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
DNA Replication: addition of a
nucleotide
DNA duplex formation
A-T hydrogen bonding
G-C hydrogen bonding
3D structure of DNA
Inverted repeats in DNA
Formation of Stem-loops
“Sticky ends”
Hairpins
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
Reannealing DNA
**DNA structure overview**
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complementary strands (antiparallel)
3 Angstrom separationof hydrogen bonds
sugar phosphate backbone held together with hydrogen bonding
between bases
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?
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?
inverted repeats, stem-loop, hairpins, sticky ends
supercoiled DNA (DNA-binding proteins)
relaxed, nicked circular DNA
Supercoiled and relaxed DNA
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
Codon and Anticodon; Wobble
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
Chaperones (heat-shock proteins)
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