Midterm 2-1 Flashcards

Question

Energy and carbon and electron source of cyanobacteria

Answer 1

Energy Source: light (phototroph) Carbon source: CO2 (autotroph) electron source: H2O - produced oxygen

Answer 2

Energy Source: organics (organotrophs) (ie cyanobacteria) Carbon source: organics (heterotrophs) electron source: organics redox acceptor = O2

Answer 3

Energy Source: Fe2+ from a lower guild (lithotroph) Carbon source: CO2 (autotroph) electron source: Fe2+ redox acceptor = oxygen

Answer 4

Energy Source: H2S (lithotroph) Carbon source: organics OR CO2 electron source: H2S Redox acceptor = F3+ or O2

Answer 5

Energy Source: light (phototrophs) Carbon source: Co2 (autotrophs) electron source: H2S (produces sulfate)

Answer 6

Energy Source: light (phototroph) Carbon source: CO2 (autotroph) electron source: H2S (produces sulfate)

Answer 7

Energy Source: Organics (Heterotroph) Carbon source: Organics (Organotroph) electron source: Organics Redox acceptor: sulfate --> source of H2S for the above guilds

Answer 8

autotrophic

Answer 9

microbes (bacteria and algae)

Answer 10

Fix carbon dioxide into organic matter consumption of CO2 carbon cycle has not been balanced between inputs and outputs to the atmosphere in recent years. CO2 production>autotrophy

Answer 11

Breaking down organic material - oxidizing it to CO2 - heterotrophy

Answer 12

They use the calvin cycle. The calvin cycle is universal to plants, not autotrophy BActeria and Archaea have 6 other autotrophic pathways that can also be used

Answer 13

When electrons in photoautotrophs come from water

Answer 14

When electrons in photoautotrophs comes from another reduced compound like H2S or NH3 instead of water. It is easier to pull electrons off of H2S than water

Answer 15

COnverts methane to CO2 (in an oxic environment)

Answer 16

Take electrons from organic material and transfer them to CO2 to produce methane one of the last resort respirations when all other electron acceptors are used up - in addition to acetogenesis

Answer 17

NH4+ --> NO3- NH4+ --> NO2- ammonium to nitrate or nitrite

Answer 18

nitrate to nitrogen gas NO3- --> Nitrogen gas nitrate - nitrogen gas detrimental in agriculture - loss of fertilizer to the atmopshere beneficial in sewage treatment - removal of nitrate which cause eutrophic waterways

Answer 19

important for nutrition nitrogen gas to ammonia ONLY CARRIED OUT BY BACTERIA

Answer 20

organic nitrogen to ammonium degradation of organic matter done by heterotrophs

Answer 21

nitrite + ammonium --> nitrogen gas NO2- + NH3 or NH4+ --> N2 anaerobic ammonia oxidation

Answer 22

N2O in the upper atmosphere is a green house has and contributes to ozone depletion NO in the lower atmosphere causes air pollution (production of O3)

Answer 23

assimilatory reduction of inorganic compounds is done to use the reduced compounds as nutrients in biosynthesis USING SOMETHING AS A NUTRIENT

Answer 24

dissimilitory reduction of inorganic compounds is their use in anaerobic respiration using inorganic compounds as a terminal electron acceptor

Answer 25

Anaerobic repiration involved the reduction of oxidised inorganic compounds as terminal electron acceptors lithotrophy involves the oxidation of reduced organic compounds for energy ***

Answer 26

Lithotrophy involves the oxidation of reduced inorganic compounds for energy

Answer 27

Uses O2 or another oxidant to oxidize H2S or S, this produces energy and electrons that are needed to reduce the carbon in carbon dioxide

Answer 28

ie phototrophic purple sulfur anaoxygenic photosynthesis --> energy comes from light but electrons come from H2S (In oxygenic phototrophs they comes from H2O)

Answer 29

Nitrogenase In symbiotic bacteria, pyruvate derrived from things donated from the plant donates electrons toward and the pmf develops ATP towards powering the nitrogenase enzyme It converts N2 gas to NH3

Answer 30

Sugars --> organic acids --> succinate, malate, fumarate uses electrons from here for the nitrogenase enzyme or use the sugars in the CAC - make ATP with oxidative phosphorylation

Answer 31

is the bacteria - the symbiotic unit inside the plant cell - the membrane is called the bacteroid membrane once it is engulfed

