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Microbiology Ch 8

Microbiology Torta,Funke,Case Ch. 8 - Microbial Genetics

Science of heredity, how information is carried and replicated Genetics
The genetic information within a cell Genome
A cell's genetic information is organized into _________? They contain DNA. Chromosomes
Chromosomes contain _________, which are segments of DNA. Genes
DNA is a macromolecule composed of these repeating units. Nucleotides
Each nucleotide includes these three things. A nitrogenous base (adenine, thymine, cytosine, guanine), deoxyribose (a pentose sugar), and a phosphate group.
Name the four bases in DNA Adenine, thymine, cytosine, guanine
The shape of a DNA molecule. Double helix
Structure of each strand of DNA. Sugar-phosphate backbone with a nitrogenous base attached to each sugar in the backbone.
Holds together the two strands of DNA Hydrogen bonds between the nitrogenous bases
Nitrogenous bases that always connect to each others in DNA Base pairs: Adenine pairs with Thyamine; cytosine pairs with guanine
Why are paired DNA strands always complementary ? The specific base pairing requires that each strand match the other's corresponding bases
Where is genetic information encoded? The linear sequence of bases along a strand of DNA: Average gene has 1000 bases.
The rules that determine how a nucleotide sequence is converted into the amino acid sequence of a protein Genetic code
Allows for precise duplication of DNA during cell division The complementary structure of DNA
A gene usually "codes" for what? A messenger RNA (mRNA) molecule which ultimately results in the formation of a protein. Alternatively, it might code for a transfer RNA (tRNA) or a ribosomal RNA (rRNA).
When the ultimate molecule for which a gene codes has been produced, it is said to be ___________? Expressed
An organism's genetic makeup; it's entire DNA. Genotype
The actual expression of the properties that a gene encodes for . . . Phenotype
Number of chromosomes in a bacteria One
How many base pairs in E. coli, a typical bacteria? 4.6 mission: If lined up would be 1mm long.
% cell volume of chromosome in E. coli 10%
Enzyme that twists and coils DNA topoisomerase II or DNA gyrase
Where is the chromosome in a bacteria? Atached at one or more points to the plasma membrane
The sequencing and molecular characterization of genomes Genomics
What makes possible the flow of genetic information from one generation to the next? DNA replication makes this possible
When does DNA replicate? Happens just before cell division.
How does genetic information contained in DNA flow in a metabolizing cell? It is transcribed into mRNA and translated into protein.
Why can one strand of DNA act as a template for the other? Because they are complementary
Describe DNA replication Two strands of parent DNA are unwound and separated one segment at a time, free nucleotides in cytoplasm match up to exposed bases of each single strand. Continues until entire DNA molecule is replicated.
In DNA replication what joins newlly added nucleotides to the growing DNA strand? DNA polymerase
In DNA replication, the point at which replication occurs. Replication fork
During DNA replication, the process in which one strand is conserved and one strand is new is called... Semiconservative replication
Study and understand Figure 8.3 and 8.4: DNA Replication Study and understand Figure 8.3 and 8.4: DNA Replication (graphics cannot be used on these flashcards)
DNA Replication requires a lot of energy. What provides the energy for DNA replication? The nucleotides provide this. They are nucleoside triphosphates. Deoxyribose is the sugar in the nucleosides used to synthesize DNA.
What happens to necleosides as they are are added to the growing strand of replicating DNA? Two phosphate groups are removed from these in a hydrolysis reaction that provides energy to make the new bonds in the DNA strand.
Study and understand Figure 8.5 and 8.6: RE: DNA replication Figure 8.5, 8.6 be ready to draw and label these items and ID all the important points
In DNA replication, what is the original strand called? Parental strand
During DNA replication, one strand is synthesized continuously. What is that strand called? Leading strand. It is synthesized in the 5' -> 3' direction.
DNA polymerase can only add new nuclotides to which end of the DNA strand? The 3' end
What overcomes the problem that DNA polymerase can only add to the 3' end? What is needed to start synthesis? RNA primer
The strand of DNA that is replicated second. Lagging strand
The lagging strand of DNA is replicated in pieces of about 1000 nucleotides each. These are called____________? Okazaki fragments
During DNA replication, what enzyme removes the RNA primer? DNA polymerase
During DNA replication, what enzymen joins the newly made DNA fragments? DNA ligase
Recall bacteria have a single chromosome that forms a loop. In DNA replication in some bacteria, the strands separate forming a replication fork in both directions. When is replication complete? When the replication forks meet.
