unit 3c

Unit 3c

Microbial Genetics

Microbial GeneticsGenetics: the science of heredityGenome: the genetic information in the cellGenomics: the sequencing and molecular characterization of genomes

• Gregor Mendel• Grew pea plants from 1856-1863.• Genetics: the science of heredity• Genome: the genetic information

in the cell• Genomics: the sequencing and

molecular characterization of genomes

A cell’s genome includes• Chromosomes and _________• Chromosomes are structures containing

the DNA

Plasmids

A bacterium has a single circular chromosome consisting of a single circular molecule of DNA

Plasmids (review)• small loops of extrachromosomal DNA in bacteria• often carry genes for virulence, bacteriocins (toxic proteins

that kill other bacteria) or drug resistance (codes for enzymes that inactivate certain drugs or toxic substances)– can recombine into new combinations

• transmitted from organism to organism

Eukaryotic DNA sites

DNA

• Fig. 2.16

Nucleotides

“Genes”

• Segments of DNA (except in some viruses, in which they are made of RNA) that code for functional products

DNA

• each gene could be several thousand or more base pairs long.– E. coli approximately 4,300 genes (4.6 million

base pairs– Humans have approximately 20,000 to 25,000

genes.• Based on Human Genome Project

Nucleic Acids• DNA and RNA

• DNA: deoxyribonucleic acid

• RNA: ribonucleic acid– Messenger RNA (mRNA)– Ribosomal RNA (rRNA)– Transfer RNA (tRNA)

• Nucleotides are the structural units of nucleic acids

Nucleotides (Review)• a nucleic acid is a long chain of nucleotides• each nucleotide has 3 parts:

– a 5-carbon ________• ribose in RNA• deoxyribose in DNA

– A __________ group– a ___________ base

Sugar

PhosphateNitrogenous

One nucleotide

RNA nucleotide with uracil

Nucleic acids

• RNA: usually a single chain of nucleotides (may be double in viruses)

• DNA: usually a double chain of nucleotides (may be single in viruses)

• 2 kinds of base pairs:

Nucleotides Complementary Base Pair

• Nucleotide bases bind to each other in a specific manner = complementary base pairing.

• Specific purines complementary base pair with specific pyrimidines.

Complementarybase pairing inDNA

DNA

• Double helix of James Watson and Frances Crick

Review of Proteins:

• long chains of amino acids: hundreds of amino acids in complex three-dimensional arrangements

• there are 20 naturally occurring kinds of amino acids

• each amino acid in a protein must be exactly the right kind of amino acid or it will be a different protein

• the function of a gene is to determine the sequence of the amino acids to make a specific protein

The genetic code• The set of rules that determine how a

nucleotide sequence is converted into the amino acid sequence

• along a mRNA, groups of 3 consecutive nucleotides is a codon, the genetic code for one amino acid

• e. g. —P—R—P—R—P—R— l l l U A C

• 64 possible mRNA codons for 20 amino acids• there can be up to 6 codons that specify the same amino acid• a few codons specify NO amino acid (start or stop codons),

signal the end of the protein molecule’s synthesis

The genetic code

An overview of genetic flow ….figure 8.2

1) DNA replication

• reproduction of a molecule • basis of continuity of life• molecule “unzips” along the hydrogen

bonds• each half attracts the nucleotides needed

to recreate the other half• if successful, both new molecules are

identical to the original and to each other

DNA Polymerase – Enzyme that connects each nucleotide together

DNA Ligase – Enzyme that connects sections of DNA together

DNA Replication

Okazaki Fragments

5’

5’

3’

3’

Lagging Strand Leading

Strand

Figure 8.6

DNA replication precedes cell division

2) Transcription

• = production of RNA by DNA• DNA produces several kinds of RNA• messenger-RNA (m-RNA) carries the genetic

code for a protein out from the chromosome to the ribosomes

• transfer-RNA (t-RNA) carries individual amino acids to the messenger RNA which puts them in the proper sequence

• ribosomal-RNA (r-RNA) links up the amino acids to form a protein

Translation• = protein synthesis, translating the genetic

code into a specific protein

chain of amino acids

Fig. 8.10

• Simultaneoustranscription andtranslation inbacteria

Becomes mRNA (messenger RNA) – this has the code for how to build a protein

_________________________Connects RNA nucleotides together (like DNA polymerase)

RNA Polymerase

Codon- A section of three nucleotides in a row that code for an amino acid

tRNA – transfer RNA anticodon & amino acid

Polypeptide Chain – all the amino acids who together

Mutations• Can be negative, neutral, or positive!• defined as a change in the base sequence of DNA• can involve one or more nucleotides• the source of new genes (such as virulence or drug

resistance)• about one mutation per million replicated genes• causes:

– errors in DNA replication– radiation– mutagenic chemicals

The electromagnetic spectrum: effective wave lengths:

• a. ultraviolet radiation– damages DNA

– optimum wave length: 260 nm– poor penetrating ability

Ames Test uses bacteria as carcinogenindicators (figure 8.22)

• Many known mutagens have been found to be carcinogens

Genetic Recombination

• The exchange of genes between 2 DNA molecules to form new combinations of genes on a chromosome.– Vertical gene transfer

• Genes are passed from an organism to its offspring

– Horizontal gene transfer• Between bacteria of the same generation!• Donor cell to recipient cell = recombinant

An overview of genetic flow ….figure 8.2

Bacterial gene transfers

• Bacteria have a number of forms of recombination:– ___________– ___________– ___________

ConjugationTransformation

Transduction

Bacterial conjugation (DNA transferred through a mating process)• 2 bacteria connected by a tube called

the sex pilus• F = fertility factor (ability to mate)• F+ is equal to being male (one that

grows the sex pilus)• F– is equal to being a female• DNA passes through the sex pilus

from the F+ to the F–• usually just the F factor, but sometimes

other genes are carried along • F– becomes F+

Figure 8.24: Griffith’s Transformation Experiment

Transduction: • Transduction: host DNA

carried from cell to cell by virus

• Figure 8.28

Biotechnology

• Restriction Enzymes – enzymes found in bacteria that cut DNA at specific sequences.

Cotton Plants with Bacillus gene inserted (left)

Bioremediation

Pharmaceuticals

Figure 9.1

DNA in diagnosis• 4. Nucleic acid hybridization • Basis of DNA probes

– Short segments of ssDNA that are complementary to the desired gene

• Complementary strands of known DNA separated by heat

• One side marked with fluorescent dye• DNA of unknown bacteria separated by heat• Will hybridize with fluorescent strand of known

DNA if same kind. After rinsing away unbound DNA, a fluorescent DNA double strand will remain

• Can hunt for complementary DNA within a massive amount of material, such as food

DNA-DNA hybridization (fig. 10.15)

DNA probe to detect Salmonella • Why use

E. coli ?

• Easilygrown &researchersare familiarwith its genetics

• Figure 10.16

DNA probe, continued

DNA probe, continued

DNA Chips (figure 10.17)An array of DNA probes arranged in a DNA chip can be used to

identify pathogens

• BUT should we?