Microbio test #2
Identify the base pairs used in the synthesis of deoxyribonucleotides
- thymine and cytosine (pyrimidines)- have single ring structure -guanine and adenine (purines) -have a double ring structure A and T go together G and C go together
the spontaneous mutation rate = ___________________ replicated base pairs or _____________ replicated genes
-1 in 10^9 - 1 in 10^6 -Mutagens increase the mutation rate to 10^-5 or 10^-3 per replicated gene.
Explain why DNA replication is bidirectional and includes both a leading and lagging strand
During replication, one strand, which is complementary to the 3' to 5' parental DNA strand, is synthesized continuously toward the replication fork because polymerase can add nucleotides in this direction. This continuously synthesized strand is known as the leading strand. The other strand, complementary to the 5' to 3' parental DNA, grows away from the replication fork, so the polymerase must move back toward the replication fork to begin adding bases to a new primer, again in the direction away from the replication fork. It does so until it bumps into the previously synthesized strand and then it moves back again (Figure 11.7). These steps produce small DNA sequence fragments known as Okazaki fragments, each separated by RNA primer. Okazaki fragments are named after the Japanese research team and married couple Reiji and Tsuneko Okazaki, who first discovered them in 1966. The strand with the Okazaki fragments is known as the lagging strand, and its synthesis is said to be discontinuous
Explain why anaerobes are killed when exposed to oxygen
Three main enzymes break down those toxic byproducts (ROS): superoxide dismutase, peroxidase, and catalase. Each one catalyzes a different reaction. Obligate anaerobes usually lack all three enzymes. Aerotolerant anaerobes do have SOD but no catalase
What method is used to determine the number of viable cells?
Typically plate count, because the bacteria won't grow if they're not alive
Individual nucleoside triphosphates combine with each other by covalent bonds known as 5ʹ-3ʹ ____________________, or linkages whereby the phosphate group attached to the 5ʹ carbon of the sugar of one nucleotide bonds to the hydroxyl group of the 3ʹ carbon of the sugar of the next nucleotide.
phosphodiester bonds
What are the two types of mutations
point and frameshift
_____ ______ is the substitution of a single base
point mutation
what is recombination
the process in which a donor DNA molecule replaces a segment of a host genome or is inserted into a host genome. Produces a new combination of alleles in prokaryotic organisms that produce asexually
what is gene therapy
the transplantation of normal genes into cells in place of missing or defective ones in order to correct genetic disorders.
what is the function of nucleic acids
they store genetic information needed for building and controlling the cell
Spacing of the backbone results in major(far apart) and minor (close together)grooves- proteins can bind to the DNA here
true
T/F mutation may be neutral, beneficial or harmful
true
what is transduction
two types: generalized- can transfer any gene from a donor to a recipient cell specialized: can transfer only a few closely linked genes between cells
what is transformation
uptake of DNA from the environment
Describe the biochemical structure of ribonucleotides
uracil replaces thymine in RNA - capable of 2 hydrogen bonds and bonds with adenine -Guanine and cytosine remain the same
Identify examples of toxin-producing algae
diatoms, dinoflagellates,
define genetic engineering
direct alteration of an organism's genes to achieve desirable traits utilizing recombinant DNA technology
Describe the formation and characteristics of biofilms
-A mature biofilm is a complex community of microorganisms attached to a surface. -They release polysaccharides, proteins, and DNA to form the extracellular polymeric substance -heterogenity is the difference in metabolic activity and location of microbes -the waste product of one organism becomes the nutrient for another -hard to treat with antibiotics
What is the importance of knowing the phases when doing research with microorganisms?
-Cells in the log phase show constant growth rate and uniform metabolic activity. For this reason, cells in the log phase are preferentially used for industrial applications and research work. The log phase is also the stage where bacteria are the most susceptible to the action of disinfectants and common antibiotics that affect protein, DNA, and cell-wall synthesis. -In certain pathogenic bacteria, the stationary phase is also associated with the expression of virulence factors, products that contribute to a microbe's ability to survive, reproduce, and cause disease in a host organism.
