microbiology exam 3 material

are viruses living things?

no
- cannot reproduce on their own
- requires host

viroids

RNA molecules that infect plants
- have no protein capsid
- are replicated by host RNA polymerase

example of viroid

potato spindle tuber disease

t/f: viroids do the same thing as viruses in terms of replication

true

one difference: viroids do not contain proteins

example of prion

mad cow disease, creutzfeldt-jakob disease

prions

proteins that infect animals
- no nucleic acid component

what is the ideal virus structure?

maximizing capacity while minimizing the required number of genes

primary distinctions of viruses

genome composition (RNA or DNA)

route used to express messenger RNA (mRNA)

what traits are used to organize viruses? (2)

conformation (ss/ds) and genome (DNA/RNA)

aka Baltimore classification of viral genomes

group I virus

double-stranded DNA

group II virus

single-stranded DNA

Group III virus

dourble-stranded RNA

group IV virus

(+) single stranded RNA

group V virus

(-) single stranded RNA

antisense

group VI virus

RNA retroviruses

group VII virus

DNA pararetroviruses

RNA bacteriophage

- found in bacteria
- many are in the (+) configuration

once in the cell, viruses must make (2)

1. genetic material (genome)
2. proteins needed for capsid coats

RNA replicase

RNA-dependent RNA polymerase

reads RNA template, makes RNA compliment to it

ss DNA bacteriophages

- some contain ss DNA in (+) configuration
- first step is to make complimentary (-) strand

bacteriophage T7

- ds DNA
- infects E. coli (common)
- genome always enters host cell in same orientation

what is one problem with linear ds-DNA replication?
how do eukaryotes and bacteria handle this differently?

DNA gets shorter everytime
- bacteria doesn't have telomeres
- concatemer: numerous genomes join together and prevent DNA shortening

T4 bacteriophage replication

- early genes are transcribed by host RNA polymerase
- rolling-circle replication: phage T4 genome is synthesized within the host cell
- late genes are induced, produce capside and tail proteins
---> late genes also encode lysozyme

t/f: the viruses that infect archaea resemble those that infect enteric bacteria

true

t/f: only ds DNA viruses can infect archaea

false

only ds DNA viruses have been identified so far, but it is not exclusive

plant RNA virus type

(+)-strand RNA virus

what does tobacco mosaic virus cause?

necrosis of plants

enlarges cymplasm

(+) strand RNA viruses of animals

replication requires conversion of the genome into a (-) strand intermediate

(+) strand RNA virus example

Covid-19, poliovirus, Hep C(liver)

RNA replicase can go back up to make (-) strand --> can make another (+) strand

(-) strand RNA viruses of animals

(-) strand RNA viruses are complementary to the mRNA; copied into mRNA by an enzyme present in the virion

RNA polymerase travels WITH the virus (not made in host)

(-) strand RNA virus examples

Rhabdovirus (rabies)

t/f: both (+) and (-) strand RNA viruses effect only Eukarya

false

only (-) strand RNA viruses are known to infect Eukarya

how does influenza replicate?

receptor-mediated endocytosis (RME)
- Endosome releases (-) strand
- segment goes to nucleus with RNA polymerase
- (+) strand is made, used to make more (-) strand and mRNAs
- genomes either return to nucleus or go for exocytosis to other cells

how does herpesvirus cause diseases in humans/animals?

- remains dormant for periods of time
- infection follows attachment of virions to specific cell receptors
- proteins inhibit macromolecular synthesis
--> turn linear DNA circular

retrovirus

RNA virus that utilizes enveloped virions and reverse transcriptase to make a DNA copy of a genome

hepadnavirus

viral replication occurs through an RNA intermediate (uses reverse transcriptase)

tiny, only partially dsDNA, circular

what happens to extra DNA on the ends following reverse transcriptase?

serves as an artifact of the process

dsDNA gets inserted into host genome via integrase

can viral genomes get orphaned throughout evolution?

yes
- genes get passed on without being a virus (remain in DNA)

t/f: humans share more retroviral insertion sites with chimps than gorillas

true

epidemiology

the study of occurrence, distribution, and determinants of health and disease in a population

how do infectious and non-infectious disease rates compare in developed v. underdeveloped countries?

diseases (both types) cause significantly more deaths in underdeveloped countries

chronic infections

host and pathogen survive

well-adapted pathogen lives in balance with its host

acute infections

pathogen can be selective force

new natural pathogens sometimes emerge for which the host has no resistance

pandemic

widespread, usually worldwide

endemic

constantly present in a population, usually at low incidences

incidence

number of new cases of a particular disease in a given period of time

prevalence

total number of new and existing cases in a population in a given period of time

outbreak

occurs when a number of cases of a disease are reported in a short period of time

subclinical infections

diseased individuals with no/mild symptoms (carriers)

steps of disease progression

1. infection: organism invades host
2. incubation period: onset of symptoms
3. acute period: worst
4. decline period: symptoms subside
5. convalescent period: regain strength

reservoirs

sites in which infectious agents remain viable and from which infection of individuals can occur

zoonosis

any disease that primarily infects animals

occasionally transmitted to humans

how do epidemiologists follow transmission of a disease?

