Exam 3 ANSWERED STUDY GUIDE LEC PDF

CHAPTER 8: MICROBIAL GENETICS Define genetics, genome, chromosome, gene: Genetics – the study of heredity and the variation of inherited traits. Genome – the complete set of genetic material in an organism, containing all its DNA. Chromosome – structures within cells made of DNA and protein that...

CHAPTER 8: MICROBIAL GENETICS Define genetics, genome, chromosome, gene: Genetics – the study of heredity and the variation of inherited traits. Genome – the complete set of genetic material in an organism, containing all its DNA. Chromosome – structures within cells made of DNA and protein that carry genes. Humans have 23 pairs of chromosomes. Gene – a segment of DNA on a chromosome that codes for a specific protein or trait. Describe the Central Dogma of Biology theory: The central dogma of biology describes the flow of genetic information within a cell 1. DNA is transcribed in RNA 2. RNA is translated into protein. This means that DNA holds instructions for making proteins which are essential for cellular functions. What are the 2 functions of DNA? Describe how it serves as genetic information: 1. Storage of genetic information – DNA has all the instruction an organism needs for growth development and replication. 2. Replication – DNA can be copied to ensure genetic information is passed to new cells or offspring. DNA serves as genetic information is passed to new cells or offspring. DNA serves as genetic information because its sequence of bases (A-T, C-G) forms a unique “code” that determines traits and protein production. Describe the structure and 3 parts of a nucleotide. What are the 4 DNA bases? RNA bases? Nucleotide: 1. Phosphate group 2. Sugar (deoxyribose in DNA) 3. Nitrogenous base (A-T, C-G in DNA) DNA bases: adenine, thymine, cytosine, guanine RNA bases: adenine, uracil, cytosine, guanine Describe 4 differences between DNA and RNA: 1. DNA is double-stranded; RNA is single-stranded. 2. DNA contains thymine; RNA contains uracil instead. 3. DNA has deoxyribose sugar; RNA has Describe the “twisted ladder” structure of DNA. What are the rails and steps of the ladder? What is meant by the term “antiparallel strands” Aka double helix is a shape in which two long strands of DNA twist around each other. Rails (sides) – the two sides of the ladder are made of alternating sugar (deoxyribose) and phosphate groups. These sugar-phosphate backbones provide structural stability and protect the inner bases. Steps (rungs) – it is made up of pairs off nitrogenous bases: (A-T), and (C-G). it is held together with hydrogen bonds contributing the stability of the DNA molecule. (5’ vs. 3’)? The term antiparallel strands describe how two strands of DNA in opposite directions: o Each strand has a directionality labeled 5’ (5 prime) end and 3’ (3 prime) end. o The 5’ end has a free phosphate group attached to the 5th carbon of the sugar molecule. o The 3’ end has a free hydroxyl group (-OH) attached to the 3rd carbon of the sugar.  o In the double helix, one strand runs 5’3’ and the complementary strand runs 3’ to 5’. This antiparallel arrangement is critical for DNA replication and various enzymatic processes, as enzymes involved in DNA synthesis and repair can only add nucleotides in the 5’3’ direction. Describe the steps of DNA replication. DNA replication is the process by which DNA makes a copy of itself before cell division. Steps: 1. Unwinding – the enzymes helicase unwinds and separates the two DNA strands by breaking the hydrogen bonds between base pairs creating a “replication fork”. 2. Priming – primase, an RNA polymerase lays down a short RNA primer to provide a starting point for DNA synthesis. 3. Elongation: o Leading strand – DNA polymerase synthesizes this strand continuously in the 5’ to 3’ direction, following the helicase as it unwinds the DNA. o Lagging strand – DNA polymerase synthesizes this strand in short, discontinuous segments because it runs in the opposite 3’ to 5’ direction relative to the replication fork. These segments are called Okazaki’s fragments. 4. Joining – DNA ligase joins the Okazaki fragments on the lagging strand by forming bonds between the fragments, completing the DNA strand. What enzymes are involved, their functions? o Helicase – unwinds the DNA double helix o Primase – lays down RNA primers to start replication o DNA polymerase – add nucleotides in the 5’ to 3’ direction, synthesizing new DNA strand. o Ligase – joins Okazaki fragments on the lagging strand to create a continuous strand. What’s leading/lagging strand? o Leading strand – synthesizes continuously in the 5’ to 3’ direction, following replication fork. o Lagging strand – synthesized discontinuously in short Okazaki fragments in the 5’ to 3’ direction but in the opposite direction of the replication fork movement. Describe the process of protein synthesis. This occurs in two main stages: 1. Transcription – it is located in nucleus (eukaryotes). Transcription is the process of creating an mRNA copy of a gene. RNA polymerase binds to the DNA at the gene’s promoter region and synthesizes a complementary strand of mRNA based on the DNA template. This result in an mRNA, a single-stranded copy of the gene that carries instructions from DNA to the ribosome. 