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Dr. Gary Andersen, 913-279-2211 Some slides used with permission from Curtis Smith, KCKCC Reference: Chapter 7,8 from (Black, J., 2005). Microbial Genetics. Genomes – the total of the genetic material in a cell.

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microbial genetics
Dr. Gary Andersen, 913-279-2211

Some slides used with permission from Curtis Smith, KCKCC

Reference: Chapter 7,8 from (Black, J., 2005)

Microbial Genetics
basic units of genetics
Genomes – the total of the genetic material in a cell.

Gene - The unit of heredity for a given genetic trait. The site on a DNA molecule that carries the code for a certain cell function.

Viruses – 4 or 5 genes, E. coli – 4228 genes, Human ~ 31,000 genes.

Basic Units of Genetics
a big question to struggle with
Which is more important… nature or nurture? Genetics or the environment? In determining the characteristics and behavior of an organism?A Big Question to Struggle With
nucleic acids
I. Nucleic acids are located in the nucleoid of bacteria, and the nucleus of eukaryotes. There are 2 kinds of nucleic acids: RNA & DNA.Nucleic Acids


E. coli cell

showing DNA


DNA (deoxyribonucleic acid) is made of subunits called nucleotides. Nucleotides are made of 3 components. These 3 components are linkedtogether with a covalent bond.

E. Coli = 4.6 million nucleotide pairs (~1mm)

Corn = 2.5 billion nucleotide pairs

Human = 3 billion nucleotide pairs (2nm wide by 2 meters long)

significance of dna structure
Maintains the code with high degree of fidelity. (double strand assures accurate replication)

Provides a method for introducing a high degree of variety. (unlimited variety of sequences possible)

Significance of DNA Structure
2 component ribose sugar

Ribose - A five carbon sugar that functions as part of the DNA backbone (ie. structural). “2, Deoxy” means without oxygen on the number 2 carbon atom.

2. COMPONENT – Ribose Sugar
3 component nitrogen bases

Function: express genetic information.

composition :


double ring structures


single ring structures

3. COMPONENT – Nitrogen Bases
nucleotide base
Nucleotide Base

Composed of one Nitrogen base, one Deoxyribose, and one Phosphate group


(Nitrogen base)



dna structure13
4. DNA is a double helix (there are 2 strands of DNA) which are intertwined with 5 base pairs per turn.

5. DNA has complimentarity

that is A always bonds with T

and G always with C

6. DNA is always antiparallel. The 2 strands of DNA are always oriented in opposite directions. ( 5’ PO3 end – 3’ OH end)


DNA Structure
b rna

Similar to DNA except:

1. RNA is single stranded

2. RNA has a ribose sugar instead of deoxyribose. (Oxygen on #2 C).

3. RNA has URACIL (u) instead of thymine

4. RNA is always shorter than DNA, ~ 1,000 nucleotides in length

c functions of rna
1. rRNA (ribosomal) - comprises the ribosome (site of protein synthesis). (60% of a ribosome is made of RNA, the rest is protein).

2. tRNA (transfer) carries amino acids to the ribosome during protein synthesis. Also known as the “ANTICODON”

3. mRNA (messenger) - a complimentary strand of RNA equal in size to 1 gene (normally ~1,000 nucleotides). “CODON” - coded info from DNA (bound for the ribosome)

dna replication
1. Where 2 parental strands of DNA are copied into 2 daughter strands. Rate = 1,000 nucs per seconds without error. This leads to binary fission in bacteria.

Cell Division) = 2 daughter cells

2. Each cell receives 1 parental strand and 1 daughter strand. (semiconservative replication)


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As the two replication forks meet, the two new chromosomes separate—each containing one new and one old strand

1 events in dna replication
DNA unwinds using the enzyme DNA Helicase

SSBP holds the 2 strands apart (single strand binding proteins)

Note: 2 replication forks. DNA replication is considered bi-directional replication.

dna repliction continued
Polymerization requires DNA Polymerase (POL III) which is an enzyme that synthesizes 2 nucleotide strands (daughter strands) from 2 parental (templates) strands.

DNA exonuclease (POL I) removes any mistaken base pairs.

DNA ligase seals any gaps and joins the 2 strands together.


Replication of DNA cont’d

  • http://www.ncc.gmu.edu/dna/repanim.htm
the central dogma of biology
There are 3 parts to the flow of information in all cells.


DNA -------------mRNA-----protein


b transcription
2nd part of the central dogma of biology

1st step in gene expression (i.e.protein synthesis).

