Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MIC 101 > MTIII > Flashcards

MTIII Flashcards

You may prefer our related Brainscape-certified flashcards:
Physics 101 flashcards Psychology 101 flashcards Chemistry 101 flashcards Biology 101 flashcards Organic Chemistry 101 flashcards Sociology 101 flashcards
0
Q

What are the gram positive biochemical tests

A

Catalase

YGC Plates

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
1
Q

What is the first biochemical test you do

A

Gram stain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are the gram positive rogues gallery bacteria

A

Micrococcus luteus
Streptococcus lactis
Staphylococcus epidermidis
Bacillus cereus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is/are gram positive rods?

A

Bacillus cereus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is/are gram positive cocci?

A

Micrococcus luteus
Staphylococcus epidermidis
Streptococcus lactis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is catalase positive

A

Micrococcus lactis

Staphylococcus epidermidis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What has white to cream colonies on YGC?

A

Staphylococcus epidermis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What produces yellow colonies on YGC

A

Micrococcus luteus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What produces acid on YGC

A

Staphylococcus epidermidis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What does not produce acid on YGC

A

Micrococcus luteus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is catalase negative

A

Streptococcus lactis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What are the gram negative rogues gallery bacteria

A

Enterobacter aerogenes
Eschiera coli
Pseudomonas putida

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is oxidase positive

A

Pseudomonas putida

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is oxidase negative

A

Enterobacter aerogenes

E. coli

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How do you confirm you have pseudomonas

A

Streak on f agar, check for fluorescence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Which bacteria displays these IMVIC results
IND MR VP CIT
- - + +

A

Enterobacter aerogenes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Which bacteria displays these IMVIC results
IND MR VP CIT
+ + - -

A

E. coli

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What does the catalase test, test?

A

Does this bacterium produce the enzyme catalase to breakdown of hydrogen peroxide?

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is the reaction displayed with a catalase positive test? Why does this happen.

A

Th addition of hydrogen peroxide to a goober of bacteria on a microscope slide produces vigorously fizzing wombat spit
- the fizzing is caused by the release of oxygen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is the reaction displayed with a catalase negative test? Why does this happen.

A

The addition of hydrogen peroxide to a goober of bacteria on a microscope slide produces absolutely more action because there is no catalase enzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What questions are you asking when you streak into YGC

A

Does this bacterium produce pigment on YGC

Doses it produce acid on YGC

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What produces a zone of clearing on YGC

A

It is produces when acidification of the YGC medium results in calcium carbonate going back into the solution (i.e. dissolving)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What is the result of Micrococcus luteus being streaked onto YGC

A

Bright lemon yellow colonies not surrounded by a zone of clearing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What is the result of streaking staphylococcus onto YGC

A

White cream colored colonies are surrounded by a zone of clearing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Why produces small colonies on YGC

A

The enzyme is catalase negative, so it’s having to grow in the presence of large amounts of hydrogen peroxide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What is the result of streaking streptococcus onto YGC

A

Really small colors surrounded by a zone of clearing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What does an oxidase test, test?

A

Does the bacterium have the enzyme cytochrome oxidase?

  • cytochrome c oxidase is an electron transport chain enzyme that transfers electrons from cytochrome c (in the periplasm) to oxygen (inside the cell). Cytochrome c oxidase is used by bacteria to catalyze the oxidation of cytochrome c.
    • so the test assesses the bacterium’s ability to catalyze the oxidation of our chromogenic agent
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What does an oxidase positive test do

A

The addition of oxidase reagent will change the color of a goober of bacteria on a piece of filter paper to dark blue within about 10 seconds
- the chromogenic agent turns blue as it is oxidized

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What does an oxidase negative test show

A

The addition of oxidase reagent will jot chafe the color of a goober of bacteria on a piece of filter paper
- the chromogenic agent remains colorless because it is not oxidized

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What does an F agar test test for

A

Does this bacterium produce fluorescent siderophores

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What is a positce f agar test? Why

A

The bacterium secretes water soluble, fluorescent siderophores to snarf up and iron that might be around
- it is merely a coincidence that pseudomonas f agar siderophores are fluorescent (E. coli produces them as well but they’re not fluorescent)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What doe the indole test for

A

Does this bacterium have the enzyme tryptophanase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What does a positive indole test indicate?

A

E. coli
The bacterium has the enzyme tryptophanase and can breakdown the amino acid tryptophan i not usable goodies
- indole is a side product of this reaction that can be detected by kovac’s reagent
- indole will react with the kovac’s reagent and form the red dye rosindole, which will form a magenta ring at the top of the tube

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What does an indole negative test indicate

A

Enterobacter aerogenes

The bacterium dies not have the enzyme tryptophanase

  • indole will not be produced
    • indole will not be present to react with kovac’s reagent. Rosindole will not be formed. There will be no magenta ring
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

What does the methyl red test test for

A

Is this bacterium a mixed acid fermenter

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What does. Positive methyl red Test indicate

A

E. coli

The bacterium is a mixed acid fermenter of glucose and producers beau coup stable organic acids
- this lowers the ph upon addition, the methyl red ph indicator will remain red

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What does a negative methyl red test indicate

A

Enterobacter aerogenes

The bacterium is not a mixed acid fermenter (strongly implying it is a butanediol fermenter)
- very few stable organic acids will be produces and the ph will be lowered but not by much. Upon addition, the methyl red ph indicator will be a somewhat yellow to orange color (dried mango)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What does the Voges-Proskauer test test for

A

I this bacterium a butanediol fermenter

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What does a positive Voges-Praskeur test indicate

A

Enterobacter aerogenes

The bacterium is a 2,3-butanediol fermenter of glucose and produces large amounts of acetoin and 2,3-butanediol
- the acetoin is detected by the addition of alpha-naphtol and KOH
It will be borked down to diacetyl, which reacts with guanidine in the medium to eventually – up to 45 min – produce a red color upper layer (grenadine over triple sec)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

What does a negative Voges-Praskeur test indicate

A

E. coli

The bacterium is not a butanediol fermenter (strongly implying that it is a mixed acid fermenter)
- neither acetoin nor 2,3 butanediol will be produced
The addition of alpha-naphthol and KOH gives no color change

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

What does the citrate test test for

A

Can this bacterium use citrate as it’s sole carbon and energy source

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

What does a positive citrate test indicate

A

Enterobacter aerogenes

The bacterium can use sodium citrate so it can grow

  • and if it can grow, it will use the ammonia salt as a nitrogen source and in so doing. Will break it down to ammonia and ammonia hydroxide, both of which are alkaline compounds
    • the bromthymol ph indicator will change to an offshore deep ocean Malibu blue
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

What does a negative citrate test indicate

A

The bacterium cannot use sodium citrate so it cannot grow

  • since it. Cannot grow, it will not use ammonia salt as a nitrogen source and no alkaline compounds will be produced.
    • the bromthymol ph indicator will remain a cool and refreshing coastal redwoods green
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

How do you determine the number of viable bacteria per hamburger?

