Download Terminology

6/30/14
CHPT 8: MICROBIAL GENETICS
Chapter summary
§  Genetics: The study of what genes are, how they carry
§  Structure and function of the genetic material:
information, how that information is expressed, and how genes
§  The flow of genetic information
are replicated.
§  DNA replication
§  Gene: A segment of DNA that encodes a functional product,
§  Transcription
§  Translation
usually a protein.
§  Regulation of bacterial gene expression
§  Operons
§  Mutation
§  Genetic transfer and recombination
§  Genes and evolution
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E. coli
Terminology
§  Genome: All of the genetic material in a cell
§  The study of genomes is called genomics.
§  Genotype: The genes of an organism
§  Phenotype: Expression of the genes
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Chromosome Map
Chromosome Map
http://bytesizebio.net/wp-content/uploads/2009/01/r-typhi.jpg
Flow of Genetic Information
Vertical flow of information WITHIN a cell
The “Central Dogma”
DNA
TRANSCRIPTION
RNA
TRANSLATION
DNA, RNA and Proteins have
their own language, via which
information is stored
Protein
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Vertical flow of information WITHIN a cell
The “Central Dogma”
Nucleotides
Vertical flow of information WITHIN a cell
That is a dog (= the original information)
DNA
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TRANSCRIPTION
RNA
Nucleotides
4
RNA
That is a dawg (= copy of the original
TRANSLATION
Protein
Amino acids
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English
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Flow of Genetic Information
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DNA
Language
How many letters
in alphabet?
Protein
information, in the same
language, but a slightly
different dialect)
Quello e’ un cane (= the original information
in a different language)
DNA
§  Polymer of nucleotides: adenine,
thymine, cytosine, and guanine
§  Double helix associated with proteins
§  Deoxyribose-phosphate (sugar
phosphate) "backbone"
§  Two strands are held together by
hydrogen bonds between AT and CG.
§  Strands are antiparallel.
Vertical flow
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DNA
DNA
DNA Replication
DNA Replication - the copying of DNA
§  DNA replication is semi-conservative.
DNA replication video
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DNA Replication - the copying of DNA
DNA Replication
§  DNA is copied by DNA polymerase
§  DNA replication is semi-conservative.
§  New DNA made in the 5' → 3' direction
§  Initiated by an RNA primer
§  Leading strand is synthesized continuously
+
§  Lagging strand is synthesized discontinuously
§  Okazaki fragments
§  RNA primers are removed and Okazaki fragments
joined by a DNA polymerase and DNA ligase
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Flow of Genetic Information
Transcription
§  The synthesis of RNA from DNA
§  DNA is transcribed to make RNA (mRNA, tRNA, rRNA).
§  Transcription begins when RNA polymerase binds to
the promoter sequence
§  Transcription proceeds in the 5' → 3' direction
(i.e., RNA made from 5' → 3').
§  Transcription stops when it reaches the
terminator sequence
Vertical flow
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Transcription
Transcription
Transcription
Bioflix video
(see part of YouTube channel
video called “Protein Synthesis”)
Transcription
1st
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Transcription
Translation
§  The synthesis of proteins by
ribosomes, using the information
in mRNA.
§  mRNA is translated in codons
(groups of 3 nucleotides)
§  Translation of mRNA begins at the
start codon - AUG
§  Translation ends at one of 3 stop
codons - UAA, UAG, UGA
Translation
Translation - mRNA to protein
• The Genetic Code
•  Each mRNA codon "codes" for
one amino acid
•  Organisms contain 20 different
amino acids, but > 60 codons…
Why?
•  There is more than one codon
for each amino acid (e.g. both
UAU and UAC code for Tyr)
•  Known as the degeneracy of
the code
Bioflix video
(see 2nd part of YouTube channel
video called “Protein Synthesis”)
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Translation
Translation
Translation
Translation
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Translation
Translation
Translation
Translation
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Translation
RNA processing in Eukaryotes
Chapter summary
Regulation of Bacterial Gene Expression
§  Structure and function of the genetic material:
§  Constitutive enzymes are expressed at a fixed rate.
§  The flow of genetic information
§  DNA replication
§  Other enzymes are expressed only as needed.
§  Transcription
§  Repressible enzymes
§  Translation
§  Inducible enzymes
§  Regulation of bacterial gene expression
§  Operons
§  Mutation
§  Genetic transfer and recombination
§  Genes and evolution
§  Pre-transcriptional control:
§  Inducible operons
§  Repressible operons (not examinable)
§  Epigenetic control (not examinable)
§  Post-transcriptional control (not examinable)
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The operon model of gene expression
• An operon
The operon model of gene expression
• An operon
•  Contain a promoter, operator and structural genes
•  Contain a promoter, operator and structural genes
•  Generally contain genes involved in a single metabolic pathway
•  Generally contain genes involved in a single metabolic pathway
•  Co-ordinated expression
•  Co-ordinated expression
The lac (lactose) operon
-  an inducible operon
Regulation of gene expression - induction or repression
Induction – the lac operon
Induction – the lac operon
lac operon animation
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Chapter summary
Mutation
§  Structure and function of the genetic material:
§  A change in the genetic material
§  The flow of genetic information
§  DNA replication
§  Transcription
§  Translation
§  Regulation of bacterial gene expression
§  Mutations may be neutral, beneficial, or harmful.
