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Study Guide Midterm 2

by: Anastassia Erudaitius

Study Guide Midterm 2 BIOL 123 001

Anastassia Erudaitius

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About this Document

As was apparent from the previous midterm, Dr. Rao focuses his exams on topics covered heavily in lecture, therefore the study guide is an organized, detailed format of the most important concepts ...
Dr. Rao
Study Guide
UCR, Bio, 123, comparative, Virology, Rao
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This 12 page Study Guide was uploaded by Anastassia Erudaitius on Monday May 2, 2016. The Study Guide belongs to BIOL 123 001 at University of California Riverside taught by Dr. Rao in Spring 2016. Since its upload, it has received 64 views. For similar materials see Virology in Biology at University of California Riverside.


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Date Created: 05/02/16
[Bio 123 - Comparative Virology] [Dr. Rao] [Midterm 2 Study Guide] Highlight =Very Important Highlight = Important Highlight = May need to know term [Lecture – Influenza Virus – Part 2]  Virus steals CAP from host cell RNA to prime its own viral RNA o This is because the viral RNA is (-) sense so it does NOT have a CAP o The viral RNA needs a CAP in order to be translated  The virus is (-) sense RNA but in the replication process it makes (+) sense RNAs o Two (+) sense RNAs made  +vmRNA  3’ polyA tail  5’cap  DIFFERENT from viral genome RNA  This one has a 5’cap because it is the RNA that gets translated to make proteins  +antigenome RNA  Exact copy of the genome  NO 3’ polyA tail  NO 5’cap  PB2 polymerases snatch the Caps from host RNAs  Viruses tag the host mRNA for cleavage of the Cap o Once the host RNA Cap is cleaved they cannot translate o Host can no longer make proteins once Cap is cleaved o The viral RNAs however are NOT tagged  Three proteins made from one mRNA virus o M1 – one long protein made from a single mRNA o M2 – result of splicing of M1 protein o M3 – result of splicing of M1 protein  Virus encodes NS1 protein o NS1 snatches Cap from host mRNAs to prevent cells from exporting to the cytoplasm (preventing them from being translated)  Virus packages 8 different (-)sense RNAs o All 8 needed to make 8 different necessary proteins  Viruses prevent re-entering the cell by cleaving sialic acid receptors on surface of host cell  Recombination occurs between multiple strains that infect the host o Each influenza strain has 8 RNAs o With recombination between two strains there can be 64 possible strains generated  Influenza is best transmitted in lower humidity and colder temperatures  2009 H1N1 Swine Flu o Mostly younger generations infected o Older generations exposed to previous influenza strains and therefore developed more antibodies to protect them from related strains [Lecture – HIV Part 1 – History]  Discovered in 1980s first in homosexuals o Found that infected patients suffering from immune deficiency  Secondary infections result once immune system is attacked  Previously named GRIDS (thought to be exclusive to homosexuals)  1982 – Two groups working independently o United States – Gallo named the virus HTLV - III o France – Montagnier named the virus LAV  AIDS is the disease caused by HIV o Note that AIDS is not the virus! o Disease name is different from virus  Patients infected with HIV died 1 month to 6 years after initial manifestation of AIDS o Based on appearance of first symptom and time until death  SIV – Simian Immunodeficiency Virus o Very similar virus existing in monkeys in Africa o Does not affect the monkeys, no symptoms o Another similar strain found in chimpanzees o Hypothesized that SIV was passed from monkeys to humans  Hunters cut themselves while preparing infected chimpanzee meat  Food would be contaminated, could touch contaminated food while cutting food/cut self  HIV is NOT transmitted by eating  HIV is transmitted via blood  Influenza infects more people than HIV because of its mode of transmission (aerosol), but it is not as serious because influenza does not attack the immune system like HIV  Education has reduced the spread of the virus [Lecture – HIV Part 2 – Life Cycle]  Retroviruses are enveloped, single stranded +RNA o Use reverse transcriptase o Many different capsid shapes depending on the virus  Retro – backwards  Onco – tumor  Spuma – foam  Lenti – slow  HIV is cone-shaped  HIV has 2 copies of the same RNA o It is unknown why there are 2 copies o No other virus has two copies of the same RNA  Encodes transcriptase and integrase  Transmission – blood or sexual contact  HIV-1 o Most prevalent throughout world  HIV-2 o Present mostly in Africa o Less easily transmitted than HIV-1 o Develops very slowly o Rarely transmitted from mother to child  Attacks immune system (CD4) o Secondary infections and other illnesses result o Cause of death is not infection from HIV but the illness associated with the comprised immune system  Treatment is expensive, not readily available  HIV is very unstable o Virus dies very quickly once it leaves the host  This is unlike influenza which can be transmitted via fomites o Can be easily broken down by soap and antiseptics  This is very different