A

You divide the number of colonies on a plate by the dilution factor of that plate

Ex) 150 colonies on your “7” nutrient agar spread plate
Divide 150 by 10^-7 = 1.5 x 10^9

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

What are nutrient agar plates used to determine

A

The number of aerobic bacteria per gram of hamburger

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

What are the MacConkey spread plates used to determine the number of

A

Enteric bacteria per gram of hamburger

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

What is the definition of an outbreak

A

A sudden, unexpected increase in to disease among a particular segment of the population

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

What is the definition of an epidemic

A

A sudden increase in a disease above the real, expected level

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

What is a pandemic

A

A sudden increase in a disease above the normal, expected level in a large percentage of a population over a large area

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

What is the incidence of a disease

A

The number of new cases of that disease over a specific period of time

If 10 people catch a disease per day then the incidence is stated as 10 new cases per day or 70 new cases per week

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

What is the prevalence of a disease

A

The total number of cases of that disease at any particular time

So if java fever has an incidence of 10 cases per day and it’s the 4th day since onset, the prevalence is 40 cases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

What is morbidity

A

The number of people in a susceptible population who contract a disease over a specific period of time

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

How do you calculate a morbidity rate

A

The number of new cases over a specific time period

Over

The number of in individuals in a susceptible population

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

What is mortality

A

The number of deaths from a specific diseased compared to the number of individuals who contracted the disease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

How do you calculate a mortality rate

A

Number of deaths from a Diane over a specific time period

Over

Number of cases of that disease over the same time period

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

Who is Ronald Ross

A

Was a doctor on a ship who got in cooked with sir Patrick Manson and ultimately became important in studying malaria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

What did Manson show Ross

A

How to repeat Laveran’s observations involving blood smears

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

What was the important thing Ross found in anopheles mosquitoes

A

Plasmodia

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

Which life cycles did Ross discover

A

The plasmodium life cycle for avian malaria and for human malaria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

What is the causative agent(s) for malaria

A

There are four species of protozoan plasmodium that infect humans:

  • plasmodium falciparum
  • plasmodium vivax
  • plasmodium Ovale
  • plasmodium malariae
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

Plasmodium falciparum

A

=scythe-like
Falcipian malaria, also called malignant tertian malaria (=bearing evil + every third (day))
The most common and the most virulent (worst) form of malaria
48 hour fever cycle
- fever on day 1 recurs on day 3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

Plasmodium vivax

A

Benign tertian malaria (=well born + every third (day))
48 hour fever cycle
- fever on day 1 recurs on day 3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
62
Q

Plasmodium Ovale

A

Ovale tertian (= every third day)
48 hour fever cycle
- fever on day 1 recurs on day 3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
63
Q

Plasmodium malariae

A

Quart an malaria (=every fourth day)
72 hour fever cycle
- fever on day 1 recurs on day 4

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
64
Q

Animal reservoir of malaria

A

Monkeys
- these are plasmodium species that infect moneys that occasionally induce a very mild form of malaria in humans. Plasmodium falciparum is very nearly genetically identical to a plasmodium species that induces malaria in chimpanzees
The Anopheles mosquito serves as a vector
- sixty of the 380 species of anopheles mosquito can transmit malaria. Plasmodium is always inside a human or inside a mosquito. It’s been said that plasmodium never sees sun

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

Mode of transmission of malaria

A

Human to mosquito to human

  • the anopheles mosquito is the primary host
  • humans are the secondary host
    • in protozoal diseases, the host in which the sexual reproductive cycle takes place is termed the primary host (Or definitive host)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
66
Q

Progression of malaria

The plasmodium life cycle in the mosquito

A

Female anopheles mosquito acquire plasmodium female gametocytes (=marriage cells) and male gametocytes inside separate red blood cells when she “bites” an infected human
- female gametocyte develops into macrogamete (large marriage cell)
- male gametocyte develops into 8 motile micro gametes
- these 8 flagellated micro gametes pinch off from the male gametocyte via exflagellation (remove flagella)
(Any meterozites that are ingested by the mosquito will be digested. Gametocyte activating factor(GAF) is necessary for gametogenesis and can be found only in sufficient concentrations in the mosquito stomach. GAF is Xanthurenic acid)
The macro gamete is fertilized by the micro gamete
- the result is a zygote
The zygote becomes a motile ookinete (=moving egg)
- ookinete penetrates the mosquito midgut and forms a non motile oocyst (=egg bladder)
Each oocyst undergoes meiosis and forms ~10000 motile sporozites
- sporozites (little animal seed) are released into the hemocoel (blood cavity) and migrate to and invade the salivary glands
When a mosquito “bites” she injects saliva as an anticoagulant
- 20-50 sporozites are injected into this “bite” along with the saliva

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
67
Q

Progression of malaria

Life cycle in humans

A

Pre-erythrocyte stage/ exoerythrocyte stage (=outside the rbc)
- sporozites are present in the formulation for about 30 min
- migrate to liver me invade hepatocytes (=liver cells)
- within approximately a week each sporozite has multiplied amd differentiated into 5000 to 10000 non motile merozoites (=numerous little animals)
(Plasmodium vivax can form hypnozites (sleeping little animals) in the liver, which can remain dormant for months or years)
- merozoites enter the bloodstream and infante RBCs
Erythrocytic Stage (blood stage)
- merozoites invade RBCs
- replicate and undergo sequential differentiations:
- ring form
- trophozoite (=growing little animal)
(Trophozoites are voracious consumers of glucose, so in severe cases the patient will become hypoglycemic (= low blood sugar). They also destroy from 25% to 75% of the hemoglobin in RBCs)
- schizont (dividing one)
- merozoites
- the cell ruptures, releasing 8 to 24 merozoites (and rbc debris)
(Plasmodium falciparum invades RBCs of all ages (so more can be targeted). Plasmodium vivax and plasmodium Ovale only invade reticulocytes (immature RBCs with an endoplasmic reticulum) while plasmodium malariae only invades mature RBCs (so these 3 Malawians can’t target as many RBCs)
- after 2 “rounds” some merozoites invading RBCs differentiate into female gametocytes or male gametocytes
- these will develop into macrogametes and micro gametes, respectively, when ingested by a mosquito
(The trigger for gametocyte production is unknown. Plasmodium falciparum gametocytes are banana shaped, all others are spherical)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
68
Q

Symptoms of malaria

A

Periodic chills and fevers
- tertian malaria = fever on day 1 recurs day 3 (48 hrs)
- quartan malaria = fever on day 1 recurs day 4 (72 hours)
(Fever seems to be the result of the synchronized rupture of erthyrocytes which increases the production of endogenous pyrogens)
Hypoglycemia
- lowered blood sugar (glucose) levels due to growing Trophozoites
Anemia (without blood)
- loss of hemoglobin to growing Trophozoites
- loss of RBCs upon release of merozoites
(The combination of hypoglycemia and anemia can result in low blood pressure (hypotension) leading to coma, shock and death)
Splenomegaly (=large spleen)
- the spleen – the body’s blood filter – becomes enlarged when it has to filter out large amounts of rbc debris
Intense headaches, cerebral damage, renal failure
- caused by capillary blockage of by rbc debris
(Plasmodium falciparum can induce (1) cerebral malaria, wherein blockage of brain capillaries can result in coma and death, and (2) black water fever, wherein so much rbc debris is filtered out that the urine turns the color of cola. This can result in kidney failure, leading or death)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

How do you diagnose malaria

A

Characteristic chills and fever
- history of travel into endemic areas
Presence of plasmodia inside RBCs on blood smears
Decreased hemoglobin levels

