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mcb 2000

mcb 2000

Description

School: University of Florida
Department: Biology
Course: UF Microbiology
Professor: Abdolkarim asghari
Term: Spring 2016
Tags: Bacteria, Viruses, replication, translation, and transcription
Cost: 50
Name: MCB2000- Exam 2 Study Guide
Description: Covers all of the material for exam 2.
Uploaded: 02/23/2018
22 Pages 14 Views 13 Unlocks
Reviews


MCB 2000 Study guide for EXAM TWO


what theory is created by francis crick in 1956?



(answers come from lecture notes and textbook chapters 8,9 and 13)  

1. Define Central Dogma of Molecular Biology (list its chain of events)

• DNA -> mRNA -> protein formation -> functional proteins  

• Theory created by Francis Crick in 1956  

• A sequence of nucleotides in DNA determines the sequence of amino acids in a protein  • Transcription: genetic information in DNA is copied, or transcribed, into a complementary base  sequence of RNA

• Translation: cell uses information encoded in the RNA to synthesize specific proteins  • Describes how DNA becomes messenger RNA, which turns into protein  

• If a mutation occurs this process is altered  

o Mutated DNA -> mutated mRNA -> altered protein structure -> altered protein function  o The change in the DNA sequence of amino acids alters the folding of the protein which  alters its ability to function  


what is chromosome?



2. Define Chromosome, gene, genome

• Chromosome: structures that contain DNA and physically carry the hereditary information o Contain genes  

• Gene: segments of DNA that encode functional products, usually proteins  Don't forget about the age old question of comm 100

o in some viruses they are made out of RNA  

• genome: all of the genetic information in a cell.  

o Includes chromosomes and plasmids  

• Genome -> chromosomes -> genes  

3. Name different RNA molecules. What is the role of each molecule? Which ones contains Codon,  anticodon

• Ribosomal RNA (rRNA)  

o Forms an integral part of ribosomes  

o Machinery for protein synthesis  

o Ribosome is made up of rRNA and protein- it sandwiches the mRNA  

• Messenger RNA (mRNA)  

o Carries the codes from the DNA  

o Provides the information for making a specific protein  If you want to learn more check out hacs themes

o Brings the information from the DNA to the ribosome (place where protein synthesis  occurs)  


what is gene?



o Carry codons  

o Synthesized by RNA polymerase (recognizes the beginning of the gene, moves 5 to 3  prime)  

o mRNA is the translated version of the DNA (in the language of proteins)  

o codons- group of 3 mRNA nucleotides that code for a particular amino acid  

o contains uracil instead of thymine  

o transcribed with RNA polymerase and a supply of RNA nucleotides  

o sequence of codons on the mRNA molecule determines the sequence of amino acids that  will be made into a protein  

• Transfer RNA (tRNA)  

o Transport the required amino acids to the ribosome  

o Recognize the specific codons  

o Carry anticodons which are commentary to the codons on the mRNA

o Anticodons bind to the codons from the mRNA and an amino acid chain is assembled  4. Briefly describe replication, transcription, and translation. What is used as template for each process? • Replication  

o One strand of DNA serves as a template for the production of a second strand  

o The strand is opened up by topoisomerase and gyrase- these enzymes relax the strand  and unwind the double helix and supercoiling  

o The strands of DNA are separated by Helicase- enzyme breaks the hydrogen bonds  between the two strands of DNA  Don't forget about the age old question of organic chemistry 1 final exam

o A replication fork is created  

o DNA polymerase adds new nucleotides in the 5’ to 3’ direction

o The leading strand (5’-3’) is synthesized continuously  

o The lagging strand (3’-5’) is synthesized discontinuously through Okazaki fragments o Primers are needed to initiate synthesis for both strands  

o The Okazaki fragments are joined together by ligase  

o DNA ligase- makes covalent bonds to join DNA strands  

o DNA polymerase- synthesizes DNA and proof reads/ repairs the DNA  

o Helicase- unwinds the double stranded DNA  

o Topoisomerase- relaxes the super coiling ahead of the replication fork and separated  DNA circles at the end of replication  

• Transcription  

o RNA polymerase copies RNA from a DNA template  

o Genetic information from DNA is rewritten with the base sequences of mRNA  

o Process begins when RNA polymerase binds to the DNA at the promoter site  

o Only one of the DNA strands is used as a template  

o Synthesized in the 5’-3’ direction  

o Synthesis stops when RNA polymerase reaches the terminator site on the DNA  o Short term copies of the gene can be made which are directly used in protein synthesis o mRNA is created  Don't forget about the age old question of extranet uc

• Translation  

o mRNA travels to the ribosome carrying the information to make a protein  

o mRNA carries the necessary codons  

o tRNA carries the anticodons and the amino acid to the ribosome  

o the sequences of the codons on the mRNA determines the sequence of the amino acids  and the protein that will be created  

o each codon codes for an amino acid  

o there are 64 codons but only 20 possible amino acids (degeneracy)  

o start codon (AUG) codes for the beginning of protein synthesis  

o three nonsense codons (UAA, UAG, and UGA) signal the end of protein synthesis and do  not code for an amino acid  

o the ribosome directs the binding of the tRNAs to the corresponding codons

o an amino acid chain begins to be assembled and a protein is produced  

o as the amino acids are brought in line one at a time, peptide bonds begin to form making  a polypeptide chain  

5. What are the products of: Replication, Transcription, Translation and Reverse Transcription? What are  the differences between DNA polymerase and RNA polymerase? What is the significance of reverse  transcriptase? What is the source of reverse transcriptase (its origin)? What does it do? • Products of…  We also discuss several other topics like atbis login

o Replication

▪ DNA

o Transcription  

▪ mRNA

o Translation  

▪ Proteins  

o Reverse transcription  

▪ DNA/ parts of a desired gene  

▪ DNA copy of mRNA is produced  

• DNA polymerase  

o Adds nucleotides to the growing DNA strand in the 5’-3’ direction  

o Synthesizes DNA, proof reads DNA, repairs DNA  

o Removes mismatched bases before the synthesis process continues  

• RNA polymerase

o Synthesizes RNA from on strand of the double-stranded DNA (serves as template)  o Binds to the promoter and allows transcription to begin  We also discuss several other topics like elite mass dichotomy system

o Recognizes the beginning of the gene and moves in the 5’-3’ direction to synthesize an  mRNA  

o Synthesis of RNA continues until the RNA polymerase reaches the terminator  

• Reverse transcriptase: origin, what does it do?