correlating geographic, climatic, social, and demographic data

how are pathogens classifed?

mechanism of transmission

steps in common: escape from host, travel, entry into host

2 modes of pathogen transmission

direct, indirect

direct host-to-host transmission

an infected individual transmits a disease directly to a host via an intermediate

indirect host-to-host transmission

transmission is facilitated by a living/non-living agent

vectors

living agents that spread disease

fomites

non-living agents that spread disease

why might the transmission of a virus peak in the summer?

a vector is required

west nile virus (mosquito)

why might the transmission of a virus peak in the winter?

a fomite is utilized

more people are indoors

common-source epidemic

result from common exposure to a single source of infection over a period of time

ex. poisoned water hole

host-to-host epidemic

the disease shows a slow, progressive rise and a gradual decline

ex. influenza, chicken pox

why is coevolution between a host and its parasite common?

parasites become less lethal overtime in order to survive

herd immunity

the resistance of a group to an attack by a disease to which a large proportion of the members of the group are immune

t/f: everyone in a population must be vaccinated to obtain herd immunity

false

the majority do (decreases ease of transmission)

how does AIDS spread?

bodily fluids

what is AIDS?

RNA retrovirus that attacks the immune system

opportunistic infections

infections that occur in individuals who do not have healthy immune systems

complicates epidemiology --> makes it difficult to determine cause of death

why is there no vaccine for RNA?

has an error rate of 10 during replication
--> quick evolution time
--> targets reverse transcriptase / RNA primer

healthcare-associated infections (HAIs)

infection acquired during admission to a healthcare facility

nosocomial infection

reasons for HAIs

- patients have low resistance
- overcrowding
- certain treatments increase risks
- use of antibiotics has selected / antibiotic-resistant organisms

controls for transmission of pathogen (4)

- immunization
- quarantine
- surveillance
- pathogen eradication

emergence factors

- human demographics/behavior
- techonology/industry
- economic development and land use
- international travel and commerce
- microbial adaptation and change
- breakdown of public health measures
- abnormal natural occurrences (climate change)

biological warfare and bioweapons

the use of biological agents to kill a military or civilian population
- easy to produce/deliver
- safe for use by offense
- able to kill in a consistent manner

why was B. anthracis used as a bioweapon?

endospores can be used as an aerosol

it is a very resilient microbe

3 forms of B. anthracis

- cutaneous (skin)
- gastrointestinal
- respiratory

how is B. anthracis treated?

ciprofloxacin

t/f: there is no prevention for anthrax infections

false; there are vaccines, however, they are only given to those at risk

unique features of archaea

- reverse gyrase of hyperthermophiles (maintains positive supercoils)

similarities of archaea and bacteria (3)

- circular genome
- gene size and density
- presence of operons

similarities of archaea and eukaryotes

- presence of intrones
- RNA polymerase
- histone homologs

t/f: archaeal phylogeny is poorly resolved

true

archaea were discovered fairly recently and live in extreme environments

t/f: archaeal metabolism is most similar to eukaryotes

false

most similar to bacteria EXCLUDING methanogenesis (unique to archaea)

euryarchaeota

- diverse archaea
- extremophiles

haloarchaea

- extremely halophilic
- REQUIRES high salt conc.
-found in salt lakes, salt evap. ponds, and saline habitats

how do archaea use light-absorbing pumps and sensors?

- use light energy to set up proton motive force to move substances
- halorhodopsin brings in chloride

how do halophiles maintain a water balance?

managing internal solutes

somtimes difficult in environments

methanogens

-archaea that produce CH4
- found in marshes
- energy yield is not great (little competition)

substrates for methanogens (3)

- CO2-type
- methyl
- acetotrophic

thermoplasmatales

- thermophilic and/or extremely acidophilic
- 3 genera (2 lack cell walls)

thermococcales and methanopyrus

- phylogenetically related genera of hyperthermophilic euryarchaeota
- branch near the root of the tree
- membrane contains degrees of unsaturation

archaeoglobales

- hyperthermophilic
- oxidize various compounds

nanoarchaeum and aciduliprofundum

- obligate symbiont of crenarchaeote
- small, contains smallest genomes
- depends on host for most cellular needs

crenarchaeota

- temperature extremes
- most cultured representatives are hyperthermophiles
- ocean is full of them

sulfobales

- order containing sulfolobus and acidianus
- from terrestrial volcanoes (convergent evolution)

sulfolobus

- grows in sulfur-rich acidic hot springs
- aerobic chemolithotrophs
- oxidize reduced sulfur/iron

acidianus

- grow in acidic sulfur hot springs
- use elemental sulfur both aerobically and anaerobically

thermoproteales

- inhabit neutral or slightly acidic hot springs or hydrothermal vents

nonthermophilic crenarchaeota

- abundant in deep ocean waters (cooler water)
- appear to be capable of nitrification (genes for it)