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

Treatment of malaria

A

Chemotherapy
- quinine and various quinine-derivative compounds
- primaquine, quinine (and quinidine), malaronea & fansidar
- the herbal extract of artemisia annua (sweet wormwood) shows enormous promise
- quinghasou (artemisinin) (costs more $ than above treatment)
- problems with anti-protozoal chemotherapy
(Plasmodium is a eukaryote, not a prokaryote. So (1) it dos ah have a cell wall, (2) it’s only 70S ribosomes are in mito (3) it’s DNA and RNA polymerases are more or less like ours. Any chemical that interferes with any plasmodium process will interfere with the same process in the patient. Treating protozoal diseases - as well as fungal and viruses - almost always involves using chemical agents with a low therapeutic index that must be administered very carefully to prevent causing too much harm to the patient)
In the absence of treatment, malaria is self limiting in adults
- recovery in adults results in immunity for approximately 1 year
(Infected Children frequently die within 72 hours of presenting symptoms. African children under the age of 5 typically contract malaria 6 times per year - malaria kills a kid every 30 seconds)

71
Q

Prevention of malaria

A

Control of anopheles mosquitoes
- in the past this had involved massive use of insectisides
- current thinking is that more limited use of insectisides and elimination of breeding areas is sufficient
(DDT is disastrous to birds and wildlife)
There are several vaccination strategies

72
Q

Anti-Erythrocytic stage vaccine

A

Receptors involved in entry have been discovered
- basigin / CD147 (rbc receptor)
- PfRh5 (plasmodium merozoite)
The anger institute involves am Anti-pfRh5 vaccin
- blocking PfRh5 has prevented all plasmodium strains from invading erythrocytes

73
Q

Anti-sporozite vaccine

A

RTS, S vaccine consists of a recombinant protein
- circumsprozite protein (CS)
(It targets plasmodium to hepatocytes)
- 56% clinical malaria reduction, 47% severe reduction.
(All finders by US military and gates foundation)

74
Q

Impact of malaria

A

It incas approximately 500 million people planet wide

  • it kills approximately 3 million people per year
    • it kills 3000 children per day
75
Q

What is a virus

A

Viruses (=poison) are obligatory intercellular parasites. They are completely dependent on host cell genetic and biochemical mechanisms for the synthesis of new virus particles.

Viruses are biological entities consisting of:

  • genome – composed of either DNA or DNA, never both)
  • capsid (=box) – is a protective covering composed of protein
  • envelope (some viruses) – a host derived lipid membrane
76
Q

DNA Virus genome

A

The genome of a DNA virus can be

  • double stranded DNA (dsDNA)
  • single stranded DNA (ssDNA)
    • single stranded DNA can be:
      • positive sense = the DNA equivalent of mRNA
      • negative sesame = template for mRNA
77
Q

RNA virus genome

A

The genome of an RNA virus can be

  • double stranded RNA (dsRNA)
  • single stranded RNA (ssDNA)
    • single stranded RNA can be
      • positive sense = analogous to mRNA (frequently serves as mRNA)
      • negative mRNA = analogous to a template for mRNA
78
Q

Capsid

A

Capsids are composed of subunits called capsomeres (=box units)
- capsomeres are sometimes (but not always) identical subunits
Capsids are usually capable of self assembly
- self assembly resembles crystallization
- the intact capsid represents a lower energy state than the collection of individual capsomeres
- self assembly is limited to regular geometric solids
- helix
- icosahedron (kinda like a soccer ball)
- so most viruses are either a helix or icosahedron (=20 heads)

79
Q

Nucleocapsid

A

The combination of genome and capsid
(This term is used to describe (1) a completely assembled virus particle in the cytoplasm prior to its release from the host cell as a virus particle, (2) an assemblage of genome and capsid in the cytoplasm prior to its extrusion through a host cell membrane during which it will obtain an envelope and become a virus particle, or (3) an assemblage of genome and capsid released into the cytoplasm infect the host cell)

80
Q

Virus Envelope

A

A host derived lipid bilayer membrane that encased the nucleocapsid
- all negative sense RNA viruses are enveloped
The envelope contains virus coded protines
(Cellular proteins are usually excluded from a virus envelope)
- envelope proteins can be important for viral attachment and entry into the host cell
The envelope can be integral to virus structure
(Think of shrink wrapped water bottle cases, the shrink wrap is like the envelope. Makes it strong etc)
Enveloped viruses tend to be sensitive to drying
(Enveloped viruses generally have to be transmitted directly from one person to another person (mucous to mucous) or have to be transmitted within some body fluid (blood or respiratory droplets) to maintain the integrity of the virus envelope (and hence the virus particle itself))

81
Q

What are non enveloped viruses sometimes called

A

Naked viruses
- they tend to be tough little beasts. Polio virus is a naked virus, it can withstand several hours in a chlorinated swimming pool

82
Q

What is the Baltimore classification system of viruses? What is it based on

A

The Baltimore classification is based on (1) what a virus uses as it’s genome and (2) how a virus goes about generating its mRNA. The Baltimore classification ins has difficult as it appears: Class I and Class II are DNA viruses (~30% of viruses are DNA viruses). Class III, IV, V, and VI are RNA viruses (~70% of animal viruses are RNA viruses).

83
Q

Class I Virus

A

Double stranded DNA
mRNA is synthesized using the negative sense DNA strand as a template
- most class I viruses use host cell RNA polymerase II (poly II)
- some class I viruses bring along their own RNA polymerases
Ex) Hepatitis B virus(serum hepatitis) , Herpes Simplex Virus(genital herpes) , Epsteinn-Barr Virus(mononucleosis), and varicella-zoster virus (chicken pox)

84
Q

Class II Virus

A

Single stranded, positive sense DNA or negative sense DNA
Double stranded DNA intermediate generated by host cell DNA polymerase
mRNA is synthesized using the negative sense DNA strand as a template
- class II viruses use host cell RNA poly II

Ex) parvovirus strain B19 (fifth disease)

85
Q

Class III Virus

A

Double stranded RNA(s)
mRNA is synthesized using the negative sense strand as template
- class III viruses bring along their own RNA polymerase
Ex) rotavirus (=wheel) – infant diarrhea

86
Q

Class IV virus

A

Single stranded positive sense RNA
Genome serves as mRNA
Ex) hepatitis a virus (infectious hepatitis), poliovirus (polio), rhinovirus (common cold), West Nile virus (west Nile fever), hepatitis c fever (post transfusion hepatitis), yellow fever hepatitis (yellow fever), SARS virus (severe acute respiratory syndrome)

87
Q

Class V virus

A

Single strand negative sense RNA(s)
mRNA is synthesized using the negative sense RNA(s) as template
- class as viruses bring their own RNA polymerases
Ex) influenza virus (influenza), measles virus (measles), mumps virus (mumps), rabies virus (rabies)

88
Q

Class VI Virus

A

Positive sense RNA
Expression and replication of the genome requires the generation, integration, and transcription of a double strained DNA intermediate
mRNA is synthesized using the negative sense DNA strand as a template
- chads VI viruses use host cell RNA poly II
Ex) HIV (AIDS)

89
Q

Virus replication

- attachment

A

Cell receptor proteins exploited by viruses
- CD155 is the poliovirus receptor protein (PVR)
- Salic acid is the influenza virus receptor
- CD4 and CXCR4 (fusin) are the HIV co-receptors on CD4+ T cells
- CD4 and CCR5 are the HIV co receptors on macrophage and monocytes
(Receptor proteins are not present for the convenience of the virus. They are present to perform a cellular function. The virus is is moly using them as a convenient, reliable way to enter an appropriate host cell)