o Artificial gene that contains only exons can be produced by using reverse transcriptase o Synthesizes complementary DNA from an mRNA strand template  

o mRNA then goes away through enzymatic digestion  

o DNA polymerase synthesizes a complementary strand of DNA- becomes double stranded  o The cDNA that is produced through reverse transcription can be combined with the other  molecules of cDNA from the same tissue or cell and be placed in the cDNA library  

o Popular method of obtaining eukaryotic genes  

o Only parts of desired gene may be transcribed if the mRNA molecule was too long  6. Define/Explain/describe: Complementary strands, Anti-parallel, Semiconservative replication, Double  helix

• Complementary strands

o Strands that make up the double helix of DNA  

o They have complementary base pairs (A and T; C and G)  

o Complementary structure of the nitrogenous bases allows one strand to serve as a  template during DNA replication  

• Anti-parallel  

o The two strands of DNA are anti-parallel because they run in opposite directions  o One strand goes from 5’-3’ the other strand goes from 3’-5’  

• Semiconservative replication  

o Each new DNA molecule contains the original strand and one new strand  

o DNA is never completely brand new; always contains one parent strand and one  daughter strand  

• Double helix

o two strands made of nucleotides make up the double helix  

o two strands of DNA are wound together around the same axis  

7. List the enzymes and their functions involved in DNA replication

• DNA ligase: makes covalent bonds to join DNA strands and Okazaki fragments  

• DNA polymerase: synthesizes DNA, proofreads and repairs  

• Helicase: unwinds double stranded DNA

• Topoisomerase: relaxes supercoiling ahead of the replication fork; separate DNA circles when DNA  replication is done  

• Gyrase: relaxes the DNA strand before replication  

8. What is the genetic material for viruses, DNA or RNA, single stranded or double stranded?  • Viruses can have DNA or RNA, but can’t have both  

• Can be double stranded or single stranded  

• Linear or circular  

9. Where in eukaryotes and prokaryotes one can find DNA?

• Eukaryotes  

o Most located in the nucleolus  

o Some in the mitochondria and some in the chloroplasts as well  

o linear chromosomes that together make up the genome  

• Prokaryotes  

o There are no membrane bound organelles, so DNA is found free floating in the cytoplasm  o In the nucleoid region

o Found in a coiled loop  

o DNA can be in the form of plasmids in certain bacteria; distinct from the chromosomal  DNA  

10. Define Operons and explain their role in gene expression (transcription) in bacteria. Give examples. • The process of turning genes on and off can save energy for the cell- only making what is  necessary at the time  

• Set of operator and promoter sites and the structural genes that they control  

• Regulated by the production of regulatory genes  

• Operator: provides the go and stop signal for transcription of structural genes  

• Promoter: place where RNA polymerase begins transcription  

• Regions of DNA that code for multiple genes  

• Genes are expressed only as needed  

• Inducible genes are lactose operons  

o They are usually off unless there is a substrate that needs to be broken down/sugar to  metabolize  

o When lactose is not available a repressor binds to the operator site and prevents  transcription  

o If lactose is available repressor binds to the metabolite of lactose and lactose-digesting  enzymes are created  

• Repressible operons are always on

o Synthesis of proteins always needs to occur unless an amino acid comes from outside the  cell  

o Structural genes are transcribed unless turned off  

11. Define catabolic Repression

• Inhibits gene expression

• Decreases the synthesis of enzymes

• a process that can override inducible operons  

• when you have lactose and glucose together the glucose is used first -> the inducible operon is  turned off  

• the lag time between using glucose and lactose -> the time it takes to turn on operon  • catabolic repression does not affect the repressible operons  

• inhibition of the metabolism of alternative carbon sources by glucose

12. What are ribosomes made of? Prokaryotes and eukaryotes have different ribosomes? What is the  significance of this difference?

• Ribosomes  

o Every cell has them; used to synthesize proteins  

o Connect amino acids together to make a polypeptide chain  

o Made of rRNA and protein  

o Sandwiches the mRNA during translation  

o Some are free floating in the cytoplasm and some are bound to the membrane of the  endoplasmic reticulum

• Prokaryotic vs. eukaryotic  

o Prokaryote: 70s ribosomes  

o Eukaryote: 80s ribosomes (60s subunit and 40s subunit)  

o Chloroplasts and mitochondria (in eukaryotes) have 70s ribosomes too  

▪ Shows that prokaryotes evolved into eukaryotes over time  

13. What is meant by recombinant DNA (technology)? Describe the use of Recombinant DNA in Producing  Insulin. What is the purpose of cloning?

• Recombinant DNA technology: the insertion/ modification of genes to produce desired proteins  • DNA from two different sources are put into one cell  

• also known as genetic engineering  

• bacteria with genes for human insulin can be used to produce insulin for diabetic patients  • vector is introduced to the bacteria and begins to multiply creating a clone  

• vector: self-replicating DNA molecules used to transport foreign DNA into a cell  • clone: population of genetically identical cells arising from one cell; each carries the vector • from this clone researchers can harvest large amounts of the gene they are interested in studying  • production of insulin  

o the insulin they used to get from animals was not as effective as the insulin they can now  produce from humans  

o synthetic genes were constructed for the two polypeptide chains that are present in  insulin  

o synthetic genes introduced to a plasmid (vector)

o these synthetic genes were linked to genes that were already coding for a different gene  (beta-galactosidase enzyme)  

o allowed the insulin enzyme to be produced at the same time as the other enzyme  o an E. coli bacteria was used to produce each of the polypeptide chains  

o polypeptides were collected from bacteria and the beta-galactosidase enzyme was  removed  

o two polypeptides were joined by chemicals to make the human insulin  

14. Explain how a technique called RFLP works in analyzing DNA

• restriction fragment link polymorphism  

• takes the genetic information of the nucleic acid/ DNA and cuts the DNA into pieces  • southern blotting: DNA probes detect specific DNA in fragments (RFLPs)  

