MCB2000 Exam 2 Study Guide
Implications of the alteration of DNA
-Diseases -Biofilms -Antibiotic resistance -Biotechnology
24. How one can amplify DNA fragments in laboratory?
-PCR (polymerase chain reaction) -involves a thermocycler that cyclically increases and decreases the temperature of the solution -94 degrees to separate DNA -60 degrees to allow primers to hydrogen-bond to their complementary sequence -72 degrees to allwo heat-stable DNA polymerase to add nucleotides to the 3' end of the primers
12. What is the genetic material for viruses, DNA or RNA, single stranded or double stranded?
-RNA or DNA that can be single or double stranded
6. What is the significance of reverse transcriptase? What is the source of reverse transcriptase (its origin)? What does it do?
-RNA-dependent DNA polymerase -retroviruses have genes that code for reverse transcriptase
33. How different types of radiation may cause mutation
-UV light causes the formation of thymine thymine dimers which form bubbles in the DNA and prevent normal transcription from occurring -ionixzixng radiation (X and gamma rays): penetrate deep in the body and affect all of the bodies cells, can cause base deletions, cross-linking, single-strand nicks, and breaking of entire chromosomes
36. What is the difference between the two forms of radiation? What type of damage (to DNA) each one causes?
-UV light creates bubbles that stop normal transcription -ionizing radiation causes a wide variety of deleterious mutations
45. What is the importance of Cyanobacteria/Algae
-a group of free-living, photosynthetic bacteria that were precursors to chloroplasts in the modern eukaryotic cell that can be either filamentous or non-filamentous but all obtain their energy through oxygenic photosynthesis
31. Define spontaneous mutation. What causes spontaneous mutation/induced mutation
-a natrually occurring mutation in the absence of a mutagen -occurs naturally due to mistakes in DNA replication -induced mutation: caused by a mutagen that directly damages DNA and produces a heritable change in the DNA nucleotide sequence
19. What is meant by recombinant DNA (technology)? Describe the use of Recombinant DNA in Producing Insulin. What is the purpose of cloning?
-a set of procedures used to combine genetic material from multiple sources and create DNA sequences that are otherwise not found in biological organisms -researcehrs have inserted the gene that codes for human insulin into E. coli and induced insulin production in bacteria which dramatically reduced the cost of obtaining insulin -cloning: obtains multiple copies of the DNA of interest which can be used to study the function of a gene, investigate the gene's characteristics, examine how mutations affect a gene's function or make large amounts of a protein coded for by a gene
54. What is tissue culture/cell culture/monolayer? What is their use? Why you always need host to grow virus. Describe three ways in which viruses are cultivated.
-a single layer of homogenized cells growing side by side but not on top of one another -do not have the capacity to self-replicate -in bacterial cell cultures, in living animals, in embryonated eggs
DNA polymerase
-adds nucleotides to the 3' end of a growing DNA strand -proofreads and repairs DNA
DNA polymerase
-adds nucleotides to the 3' end of a growing DNA strand, using DNA as a template -proofreading function
25. What is synthetic DNA
-artificial DNA that scientists create from scratch in the laboratory that can in theory be used to replace absent or defective genes during gene therapy
55. What is the order of virus life cycle? What occurs during adsorption, un-coating and assembly (maturation). Describe ONE-STEP growth cycle? How one grows viruses in lab?
-attachment/adsorption -penetration -biosynthesis/replication -assembly/maturation -release
42. Compare the general features of Bacteria, Archaea and Eukarya.
-bacteria and archaea: prokaryotes -archaea: no peptidoglycan -bacteria: peptidoglycan -bacteria: sensitive to antibiotics -eukarya: 80S, mitosis, linear chromosome
50. List the differences between bacteria and viruses. Where in nature viruses can be found
-bacteria can self-replicate -viruses are intracellular parasites -bacteria replicate through binary fission -bacteria always have double-stranded DNA -bacteria have ribosomes -bacteria are sensitive to antibiotics -viruses: sensitive to interferons
43.Describe general features of Bacteria, Protozoa, Fungi, Viruses, and Archaea
-bacteria: single-cell prokaryotes with cell walls of peptidoglycan and a singular circular double-stranded DNA molecule, anddivide by binary fission -protozoa: unicellular eukaryotes that inhabit water and soil and have a life cycle that alternates between cysts and trophozoites -fungi: eukaryotic chemoheterotrophs that can be uni or multicellular that develop either sexually or asexually from spores or hyphal fragments, made of chitin -viruses: obligat, intracellular parasites that are sub-microscopic and have a specific range of hosts, acellular and non-living -archaea: single celled prokaryotes that do not have peptidoglycan and are often extremophiles
38. What is the connection between horizontal gene transfer and antibiotic resistance genes? What is the role of plasmids in this process?