90
Q

Virus replication

- uptake

A

Direct entry (poliovirus)
- the genome only is Inserted into the cytoplasm
- analogous to bacteriophage genome entry
(The empty capsid stays on the surface but will eventually be take up by Endocytosis)
Receptor mediated Endocytosis (influenza)
- attachment induces Endocytosis of intact virus
- enveloped virus (influenza).
- lowered pH in endosome results in the fusion of the virus envelope with the endosome membrane
- the nucleocapsid(s) enter the cytoplasm
- non envelope virus
- lowered pH in endosome results in the fusion of the nucleocapsid(s) with the endosome membrane
- the genome enters the cytoplasm
Membrane fusion (HIV)
- attachment induces fusion of the virus envelope and host cell membrane
- the nucleocapsid enters the cytoplasm

91
Q

Synthesis (transcription) of viral mRNA

A

Class I, class II, and class VI
- host cell RNA poly II synthesized virus mRNA
Class III and class V
- virus coded RNA polymerase synthesizes virus mRNA
Class IV
- virus genome serves as mRNA

92
Q

Translation of viral mRNA

A 
Non structural proteins (early proteins)
- non structural proteins are enzymes, polymerases, regulatory proteins and scaffolding proteins that will not be a structural component in the virus capsid or envelope 
(Non structural protein synthesis usually occurs late in viral replication. Viruses need relatively small amounts of non structural proteins)
Structural proteins (late protein s)
- structural proteins are capsid and envelope proteins 
(Structural protein synthesis usually occurs late in viral replication. Viruses need massive amounts of structural proteins)
93
Q

What are non structural proteins

A

Early proteins
- non structural proteins are enzymes, poly me raises, regulatory proteins and scaffolding proteins that will not be a structural component in the virus capsid or envelope

94
Q

What are structural proteins

A

Late proteins

- structural protein is are capsid and envelope proteins

95
Q

Synthesis of viral genome

A

Class I
- host cell DNA polymerase synthesizes new virus genome
Class II
- host cell DNA polymerase synthesizes new virus genome
Class III, IV and V
- virus coded RNA polymerase synthesizes new virus genome
Class VI
1. virus coded reverse transcriptase synthesizes fan intermediate
–and then –
2. Host cell RNA polymerase II synthesizes virus genome using this DNA intermediate as a template

96
Q

Assembly of virus

A

New virus particles are assembled within the host cell
- icosahedreal capsids are usually assembled as empty shells
- capsomeres are assembled into “faces”
- the genome is packed into the completed icosahedron
(The massive amounts of structural proteins are frequently in and of themselves sufficient to change to change conditions. Within the host cell such that these structural proteins self assemble (“crystallize”)8!59 nucleocapsid)

97
Q

Research of virus

A

Non enveloped virus (poliovirus)
- the host cells lysed
- virus particles are released with cell cell contents
Enveloped virus
- the host cell is not lysed
- budding (influenza virus, HIV)
- nucleocapsid components bind to cytoplasmic domains of envelope proteins
- the host cell membrane is molded around the nucleocapsid
- the virus acquires its envelope as it extrudes through the cell membrane
(A very big problem with budding is that the virus coded envelope proteins in the host cell membrane act like a flashing neon sign advertising “virus infected cell” to natural killer cells and cytotoxic T cells. So some viruses have learned to very quilt sneak out the back door…)
- exocytosis (hepatitis B virus)
- the virus “buds” through an internal cell membrane, such as the Golgi or endoplasmic reticulum
- the virus is transported via vesicles to the cell membrane and released from the cell
(Th virus coded envelope proteins are never visible to the surfaces of the cell so it’s difficult for the immune system to “see” that a cell is incited with a virus)

98
Q

What is NFIP

A

National foundation for infantile paralysis

  • the largest privately funded program to abolish an infectious disease
      • big deal because for had polio
99
Q

What is the Salk vaccine

A

It is a killed/inactivated virus
- injected
- ~70-90% effective
- the inactivated virus “looks” different to the immune system
- so your immune system will have a bit if trouble when it encounters the real thing
(Killed virus vaccines are the equivalent to using road kill for a survey course in California wildlife)0
A Salk vaccine injection introduces inactivated poliovirus into your circulation
- results in the production of IgM and (primarily) IgG
- IgG is the major antibody class found in the circulation
- invading poliovirus will encounter antibody only when the infection has progressed as far as entering the circulation

100
Q

What is the Sabin vaccine

A

Live virus/attenuated virus
- oral
- virtually 100% effective
- the attenuated virus looks the same as the normal polio virus to the immune system
- so your immune system will respond exactly like it would respond to the real virus
- the Sabin vaccine actually sets up an infection within the intestine
- result sin the production of sIgA (secretory IgA)
- sIgA is the major antibody class secreted by mucosal surfaces
- invading poliovirus will be prevented from entering the body by sIgA in the intestine
- this process is termed immune exclusion
(However, due to virulence, 1 in 8 million patients receiving the Sabin vaccine will develop paralytic polio. Eighty such cases have occurs in the USA since 1980. The Sabin vaccine is the major source of paralytic polio in the USA)

101
Q

Causative agent of polio

A

Polio virus

  • picornavirus (small RNA virus)
  • simple,naked icosahedron
    • polio virus does not have an envelope
  • contains single stranded, positive sense 7.5 Kb RNA genome
102
Q

Animal reservoir of polio

A

None

103
Q

Mode of transmission of polio virus

A

Fecal-oral
- usually occur sin contaminated food or water
(A surprising mode of transmission was through swimming pools. Polio Venus is an if reddish stable virus that’s able to survive for several hours In a chlorinated swimming pools. In the 1930s 40s and 50s public swimming pools were close due to Polio outbreaks)

104
Q

Progression and symptoms of polio (quick version)

A

Poliovirus first infects the upper throat and the intestines
- the immune system will produce lots of IgA
- there won’t be any symptoms
Poliovirus will sometimes get into the bloodstream
- the Immune system will produce lots of IgG
- the symptoms will be cold like
Poliovirus somewhat rarely can cross the meninges
- th immune system cannot access the meninges
- the classic symptom is a stiff neck
Poliovirus much more rarely infects motor neurons
- the immune system cannot access motor neurons
- the symptom will be paralysis
Poliovirus very, very rarely infects cranial neurons
- the immune system cannot access the brain
- the symptom will be respiratory arrest

105
Q

Symptoms of asymptomatic infection(polio)

A

Sub-clinical

~95% of infections

106
Q

Symptoms of abortive polio

A 
Viremia
Cold like symptoms lasting 1-4 days
- headache
- fever
- sore throat
~5% of infections
107
Q

Symptoms of non Paralytic polio (aseptic meningitis)

A

Polio virus infects the meninges
Symptoms of abortive polio, plus
- pain and spasms in the neck, back, arms, and abdomen
- resistance to neck movements is the most highly characteristic symptom
- pain and spasms last ~2 weeks
~1% of infections

108
Q

Symptoms of paralytic polio (acute flaccid paralysis)

A

Polio virus infects motor neurons
Symptoms of non paralytic polio, plus
- asymmetrical muscle weakness and loss of reflexes
(Boys are much more susceptible to paralysis than girls)
~0.5% of infections

109
Q

Symptoms of bulbar paralytic polio

A

Polio virus infects cranial neurons
Symposium of paralytic polio plus
- weakness of Muscles supplied by cranial nerve
- respiratory arrest
~5-10% of all paralytic polio cases (very small number)

110
Q

Diagnosis of polio

A

Requires the isolation and antigenic detection of poliovirus in throat swabs, stool samples and/or cerebrospinal fluid
(The parts of the planet where polio is encountered, such as Afghanistan, India, Indonesia, Nigeria and Pakistan, rarely have access to sophisticated diagnostic facilities)