o DNA is first digested by a restriction enzyme -> creates thousands of fragments of  different sizes  

o Fragments separated by gel electrophoresis  

o take DNA cut it up, put it in gel, transfer it to paper, a make a probe  

o probe binds to certain fragments and this can be seen by colored dye  

o genes can be tested for mutations  

o can be compared to the DNA from a father and child for a paternity test

o important in genetic testing  

15. List scientific and agricultural applications of recombinant DNA.

• Scientific  

o Create human enzymes and proteins  

o Create medications such as insulin and HGH  

o Subunit vaccines: made from pathogen proteins in genetically modified yeast  

o Gene therapy to replace defective or missing genes  

o Vaccines for cervical cancer  

o CSF- colony stimulating factor to help patients with AIDs  

o Interferons to help people with cancer and the creation of the hepatitis B vaccine  o Flu virus vaccine  

o Tumor Necrosis factor to disintegrate tumors  

o Gene silencing: use RNA to break down mRNA and stop diseases from happening  o Bioinformatics: understanding gene function via computer-assisted analysis  

o Proteomics- determining proteins expressed in a cell  

o Reverse genetics- discovering gene function from a genetic sequence  

o Restriction enzymes used to cut DNA  

o Viruses and gene guns can be used to insert DNA  

o Southern blotting: DNA probes detect specific DNA in fragments (RFLPs) separated by gel  electrophoresis  

o Take DNA from different places, cut it up, put it in gel, transfer genes to solution w/probe  o Probe will attach and show on x-ray  

o RFLP- restriction fragment link polymorphism  

▪ Take DNA cut it up, put it on gel, transfer to paper, make a probe  

▪ Then take DNA from the father and child and compare  

▪ Prove paternity with test  

• Agricultural  

o Bt toxin: produced by bacteria and kills pests  

▪ Took gene and introduced it to plants  

▪ Introduced into corn and cotton -> bugs can’t eat plants, or they will die  

▪ No need for pesticides  

▪ Plant has the toxin producing genes in it  

o Added roundup material into plants- produce genes  

o Rhizobium meliloti bacterium- modified for enhanced nitrogen fixation  

o Suppression of genes- antisense DNA (block DNA to increase shelf life of plants)  o Nutrition- human proteins added to plants to increase our nutrient intake  

o bGH hormone- makes cows produced more milk and gain more weight  

o Make cellulose- enzyme that degrades cellulose to make animal feedstock  

▪ Produced by E. Coli

16. Name the tools used to make a recombinant DNA. Example; how you cut DNA, how you introduce the  DNA to the host cell, how to track the DNA. What is meant by gene library? Protoplast fusion? • How do you cut DNA- restriction enzymes  

o Cut specific sequence of DNA  

o Destroy bacteriophage DNA in bacterial cells  

o Methylated cytosine in bacteria protect their own DNA from digestion  

o Create blunt ends (straight cuts) or sticky ends (staggered cuts)  

o Recognizes and cuts the same DNA sequence each time  

o Sticky ends are most useful- can join two pieces of DNA in vitro cut by same restriction  enzyme (join by hydrogen bonding)

o DNA ligase links the backbones of the two pieces of DNA with covalent bonds  

• Introducing DNA to the host cell- vectors  

o Carry new DNA to desired cells  

o Must be able to self-replicate  

o Plasmids and viruses can be used as vectors  

o Shuttle vectors: exist in several different species and can move cloned sequences among  various organisms  

• Bacteria, yeast, and mammalian cells, or bacterial, fungal and plant cells  

o Carry genes between or into eukaryotes and prokaryotes  

o Plasmids can be cut with same restriction enzymes as the DNA-> same sticky ends so they  can be joined together easily  

• How to track DNA  

o PCR can detect infectious agents when no other detection method would be possible  • Gene library  

o Collection of bacterial cells  

o Each collection from library has segments of DNA in it that can be studied  

o Collection of clones containing different DNA fragments  

o DNA is digested and spliced into plasmid or phage vectors and introduced into bacteria  o At least one clone exists for every gene in the organism  

o Use a restriction enzyme to cut into pieces and place in different cells  

o Helps to understand what different genes do- different gens in each bacteria  

• Protoplast fusion  

o Removing cell walls from. Two bacteria allows them to fuse (fungi mostly)  

o When placed in solution protoplasts fuse at a low rate  

o Polyethylene glycol increased the speed of the fusion process  

o Use to manipulate plant and algae

o DNA from two parent cells may combine  

17. Describe how DNA can be inserted into a cells; By: Gene Gun, Microinjection

• gene gun: DNA-coated “bullet” that goes into a cell  

o shoot plant through cellulose wall  

o tungsten or gold are coated with DNA  

o helium propels them into the plant cell wall  

o some cells can express the DNA the same way they express their own DNA  

• Microinjection: foreign DNA goes into an egg  

o Dolly the Sheep was created this way  

o Goes directly into an animal cell  

o Micropipette is really small in comparison to the cell  

o Punctures the plasma membrane and DNA is injected  

18. Define spontaneous mutation. What causes spontaneous mutation/induced mutation • Spontaneous mutation  

o Occur in the absence of a mutagen  

o Small amount of spontaneous mutations is important for genetic diversity  

o Caused by mistakes made in DNA replication  

o Deamination of cytosine to uracil can be one cause  

• factors that Induce mutation  

o change in base pairs  

o radiation

▪ ionizing radiation (x-ray/gamma rays)

▪ UV radiation  

o chemicals

▪ nitrous acid  

▪ nucleoside analog  

o missense mutation: base substitution results in change in amino acids  

o nonsense mutation: base mutation results in nonsense stop codon  

o frameshift mutation: insertion or deletion of one or more nucleotide pairs  

o deletion: removing one base pair  

19. Define base analogs and explain how they may induce mutation

• Chemical mutagens that mimic base pairs  

• Can be incorporated into DNA instead of a normal base  

• Increases the rate of mutated protein formation  

• Matches up to the wrong base more than normal base it often replaces  

• Leads to base pair substitutions

• Nucleoside analog: structurally similar to normal base pair but altering properties  o Used to make antitumor, antiviral and HIV drugs  

