BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
This outline is intended to facilitate your preparation for lecture. This outline will NOT
substitute for regular lecture attendance.
Unit 3
I. Patterns of Information Flow in the Microbial World Fig. 8.2


Within one organism (cell)
From one organism to another:
o from one generation to the next (vertical transfer)
o between cells of the same generation (horizontal transfer)
A. Basic genetics review:
1. Structure of nucleotides and nucleic acids
Nucleotides are
composed of 3 basic parts (label drawing on next page):
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
Base
O
C
O
O
P
O
O
P
O
O
P
O
O
O
H
H
H
3 phosphates
= triphosphate
O
N
C
C
C
O
O
C
N
C
C
C
C
O
O
H
H
5 carbon sugar
= ribose
Fig. 2.17 - modified
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
The base of a nucleotide can be one of 5 kinds:
Adenine –
Guanine –
Thymine –
Cytosine –
Uracil –
A nucleic acid is a
There are 2 kinds of nucleic acids:
1. RNA – Ribonucleic acid
Sugar Bases 3 kinds of RNA molecules:
transfer RNA (tRNA)
messenger RNA (mRNA)
ribosomal RNA (rRNA)
RNA molecules are generally
2. DNA – deoxyribonucleic acid
Sugar Bases –
DNA molecules are generally
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
A nucleic acid is a polymer of nucleotides. (shown with DNA nucleotides):
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
Nucleotides continue to be added until a long polymer is formed:
H3C
H
H
H
H
Notice a couple things about this polymer:
1.
2.
3.
4.
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
6
The sequence of the nucleotide bases in a nucleic acid has meaning. The S-P backbone is constant, the
same in all DNA molecules.
**It is the sequence of the nucleotide bases that carries the information.
Base pairing -
In the example shown here:
BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
Joining of nucleotides to make a nucleic acid
Fig. 8.4
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
The two strands of nucleic acid are complementary in base sequence and also antiparallel or of
opposite orientation with respect to 5’  3’.
Fig. 8.3b
The 2 strands twist around each other to form a double helix
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
The double helix of DNA has to be organized and packed to fit inside the cell. Fig. 8.1a
In all cells, DNA is organized into chromosomes, but the size of the DNA molecule, the number,
structure, and packaging of the chromosome varies among the 3 Domains:
how many base pairs
are in the DNA?
how many
chromosomes does cell
have?
what is the structure of
chromosome?
how is chromosome
packed to fit in cell?
Archaea
5 x 105 to 5 x 106
Bacteria
2 x 106
Eukarya
1 x 107 and more
1
1
many
closed circle
closed circle
linear
histones,
nucleosome-like
supercoiling,
DNA binding
proteins
histones,
nucleosomes,
chromatin
B. Flow of information from one generation to the next ( = vertical transfer)
1. Overview DNA Replication (repl.) (pp. 212-216)
DNA replication is semiconservative – resulting ds DNA after replication is made up of 1 old
strand of DNA and 1 new strand of DNA.
Fig. 8.3
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
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Fig. 8.5 Review of DNA replication - Events at the DNA Replication Fork
1. Notice the orientation of each of the strands of DNA
2. Enzymes (helicases) unwind the parental double helix
3. Proteins stabilize the unwound, single stranded parental DNA (otherwise it would just re-pair
and coil back up)
4. DNA polymerase catalyzes the addition of new nucleotides to the new strand
5. DNA polymerase can only add nucleotides to an exposed 3’OH
6. The new strand of DNA is synthesized with the new strand extending in a 5’ to 3’ direction.
7. But what about the other strand, how is it copied?
8. The other strand has no exposed 3’OH so DNA polymerase cannot act
9. But RNA polymerase does not need an exposed 3’OH in order to add nucleotides
10. RNA polymerase brings in complementary RNA nucleotides to make a short section of RNA
called a “primer”
11. These RNA primers have exposed 3’OH so now DNA polymerase can work.
12. DNA polymerase adds nucleotides causing the new strand to grow in a 5’ to 3’ direction (as on
the other strand).
