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فسيولوجيا الميكروبات Microbial Physiology Microbial Genetic دكتور محمد عبده مسلم أستاذ بيئة وفسيولوجيا الميكروبات المشارك
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دكتور محمد عبده مسلمالمشارك الميكروبات وفسيولوجيا بيئة المشارك أستاذ الميكروبات وفسيولوجيا بيئة أستاذ
الدقيقة واألحياء النبات الدقيقة قسم واألحياء النبات قسم
العلوم العلوم كلية كلية
سعو الملك سعو جامعة الملك دجامعة
Structure and Function of Genetic Structure and Function of Genetic MaterialMaterial
• 1. Genetics is the study genes, genetic information, the expression of the genetic information, replication of genetic information and passing it to subsequent generations or other organisms.
• 2. DNA in cells exists as a double-stranded helix; the two strands are held together by hydrogen bonds between specific nitrogenous base pairs. – Base pairing principle: A-T and C-G.
– Complementary bases
The Double Helix & Base PairingThe Double Helix & Base Pairing
Structure and Function of Genetic Structure and Function of Genetic MaterialMaterial
• 3. A gene is a segment of DNA, a sequence of nucleotides, that codes for a protein.
• 4. When a gene is expressed, DNA is transcribed to produce mRNA; mRNA is then translated into proteins.
• 5. The DNA in a cell is replicated before the cell divides, so each daughter cell receives the same genetic information.
GenotypeGenotype andand PhenotypePhenotype
• 1. Genotype is the genetic composition of an organism—its entire DNA.
• 2. Phenotype is the expression of the genes—the proteins of the cell and the properties they confer on the organism.
DNADNA andand ChromosomesChromosomes
• 1. The DNA in a chromosome exists as one long double helix associated with various proteins that regulate genetic activity.
• 2. Bacterial DNA is circular; the chromosome of E. coli, for example, contains about 4 million base pairs and is approximately 1000 times longer than the cell.
• 3. Genomics is the molecular characterization of genomes.
Some Types of DNA: Chromosomal Some Types of DNA: Chromosomal (circular or linear) and Plasmid (Vector)
DNADNA ReplicationReplication• 1. During DNA replication, the two strands of the double
helix separate at a point called the replication fork, and each strand is used as a template by an enzyme DNA polymerase 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.
• 4. DNA polymerase proofreads new molecules of DNA and removes mismatched bases before continuing DNA synthesis. Statistically, errors only occur ~1 time for every 1010 bases added.
• 5. Each daughter bacterium receives a chromosome identical to the parent's.
DNADNA ReplicationReplication
Protein SynthesisProtein Synthesis
• DNA mRNA Protein
Transcription Translation
• Central Dogma of Molecular Genetics
Gene Expression: Gene Expression: Transcription and TranslationTranscription and Translation
RNARNA andand ProteinProtein SynthesisSynthesis
• 1. During transcription, the enzyme RNA polymerase synthesizes a strand of mRNA from one strand of double-stranded DNA, which serves as a template.
• 2. RNA is synthesized from nucleotides containing the bases A, C, G, and U, which pair with the bases of the DNA sense strand.
• 3. Promoter site: – The starting point for transcription, where RNA
polymerase binds to DNA • 4. Terminator site:
– The region of DNA that is the endpoint of transcription; – RNA is synthesized in the 5' —> 3' direction.
• 5. Translation:– The process in which the information in the nucleotide base
sequence of mRNA is used to assemble a protein with a specific amino acid sequence.
• 6. The mRNA associates with ribosomes, which consist of rRNA and protein.
PromoterPromoter
Translation
RNA and Protein Synthesis - Continue
• 6. Three-base segments of mRNA that specify amino acids are called codons.
• 7. The 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.
RNA and Protein Synthesis - Continue
• 8. The genetic code is degenerate; that is, most amino acids are coded for by more than one codon.
• 9. Of the 64 codons, 61 are sense codons (which code for amino acids), and 3 are nonsense codons (stop codons) which do not code for amino acids and are stop signals for translation.
• 10. The start codon, AUG, normally codes for methionine (formylmethionine at the beginning or a protein).
Base Substitution MutationBase Substitution Mutation
Frame Shift Mutation• In a frameshift mutation, one or a few base pairs
are deleted or added to DNA:• Normal DNA:
– ATG CAT GCA TGC ATT TCC TGC TTA AAA
• Addition Mutation (A is added):– AAT GCA TGC ATG CAT TTT CCT GCT TAA
Reading Frame is Shifted (to the right)
• Deletion Mutation (A in normal DNA is deleted)– TGC ATG CAT GCA TTT CCT GCT TAA
Reading Frame is Shifted (to the left)
Mutations - ContinueMutations - Continue
• Spontaneous mutations occur without the presence of a mutagen. The spontaneous mutation rate varies from genome to genome.– Copying errors in the genetic material during cell
division
• Induced mutations occur as a result of applying mutagens.
MutagensMutagens
• Mutagens are agents in the environment that cause permanent changes in DNA:
– 1. Chemical mutagens for example, nitrous acid, 2-aminopurine and 5-bromouracil and benzpyrene.