Explain several laboratory methods used to determine viable and total cell counts in populations undergoing exponential growth
-Direct cell count counting chambers electronic cell counting device (flow cytometry) on membrane filters -Plate count spread and pour plate techniques (ideal number 30-300 CFUs) diluted sample of bacteria is spread or poured into a Petri dish numbers are determined by counting the number of colonies formed multiplied by the dilutionfactor results expressed as colony forming units -the most Probable number Tubes inoculated with different amounts of sample are assessed for bacteria growth and the numbers are plotted in a chart -Indirect cell count (used to compare cell densities) spectrophotometer dry weight of a culture sample metabolic activity
Identify examples helminths' mode of transmission.
-Soil-transmitted helminthiases -Roundworm infections such as lymphatic filariasis, dracunculiasis, and onchocerciasis -Trematode infections, such as schistosomiasis, and food-borne trematodiases, including fascioliasis, clonorchiasis, opisthorchiasis, and paragonimiasis -Tapeworm infections such as cysticercosis, taeniasis, and echinococcosis
what happens during the log phase
-cells are dividing exponentially -maximum gene expression -Generation time is genetically determined by intrinsic growth rate (growth rate varies by species)
Describe quorum sensing and its role in cell-to-cell communication and coordination of cellular activities.
-in some pathogens, synthesis of virulence factors only begins when enough cells are present to overwhelm the immune defenses of the host
What happens during the stationary phase
-total number of viable cells stays constant -synthesis of important components in the cell slows down -endospore formation
what is conjugation
A process in which 2 organisms exchange genetic material following cell to cell contact Donor cells carry the plasmid (F factor) and are called F+ cells • Plasmids are copied and one copy is transferred thru the mating bridge to the other cell where the plasmid regain the original circular shape. When an F factor (a plasmid) is transferred from a donor (F+) to a recipient (F-), the F- cell is converted to an F+ cell
thymine and adenine have ________ hydrogen bonds
2
guanine and cytosine have _____ hydrogen bonds
3
Summarize the general characteristics of unicellular eukaryotic parasites
??
What are the uses of genomic libraries?
A genomic library is a collection of the total genomic DNA from a single organism Used to: determine DNA sequence, analyze gene function, detection of related genes from different sources
What is DNA analysis using agarose gel electrophoresis
Agarose gel electrophoresis is widely used to separate DNA (or RNA) of varying sizes that may be generated by restriction enzyme digestion or by other means, such as the PCR. -a technique used to separate biological molecules based on size and biochemical characteristics (charge and polarity) -DNA has a negatively charged backbone that is attracted to the positively charged electrode• Samples are loaded into wells within the agarose gel
Explain how RNA can serve as hereditary information
Although RNA does not serve as the hereditary information in most cells, RNA does hold this function for many viruses that do not contain DNA. Thus, RNA clearly does have the additional capacity to serve as genetic information. Although RNA is typically single stranded within cells, there is significant diversity in viruses. Rhinoviruses, which cause the common cold; influenza viruses; and the Ebola virus are single-stranded RNA viruses. Rotaviruses, which cause severe gastroenteritis in children and other immunocompromised individuals, are examples of double-stranded RNA viruses. Because double-stranded RNA is uncommon in eukaryotic cells, its presence serves as an indicator of viral infection. The implications for a virus having an RNA genome instead of a DNA genome are discussed in more detail in Viruses
define biotechnology
Biotechology is the science of utilizing living systems to benefit humankind
Describe the characteristics of parasitic platyhelminths
Cestodes "tapeworms" - Eggs are ingested and hatch into larvae - Attach to intestines with scolex - Reproductive segments (proglodds) - Intermediate host may be involved
______ and __________ can be used to identify organisms
DNA and RNA
define transgenic
DNA introduced from a different species
define recombinant
DNA molecules: new combinations of genetic material
what is the process of cytokinesis directed by
FtsZ
Define gene and genotype and differentiate genotype from phenotype
Gene: segments of DNA molecules that contain the instructional code necessary for synthesizing various proteins, enzymes or stable RNA molecules Genotype: a full collection of genes that a cell contains within it's genome phenotype: The set of genes being expressed at any given point in time determines the cell's activities and its observable characteristics
How can UV radiation act as a mutagen?