In bacteria, evidence indicates that replications begins where? In the portion of the circular chromosome attached to the plasma membrane
Error rate of DNA replicaton One in 10 to the 10th power (one in ten billion) bases.
The accuracy of DNA replication is due largely to the "proofreading" capabiloity of what enzyme? DNA polymerase
How does DNA polymerase perform proofreading of a newly formed DNA strand? As each new base is added, it evaluates to be sure the proper complimentary base-pairing structure is formed. If not, it excises the improper base and replaces it with the correct one.
What is the "starting point" of DNA replication called? Point of origin
The transfer of information from the DNA strand to RNA Transcription
The process of protein synthesis from the information encoded on the RNA Translation
The three kinds of RNA in bacterial cells Messenger RNA, ribosomal RNA, transfer RNA
The cellular machinery of protein synthesis Ribosomes; contain ribosomal RNA
What carries the coded information for making specific proteins from DNA to the ribosomes where they are made? Messenger RNA (mRNA)
What is a gene? A portion of a cell's DNA
What happens during transcription? A strand of mRNA is synthesized using a specific gene - a portion of the cell's DNA - as a template
What base does RNA contain instead of Thymine? Uracil
Name the complimentary bases in RNA Guanine pairs with Cytosine; Anine pairs with uracil
In RNA, what would be the complement of the DNA base sequence ATGCAT UACGUA
Transcription requires what enzyme? RNA polymerase
In transcription, the DNA site that RNA binds to is called the? Promoter
RNA systhesis is completed when RNA polymerase reaches a site on DNA called _________? Terminator
Steps of RNA replication RN polymerase bomds to promoter on DNA, RNA polymerase assembles free nucleotides into a new chain, RNA polymerase moves along the DNA and continues until it reaches the terminator site, released.
How many strands does RNA (including mRNA) have? One, not two like DNA.
Steps of DNA replication DNA is unwound, replication fork forms at orgin of replication, leading strand synthesized continuously, lagging strand synthesized in pieces called Okazaki fragments with help from RNA primer
mRNA uses groups of three nucleotides to code information. These groups are called _________? Codons
The sequence of codons in mRNA determines what? The sequence of amino acids in the protein being synthesized. Each codon codes for a particular amino acid. This is the genetic code.
There are 64 possible codons and 20 amino acids. Most amino acids are signaled by several alternative codons. What is this situation called? degeracy of the code
Why is degeneracy and advantage? It allows for a certain amount of change or mutation in the DNA without affecting the protein produced.
Of 64 codons 61 are sense codons, 3 are nonsense codons (stop codons). What are sense codons for? They code for amino acids
What are nonsense codons (stop codons) for? They signal the end of protein molecule synthesis
The start codon (also the codon for methionine) is what? AUG, in bacteria it codes formylethione rather than methionine.
At what site in a cell are the mRNA codons read and the appropriate protein assembled? Ribosome, the site of protein synthesis
In the ribosomes, what recognizes specific codons and transports the required amino acids for the synthesys of protein? transfer RNA (tRNA)
Each tRNA has a sequence of three bases that is complementary to a codon. What is this called? anticodon
Ribosomes produce proteins. What functions does it provide to do this? It directs the orderly binding of tRNAs to codons and assembles the amino acids brought there into a chain, ultimately producing a protein. Be sure and see figure 8.10.
The ribosome moves along the mRNA in what direction? The 5' -> 3' direction
Briefly describe translation (in bacterial ribosome) tRNA binds to start codon, bring with it formylmethione, tRNA for 2nd codon moves into place, 1st amino acid xferred by ribosome(r), r moves along mRNA to next codon, continues and assembles protein until three nonsense codons reached. See Figure 8.10.
Why can translation begin before transcription is complete (in bacteria)? mRNA is produced in the cytoplasm, start codons being transcribed are available to ribosomes before the entire mRNA molecule is complete.
In eukaryotic cells, translation cannot begin before transcription is complete. Why is this? In eukaryotes transcription takes place in the nucleus. The mRNA must be completed and moved through the nuclear membrane to the cytoplasm before translation can begin. Plus RNA undergoes processing before leaving nucleus.