20. How different types of radiation may cause mutation

• Ionizing radiation (x-ray and gamma rays) cause the formation of ions that can oxidize nucleotides  and break the deoxyribose-phosphate backbone  

• UV radiation causes thymine dimers (fusing two Thymine together)  

• Repair UV damage by…

o Photolyases separates thymine dimers  

o Nucleotide excision repair: enzymes cut out incorrect bases and fill in correct bases  • Sunlight -> UV and infer-red  

o When exposed we need to come into the shade to let the cells repair themselves or else  permanent damage can occur over time  

• Ionizing radiation causes electrons to come out of their shell abnormally  

o Oxidize DNA bases which leads to mutations  

o Can even cause phosphate bond in DNA to break which destroys chromosomes  • UV radiation

o Harmful covalent bonds form between the pyrimidine bases in DNA  

o Can cause damage or death  

21. Define frame shift mutation, missense/nonsense mutation

• missense mutation: base substitution results in change in amino acids  

o carrying incorrect base at that position on the mRNA  

• nonsense mutation: base mutation results in nonsense stop codon  

o protein isn’t fully synthesized  

o it is shorter in length -> can’t fold the same way -> doesn’t serve the same function  • frameshift mutation: insertion or deletion of one or more nucleotide pairs  

o shifts the reading frame  

o inserting/deleting one amino acid with alter all of the codons from that point on  o nonsense codon might come up and the protein would be shortened  

22. List some chemical agents that can cause cancer (mutagens) and describe their mechanism of action? • Carcinogens- substances that cause cancer  

• Nitrous acid: causes adenine to bine with cytosine instead of thymine  

o One of the daughter strands of the DNA will have base pairs that differ from the parent  DNA  

o Alters DNA at random locations

• Nucleoside analog: incorporates into DNA in place of a normal base; cause mistakes in base pairing  o Similar to normal bases but alterations in base pairing  

o Randomly placed in DNA instead of a normal base  

o Base substitutions will continue in the future  

• Benzopyrene: found in smoke can cause a frameshift mutation  

• Aflatoxin: produced by mold and causes a frameshift mutation in peanuts and grain  23. State the difference between and give examples of vertical and horizontal gene transfer? • Vertical gene transfer

o transfer of genes from an organism to its offspring

o present in plants and animals  

• Horizontal gene transfer  

o transfer of genes between cells of the same generation

o only in bacteria  

o donor cell: gives part of DNA  

o recipient cell: gets part of DNA from another cell  

o DNA is then incorporated  

o Occurs in only 1% of bacteria  

o humans and plants do not have horizontal gene transfer  

o Transformation- picking up DNA from environment  

o Transduction- virus pass DNA from one bacteria to another  

▪ Virus goes into one bacteria -> pick up genes and carry to another bacteria  

▪ Put genes in plasmid -> put plasmid in humans  

▪ Has allowed us to create cheaper insulin  

▪ Plasmids: self-replicating circular pieces of DNA  

o Conjugation- two bacteria come in direct contact; DNA transfer through pili (sex pili)  ▪ Plasmid transfer from one bacterium to another  

▪ Plasmids carry genes that cause diseases and make antibiotic resistant genes

o Transpons and plasmids  

▪ Transpons are segments of DNA that can move from one region of DNA to another  ▪ Contain insertion sequence that code for transposase that cuts and reseals DNA  ▪ Complex transpons carry other genes (ex: antibiotic resistance)  

▪ Mobile gene elements- can jump off chromosome to other parts of chromosome to  plasmids  

24. Describe the role of Yeast cells, Plant cells, and Mammalian cells in making gene products • Saccharomyces cerevisiae (yeast)  

o Easily grown, larger genome than bacteria  

o Express eukaryotic genes easily  

o Can carry plasmids- makes it easy to transfer into another yeast cell that no longer has a  cell wall  

o Can continuously secrete product  

o Better at expressing foreign genes than bacteria  

• Plant cells/ whole plants  

o Express eukaryotic genes easily

o Plants are easily grown, large-scale, low cost  

o Make genetically modified plants  

o Used to make codeine (alkaloids), rubber (isoprenoids), and sunscreen (melanin)  o Good for making vaccines and antibodies  

o Low risk of contamination and cancer-causing genes

• Mammalian cells- hard to work with  

o Express eukaryotic genes easily  

o Can make products for medical use  

o Harder to grow  

o Can be hosts for growing viruses  

o Genes must be cloned in bacteria first to make mass amounts  

o Genes inserted into a plasmid -> plasmid is copied by bacteria -> recombinant plasmids  are then put into the mammalian cell again  

25. List the therapeutic application of genetic engineering discussed in class.

• Human enzymes and other proteins such as insulin

• Subunit vaccines: made from pathogen proteins in genetically modified yeasts  • Nonpathogenic viruses carrying genes for pathogen’s antigens as DNA vaccines • Gene therapy to replace defective or missing genes  

• Vaccines for cervical cancer  

o Viral protein produced in yeast

• CSF- colony stimulating factor  

o Helps AIDs patients

o Made with E. Coli or yeast

• Interferons  

o Help with cancer- E. Coli or yeast

o Hepatitis B vaccine- yeast

• Human insulin

• Human growth hormone  

• Flu virus vaccine  

• Tumor Necrosis Factor- disintegration of tumors, helps with cancer

26. What is the significance of Ti Plasmid

• Using the Ti plasmid as a vector for genetic modification in plants  

o Ti plasmid- occurs in agrobacterium tumefaciens (infects plants)  

o Integrates into the plant genome and causes a tumor-like growth  

o Can be used to introduce rDNA into a plant  

o Makes the shelf life of vegetables longer  

o Grow bacteria -> take plasmid out -> open plasmid -> put genes into plasmid -> put  plasmid back in bacteria  

o Make it benign- infect plant but doesn’t cause disease  

o Plant grows and expresses genes we put in it  

o Transfer genes from prokaryotes to eukaryotes

o infects plants and causes crown gall tumor growths  

o T-DNA from the Ti plasmid gets integrated into the genome of the plant that is infected  o T-DNA leads to the growth of the crown gall and causes the production of bacteria  ▪ Serves as a source of nutritional carbon and nitrogen  