111
Q

Treatment of polio

A

Supportive
- this is med speak for “there is no treatment”
Long term (and expensive) rehabilitation is frequently required
(The cost of preventing polio is essentially extremely minute to the cost of dealing with the costs)
- braces
- physical therapy
- drinker respirator (“iron lung”)

112
Q

Prevention of polio

A

Salk inactivated polio vaccine
Sabin oral polio vaccine (OPV)
- the use of OPV has not been recommended in the us since 2000

113
Q

Impact of polio

A

Polio is no longer A serious threat in the us
Polio still reminds a threat in developing countries
- polio is still a problem in Afghanistan, Pakistan, Nigeria, and to a much lesser extent, Indonesia
- the WHO is attempting to eradicate polio

114
Q

Polio virus

A

Naked icosahedral nucleocapsid approximately 30 nm in diameter

  • the capsid is composed of 4 different proteins (“structural proteins”)
    • VP1, VP2, VP3 and VP4 (vp= virus protein)
    • there are 60 molecules of each protein in the capsid
  • single stranded positive sense 7.5 Kb RNA genome
    • VPg (22-24 amino acids) attached to the Poly-U at 5’ end (VPg = virus protein associated with the genome)
    • internal ribosome entry site (IRES) within 5’ non coding region
      • poliovirus uses its IRES – not its VPg – to bind to ribosomes
      • the IRES contains extensive secondary and tertiary structure
  • poly 3’ end
115
Q

Poliovirus entry

A

Polio virus vp1 binds to poliovirus receptor (PVR (CD155)) on epithelial cells, fibroblast and endothelial cells
- N terminus of five vp1 molecules forms a transmembrane channel
- the RNA genome enters the cell
(The genome alone seems to enter via a transmembrane channel created by these five vp1 molecules. The empty capsid remains outside the cell)

116
Q

Poliovirus mRNA

A

Poliovirus positive sense RNA genome first serves as mRNA
Poliovirus RNA binds to ribosomes via its IRES
- allows the translation of poliovirus-coded proteases and poliovirus coded RNA polymerase (“non structural proteins”)
A poliovirus coded protease (2A) cleaves host cell initiation factors
- prevent host cell mRNA from binding to ribosomes
- effectively shuts-down translation of host cell mRNA in ~30 minute
- “frees-up” host cell ribosomes for unrestricted translation of poliovirus mRNA
- particularly poliovirus RNA polymerase and new VPg

117
Q

Poliovirus protein synthesis

A

Occurs in host cell cytoplasmic ribosomes
- poliovirus acts like a single 7.5Kb mRNA
- individual poliovirus proteins are products of nascent (=to be born) and post translational cleavage of larger precursors polypeptides
- the polio virus 247kD (~2300 AA) precursor polypeptide is translated and cleaved within approximately 15 min to produce different proteins
(This 247 kd precursors polypeptide never exists intact in the host cell. Nascent cleavages by 2A and 3C “chop” it up while it’s being translated (“born”) and post translational cleavages in turn “chop” these up after translation)
- nascent cleavages produce 3 poly proteins
- P1 (97 kD)
- P2 (65 kD)
- P3 (85 kD)
- post translational cleavages of P1 produces structural proteins
- P1 is cleaved into VP1, VP3 and VP0
- VP0 is later cleaved into VP2 and VP4
- post translational cleavages of P2 and P3 produce non structural proteins
- P2 is cleaved. Into proteases
- P3 is cleaved into proteases, VPg, and poliovirus RNA polymerases

118
Q

Poliovirus genome replication

A

Occurs in modified host cell ER vesicles

(1) positive sense RNA gene serves as template
- VPg poly U binds to poly A. 3’ end of genome to serve as primer
- poliovirus RNA polymerase (3D) makes a negative sense RNA replicative intermediate (RI) then…
(2) negative sense replicative intermediate (RI) serves as template
- VPg poly u binds to poly A at 3’ end of RI to serve as primer
- poliovirus RNA polymerase (3D) makes positive sense strands
- each RI can simultaneously serve as template for multiple VPg poly U and poliovirus RNA polymerase (3D) molecules
- this results in the rapid production of large numbers of positive sens RNA molecules that can act as:
- mRNA …or
- template for more RI synthesis …or
- genome for new poliovirus

119
Q

Poliovirus assembly

A

Occurs in the host cell cytoplasm
Velocity gradient sedimentation (“ultracentrifugation”) of homogenates of cells infected with polio virus at different times allowed virologists to detect the ordered appearance of ever larger particles
- 5S (first to be detected)
- 14S
- 80S
- 150S
- 160S (last to be detected)
Polio virus assembly entails an ordered assembly of subunit components
- P1 is cleaved into vp1 and vp3-vp0
- vp0-vp3-vp1 form capsid protomers (5S particle)
- 5 protomers to interact–
- (vp0-vp3-vp1)5 form a pentamer (14S particle)
- twelve pentamers combine –
(Vp0-vp3-vp1)60 form a procapsid (80S particle)
- The RNA genome is added–
- (Vp0-vp3-vp1)60 form a provirion (150S particle)
- maturation cleavage cleaves vp0 into vp2 and vp4–
- (Vp2-vp4-vp3-vp1)60 form a virus particle (160S particle)
(The protease involved in this maturation cleavage is unknown. It could be the capsid proteins themselves or the RNA molecule)
Within 6 hours a cell can produce approximately 100,000 virus particles

120
Q

Poliovirus release

A

Virus particles are released when the host cell lyses

- this is typical of naked icosahedral lyses

121
Q

Tests for environmental and recreational water quality

A

These involve enumerating coliforms (particularly E. coli and enterobacter)

  • the operational definition for water quality testing: coli form bacteria are non spore forming gram negative rods that ferment lactose to form acid and gas in 24 to 48 hours at 35 C
  • coli from bacteria are used as indicator bacteria
    • the presence of coliforms indicate sewage contamination and implies that pathogens are present
122
Q

Most probable number (MPN)

A

MPN is a statistical elimination of the number of coliform bacteria present per 100 ml of water. MPN would be used to test water for environmental or recreational purposes - but not for potability(drinking)
- each of 3 large test tubes containing 10 ml of double strength lactose birth and a Durham tube is inoculated with 10 ml of a water sample
- each of 3 standard test tubes of lactose broth is inoculated with 1.0 ml of this water sample
- each of 3 standard test tubes of lactose broth is inoculated with 0.1 ml of this water sample
- these 9 samples are then Incubated at 35C for 24 hours +/- 2 hours
- turbidity (mixed up) (“cloudiness”) and has production (a bubble of hydrogen in the Durham tube) in any tube is positive for the presence of coliforms
(Each set of tubes generates a number between 0 and 3 so an mom test will generate three numbers and these can be used to determine MPN from statistical charts)

123
Q

Test for water drinking water quality

A

Multiple tube fermentation method
=the multiple tube fermentation method of water quality testing would be used to test drinking water. You might notice that the first stage of this test (presumptive test) is simple an MPN – but all tubes must be negative.
- presumptive test
- tubes containing lactose broth are inoculated with 10ml, 1ml and 0.1 ml of sample water
- incubated at 35C for 24 +/- 2 hours
- gas production is presumptive of the presence of coliforms
Confirmed test
- the most dilute gas producing tubes are streaked onto eosin-methylene blue (EMB) plates
- incubated at 35C for 24 +/- 2 hours
- dark centered colonies (frequently surrounded by a fly butt metallic green sheen) confirms the presence of coliforms (indicates E. coli)
Completed test
- tubes containing lactose broth are inoculated with dark centered colonies
- incubated at 35C for 24 +/- 2 hours
- gas production and acid production is positce
- agar slants are inoculated with dark centered colonies
- incubated at 35C for 24 +/- 2 hours
- presence of gram negative, non spore forming rods is positive
- the presence of gram negative, non spore forming rods that produce gas and ferment lactic acid constitutes a positive completed test
All samples invoiced in the multiple tube fermentation should test negative. Any positive results indicate a serious breakdown in water treatment, usually involving chlorination problems or water main breaks (an increasing problem with this country’s aging infrastructure)