-bacterial plasmids often have antibacterial resistance genes and these genes can be transferred to other bacteria via horizontal gene transfer -antibiotic resistance increases the more you are exposed to antibiotics
Describe economic impact of fungi.
-bakers yeast used to brew wine and make bread -bakers yeast hep b vaccine -trichoderma make denim -taxol for cancer patients -entomophaga kills pests
21. List scientific and agricultural applications of recombinant DNA.
-bioinformatics -proteomics: study of all the proteins that can be expressed by the human genome -reverse genetics -southern blotting: uses radioactive DNA hybridization probes and autoradiography to identify the presence or absence of a specific gene -DNA fingerprinting: analysis of an organisms DNA by creating restriction fragments and running those fragments through an electrophoretic gel -nanotechnology: involves the design and manufacture of extremely small mechanical devices and electronic circuits built at the molecular level
6. What are the differences between DNA polymerase and RNA polymerase?
-both use DNA as a template -DNA polymerase synthesizes new DNA -RNA polymerase synthesizes new RNA -DNA polymerase needs a RNA primer but RNA polymerase does not
30. List some important agricultural products produced using recombinant DNA technology. (Table 9.3)
-bt cotton and bt corn -genetically modified tomatoes and raspberries -roudup-resistant crops
46. List features of Chlamydia, Spirochetes, and Mycoplasma discussed in lecture
-chlamydiae: gram-negative, no peptidoglycan, obligate intracellular organisms, cause STDs -spirochete: highly coiled cells that move via axial filaments that can constrict -mycoplasma: a genus of bacteria that lack a cell wall around their cell membranes, which means they need to be gram-stained to be identified
Examples of horizontal gene transfer include: _______. _______. _______
-conjugation -transduction -transformation
types of horizontal gene transfer
-conjugation: transfer of genetic material between bacteria through direct contact (plasmid - pilus) -transformation: direct uptake of genetic material from a bacteriums surroundings -transduction: transfer of genetic information from one bacterium to another via bacteriophage
Topoisomerase
-contributes to or relieves "supercoiling" of DNA ahead of replication fork -separates DNA circles at the end of replication
51. What is meant by obligate intracellular pathogens? Which groups of infectious agents are included?
-disease-causing microorganism that cannot reproduce outside its host cell -viruses, bacteria, fungi, and protozoans
13. Where in eukaryotes and prokaryotes one can find DNA?
-eukaryotes: nucleus -prokaryotes: nucleoid
44. Compare general features of prokaryotic and eukaryotic cells
-eukaryotic larger -eukaryotes have DNA in a membran-bound nucleus vs a nucleoid -membrane-bound organelles -eukaryotic DNA is linear, prokaryotes have plasmids -pro and eu can have cell walls but not all do -both have flagella only eukaryotes have cilia
32. Define base analogs and explain how they may induce mutation
-fit into the DNA molecule like a "normal" base but do not have the same function -randomly incorporated into cellular DNA in place of the normal bases
Outcome of ionizing radiation (X-ray):___________
-formation of ions that oxidize nucleotides and break apart the deoxiribose-phosphate background -base deletions -cross-linking -single-stranded nicks -breaking of entire chromosomes
15. Define Operons and explain their role in gene expression (transcription) in bacteria. Give examples.
-functioning units of DNA containing a cluster of functionally related genes under the control of a single promoter -single "switch" sequence controls transcription of the entire operon -primarily found in prokaryotes -inducible operons: normally turned off but can be turned on -repressible operons: normally turned on and can be regulated by being turned off
23. Describe how DNA can be inserted into a cell; By: Gene Gun, Microinjection
-gene guns: shoot foreign DNA into plant cells with a burst of helium and tungsten or gold-coated DNA -microinjection: glass micropipette punctures the plasma membrane and inject foreign DNA into an animal cell
2. What are the important points discussed in "Big Picture-Genetics"?
-genetics: the study of heredity, how genes are replicated, expressed, and passed from one generation to the next -mutations in the DNA alter the mRNA, which alters the protein and its function -frameshift mutations and base substitutions