The cells genetic plan contained in DNA is transcribed into a complimentary base sequence called messenger RNA (mRNA).

The region of DNA that produces or serves as a template for mRNA is called a gene. A gene normally consists of around 1,000 base pairs. It is the smallest segment of DNA that codes for mRNA.

transcription continued33
7. Example:




8. mRNA is a blueprint of DNA or a transcript or code.

9. One code word consists of three letters.

Transcription continued
animation of transcription
Animation of Transcription
  • http://www.ncc.gmu.edu/dna/mRNAanim.htm
c translation
Translation is the 3rd part of the central dogma of biology (2nd step in gene expression or protein synthesis).

After transcription, the coded information in mRNA is translated into an enzyme (protein).

This process takes place on the ribosome. Note that the ribosome is made of rRNA and protein.

translation continued

tRNA utilizes the information in mRNA to determine the sequence of amino acids in a protein. tRNA has a cloverleaf shape. The amino acid end binds one specific amino acid in the cytoplasm. The anticodon end pairs with the codon on mRNA.

translation continued39
The mechanics of translation

Initiation; mRNA bumps into the small subunit and triggers the two ribosomal subunits to bind together. The first tRNA anticodon (UAC) carrying the amino acid methionine hydrogen bonds with the codon AUG on mRNA.

translation continued40
b. Elongation – The second tRNA binds to the second code word on mRNA. A peptide bond forms between the two amino acids. The first tRNA leaves, and the enzyme translocase moves the ribosome down one code word of mRNA at a time. This repeats ~ 300X.TRANSLATION CONTINUED
translation continued41
C. In termination, one of three possible stop codons is reached. The last tRNA falls away and the two ribosomal subunits fall apart.TRANSLATION CONTINUED
d the genetic code
61 sense codons for 20 amino acids

3 nonsense (or stop codons)

total codons

Pg 180 (Black, J., 2005)

d. The Genetic Code
translation animation
Translation - Animation
  • http://www.ncc.gmu.edu/dna/ANIMPROT.htm

Translation Animation - http://www.wehi.edu.au/wehi-tv/dna/movies/Translation.mov.gz

translation blockers
Streptomycin – (SM) blocks assembly of the ribosome during initiation.

Chloroamphenicol – (CA) blocks peptide bond formation during elongation.

Tetracycline – TC – blocks the 2nd site on the ribosome during elongation.

Erythromycin EM – blocks translocase during elongation.

Translation Blockers

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gene regulation
How can genes be turned off and on?

Examples from E. coli

Inducer – example is lactose (lac operon), pg 187 of (Black, J., 2005)

Repressor – argenine (arg operon), pg 187-188 of (Black, J., 2005)

Gene Regulation
iii 5 ways of creating genetic diversity in bacteria
A. Mutations

B. Transformation

C. Conjugation

D. Transposition

E. Transduction

III. 5 Ways of Creating Genetic Diversity in Bacteria
a mutations
1. Changes in the nucleotide sequence usually due to an error in DNA replication. These occur naturally at low levels (also known as spontaneous mutations); or by the effects of chemical agentscalled mutagens; or by physical agents like radiation. A. Mutations
results of mutations
2. Most mutations are neutral - they have no effect on the polypeptide. Some mutations result in a less active product; Less often an inactive product; Very few mutations are beneficial. However, these would be passed on!Results of Mutations
types of mutations
3. Point mutations - a one base change in DNA. There are 3 types:

a. silent mutations - single base substitution in the 3rd base nucleotide position of a codon. This results in NO change in amino acid. Note that the first 2 letters of the genetic code are the most critical.

Types of Mutations
b.missense mutations - single base substitution in 1st or 2nd base nucleotide position. This results in a changed amino acid. A change in one amino acid usually will have little effect depending on where in the polypeptide it occurs.

nonsense mutations - single base substitutions that yield a stop codon. Note: there are 3 nonsense codons in the genetic code = NO PROTEIN

4. Frame Shift Mutations - the addition or deletion of 1 or more bases. These are due to powerful mutagens; chemical or physical.

a.Chemical mutagens - (used in research to study mutagenesis). There are 3 kinds of chemical mutagens.

1. alkylating agents. Adds alkyl group, CnH(2n+1) Ex. formalin, nitrogen, mustard, and ethylene oxide (reacts with G changing it to bind with T).

2. base analogs. Mimics a nitrogen base. Ex. AZT is a modified sugar that substitutes for T. Ex. 5 - bromouracil binds with A or G.