from polio which is extremely stable and cannot be broken down by acids  You need very many virus particles in order to initiate the infection  Viral replication – Attachment o Surface receptor cells on virus – glycoprotein o Co-receptors: CD4, CCr5, CXCr4  In contrast – poliovirus only has one receptor (sialic acid)  T-cell uses CxCr4 receptor  Macrophages use CCr5 receptor o First binds to receptors on host cell o Then penetrates via endocytosis and enters the cell  Macrophage – any foreign material is engulfed and killed  Viral replication – Step 2: Replication o Many RNA mutations occur because RNA Pol doesn’t have proofreading capability  In each round of replication 4 mutations are introduced  New viruses constantly being produced once HIV infects a host o One large polyprotein made o Integrase integrates the viral DNA into host DNA o Although RNAs are (+) sense they do not act as mRNA (do not get translated)  RNA is used as a template to make +ssDNA  In order to use RNA as a template tRNA from the host cell is used as a primer, then the RNA is transcribed into ssDNA  RNase H cleaves RNA at certain places – each piece functions as a primer o dsDNA is made and integrase takes the DNA to the nucleus and ligates into the host chromosome o dsDNA is transcribed by DNA Pol into viral RNA o viral RNA then exits the nucleus, enters the cytoplasm and is translated  HIV is very different from viruses like TMV o TMV – only one virus particle is needed to infect host  The virus also replicates so quickly and efficiently [Lecture – HIV Part 3]  35.3 million currently living with AIDS  Infections mainly coming from Africa due to lack of education and sanitation  Major mode of HIV transmission is via sexual contact  Chart in lecture slides show most common form of HIV transmission going to least common mode of transmission, left to right  Symptoms often appear flu-like o Appear within 1-4 weeks after exposure  HIV is NOT transmitted via insects  PEP drugs help prevent infects AFTER exposure  Three phases of clinical symptoms o First 30 days after exposure – HIV RNA is detectable  NOT antibodies  takes almost one month to detect antibodies, because the virus is not active soon after infection o Asymptomatic stage – virus is extremely active, but person does not show symptoms  Can last for 10 years o AIDS stage – patient dies within 2-3 years if not receiving treatment  The lymphocyte counts decrease to 50cells/microliter  At this point opportunistic infections result  Wasting syndrome – person will start drastically losing weight  Even before AIDS fully develops in the person an opportunistic infection can still be fatal  AIDS dementia – impairment of cognitive reasoning, behavioral changes  Can measure how many given virus particles per microliter of blood  AZT – prevents the conversion of RNA to DNA  so DNA cannot get integrated into your chromosomes  HAART – Highly Active Retroviral Therapy – mixture of three drugs, one is to block HIV reverse transcriptase, another inhibits protease activity (as a result the virus cannot assemble into mature virus), the other prevents the integration of the viral genome into the host chromosome (blocks integrase)  Fusion inhibitor prevents virus from fusing with the cell membrane so the virus cannot enter the host cell  Studies of HIV vaccine have been conducted o Mixture of two antibodies o Have made vaccines that can protect monkeys from SIV o Only inactivated virus used to develop HIV vaccine [Lecture – Prions and Viroids] [Prions]  Prions attack nerve and brain tissue  Prions are found ONLY in mammals o No known prion diseases in plants  Prions are only transmitted via food  Result in slowly progressing disease  Human Prion disease – CJD  Animal Prion disease o Found mostly in goats o CWD – found in deer, elk, and moose o BSE – found in cattle  causes mad cow disease  Resistant to nucleases  Hosts infected do not produce antibodies – no immune response to prions  No nucleic acid genome  The infectious agent is the PROTEIN o Proteins do not replicate (need nucleic acids to replicate) o The protein binds to the host protein in the brain  prion protein changes host protein conformation  normal host protein is modified to become a highly pathogenic prion protein  protein is released to infect/bind to other proteins  PRION -- “proteinaceous infectious particle”  Transmission within species o Vertical or horizontal transmission o Uncommon – foodborne  Species barrier concept o They do transmit from animals to humans, and humans to animals  BSE o Mainly transmitted through food o These cases mostly found in Europe o Mostly found in “beef-eating countries”  U.S. and Europe o In U.S.  ban on feeding cattle meat and bone meal  TSE pathogenesis o Oral route o Migrates to the nervous system o The prion attacks your NERVOUS SYSTEM o It is a very slow generating disease o Because it affects the brain, they look at the brain tissue and compare it to normal brain tissue o Prp – normal protein o PrP-Sc – srapie protein  Scrapie o First found in sheep o When the sheep get infected by scrapie they get very itchy  Mad Cow disease o The cows are slaughtered when they are 2 years old  Slow progressing disease so it is very difficult to detect in