In eukaryotes regions of genes that code for proteins are often interrupted by noncoding DNA. Describe eukaryotic genes They are composed of exons (regions of DNA expressed) and introns (intervening regions of DNA that do not code protein)
What are exons? Regions of eukaryotic DNA expressed
What are introns? Intervening regions of eukaryotic DNA that do not code protein
Briefly describe eukaryotic mRNA synthesis RNA polymerase synthesizes RNA in nucleus that contains exons and introns (RNA transcript), ribozymes remove intron-derived RNA & splicetogether exon-derived RNA -> mRNA, mRNA leaves nucleus
What's a common feature of all metabolic reactions? They are catalyzed by enzymes.
What stops a cell from performing unneded chemical reactions? feedback inhibition
Why is regulation of a cell's protein synthesis important to a cell? It conserves energy and prevents buildup of unneeded components
Many genes - perhaps 60-80% are not regulated but their products are produced at a fixed rate. What are these called? Constitutive genes
What trick does protozoan Trypanosoma use to prevent destruction by a hosts immune system? It turns on one surface glycoprotein at a time as the host's immune system kills parasites with only one type of surface molecule.
What two genetic control mechanisms regulate the transcription of mRNA and the synthesys of proteins from them? Repression and induction
What is repression The regulatory mechanism that inhibits gene expression and decreases the synthesis of enzymes. Usually a response to over-abundance of end-product in a metabolic pathway.
What regulatory proteins mediate repression? Repressors. These block the ability of RNA polymerase to initiate transcription from the repressed genes.
A process that turns on the transcription of a gene or genes is called __________? Induction
A substance that acts to induce transcription of a gene is called a/n __________? Inducer
What are enzymes called that are synthesized in the presence of inducers? Inductible enzymes
When the presence of compound, such as lactose indirectly induces a cell to synthesize more enzyme, this response is called ____________? Enzyme induction
Genes which determine the structure of proteins are called _______? Structural genes
DNA segments that do not code for proteins but do provide control functions. Control region
The portion of a control region where RNA polymerase initiates transcription. Promoter
A portion of a control region of DNA that acts as a go or stop signal for transcription of the structural genes. Operator
A set of operator and promoter sites and the structural genes they control. Operon
Who invented the operon theory of gene expression? Francois Jacob and Jacques Monod in 1961
What prevents E. coli from producing the enzyme to split lactose when lactose is not present? Near the lac operon on the bacterial DNA is a regulator gene (I gene) which codes for a repressor protein. When lactose is absent, it binds binds tightly to the operator site, preventing RNA polymerase from transcribing the genes, and no mRNA is made.
Briefly describe how the presence of lactose for E. coli switches on the production of the enzyme that splits lactose. Lactos is transported into the cell, converted into the inducer allocactose. The inducer binds to the repressor protein so it cannot bind to the operator site, thus enabling the operator. RNA polymerase can then transcribe structural genes onto mRNA.
What is a repressed operon? Turned off
What is cAMP? What does it do? It is cyclic AMP. It is an alarmone - a cellular alarm signal. cAMP signals a shortage of and a lowered level of ATP.
cAMP binds to the _________? cAMP receptor protein (CRP)
What is an alarmone? A cellular alarm signal . Used to respond to environmental or nutritional stress.
Inhibition of metabolism of alternative carbon sources by glucose is called _______? Catabolite repression - or the "glucose effect"
Describe the structure of an operon. It is a segment of DNA that follows a regulatory gene and consists of a control region and structural geners. The control region contains a promoter and an operator in that order. It is followed by the structural genes which code for proteins.
In the operon model, what happens if the repressor is active and the operon is off? No protein is produced. The repressor binds to the operator site and blocks RNA transcriptase from moving on to the structural genes. No protein produced.
In the operon model of gene regulation, what happens if the repressor is inactive and the operon is on? Protein is produced.
What is a mutation? A change in the base sequence of DNA.
What is a "silent" mutation? One that causes no change in the activity of the product encoded by the gene.
The most common type of mutation. Base substitution - point mutation
A mutation that results in an amino acid substitution in the synthesized protein is callded a __________ mutation? missense
Name a common disease caused by a missense mutation. Sickle-cell anemia
A base substitution resulting in a nonsense codon is called a __________? Nonsense mutation. When transcribed to mRNA, it creates a nonsense or stop codon that stops the production of the protein, sometimes producing a protein fragment.