Answer 32

a protein that scavenges oxygen out of the system The nitrogenase enzyme within the bacteroid is harmed by oxygen. So the cell has just enough oxygen to aerobically respire but not too much - and this is regulated by Lb

Answer 33

ie the plasmid DNA is integrated into the chromosome - bc the plasmid genes are still expression - the F pilus is created Plasmid DNA is then nicked at the oriT - and rolling circle replication begins moving chromosomal DNA into the recipient cell - it is unlikely, however, that the entire chromosome will cross over - only a small portion of will - tra genes are unlikely to be passed over and thus the recipient of Hfr conjugation is F- the donor will remain Hfr

Answer 34

How we refer to a plasmid that has taken some chromosomal DNA with it when it excised itself from the chromosome Sometimes when the F plasmid is removing itself, it takes chromosomal genes with it. So the cell is going from Hfr to F+ but bc the chromosome has lots of insertion sequences, the plasmid DNA may use a different IS to excise and as a result, take some chromosomal DNA with it F' is full functional can move via conjugation still.

Answer 35

Plasmids often contain transposons in addition to insertion sequences transposons are jumping genes that can jump, independently into the chromosome Transposons are mobile genetic elements that move between different host DNA molecules, including chromosomes, plasmids, and viruses

Answer 36

a virion. This is the infectious form of the virus.

Answer 37

not infectious in nature. Replicating genome In a lab it can be used to unnaturally infect something

Answer 38

Helical, icosahedral (20 sides, efficient), complex (non-symmetrical)

Answer 39

All viruses have a capsid, a protein coat that surrounds genomic material. It is composed of capsomeres

Answer 40

By counting the number of plaques, one can calculate the titer of the virus sample. The titer is typically expressed as the number of “plaque-forming units” per milliliter a way to enumerate the number of viral particles in liquid, underestimates the number of viral particles though

Answer 41

viruses of bacteria and archaea a complex, filamentous virion attaches to host cell receptors with tail fibres injects genome into host cytosol, leaving capsid on cell surface. icosahedral head group

Answer 42

eclipse + maturation = latent period eclipse - when the virus is taking over the host maturation - when assembly happens latent period = time from infection to the release of progeny virus

Answer 43

A virulent phage

Answer 44

Class: l linear dsDNA Infects Ecoli host by attaching to lipid polysaccharides

Answer 45

Anti-sigma factor proteins - inhibit host sigma factors so that the host stops transcribing its own genes phage-specific replisome as well. includes enzymes that degrade the host DNA to ncts and then they transcribe a diff sigma factor that will help transcribe the middle and late genes.

Answer 46

positive! plus sense configuration plus sense mRNA/strand

Answer 47

l, ll, Vll

Answer 48

lll, lV, V, Vl

Answer 49

dsDNA t4, lamda, variola major (small pox) mRNA is synthesized from the negative sense strand of the DNA. RNA Polymerase in either host or viral encoded DNA replication following semiconservative or rolling circle replication

Answer 50

ssDNA (+) genomes (99% of these viruses are positive sense DNA but there are couple negative sense) ΦX174 and M13 (both are bacteriophage), parvovirus (-) sense DNA must be made first and then the (+) mRNA can be transcribed from this DNA replication follows semiconservative or rolling circle replication

Answer 51

Φ6 (phage) and rotavirus (stomach flu) dsRNA genome RNA strand separate and the virus will make RNA replicase. RNA-dependent DNA polymerase (needs to be packaged with this specialty molecule because there is no eukaryotic enzyme that can replicate RNA from RNA. (-) RNA is copied while (+) RNA is copied and translated (mRNA)

Answer 52

single stranded (+) RNA genomes Poliovirus, rhinoviruses (cause the common cold), corona viruses the genome is used directly as mRNA RNA replicase synthesizes (-) RNA strands to then use as a template to synthesize mRNA and genome

Answer 53

ssRNA (-) genomes Rabies, influenza RNA replicase synthesizes (+) RNA strands (mRNA) RNA replicase uses (+) RNA as a template for (-) RNA to synthesize the genome

Answer 54

ssRNA (+) retroviruses HIV Reverse transcriptase synthesizes dsDNA The negative sense DNA strand is then used as a template to synthesize mRNA and genome