cows at 2 years of age o Individuals eat the infected meat  the protein enters your body o Cow farms feed cows and sheep meat from other cows or sheep  The dead cows or dead sheep may carry the protein and the cows/sheep eating that meat get infected because the virus spreads orally  In 1997 they banned these practices o The protein is very stable so cooking the meat may not prevent infection  Kuru o Confined only to specific tribe o Tribe members had very unusual symptoms  instability (cannot walk), biting their own hands o Ambulant stage first  sedentary stage  terminal stage  Very long process (30-40 years) o One of the rituals of this tribe: when the person dies they eat the meat of the dead  they only eat women and children  The disease is found manly in women and children (within families), and not in men  As a result of infection holes form in the brain  No treatment is available [Viroids]  Free nucleic acids, ssRNA o Susceptible to nucleases  Easily degradable by ribonucleases o Do not encode any proteins (unlike viruses)  Replicate using host proteins ONLY  Replicates in the nuclease (because it needs host Pol in order to replicate)  No capsid o No capsid to protect viroid from nucleases o They are instead protected by their secondary structure  Secondary structure results in a double stranded form like dsRNA  dsRNAs are resistant to nucleases  Genome only 400 nucleic acids long  Only in plants o Not found in any mammals (like prions)  Potato spindle tuber o First viroid discovered o Theodore Diener received credit for discovering viroids, but his competitor discovered it first  Hepatitis delta virus – satellite virus associated with Hepatitis virus [Lecture – Viral Evolution]  Viruses evolve very rapidly  TMV completes its life cycle within a few hours after infection  High rates of mutation are extremely common for RNA viruses o Because RNA Pol does not have proofreading ability  Plasma – means blood  HIV has a 90% daily turnover rate  this is one of the reasons HIV cannot be controlled o It generates so many copies, and so many mutants so quickly  Hepatitus B has a turnover rate of 50% daily  In table 18-1, the asterisks represent re-emerging viruses o Viruses that have been gone, but are now coming back o Polio virus is a re-emerging virus  Emerging viruses – viruses that have newly enterd the human population for the first time  Re-emerging viruses – viruses that have reappeared in the human population after being absent  Antigenic drift – only nucleic substitutions  Antigenic shift – entire segment is swapped with another  Influenza virus underwent a lot of evolution because it has been around so long and has so many hosts o One swine can carry avian influenza, another swine can carry human influenza, the two viruses come together and generate a completely new virus  this is how H1N1 developed o Antigenic shift can occur  Some viruses are highly restricted to just one species  Bats have a certain virus that used to be restricted to bats o Because of deforestation the bats came into the villages, and came in contact with humans, the virus was introduced to the human population  Many viruses present in sub-tropical areas because most viruses replicate well in warm climates  Influenza mode of transmission – airborne  Polio virus – transmission through food  SARS and H5N1 was spread via human travel  Mosquitos and other bugs can get on the plane and introduce the virus it carries to a new population o Mosquitos are very important vectors for many viruses  Cholera gets spread very easily through water – hurricanes were a concern for the spread of cholera (as well as accumulation of mosquitos due to stagnant water) [Lecture –Ebola]  (-)ssRNA virus o Same as influenza o Very deadly  Lipid membrane  Encodes its own Pol o It is (-) sense so it must encode its own polymerase in order to be transcribed  Incubation period: 2-21 days  Transmitted via fruit bats  Highly contagious, but not airborne  Can use ELISA to detect viral protein  Can use PCR to detect viral nucleic acid  No treatment  Name of Ebola came from the river (the origin)  Death rate is 50-90%  worse than smallpox  smallpox is very deadly but compared to Ebola, Ebola is worse  Ebola – internally, all the organs are disintegrated  whoever is infected with the virus will not survive  Humans and non-humans (chimps, monkeys) get infected by Ebola  Out of all 5 species the most deadly Is the ZAIRE virus o About 68% death rate o Reston death rate is 0  No specific symptoms to Ebola o Maculopapular rash – rash on the skin o Hemorrhage – person bleeds to death through any possible openings o Death rate 50-90%  Since this virus is highly contagious: o Isolate the patient o Restricted entry o PPE – cover everything  If you think a person MAY be infected with Ebola the sample must be labeled with “Suspect Ebola”  Lab Sample: o Collect 4 ml blood o Wrap in tissue paper o Triple layer seal it o Put in leak-proof boxes  Anytime you have a sample you must separate it from the other equipment  Yellow bags are the ones they normally use under lab conditions  they are autoclavable, can seal them and use them under autoclave  Need BSL-4 lab to work with Ebola


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