2. Translation – located in the ribosome (in the cytoplasm). Translation is the process of reading the mRNA sequence to build a protein. The mRNA binds to a ribosome, and tRNA molecules bring amino acids corresponding to each mRNA codon. The ribosome links the amino acids together to form a polypeptide chain. As a result, a polypeptide chain, which folds into a functional protein. Differentiate transcription vs. translation. Transcription converts DNA into mRNA; occurs in the nucleus and it involves RNA polymerase. Translation converts mRNA into a protein; occurs in the ribosome and it involves (rRNA), mRNA, and tRNA. Describe process steps of transcription. Transcription is the first step in protein synthesis where DNA is transcribed into mRNA. Steps: 1. Initiation - RNA polymerase, the main enzyme involved in transcription binds to the promoter region of the DNA 2. Elongation – RNA polymerase unwinds the DNA and reads one strand synthesizing a complementary strand of mRNA by adding RNA nucleotides (A, U, C, G) that match the DNA template.  3. Termination – when RNA polymerase reaches a termination signal in the DNA sequence, it releases the newly synthesized mRNA strand, and transcription stops. The DNA rewinds, returning to its double-helix structure. What enzyme(s) are involved and their function? RNA polymerase – binds to DNA, unwinds double helix, reads the DNA template strand, and synthesizes a complementary mRNA strand. High level, how does translation work? Translation is the process by which the mRNA sequence is converted into a protein, and it takes place in the ribosome. What are the three steps of translation and what happens in each step? Steps: 1. Initiation – the ribosome assembles around the mRNA strand. A tRNA with an anticodon complementary to the mRNA’s start codon (usually AUG) binds, bringing the first amino acid. 2. Elongation – as the ribosome moves along the mRNA, each codon pairs with tRNA anticodon. Each tRNA brings a specific amino acid which the ribosome link into a growing polypeptide chain. 3. Termination – when the ribosome reaches a stop codon on the mRNA, no corresponding tRNA binds. This signals the ribosome to release the polypeptide completing the process. What are the major molecules involved in translation and what are their functions? o mRNA – carries the genetic code from DNA to the ribosome, serving as a template for protein synthesis o tRNA – carries amino acids to the ribosome. Each tRNA has an anticodon that pairs with a codon on the mRNA ensuring the correct amino acid is added to the chain. o Ribosome – a molecular complex made of rRNA and proteins. It facilitates the alignment of tRNA and mRNA and catalyzes the formation of peptide bonds between amino acids to build the protein. Describe a codon and anticodon. Where is each found and what is the function of each? o Codon – a sequence of 3 nucleotide bases on the mRNA that codes for a specific amino acid. Found on the mRNA, each codon specifies one amino acid or a stop signal. o Anticodon – a complementary sequence of 3 bases on the tRNA. Each tRNA’s anticodon pairs with a specific codon on the mRNA ensuring that the correct amino acid is added to the protein chain. How do you read the codon table? o Codon table – to read a codon table, locate the first base of the codon along the left side, the second base along the top and the 3 rd base on the right. The intersection of these 3 coordinates provides the amino acid specified by that codon. If given a DNA sequence and codon table, can you provide the complementary DNA sequence? the mRNA sequence? The amino acid sequence from the mRNA sequence? 