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Ch.8 - Microbiology
Microbial Genetics
| Question | Answer |
|---|---|
| Plasmid DNA from E. coli. | Plasmids are transferrable pieces of DNA that bacteria can exchange with other bacteria. Can carry things like antibiotic resistance and toxin production. |
| Big Picture: Genetics. | The science of heredity. Central dogma of molecular biology. Mutations. Gene expression controlled by operons. |
| Typical chain of events described by central dogma: | DNA, (transcription), mRNA, (translation), Protein, Function. |
| How mutations alter a genome: | Mutated DNA, Mutated mRNA, Altered Protein, Altered Function. |
| In base substitution mutations. | A single DNA base pair is altered. |
| In frame-shift mutations. | DNA base pairs are added or removed from the sequence, causing a shift insequence reading. |
| Inducible operon. | Includes genes that are in the "off" mode with the repressor bound to the DNA, and its turned "on" by the environmental inducer. |
| Repressible operon. | Includes genes that are in the "on" mode without the repressor bound to the DNA, and its turned "off" by the environmental corepressor and repressor. |
| Alteration of bacterial genes and gene expression. | Cause of disease. Prevent disease treatment. Manipulated for human benefit. |
| Diseases. | Many bacterial diseases are caused by the presence of toxic proteins that damage human tissue. These toxic proteins are coded for by bacterial genes. |
| Vibrio cholerae. | Produces an enterotoxin that causes diarrhea and severe dehydration, which can be fatal if left untreated. |
| Antibiotic Resistance. | Mutations in the bacterial genome are one of the 1st steps toward the development of antibiotic resistance. This process has occurred in Staphylococcus aureus, which is currently resistant to beta-lactam antibiotics such as penicillin. |
| Methicillin. | Was introduced to treat penicillin-resistant S. aureus. Methicillin-resistant S. aureus, (MRSA), is now a leading cause of healthcare-associated infections. |
| Biotechnology. | Scientist can alter a microorganism’s genome, adding genes that will produce human proteins used in treating disease. Insulin, used for treatment of diabetes, is produced in this manner. |
| DNA expression. | Leads to cell function via the production of proteins. Can be controlled by operons. |
| Mutations. | Alter DNA sequence. |
| DNA mutations. | Can change bacterial function. |
| Genetics. | Study of genes, how they carry information, how information is expressed, and how genes are replicated. |
| Chromosomes. | Structures containing DNA that physically carry hereditary information; the chromosomes contain genes. |
| Genes. | Segments of DNA that encode functional products, usually proteins. |
| Genome. | All the genetic information in a cell. |
| Genetic code. | Set of rules that determines how a nucleotide sequence is converted to an amino acid sequence of a protein. |
| Genotype. | Genetic makeup of an organism. We can NOT physically see the genotype of an organism. |
| Phenotype. | Expression of the genes We can physically see the phenotype of an organism. |
| Bacteria usually have: | Single circular chromosome made of DNA and associated proteins. |
| Short tandem repeats (STRs). | Repeating sequences of non-coding DNA homologous to introns in eukaryotes. |
| Vertical gene transfer. | Flow of genetic information from one generation to the next. |
| DNA Expression. | Genetic information is used within a cell to produce for proteins including enzymes for the cell to function (Blueprint). |
| DNA Recombination | Genetic information can be obtained (and transferred horizontally) from another cell in the same generation or from a parent cell during cell division. |
| DNA Replication. | Genetic information can be expressed within a cell or transferred to another cell. |
| Double helix (Replication): | "Backbone" consists of deoxyribose-phosphate (sugar). Two strands of nucleotides are held together by hydrogen bonds between A-T and C-G. Strands are antiparallel (5’-3’ and 3’-5’). |
