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Chapter 6
Lectures by
John Zamora
Middle Tennessee State University
2012 Pearson Education, Inc.
Molecular Biology
of Bacteria
Figure 6.3
DNA
REPLICATION
TRANSCRIPTION OF
BOTTOM STRAND
RNA
TRANSLATION
Protein
2012 Pearson Education, Inc.
Adenine (A)
Guanine (G)
Cytosine (C)
Thymine (T)
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
Figure 6.4
3-Hydroxyl
5-Phosphate
Hydrogen
bonds
Phosphodiester
bond
5-Phosphate
3-Hydroxyl
2012 Pearson Education, Inc.
Figure 6.5
Sugar
phosphate
backbone
3.4
nm
Major
groove
Figure 6.6
Inverted repeats
Loop
Stemloop
structure
Stem
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
Figure 6.8
Break one strand
Supercoiled
domain
Seal
Nick
Figure 6.9
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
Figure 6.10
lac operon
(lactose
degradation)
100/0
Origin of
replication
HfrH
P804
10
90
HfrC
20
Not1 restriction
sites, in kbp
80
70
KL14
trp operon
60
Hfr44
40
(tryptophan
biosynthesis
50
his operon
(histidine
biosynthesis)
2012 Pearson Education, Inc.
Figure 6.11
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
Figure 6.13
Semiconservative
replication
Parental
strand
New
strand
Figure 6.14
Base
Base
Growing
point
DNA
polymerase
activity
Deoxyribonucleoside
triphosphate
Base
Figure 6.16
RNA primer
Lagging
strand
Primase
Helicase
Free 3-OH
Single-strand
binding protein
DNA polymerase III
Leading
strand
RNA primer
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 helicase
Leading strand
template
Tau
Parental DNA
RNA primer
DNA primase
Lagging
strand
template
Single-strand
DNA-binding
proteins
DNA gyrase
Figure 6.24
Target sequence
DNA
polymerase
Heat
PCR
cycle
Copies of
target
sequence
Primers
Repeat cycle
Repeat cycle
Primer extension
108
107
106
105
104
103
102
10
2 4 6 8 10 12 14 16 18 20
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
Longer transcripts
Figure 6.26
RNA polymerase
(core enzyme)
Transcription
Sigma
mRNA start
1.
2.
3.
4.
5.
6.
35 sequence
Pribnow box
Consensus
Promoter sequence
2012 Pearson Education, Inc.
Figure 6.30
C-terminus
N-terminus
Peptide
bond
2012 Pearson Education, Inc.
Figure 6.29
-Carbon
Carboxylic
acid group
Amino
group
General structure of an
amino acid
Trp Tryptophan(W)
Ionizable: acidic
Ionizable: basic
Nonionizable polar
Nonpolar
(hydrophobic)
Figure 6.31
Alanine
tRNA
Anticodon
Wobble position;
base pairing more
flexible here
mRNA
Codon
2012 Pearson Education, Inc.
Figure 6.32
mRNA
Correct
0
Incorrect
1
Incorrect
1
2012 Pearson Education, Inc.
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
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
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
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
Figure 6.40
ATP
Improperly
folded
protein
ADP
DnaK
DnaJ
GroEL
GroES
Properly folded
(active) protein
ATP
ADP
Properly folded
(active) protein
2012 Pearson Education, Inc.
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