o Plant cell with the foreign DNA can generate a new plant eventually  

o Example: resistance to glyphosate herbicide  

o Example: the development of Bt toxin in plants which is toxic to insects  

o Example: MacGregor tomatoes can stay firm after they are harvested

▪ Suppression of enzyme that breaks down pectin  

27. Compare the general features of Bacteria, Archaea and Eukarya.

• Archaea  

o Prokaryotic

o Cell wall with peptidoglycan  

o Branched carbon chains attached to glycerol by ether linkage (membrane lipids)  o First amino acid in protein synthesis- methionine  

o Not antibiotic sensitive  

o No tRNA loop  

o Common arm of rRNA- lacking  

• Bacteria  

o Prokaryotic  

o Peptidoglycan cell wall  

o Straight carbon chain attached to glycerol by ester linkage (membrane lipids)  o First amino acid for protein synthesis- formyl methionine  

o Sensitive to antibiotics  

o Has tRNA loop  

o Has common arm of rRNA  

• Eukarya  

o Eukaryotic  

o Cell call- varies in composition; contains carbs (cellulose, chitin)  

o Membrane lipids- straight carbon chains, attached to glycerol with ester linkage  o First amino acid for protein synthesis- methionine  

o No antibiotic sensitivity  

o Lacks rRNA loops  

o Common arm of tRNA is present  

28. Describe general features of Bacteria, Protozoa, Fungi, Viruses, and Archaea • Bacteria  

o Prokaryotic  

o Peptidoglycan cell wall  

o Straight carbon chain attached to glycerol by ester linkage (membrane lipids)  

o First amino acid for protein synthesis- formyl methionine  

o Sensitive to antibiotics  

o Has tRNA loop  

o Has common arm of rRNA  

• Protozoa  

o Unicellular eukaryotes  

o Inhabit water and soil  

o Animal-like nutrition  

o Cysts and trophozotic  

▪ Trophozotic: growing, active, multiplying  

▪ Cysts- transmission, inactive, resistant to elements  

o Human/ animal pathogens  

▪ Amebae, malaria, giardia, cryptosporidium (outbreaks with water contamination)  ▪ Most cause diarrhea  

o Helminths

▪ Parasitic worms  

▪ Multicellular eukaryotic animals  

▪ Specialized to live in host  

• Fungi

o Mycology- study of fungi  

o Chemoheterotrophs  

o Decompose organic matter- recycle organic matter

o Unicellular or multicellular  

o Aerobic or facultative anaerobic  

o Yeast vs. mold  

o Reproduce by spores- sexual or asexual spores  

o Septate hypha- branching and segmented  

o Coenocytic hyphe- branching but not segmented  

o Grow better at pH of 5, high sugar or salt concentration  

o Spores are different from endospores (from bacteria)  

o Endospores- survive adverse conditions  

o Spores- used for reproduction  

o Metabolize complex molecules  

o Yeasts  

▪ Non-filament and unicellular  

▪ Budding yeast- divide unevenly  

▪ Fission yeast- divide evenly  

▪ Yeast like at 37 C, Mold like at 25 C  

▪ Dry and chalky  

• Viruses  

o Contain DNA or RNA (can’t be both), single or double stranded  

o Contain a protein coat- capsid  

o No ribosomes  

o No ATP- generating mechanism  

o nucleic acid covered by capsid

o Rely on host for replication, transcription, translation  

o No metabolism  

o May have enzymes, but energy comes from host cell  

• Archaea  

o Distinct taxonomic grouping- lacks peptidoglycan  

o Extremophiles  

▪ Halophiles- require salt concentration > 25%  

▪ Thermophiles- requires growth temp >80C  

o Methanogens- anaerobic and produced methane ( CH4)  

o Hyperthermophiles- above boiling temperature  

o Methanotrophs- eat methane/ consume methane  

o Bacteria helps to balance Co2 and methane concentration  

29. Compare general features of prokaryotic and eukaryotic cells

• Eukaryotes  

o Nucleus (membrane bound)  

o More than one chromosome  

o Usually multicellular  

o Lysosomes and peroxisomes  

o Microtubules  

o ER, mitochondria, cytoskeleton, vesicles, Golgi apparatus, chloroplast in plants  o DNA wrapped around histones  

o 80s ribosomes  

o microscopic flagella- membrane bound  

o selective permeability of nuclear membrane  

o plasma membrane with steroids  

o cell wall only in plant cells and fungi

o vacuoles  

• Prokaryotes  

o one chromosome in plasmids  

o usually unicellular  

o NO membrane bound nucleus  

o NO lysosomes, peroxisomes, microtubules, ER, mitochondria, Golgi, chloroplasts  (chlorophyll scattered in cytoplasm), permeable nuclear membrane, steroids in plasma  membrane

o Vacuoles  

o Cell wall  

o 70s ribosomes  

o folded DNA organized into a variety of conformations that are supercoiled and wound  around tetramers of the HU protein  

30. What is the importance of Cyanobacteria/Algae  

• Both play an important role in oxygenating the environment  

• Cyanobacteria

o Primary producers  

o Fix co2 through photosynthesis  

o Oxygenate the environment  

o Photosynthetic bacteria  

• Algae  

o Produce and secrete carbohydrates  

o Primary producers- can live deep in ocean  

o Photoautotrophs: fix co2 -> oxygen  

o No roots/ stems  

o Mostly aquatic, make biomass from Co2  

o Produced 80% of Earth’s oxygen  

o Algal blooms: increased in planktonic algae that can result in toxin release or die and  consume oxygen  

