BIOS2150 Microbiology Exam 3 Study Guide PDF

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Exam 3 study guide 3. Dr. Lance Johnson Metropolitan community college Spring 2019....

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BIOS2150 Microbiology Exam 3 Study Guide Ch. 8 Microbial Genetics What is the difference between prokaryote and eukaryote chromosomes? In prokaryotes the circular chromosome is contained in the cytoplasm in the nucleoid. In eukaryotes all of the cells chromosomes are stored inside a structure called the nucleus. What is a gene? A gene is the passable genetic information from one cell to another. What is the central dogma of biology? It is the natural order of how genes become proteins. They go from DNA to RNA and then to proteins. What is expression? It is when genes is used in the functional gene product. They are mostly proteins but if it is a non-protein coding genes then it is functional RNA. What three parts make up a nucleotide? They are the nitrogenous base, Pentose sugar, and phosphate group What are the 4 bases used in DNA? Adenine, Thymine, Cysteine, and Guanine. What is the structural difference between deoxyribose and ribose? The sugar in DNA does not have oxygen atom on the carbon 2 of sugar ring. Ribose has a hydroxyl group on carbon 2 sugar ring. What makes up the backbone of DNA? It is made of a repeated pattern containing the sugar deoxyriose and a phosphate group. What makes up the rungs of DNA? Nitrogenous bases. What are the complementary base pairings and what holds them together? They are complementary nitrogenous base pairs. The double nitrogenous pairs are linked by hydrogen bonds. What reaction is used to connect nucleotides to form DNA strands? Hydrolyze? What is the orientation of the two strands of DNA? Counter parallel How does replication take place? It takes place in the nucleus of eukaryotic cells and in the cytoplasm of prokaryotic cells. It is similar in all cells. The enzyme gyrase starts. It cuts the double stranded part to prepare it. Then helicase unzips the DNA. Proteins bind to each side keeping them apart. Polymerase pairs nucleotides together. This makes 2 double helixes from 1. Polymerase also proofreads during this. Ligase then zips DNA into its double helix again. What is a mutation? It is when genetic information is messed up and results in a piece that has messed up the offspring. What is the role of proofreading enzymes? They double check the chemical bonds to make sure there is no errors. What are thymine dimers and how are they fixed? When ultraviolet light is absorbed by genetic information and it changes a bond it will end up reacting with the neighboring molecule base. If it is a thymine or cytosine that is next to them then it can form a covalent bond. What is the difference between the leading and the lagging strand? The synthesis of lagging strand is discontinuous and it occurs in the direction opposite to the growing replication fork while the synthesis of the leading strand is continuous and it occurs in the same direction as the growing replication fork.

What is an Okazaki fragment? They are fragments of DNA that are formed on the lagging strand of DNA which get paired together. What enzyme replicated DNA? Helicase. What enzyme makes the primers and what is the primers role? Primers are DNA pieces that are built in a lab. They can code for anything that is wanted. What is the role of DNA ligase? It repairs irregularities or breaks the backbone of double stranded DNA molecules. What is a plasmid? A genetic structure in a cell that can replicate independently from a chromosome. Typically a small circular DNA strand in the cytoplasm of a bacterium or protozoan. What happens during transcription? It is the process of DNA being copied into a new messenger RNA. The newly formed mRNA copies the gene, then serves as a blueprint for protein synthesis during the process of translation. What enzyme performs transcription? RNA polymerase Is there proofreading in transcription? No only translation? What bases are used in RNA? Adenine, guanine, cysteine, uracil. What are the differences between RNA and DNA? Thymine, and Uracil. What is mRNA, tRNA, and rRNA? Messenger RNA, Transfer RNA, and Ribosomal RNA. How does transcription know where to start and where to end? Promoter regions vs. termination region which is usually row of t’s. It is because the A and T bonds have 2 hydrogen instead of G and C’s 3 bonds so therefore it is weaker and can be broken easier. What are introns vs. exons? Coding regions are exons and non-coding are introns. In transcription the entire gene is copied into a pre- mRNA, which includes exons and introns. During RNA splicing, introns are removed and exons joined to form a contiguous coding sequence. What is splicing and what enzyme performs it? It is when introns are removed, leaving only the yellow, and protein coded regions called exons. RNA splicing being with assembly of helper proteins at the intron/ exon borders. What is a codon? It is a specific gene sequence or sequence of 3 nucleotides which together is a genetic code in either DNA or RNA. Where does translation take place and what enzyme performs it? It takes place outside of the nucleus in the cytoplasm. It is catalyzed by ribosome. How many amino acids are there? 20 essential amino acids in humans. What is the start codon? UAG What are stop codons? UGA, UAA, and UAG. What is meant by a degenerate code? It is a genetic code in which several code words have the same meaning. The genetic code is degenerate because many different instances in which codons specify the same amino acid. Be able to use the mRNA codon dictionary.https://www.google.com/url? sa=i&source=images&cd=&ved=2ahUKEwiX5u65_8bjAhUKheAKHVaMDjsQjRx6BA