13. Synthesis on this strand is discontinuous, not continuous as on the other strand.
14. Discontinuous synthesis, because there are more steps, is slower.
15. The synthesis on this strand will lag behind, so this strand can be called the “lagging strand”, the
other strand can be called the “leading strand”.
16. Eventually, on the lagging strand, the DNA polymerase will run into the back of an RNA primer.
17. The DNA polymerase removes the RNA nucleotides and replaces them with DNA nucleotides.
18. Another enzyme called DNA ligase joins the fragments of the lagging strand.
BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
In Eukarya the chromosome is linear, but in Bacteria and Archaea the chromosome is
circular.
How do you replicate a circular DNA?
2. DNA replication in Bacteria Fig. 8.6
Origin of replication –
2 repl. forks form.
Bidirectional –
**Consequences –
DNA replication in Archaea -
C. Flow of information within a single cell
**DNA contains sequences of nucleotides (specifically nucleotide bases) that code for
functional products – these functional products are called genes.
Gene –
Functional products may be:
Structural RNAs
Proteins
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
How does information stored in DNA ultimately become a functional product?
1. Transcription (transc.) (p. 216)
Transc. will require:
 DNA template
 RNA nucleotides (with the bases A, U, C, G)
DNA template sequence (of nucleotide bases)
5’-A-C-G-T-T-C-G-T-A-A-C-G-G-G-C-T-A-3’
The RNA copy of this

The enzyme RNA polymerase (RNA pol) – A large DNA binding protein whose job is to
catalyze the addition of RNA nucleotides. The RNA polymerase of Archaea is more
similar to that of Eukarya than to Bacteria.

2 kinds of informational DNA nucleotide sequences:
Promoter –
Terminator –
DNA
Initial
binding site
Pribnow
sequence
Promoter
First nucleotide
transcribed
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
Review the process of transcription Fig. 8.7
The orientation of the RNA copy (= the transcript) produced is complementary and antiparallel to the template DNA.
The RNA transcript may be:
ribosomal RNA (rRNA)
transfer RNA (tRNA)
messenger RNA (mRNA)
What happens next to the RNA transcript? – is the transcript modified after it is made? (called
post-transcriptional modification)
rRNA / tRNA molecules
mRNA
Bacteria and Archaea
modified
not modified
Eukarya
modified
extensively modified
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
2. Translation (transl.) (pp. 217-221)
How does the information in RNA get passed on to proteins? Translate the information carried
in the mRNA molecule and use that information to build a protein (a protein is a polymer of
amino acids).
Transl. will require:
 mRNA –
 genetic code
 tRNA  rRNA mRNA
AU G
5’
3’
codon
Codon – 3 RNA bases in sequence, read as 3 together, a triplet
tRNA – the translator –
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
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mRNA codon sequence
5’
3’
How does translation get started? – there is a specific transl. start in the mRNA– how the cell
“knows” where to start translating mRNA into a protein.
There are similarities and differences among the 3 Domains what the transl. start is
Bacteria
1 mRNA  several
proteins (operon)
consensus sequence
Archaea
1 mRNA  several
proteins
consensus sequence
Transl.
start
1st aa
N-formylmethionine
Methionine
1st a.a. – the first amino acid in the newly formed protein.
Eukarya
1 mRNA 
1 protein
5’-P end of
mRNA
Methionine
BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
Where does translation take place?
Ribosomes are complex molecules composed of rRNA and proteins. Ribosomes will selfassemble on the mRNA molecule.
Subunit sizes
rRNA sizes
# of proteins
Complete ribosome
Bacteria and Archaea
50S
30S
16S*
5S
23S
52
Eukarya
60S
40S
18S*
5S
5.8S
28S
82
70S
80S
Remember that S stands for “Svedberg”, which refers to how the molecule moves in a
centrifugal force.
* it was the DNA coding for these rRNA that Carl Woese sequenced to discover the 3
Domains of Life.