58. What is the role of viruses in cancer? Name the cancers caused by viruses.
-hep b, hep c, hpv, htlv-1, htlv-2
1. Define Central Dogma of Molecular Biology (list its chain of events)
-holds that DNA is transcribed into a complementary strand of RNA, which is translated into a specific sequence of amino acids that results in the creation of a protein -DNA - transcription - RNA - translation - Protein
28. Define nanotechnology
-involves the design and manufacture of extremely small mechanical devices and electronic circuits built at the molecular level -bacteria produce nanospheres from elements like gold, silver, cadmium, and selenium
57. Name different shapes of viruses. Which one is unique to viruses?
-isacohedron shape: polyehdron with 20 triangular faces, 30 edges, 12 vertices
Ligase
-joins fragments of DNA together, including Okazaki fragments and newly formed segments during DNA repair
61. Define and compare latent viral infections and persistent viral infections.
-latent: virus remains in the host cell in a dormant state until a trigger activates it -Persistent: produced and released slowly over time without killing the host
Primase
-lays down RNA primers to allow DNA synthesis to begin
10. What is meant by post-transcriptional control?
-mRNA has to be exported from the nucleus via the nuclear pores -addition of a guanine cap and a poly-A tail -removal of introns: intervening sequences of non-coding RNA
4. Name different RNA molecules. What is the role of each molecule? Which ones contains Codon, anticodon
-mRNA: carries genetic information from the DNA to the ribosomes -tRNA: used to carry amino acids during protein synthesis -rRNA: structural components of ribosomes -codons: mRNA -anticodons: tRNA
35. List some chemical agents that can cause cancer (mutagens) and describe their mechanism of action?
-nitrous acid (adenine to cytosine instead of thymine) -base analogs (cause mistakes in base pairing) -benzopyrene (frameshift mutation) -aflatoxin (fameshift mutation)
52. Name different components of a virus. Name the two that every virus must have
-nucleic acid and capsid -viral envelope (composed of lipids, proteins, and carbs -spike (protein that assists in the recognition and attachment to the host cell
Semiconservative replication
-one of the strands of the daughter DNA is a "new" strand while the other is an old strand -daughter strand will always have a correct template even if there was an error in DNA replication
Antiparallel
-parallel with one another but run in opposite directions -5' is directly across from 3' and vice versa
26. List therapeutic applications of Recombinant DNA technology
-production of human enzmes and other gene products -subunit vaccines: only uses a fragment of a pathogen -DNA vaccine: contains the DNA that codes for specific antigens -gene therapy: involves the transplantation of normal genes into cells in place of missing or defective ones in order to correct genetic disorders -gene silencing and RNA interference: siRNAs can stop the expression of those genes
18. What are ribosomes made of? Prokaryotes and eukaryotes have different ribosomes? What is the significance of this difference?
-proteins and rRNA -prokaryotes: 70S -eukaryotes: 80S -we can make drugs attack prokaryotic ribosomes without attacking eukaryotic ribosomes which allows us to kill bacterial cells without killing human cells
29. Describe the use of human microbiome in crime scene investigation.
-refers to the aggregation of microbes that reside on or within human tissues -each person has a unique microbiome fingerprint -can be used as a forensic evidence
14. What is meant by pre-transcriptional control?
-regulates gene expression before transcription has occurred -presence of or absence of a regulatory molecule in the cell can control whether these genes are transcribed -epigenix control via methylation of DNA, bacterial operons
6.What are the products of: Replication, Transcription, Translation and Reverse Transcription?
-replication: double-stranded DNA -transcription: single-stranded RNA -translation: polypeptide (protein) -reverse transcription: DNA
22. Name the tools used to make a recombinant DNA. Example; how you cut DNA, how to track the DNA.
-restriction enzymes: cut DNA st restriction sites -can be used to cut the DNA of interest and a plasmid vector, and then the DNA can be inserted into the plasmid vector -ligase can seal the strands together
20. Explain how a technique called RFLP works in analyzing DNA
-restriction fragment length polymorphism -isolate DNA of interest -amplify using PCR techniques -cut the DNA with restriction enzymes to creat restriction fragments -use gel electrophoresis to separate restriction fragments according to their lengths on an agarose gel -use computers to analyze
39. Describe the role of Yeast cells, Plant cells, and Mammalian cells in making gene products
-saccharomyces cerevisiae: can more easily express eukaryotic genes than prokaryotic vehicles like e. coli -plant cells and whole plants: can be grown in culture and manipulated to produce genetically modified plants -more difficult to grow in culture but they express eukaryotic genes easily and have a low risk of toxin or allergens