124
Q

Membrane filtration method

A

100 ml of sample water is drawn through a 0.45 mi from sterile membrane filter
The membrane filter is then incubated on a pad saturate with growth medium
Any colonies that grow can be further tested
- the presence of more than 1 colony generally indicates the water is not safe to drink

125
Q

Colilert defined substrate test (ONPG and MUG test)

A

Tests for both coliforms and E. coli
Reagent pack containing ONPG and mug as the only nutrients (“substrates”) is added to 100ml of sample water
- ONPG is a colorimetric (measure with color) compound that will produce a yellow product when it’s broken down by the enzyme beta galactosidase in coliforms
- MUG is a fluorogenic (produce fluorescence) compound that will produce a blue fluorescent product when broken down by the enzyme beta-delta-glucuronidase in E. coli
After 24 hour incubation at 35C–
- any coliforms that grow will produce Beta galactosidase
- beta galactosidase produced by these coliforms will hydrolyses ONPG to a yellow product (E. coli is a coliform and will produce this)
- any E. coli that grows will produce the enzyme beta-glucuronidase
- beta delta glucuronidase produced by these E. coli will hydrolyses MUG to a blue fluorescent product under uv illumination
(E cooling is the only coli form that produces the enzyme Beta delta… Blah)

126
Q

Water treatment

- sedimentation

A

Settling tanks
- allows leaves, sand, and gravel to sink
Flocculation (little tuft (flock) of wool)
- addition of aluminum sulfate (alum) or iron sulfate causes precipitation of suspended materials

127
Q

Water treatment

- filtration

A

Slow sand filter
- fine particles of sand several feet deep
- develop a dirty cover of microbes that acts as a bio filter
- slow sand filters effectively remove giardia
- can filter ~3 million gallons of water per day
Rapid sand filter
- contains coarse gravel as well as sand
- does not develop a dirty cover of microbes and so must be cleaned more often
- these do not remove giardia
- can filter ~200 million gallons of water per day
Charcoal
- removes organic chemicals,as well as microbes
Filtration removes approximately 99% of microbes

128
Q

Water treatment

Chlorination

A

Addition of chlorine (usually as a gas) to 0.2 to 1.0ppm

  • kills most bacteria within 30 min
  • the more organics in the water, the more chlorine must be used
129
Q

Causative agent of influenza

A

Influenza virus
- orthomyxovirus (Baltimore class V virus)
- enveloped virus containing segmented, negative sense
- usually spherical morphology (about 100nm diameter)
- influenza is extremely sensitive to acid heat and drying
(Transmission of influenza basically requires that the virus go from mucous to mucous, or from mucous to droplet to mucous. The fact that transmission of influenza occurs so readily, is disgusting)

130
Q

Influenza strains

A 
Type A (most common, many species, including humans)
Type B (humans only)
Type C (humans (mostly children) and other primates)
131
Q

WHO Influenza nomenclature

A
  1. Type A,B or C
  2. Animal host (if non human)
  3. Geographical origin
  4. Laboratory (strain) number
  5. Isolation year
  6. Antigens description (type a only)
132
Q

Animal reservoir of influenza

A
  • wild birds seem to be the natural host for type a
  • domestic pigs, horses, ducks,chickens are common reservoirs
    (A given influenza virus tends to only infect a particular type of an imal. There are swine equine, avian and human influenza viruses and each tends to infect pigs, horses, birds or humans)
    (Pigs in particular can serve as host for influenza viruses from different species (such as avian and human) and thus serve as important “mixing vessels” for antigenic shift)
133
Q

Mode of transmission for influenza

A

Inhalation of respiratory droplets containing virus particles
Hand contact with contaminated materials,followed by involuntary hand to eye contact

134
Q

Progression of influenza

A
  • Influenza infects primarily respiratory epithelial cells
  • – results in the loss of ciliated epithelial
  • Localized symptoms are produced when immune system cells eliminate those infected respiratory epithelial cells
  • Constitutional symptoms are produced by frantic cytokine signaling by infected cells and immune system cells
135
Q

Symptoms of influenza

A

Fever(sudden onset), malaise(severe), headache, vomiting, diarrhea

  • malaise= general feeling of discomfort
  • diarrhea is common in children, rare in adults
136
Q

Diagnosis of influenza

A

Difficult to confrim
- if an influenza epidemic is in progress, it’s probably influenza
- if the constitutional symptoms (“malaise”) overwhelm the localized symptoms, it’s probably influenza
(Like y feel like crap with the flu, not really as much with a cold)
Influenza can be diagnosed via Serology

137
Q

Treatment of influenza

A

For the average healthy person:
- rest (complete recovery takes about 2 weeks)
For high risk groups (people with heart/respiratory problems)
- amantadines (“M2 inhibitors”) help alleviate the symptoms
- amantadine, rimantadine
- neuriminidase inhibitors (NAIs)
- Oseltamivir (Tamiflu), Zanamivir (Relenza)

138
Q

Prevention of influenza

A

Influenza vaccines (70-90% effective)
- split virus vaccines (trivalent inactivated vaccine/TIV)
(Consist of hemagglutinin (HA) and neuraminidase(NA). Fluzone is a concentrated (4X) vaccine that confers greater protection for people 65 years and older)
- intradermal vaccine (Fluzone intradermal)
(Fluzone intradermal is injected into the skin using a much smaller needle. It activate dendritic cells)
- attenuated virus vaccine (FluMist)
(FluMist is administered by being sprayed up the nose. It consists of attenuated, temperature-sensitive virus strains that can only replicate in the nose, where the temperature is below 37C)

139
Q

Antigenic Drift

- influenza

A

Type A and B only
Minor changes in HA and an genes causing minor influenza epidemics that occur approximately every 2 years
- cause by spontaneous point mutations
— RNA polymerases cannot proofread so there is no way for these mutations to be corrected
The immune system is a bit slow to catch onto these changes, so you’ll catch a very mild flu

140
Q

Antigenic shift

- influenza

A

Type A only
Major changes in HA and NA causing influenza pandemics that occur approximately every 10-15 years
- caused by the genetic re assortment between virus particles from different species hosts
— pigs, horses, ducks, and chickens are common “mixing vessels”
The immune system is blind-side by these changes, so you’ll probably catch the flu

141
Q

Impact of influenza

A

Since influenza epidemics involve very large numbers of individuals, the number of deaths can be surprising (~55 million in 1918)

