Definitions
Genetics
the study of heredity, genes and the
mechanisms that they carry this information
Replication
Expression
Genome
Complete genetic information of the cell
Definitions
Chromosome
The structures that are composed of DNA that carry
the hereditary information
Gene
Segments of the chromosome that code for a specific
product (usually a protein)
Genomics
Sequencing and molecular characterization of
genomes
DNA
Base sequence codes for protein
4 letter alphabet (A, T, G and C)
Genetic code
Determines how nucleotide sequence is
converted into amino acid sequences
Complementary strand allow precise
duplication
DNA to proteins
Gene on DNA
Converted to mRNA
mRNA on ribosome
tRNA brings amino acids to ribosome for
protein synthesis
Definitions
Genotype
Genetic information of the organism
Information that codes for characteristics of
the organism
Phenotype
The expressed or physical characteristics of
the organism
The expression of the genotype
Bacterial Chromosome (DNA)
Bacterial
chromosome
Single
Circular
Attached one or many
sites to plasma
membrane
Bacteria chromosome
Escherichia coli
4.6 million base pairs
4300 genes
1mm long
1,000 X length of cell
Supercoiled
Topoisomerase II
DNA gyrase
Bacterial chromosome
Genetic map
Mapped in minutes
Based on time for
chromosome
exchanged between
two cells
DNA replication
Parental strand
Two new “daughter
strands”
Each strand acts as
template for new
strands
Semiconservative
replication
DNA Replication
Carbons in nucleotide numbered 1`-5`
Complementary sugars are upside down to one
another
Strands run 5`3` on each side
DNA Replication
Steps in replication
DNA unwinds
DNA polymerase
Adds nucleotides to 3`
end
Replication fork forms
Leading strand forms
towards the fork
5`3`
DNA Replication
DNA replication
Lagging strand
Needs RNA primer
Removed by DNA
polymerase
Synthesized
discontinuously
Moves away from fork
Okazaki fragments
1000 nucleotides
DNA ligase fuses
segments
Bacterial DNA Replication
Bacterial DNA
replication
E. coli
Occurs bidirectionally
Two replication forks
Continues until forks
meet
RNA Synthesis
Transcription
Process of taking DNA code and converting to
RNA code
Translation
Converting RNA (mRNA) with tRNA to form
amino acid sequences and proteins
Occurs at ribosome
Protein Synthesis
Three types of RNA
mRNA - messenger
tRNA - transfer
rRNA – ribosomal
DNA unzips at gene
Transcription
RNA polymerase
binds to DNA at
promoter
Only coding strand of
DNA is template
5`3` direction
RNA polymerase
assembles RNA
nucleotides
Transcription
RNA chain grows
RNA stops growing at
terminator site
mRNA strand released
from DNA
DNA zips up
mRNA intermediate
between DNA and
translation
Translation
Bacterial translation
Protein synthesis
Decoding mRNA to amino
acids and proteins
Codons
Groups of 3 nucleotides
Sequence of codons
determines amino acid
sequence
Several codons for a
single amino acid
Degeneracy
Allows for
mutations
Translation
64 codons
(4
3
)
Sense codons
Code for amino acids
61 codons
Nonsense codons
Stop codons
UAG, UAA, UGA
Signal end of protein
synthesis
AUG
Start codon
Formylmethionine
Usually removed from protein
Translation
tRNA
Transfer RNA
Anticodon
Complementary to
codon
Amino acid attached
Brings amino acid to
ribosome
Translation
1 – components
needed come
together
Ribosome
tRNA
mRNA
2 – tRNA carries first
amino acid ( ?) to
ribosome and mRNA
Translation
3 – second amino
acid brought to
ribosome
P – site
Site of first amino acid
A – site
Site of second amino
acid
Peptide bond forms
Translation
4 – after peptide bond
first tRNA is released
to find amino acid
Translation
5 – ribosome moves
along mRNA until
tRNA is in P site
Process continues
down mRNA
Translation
6 – ribosome
continues down
mRNA
Peptide chain
elongates
Translation
7- polypeptide
(protein) released
Ribosome moves
down mRNA until stop
codon
UAG, UAA, UGA
Polypeptide released
Translation
8 – tRNA is released
and ribosome
disassembles
tRNA, mRNA, and
ribosome can be used
again
Review
Other points
Ribosome moves
5`3` direction
Additional ribosome
may attach and begin
synthesizing protein
Prokaryotes can start
translation before
transcription is
complete
Eukaryotic differences
Transcription takes place
in nucleus
mRNA completed prior to
entry in cytoplasm
Exons – Expressed DNA,
code for protein
Introns – intervening DNA,
do not code for protein
Removed by ribozymes
Regulation of Bacterial Gene
Expression
All metabolic reactions are catalyzed by
enzymes (proteins)
Feedback inhibition stops a cell from
performing unneeded chemical reactions
Stops enzymes that are already synthesized
What prevents synthesis of enzymes that
are not needed?