31. List features of Chlamydia, Spirochetes, and Mycoplasma discussed in lecture • Chlamydiae- obligate intracellular bacteria  

o Cause chlamydia and eye infections  

o Elementary body- small inactive used for transmission of disease (outside form of  bacteria)  

o Reticulate body- large, active, inside human cells  

o Elementary body -> enters human cell -> reticulate body  

o Chlamydia trachomatis- causes trachoma and urethritis  

o Chlamydophilia psittachi- causes respiratory psittacosis  

• Spirochaetas  

o Syphilis (T. Pallidum)  

o Lyme disease (borrelia)  

o Axial filament- allows organism to move around  

• Mycoplasma  

o No cell wall in this bacteria  

32. List forms of fungi listed in the lecture notes. Describe economic impact of fungi • Mycology- study of fungi  

• Chemoheterotrophs  

• Decompose organic matter- recycle organic matter

• Unicellular or multicellular  

• Aerobic or facultative anaerobic  

• Yeast vs. mold  

• Reproduce by spores- sexual or asexual spores  

• Septate hypha- branching and segmented  

• Coenocytic hyphe- branching but not segmented  

• Grow better at pH of 5, high sugar or salt concentration  

• Spores are different from endospores (from bacteria)  

• Endospores- survive adverse conditions  

• Spores- used for reproduction  

• Metabolize complex molecules  

• Yeasts  

o Non-filament and unicellular  

o Budding yeast- divide unevenly  

o Fission yeast- divide evenly  

o Yeast like at 37 C, Mold like at 25 C  

o Dry and chalky  

33. List fungal diseases listed in lecture notes

• Mycosis- fungal infections  

• Systemic mycoses- deep within body  

• Subcutaneous mycoses- beneath skin  

• Cutaneous mycoses- affect skin, hair, nails  

• Superficial mycoses- localized (example: hair shaft)  

• Opportunistic mycoses- harmless in normal habitat but pathogenic in a compromised host  o HIV/AIDS  

o Immunocompromised patients are at risk  

34. What are the general features of Protozoa? Compare Cyst vs. Trophozoite  • Unicellular eukaryotes  

• Inhabit water and soil  

• Animal-like nutrition  

• Cysts and trophozotic  

o Trophozotic: growing, active, multiplying  

o Cysts- transmission, inactive, resistant to elements  

• Human/ animal pathogens  

o Amebae, malaria, giardia, cryptosporidium (outbreaks with water contamination)  o Most cause diarrhea  

• Helminths

o Parasitic worms  

o Multicellular eukaryotic animals  

o Specialized to live in host  

35. List the differences between bacteria and viruses. Where in nature viruses can be found • Bacteria and viruses are both capable of being intercellular parasites  

o Only chlamydia and rickettsia are intracellular parasites for bacteria  

o Bacteria still do their own metabolism and perform some functions- viruses do not  • Viruses have no cell membrane and no binary fission  

• No ribosomes in viruses  

• Not sensitive to antibiotics

• Viruses are sensitive to interferons, but bacteria are not  

36. What is meant by obligate intracellular pathogens? Which groups of infectious agents are included? Viruses may attack which groups of organisms… Humans, animals………….

• Obligate intracellular pathogens/ parasites  

o Require a host to live, grow and multiply  

o Viruses: multiply inside of a cell; use the cell to get energy

o Viroids  

o Prions  

o Other cell structures can act as intercellular parasites as well  

▪ Some fungi, protozoa and bacteria can replicate inside of a host cell  

▪ small bacteria and some rickettsia

• Viruses can attack…  

o can attack animals, humans, bacteria, archaea and some plants (plants also infected by  viroids)  

37. Name different components of a virus. Name the two that every virus must have • Contain DNA or RNA (can’t be both), single or double stranded  

• Contain a protein coat- capsid  

• No ribosomes  

• No ATP- generating mechanism  

• nucleic acid covered by capsid

• Rely on host for replication, transcription, translation  

• No metabolism  

• May have enzymes, but energy comes from host cell  

• Viron- complete, fully developed viral particle

• Nucleic acid- DNA or RNA can be single or double stranded; linear or circular  

• Few hundreds of genes in genome; prokaryotes have 1,000s

• Capsid- protein coat made of capsomeres (subunits)

o Most of the mass of the virus  

o Arrangement of the capsomeres is what makes the morphology  

• Envelope- lipids, protein, and carbohydrate coating on some viruses  

o Animal viruses can have an envelope made of the host’s plasma membrane that they get  when they are released from the host cell  

o Some viruses are nonenveloped  

• Spikes- projections form outer surface  

o Can be used for identification/ communication  

o Carbohydrate-protein complexes  

• All viruses must have…

o DNA or RNA  

o Capsid  

38. Distinguish between transforming, persistent, latent, lysogenic, and lytic viral infection  • Transforming

o virus has capacity to alter nucleic acid of host, may cause DNA changes in host (cancer) o Activation of host proto-oncogene (human) or insertion of oncogene (animals)  o Oncogenes are in charge of cell division  

o If you mess it up cell divides indefinitely = cancer  

• Persistent  

o virus gets in, attacks host but does not kill host (remains with host)

o occurs gradually over a long period and is generally fatal

o subacute sclerosing panencephalitits (measles virus)  

o Cervical cancer- HPV virus  

o HIV/AIDs- HIV1 and 2 (lentivirus)  

o Liver cancer- Hepatitis B virus  

o Persistent enterovirus- echoviruses  

o Progressive encephalitis- rubella  

• Latent  

o no virus produced  

o no host dies  

o virus becomes part of host

o virus remains inactive for a while  

o can show up later  

o virus remains in asymptomatic host cell for long periods  

o may reactivate due to changes in immunity (cold sores, shingles)  

o Cold sores- herpes simplex 1 and 2  

o Leukemia- HTLV-1 and 2  

o Shingles- varicellovirus  

o No symptoms during latency  

• Lysogenic  

o phage DNA is incorporated in the host DNA  

o phage conversion  

o specialized transduction  

o go inside and become part of bacteria and stay in indefinitely  

o no cell death

o no virus produced  

o host chromosomes stay and multiply with the host  

o induction: virus leaves if the host dies  

o Phage DNA incorporates into host cell DNA  

o Inserted phage DNA is known as a prophage (provirus)  

o When the host cell replicates its chromosomes, it also replicates prophage DNA  o Results in phage conversion- the host cell exhibits new properties  

o Resistant to antibodies  

o Can become pathogens/cause disease  

o Attachment  

o Penetration: virial nucleic acid goes inside  

o Incorporate DNA with the host and keep growing with the host

o Virus becomes part of chromosome with its host  

o Human genetic material may have been introduced to humans through viruses  • Lytic  

o Phage causes lysis and death of the host (infected bacteria and kill host)  o viron is released

o attachment and absorption  

o penetration- injecting DNA into host  

o synthesizing virial components- making nucleoid acid, capsid  

o maturation/ assembly: components put together  

o release/ exit; cell dies  

o Attachment  

o Penetration- phage penetrates host cell and injects its DNA (capsid remains outside)  o Biosynthesis: takes over the host, redirects host to make more virus components

o Maturation: packaging of a new virus  

o Release- viruses are released (started with 1 now there are 100’s)  

39. 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.