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
Review the process of translation - Fig. 8.9, 8.8
Summarizing where transcription and translation happen in the 3 Domains and what the
consequences of where are.
Bacteria and Archaea
Eukarya
Site of transcription
cytoplasm
nucleus
Site of translation
cytoplasm
cytoplasm
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
3. Gene Expression and Regulation
In Eukarya the mRNA transcript is formed in the nucleus and then leaves the nucleus,
traveling to the ribosomes in the cytoplasm.
**In Bacteria and Archaea – transcription and translation both occur in the cytoplasm – this
means that transcription and translation occur simultaneously.
Expression –
Eukarya regulate gene expression by regulating whether or not translation occurs (an event
physically separated from transcription in the cell).
But how can Bacteria and Archaea regulate gene expression?
Regulation of gene expression in Bacteria and Archaea - happens by regulating whether or
not transcription occurs. (pp. 221-226).
How can they do this?
Bacteria have 2 kinds of genes:
Constitutive –
Ex. Genes for enzymes necessary to break down glucose
Inducible –
Ex. Genes for enzymes for break down of lactose
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
**Example of regulation of inducible genes - Lactose Operon of E. coli
Operon –
1. Structure of lac operon of E. coli
Fig. 8.12 modified
a. 3 Structural genes - encode enzymes
Gene
Enzyme
Z
-galactosidase
Y
Lactose permease
A
Transacetylase
b. Promoter and Operator
Operator –
c. I gene – codes for a repressor protein
RNA polymerase also involved
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
2. How does E. coli control expression of these genes?
a. If have glucose but no lactose – don’t want structural genes for lactose use to be expressed.
I gene is transc. & transl. into repressor protein that binds to DNA at the operator region –
physically blocks the movement of the RNA polymerase so the structural genes are NOT
expressed.
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
b. If there is no glucose but there is lactose:
I gene is transc. & transl. into repressor protein, as above. But lactose is transported into cell
where it is converted into allolactose (which is called an inducer) – allolactose binds to the
repressor protein. Now the repressor protein can’t bind to the operator sequence. The RNA
polymerase is not blocked. The structural genes are expressed and the 3 enzymes needed to
breakdown lactose are made.
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
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D. Flow of information from one cell to another cell of the same generation
**Flow of information between cells of the same generation (called horizontal gene transfer =
HGT) (pp. 233-241)
**Unlike Eukarya, which evolve principally through the modification of existing genetic
information, Bacteria and Archaea have obtained a significant proportion of their genetic
diversity by taking genetic material from distantly related organisms.
Importance of HGT:
•
•
•
•
May account for 10 to 50% of all the genes in the genome of a Bacteria or Archaea.
Has occurred between diverse species and even across the boundaries of Domains (i.e.,
Bacteria have acquired genes from Eukarya).
Produces extremely dynamic genomes in which substantial amounts of DNA are introduced
into and deleted from the chromosome.
Has led to the emergence of new pathogenic microbes.
How do microbes of the same generation exchange DNA?
Overall process involves:
Recombination –
Recombination always requires:
Donor –
Recipient –
Recombinant
BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
**3 Mechanisms of Horizontal Gene Transfer (HGT)
1. Transformation – DNA released by one bacterium (naked DNA) is taken up by a 2nd
Fig. 8.25
Ex. Streptococcus pneumoniae -
2. Conjugation – DNA transfer is mediated by a plasmid (introduced in Unit 1)
Conjugation requires direct cell to cell contact via a pilus (introduced in Unit 1)
Fig. 8.27
Examples:
Pseudomonas –
Clostridium tetani –
Bacillus anthracis –
Many, many antibiotic resistance
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BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World
3. Transduction – bacterial DNA is transferred from donor to recipient inside a virus that
specifically infects bacterial cells (a bacteriophage or phage; more about these later in this
Unit)
Fig. 8.28
Examples:
Corynebacterium diphtheriae –
Streptococcus pyogenes –
E. coli O157:H7 -
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