| Order of the nitrogen-containing bases: | Forms the genetic instructions of the organism (Genotype). |
| DNA: | Adenine, Thymine, Cystonine, Guanine (plus deoxyribose sugar and phosphate). |
| Replication. | One strand serves as a template for the production of a second strand. Topoisomerase and gyrase relax the strands. Helicase separates the strands. A replication fork is created. |
| DNA Replication: Step 1. | Double helix of the parental DNA separates as weak hydrogen bonds between the nucleotides on opposite strands break in response to the action of replication enzymes. |
| DNA Replication: Step 2. | Hydrogen bonds form between new complementary nucleotides and each strand of the parental template to form new base pairs (2). |
| DNA Replication: Step 3. | Enzymes catalyze the formation of sugar-phosphate bonds between sequential nucleotides on each resulting daughter strand (3). |
| DNA polymerase adds nucleotides to the growing DNA strand. | In the 5'-> 3' direction. Started by an RNA primer. Leading strand is synth. continuously. Lagging strand is synth. discontinuously, creating Okazaki fragments. DNA polym. removes RNA primers; Okazaki fragments are joined by the DNA polym. and DNA ligase. |
| DNA Gyrase. | Relaxes supercoiling ahead of the replication fork. |
| Makes covalent bonds to join DNA strands; Okazaki fragments, and new segments in excision repair. | |
| DNA Polymerases. | Synthesizes DNA; proofreads and repairs DNA. |
| Endonucleases. | Cut DNA backbone in a strand of DNA; facilitate repair and insertions. |
| Exonucleases. | Cut DNA from an exposed end of DNA; facilitate repair. |
| Helicase. | Unwinds double-stranded DNA. |
| Methylase. | Adds methyl group to selected bases in newly made DNA. |
| Photolyase. | Uses visible light energy to separate UV-induced pyrimidine dimers. |
| Primase. | An RNA polymerase that makes RNA primers from a DNA template. |
| Ribozyme. | RNA enzyme that removes introns and splices exons together. |
| RNA Polymerase. | Copies RNA from a DNA template. |
| snRNP. | RNA-protein complex that removes introns and splices exons together. |
| Topoisomerase. | Relaxes supercoiling ahead of the replication fork; separates DNA circles at the end of DNA replication. |
| Transposase. | Cuts DNA backbone, leaving single-stranded “sticky ends”. |
| Important Enzymes in DNA Replication, Expression, and Repair. | DNA Gyrase, DNA Ligase, DNA Polymerases, Endonucleases, Exonucleases, Helicase, Methylase, Photolyase, Primase, Ribozyme, RNA Polymerase, snRNP, Topoisomerase, Transposase. |
| Summary of Events at the DNA Replication Fork # 1 Helix: | Enzyme unwinds the parental double helix. |
| Summary of Events at the DNA Replication Fork # 2 Unwound: | Proteins stabilize unwound parental DNA. |
| Summary of Events at the DNA Replication Fork # 3 Cont. Synth: | Leading strand is synthesized continuously. |
| Summary of Events at the DNA Replication Fork # 4Disc Synth : | Lagging strand is synthesized discontinuously. Primase, an RNA polymerase, synthesizes a shortRNA primer, which is then extended by DNA polymerase. |
| Summary of Events at the DNA Replication Fork #5 Primer digest: | DNA polymeraze digests RNA primer, replaces it with DNA. |
| Summary of Events at the DNA Replication Fork #6 Ligaze joins: | DNA ligaze joins the disconitnuous fragments of the lagging strand. |
| Nucleotides. | Supply Energy for replication. |
| Provides energy. | Hydrolysis of two phosphate groups on ATP. |
| When a nucleoside triphosphate bonds to the sugar. | Loss of 2 phosphates. |
| Origin of Replication (ORI). | Most bacterial DNA replication is bidirectional. |
| Each offspring cell receives___ of the DNA molecule. | One copy. |
| Replication is highly accurate due to. | Proofreading capability of DNA polymerase. |
| Ribonucleic acid. | Single-stranded nucleotide. 5-carbon ribose sugar. Contains uracil (U) instead of thymine (T). |
