Chapter 8 – Microbial Genetics
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Most microbial traits are controlled or influenced by genetics/heredity.
Structure and Function of the Genetic Material
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Genetics – the science of heredity.
o What genes are, how they carry information, how they are replicated and passed
on.
o The genetic information is called the genome
 It includes chromosomes and plasmids
 Chromosomes – the DNA that carries the hereditary information,
in the form of genes
 Genes – the segments of DNA that code functional products
o DNA’s structure is allows it to be used similar to language,
with the letters forming “words” and sentences.
 This is called the genetic code.
 The complementary nature of DNA allows for
precise duplication
o Genotype and Phenotype
 Genotype = genetic makeup; potential properties
 Phenotype = actual, expressed traits
DNA and Chromosomes
o Bacteria have a single, circular chromosome consisting of a single, circular
molecule of DNA with associated proteins.
 Genomics – the sequencing of genomes, has allowed scientist to figure
out the entire genetic sequences and open reading frames of many
microbes/organisms.
Flow of Genetic Information
 Gene expression – DNA  RNA  protein
 Recombination – transfer of genetic information between cells
 Replication – transfer of genetic information from parent cell to offspring
DNA replication – one double stranded, parental DNA molecule is converted into 2
identical daughter molecules
Steps:
1. During DNA replication, the two strands of the double helix separate at the replication
fork, and each strand is used as a template by DNA polymerases to synthesize two new
strands of DNA according to the rules of nitrogenous base pairing.
2. The result of DNA replication is two new strands of DNA, each having a base sequence
complementary to one of the original strands.
3. Because each double-stranded DNA molecule contains one original and one new strand,
the replication process is called semiconservative.
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leading strand is synthesized continuously and the lagging strand discontinuously.
5. DNA polymerase proofreads new molecules of DNA and removes mismatched bases
before continuing DNA synthesis.
6. Each daughter bacterium receives a chromosome that is virtually identical to the
parent’s
o DNA replication in bacteria can sometimes be bidirectional
o It is really accurate; only about 1 in every 1010 contains a mistake
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RNA and Protein Synthesis
o Transcription – DNA to RNA
o RNA is synthesized from nucleotides containing the bases A, C, G, and U, which
pair with the bases of the DNA strand being transcribed
 mRNA – contains the info to make a protein
 tRNA – brings in the correct amino acid to make the protein
 rRNA – makes up ribosomes where protein synthesis occurs
o Translation – RNA to protein
 Transcription plus Translation = gene expression
Information you need to know:
1. RNA polymerase binds the promoter; transcription begins at AUG; the region of DNA
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direction.
The mRNA associates with ribosomes, which consist of rRNA and protein.
Three-base segments of mRNA that specify amino acids are called codons.
he genetic code refers to the relationship among the nucleotide base sequence of DNA,
the corresponding codons of mRNA, and the amino acids for which the codons code.
The genetic code is degenerate; that is, most amino acids are coded for by more than
one codon.
Of the 64 codons, 61 are sense codons (which code for amino acids), and 3 are nonsense
codons (which do not code for amino acids and are stop signals for translation).
7. The start codon, AUG, codes for methionine.
8. Specific amino acids are attached to molecules of tRNA. Another portion of the tRNA
has a base triplet called an anticodon.
9. The base pairing of codon and anticodon at the ribosome results in specific amino acids
being brought to the site of protein synthesis.
10. The ribosome moves along the mRNA strand as amino acids are joined to form a
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11. Translation ends when the ribosome reaches a stop codon on the mRNA.
o In prokaryotes, transcription and translation take place in the cytoplasm. In
eukaryotes, transcription takes place in the nucleus and translation takes place
in the cytoplasm.
o In eukaryotes, genes are often interrupted by sequences that don’t mean
anything (introns). These introns are cut out, leaving only the sequences that
actually code for the protein (exons).
 The introns are removed by particles called small nuclear
ribonucleoproteins (snRNPs). These snRNPs also splice the exons back
together.
Regulation of Bacterial Genes – the Lac Operon in E. coli
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Many genes are not regulated, they are constitutive (turned on all the time) because
whatever they code for, the cell needs most or all of the time.