142
Q

Type A influenza virus

A

100nm diameter, 13.2 Kb,p negative sense splint RNA virus
Each particle consists of:
- “shrink wrapped” lipid bilayer envelope containing:
— hemagglutinin (HA)
- hemagglutinin is a rod shaped trimer
- each virus particle contains approximately 500 trimers
(There are 16 different types of HA. All 500 of these HAs will be the same type of HA)
— Neuraminidase (NA)
- neuraminidase is a mushroom shaped tetramer
- each virus particle contains approximately 100 NA trimers
(There are 9 different types of NA. All of these NAs will be the same type of NA)
— membrane protein (M2) (M=”membrane”)
- M2 tetramers form transmembrane proton channels that promote release of nucleocapsids into the cytoplasm
- Matix protein (M1) (M=”matrix”)
- eight helical nucleocapside
— each with its own single strand of negative sense RNA protected by nucleoprotein (NP)
- each contains its own set of RNA polymerase components (PA,PB1, PB2)
- 5’ and 3’ ends of RNA bind to PB1

143
Q

Influenza virus entry

A
  • NA digests mucous on the surface of respiratory epithelial cells,exposing the cell membrane
  • HA binds to Sialic acid residues on surface glycoproteins
    • HA binding induces Endocytosis into vesicles
      • these vesicles are delivered to endosomes
  • acidification of endosomes causes a conformational change in HA
    • this exposes the fusion-promoting region on HA
      • virus envelope and endosome membrane fuse
        (At the same time an ion channel formed by m2 tetramers promotes acidification inside the virus particle. This weakens the interactions of M1’s and NPs, which allow the nucleocapsids to be released into the cytoplasm)
  • the 8 helical nucleocapsids go to the nucleus
    • NP and Polymerase components contain nuclear localization signals
144
Q

Influenza virus mRNA synthesis

A

Influenza transcriptase uses negative sense influenza genome RNA segments as template
- primed RNA synthesis
- PA, PB1, and PB2 function as trimeric transcriptase complex
- PB2 binds to the cap at the 5’ end of a host cell mRNA (“cap snatching”)
- PB1 cleaves this host cell mRNA 10-13 bases from the Cao (at an A) and uses this capped RNA fragment as a primer
- the 3’ A of the host cell RNA fragment is bound to the 3’ U of the influenza genome RNA
- PB1 acts as an RNA polymerase (“primed RNA synthesis”)
(The function of PA during transcription is unnknown)
- Poly A tails are added by repeated slippage (“chattering”) of PB1 over a short poly-U tract ~20 bases from the 5’ end of the genome
- so PB1 polymerizes a slightly truncated copy of the genome
- resultant influenza mRNA molecule are transported to the cytoplasm

145
Q

Influenza virus protein synthesis

A

Most influenza virus proteins are made on “free” ribosomes in the host cell cytoplasm
- PB1, PB2, PA, NP, M1, NS1, NS2
- NS1 is the most abundant virus protein in infected cells
Influenza virus embrace proteins are made on ribosomes associated with the host cell rough endoplasmic reticulum (RER) for transport via the Golgi to the cell membrane
- HA, NA, and M2

146
Q

Influenza genome synthesis

A

Newly synthesized NP, PB1, PB2, PA, M1 and NS2 migrate to the nucleus
- increased levels of NP trigger genome synthesis
Influenza replicase uses negative sense influenza genome RNA segments as template
- unprimed RNA synthesis

147
Q

Unprimed RNA synthesis

A

PA, PB1 and PB2 function as trimeric replicase complex
- PB1 – in the presence of increased levels of NP – acts as RNA polymerase (“unprimed RNA synthesis”)
(The functions of PA and PB2 during replication are unknown)
- PB1 “reads through” the short Poly U tract
- so PB1 polymerizes a full length copy of the genome
- read through requires the presence of NP
- resultant positive sense cRNA molecule serves as template
- PB1 – in the presence of NP – again acts as an RNA polymerase
- resultant negative sense RNA molecules are genome
Each genomic RNA is assembled into a nucleocapsid (NP)
- nucleocapsids associate with M1 and NS2
- Ns2 serves as nuclear export signal

148
Q

Influenza virus assembly

A

HA, NA and M2 form patches in the host cell membrane
- HA, NA and M2 patches exclude host cell membrane proteins
- NA digest host cell Sialic acid residues in the membrane
Selective nucleocapsid incorporation model
Random nucleocapsid incorporation model

149
Q

Selective nucleocapsid incorporation model

A

Eight nucleocapsids associate PRIOR to budding
- each virus particle will contain the complete genome
- viral proteins recognize and interact sequentially with specific signal sequences on 5’ and 3’ ends of genome RNA
- these signal sequences may control –
- individual nucleocapsid recruitment
- nucleocapsid to nucleocapsid associations
- seven nucleocapsids are arranged in a cylinder
- the eighth is inside the cylinder
(The evidence is largely from electron microscopy. While the images are enticing, electron microscopy is notorious for generating artifacts)

150
Q

Random nucleocapsid incorporation model

A

Approximately 11 nucleocapsids are randomly incorporated DURING budding
- only 10% of virus particles will contain the complete genome
(Randomly packaging about 11 nucleocapsids into each virus particle would work well enough and save the virus the trouble of having to deal with a complex packaging scheme. This would also explain why it takes more than one influenza virus to initiate an infection)

151
Q

Influenza virus budding

A

M1 attached to nucleocapsids interacts with cytoplasmic tails of HA in the host cell membrane
- as nucleocapsids bind to more HAs, the virus buds from the host cell, swiping some host cell membrane for its envelope
The influenza virus particle buds from the host cell
- NA reverses HA binding to Sialic acid and digests mucous so the virus particle can get out from underneath the mucous
(NA inhibitors interfere with the release of influenza virus particles)

152
Q

During kidney transplants, what was found in the blood to be indicative of immunosuppression

A

Kaposi’s sarcoma

153
Q

What is the causative agent of AIDS

A

Human immunodeficiency virus

- 100nm in diameter, 9.3 Kb positive sense RNA virus

154
Q

Animal reservoir of HIV

A

None

- HIV only infects humans so it could be eradicated

155
Q

Mode of transmission of HIV

A

Transmission via contaminated blood

  • IV drug use
  • sexual transmission
  • mother to child
  • blood transfusion
  • occupational risk (health care workers)
156
Q

HIV induced immunosuppression

A
  1. CD4+ T cell depletion
    - the reduction of these cells seems to be the major factor inducing immunosuppression
  2. Lymph node disruptions
    - lymphoid architecture will eventually become disrupted
    (The architecture is important for providing a suitable environment for various lymphocyte interactions, including the activation of both T cells and B cells. Disruption of this critical structure weakens the immune system. The first name of HIV was lymphadenopathy virus)
  3. Cytokine imbalances
    - expression of TH1 inflammatory T cells is down regulated
    — depresses cell mediated responses
    - expression of TH2 helper T cells is up regulated
    — elevates antibody mediated responses
157
Q

Diagnosis of HIV

A

HIV antibody test
(Tests for the presence of a Anti-SU and Anti-TM antibodies in blood, urine or saliva – usually appear 3 months after infection)
Plasma HIV RNA test (viral load test)
(Tests for the presence of HIV RNA and/or DNA in blood -9 days after infection)
Western blot
(Tests for the presence of HIV proteins in blood (TM and CA). Western blots are used to confirm positive HIV antibody test or viral load test results)

158
Q

Treatment of HIV

A

Antiretroviral treatment (ART) or highly active antiretroviral treatment (HAART) employs a combination of 5 classes of antiretroviral agents:

  • reverse transcriptase inhibitors (RTIs)
  • protease inhibitors (PIs)
  • fusion inhibitors
  • CCR5 Antagonists
  • integrase inhibitors
159
Q

Prevention of HIV

A
  • Current data indicate that early and strict adherence to HAART can help prevent the transmission of HIV
  • avoidance of risky sexual practices
  • avoidance of IV drug use
160
Q