– 2. Ionizing radiation causes the formation of ions and free radicals that react with DNA; base substitutions or breakage of the sugar-phosphate backbone result.
– 3. Ultraviolet radiation is nonionizing, causing bonding between adjacent thymines (thymine dimers).
Repair of Mutated DNARepair of Mutated DNA
• 1. Damage to DNA caused by UV radiation can be repaired by enzymes that cut out and replace the damaged portion of DNA.
• 2. Light-repair enzymes repair thymine dimers in the presence of visible light.
FrequencyFrequency ofof MutationMutation
• 1. Mutation rate is the probability that a gene will mutate when a cell divides;
• Spontaneous mutations are at a rate of 10-6 per replicated genes.
• 2. Mutations occur randomly along a chromosome.
• 3. A low rate of spontaneous mutation is beneficial, providing genetic diversity needed for evolution.
IdentifyingIdentifying MutantsMutants
• 1. Mutants can be detected by selecting or testing for an altered phenotype.
• 2. Positive selection involves the selection of mutant cells and rejection of nonmutated cells.
• 3. Replica plating is used for negative selection—to detect, for example, auxotrophs that have nutritional requirements not possessed by the parent (nonmutated) cell. For example, a histidine dependent bacterium.
Replica Plating
Identifying Chemical CarcinogensIdentifying Chemical Carcinogens• 1. The Ames test is an inexpensive and rapid test for
identifying possible chemical carcinogens.• 2. The test assumes that a mutant cell can revert to
a normal cell in the presence of a mutagen and that many mutagens are carcinogens.
• 3. Histidine auxotrophs (Histidine dependent Salmonella) are exposed to an enzymatically treated potential carcinogen; reversions to the nonmutant state indicates a chemical mutagen – suspected carcinogen.
The Ames Test The Ames Test (Use of Robotics)(Use of Robotics)
Genetic Transfer and Genetic Transfer and Recombination of DNARecombination of DNA
• 1. Genetic recombination, the rearrangement of genes from separate groups of genes, usually involves DNA from different organisms; it contributes to genetic diversity. The resultant DNA is recombinant DNA or rDNA
• 2. In crossing over, genes from two chromosomes are recombined into one chromosome containing some genes from each original chromosome.
Genetic Transfer and Genetic Transfer and Recombination of DNA - ContinueRecombination of DNA - Continue
• 3. Vertical gene transfer occurs during reproduction when genes are passed from an organism to its offspring.
• 4. Horizontal gene transfer in bacteria involves a portion of the cell's DNA being transferred from donor to recipient.– When some of the donor's DNA has been
integrated into the recipient's DNA, the resultant cell is called a recombinant cell and the DNA is recombinant DNA or rDNA
TransformationTransformation inin BacteriaBacteria• 1. During this process, genes are transferred
from one bacterium to another as "naked" DNA in solution.
• 2. This process was first demonstrated in Streptococcus pneumoniae, and occurs naturally among a few genera of bacteria.
Conjugation in BacteriaConjugation in Bacteria
• This process requires contact between living cells assisted by the pilus ('bacterial sex').
F (Fertility) Gene in ConjugationF (Fertility) Gene in Conjugation
Conjugation - ContinueConjugation - Continue
• 2. One type of genetic donor cell is an F+; recipient cells are F-. F+ cells contain plasmids called F factors; these plasmids are transferred to the F- cells during conjugation.
Conjugation: Mating FConjugation: Mating F++ x F x F--
ConjugationConjugation
• 3. When the plasmid becomes incorporated into the chromosome, the cell is called an Hfr (high-frequency recombinant).
• 4. During conjugation, an Hfr can transfer chromosomal DNA to an F-. Usually, the Hfr chromosome breaks before it is fully transferred
Conjugation: Mating Hfr x FConjugation: Mating Hfr x F--
Transduction in BacteriaTransduction in Bacteria
• 1. In this process, DNA is passed from one bacterium to another via a bacteriophage (bacterial virus) and is then incorporated into the recipient's DNA.
• 2. In generalized transduction, any bacterial genes can be transferred.
Generalized Transduction in Generalized Transduction in Bacteria - ContinueBacteria - Continue
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PlasmidsPlasmids
• Plasmids are self-replicating, closed circular extrachromosomal molecules of DNA carrying genes that are not usually essential for survival of the cell.
• Plasmid are mobile.
• There are several types of plasmids such as, conjugative plasmids and those carrying genes for antibiotics or heavy metals resistance
pBR322 PlasmidpBR322 Plasmid
Transposons Transposons (“Jumping Genes” or Mobile DNA)
• 1. Transposons are small segments of DNA that can move from one region of a chromosome to another region of the same chromosome or to a different chromosome or a plasmid.
Transposons - ContinueTransposons - Continue
• 2. Transposons are located in the chromosomes of organisms, in plasmids, and in the genetic material of viruses. They may be simple (insertion sequences) to complex.
• 3. 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.
The reddish streaks on these corn grains are caused by transposons.
GenesGenes andand EvolutionEvolution
• 1. Diversity is the precondition of evolution.
• 2. Genetic mutation and recombination provide a diversity of organisms, and the process of natural selection allows the growth of those best adapted for a given environment.