Answer 55

dsDNA genomes Hepatitis B mRNA synthesized from (-) DNA strand mRNA is then used as a template by reverse transcriptase to synthesize dsDNA Doesn't use the original genome for DNA replication because its virion does not come prepackaged with enzymes to take over host cells. Has to first make the mRNA to make these enzymes

Answer 56

A class lV ssRNA (+) genome with a polA tail to prevent host endonuclease from breaking it down . Naked icosohedral virion , very small oral-fecal contamination, aerosols ~1/100 cases develop neurological damage when virus moves to the CNS highly infectious, Replicates in the stomach but can spread into other tissues in the body Host: humans only

Answer 57

A host with integrated viral DNA

Answer 58

viral DNA that is integrated into the host genome

Answer 59

A viral genome which integrates into a eukaryotic genome

Answer 60

Lamda tail attaches to a host maltose transport protein The 5' ends of the lamda DNA contain short, single-stranded complimentary, cohesive ends (form the cos site when fused) Following entry into the host cytosol, lamda DNA circularizes, forming a cos site (cohesion site)

Answer 61

If there is lysogeny promoting conditions, the cl genes will be transcribed rapidly. cl accumulates, and causes most lamda genes to be repressed. One of the genes that is expressed - the product monitors stress levels - if stress is detected, proteins build up - interact with the lamda proteins to signal a response. DNA will then integrate into the chromosome Lysogeny promoted!

Answer 62

Conditions not right for lysogeny, the cl repressor gene is not going to transcribed very fast and instead the cro gene will be made -- and inhibit cl cro accumulates, and the cl gene is repressed. Lamda enters the lytic cycle

Answer 63

att sequences. Attachment sites. Both the host and lamda contain att sequences like insertion sequences, share short stretches of homology

Answer 64

Nicks at the att sites DNA ligase helps to insert.

Answer 65

The circular lamda DNA is copied by rolling circle replication. It is synthesized as a longer concatemer. Idvll genomes are cut at each cos site and are assembled into phage heads. So all progeny of lamda will have the exact same molecules because they are cut at a very specific site.

Answer 66

During a lytic infection by a virulent phage. Occurs during assembly when a chunk of the host DNA gets packaged instead of the viral genome. This phage will then adsorb to another cell - can get random genes passed over if there is homology between the regions. success is rare! uptake of a functional host gene is rare by a phage. Lots of factors must be lined up correctly

Answer 67

Occurs during a lysogenic infection by a temperate phage.

Answer 68

Infection cycle of a temperate phage - can do lytic or lysogenic

Answer 69

Occurs during lysogenic infection by a temperate phage During lysogeny, viral DNA is inserted at a specific (att) site During induction, host chromosomal DNA - adjacent to the att site (NOT RANDOM) - can be excised with the viral DNA During the next round of lysogeny, those prokaryotic genes can be inserted into the next host genome. If this changes the phenotype of the host, we say that phage-conversion has occurred.

Answer 70

When integrated viral DNA loses its ability to leave the chromosome. It becomes junk DNA part of the bacterial chromosome -defective prophage prokaryotes use this for horizontal gene transfer Upon entering stationary phage, genes for GTA production (on host chromosome) are induced A small number of cells undergo programmed cell death and package stretches of their DNA into the GTAs The rest of the population express GTA receptor genes as well as genes to become competent to their uptake The genes for capsid and tail function are forever integrated under control of the promoter. ~20% of these generate GTA - sacrifice themselves to increase genetic diversity

Answer 71

many viruses are specific to certain tissues

Answer 72

In eukaryotic viruses: -nucleocapsid enters the host -host cells have a nucleus so the virus has to get in and out of this - viral genome (sometimes) "hides" in a membrane-bound viral factory or viralplasm.

Answer 73

1. Cell lysis (most common) 2. Latent infection (viral genome becomes a provirus) 3. Persistent infection (virion leave the host by budding out the cell membrane - this doesn't kill the cell but the cell remains infected) 4. Transformation (infection can result in cancer if DNA is integrated such that it disrupts cell cycle genes)

Answer 74

Plant viruses have a broad- host range. Same virus can infect multiple diff plants Most plant viruses are not enveloped Plant cells are harder to infect - need something else to punch a hole in the the plant cells first Viruses can infect adjacent cells through plasmadesmata. So once a plant cell does infect, it infects the entire plant.

Midterm 2-1 Flashcards

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