Impact of HIV

A

Approximately 34 million people are infected with HIV worldwide
- approximately 1.8 million people die each year due to HIV
Approximately 1.2 Million are infected in the US
- 1 in 5 are unaware that they are infected

161
Q

Each HIV particle consists of:

A

“Shrink wrapped” lipid bilayer envelope containing trimeric complexes of: - surface protein/ SU/ gp 120 (120 kD glycoproteins)
- transmembrane protein/ TM/ gp 41
Icosahedral matrix
- Matrix/ MA/ p17 (17 kD protein)
Tapered cylindrical core
- capsid protein / CA/ p24
(This is unique to HIV. Other retrovirus have an isocahedral core)
- core contrains:
— diameric RNA genome
- two identical single stranded 9.3 Kb positive sense RNA molecules
- complexed with nucleocapsid protein/ NC / p7
- two cellular tRNAs ( tRNA (lys))
- these are base paired to the genome and serve as primers for reverse transcriptase
- reverse transcriptase / RT / p66
- concerts ssRNA genome to dsDNA
- protease / PR / p14
- cleaves poly proteins into functional proteins
- integrase / IN / p32
- integrates dsDNA into host cell genome

162
Q

What and how many major genes does the HIV genome have. What do they code for

A

The HIV genome contains 3 major genes which code for 3 poly proteins (Gag, Gag-Pol, and Env) that will be cleaved into individual proteins

163
Q

Gag polyprotein

A

Group Antigen Genes (gag) for capsid proteins

  • p17 Matrix protein (MA)
  • p24 capsid protein (CA)
  • p7 nucleocapsid protein (NC)
164
Q

Pol polyprotein

A

POLymerase (pol) for enzymes

  • p14 protease (PR)
  • p66 reverse transcriptase (RT)
  • p32 integrase (IN)
165
Q

Env polyprotein

A

ENVelope (Env) proteins for envelope proteins

  • gp120 surface protein (SU)
  • gp41 transmembrane protein (TM)
166
Q

What is the sequence of the genome/mRNA of HIV

KNOW THIS!!!

A

Gag pol Env

5’ MA-CA-NC - PR-RT-IN - SU-TM 3’

(“Mangy cars munch prechilled rats in summer time)

167
Q

HIV entry

A

SU burning to CD4 induces a conformation change in SU, allowing it to bind to a co receptor protein
- Fusin (CXCR4) on CD4+ T cells
- CCR5 on macrophage and monocytes
SU binding to co-receptor induces a conformation change in TM
- TM pierces host cell membrane and induces fusion of host cell membrane with HIV envelope
Matrix and core disassemble in the cytoplasm

168
Q

HIV genome converted to preintegration complex

A

HIV RT converts the single stranded positive sense RNA HIV genome into the double strained DNA HIV double stranded DNA. It accomplishes this via three separate enzymatic activities
1. First, RT acts as an RNA dependent DNA polymerase (reverse transcriptase activity) and…
- RT synthesizes negative sense strand DNA using the positive sense RNA genome as template
- tRNA(lys) bound to the genome serves as primer
2. RT simultaneously acts as an RNA nuclease (RNase activity) and…
- RT degrades almost all of the RNA genome
- a small RNA oligomer of the genome remains intact
3. Finally, RT acts as a DNA dependent DNA polymerase and…
- RT synthesizes positive sesame DNA strand using the newly synthesized negative sense DNA as a template
- the small RNA oligomer remaining from the genome serves as primer
(Remember, RT is a DNA polymerase. It can use RNA or DNA as a template but what it polymerizes is always DNA)
Double stranded DNA, MA, and IN are associated in a preintegration complex
- preintegration complex is transported into the nucleus via nuclear pores

169
Q

HIV DNA integrates into the host genome

A

Integration requires IN
- integration is a required step in HIV replication
Integrated HIV DNA is termed a provirus
- provirus is a stable genetic element in the host genome
(The provirus is replicated whenever the chromosome is replicated)
(As with insertion sequences and transposons, integration generates a direct repeat of host DNA target sequences on either side of the provirus)

170
Q

HIV mRNA

A

Host RNA pol II obligingly transcribes provirus DNA producing more than 25 different mRNAs that fall into three categories

  • 2 Kb spliced for regulatory proteins
  • 4 Kb spliced for Env proteins
  • 9 Kb un spliced for gag and gag-pol polyproteinsn
171
Q

HIV protein synthesis

A

HIV proteins – like polio virus proteins – are initially produced as Env polyprotein,gag polyprotein and gag-pol polyprotein
- the 4 Kb mRNA for Env proteins targets rough endoplasmic reticulum
- Env polyprotein – like influenza envelope proteins – is synthesized on (i.e extruded into) RER and transported to the cell membrane
- glycosylated and cleaved during transit by host cell enzymes in to SU and TM
- form patches of SU/TM trimers on the cell membrane
- the 9 Kb mRNA for gag and gag-pol poly proteins targets “free” ribosomes in the cytoplasm
- gag and gag-pol are made on cytoplasmic ribosomes
- approximately 20 times more gag polyprotein is synthesized than is gag-pol polyprotein
(The gag and pol polyprotein sequence on the 9 Kb unspliced ,RNA are (1) separated by a single stop codon, and (2) read in different reading frames. The frame shift occurs when the ribosome reaches a heptamer sequence (U UUU UUA) and a stem-loop which occasionally shifts the readin frame back by one nucleotide such that the ribosome will no longer recognize the stop codon. But this doesn’t happen very often so there’s about 20 times as many gag polyproteins than there are gag-pol polyproteins)
- gag and gag-pol polyproteins will not be cleaved into capsid proteins and enzymes by until PR becomes activated during HIV maturation following budding

172
Q

HIV gene synthesis

A

Host RNA pol II obliging transcribes provirus DNA producing –
- full length transcripts that serve as HIV genome

173
Q

HIV assembly into immature virus particles

A

MA portion of Gag (and gag-pol) polyprotein binds to cytoplasmic domains of TM trimers
(MA almost certainly binds to the cytoplasmic domain of TM trimers)
Gag polyproteins oligomerize via CA-CA interactions
- gag-pol polyproteins likewise bind via Ca-CA interactions with Gag polyproteins
NC portion of gag polyprotein binds to 5’ end of full length dimers (genomic) RNA
Cellular tRNA(lys) binds to RT and NC portions of gag-pol
Immature virus particle buds from the cell
- budding immature virus particles swipes hits cell membrane for its envelope
At the time of budding these immature virus particles have nested layers (outermost layer)
- host cell membrane (now the virus envelope with SU/TM trimers)
- MA portion of gag polyproteins
- CA portion of gag polyproteins
- NC portion of gag polyproteins,closely associated with…
- RNA dimer
- PR-RT-IN of a small number of gag-pol polyproteins
(Innermost layer)

174
Q

HIV maturation into mature (infectious) virus particles

A

Auto catalytic cleavage releases PR from gag-pol polyprotein

  • PR becomes active as virus is budding
    • sequential cleavages separate individual MA, CA, NC proteins (as well as RT and IN)
  • CA undergoes conformational change when cleaved
    • CA form tapered cylindrical core around RNA dimers
      • RNA dimers are bound to NC
  • MA remains (loosely) associated with the virus envelope
  • SU/ TM trimers remain in virus envelope
175
Q

Animal reservoir of hepatitis

A

None

- could in theory be eradicated

176
Q

Mode of transmission of hepatitis

A

Via contaminated blood

MIC 101 (3 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions