Lecture 6

6.1 Macromolecules and Genetic

Information
6.2 DNA Structure: The Double Helix
6.3 DNA Structure: Supercoiling
6.4 Genetic Elements
Figure 6.1
Figure 6.2a
Figure 6.2b
Figure 6.3
Base pairing between A and T
Figure 6.4
Base pairing between G and C
Figure 6.4
Hydrogen bonds
Figure 6.5
Complementary,
antiparallel,
twisted in a helix
(10 bp/turn)
The Double Helix
Figure 6.6
Figure 6.7a
Secondary Structure
Figure 6.7b
Figure 6.8
Sticky ends
Figure 6.9
hairpin
Figure 6.10
Figure 6.12
Genetic Elements (Table 6.1)
Chromosome
long, usually circular, double-stranded DNA
Plasmid
short, usually circular, double-stranded DNA
Viral genome
single- or double-stranded DNA or RNA
Transposable element
double-stranded DNA, found within another DNA
molecule, can move from one site to another
Inset Figure 1
Isolation of DNA
Inset Figure 2
UV Absorbance of DNA
Fluorescent Dye for DNA
Density Gradient Centrifugation
Agarose Gel Electrophoresis
Inset Figure 3
Insert Figure 5
Reassociation of Denatured DNA
Insert Figure 7
Lecture 6
6.5 Restriction and Modification of DNA
6.6 DNA Replication
6.7 Transcription: The Basic Process in
Bacteria
6.8 Transcription: Other Patterns and
Inhibition
Restriction and Modification of
DNA
Restriction enzymes cleave DNA at specific
sequences (usually palindromes), are meant
to protect the cell from foreign DNA
Their own DNA is protected by methylation
(i.e. modification) of the specific sequence
EcoR1 Recognition Site
Figure 6.13
see http://www.neb.com for detailed information about restriction enzymes
Figure 6.14
Initiation of DNA synthesis
Figure 6.15
template
new
DNA polymerase carries out
this reaction -- cannot begin
a new chain
Primer added by
primase enzyme
Figure 6.16
Bidirectional replication
DNA Replication Fork
Figure 6.17
leading strand
Figure 6.18
The Lagging Strand
Polymerase III
Figure 6.18
Ligase
Figure 6.19
Figure 6.20
Figure 6.21
35 exonuclease
activity of DNA pol III
Proofreading
Figure 6.22
Replication of Linear DNA
Transcription
Figure 6.25
Note: no requirement for primer
Figure 6.26
Promoter
Transcription Termination
Figure 6.27
Figure 6.29
Typical Archaeal Promoter
Lecture 6
6.10 The Genetic Code
6.11 Transfer RNA
6.12 Translation: The Process of Protein
Synthesis
6.13 Translation: Alternatives and Errors
Figure 6.34
The Wobble Concept
3 Different Reading Frames
Figure 6.35
Figure 6.36a
Structure of Transfer RNA
Figure 6.36b
Figure 6.37
Aminoacyl-tRNA synthetase
activity
Table 6.6 Ribosome Structure
Property Prokaryote Eukaryote
Overall Size 70S 80S
Small subunit 30S 40S
No. of proteins ~21 ~30
RNA size (No. of bases) 16S (1500) 18S (2300)
Large subunit 50S 60S
No. of proteins ~34 ~50
RNA size (No of bases) 23S (2900)
5S (120
28s (4200
5.8S (160)
5S (120)
Figure 6.38
Figure 6.39
Polysome
Figure 6.40
Molecular Chaperone
Codon Usage
Organisms have preferred codons for each
amino acid
For a given organism, some codons are
used very often, while others are used rarely
This codon preference is a unique trait of
the organism
Codon preference can be used to determine
whether a newly sequenced region actually
encodes a gene