Some are regulated, to save energy.
o Repression – a regulatory mechanism that inhibits gene expression
o Induction – the process that turns on the transcription of a gene or genes.
 Requires an inducer molecule.
 There is an “on-off” switch that transcribes and then translates the 3
genes when lactose is present, and “turns off” the gene when lactose is
not there (Operator).
 There is a promoter, which is a DNA sequence that recognizes the
enzyme RNA polymerase, and thus promotes transcription.
 There are structural genes present that code for particular polypeptides
(enzymes) to be made when lactose is present.
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A group of genes that code for enzymes involved in the same
function (structural genes), their promoter site, and the operator,
all make up the operon.
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The operon that controls the metabolism of lactose is called the
lac operon.
When you eat or drink a dairy product, E. coli in your stomach absorbs the lactose and
breaks down into its 2 parts, glucose and galactose. This requires 3 different enzymes,
which are each coded for by 3 different genes.
Steps:
- When there is no lactose present, a protein called a repressor turns off the operon.
 A repressor is a protein that binds to an operator and physically blocks
RNA polymerase from binding to a promoter site (it inhibits the gene
from being expressed).
 The blocking of RNA polymerase consequently stops the transcription of
the genes in the operon.
 This makes the lac operon an inducible operon
o Transcription of the structural genes is ultimately
controlled by a regulatory gene, called the I gene. It codes
for the production of the repressor protein.
- When lactose is present, the lactose binds to the repressor and changes the shape of
the repressor. The change in shape causes the repressor to fall off of the operator.
Now RNA polymerase can attach to the promoter and begin transcribing the genes that
code for lactose-metabolizing enzymes.
o Because it activates, or induces, transcription, lactose acts as an inducer.
- There are also repressible operons, which are turned on until they are repressed.
o Example: the genes responsible for tryptophan synthesis. Tryptophan is
produced until there is an excess, then it acts as a corepressor, binding to the
repressor protein so it can now bind to the operator, thus stopping tryptophan
synthesis.
- Genes can also be positively regulated.
o Transcription of structural genes for catabolic enzymes which break down other
carbohydrates is induced by the absence of glucose.
 Cyclic AMP and CAP must bind to a promoter in the presence of an
alternative carbohydrate.
 Cyclic AMP is an alarmone, a chemical alarm that promotes a
cells’ response to environmental or nutrient stress
o The presence of glucose inhibits the metabolism of alternative carbon sources by
catabolite repression
Mutations
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A change in the base sequence of DNA.
Can cause a different end product, can be beneficial, can be silent, or lethal
Types: base substitutions, missense mutation, nonsense mutation, frameshift mutation,
and spontaneous mutations.
o Base mutations – aka point mutation. A single base is replaced with a different
base
o Missense mutation – occurs when the point mutation results in a different amino
acid being put into the growing peptide chain.
o Nonsense mutation - a base substitution that puts a stop codon in the middle of
mRNA molecule, so the entire sequence isn’t made.
o Frameshift mutations – one or a few nucleotides are deleted or inserted,
resulting in a different reading frame of the DNA molecule.
o Spontaneous mutations – base or frameshift mutations that occur during DNA
replication, which may occur in the absence of any mutation-causing agent
 Mutagen – an agent in the environment that can directly or indirectly
bring about a mutation.
 Chemical mutagens
o Nitrous acid – converts A to a form that can no longer pair
with T, but instead pairs with C.
o Nucleoside analog – similar to nitrous acid in that it causes
incorrect base pairing
o Benzopyrene and Aflotoxin – a frameshift mutagen; causes
deletions or insertions.
 Radiation – ionize atoms and molecules, causing electrons to pop
out of their shells. These free electrons then cause damage to
other molecules, creating highly reactive free radicals, et cetera.
o Bacteria and other organisms have enzymes that can
repair UV damage
 Photolyases – light repair enzymes use visible light
to repair damage
 Nucleotide excision repair – enzymes cut out the
incorrect base and ill in the gap with newly
synthesized DNA that is complementary to correct
strand.
 Methylases – enzymes that add methyl
groups to select bases after DNA is made. If
a group remains unmethylated, it is
perceived as being the incorrect base pair
and it cut out, only to be replaced by the
correct, methylated one.
