Microbial Genetics Chapter 8 PDF

Chapter 8: Microbial Genetics ============================= Introduction to Genetics and Genes ---------------------------------- Genetics: study of inheritance, structure of nucleic acid and how is express List the four areas that genetics explores. ( 1. Transmission of traits from parent to o...

Chapter 8: Microbial Genetics ============================= Introduction to Genetics and Genes ---------------------------------- Genetics: study of inheritance, structure of nucleic acid and how is express List the four areas that genetics explores. ( 1. Transmission of traits from parent to offspring 2. Expression ad variation of traits 3. Structure and function of genetic material 4. How genetic material changes The Nature of the Genetic Material ---------------------------------- Genome: All the genetic material, All DNA Fig 8.1 Most of the genome exists in the form of chromosomes List the location(s) of the genome components. Plasmids or in organelles(mitochondria DNA) of eukaryotes Genome of cells composed entirely of DNA Genome of [viruses] can contain either DNA or RNA. Chromosome: (pack of DNA); contains genes List and describe the three categories of genes. 1. **Structural genes:** code for proteins 2. **Genes that code for RNA machinery** 3. **Regulatory genes:** control gene expression Genotype vs Phenotype DNA Recombination Events ------------------------ Recombination: Def: how does bacterial material change? [Recombination] ( this is different than transcript, translation) - A bacteria donates DNA to a recipient cell. End result is a new strain different from both the donor and the original recipients - Recombinant: an **organism with new genetic material received from a donor. Now, it could be resistant to drugs.** Dependent on the fact that bacteria have plasmids and are adept at interchanging genes Provide genes for resistance to drugs and metabolic poisons, new nutritional and metabolic capabilities, and increased virulence and adaptation to the environment **[Horizontal]** Gene Transfer in Bacteria **(Table 8.7)** - Define: **gene movement** only between the same generation. - This is a type of recombination. - Process is independent from asexual replication - Transferred DNA may be in the form of plasmids or chromosomal fragments. - Ex: this movement can be little pieces of chromosomes between cells in a population. - Ex: Chromosomal fragments can break inside recipient plasma and it can recycle the genetic material. Plasmids: - Small, circular pieces of DNA - Replicate independently - Not necessary for survival - Can carry useful traits - Move eseier than chromosomes **Chromosomal fragments must integrate into the bacterial chromosome in order to be replicated** 1. **[Conjugation] (Fig 8.11). DIRECT** - DNA is transferred by a donor to a recipient cell via a direct connection - DNA is duplicated and a copy is transferred to another bacteria - Gram-negative conjugation: - *What is an F factor?* Is a type of plasmid and gene for the pilus is found here. - The recipient cell has a recognition site on its surface. - Pilus grows out from the F^+^ cell, attaches to the surface of the F^-^ cell, contracts, and draws the two cells together. - Gram-positive conjugation: - Do gram positive bacteria make a pilus? ***[NO]*** - An opening is created between two adjacent cells - Replicated DNA passes across from one cell to another - Conjugation is a conservative process in which the donor bacterium retains (conserves) a copy of the genetic material being transferred. - F factor in *E. coli:* - The donor (F^+^) cell makes a copy of its F factor. - Transmits this to a recipient (F^-^) cell - The transferred DNA does not include chromosomal genes, only the F factor itself. - What is the impact on the recipient cell after conjugation is complete? Now it is F+ - High-frequency recombination (Hfr) donors: - Where are the F genes located? (Insert answer) - Some chromosomal genes get transferred to the recipient. - Does the recipient cell become F^+^? (Insert answer) - **[F factor integrates into the chromosome of bacteria and NOT as a SEPARATE PLASMID like F factor ]** - **[Long process bridge can break and recipient cell remains F- ]** - **Resistance (R) factors** (plasmids) can be passed between bacteria during conjugation. R factors can contain genes for resistance to antibiotics or heavy metals or genes that increase the cell's pathogenicity (synthesis of toxins, enzymes, or adhesion molecules). 