However, nonionizing radiation (like UV light) can induce dimer formation between two adjacent pyrimidine bases, commonly two thymines, within a nucleotide strand. During thymine dimer formation, the two adjacent thymines become covalently linked and, if left unrepaired, both DNA replication and transcription are stalled at this point. DNA polymerase may proceed and replicate the dimer incorrectly, potentially leading to frameshift or point mutations
it is possible to maintain a culture in log phase with a
chemostat in lab
Define generation time for growth based on binary fission
In prokaryotes (Bacteria and Archaea), the generation time is also called the doubling time and is defined as the time it takes for the population to double through one round of binary fission
What is the importance of plasmids in biotechnology?
In recombinant DNA technology, plasmids are often used as vectors: DNA molecules that carry DNA fragments from one organism to another. Plasmids used as vectors can be genetically engineered by researchers and scientific supply companies to have specialized properties. Some plasmid vectors contain genes that confer antibiotic resistance; these resistance genes allow researchers to easily find plasmid-containing colonies by plating them on media containing the corresponding antibiotic. The antibiotic kills all host cells that do not harbor the desired plasmid vector, but those that contain the vector are able to survive and grow
Explain the meaning of semiconservative DNA replication
In semiconservative replication, the two strands of the double helix separate during DNA replication, and each strand serves as a template from which the new complementary strand is copied; after replication, each double-stranded DNA includes one parental or "old" strand and one "new" strand.
Identify and describe different categories of microbes with specific growth such as altered light.
Light - photosynthetic bacteria depend on light to grow. Free on aquatic environments, in soil, or in symbiosis with fungi and lichens
Identify the Protista groups and their importance as pathogens
Many protists are pathogenic parasites that must infect other organisms to survive and propagate
Explain the principle of restriction fragment length polymorphism analysis and its uses
RFLP analysis has many practical applications in both medicine and forensic science. For example, epidemiologists use RFLP analysis to track and identify the source of specific microorganisms implicated in outbreaks of food poisoning or certain infectious diseases. RFLP analysis can also be used on human DNA to determine inheritance patterns of chromosomes with variant genes, including those associated with heritable diseases or to establish paternity -fingerprinting also
Identify and describe different categories of microbes with temperature requirements for growth: psychrophile, psychrotrophs, mesophile,thermophile, hyperthermophile
Mesophiles: love moderate temps 20-45 degrees psychrotrophs (psychrotolerant) : like cooler temperatures 4-25 degrees psychrophiles: cold loving Psychrophiles are microorganisms that can grow at 0 °C and below, have an optimum growth temperature close to 15 °C, and usually do not survive at temperatures above 20 °C Thermophiles: Organisms that grow at optimum temperatures of 50 °C to a maximum of 80 °C are called thermophiles ("heat loving") hyperthermophiles, which are characterized by growth ranges from 80 °C to a maximum of 110 °C, with some extreme examples that survive temperatures above 121 °C
Define mutation and describe the mutagens that can cause them
Mutation: a permanent change in the base sequence of DNA Mutagens: agents that cause mutations (can often be carcinogens)• Chemical: nitrites, cigarette smoke • Physical: UV light, X rays
Describe the characteristics of parasitic nematodes
Nematode larvae that infect humans:- Hookworm enters through the skin and moves to the lungs• Swallowed infected sputum carries it to the intestines- Heartworm is spread by mosquitoes• Infects heart of cats and dogs• Infect skin & eyes of humans• Nematode larvae that infect animals:- Threadworms are entomopathogenic nematodes (EPN) that kill insects• Bio pesRcide applicaRonsHeartwormohioline.osu.edu, soybean cist nematode• Nematode infect plants- Can damage roots, foliage, seeds
noncoding DNA
Noncoding DNA: areas do not encode proteins or stable RNA products• Before coding sequences and between genes (intergenic regions) -Prokaryotes appear to use their genomes very efficiently, with only an average of 12% of the genome being taken up by noncoding sequences. In contrast, noncoding DNA can represent about 98% of the genome in eukaryotes, as seen in humans, but the percentage of noncoding DNA varies between species
Distinguish between transcription in prokaryotes and eukaryotes
One critical difference in activity between DNA polymerase and RNA polymerase is the requirement for a 3'-OH onto which to add nucleotides: DNA polymerase requires such a 3'-OH group, thus necessitating a primer, whereas RNA polymerase does not
Why are persisters medically important? (death phase)
Persister cells are medically important because they are associated with certain chronic infections, such as tuberculosis, that do not respond to antibiotic treatment. (death phase)
Explain the structure and consequences for bacterial genetic diversity of transposons
Process whereby DNA independently excises from one location in a DNA molecule and integrates elsewhere using transposans Because transposons can move within a DNA molecule, from one DNA molecule to another, or even from one cell to another, they have the ability to introduce genetic diversity. Movement within the same DNA molecule can alter phenotype by inactivating or activating a gene -tranposan can cause multiple antibiotic resistance genes on a single R plasmid in Shigella strains causing bacterial dysentery. Such an R plasmid can then be easily transferred among a bacterial population through the process of conjugation.