When one or a few nucleotide pairs are deleted or inserted in the DNA the mutation is called a ___________ mutation. frameshift
Chemicals and radiation that directly or indirectly bring about mutations are called _____? mutagens
What type of mutation in Salmonella typhimiruium allows it to survive in phagocytes? An altered outer membrane
What organisms have a mutation in the capsule-encoding gene that results in decreased pathogenicity because phagocytes can destroy them? Streptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis.
Nitrous acid is a mutagen. What does it do? It alters the base adenine (A) to a form that no longer pairs with thymine (T) but instead pairs with cytosine (C).
Mutagens that have molecules that are structurally similar to normal bases but have slightly altered base-pairing properties are called? nucleoside analog mutagens
Give an example of a drug that is a nucleoside analog. AZT (azidothymidine) used in the treatments of HIV infection.
What component of smoke, soot is an effective frameshift mutagen? Benzpyrene
What organism produces Aflatoxin, a frameshift mutagen? Aspergillus flavus. Grows on peanuts and grain
Frameshift mutagens used against herpesvirus infections? acridine dyes.
How do most frameshift mutagens do their damage? They have the right size and chemical properties to slip between the stacked base pairs of the DNA double helix, slightly offsetting two strands, leaving a gap or bulge in one strand. When copied, bases are inserted in the copy.
How does radiation cause mutation? It excites some electrons, which bombard other molecules producing ions and free radicals. These are very reactive. Some combine with bases in DNA, resulting in errors in replication and repair that produce mutations.
How does UV light cause mutation? It causes the formation of covalent bonds between certain bases. Adjacent thymines in a DNA strand can cross-link to form thymine dimers. These dimers, unless repaired, may cause serious damage to the cell because it cannot properly transcribe it.
What special mechanism do bacteria and some other organisms have to repair UV-induced damage? Light-repair enzymes called photolyases. These use visible light energy to separate the dime back to the original two thymine.
What repair mechanism is not restricted to UV-induced damage but can repair mutations from other causes as well? Nucleotide excision repair. Enzymes cut out distorted cross-linked thymines by opening a wide gap. They fill the gap with newly synthesized DNA that is complementary to the undamaged strand. Then DNA lygase seals the DNA backbone's covalent bonds.
UV exposure of human skin causes sunburn. What is sunburn? A large number of thymine dimers form in skin cells. Unrepaired dimers may result in skin cancers.
The inherited xeroderma pigmentosum results to increased sensitivity to UV. What causes it? A defect in the nucleotide excision repair. Patients with this disorder have an increased risk of skin cancer.
What is the "mutation rate"? The probability that a gene will mutate when a cell divides.
What is the average mutation rate for a single base? 10 to the minus 9 (one in one billion)
The average gene has how many base pairs? 1,000
What is the spontaneous rate of mutation for a gene? 10 to the minus 6 (one in one million)
How much does a mutagen typically increase the mutation rate? 10 to 1000 times
What two common methods are used to select mutant cells from a colony? Positive Direct Selection - the selected cells thive in a selective environment. And Negative (indirect) Selection - selects cells that cannot perform a certain function.
How does "replica plating" perform negative selection? A plate is grown with about 100 bacteria. Paper or velvet is used to transfer the colony print to other plates, some with and some without the target chemical. Cells that grow on the media with the target substance but not on the other media are saved.
A mutant microorganism that has a nutritional requirement that is absent in the parent is know as an _________? Auxotroph
What are substances called that cause cancer in animals, including humans? Carcinogens
Test that uses suxotrophs of Salmonella to test to see if a substance is a carcinogen? Ames test. They use cells that have lost the ability to synthesize histidine. Cells retested after exposure to test substance.
When a new mutation reverses the effect of a previous mutation what is this called? A reversion
The exchange of genes between two DNA molecules to form new combinations of genes on a chromosome. Genetic recombination
When two chromosomes break and rejoin and shuffle chromosomes. Crossing over. In eukaryotes, this happens during formation of reproductive cells. Also is used in bacteria.
Mutation and recombination contribute to a populations genetic __________? Diversity
When genes transfer from a microbe to its offspring. Vertical gene transfer
When a microbe transfers its genes to microbes of the same generation. Horizontal gene transfer
The cell that provides DNA to another cell. Donor cell
The cell that receives DNA from another cell. Recipient cell
A recipient cell that incorporates part of a donor's DNA into it's own DNA is called a _________? Recombinant
How common is the transfer of genetic material between cells? Not common. It may occur in less than one percent or less of an entire population.
