related to their side chain (Figure 6.29)
The diversity of amino acids make possible
an enormous number of unique proteins with
different biochemical properties
Figure 6.29
-Carbon
Carboxylic
acid group
Amino
group
Gly Glycine (G)

Asp Aspartate (D)
General structure of an
amino acid
Ala Alanine (A)

Glu Glutamate (E)
Val Valine (V)
Lys Lysine (K)
Leu Leucine (L)
Pyl Pyrrolysine (O)
Ser Serine (S)
Ile Isoleucine (I)
Thr Threonine (T)
Met Methionine (M)
Asn Asparagine (N)
Arg Arginine (R)

Phe Phenylalanine(F)
His Histidine (H)
Gln Glutamine (Q)
Trp Tryptophan(W)
Cys Cysteine (C)

Sec Selenocysteine (U)
Ionizable: acidic
Ionizable: basic
Tyr Tyrosine (Y)
Nonionizable polar
Nonpolar
(hydrophobic)
Structure of the amino acid

R groups
Pro Proline (P)
(Note: Because proline lacks a free amino

group, the entire structure of this amino
acid is shown, not just the R group).

Translation: the synthesis of proteins from RNA
Genetic code: a triplet of nucleic acid bases
(codon) encodes a single amino acid
Specific codons for starting and stopping
translation
Degenerate code: multiple codons encode a
single amino acid
Anticodon on tRNA recognizes codon
Wobble: irregular base pairing allowed at third
position of tRNA (Figure 6.31)
Figure 6.31
Alanine
tRNA
Anticodon
Wobble position;
base pairing more
flexible here
Key bases in codon:

anticodon pairing
mRNA
Codon

Stop codons: terminate translation (UAA, UAG,
and UGA)
Start codon: translation begins with AUG
Reading frame: triplet code requires translation to
begin at the correct nucleotide (Figure 6.32)
ShineDalgarno sequence: ensures proper
reading frame
Open reading frame (ORF): AUG followed by a
number of codons and a stop codon in the same
reading frame
Figure 6.32
mRNA
Correct
0
Incorrect
1
Incorrect
1

Codon bias: multiple codons for the same
amino acid are not used equally
Varies with organism
Correlated with tRNA availability
Cloned genes from one organism may not be
translated by recipient organism because of
codon bias
Some organelles and a few cells have

slight variations of the genetic code
(e.g., mitochondria of animals, Mycoplasma,
and Paramecium)
6.18 Transfer RNA

Transfer RNA: at least one tRNA per amino acid
Bacterial cells have 60 different tRNAs
Mammalian cells have 100110 different tRNAs
Specific for both a codon and its cognate

amino acid
tRNA and amino acid brought together by
aminoacyl-tRNA synthetases
ATP is required to attach amino acid to tRNA
tRNA is cloverleaf in shape (Figure 6.33)
Figure 6.33
Acceptor stem
Acceptor
end
TC loop
Acceptor
end
Acceptor
stem
D loop
D loop
Anticodon
stem
TC loop
Anticodon
stem
Anticodon
Codon
mRNA
Anticodon loop
A
A Anticodon
mG
6.18 Transfer RNA

Anticodon: three bases of tRNA that
recognize three complementary bases on
mRNA
Fidelity of recognition process between tRNA
and aminoacyl-tRNA synthetase is critical
(Figure 6.34)
Incorrect amino acid could result in a faulty or
nonfunctioning protein
Figure 6.34
Uncharged
tRNA-specific
for valine
(tRNAVal)
Amino acid
(valine)
tRNA acceptor stem
Anticodon
region
AMP
C
A
C
Linkage of valine
to tRNAVal
Aminoacyl-tRNA
synthetase for
valine
AMP
Valine
Charged
valyl tRNA,
ready for
protein
synthesis
Anticodon
loop
C
A
C

Ribosomes: sites of protein synthesis
Thousands of ribosomes per cell
Composed of two subunits (30S and 50S in
prokaryotes)
S = Svedberg units
Combination of rRNA and protein
E. coli has 52 distinct ribosomal proteins

Translation (Figure 6.35) is broken down into
three main steps:
1. Initiation: two ribosomal subunits assemble with
mRNA
Begins at an AUG start codon
2. Elongation: amino acids are brought to the

ribosome and are added to the growing
polypeptide
Occurs in the A and P sites of ribosome
Translocation: movement of the tRNA holding the
polypeptide from the A to the P site

Steps of Translation (contd)
3. Termination: occurs when ribosome reaches
a stop codon
Release factors (RF): recognize stop codon and
cleave polypeptide from tRNA
Ribosome subunits then dissociate
Subunits free to form new initiation complex and
repeat process
Polysomes: a complex formed by ribosomes

simultaneously translating mRNA (Figure 6.36)
Figure 6.35
TRANSLATION: Initiation
A site
Initiator
tRNA
P site
GTP
mRNA
Large 50S
subunit
E site
Add large
subunit
Ribosome
binding site
(RBS)
Small 30S
subunit
Small 30S
subunit
Initiation complex
TRANSLATION: Elongation
Gro
w
ing
po
lyp
ept
id
Incoming
tRNA
E site
e
mRNA
Codon
recognition
GTP
P site
P site
A site
A site
Cycle continues
three times
P site
GTP
Peptide bond
formation
Translocation
P site
A site
P site
A site
A site
Figure 6.36
Growing polypeptide
mRNA
Nearly finished
polypeptide

