The document discusses molecular information flow in microorganisms. It describes the central dogma of DNA to RNA to protein, with the three main steps being replication, transcription, and translation. Replication copies DNA, transcription transfers genetic information from DNA to RNA, and translation uses the information in mRNA to form a polypeptide on the ribosome. The genetic elements in bacteria are usually a single circular chromosome and sometimes additional plasmids.

1. Molecular Information Flow
in Microorganisms

2. Gene, Genetic Elements, and Genomes
• The functional unit of genetic information
is the gene
• Genes make up parts of chromosomes or
other large molecules known collectively
as genetic elements
• The total complement of genetic elements
is the genome (chromosome)

3. Central Dogma
DNA begets RNA begets Protein

4. Central Dogma
1. Replication. During replication, the
DNA double helix is duplicated.
Replication is catalyzed by the
enzyme DNA polymerase.
2. Transcription. The transfer of
genetic information from DNA to
RNA. Transcription is catalyzed by
the enzyme RNA polymerase.
3. Translation. The formation of a
polypeptide using the genetic
information transferred to mRNA by
DNA is a process that occurs on the
ribosome.

5. Central Dogma
• In Eukaryotes, replication and
transcription occur in nucleus
(because no ribosomes there).
• In Bacteria and Archaea, it all
happens in cytoplasm, and a
ribosome initiates translation of
an mRNA before RNA
polymerase has finished
synthesizing it.
• Allows for rapid cell growth

6. Genetic Elements

7. Chromosomes
• Bacteria and Archaea
(mostly) have a single,
circular chromosome.
• Contains all (or most) of the
organism’s genes
• Eukaryotes have (multiple),
linear chromosomes.

8. Plasmids
• Many Bacteria and Archaea
contain plasmids in addition
to their chromosome
• Thousands of different
plasmids are known
• Most plasmids are circular,
but many are linear and vary
in size from approximately 1
kbp to more than 1 Mbp

9. Plasmids
• Pathogenic bacteria express a
variety of plasmid-encoded
virulence factors that assist them
in establishing infections.
• Sometimes plasmids encode
properties essential to the
ecology of the bacterium.
• Nitrogen fixation in Rhizobium
• Genes for degradation of
hydrocarbons or toxic pollutants,
such as polychlorinated biphenyls
(PCBs) and herbicides or other
pesticides

10. DNA Replication
• Replication is a
semiconservative process
• The two resulting double helices
each consist of one new strand
and one parental strand
• DNA replication always
proceeds from the 5’ end to
the 3’ end
• the 5’-phosphate of the incoming
nucleotide being attached to the
3’-hydroxyl of the previously
added nucleotide

11. DNA Replication
• Enzymes that catalyze the
polymerization of deoxynucleotides
are called DNA polymerases
• All DNA polymerases synthesize DNA
in the 5’ to 3’ direction, but none of
them can initiate a new chain de novo
• They can only add a nucleotide
onto a preexisting 3’-OH group
• To start a new DNA chain, a
primer is required
• A nucleic acid molecule to which DNA
polymerase can attach the first
nucleotide

12. Transcription
• Transcription transforms the
genetic information inscribed in
DNA into RNA
• Yields three main forms of RNA:
• messenger (mRNA),
• transfer (tRNA),
• ribosomal (rRNA)

13. Transcription in Bacteria
• Transcription is catalyzed by
the enzyme RNA
polymerase
• During elongation of an RNA
chain, ribonucleoside
triphosphates are added to
the 3’-OH of the ribose of the
preceding nucleotide.
• Thus chain growth is 5’ to 3’,
just as in DNA synthesis

14. Transcription in Bacteria
• RNA polymerase uses DNA as a
template
• For any given gene, only one of
the two strands is transcribed
• Unlike DNA polymerase, RNA
polymerase can initiate new
RNA on its own
• Unlike DNA replication,
transcription occurs on much
smaller units of DNA, often as
little as a single gene
Cryo-electron micrograph of Escherichia coli RNA polymerase
with sigma factor

15. Transcription in Bacteria
• Gene expression is a highly regulated
process
• To begin transcription, RNA polymerase
must first recognize initiation sites on the
DNA
• Sites are called promoters
• The DNA helix at the promoter site is
opened up by RNA polymerase
• As the polymerase moves, it unwinds the
DNA in short segments to expose template
DNA