• Tissue culture/ cell culture/ monolayer  

o Tissues are treated w/ enzymes to separate cells  

o Virally infected cells are detected via their deterioration, known as the cytopathic effect  (CPE)  

o Continuous cell lines are used  

o Put solution in flat bottom flask -> cells attack to bottom and grow  

o Dissect tissue from animal -> homogenize it -> put in flask and grow a layer on bottom  (monolayer)  

o Monolayer is healthy layer of cells  

o Add virus and you can see monolayer dislodging cells from bottom of flask and killing  them  

o Cell culture: take liquid from flask  

o Cells die after a while from being in flask with virus  

o Hyuridoma  

▪ Mix of normal cells with cancer cells  

▪ Allow normal cells to grow unlimited  

▪ Take it off bottom -> put in two flasks (passing the cells)  

▪ Allows you to make unlimited # of cells  

▪ Provides growing cells for viruses  

▪ Transformed cells (cancer cells)  

▪ Normal cells- came from the animal

▪ Normal cells do not grow forever  

▪ Cancer cells grow forever, but can’t make monolayer  

▪ Combine the two and they can grow forever and make monolayer  

▪ Collect virus sample from monolayer after a few days  

o Preferred type of growth medium  

o Can be grown similar to the way that bacteria are grown  

o Cells suspended in a solution that provides everything they need to grow- form a  monolayer and adhere to the container  

o Cytopathic effect: viruses cause cells of the monolayer to deteriorate  

o The CPE can be counted like plaques are counted using the PFU/ml

• Why do you need a host to grow viruses?

o Viruses don’t have any way of making ATP on their own  

o Need a host for replication, transcription and translation  

o No ribosomes  

o Non metabolism  

o Can’t multiply without a host cell  

• Three ways that viruses are cultivated  

o In animals

▪ Inject directly into small animals  

▪ Take their cells

o In embryonated eggs

• Virus injected into egg  

• Viral growth is signaled by changes or death of the embryo

• Embryo will die -> crack into egg and get sample  

• How they multiply the flu virus  

o in cell cultures  

40. 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? • Life cycle  

o Attachment: virion attaches to host cell  

o penetration

o Entry and uncoating: virion enters cell, and its DNA is uncoated  

o Synthesis/replication: viral DNA is replicated, and some viral proteins are made.  ▪ Replication  

▪ Protein synthesis  

o Assembly  

▪ Maturation: virions mature

▪ Packaging  

o Exit/Release: virions are released.  

• Absorption

o virus attaches to host and injected DNA in host

• Un-coating  

o nucleic acid of virus is released inside

• Assembly/ maturation  

o components put together

• One step growth cycle  

o Eclipse period (no virus detected)  

o Virions released from host cell  

o Acute infection  

o Loosening of capsid and nucleic acid go into host (no complete virus is detected)  o Made of pre-formed components  

• How to grow viruses in the lab  

o Animals  

o Cell cultures  

o Embryonated eggs  

o Must be grown in living cells  

41. List Congenital infections caused by viruses

• Rubella  

• Herpes  

• Cytomegalovirus (CMV)  

• Parvovirus  

• Varicella (chickenpox)  

• Enteroviruses  

42. Name different shapes of viruses. Which one is unique to viruses?

• Polyhedral virus

o Multiple faces  

o 20 triangle faces; 12 corners  

• Helical virus  

o Ebola

o long rods  

o ridged or flexible

o nucleic acid inside of a hollow capsid  

• bacteriophages and complex viruses (head and tail)  

o capsid with additional structures attached  

o can have a capsid head that is polyhedral and a tail that is helical  

o has a tail and a head  

o shape that is unique to viruses  

• enveloped viruses  

o spherical  

o there can be enveloped helical (influenza) and enveloped polyhedral (herpes) as well  43. What is the role of viruses in cancer? Name the cancers caused by viruses.

• roles of viruses  

o alterations in eukaryotic cells creates cancer  

o oncogenes: transform normal cells into cancerous cells  

▪ can be activated by chemicals, radiation and viruses  

o oncogenic viruses- become integrated into the host cell’s DNA and induce tumor  formation  

o tumor cells undergo transformation and acquire unique properties  

o A transformed cell harbors a tumor- specific transplant antigen (TSTA) on the surface or a T  antigen in the nucleus  

• cancers caused by viruses  

o sarcoma- cancer of connective tissue  

o adenocarcinomas- cancers of glandular epithelial tissues  

o Leukemia and lymphoma can be caused by HTLV-1 and HTLV-2  

o Cervical cancer- HPV  

o Liver cancer- hepatitis B virus  

• Viruses that cause cancer  

o Adenoviridae  

o Herpesviridae  

o Poxviridae  

o Papovaviridae- papilomavirius causes cervical cancer  

o Hepadnaviridae  

44. What is plaque assay and what is used for? What is CPE? Give an example

• Plaque assay  

o Plaque: a clearing in a bacterial lawn that results from the lysis by a phage  

o Used to determine virus concentration  

o Determine the number of plaque forming units

o Purifies the colony to understand how much of a virus is in a solution and it can be  properly used in lab work  

o You can see plaque formation when virus is introduced to a bacteria

▪ Each plaque corresponds to a single virus and can be expressed as PFU (plaque  forming units)  

▪ Plaque shows up as a clear zone in the bacteria  

• CPE  

o Effects of a viral infection that are visible- inhibition of the host DNA/RNA and protein  synthesis  

o Cytocidal effects: result in cell death  

o Noncytocial effects: result in cell damage  

o Types of effects  

▪ Macromolecule synthesis stops

▪ Host cell lysosomes release enzymes and the cell destroys itself  

▪ Inclusion bodies: cause acidophilic or basophilic staining which can be used to  

identify the virus  

▪ Syncytium: a large cell forms between multiple infected cells  

▪ Changes to the host cell’s ability to function  

▪ Changes to the surface of the cell  

▪ Chromosomal changes to the host cell  

▪ Cancer causing viruses transform the cell  

▪ Alpha and beta interferons- protect neighboring cells from infection by virus  

45. Define lysogeny and describe its role in passing disease causing genes from one bacteria to another. What other genes may be exchanged using lysogenic viruses.