1. Complementary DNA sequence – given a DNA sequence, we can create its complementary strand by pairing each base with its complement: o A-T o C-G 2. mRNA sequence – to transcribe DNA into mRNA, replace each T in the DNA template with U in the mRNA keeping the complementary bases. o A–U o T–A o C–G o G–C  3. Amino acid sequence – using the mRNA sequence and codon table, you can determine the sequence of amino acids. Each 3-base codon corresponds to specific amino acid, and you can decode it using the table. Compare protein synthesis in prokaryotes and eukaryotes Prokaryotes: o Transcription and translation occur simultaneously in the cytoplasm as they lack a nucleus. o mRNA is often polycistronic (coding for multiple proteins), allowing related genes to be expressed together. o No mRNA processing (like splicing, capping, or polyadenylation) occurs. Eukaryotes: o Transcription occurs in the nucleus, while translation occurs in the nucleus while translation occurs in the cytoplasm. o mRNA is usually monocistronic (coding for one protein) o mRNA undergoes processing – introns are spliced out 5’ cap is added and 3’ poly-A tail is attached. What can prokaryotes do in protein synthesis that eukaryotes cannot? A unique feature in prokaryotes is that it can couple transcription and translation, meaning ribosomes can start translating mRNA while it’s still being transcribed. This allows faster protein production. Define an operon. Describe the parts of an operon and their function- promoter sequence, operator sequence, repressor protein, RNA polym. An operon is a set of genes in prokaryotes controlled by a single promoter and regulated together. Components: o Promoter - a sequence where RNA polymerase binds to start transcription o Operator - a regulatory sequence where a repressor protein can bind to block transcription o Repressor protein - a molecule that binds to the operator to prevent RNA polymerase from transcribing the genes o RNA polymerase - the enzyme that transcribes DNA into M RNA when it can access the promoter and operator Compare and contrast inducible vs. repressible operon. o Inducible operon - typically off but can be turned on in response to a specific molecule (inducer). Example Lac operon o repressible operon - typically on but can be turned off when a specific molecule (corepressor) is present. Example TRP operon How does the E. coli lac operon work? What type of operon is the lac operon? How is it turned on? off? The lac operon an E. coli is an inducible operon used to breakdown lactose o Turned on - when lactose is present, it binds to the repressor protein causing it to release from the operator. This allows RNA polymerase to transcribe the genes needed to metabolize lactose o Turned off - when lactose is absent, the repressor binds to the operator blocking RNA polymerase and preventing transcription Describe the 2 major DNA mutation types and their effect on the resulting protein(s). Point mutations – silent, missense, nonsense and frameshift mutations- insertions or deletions There are two major types of mutation: 1. Point mutations - a change in a single base o Silent mutation - no change in the resulting protein (due to redundancy in the genetic code) o Missense mutation - a change in one amino acid in the protein, potentially altering protein function. o Nonsense mutation - introduces a premature stop codon leading to a truncated (shortened) and usually nonfunctional protein  2. Frameshift mutation - insertions or deletions that shift the reading frame, changing every subsequent codon and usually resulting in a nonfunctional protein due to extensive changes in the amino sequence Compare and contrast vertical vs. horizontal gene transfer. o Vertical gene transfer - this is the transmission of genetic material from parent to offspring during reproduction. It occurs during cell division (e.g., binary fission in bacteria or mitosis/meiosis in eukaryotes) and it's this standard means of passing genetic information down generations. Vertical gene transfer ensures that offspring inherited traits from their ancestors o Horizontal gene transfer - this involves the transfer of genetic material between organisms that are not parent and offspring. It allows genes to move between unrelated individuals or even different species. Horizontal gene transfer is especially common in prokaryotes (e.g., bacteria) and contributes to genetic diversity and rapid adaptation such as antibiotic resistance o Key difference - vertical gene transfer passes genes from parent to offspring, while horizontal gene transfer occurs between unrelated individuals often within the same generation Describe two methods of horizontal gene transfer. 1. Transformation: o In transformation the bacterium takes up 3 DNA fragments from its environment, often released by other bacteria when they die o The DNA is compatible, it can integrate into the bacterium’s genome providing new traits, such as antibiotic resistance. o Transformation is significant in bacterial adaptation and genetic diversity. 