Download Binary fission of bacteria

Central dogma: Information flow
in cells
Nucleotides
• Pyrimidine bases: Cytosine (C), Thymine
(T), Uracil (U, in RNA)
• Purine bases: Adenine (A), Guanine (U)
Prokaryotic gene coding
Eukaryotic processing of rRNA
A-T hydrogen bonding
G-C hydrogen bonding
Genetic Elements
• Prokaryotes: Chromosome, plasmid, viral
genome, transposable elements
• Eukaryotes: Chromosomes, plasmid,
mitochondrion or chloroplast genome, viral
genome, transposable elements
Melting of DNA
• Melting means separation of two strands from the
heteroduplex
• Melting temperature of DNA is dependent on the
relative number of AT and GC pairs
• Melted DNA can hybridize at temperatures below
melting temperature
– This process can be used to test relatedness between
species (interspecies DNA-DNA hybridization)
– It is also possible to reanneal DNA with rRNA to test
relatedness of one species rRNA with the rRNA genes
of another species
**DNA structure overview**
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complementary strands (antiparallel)
3 Angstrom separation of hydrogen bonds
sugar phosphate backbone held together with hydrogen bonding
between bases
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size is expressed in nucleotide bases pairs. E. coli has 4600 kbp.
(E. coli chromosome is > 1mm, about 500X longer than the cell itself.
How can the organism pack so much DNA into its cell?
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each bp takes up to 0.34nm, and each helix turn is 10bp(or 34
Angstroms), therefore how long is l kb of DNA? and how many turns
does it have?
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supercoiled DNA (DNA-binding proteins)
DNA Organization
• In prokaryotes: naked circular DNA with negative
supercoiling
– Negative supercoiling is introduced by DNA gyrase
(topoisomerase II)
– Topoisomerase I relaxes supercoiling by way of singlestrand nicks
• In eukaryotes: linear DNA packaged around
histones in units called nucleosomes
– The coiling around histones causes negative
supercoiling
Restriction and modification
DNA Replication: addition of a
nucleotide
Semiconservative replication
Initiation of DNA replication
Origin of replication= oriC = ~300bp
Templates, primers, polymerase, primase
DNA Replication
Bidirectional replication
Okazaki fragments
Proofreading by DNA
polymerase III
Replication overview
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1. origin of replication+ 300 bases, recognized by specific initiation proteins =
replication fork
2. bidirectional, therefore leading and lagging strands
helicase unwinds the DNA a little (ATP-dependant)
single-strand binding protein prevents single strand from reannealing
Primase, DNA polymerase III and DNA polymerase I (also 5' to 3'
exonuclease activity), ligase
Okazaki fragments
Topoisomerases, and supercoiling regulation
3. Proofreading (3 to 5' exonuclease activity by DNA pol III)
DNA Sequencing
Transcription
• RNA plays an important role
• tRNA, mRNA, rRNA
• Name three differences between chemistry
of RNA and DNA
• RNA has both functional and genetic roles
Initiation of Transcription
Pribnow box=tataat
Transcription
Completion of transcription
Example of termination sequence
More transcription
• Polycistronic mRNA
• How can mRNA be used in microbial
ecology?
• Antibiotics and RNA polymerases
RNA processing
• Removal of introns
• Ribozymes (nobel prize-Tom Cech and Sid
Altman)
• RNA-splicing enzymes
• Origins of life? Which came first RNA or
DNA?
The genetic code
• Notice that the wobble base generally
makes minor changes in the amino acid
• AUG is the start code (formyl methionine)
for bacteria
• UAA, UAG, UGA are stop codons
• Specific tRNA for each other codon
tRNA associated with codon
~60 specific tRNAs
in prokaryotes
mRNA, tRNA and ribosomes
Shine Dalgarno sequence
GTP and Elongation Factors (EF)
Growing protein polymer
Translocation
Role of rRNA in protein
synthesis
• Structural and functional role
• 16S rRNA involved in initiation
– Base pairing occurs between ribosome binding
sequence on the mRNA and a complementary
seq on the 16S rRNA
• 23S rRNA involved in elongation
– Interacts with EFs
Overview of today
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Summarized basic DNA structure
DNA replication
DNA sequencing
Transcription
RNA processing
Translation
Role of rRNA in protein synthesis