• Lysogeny  

o the phage remains latent  

o Phage DNA incorporates into host cell DNA  

o Inserted phage DNA is known as a prophage (provirus)  

o When the host cell replicates its chromosomes, it also replicates prophage DNA  

o Results in phage conversion- the host cell exhibits new properties  

o Resistant to antibodies  

o Can become pathogens/cause disease  

o Attachment  

o Penetration: virial nucleic acid goes inside  

o Incorporate DNA with the host and keep growing with the host

o Virus becomes part of chromosome with its host  

• Genes exchanged using lysogenic viruses  

o cancer causing genes are exchanged by lysogenic viruses  

46. Which of the three domains of microbes are prokaryotes and which ones are eukaryotes? • Prokaryotes  

o Bacteria  

o Archaea  

• Eukaryotes  

o Eukaryota  

47. Important terms relevant to exam TWO: Define/Describe/Explain the following terms: • Chromosome, Gene, genome, Extra-Chromosomal DNA (Plasmids, etc.)

o Chromosome: carries hereditary info and contains the genes  

o Gene: DNA segment that encodes for functioning; made up of DNA and nucleotides  o Genome: all of the genetic information in a cell  

o Extra-chromosomal DNA: DNA that exists outside of the nucleus (plasmids in bacteria are  also extrachromosomal DNA)  

o Plasmids: circular molecule of DNA that exists and replicates independently of the  chromosome.  

• Replication, Transcription, Translation

o Replication: one strand of DNA serves as the template to create another strand of DNA;  the process of making more DNA that will be passed on to future generation  

o Transcription: synthesizing RNA from a strand of DNA that is used as a template  o Translation: mRNA being used as a template to create a protein. (amino acids are carried  by tRNA to the mRNA and matched up by codons and anticodons)  

• DNA Polymerase vs. RNA Polymerase

o DNA polymerase: an enzyme that synthesizes DNA; copies a DNA template  

o RNA polymerase: an enzyme that creates RNA from a template of DNA

• Ribosome, Codon/Anticodon / Genetic code

o Ribosome: the site where protein synthesis occurs; made up of RNA and protein  o Codon: three nucleotide bases in a strand of mRNA that code for the insertion a certain  amino acid into the polypeptide chain.  

o Anticodon: three nucleotide bases carried by tRNA that recognize the mRNA codons.  o Genetic code: the mRNA codons and the amino acids they code for.  

• Ligase / Helicase, Reverse transcription, exonuclease/exonuclease activity (adding/removing  nucleotides)

o Ligase: makes covalent bonds to join DNA strands (Okazaki fragments)  

o Helicase: separates the strands of DNA by breaking hydrogen bonds; unwinds double stranded DNA  

o Reverse transcription: sequences of nucleotides are copied from RNA to make DNA; in  PCR mRNA is used as a template to make DNA again  

o Exonuclease/ exonuclease activity: also known as proofreading; when DNA polymerase  recognizes an incorrect base pair, it makes backwards one base pair to make the  correction  

• Mutagens/Carcinogens/Ames Test

o Mutagens: an agent in the environment that brings mutation  

o Carcinogens: something capable of causing cancer (chemical, radiation, virus)  o Ames test: exposes mutant bacteria to mutagenic substances to measure the rate of  reversal of the mutation  

• Cloning, Recombinant DNA, Genomic library, Synthetic DNA

o Cloning: making a populations of cells that arise from one single parent cell; making  identical copies  

o Recombinant DNA: DNA molecule produced by combining DNA from two different  sources  

o Genomic library: collection of the total genomic DNA from a single bacteria.  o Synthetic DNA: artificial genes that are created in a laboratory.  

• Gel electrophoresis, PCR, Restriction enzymes, vectors,  

o Gel electrophoresis: separation of substances by the rate of movement through an  electrical field (used in PCR)  

o PCR: a technique used to amplify DNA using DNA polymerase; makes multiple copies of a  template  

o Restriction enzymes: enzymes that cut DNA at specific sites between two nucleotides  o Vectors: inserted into genes during genetic engineering; a plasmid or virus  • Subunit vaccine, DNA vaccine, Gene therapy, gene silencing

o Subunit vaccine: a vaccine that has antigenetic fragments.  

o DNA vaccine: injection of genetically engineered DNA; allows cells to produce an antigen  directly and produces a protective response  

o Gene therapy: treating a disease by replacing abnormal genes

o Gene silencing: using an RNAi to inhibit gene expression (stops transcription using short  interfering RNA to make double stranded RNA)  

• Shotgun sequencing, metagenomics,  

o Shotgun sequencing: used to determine the nucleotide sequence in an organism’s  genome.  

o Metagenomics: study of genomes of uncultured organisms; sequences of DNA are  collected from environmental samples.  

• Viruses: Capsid / Spike / Envelope / Icosahedra, Plaques assay/ Un-coating

o Capsid: protein coat made of capsomers subunits in a virus  

o Spike: projections from the outer surface of a virus  

o Envelope: lipids, proteins and carbohydrates that coat some viruses  

o Icosahedra: virus with twenty faces made of equilateral triangles  

o Plaques assay: technique used to purify population of viruses and determine the amount  of plaque forming units in the sample  

o Un-coating: separation of the nucleic acid from the protein coat in a virus  • Examples of acellular structures; Virus (Virion) / Viroid / Prion

o Virus: a submicroscopic and parasitic agent that is made of nucleic acid and a protein  coat (capsid)  

o Virion: a fully developed viral particle  

o Viroid: infectious RNA  

o Prion: infectious agent; protein but no nucleic acid

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