11. What is the function of microRNAs (miRNAs)?
-small, single-stranded bits of RNA that inhibit protein production in eukaryotic cells -facilitate cell differentiation by producing different proteins
Single-stranded binding protein
-stabilizes single-stranded DNA once it is unwound
48. List fungal diseases listed in lecture notes.
-superficial mycosis: localized -cutaneous mycosis: affects the hair, skin, or nails -subcutaneous mycosis: found beneath the skin -opportunistic mycoses: fungal infections that are harmless in normal people but pathogenic in immunocompromised hosts
17. Cells Prefer glucose over lactose. How genes are expressed to facilitate this preference?
-the genes that produce the enzymes needed to break down lactose will not be produced as long as glucose is also present in the medium -diauxic growth: a two phased growh pattern in which two periods of exponential growth are separated by a brief lag phase -glucose used first, then lactose
5. Briefly describe replication. What is used as template for each process?
-the process in which double-stranded DNA is copied to produce two identical DNA molecules -DNA is the template in this process
5. Briefly describe transcription. What is used as template for each process?
-the process in which information in a strand of DNA is copied into a new molecule of mRNA -DNA is template
5. Briefly describe translation. What is used as template for each process?
-the process in which the information in mRNA is used to synthesize polypeptides -mRNA is the template
27. What is the goal/purpose of Genome Project?
-to provide a complete and accurate sequence of the 3 billion DNA base pairs that make up the human genome and to find all the estimated 20,000 to 25,000 human genes
How you introduce the DNA to the host cell
-transformation: cell pick up "naked" DNA from the environment -electroporation: makes a cell competent to pick up DNA from the environment by applying an electrical shock to it -protoplast fusion: involves the removal of cell walls from two cells and then treating them with polyethylene glycol in solution which causes the cells to fuse and their chromosomes to recombine -gene guns: shoot foreign DNA into plant cells -microinjection: involves the use of a glass micropipette to puncture the plasma membrane and inject foreign DNA into animal cell
53. Distinguish between transforming, persistent, latent, lysogenic, and lytic viral infection
-transforming infection: virus affects the hosts' genetic makeup w a mutation -persistent: viral particles are produced and released slowly overtime without killing the host -latent: remains in a dormant state until a trigger activates it and causes it to make more copies of itself -lysogenic: phage genome becomes incorporated into the host chromosome as a prophage and does not kill -lytic: virus produces more phage particles until the cell eventually lyses
41. What is the significance of Ti Plasmid
-tumor-inducing plasmid induces the formation of tumors in hundreds of plant species, but can also be used as a cloning vector that carries the DNA of interest and a selectable marker
Complementary strands
-two DNA strands that make up DNA molecules are complementary, which means that the nucleotideso n one side always pair up with the nucleotide bases on the other strand -adenine & thymine -cytosine & guanine
Double helix
-two strands wound around each other like a twisted ladder -sugar-phosphate backbone of each strand forms the sides of the ladder -nucleotide bases form the rungs
49. What are the general features of Protozoa? Compare Cyst vs. Trophozoite
-unicellular eukaryotes with complex life cycles and animal-like nutrition -cysts: small non-dividing, inactive forms that are involved in transmission to a new host, rigid cell coat that makes them resistant to harsh environmental conditions which allows the protozoan to survive outside the host in most ambient conditions -trophozoites: larger dividing active forms that cause diseases, cannot survive outside the host
Helicase
-unwinds the double helix at the replication fork
62. What is plaque assay and what is used for? What is CPE? Give an example
-used to quantify viruses
RNA interference (RNAi)
-uses gene silencing to treat genetic diseases
37. State the difference between and give examples of vertical and horizontal gene transfer?
-vertical: transmission of genetic information from parent to offspring in sexual or asexual reproduction -horizontal: transmission of genetic information between organisms in a manner other than traditional sexual or asexual reproduction
47. List forms of fungi listed in the lecture notes.
-yeast: single cells, non-filamentous, fission divide evenly, budding do not -molds: grow in multicellular filaments called hyphae, can be septate with walls and membranes, or coenocytic (lack walls or membranes)
56. List Congenital infections caused by viruses
-zika, herpes, cytomegalovirus, rubella, varicella, enteroviruses
Biofilm
A surface-coating colony of one or more species of prokaryotes that engage in metabolic cooperation.