2. Conjugation: o Conjugation is the transfer of genetic material directly between two bacterial cells, usually through a structure called a pilus. o Plasmid in a donor cell replicate and is transferred to a recipient cell through the pilus. o Conjugation allows bacteria to share genes rapidly, especially those on plasmids such as genes for antibiotic resistance. Additional method: Transduction o In transduction, a virus (bacteriophage) transfers genetic material between bacteria. o During infection, the virus may accidentally package bacterial DNA instead of its own and when it infects another bacterium it transfers this DNA to a new host o transduction enables gene transfer across bacterial species and is an important mechanism for spreading new traits. CHAPTER 9: BIOTECHNOLOGY Describe the following terms: genome, clone, and transgenic organism. o Genome – the complete set DNA in an organism, containing all its genes and the information needed for its growth, development, and function. The genome includes both the coding (genes) and non-coding sequences of DNA. o Clone – a genetically identical copy of a gene, cell, or entire organism derived from a single original ancestor. o Transgenic organism - an Organism that has been genetically modified to contain DNA from other species. This foreign DNA is introduced into its genome to give the organism new traits. Define restriction enzymes – where do they come from and what do they do? o Restriction enzymes also known as restriction endonucleases are enzymes that cut DNA at specific sequences called recognition sites. They are naturally found in bacteria where they serve as a defense mechanism against viruses by cutting viral DNA into fragments thus preventing infection. o Each restriction enzyme recognizes a specific DNA sequence typically 4 - 8 base pairs long and makes a cut at or near this site. This allows for precise cutting of DNA into defined fragments. Describe how they are a valuable tool used to create recombinant DNA.  Restriction enzymes are essential in genetic engineering for creating recombinant DNA (DNA formed by combining DNA from different organisms). By cutting DNA from different sources with the same enzyme, scientists produce fragments with compatible ends that can be joined together. This allows genes the DNA segments from different sources to be inserted into plasmids or other vectors forming recombinant DNA. Describe the terms recognition site and “sticky ends” relative to restriction enzymes. o Recognition site - the specific sequence of DNA that a restriction enzyme recognizes and cuts. Each enzyme has a unique recognition sequence (e.g., the enzyme EcoRI recognizes capital GAATTC). o Sticky ends - when some restriction enzymes cut DNA, they leave overhanging single stranded ends called “sticky ends”. These sticky ends can easily pair with complementary sticky ends of other DNA fragments cut by the same enzyme, facilitating the joining of DNA pieces. Why are “sticky ends” advantageous? Sticky ends allow for easy pairing between complementary DNA fragments ensuring accurate and stable integration of new DNA sequences into plasmids or other vectors. This is important for constructing recombinant DNA molecules. Describe the use of recombinant plasmids in transferring genes. Plasmids are small, circular DNA molecules found in bacteria that replicate independently of the bacterial chromosome. In genetic engineering, scientists use plasmid as vectors (carriers) to transfer genes. By inserting a gene of interest into a plasmid they create a recombinant plasmid which can then be introduced into bacteria or other cells. These cells can then replicate the plasmid producing copies of the gene or expressing the gene to produce a protein. Why is their always and antibiotic resistance gene in the plasmid? Recombinant plasmids often include an antibiotic resistance gene as a selection marker. After the plasmid is introduced into bacterial cells the bacteria are grown on a medium containing the antibiotic. Only the cells that successfully take up the plasmid with the antibiotic resistance gene will survive in this environment while others without the plasmid will be killed by the antibiotic. This selection process allows scientists to easily identify and isolate the cells that have taken up the recombinant plasmid as only those cells will grow in the presence of the antibiotic. This ensures that only the modified cells with the gene of interest are retained for further study or production. PCR – what is that? PCR, or polymerase chain reaction is a technique used to amplify (make many copies of) a specific DNA sequence. It is widely used in molecular biology, forensic science, and diagnostics. Discuss the four key ingredients of PCR 1. DNA template - the DNA sample that contains the target sequence to be copied 2. DNA primers - short DNA sequences that are complementary to the target DNA sequence. They bind to specific sites on the template guiding DNA polymerase to where amplification should start. 