2. ### **[Transformation -- INDIRECT ]** - DEAD CELL HAS FREE DNA - Organism do not have do be related in generation - A chromosome released by a lysed cell breaks into fragments small enough to be accepted by a recipient cell. - Transformation: - Process: A bacterium dies, and plasmids are released. A bacterium that is proximal can scavenge this free-floating DNA and incorporate the properties if the dead bacteria 3\. **[Transduction] (Fig 8.12) - INDIRECT** - Generalized Transduction: - Bacteriophages, bacterial DNA is incorporated into the bacteriophage. Upon lysis this bacteriophage go to attack new bacteria. - Virtually any gene from the bacterium can be transmitted, usually between cells in the same species Mutations: Changes in the Genetic Code -------------------------------------- Mutation: Any change to the nucleotide sequence in the genome Does it always change the phenotype? No Can involve the loss of base pairs, the addition of base pairs, or a rearrangement in the order of base pairs ### Causes of Mutations - Spontaneous mutation: errors in DNA replication, out in the right nucleotide, it is not super common. Bacteria have more opportunity for error because the rate of speed is higher than in eukarts. - Do bacteria mutate at a higher or lower rate than other organisms? higher - Induced mutations: result from exposure to known *mutagens* - Mutagens: anything that increases mutation rates - Ex: UV light or Chemicals ### Repair of Mutations - DNA has a proofreading mechanism to repair mistakes in replication. - The cell has additional systems for finding and repairing DNA that has been damaged. - UV damage repair: Photoactivation/light repair through photolyase.  photolyase directly reverses the DNA lesion without removing or replacing nucleotides. -  **Not found in humans:** While bacteria, plants, and some animals have photolyase - Successful only for a small number of UV mutations - Cells cannot repair severe, widespread damage and will die. - NO poof reading for RNA, an error stay and is passed on, that why virus replicate quick - Excision repair: - Incorrect bases are removed and replaced by correct bases using a series of enzymes 1. **Base Excision Repair (BER)** -- Corrects small, non-helix-distorting lesions (e.g., single-base damage from oxidation or deamination). 2. **Nucleotide Excision Repair (NER)** -- Removes bulky lesions, such as **thymine dimers** caused by UV radiation. ### Steps of Excision Repair #### 1. Recognition of Damage - Specific repair proteins **detect the DNA damage** (e.g., mismatched or chemically altered bases). #### 2. Excision of the Damaged Region - **For BER**: - A **DNA glycosylase** removes the incorrect base, leaving an **AP site (apurinic/apyrimidinic site)**. - An **AP endonuclease** then **cuts the DNA backbone** at this site. - **For NER**: - A multi-enzyme complex (**excinuclease**) **cuts out a short segment** of the DNA surrounding the damage (about 12--24 nucleotides). #### 3. DNA Synthesis (Filling the Gap) - **DNA polymerase** synthesizes a new, correct DNA strand using the undamaged strand as a **template**. #### 4. Ligation (Sealing the DNA) - **DNA ligase** seals the final **nick in the backbone**, restoring the DNA to its original state. ### Positive and Negative Effects of Mutations Unrepaired mutations are heritable (will be passed on to the offspring of organisms and viruses) Mutations may be - Silent - Helpful - Harmful/lethal As long as the environment is stable, mutants only comprise a small percentage of the population: When the environment changes, some mutants will be equipped to survive in the new environment. Acquired drug resistance is a clear model for this type of selection and adaptation. Question: An event in which one bacterium donates DNA to another bacterium, resulting in a strain that differs from both donor and recipient, is a type of genetic transfer called conjugationField 1Field 1 conjugation , Incorrect Unavailable. Correct AnswerQuestion ---------------------- - **Field 1: **recombination A(n) Blank\_\_\_\_\_\_ cell has a separate fertility plasmid, whereas a(n) Blank\_\_\_\_\_\_ cell has the F factor incorporated into its chromosome. Multiple choice question. HfrHfr; F−F- HfrHfr; F+F+ F−F-; HfrHfr Reason:  F−F- is a recipient cell that does not contain an F plasmid. F+F+; Hfr Which is an agent that induces changes in DNA? Multiple choice question. a.Mutation Reason:  A mutation is a change in DNA. b\. Mutagen correct c.Mutant Reason:  A mutant is an organism with a mutation. A(n) Blank\_\_\_\_\_\_ is a bacterial virus involved in Blank\_\_\_\_\_\_, a means of horizontal gene transfer. Multiple choice question. a. bacteriophage; transduction correct b. bacteriophage; transformation Reason:  Incorrect: Transformation is the uptake of naked DNA. c. plasmid; transduction Reason:  Incorrect: Bacteriophage are involved in transduction. d. F factor; transduction Reason:  Incorrect: F factor is transferred through conjugation. Which cell can transfer both chromosomal and plasma DNA? **a.** Hfr **b.** F+ What enzyme is often used to repair UV damage to DNA?\ photolyase READ about: Repair Hfr