Describe the different mechanisms of DNA repair.
Proofreading: most of the mistakes introduced during DNA replication are promptly corrected by most DNA polymerases through a function called proofreading Mismatch repair: Some errors introduced during replication are corrected shortly after the replication machinery has moved. The enzymes involved in this mechanism recognize the incorrectly added nucleotide, excise it, and replace it with the correct base Nucleotide excision repair (1st type of thymine dimer repair): enzymes recognize the distortion introduced by the pyrimidine dimer and replace the damaged strand with the correct bases, using the undamaged DNA strand as a template Direct repair (second type of thymine dimer repair): occurs through the process of photoreactivation in the presence of visible light. An enzyme called photolyase recognizes the distortion in the DNA helix caused by the thymine dimer and binds to the dimer. Then, in the presence of visible light, the photolyase enzyme changes conformation and breaks apart the thymine dimer, allowing the thymines to again correctly base pair with the adenines on the complementary strand
Identify health risks associated with biofilms and how they are addressed
Some of the methods used to control biofilm formation include mechanical and manual cleaning, chemical cleaning and sanitation, and application of hot water.
How can we access mutation rate among bacteria?
The Ames test and replica plating. The Ames test is used to measures the mutation rate associated with exposure to the carcinogenic compounds Replica plating: This technique is used to detect nutritional mutants, called auxotrophs, which have a mutation in a gene encoding an enzyme in the biosynthesis pathway of a specific nutrient, such as an amino acid. As a result, whereas wild-type cells retain the ability to grow normally on a medium lacking the specific nutrient, auxotrophs are unable to grow on such a medium
Explain the central dogma
The central dogma describes the two-step process, transcription and translation, by which the information in genes flows into proteins: DNA → RNA → protein.
Identify and describe different categories of microbes with requirements for growth with or without oxygen: obligate aerobe, obligate anaerobe,facultative anaerobe, aerotolerant anaerobe, and microaerophile
The growth of bacteria with varying oxygen requirements in thioglycolate tubes is illustrated in Figure 9.20. In tube A, all the growth is seen at the top of the tube. The bacteria are obligate (strict) aerobes that cannot grow without an abundant supply of oxygen. Tube B looks like the opposite of tube A. Bacteria grow at the bottom of tube B. Those are obligate anaerobes, which are killed by oxygen. Tube C shows heavy growth at the top of the tube and growth throughout the tube, a typical result with facultative anaerobes. Facultative anaerobes are organisms that thrive in the presence of oxygen but also grow in its absence by relying on fermentation or anaerobic respiration, if there is a suitable electron acceptor other than oxygen and the organism is able to perform anaerobic respiration. The aerotolerant anaerobes in tube D are indifferent to the presence of oxygen. They do not use oxygen because they usually have a fermentative metabolism, but they are not harmed by the presence of oxygen as obligate anaerobes are. Tube E on the right shows a "Goldilocks" culture. The oxygen level has to be just right for growth, not too much and not too little. These microaerophiles are bacteria that require a minimum level of oxygen for growth, about 1%-10%, well below the 21% found in the atmosphere.
Illustrate and briefly describe minimum, optimum, and maximum temperature requirements for growth.
The growth rates are the highest at the optimum growth temperature for the organism. The lowest temperature at which the organism can survive and replicate is its minimum growth temperature. The highest temperature at which growth can occur is its maximum growth temperature.