| Ribosomal RNA (rRNA): | Integral part of ribosomes. Produced inside the nucleus of the cell. |
| Transfer RNA (tRNA): | Transports amino acids during protein synthesis. |
| Messenger RNA (mRNA): | Carries coded information from DNA to ribosomes. |
| Transcription in Prokaryotes. | Synthesis of a complementary mRNA strand from a DNA template. |
| Transcription begins when. | RNA polymerase binds to the promoter sequence on DNA. |
| Transcription proceeds in the 5'-3' direction. | Only one of the two DNA strands is transcribed. |
| Transcription stops when. | Reaches the terminator sequence on DNA. |
| Translation. | mRNA is translated into the "language" of proteins. |
| Codons. | Groups of three mRNA nucleotides that code for a particular amino acid. |
| 61 sense codons. | Encode the 20 amino acids. |
| Genetic code. | Involves redundancy, meaning each amino acid is coded by several codons. The genetic code has no ambiguity, each codon codes for only one amino acid. |
| Know Start and Stop codons. | Prokaryotes use N-Formylmethionine. Eukaryotes use Methionine for their respective start codons. |
| Translation of mRNA begins at the start codon: | AUG. |
| Translation ends at stop codons: | UAA, UAG, UGA. |
| Codons of mRNA are "read". | Sequentially. |
| tRNA molecules transport the required amino acids to. | Ribosome. |
| tRNA molecules also have an anti-codon. | Base-pairs with the codon. |
| Amino acids are joined by. | Peptide bonds. |
| A site. | Aminoacyl site (acceptor site). |
| P site. | Peptidyl site (peptide bond site). |
| E site. | Exit site. |
| Translation process. | Good target for antibiotic therapy against bacteria. Why is that? |
| In bacteria. | Translation can begin before transcription is complete. |
| In eukaryotes. | Transcription occurs in the nucleus, whereas translation occurs in the cytoplasm. |
| Exons. | Are regions of DNA that code for proteins. |
| Introns. | Regions of DNA that do not code for proteins. |
| What structure in prokaryotes is homologous to introns in eukaryotes? | Short tandem repeats (STRs). |
| Small nuclear ribonucleoproteins (snRNPs). | Remove introns and splice exons together. |
| In the nucleus. | A gene composed of exons and introns is transcribed to RNA by RNA polymerase. |
| Processing involves snRNPs in the nucleus to remove. | Intron-derived RNA and splice together the exon-derived rNA into mRNA. |
| After further modification, the mature mRNA. | Travels to the cytoplasm, where it directs protein synthesis. |
| RNA Processing in Eukaryotic Cells. | RNA editing. |
| Constitutive genes. | Are expressed at a fixed rate. Also termed housekeeping genes. Important for basic cell maintenance and processes. |
| Inducible genes. Repressible genes. Catabolite repression. | Genes expressed only as needed. |
| Catabolite repression. | Carbon based energy breakdown. Metabolites produced from those reactions. |
| Repression. | Inhibits gene expression and decreases enzyme synthesis. Mediated by repressors, proteins that block transcription. Default position of a repressible gene is on. |
| Induction. | Turns on gene expression. Initiated by an inducer. Default position of an inducible gene is off. |
| Pre-transcriptional Control. | Repression. Induction. |
| Promoter. | Segment of DNA where RNA polymerase initiates transcription of structural genes. |
| Operator. | Segment of DNA that controls transcription of structural genes. |
| Operon. | Set of operator and promoter sites and the structural genes they control. |
| Inducible operon, | Structural genes are not transcribed unless an inducer is present. |
| In the presence of lactose. | Lactose (inducer) binds to the repressor; the repressor cannot bind to the operator and transcription occurs. |
| In the absence of lactose. | The repressor binds to the operator, preventing transcription. |
| Structure of the operon - (inducible operon). | Consists of the promoter and operator sites and structural genes. It is regulated by the product of the regulatory gene. |