gBEAU&url=https%3A%2F%2Fbiologywise.com%2Fcodonchart&psig=AOvVaw0UZjgS3JZsAZl9AdvNfSS_&ust=1563832301280144 What is the structure of tRNA? It has a distinctive folded structure with 3 hairpin loops that form the shape of a 3 leaf clover. 1 of the hairpin loops contain a sequence called anticodon, which can recognize and decode an mRNA codon. Each tRNA has its corresponding amino acid attached to its end. How does translation take place? It occurs in the nucleus where the DNA in the cell is located. MRNA is read from the genetic code, which relates the DNA sequence to the amino acid sequence in proteins. Each group of 3 bases in mRNA constitutes a codon, and each codon specifies a particular amino acid. MRNA sequence is used as a template to assemble a protein from amino acids in order. What does it mean if a tRNA is charged? Before an amino acid can be incorporated into a growing polypeptide, it must first be attached to a molecule called transfer RNA, or tRNA, in a process called charging. The charged tRNA will then carry the activated amino acid to the ribosome. What are the parts of a ribosome? 2 major parts: small ribosomal subunits, which read mRNA, and the large subunits, which join amino acids to form a polypeptide chain. In which site does the start codon begin in? P site??? It occurs in the AUG order in most circumstances in eukaryotes. What are the roles of the A. P, and E sites? 3 tRNA sites. P= peptidlyl site and binds to tRNA holding the growing polypeptide chain of amino acids. The A site or acceptor site binds to amino acyl tRNA, which holds the new amino acid to be added to the polypeptide chain. E site= exit site. It serves as a threshold, the final transitory step before a tRNA now bereft of its amino acid is let go by the ribosome. When does the ribosome know when to stop? It has a stop codon. They are UAG, UAA, and UGA. In DNA the uracil is replaced with thymine. What must happen to the protein to become functional after being made by the ribosome? It must fold in a specific way. What is a polyribosome? A cluster of ribosomes held together by a strand of messenger RNA that each ribosome is translating. What is mutation and are they good, bad, or neutral? Mutation is when the translation, or transcription is coded wrong. If this happens it usually is a very bad thing. In very rare occasions is it good, and many times it is neutral because it will kill the cell and it can restart creating a gene with better DNA. What are mutagens (with examples)? Radiation, or chemical. Can be Deletions, insertions, missense mutation, nonsense mutation, duplications, frame shift mutations, or repeat expansion. What is a point mutation and how does that possible cause a problem? A mutation affecting only one or very few nucleotides in a gene sequence. What is a silent mutation? Is a change in the sequence of nucleotide bases which constitutes DNA without a subsequent change in the amino acid or the function of the