3. DNA polymerase - an enzyme that synthesizes new DNA strands by adding nucleotides to the primers. The most commonly used enzyme is Taq polymerase which is a heat stable. 4. Nucleotides (dNTPs) - the building blocks (A, T, C, G) that DNA polymerase uses to create the new DNA strands. What ingredient allows for PCR to work? What’s it called and what is special about it? Taq polymerase - is what allows PCR to work period it is derived from thermos aquaticus a bacterium that thrives in hot springs. Taq polymerase is special because it is heat stable, meaning it can withstand the high temperatures used in PCR without denaturing, making it ideal for cyclic heating and cooling required. Describe the 3 steps of PCR. What is the role of the different temperature used in each step. 1. Denaturation (94 - 98C) - the double stranded DNA template is heated to separate it into two single strands. 2. Annealing (50 - 65C) - the temperature is lowered so that the primers can bind (anneal) to their complementary sequences on the single stranded DNA. 3. Extension (72C) - DNA polymerase extends the primers by adding new tides, creating a new strand of DNA complementary to the template. Temperature role - each temperature is carefully chosen to achieve a specific function: o High temperature (denaturation) breaks the hydrogen bonds between strands. o Moderate temperature (annealing) allows primers to bind to target sequences. o Optimal temperature for Taq polymerase (extension) enables efficient DNA synthesis. What is “real-time” PCR? How can it be used to directly determine the presence of a pathogenic organism? o Real time PCR (qPCR) - this variant of PCR allows the amplification and quantification of DNA in real time, using fluorescent dyes or probes to monitor the DNA amplification as it occurs. o By designing primers specific to a pathogens DNA sequence, qPCR can directly detect the presence of pathogenic DNA in a sample. The amount of fluorescence increases with the DNA quantity allowing for rapid quantitative detection of the pathogen. Discuss the process of Blue-white screening – what is it used for and how is it done? Blue - white screening is used to identify bacterial colonies that have successfully taken up a plasmid with a gene of interest inserted into it. This method helps distinguish between bacteria with recombinant plasmids Thomas (containing the gene of interest) and non-recombinant plasmids. Be sure to include the role of each of the following: 1. Ampicillin resistance gene - the plasmid includes an ampicillin resistance gene, which allows only bacteria that have taken up the plasmid to grow on Agar plates containing ampicillin. 2. lacZ gene in the plasmid - the plasmid also contains part of the lacZ gene, which encodes the enzyme beta galactosidase. When active, this enzyme can break down a substrate called X-gal producing a blue color. Ampicillin and X-gal in the agar o Ampicillin - ensures that only bacteria with the plasmid survive. o X-gal - Acts as a substrate for beta galactosidase. When cleaved by the enzyme it produces a blue color. Why and how do colonies become blue or white? What does that mean? o Blue colonies – if the lacZ gene is intact (no insert in the plasmid), the enzyme beta galactosidase is produced, and the colonies turn blue upon breaking down X gal. o White colonies - if a gene of interest is inserted into the plasmid, it disrupts the Lac Z gene preventing beta galactosidase production. These colonies remain white indicating successful insertion of the desired gene. White colonies indicate successful insertion of the target gene (recombinant plasmid) while blue colonies indicate non recombinant plasmids. This visual differentiation allows easy identification of colonies with a desired genetic modification. CHAPTER 11: PROKARYOTES  Define and differentiate - prokaryotic genus, species and strain. o Genus - a taxonomic rank grouping closely related species that share common traits. For example, Escherichia is a genus that includes several species like E. coli. o Species - a specific group of organisms within a genus that shared significant genetic, structural, and functional similarities. Members of a species can usually interbreed. For example, E. coli is a species within the genus Escherichia. o Strain - genetic variant or subtype within a species often with distinct characteristics. Strains can arise