| Repressor active, operon off - (inducible operon). | Repressor protein binds with the operator, preventing transcription from the operon. |
| Repressor inactive, operon on - (inducible operon). | When the inducer alloctalose, binds to the repressor protein, the inactivated repressor can no longer block transcription. The structural genes are transcribed, ultimately resulting in the production of the enzymes needed for lactose catabolism. |
| In repressible operons. | Structural genes are transcribed until they are turned off. |
| Excess tryptophan (corepressor). | Binds and activates the repressor to bind to the operator, stopping tryptophan synthesis. |
| Repressor inactive, operon on - (Repressible operon). | The repressor is inactive, and transcription and translation proceed, leading to synthesis of Tryptophan. |
| Repressor active, operon off - (Repressible operon). | When the corepressor tryptophan binds to the repressor protein, the activated repressor binds with the operator, preventing transcription from the operon. |
| Catabolite repression (Positive Regulation). | Inhibits cells from using carbon sources other than glucose. |
| Cyclic AMP (cAMP) (Positive Regulation). | Builds up in a cell when glucose is not available. |
| cAMP binds to the lac promoter (Positive Regulation). | Initiating transcription and allowing the cell to use lactose. |
| Bacteria growing on glucose as the sole carbon source. | Grows faster than on lactose. |
| Bacteria growing in medium containing both glucose and lactose. | Consume glucose first, and the after a short lag time, the lactose. |
| During lag time. | Intracellular cAMP increases the lac operon is transcribed, more lactose is transported into the cell, and B-galacto-sidases synthetize to break down lactose. |
| Lactose present, glucose scarce (cAMP level high). | Activated CAP, and the lac operon produces large amounts of mRNA for lactose digestion. |
| Lactose present, glucose present (cAMP level low). | Glucose is present, cAMP is scarce, and CAP is unable to stimulate transcription. |
| Epigenetic Control. | Methylating nucleotides turns genes off. Why does this turn genes off? Methylated (off) genes can be passed to offspring cells. Not permanent. |
| Post-Transcriptional Control. | microRNAs (miRNAs) base pair with mRNA to make it double-stranded. Double-stranded RNA is enzymatically destroyed, preventing production of a protein. Essentially tagging mRNA for destruction, siRNA is a subset of microRNA’s. Area of medical research. |
| MicroRNAs Control a Wide Range of Activities in Cells. | Transcription of miRNA occurs. miRNA binds to target mRNA that has at least 6 complementary bases. mRNA is degraded. |
| Spontaneous mutations. | Occur in the absence of a mutagen. |
| Mutagens. | Agents that cause mutations. |
| Mutations. | A permanent change in the base sequence of DNA. Mutations may be neutral, beneficial, or harmful. |
| Base substitution (point mutation). | Change in one base in DNA. |
| Base Substitutions 1 (Mistake). | During DNA replication, a thymine is incorporated opposite guanine by mistake. |
| Base Substitutions 2 (New). | If not corrected, in the next round of replication, adenine pairs with the new thymine, yielding an AT pair in place of the original GC pair. |
| Base Substitutions 3 (Tyrosine). | When mRNA is transcribed from the DNA containing this substitution, a codon is produced that, during translation, encodes a different amino acid: tyrosine instead of cysteine. |
| Missense mutation. | Base substitution results in change in an amino acid. |
| Nonsense mutation. | Base substitution results in a nonsense (stop) codon. |
| Frameshift mutation. | Insertion or deletion of one or more nucleotide pairs Shifts the translational "reading frame“. |
| Chemical Mutagens. | Nitrous acid. Nucleoside analog. |
| Nitrous acid. | Causes adenine to bind with cytosine instead of thymine. |
| Nucleoside analog. | Incorporates into DNA in place of a normal base; causes mistakes in base pairing. |