The process by which DNA are transferred from one bacterium to another as "naked" DNA in solution. Transformation
Who discovered transformation? When? What microbe? Frederick Griffith, 1928, Streptococcus pneumoniae
Transformation occurs naturally among very few genera of bacteria. Name some. Bacillus, Haemophilus, Neisseria, Acinetobacter and some Streptococcus and Staphylococcus
Transformation works best when the donor and recipient are _________? Very closely related.
When a recipient cell is in a physiological state in which it can take up donor DNA it is said to be _________? Competent
What does cell competence result from? Alterations in the cell wall that make it permeable to large DNA molecules.
What method of exchanging DNA requires direct cell-to-cell contact? Conjugation. With sex pili in gram negative or with sticky surface molecules in gram positive cells.
When gram negative cells conjugate, what two types of cells are required? One with the gene for sex pili, and one without (no pili)
First plasmid observed to be transferreb between cells during conjugation? F factor (fertility factor) in E. coli
Cells that incorporate the F factor into their chromosome are called____? Hfr cell (high frequency of recombination
In conjugation when the donor is sharing part of its chromosome, usually the chromosome breaks before it is completly transferred. How is this useful? It can be used to map the location of genes on the chromosome, by timing how long the conjugation took place, mapping genes by transfer time from the beginning of conjugation.
A virus that infects a bacteria is called a __________? Bacteriophage, or phage
What method of genetic transfer between bacteris involves a bacteriophage? Transduction
What type of transduction results in the replication of the original virus plus the dismembering and inclusion in viral capsules bits of DNA found within the invaded cell? General transduction
What type of transduction results in the transfer of a specific trait, such as the production of a toxin? Specialized transduction
Name some bacteria that use specialized transduction to transfer toxin production genes. Corynebacterium diphtheriae for diphtheria toxin; Streptococcus pyogenes for erythrogenic toxin; and E. coli O157:H7 for Shiga toxin.
What is the F factor for in a cell? It carries genes for sex pili and for the transfer of the plasmit to another cell.
Are most plasmids essential? No.
What type of plasmid is the F factor plasmid? Conjugative plasmid
Plasmids that code for enzymes that trigger the catabolism of certain unusual sugars and hydrocarbons are called _____? dissimilation plasmids
What genus of microbe can use exotic substances like toluene, camphor, and hydrocarbons for energy sources? Pseudomonas. They are used in bioremediation for this reason.
Name some plasmid-coded toxins that are important to disease. E. coli - bacterial attachment "travelers diarrhea"; exfoliative toxin of Staphylococcus aureus; neuro toxins from Clostridium tetani; Bacillus anthracis toxins.
Plasmids that contain genes for the synthesis of proteins that kill other bacteria are called _______? Bacteriocins
Factors transmitted by plasmids that cause antibiotic resistance, heavy metals, or cellular toxins. Resistance factors (R factors)
Many R factors have two groups of genes. What are they? Resistance transfer factor (RTF) that includes plasmid replication and conjugation; r-determinant - which has the resistance genes and codes for the production of enzymes.
The R100 plasmid provides resistance for what? Sulfonamides, streptomycin, chloramphenicol, tetracycline, and resistance to mercury.
What microbes can share the R100 plasmid? Escherichia, Klebsiella, Salmonella.
Small segments of DNA molecules that can move from one region of a DNA molecule to another. Transposons. They may move from one site to another site on the same chromosome or to another chromosome or plasmid.
How many base pairs are in a transposon? 770 to 40,000 base pairs
Who discovered transposons? Barbara McClintock in the 1950s
How often do transpositions of transposons happen? Comparable to the mutation rate of bacteria: From one in 100,000 to one in ten million per generation.
What information do all transposons contain? Information for their own transposition.
The simplest transposons code for an enzyme and are also called________? Insertion sequences (IS) - enzymen transposase, which catalyzes the cutting and resealing of DNA that occurs in transposition and recognition sites.
What are "recognition sites"? Short inverted repeat sequences of DNA that transposace recognizes as recombination sites between the transposon and the chromosome.
True or false: Tranposons can be carried between cells - even of different species? True. They may be carried by plasmids or viruses. Thus are a powerful mediator of evolution in organisms.
Created by: timm



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