through mutations or genetic adaptation. For example, E. coli O157:H7 is a pathogenic strain of a species Escherichia coli. Differentiate bacteria from archaea o Cell wall composition - bacteria typically have peptidoglycan in the cell walls, while Archaea lack peptidoglycan and have unique cell wall structures. o Membrane lipids - bacteria have Esther-linked lipids, while Archaea have ether-linked lipids in their cell membranes which are more resistant to extreme conditions. o Genetic machinery - archaeal genetic processes (Such as transcription and translation) are more similar to eukaryotes then to bacteria despite being prokaryotic. o Environment - Archaea are often extremophiles living in harsh conditions like high temperatures, acidity, all or salinity, while bacteria are found in a wider range of environments. Who were the first bacteria group to evolve? Who are the latest bacteria group to evolve? o First bacterial group to evolve – Cyanobacteria are among the earliest known bacteria to evolve playing a major role in oxygenating Earth’s atmosphere through photosynthesis. o Latest bacterial group to evolve – Proteobacteria Are considered one of the more recently evolved bacterial groups displaying a high level of diversity and including many modern bacterial species. Describe, compare and contrast: non-proteobacteria vs. proteobacteria o Proteobacteria - this is a large and diverse phylum of gram-negative bacteria that includes many known bacteria such as E coli and salmonella. They are primarily chemoheterotrophs and include groups like alpha, beta, gamma beta delta, and epsilon proteobacteria with varied lifestyles ranging from nitrogen fixation to pathogenicity o Non proteobacteria - a broad category of gram-negative bacteria that do not belong to the proteobacteria phylum. They exhibited a wide range of metabolic types, including phototrophs, anaerobes, and extremophiles. Examples include cyanobacteria, Bacteroides, and Spirochetes. Describe provide a characteristic for each of the following groups of non-proteobacteria: 1. Bacteroides - they are anaerobic bacteria commonly found in the intestines of animals where they play an essential role in digesting complex molecules and contribute to gut health. 2. Purple sulfur and purple non sulfur bacteria: o Purple Sulfur bacteria - these are phototropic bacteria that use hydrogen sulfide (H 2S) as an electron donor for photosynthesis producing sulfur as a byproduct. They are typically found in Sulfur rich environments. o Purple non sulfur bacteria - Similar to purple sulfur bacteria but can use organic compounds instead of H 2S as an electron donor. They are more versatile and can survive in environments with less sulfur. o Difference from green sulfur and green non sulfur bacteria - green sulfur bacteria (obligate anaerobes) also use H2S as an electron donor while green non sulfur bacteria are more flexible in their photosynthetic and metabolic processes. 3. Spirochetes – they are spiral-shaped bacteria known for their unique corkscrew motion facilitated by axial filaments. Many spirochetes are pathogenic such as syphilis and Lyme disease.  4. Chlamydias – Chlamydias are obligate intracellular parasites, meaning they only grow within host cells. They cause various disease in humans including Chlamydia and respiratory infections Describe and provide a characteristic for each of the following groups of proteobacteria: 1. Green sulfur and green non sulfur bacteria: o Green sulfur bacteria - these bacteria are obligate anaerobes that perform photosynthesis using hydrogen sulfide (H 2S) As an electron donor, producing sulfur as a byproduct. They have chloroforms specialized structures for capturing light, allowing them to thrive in low light, sulfur rich environments. o Green non-sulfur bacteria – these are more metabolically versatile, capable of photosynthesis in light and aerobic respiration in the absence of light. They use organic compounds instead of H 2S as an electron donor. o Difference from Cyanobacteria - unlike cyanobacteria which perform oxygenic photosynthesis and release oxygen, green sulfur and non-sulfur bacteria perform anoxygenic photosynthesis (do not produce oxygen). 2. Cyanobacteria: o Cyanobacteria are known for oxygenic photosynthesis (using water as an electron donor and releasing oxygen). They were crucial in oxygenating Earth's atmosphere billions of years ago allowing aerobic life to evolve. They also fixed atmospheric nitrogen converting it into a usable form for plants and other organisms. Cyanobacteria they're often found in aquatic environment and can sometimes form harmful algal blooms. 3. Enterobacteriaceae: o Enterobacteriaceae Is a large family of gram negative facultatively anaerobic bacteria that primarily inhabit the intestines of animals, including humans. This group includes species like E coli, Salmonella, and Klebsiella. o They are commonly found in the intestinal tract of animals and humans as well as in soil, water, and plants. Describe the significance (positive and negative) of this bacteria group. o Positive - some members like certain strains of E coli are beneficial for gut health, aiding in digestion and vitamin production. o Negative - other members are pathogenic causing diseases such as food poisoning Salmonella, UTI (Proteus), and pneumonia (Klebsiella). Pathogenic strains of E coli like E. coli O17:H7, can cause severe foodborne illness. What is a fecal coliform? o Fecal coliforms are subgroup of coliform bacteria that originate specifically from the intestines of warm-blooded animals, including humans. They are used as indicator of fecal contamination in water sources because their presence suggests that pathogens from fecal matter might be present. How are they related to Enterobacteriaceae? o Relation to Enterobacteriaceae - fecal coliforms are part of the Enterobacteriaceae family., for example, E coli is well known fecal coliform and is commonly used as an indicator of water quality and potential contamination. How are they related to infectious disease? o Relation to infectious disease - the presence of fecal coliforms in water sources indicates potential contamination by fecal pathogens, increasing the risk of infectious diseases such as cholera dysentery, and hepatitis. Provide a reason why there are rapid tests designed to specifically identify Enterobacteriaceae? Rapid tests are designed to specifically identify Enterobacteriaceae because they serve as indicators of potential fecal contamination, food safety, and water quality. Quickly detecting Enterobacteriaceae particularly fecal coliforms like E coli, helps prevent disease outbreaks by ensuring water and food safety. Additionally, since some members are pathogens rapid identification aids in diagnosing infections and initiating appropriate treatment. Gram Positive Bacteria – when did they evolve? Gram positive bacteria are considered to be among some of the earliest bacterial groups, evolving after cyanobacteria contributed to the oxygenation of Earth's atmosphere approximately 2.5 to 3 billion years ago. They have persisted through time due to their tough cell wall structure, allowing them to adapt to a wide range environment. Compare and contrast firmicutes and actinobacteria. Firmicutes: o Characterized by low G C 10th (guanine-cytosine) in their DNA. o Many firmicutes form endospores, which are resistant to extreme conditions. o Generally, these bacteria have simpler cell wall structures. o Examples: bacillus, Clostridium, Staphylococcus. Actinobacteria: o Characterized by high GC content in their DNA. o Often have complex life cycles with some forming filamentous structures similar to fungi. o Actinobacteria have thicker, more complex cell walls and are known for producing many antibiotics. o Examples: streptomyces and mycobacterium. What are the two groupings of gram-positive bacteria based on? Gram positive bacteria are often grouped based on their GC content (percentage of guanine and cytosine nucleotides) in their DNA. 1. Low-GC gram-positives: firmicutes 2. Hi GC-gram-positives: actinobacteria What structurally differentiates the two? (cell wall differences) The main structural difference between the two groups lies in their cell wall composition: o Firmicutes - have a relatively simpler and thick peptidoglycan layer in the cell wall which provides protection and rigidity. o Actinobacteria - have a more complex, thicker peptidoglycan layer with additional components like mycolic acids (in certain species such as mycobacterium) that make the cell wall more robust and resistant to desiccation. Describe and give an example of a species that represent the firmicutes. o Species: bacillus subtilis o bacillus subtilis is a rod shaped, and the spore forming bacterium commonly found in soil. It is known for its ability to form tough, protective spores that helps it survive environmental conditions. Bacillus species are wildly used in research and industry due to the robustness and ability to produce enzymes and antibiotics. Describe and give an example of a species that represent the actinobacteria. o Species: streptomyces griseus o streptomyces griseus is a filamentous bacterium known for its soil dwelling, “earthly” odor and for producing antibiotics including streptomycin. Streptomyces species have a high GC content forming branching filaments and play a critical role in soil health by decomposing organic matter and inhibiting the growth of other microorganisms through antibiotic production. Describe the unique characteristics of archaea. Archaea are distinct group of prokaryotes with several unique characteristics: o Extreme environment adaptation - many Archaea are extremophiles thriving in harsh environments such as hot-springs, salt flats, acidic or alkaline waters, and even deep-sea hydrothermal vents.  o Unique membrane lipids - archaeal cell membranes contain linked lipids (rather than ester-linked as in bacteria), which are more stable and suited to extreme conditions. o Genetic and biochemical differences - archaeal genetic machinery (DNA replication, transcription, and translation processes) is more similar to that of eukaryotes in bacteria even though they are prokaryotic. Differentiate the cell wall of archaea with that of bacteria. o Archaea - lack peptidoglycan, the primary component in bacterial cell walls. Instead, they have a unique substance called pseudopeptidoglycan (or pseudomurein) or other structural polymers in their cell walls which helps them maintain stability in extreme environments. o Bacteria - typically have a cell wall made of peptidoglycan which provides rigidity and protection. The structure of bacterial peptidoglycan is highly conserved across bacterial species. Discuss why many archaea species have yet to be discovered and characterized. Many archaeal species have yet to be discovered and characterized because: o Difficulty culturing - Archaea often live in extreme environments that are challenging to replicate in laboratory settings, making them difficult to culture and study. o Unique environmental needs - some Archaea require very specific conditions (e.g., high temperatures, acidity, or salinity) that are not easily maintained outside their natural habitat. o Limited tools for study - traditional microbial research techniques, which works well for bacteria are often less effective for archaea due to their unique characteristics and resistance to standard culturing methods. What is unique about archaea relative to pathogenicity and infectious disease? One unique aspect of Archaea is that to date, no archaeal species has been identified as pathogenic or directly associated with infectious disease in humans, animals, or plants. Unlike bacteria which include many pathogenic species, Archaea are generally nonpathogenic likely due to their differences in cell structure, lack of traditional virulence factors, and their distinct ecological roles. Describe three differences between bacteria vs. archaea. 1. Cell wall composition - bacteria have Peptidoglycan in their cell walls while Archaea do not. Archaea may have pseudo peptidoglycan or other unique cell wall materials. 2. Membrane lipids - bacteria have ester-linked membrane lipids while Archaea have ether-linked lipids making their membrane more resilient in extreme environments. 3. Genetic machinery - archaeal processes of DNA replication, transcript, and translation are more similar to eukaryotes than bacteria with different enzymes and protein structures involved. Describe and differentiate resident bacteria vs. transient bacteria o Resident bacteria - these are stable, long-term microbes that live on or within our bodies particularly in areas like the gut, skin, and respiratory tract. Replace essential roles in maintaining health, aiding in digestion, and protecting against pathogen. o Transient bacteria - these are temporary bacteria that do not permanently colonize the body. They may come from the environment or food that can be present for a short time before being cleared or outcompeted by resident bacteria. What are a pathogenic bacteria? Are most bacteria pathogenic? Can resident bacteria be pathogenic? o Pathogenic bacteria are bacteria that can cause disease by invading host tissues, producing toxins, or evading the immune system. These bacteria have specific virulence factors that allows them to infect and harm the host. o Prevalence of pathogenic bacteria - most bacteria are not pathogenic the vast majority are either beneficial or neutral to humans and other organisms. Pathogenic bacteria represent a small fraction of bacterial kingdom. o Resident bacteria and pathogenicity - some resident bacteria can become pathogenic under certain conditions. For example, E. coli is usually harmless in the intestines but can cause UTI if it enters the urinary tract. This concept is known as opportunistic pathogenicity where normally harmless bacteria cause infections when they are in the wrong location or if the host immune system is compromised.