Regulation of Bacterial Gene
Expression
Protein synthesis requires tremendous
energy
Cell does not waste energy
Regulating protein synthesis economizes cells
energy
Regulation of Bacterial Gene
Expression
Genes
60-80% are constitutive
Not regulated
Products produced at fixed rate
Genes turned on all the time
Code for enzymes essential to major life processes
Enzymes needed for glycolysis
Regulation of Bacterial Gene
Expression
Genes
Inducible genes
Production of enzymes is regulated
Inducible enzymes
Present only when needed
Trypanosoma
Surface glycoproteins
Produces one glycoprotein at a time
Eludes immune system
Regulation of Bacterial Gene
Expression
Regulation of
transcription
Repression
Decreases gene
expression
Decrease enzyme
synthesis
Response to
overabundance of an end
product
Regulatory proteins called
repressors
Block RNA polymerase
Regulation of Bacterial Gene
Expression
Regulation of transcription
Induction
Turns on genes
Substance that turns on gene
Inducer
Inducible enzymes
Regulation of Bacterial Gene
Expression
Induction enzymes
β-galactosidase (E. coli)
Cleaves lactose
Medium without lactose = little to no β-galactosidase
Lactose added to medium large amounts of β-
galactosidase produced
Lactose is converted to allolactose
Allolactose is the inducer
Enzyme reduction
Operon Model
Three genes for lactose
utilization
Located next to each other
on bacterial chromosome
Regulated together
Called structural genes
lac structural enzymes are
transcribed and translated
lac for lactose
Operon Model
Operon model
lac operon
Promoter region
Region of DNA where
RNA polymerase
initiates transcription
Operator region
Go or stop signal for
transcription of the
structural genes
Structural genes
Genes for metabolism of
lactose
Operon Model
Inducible operon
Near lac operon is
regulatory gene
I gene
Codes for repressor
protein
Operon Model
Lactose is absent
Repressor binds to
operator site
RNA polymerase is
inhibited
No transcription of
structural genes
No mRNA
No enzymes are
synthesized
Operon Model
Lactose is present
Converted to allolactose
Inducer
Inducer binds to receptor
protein
Receptor protein altered
Does not fit into operator site
RNA polymerase is not
inhibited
Structural genes are
transcribed to mRNA then
translated into enzymes
An inducible operon
Operon Model
Repressible operon
Tryptophan synthesis
EDCBA structural
genes
Also has promoter and
operator region
Operon Model
Repressible operon
Structural genes
transcribed and
translated
Tryptophan is
synthesized
Operon Model
Repressible operon
Excessive tryptophan
accumulates
Tryptophan acts as
corepressor
Corepressor binds to
repressor protein
Repressor protein binds
operator and structural
genes no longer
transcribed
Lactose regulation
Lactose operon
Depends on level of glucose in medium
Enzymes for glucose metabolism are constitutive
When glucose is absent cAMP (cyclic AMP) accumulates in cell
cAMP binds to cAMP receptor protein (CRP)
This binds to lac promoter
Initiates transcription by allowing mRNA polymerase to bind to the promoter
Transcription of lac operon requires
Presence of lactose
Absence of glucose
cAMP is an alarmone
Chemical alarm signal the cell uses to respond to environmental or
nutritional stress
lac operon
Lac operon
Catabolite repression
Inhibition of the metabolism of other carbon
sources by glucose
Glucose effect
Mutation
Mutation
Change in the base sequence of DNA
may cause change in the product coded by the
gene
Beneficial
Lethal
Neutral
Occur commonly
Degeneracy
Mutations
Types of mutations
Base substitution (point mutation)
AT substituted for CG
mRNA carries incorrect base
Translation
Insertion of incorrect amino acid into protein
Missense mutation, nonsense mutation, frame
shift mutation, and spontaneous mutations
Base substitution
Mutations
Normal
No mutations
DNA strand properly
transcribed by mRNA
Correct sequence of
amino acids for protein
Mutations