| Oxidation of Nucleotides Makes a Mutagen. | Adenosine nucleoside normally base pairs by hydrogen bonds with an O and a H of a thymine or uracil nucleotide. Altered adenine will H bond with an H and a N of a cytosine nucleotide. |
| Nucleoside Analogs and the Nitrogenous Bases They Replace 1. | 2-aminopurine is incorporated into DNA in place of adenine but can pair with cytosine, so an AT become a CG pair. |
| Nucleoside Analogs and the Nitrogenous Bases They Replace 2. | 5-bromouracil is used as an anticancer drug (mistaken for thymine) by cellular enzymes but pairs with cytosine. Next DNA replication, an AT becomes a GC pair. |
| Ionizing radiation. | (X rays and gamma rays) causes the formation of ions that can oxidize nucleotides and break the deoxyribose-phosphate backbone. |
| UV radiation. | Causes thymine dimers (Pyrimidine dimers). Thymine dimers have been impacted as a leading cause of melanoma. |
| Photolyases. | Separate (repair) thymine dimers. |
| Nucleotide excision repair. | Enzymes cut out incorrect bases and fill in correct bases. |
| The Frequency of Mutation. | Spontaneous mutation rate + 1 in 10 expo 9 replicated base apirs of 1 in 10 expo 6 replicated genes. Mutagens increase the mutation rate to per 10 expo -5 or 10 expo -3 replicated gene. |
| Positive (direct) selection. | Detects mutant cells because they grow or appear different than unmutated cells. |
| Negative (indirect) selection. | Detects mutant cells that cannot grow or perform a certain function. |
| Auxtotroph. | Mutant that has a nutritional requirement absent in the parent. Use of replica plating. |
| The Ames test (Identifying Chemical Carcinogens). | Exposes mutant bacteria to mutagenic substances to measure the rate of reversal of the mutation. Indicates degree to which a substance is mutagenic. |
| Crossing over. | Two chromosomes break and rejoin, resulting in the insertion of foreign DNA into the chromosome. |
| Genetic recombination. | Exchange of genes between two DNA molecules; creates genetic diversity. |
| Horizontal gene transfer. | Transfer of genes between cells of the same generation. |
| Vertical gene transfer. | Transfer of genes from an organism to its offspring. |
| Transformation (mouse experiment with encapsulated bacteria). | Genes transferred from one bacterium to another as "naked" DNA. |
| Conjugation. | Plasmids transferred from one bacterium to another. Requires cell-to-cell contact via sex pili. |
| Donor cells carry the plasmid (F factor) and are called. | F+ cells. |
| Hfr cells contain ___ on the chromosome. | The F factor. |
| Conjugation can be used. | To map the location of genes on a chromosome. |
| Transduction in Bacteria. | DNA is transferred from a donor cell to a recipient via a bacteriophage. |
| Generalized transduction. | Random bacterial DNA is packaged inside a phage and transferred to a recipient cell. |
| Specialized transduction. | Specific bacterial genes are packaged inside a phage and transferred to a recipient cell. |
| Plasmids. | Self-replicating circular pieces of DNA. 1 to 5% the size of a bacterial chromosome. Often code for proteins that enhance the pathogenicity of a bacterium. |
| Resistance factors (R factors): | Encode antibiotic resistance. |
| Dissimilation plasmids. | Encode enzymes for the catabolism of unusual compounds. |
| Conjugative plasmid. | Carries genes for sex pili and transfer of the plasmid. |
| Complex transposons. | Carry other genes (e.g, in antibiotic resistance). |
| Insertion sequences (IS) - (transposons). | Code for transposase that cuts and reseals DNA. |
| Transposons. | Segments of DNA that can move from one region of DNA to another. |
| Genes and Evolution. | Mutations and recombination create cell diversity. Diversity is the raw material for evolution. Natural selection acts on populations of organisms to ensure the survival of organisms fit for a particular environment. |
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