§  Mutagen: Agent that causes mutations
§  Spontaneous mutations: Occur in the absence of a
mutagen
§  Operons
§  Mutation
§  Genetic transfer and recombination
§  Genes and evolution
Mutation
Mutation - base substitution
§  A change in the genetic material
§  Mutations may be neutral, beneficial, or harmful.
§  Mutagen: Agent that causes mutations
§  Spontaneous mutations: Occur in the absence of a
mutagen
§  Types of mutations:
§  Base substitution (aka point mutation) - silent, missense or
nonsense
§  Frameshift mutation
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Mutation - base substitution
Mutation - base substitution
§  Silent (neutral) mutation
§  Missense mutation
§  Change in one base
§  Change in one base
§  Does NOT result in an amino acid change in the
§  Results in change in amino acid
protein
§  No effect on protein function
template
template
Mutation - base substitution
Mutation - frameshift mutation
§  Nonsense mutation
§  Frameshift mutation
§  Change in one base
§  Insertion or deletion of one or more nucleotide pairs
§  Results in a stop (nonsense) codon
template
template
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Causes of Mutations
Mutation: ionizing radiation
1.  Spontaneous
§  Ionizing radiation (e.g. X rays and gamma rays):
2.  Mutagens:
§ 
Radiation
§ 
Chemical mutagens
§  causes the formation of ions that can react with nucleotides
and the deoxyribose-phosphate backbone.
§  Nucleotide excision repairs mutations.
Mutation: non-ionizing radiation
Chemical Mutagens:
e.g. Nitrous acid as a mutagen
§  UV radiation causes
thymine dimers.
§  Light-repair
separates thymine
dimers.
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Nucleoside analogs
The Frequency of Mutation
§  Spontaneous mutation rate = 1 in 109 replicated base
pairs (= 1 in 106 replicated genes).
§  Mutagens increase the mutation rate to one in every
103 - 105 replicated genes.
Identifying mutants experimentally
§ 
Negative selection via Replica Plating
Can test for mutants with an altered phenotype, by using
either:
1.  Positive (direct) selection:
§ 
detects mutant cells because they grow or appear different.
2.  Negative (indirect) selection
§ 
detects mutant cells because they do not grow.
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Chapter summary
Flow of Genetic Information
§  Structure and function of the genetic material:
§  The flow of genetic information
§  DNA replication
Horizontal flow
§  Transcription
§  Translation
§  Regulation of bacterial gene expression
§  Operons
§  Mutation
§  Genetic transfer and recombination
§  Genes and evolution
Genetic Recombination
Recombination: Exchange of genes between two DNA molecules
Genetic Transfer
§  Vertical gene transfer: Occurs during reproduction
between generations of cells.
§  Crossing over §  occurs when two DNA
molecules break and
rejoin (at regions where
their sequences are
identical or very
similar)
§  Horizontal gene transfer: The transfer of genes between
cells of the same generation (between a donor cell and a
recipient cell). Three types:
§  Transformation
§  Conjugation
§  Transduction
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Transformation
Transformation
"Naked"
DNA
Conjugation
Conjugation
Animation
Sex pilus in Gram negatives
Mating bridge in Gram positives
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Conjugation
Conjugation
Transduction in bacteria
Plasmids
Generalised or Specialized Transduction
Generalised:
•  Small, circular, extrachromosomal DNA; contain genes
•  Replicates independently from the cell’s chromosome
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Plasmid categories
§  Conjugative plasmid:
§  Carries genes for sex pili and transfer of the plasmid
Transposons and Insertion sequences
§  Transposons: segments of
DNA that can move from one
region of DNA to another.
§  Dissimilation plasmids:
§  Encode enzymes for catabolism of unusual compounds
§  Contain insertion sequences
for cutting and resealing DNA
(transposase).
§  R factors:
§  Encode enzymes for antibiotic resistance
§  Complex transposons carry
other genes…
Transposons and Insertion sequences
Chapter summary
§  Structure and function of the genetic material:
§  The flow of genetic information
§  DNA replication
Transposition
of a transposon
into a plasmid
§  Transcription
§  Translation
§  Regulation of bacterial gene expression
§  Operons
§  Mutation
§  Genetic transfer and recombination
§  Genes and evolution
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