_________ is used to identify chemical carcinogens
Ames test
-
Chromosome, Gene, genome, Extra-Chromosomal DNA (Plasmids, Mitochondria, Chloroplast)
-
Cloning, Recombinant DNA, Genomic library, Synthetic DNA
-
DNA Polymerase vs. RNA Polymerase
-
Define Microbiome
-
Examples of acellular structures; Virus (Virion) / Viroid / Prion
-
Gel electrophoresis, PCR, Restriction enzymes, vectors
Enzyme________ unwinds double-stranded DNA
Helicase
-
Ligase / Helicase, Reverse transcription, endoonuclease/exonuclease activity (adding/removing nucleotides)
-
Mutagens/Carcinogens/Ames Test
-
Replication, Transcription, Translation
-
Ribosome, Codon/Anticodon / Genetic code
-
Shotgun sequencing, metagenomics,
-
Subunit vaccine, DNA vaccine, Gene therapy, gene silencing
-
Viruses: Capsid / Spike / Envelope / Icosahedra, Plaques assay/ Un-coating
Missense mutation
a change in the nucleotide sequence that causes the change of a single amino acid
nonsense mutation
a change in the nucleotide sequence that converts a "sense" codon to a stop codon
Genomic library
a collection of an organism's entire genomic DNA which is stored in a population of identical vectors, each of which has a fragment of the DNA -contains multiple vectors
Gene
a segment of DNA that carries the genetic information to code for a functional product which could be a polypeptide, a ribosomal RNA, or a tRNA
Chromosome
a structure that physically carries hereditary information in the form of DNA
16. Define catabolic Repression.
a system that overrides inducible operons such as the lactose operon
DNA ligase
an enzyme that joins fragments of DNA together, including Okazaki fragments and newly formed segments
Viruses may attack which groups of organisms... Humans, animals.............
any type of organism
34. Define frame shift mutation
caused by the insertion or deletion of bases in a way that throws off the reading frame
Restriction enzymes are used to ______ DNA
cut DNA at restriction sites
Post-transcriptional control requires DNA polymerase enzyme. (T/F)
false
Mutations are always harmful (T/F)
false, not always harmful
Mycosis is a form of _______ infection
fungal
Segments of DNA that encode functional products are called______
genes
Operon
group of genes operating together
Cold sores and shingles are two examples of __________ viral infections
latent
Codons are located on ________
mRNA
________: agents that cause mutations
mutagens
Repressible operon
normally "on" but can be turned "off"
Inducible operon
normally off but can be turned "on"
59. How viruses may transform a normal cell into a tumor cell?
oncogenes have the capacity to cause cancer if they are activated
60.How viruses may be used to treat cancer by killing cancer cells?
oncolytic viruses: have the capacity to destroy tumor cells
Cervical cancer and liver cancer are two examples of _______ viral infections
persistent
_________ may result in missense or nonsense mutation
point mutations
Cyst and Trophozoite are two forms of _________
protozoans
DNA gyrase
relieves "supercoiling: ahead of the replication bubble by breaking and joining DNA strands
Anticodon is located on _______
tRNA
__________ transports amino acids during protein synthesis
tRNA
RNA polymerase
the enzyme that adds nucleotides to the 3' end of a growing RNA strand, using RNA as a template
Genome
the total complex of DNA in a cell
Outcome of UV radiation: __________
thymine-thymine dimers
Process of protein synthesis is called__________
translation
All viruses are considered obligate intracellular parasites (T/F)
true
Catabolic repression allows bacteria to prefer glucose over other sugar sources (T/F)
true
DNA in prokaryotes is found in both chromosome and plasmid (T/F)
true
DNA is eukaryotes is found in chromosome, chloroplast, and mitochondria (T/F)
true
During the conjugation process, plasmids can carry antibiotic resistance genes from one bacteria to another (T/F)
true
During the lysogenic cycle, phage (virus) DNA is incorporated into host cell DNA (T/F)
true
Nitrous acid causes adenine to bind with cytosine instead of thymine (T/F)
true
Ribosome is made of protein and RNA molecules (T/F)
true
Ribosome is the site of protein synthesis (T/F)
true
Some fungi can kill termites (T/F)
true
Ti Plasmid are used to genetically modify plants (T/F)
true
Transduction is a form of horizontal gene transfer, made possible by help of viruses (bacteriophages). (T/F)
true
_______used to transport (carry) DNA into a cell
vectors
_________________transfer of genes from an organism to its offspring
vertical
Embryonated eggs are used to grow _____ in lab
viruses