3. intercalating agents. Inserts into DNA and pushes bases apart. Ex. AFLATOXIN - a chemical produced by peanut and grain molds. The mold is Aspergillus flavus (fungus).

GA fall08

b. Physical mutagens:

1. nonionizing radiation - Causes the formation of T= T dimers. UV light @ 260 nm.

2. Ionizing radiation - damages DNA by causing the formation of “free radicals” leading to mutations. 3 Ex. X-rays. Gamma rays from radioactive fallout penetrates the body. Alpha rays from inhaled dust containing radioactive fallout.

b transformation
The passage of homologous DNA from a dead donor cell to a living recipient cell. Occurs in Streptococcus pneumoniae. When S. pneumo dies the DNA can be absorbed by a living S. pneumo and recombined into the chromosome. The gene for capsule formation is obtained in this way, as is agene for penicillin resistance. Discovered in 1929 by Fredrick Griffith. B. TRANSFORMATION

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c conjugation
1. A “mating” process between a donor F+ (bacteria with fertility factor =plasmid) and an F- recipient cell.

2. Occurs in Gram - enteric bacteria like E.coli

3. Discovered in 1946 by Joshua Lederberg and Edward Tatum.

4. Plasmids carry genes that are nonessential for the life of bacteria. Ex. gene for pili (sex pilus). Ex. plasmid replication enzymes. Ex. Medical Problem: R-Factor = antibiotic resistance!

conjugation continued
“Normal - Sex” plasmid transfer (usually ~20 of 100 genes).

a. Requires a sex pilus

b. F + bacteria transmits a copy of the plasmid to F- bacteria. This converts the F- cell into an F + cell. Medical Problem: The R factor (antibiotic resistance) on the F factor is transmitted! http://www.cat.cc.md.us/courses/bio141/lecguide/unit4/genetics/recombination/conjugation/f.html

Conjugation continued
6. Hfr (High Frequency Recombination)

a. Hfr- bacterial plasmid integrates into the chromosome.

b. Medical Problem:Hfr antibiotic resistance genes are passed during binary fission (every time the cell divides). Therefore, antibiotic resistance spreads very rapidly!

c. When Hfr mate with F – bacteria, only the bacterial genes cross NOT plasmid genes. Genetic diversity results in this case due to recombination. http://www.cat.cc.md.us/courses/bio141/lecguide/unit4/genetics/recombination/conjugation/hfr.html

d transposition p 285
Transposons (jumping genes) are big chunks of DNA that randomly excise and relocate on the chromosome.

Transposons were discovered in 1950 by Barbara McLintock in corn.

Causes antibiotic resistance in Staph. aureus, the famous methicillin resistant Staphlococcus aureus (MRSA) strain!

e transduction
the transfer of genetic material from donor bacteria to recipient bacteria via a transducing agent (virus!). Bacterial viruses are called bacteriophage.

1. Discovered in 1952 by Zinder & Lederberg.

2. Two kinds of transduction: generalized and specialized.

2. Generalized transduction: Starts with the LYTIC CYCLE where a T- evenphage (Fig. 8.5 pg 210) infects E.coli killing the host cell, and synthesizing 2,000 copies of itself. The T-even phage randomly packages bacterial DNA in a few defective phages. Once a T –even phage infects another E. coli, this genetic information can be recombined into the host cell without causing the lytic cycle. New genetic information is thereby transduced from one bacteria to another.
specialized transduction
3.Specialized transduction

Lambda phage infects E.coli. The phage does not lyse the cell immediately. Instead it integrates into chromosome of the bacteria as a prophage and remains dormant. This is called the LYSOGENIC CYCLE. Phage genes are replicated and passed to all daughter cells until the bacteria is under environmental stress, from lack of nutrients, etc. Then phage gene will excise from the nucleoid and enter the LYTIC CYLE taking one adjacent gene for galactose metabolism.

Specialized Transduction
specialized transduction cont
The gal transducing phage (lambda) makes ~ 2,000 copies of itself with the gal gene, and infects other E.coli. When gal integrates into the nucleoid of other E. coli, it may provide these bacteria with a new capacity to metabolize galactose. Specialized Transduction Cont.
comparison of bacteriophage
3. Comparison of bacteriophage transduction in E.coli.

Generalized Specialized

T even phage lambda phage

lytic cycle lysogenic

random packaging specific gal gene

Comparison of Bacteriophage