16. Transcription in Bacteria
• Promoters are specific DNA
sequences
• In Bacteria, promoters are
recognized by sigma.
• Sigma recognizes two highly
conserved regions within the
promoter
These sequences are recognized by the same E. coli sigma
factor called 𝜎70

17. Transcription in Bacteria
• Genetic information is organized into
transcriptional units
• Segments of DNA that are transcribed
into a single RNA molecule bounded by
their initiation and termination sites.
• Can be:
• A single gene
• Multiple genes
• An operon is a unit of two or more genes
transcribed into a single RNA, and under
the control of a single regulatory site
(promotor)

18. Transcription in Bacteria
• Termination of transcription
is governed by specific base
sequences on the DNA.
• In Bacteria a common
termination signal is a GC-
rich sequence containing an
inverted repeat.
• When this DNA sequence is
transcribed, the RNA forms a
stem–loop structure by intra-
strand base pairing

19. Translation in Bacteria
• Once transcription has occurred,
the mRNAs are translated into
protein
• Transfer RNAs function to carry
amino acids to the translation
machinery
• Each tRNA contains a specific
three-nucleotide sequence called
the anticodon
• Group of three bases that
recognizes a codon (a three-base
code for an amino acid) on the
mRNA

20. Translation in Bacteria
• The correct amino acid (aka. cognate
amino acid) is linked to a specific
tRNA by an enzyme called an
aminoacyl-tRNA synthetase
• For each amino acid, a separate
aminoacyl-tRNA synthetase exists
• Specifically binds both the cognate
amino acid and the tRNA
containing the corresponding
anticodon

21. Translation in Bacteria
• An mRNA triplet of three bases,
called a codon, encodes each
specific amino acid
• Codons themselves are encoded
by the organism’s genome
• There are 64 possible codons (4
DNA bases taken 3 at a time = 43)
• In addition to the codons for amino
acids, there are also codons for
starting and stopping translation
• There are 22 naturally occurring
amino acids
• Several amino acids can be encoded
by more than one codon
• Called degenerate code

22. Translation in Bacteria
• A codon is recognized by specific
base pairing with a complementary
sequence on the anticodon,
located on a tRNA
• If this base pairing were always
the standard pairing of A with U
and G with C, then at least one
specific tRNA would be needed to
recognize each codon.
• True for leucine in E. coli
• Not true for lysine
• One tRNA that recognizes AAA or AAG
• This phenomenon is called wobble

23. Translation in Bacteria
• Messenger RNA is translated beginning with
its start codon (AUG)
• Encodes a chemically modified methionine in Bacteria
called N-formylmethionine
• With triplet code, its important that a peptide
sequence starts in the right place.
• The reading frame that when translated
yields the polypeptide encoded by the gene
is called the 0 (zero) frame
• In Bacteria, ribosomal RNA recognizes a
specific AUG on the mRNA as a start codon

24. Translation in Bacteria
• If an mRNA can be translated, it is
because it contains an open reading
frame (ORF)
• A start codon followed by a number of
codons and then a stop codon in the
same reading frame as the start codon.
• The codons UAA, UAG, and UGA
are stop codons
• Using computational methods, a
DNA base sequence can be scanned
to search for open reading frames.
• The search for ORFs is central to the
field of genomics

25. Translation in Bacteria
• Ribosomes are the sites of protein
synthesis.
• Bacteria and Archaea have 30S and
50S ribosomal subunits that yield
intact 70S ribosomes.
• The 30S subunit contains 16S rRNA and
21 proteins, and the 50S subunit contains
5S and 23S rRNA and 31 proteins.
• In Bacteria, initiation of protein
synthesis begins with a free 30S
ribosomal subunit
• Next, a 50S ribosomal subunit is added to
the initiation complex to form the active
70S ribosome.

26. Translation in Bacteria
• During translation, the mRNA threads through the
ribosome bound to the 30S subunit
• The A site is where the incoming charged tRNA first
attaches.
• The P site is where the growing polypeptide chain is
attached to the prior tRNA
• During peptide bond formation, the growing
polypeptide chain moves to the tRNA at the A site
• Following elongation, the tRNA holding the
polypeptide is translocated from the A site to the P
site, opening the A site for a new charged tRNA.
• Translocation pushes the now amino acid–free
tRNA to a third site, called the E (exit) site
• It is from here that the tRNA is released