Mis sense mutation
Base substitution
results in an amino
acid substitution in
protein
Sickle cell anemia
A to T
Glutamic acid to valine
Hb shape changed
during low oxygen
Mutations
Non sense mutation
Base substitution
creates a nonsense or
stop codon
Protein is not
produced
Only a fragment of
protein is produced
Mutations
Frame shift mutation
One or a few nucleotide
pairs are deleted or
inserted in the DNA
Shifts the translation
reading frame
Almost always result in a
long stretch of altered
amino acids
Inactive protein
Mutations
Insertion of extra bases into a gene
Huntington's disease
Spontaneous mutations
Occur occasionally in DNA replication
Mutagens
Chemically of physically alters DNA and
effects a change is called a mutagen
Radiation, ultraviolet light
Mutagens
Chemical Mutagens
Nitrous acid
Converts adenine (A) to a form that doesn’t bind with thymine
(T), but instead binds with cytosine (C)
Alters base pair on DNA, works on random locations
Mutagens
Chemical mutagens
(cont)
Nucleoside analogs
Structurally similar to
normal nitrogenous
bases
2 - aminopurine
Adenine
5 – bromouracil
Thymine analog
Will bind with guanine
Mutagens
Chemical mutagens
(cont)
During replication
analogs cause base
pairing mistakes
Antiviral and antitumor
drugs
AZT (azidothymidine)
Mutagens
Chemical mutagens (cont)
Other chemicals cause deletions, frameshifts,
or insertions
Benzyprene – present in smoke and soot
Frameshift
Aflatoxin – Aspergillus flavus
Frameshift
Mutagens
Radiation mutagens
X – rays
Gamma rays
Ultraviolet
Forms covalent bond
between certain bases
Thymine dimers
Death of damage to cell
Light repair enzymes
Photolyases
Use visible light
energy to separate
dimer
Mutagens
Ultraviolet damage
Nucleotide excision
repair
Enzymes cut out
distorted thymines
Creates gap
Gap is filled with newly
synthesized DNA
DNA ligase joins strand
to surrounding
backbone
Mutation frequency
Mutation rate
Probability that a gene will mutate when a cell divides
Expressed in power of 10
10
-4
mutation rate (1 in 10,000 chance of mutation)
10
-6
( 1 in 1,000,000)
Mutagens
Increase spontaneous mutation by 10 – 10,000 times
10
-6
becomes 10
-3
to 10
-5
Identifying Mutants
Positive (direct) selection
Detection of mutant cells by rejection of
unmutated parent cells
Penicillin in agar
Unmutated parental cell will not grow
Only mutated cells grow
Replica plating
Auxotroph
A mutant microorganism having a nutritional
requirement that is absent in the parent.
Identifying Chemical Carcinogens
Carcinogen
A substance found to cause cancer in animals
Often mutagens are carcinogens as well
Previously used animal testing
Time consuming
Expensive
Ames test
Ames test utilizes
bacteria to act as
carcinogen indicator
Based on observation
that exposure to
mutant bacteria to
mutagenic substance
may reverse effect of
the original mutation
Ames test
These are called reversions
Back mutations
Measures the reversion of Salmonella
Auxotrophs
Have lost there ability to synthesize histidine (his
-
)
(his
+
) bacteria have ability to synthesize histidine
90% of substances that cause reversion
have been shown to be carcinogens
Ames Test
Genetic Transfer and
Recombination
Genetic recombination
Exchange of genes
between two DNA
molecules to form new
combinations of genes on
a chromosome
Crossing over
Two chromosomes break
and rejoin
Adds to genetic diversity
Genetic transfer and recombination
Eukaryotes
Meiosis
Prophase I
Prokaryotes
Numerous different
ways
Genetic Transfer and
Recombination
Vertical gene transfer
Genetic information passed from an organism
to its offspring
Plants and animals
Horizontal gene transfer
Bacteria transfer genetic information form one
organism to another in the same generation
Genetic information passed laterally
Horizontal Gene Transfer
Horizontal gene transfer
Donor cell
Organism gives up its entire DNA
Part goes to recipient cell
Part is degraded by cellular enzymes
Recipient cell
Receives portion of donor cells DNA
Incorporates donor DNA into its own DNA
Recombinant DNA
Less than 1 % of population
Transformation
Genes transferred from one bacterium to
another in solution
Naked DNA
Discovered by Griffith
Used Streptococcus pneumoniae
Two strains
Virulent (pathologic) strain
Had a polysaccharide capsule resists phagocytosis
Avirulent (non- pathogenic) strain
Lacked a capsule
Griffith’s Experiment
Transformation
Bacteria after cell death and lysis could release
DNA into environment
Recipient cell can take up DNA fragments and
incorporate into their own DNA
Resulting in a hybrid (recombinant cell)
Recombinant cell must be competent
Able to alter cell wall to allow DNA (large molecule) to enter
Bacillus, Haemophilus, Neisseria, Acinetobacter, and some
Staph and Strep
Genetic Transformation
Conjugation
Conjugation
Involves plasmid
Circular piece of DNA
Replicates independent of
chromosome
Non essential for growth
genes
Requires cell to cell contact
Opposite mating type
Donor cell carries plasmid
Recipient cell lacks
plasmid
Conjugation
Gram positive
Sticky surfaces cause
bacteria to come in
contact with one
another
Gram negative
Utilize sex pili
Conjugation
E coli model
F factor plasmid
Fertility factor
Donors (F
+
)
Recipients (F
-
)
Converted to (F
+
)
F
+
factor integrated
into chromosome
Becomes Hfr (high
frequency of
recombination) cell
Bacterial Conjugation
Hfr conjugates with F
-
cell
Chromosomal strand
replicates and transferred
to recipient
Incomplete transfer of
donor DNA
Recipient integrates new
DNA
Acquires new versions of
chromosome
Remains F
-
cell
Conjugation in E. coli
Conjugation
Minutes and
conjugation
Identify locations of
various genes
Hfr
His, pro, thr, leu, and
F (+)
F(
-
)
His, pro, thr, leu, and
F(
-
)
Transduction in Bacteria
Transfer of bacterial
DNA transferred via
bacteriophage
Bacteriophage
Virus that infects
bacteria
Transduction
Steps of transduction
1- bacteriophage infects donor bacterial cell
2- Phage DNA and proteins, and bacterial
chromosome is broken into pieces
Transduction
Steps of transduction
3- during phage reassembly, bacterial DNA incorporated
in capsid of bacteriophage
4 – donor cell lysis releasing new bacteriophage particles
Transduction
Steps in transduction
5- phage carrying donor DNA infects new recipient cell
6- recombination can occur
Producing bacteria with genotype different than donor and recipient
Transduction
Generalized transduction
Previously explained
Specialized transduction
Only certain genes are transferred
i.e. phage codes for toxins to be produced
Cornybacterium diphtheriae – diphtheria toxin
Streptococcus pyogenes – erythrogenic toxin
Escherichia coli – Shiga toxin (hemorrhagic diarrhea)
Plasmids
Plasmids
Self replicating rings of DNA
1-5% size of chromosomal
DNA
Non – essential genes
Conjugative plasmid
F factor
Dissimilation plasmids
Code for enzymes to
breakdown unusual sugars
and hydrocarbons
Help in survival of unusual
environments
Plasmids
Other plasmids
Toxins (Anthrax, tetanus, Staph)
Bacterial attachment
Bacteriocins
Toxic proteins that kill other bacteria
Resistance factors (R factors)
Resistance to antibiotics, heavy metals, cellular
toxins
Plasmids
Resistance factors
Two groups
RTF – resistance transfer factor
Includes genes for plasmid replication and conjugation
r-determinant
Resistance genes
Codes for production of enzymes that inactivate drugs or toxic
substances
Bacteria can conjugate and transfer plasmids between
species
Neisseria
Penicillinase resists penicillin
R factor Plasmids
Transpoons
Transpoons
Small segments of DNA that move from one region to
another
700-40,000 base pairs
Occur in all organisms
Can insert within genes
Disrupt transcription of gene
Occurs rarely (similar to spontaneous mutation rate)
Transpoons
Transpoons
Contain gene for transposition
Insertion sequence (IS)
Codes for transposase
Cuts and seals DNA for transpoons