Many antibiotics inhibit translation by interacting
with ribosomes
Streptomycin, chloramphenicol, tetracycline, etc.
Many antibiotics are specific for organisms from
one or two domains (e.g., chloramphenicol is
specific for Bacteria)
Animation: The Process of Translation

6.20 The Incorporation of Selenocysteine

and Pyrrolysine
Universal genetic code encodes 20 amino acids
More than 100 different amino acids have been
found in proteins
Most are made through posttranslational
modification
Others are inserted during protein synthesis

Once formed, a polypeptide folds to form a more
stable structure.
Secondary structure
Interactions of the R groups force the molecule to
twist and fold in a certain way (Figure 6.38)
Tertiary structure
3-dimensional shape of polypeptide (Figure 6.39)
Quaternary structure
Number and types of polypeptides that make a
protein
Figure 6.38
Amino
terminus
Hydrogen
bonds
between
nearby
amino acids
Amino acids in
a polypeptide
-Helix
-Sheet
Hydrogen bonds
between distant
amino acids
Figure 6.39
A chain
-Helix
B chain
-Sheet
Insulin
Ribonuclease

Denaturation
When proteins are exposed to extremes of
heat, pH, or certain chemicals
Causes the polypeptide chain to unfold
Destroys the secondary, tertiary, and/or
quaternary structure of the protein
The biological properties of a protein are

usually lost when it is denatured

Most polypeptides fold spontaneously into
their active form
Some require assistance from molecular
chaperones or chaperonins for folding to
occur (Figure 6.40)
They only assist in the folding, are not
incorporated into protein
Can also aid in refolding partially denatured
proteins
Figure 6.40
ATP
Improperly
folded
protein
ADP
DnaK
DnaJ
GroEL
GroES
Properly folded
(active) protein
ATP
ADP
Properly folded
(active) protein

Signal sequences: found on proteins requiring
transport from cell (Figure 6.41)
1520 residues long

Found at the beginning of the protein molecule
Signal the cells secretory system (Sec system)
Prevent protein from completely folding
Figure 6.41
Membrane
Translational
apparatus
SecA
Periplasm
Protein
Protein secreted
into periplasm
Ribosome
Protein contains
signal sequence
mRNA
Protein inserted
into membrane
Signal
recognition
particle
Protein does
not contain
signal sequence
Membrane
secretion
system

Secretion of Folded Proteins: The Tat System
Proteins that fold in the cytoplasm are
exported by a transport system distinct from
Sec, called the Tat protein export system
Ironsulfur proteins
Redox proteins

Molecular Biology of Bacteria

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Molecular Biology of Bacteria

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LECTURE PRESENTATIONS

For BROCK BIOLOGY OF MICROORGANISMS, THIRTEENTH EDITION

I. DNA Structure and Genetic Information

6.1 Macromolecules and Genes

2012 Pearson Education, Inc.

6.1 Macromolecules and Genes

2012 Pearson Education, Inc.

6.1 Macromolecules and Genes

2012 Pearson Education, Inc.

6.1 Macromolecules and Genes

Translation: information in RNA is used to build

6.1 Macromolecules and Genes

Eukaryotes: each gene is transcribed

2012 Pearson Education, Inc.

6.2 The Double Helix

Backbone of DNA chain is alternating phosphates

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2012 Pearson Education, Inc.

6.2 The Double Helix

Two strands form a double helix (Figure 6.5)

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One helical turn

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6.2 The Double Helix

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6.2 The Double Helix

Stem Loops (Figure 6.6)

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2012 Pearson Education, Inc.

6.2 The Double Helix

High heat breaks hydrogen bonds, causing

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Relaxed DNA: DNA has number of turns

Rotate one end of broken

Supercoiled circular DNA

Relaxed, nicked circular DNA

DNA gyrase makes

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6.4 Chromosomes and Other Genetic

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6.4 Chromosomes and Other Genetic

Plasmids: replicate separately from chromosome

6.4 Chromosomes and Other Genetic

Plasmid is a genetic element that is

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6.4 Chromosomes and Other Genetic

II. Chromosomes and Plasmids

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6.5 The Escherichia coli Chromosome

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Escherichia coli K-12

6.5 The Escherichia coli Chromosome

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6.6 Plasmids: General Principles

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2012 Pearson Education, Inc.

6.6 Plasmids: General Principles

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6.6 Plasmids: General Principles

6.7 The Biology of Plasmids

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6.7 The Biology of Plasmids

2012 Pearson Education, Inc.