overall protein? What is a nonsense and a missense mutation? Missense mutation are when a change in 1 DNA base pair results in substations of 1 amino acid for another in the protein made by a gene. Nonsense mutation is a change in 1 DNA base pair. It prematurely signals a stop sequence instead of substituting an amino acid. What is a frame shift mutation? It is when the frames of 3 codons that code for amino acids get shifted and it messes up how the groups of codons code. What is a deletion mutation? It removes DNA. What are constitutive genes? Is transcribed continually as opposed to a facultative gene, which is only transcribed when needed. What is repression vs. induction? Both focus on binding of RNA polymerase to DNA. This effect is known as repression. Enzyme induction is when an enzyme is manufactured in response to the presence of a specific molecule. This molecule is termed an inducer. Ch. 9. Viruses Are viruses dangerous and if so how? Viruses are dangerous because it can actually change the gene coding and cause many errors in the information. It is the cause of cancers, etc. What is their relative size? Viruses are much smaller than cells, and are smaller than bacteria. Why are viruses not considered cells? They have genetic information, but cannot live and reproduce as a normal organism on their own. They must have a host cell to live in and destroy. Why are viruses not considered living? They do not meet criteria for living organisms. They cannot live and survive without the help of other organisms. What is the structural makeup of a virus (capsid, capsomere, genetic material)? Capsid is the protein shell of a virus. Capsomere is the subunit of the capsid, or an outer covering of protein that protects the genetic material of a virus. Capsomere self-assemble to form the capsid. Most viruses have either RNA or DNA as their genetic material. Nucleic acid may be single or double stranded. The entire infectious virus particle, called a virion, consists of the nucleic acid and an outer shell of protein. What are the different virus shapes? Icosahedral, enveloped, complex, or helical. These viruses appear spherical in shape, but are actually icosahedron. Icosahedron is made of equilateral triangles fused together in a spherical shape. What are virus spikes, knobs, and hooks used for? They are used for identification, and there main function is to attach to certain types of cells. What is a viral envelope? Envelopes are derived from portions of the host cell membranes, but include some viral glycoproteins. They may help viruses avoid the host immune system. Glycoproteins on the surface of the envelope serve to identify and bind to receptor sites. What is a retrovirus and what is reverse transcriptase? Reverse transcriptase is an enzyme

that does backward transcription. Retroviruses use reverse transcriptase to transform their single stranded RNA into double stranded DNA. What is meant by a virus host? It is where the virus can live within and take over the genetic material to infect it for itself. It cannot live and reproduce without this. How are viruses classified? They are not classified as living organisms. How are viruses propagated (replicated) in the lab? Viruses are replicated in the lab with certain cells to use as the host for them to replicate with. What are phages and how can you see them? Phages are viruses for bacteria. They can be seen under certain microscopes. Explain the steps in lytic viral replication. 1. Attachment: attaches to the surface of host cell 2. Penetration: injects DNA into the host cell by penetrating through the cell membrane 3. Transcription: hosts cell DNA is degraded and cell’s metabolism is directed to initiate phage biosynthesis. 4. Biosynthesis: phage DNA replicates inside the cell synthesizing new phage DNA and proteins 5. Maturation: the replicated material assembles into fully formed viral phages. 6. The new phages are released from the infected cell to find a new cell. Explain the steps in lysogenic viral replication. Lysogenic means DNA is only replicated, not translated into proteins. What is transduction? Is the process by which foreign DNA is introduced into a cell by a virus or viral vector? How do animal viruses differ in their process? The virus must be able replicate in the nucleus instead of the cytoplasm. Animal cells don’t have cell walls, so often the entire virus will enter the cell by means of endocytosis and the virus must also uncoat. What is uncoating? A process in which the viral capsid of a virus is removed, leading to the release of the viral genomic nucleic acid. How are viruses released? Enveloped viruses are released by budding. It is when the virus acquires its envelope, which is a modified piece of the host’s plasma, or other internal membrane. What is a provirus? The genetic material of a virus as incorporated into, and able to replicate with, the genome of a host cell. How does HIV function? It gradually destroys the immune system by attacking and destroying a type of white blood cell called a CD4 cell. CD4 cells play a major role in protecting the body from infection. HIV uses the machinery of the CD4 cells to multiply and spread through the body. How do plant viruses get into plant cells? Plant cells have cell walls viruses cannot get through so some viruses can be transmitted through pollen to the seed. What are viroids? An infectious entity affecting plants, smaller than a virus and consist only of nucleic acid without a protein coat.