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Frequency of Mutation
o Mutation rate – the probability that a gene will mutate when a cell divides.
 Expressed as a base of 10, with a negative exponent (ex. 10-6)
 Many harmful mutations are not passed on, whereas many beneficial
ones are.
 Mutagens increase the rate of mutations usually by 10-1000 times.
Identifying mutants
o Mutants can be detected by selecting or testing for an altered phenotype.
o Positive selection involves the selection of mutant cells and the rejection of
nonmutated cells.
 Example: cells that grow on media containing penicillin
o Replica plating is used for negative selection—to detect, for example,
auxotrophs that have nutritional requirements not possessed by the parent
(nonmutated) cell.
 Going back to the master plate which contains all of the nutritional needs
the microbe needs and finding the colony that didn’t grow on the
nutritionally restricted media.
Identifying Chemical Carcinogen
o Carcinogen – a substance which causes cancer in animals, including humans
 Testing on animals to check for carcinogens is timely and expensive. This
is being replaced by using bacterial cultures.
 The Ames test is a relatively inexpensive and rapid test for
identifying possible chemical carcinogens.
 The test assumes that a mutant salmonella cell can revert to a
normal cell in the presence of a suspected mutagen and that
many mutagens are carcinogens.
Genetic Transfer and Recombination
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Genetic recombination – the exchange of genes between 2 DNA molecules to form new
combinations of genes on a chromosome
o Types: crossing-over, vertical gene transfer, horizontal gene transfer,
transformation, conjugation, transduction, plasmids, and transposons.
 Crossing-over: genes from two chromosomes are recombined into one
chromosome containing some genes from each original chromosome
 Vertical gene transfer: occurs during reproduction when genes are
passed from an organism to its offspring.
 Horizontal gene transfer: involves a portion of the cell’s DNA being
transferred from donor to recipient.
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When some of the donor’s DNA has been integrated into the
recipient’s DNA, the resultant cell is called a recombinant
Transformation: genes are transferred from one bacterium to another as
“naked” DNA in solution
Conjugation: genetic material is transferred from one bacterium to
another; plasmids are transferred.
 This process requires contact between living cells.
 One type of genetic donor cell is an F+; recipient cells are F–. F cells
contain plasmids called F factors; these are transferred to the F –
cells during conjugation.
 When the plasmid becomes incorporated into the chromosome,
the cell is called an Hfr (high frequency of recombination) cell.
 During conjugation, an Hfr (high frequency of recombination cell
can transfer chromosomal DNA to an F– cell. Usually, the Hfr
chromosome breaks before it is fully transferred.
Transduction: DNA is passed from one bacterium to another in a
bacteriophage and is then incorporated into the recipient’s DNA.
 In generalized transduction, any bacterial genes can be
transferred
 In specialized transduction, only certain bacterial genes can be
transferred
o Example: the genes for certain toxins
Plasmids: are self-replicating circular molecules of DNA carrying genes
that are not usually essential for the cell’s survival.
 There are several types of plasmids, including conjugative
plasmids (F plasmid), dissimilation plasmids (code for enzymes),
plasmids carrying genes for toxins or bacteriocins (toxic proteins
that kill other bacteria), and resistance factors/genes (aka R
factors; resistance to antibiotic).
o Resistance transfer factor (RTF) – includes genes for
plasmid replication and conjugation
o R-determinant – has the resistance genes.
Transposons: are small segments of DNA that can move from one region
to another region of the same chromosome or to a different
chromosome or a plasmid.
 Transposons are found in chromosomes, in plasmids, and in the
genetic material of viruses. They vary from simple (insertion
sequences) to complex.
o Insertion sequences – contain only a gene that codes for
an enzyme (transposase) and the recognition site.
o Complex transposons can carry any type of gene, including
antibiotic-resistance genes, and are thus a natural
mechanism for moving genes from one chromosome to
another.
Genes and Evolution
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Diversity is the precondition for evolution.
Genetic mutation and recombination provide a diversity of organisms, and the process
of natural selection allows the growth of those best adapted to a given environment.