Describe the genetic code and explain why it is considered almost universal
The relationship between an mRNA codon and its corresponding amino acid is called the genetic code. The genetic code is nearly universal. With a few exceptions, virtually all species use the same genetic code for protein synthesis, which is powerful evidence that all extant life on earth shares a common origin
the _____________ is conserved in all cellular forms of life
central dogma. DNA to RNA to proteins
what is a protein signature
all proteins that are made in blood,other body fluids, or tissues, at certain times.. Can helpiIdentify how cell is responding to disease
What is CRISPR-Cas9?
applications of CRISPR-Cas9: -Add/replace/silence genes or parts of genes (substitutions, insertions, deletions) • Move genes (inversions or translocations)
Describe some of the adaptations microorganisms developed to survive in harsh environments
biofilms ?
What happens during the lag phase
cells are synthesizing new components
Describe examples of cell division not involving binary fission, such as budding or fragmentation
fragmentation: In some cyanobacteria, many nucleoids may accumulate in an enlarged round cell or along a filament, leading to the generation of many new cells at once. The new cells often split from the parent filament and float away in a process called fragmentation Budding: Other species may form a long narrow extension at one pole in a process called budding. The tip of the extension swells and forms a smaller cell, the bud that eventually detaches from the parent cell. Budding is most common in yeast
what are constitute genes?
genes that are always expressed
State the biotechnology applications
genomics: study of entire genomes. Development of antibiotics, diagnostic tools, vaccines, medical treatments and environmental bioremediation transcriptomics: study of the entire collection of mRNA. helps compare gene expression meta analysis: genomics or transcriptomics applied to an entire community, gene expression from multiple species Pharmacogenomics (toxicogenomic): evaluating effectiveness and safety of drugs• Gene expression changes in response to drug Proteomics: study entire complement of organism's proteins • Expression under environmental conditions • Biomarkers: proteins whose expression changes during disease process Bioinformatics: analysis of genetic information
define Capnophiles
grows better in a higher concentration of CO2 and a lower concentration of oxygen
Explain horizontal gene transfer and define recombinants.
horizontal gene transfer (HGT), the introduction of genetic material from one organism to another organism within the same generation It happens between one independent, mature organism to another Genes can be transferred to the same or different species. Recombination is the process in which a donor DNA molecule replaces a segment of a host genome or is inserted into a host genome. Recombinants are an organism, cell or haplotype formed by genetic recombination
what is a frameshift mutation
insertion or deletion of one or more bases. these result in a shift in the reading frame. caused by insertions or deletions of a number of nucleotides that are not a multiple of three are extremely problematic because they result in a shift in the reading frame. Because ribosomes read the mRNA in triplet codons, frameshift mutations can change every amino acid after the point of the mutation. The new reading frame may also include a stop codon before the end of the coding sequence. Consequently, proteins made from genes containing frameshift mutations are nearly always nonfunctional
What is gene silencing
interruption or suppression of gene expression at transcriptional or translational level
Describe the functions of the three main types of RNA used in protein synthesis
messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA) . information from DNA is transmitted to the ribosome for protein synthesis using mRNA. mRNA directs synthesis of proteins when needed. mRNA is relatively unstable and short-lived in the cell. rRNA and tRNA are stable types of RNA. rRNA is a major constituent of ribosomes, composing up to about 60% of the ribosome by mass and providing the location where the mRNA binds. The rRNA ensures the proper alignment of the mRNA, tRNA, and the ribosomes. tRNA carries the correct amino acid to the site of protein synthesis in the ribosome. It is the base pairing between the tRNA and mRNA that allows for the correct amino acid to be inserted in the polypeptide chain being synthesized
DNA strands with more G-C bonds require _____________ to break apart (denature) than those with more A-T bonds
more energy
identify nucleic acids and describe nucleotides' structure.