What are prions and how do they work? Prions are misfolded proteins that can cause other proteins to misform and can cause irreparable damage to tissue and brains. What human disease involves prions? Kuru, and possibly Alzheimer’s or Parkinson’s how/why did the Kuru tribe keep passing on prions? Because they kept eating the dead corpse. How can we prevent prions? Don’t be a cannibals and don’t be around meat that has been infected. Ch. 13 Biotechnology What is biotechnology and recombinant DNA technology? DNA that has been formed artificially by combining constituents from different organisms. What is a vector and a clone? It is a small piece of DNA that can be stably maintained in an organism, and into which foreign DNA fragment can be inserted for cloning purposes. After a DNA fragment has been cloned into a cloning vector it may be sub cloned into another vector designed for more specific use. What is a plasmid and how does it work? It is a small circular, double stranded DNA molecule that is distinct from a cells chromosomal DNA. Scientists have taken advantage of plasmids to use them as tools to clone, transfer, and manipulate genes. Plasmids that are used experimentally for these purposes are called vectors. What is site-directed mutagenesis? Specific changes in the DNA of organisms. What are restriction enzymes and how do they work? An enzyme produced chiefly by certain bacteria, having the property of cleaving DNA molecules at or near a specific sequence of bases. What is PCR and how does it work? Heating DNA so it denatures, then taq polymerase synthesizes 2 new stands of DNA using the original strands as templates. What is transformation vs. electroporation vs. protoplast fusion? Transformation is genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane. Electroporation is allows transformation of bacteria and yeasts and transfection of tissue culture through non chemical means. Protoplast fusion is a type of genetic modification in plants by which 2 distinct species of plants are fused together to form a new hybrid plant with characteristics of both. A somatic hybrid. What is a gene gun vs. microinjection? Gene gun delivers exogenous DNA to cells. It uses an elemental partial covered with DNA (usually plasmid). It fires actual projectiles in an effort to combine DNA. Microinjection is when they take a tiny needle and inject the DNA directly into the nucleus. What is a genomic library? Is a collection of the total genomic DNA from a single organism? What is cDNA and how is it made? Complimentary DNA is DNA synthesized from a single stranded RNA template in a reaction catalyzed by the enzyme reverse transcriptase. CDNA is often used to clone eukaryotic genes in prokaryotes.

What is blue-white (lacZ) screening? Is a rapid and efficient technique for the identification of recombinant bacteria? It relies on the activity of B-galactosidase. AN enzyme from E. coli, which cleaves lactose into glucose and galactose. What is colony hybridization (DNA probes)? Is a method of selecting bacterial colonies with desired genes? What are the different cells that can be used to make proteins? Ribosome performs translation, this makes amino acids. What are vaccines? A substance used to stimulate the production of antibodies and provide immunity against 1 or several diseases What is gene therapy? Experimental technique to use genes to treat or prevent disease. What is the human genome project? It was a project to identify the number of genes in a human and then figure out what genes do what process. What is bioinformatics and proteomics? Bioinformatics is the science of collecting and analyzing complex biological data such as genetic codes. Proteomics is studying a major group of animals defined by embryonic development. What is BT? Bacillus thuringiensis is a spore forming bacterium that produces crystals protein which is toxic to many insects. What are some of the ethical issues in using genetically modified organisms? social concerns, extrinsic concerns, intrinsic concerns,...