nucleotides are monomers that make up nucleic acids (consist of a 5 carbon sugar, phosphate group and 4 nitrogenous bases), nucleic acids = DNA and RNA- the difference between DNA and RNA is determined on the 2' carbon. DNA has a hydrogen and RNA has a OH group
Identify and describe different categories of microbes with specific growth such as altered osmotic pressure,
osmotic pressure halophiles require high levels of salt to survive
what are the environmental factors that impact growth
oxygen, pH, temperature, atmospheric pressure and light
Explain the method and uses of polymerase chain reaction and DNA sequencing
polymerase chain reaction (PCR) permits rapid amplification in the number of copies of specific DNA sequences for further analysis PCR occurs over multiple cycles, each containing three steps: denaturation, annealing, and extension. Machines called thermal cyclers are used for PCR; these machines can be programmed to automatically cycle through the temperatures required at each step (Figure 12.1). First, double-stranded template DNA containing the target sequence is denatured at approximately 95 °C. The high temperature required to physically (rather than enzymatically) separate the DNA strands is the reason the heat-stable DNA polymerase is required. Next, the temperature is lowered to approximately 50 °C. This allows the DNA primers complementary to the ends of the target sequence to anneal (stick) to the template strands, with one primer annealing to each strand. Finally, the temperature is raised to 72 °C, the optimal temperature for the activity of the heat-stable DNA polymerase, allowing for the addition of nucleotides to the primer using the single-stranded target as a template. Each cycle doubles the number of double-stranded target DNA copies. Typically, PCR protocols include 25-40 cycles, allowing for the amplification of a single target sequence by tens of millions to over a trillion.
___________________ contributes energy to drivepolymerization
pyrophosphate
what happens in the death phase
reduction of nutrients and accumulation of toxic waste cause cell death -programmed cell death -few cells remain alive, the persisters (Many cells lyse and release nutrients into the medium, allowing surviving cells to maintain viability and form endospores. The persisters are characterized by slow metabolic rate)
What are restriction endonucleases and how can they be used?
restriction endonucleases are bacterial enzymes produced as a protection mechanism to cut and destroy foreign cytoplasmic DNA. Today, we use restriction enzymes extensively for cutting DNA fragments that can then be spliced into another DNA molecule to form recombinant molecules.
Explain the process of plasmid replication
rolling circle replication (Figure 11.10). The circular nature of plasmids and the circularization of some viral genomes on infection make this possible. Rolling circle replication begins with the enzymatic nicking of one strand of the double-stranded circular molecule at the double-stranded origin (dso) site. In bacteria, DNA polymerase III binds to the 3'-OH group of the nicked strand and begins to unidirectionally replicate the DNA using the un-nicked strand as a template, displacing the nicked strand as it does so.
DNA analysis - sequencing
shotgun, pyrosequencing, illumina
Describe the differences between missense, nonsense, and silent mutations.
silent mutation : a point mutation will commonly result in the same amino acid being incorporated into the resulting polypeptide despite the sequence change Missense mutation: A missense mutation results in a different amino acid being incorporated into the resulting polypeptide. The effect of a missense mutation depends on how chemically different the new amino acid is from the wild-type amino acid. nonsense mutation: converts a codon encoding an amino acid (a sense codon) into a stop codon (a nonsense codon). Nonsense mutations result in the synthesis of proteins that are shorter than the wild type and typically not functional.
Explain why extrachromosomal DNA is important in a cell
some prokaryotes also have smaller loops of DNA called plasmids that may contain one or a few genes not essential for normal growth (Figure 3.12). Bacteria can exchange these plasmids with other bacteria in a process known as horizontal gene transfer HGT). The exchange of genetic material on plasmids sometimes provides microbes with new genes beneficial for growth and survival under special conditions.
mutations can be _____________ or _____________
spontaneous (occur in the absence of a mutagen) or induced (presence of a mutagen)
what is point mutation?
substitution of single base - silent, missense and nonsense mutations
the ______ and _____ form the backbone of DNA
sugars and phosphates
What is a karyotype
the number and visual appearance of chromosomes in the nuclei of specific organisms
Interpret visual data demonstrating minimum, optimum, and maximum oxygen or carbon dioxide requirements for growth
the optimum oxygen concentration, as the name implies, is the ideal concentration of oxygen for a particular microorganism. The lowest concentration of oxygen that allows growth is called the minimum permissive oxygen concentration. The highest tolerated concentration of oxygen is the maximum permissive oxygen concentration. The organism will not grow outside the range of oxygen levels found between the minimum and maximum permissive oxygen concentrations.
