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CMMB 343 > Midterm 2-1 > Flashcards

Midterm 2-1 Flashcards

1
Q

Anabolism

A

Energy-requiring metabolic reactions
Synthesis new cell material

The building of polymers - connecting of smaller units to generate larger units

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2
Q

What does a cell need to grow?

A

Carbon (hetero vs auto)
Water
Oxygen or another redox acceptor
Nutrients - other building blocks (macro and micronutrients)
Electrons (come from the energy source or else a chemical source if the organism is a phototroph)

Energy source (organotrophs, lithotrophs, phototrophs)

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3
Q

Heterotrophs vs Autotrophs

A

HETEROTROPHS - Obtain their carbon from organic compounds

AUTOTROPHS - obtain their carbon from CO2

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4
Q

What does reduction of carbon mean?

A

Typically means building carbon up to build something like cell components.

THis requires electrons!!

Ie. reducing carbon dioxide (electrons usually obtained from H20 or H2S in this case)

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5
Q

Do catabolic pathways use up or generate free energy?

A

Catabolism - breaking down of larger polymers into smaller units

THis is exergonic and thus generates free energy

Free energy is conserved by synthesizing energy rich molecules like ATP

ATP formation required = =31.8kJ/mol

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6
Q

Is the electron donor reduced or oxidized?

A

Loses electrons so it is oxidized

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7
Q

IS the electron acceptor reduced or oxidized?

A

It is reduced because it gains electrons

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8
Q

If the reduction potential of a half reduction is MORE NEGATIVE…

A

ie. closer to the top of the table, the compound is more likely to DONATE electrons to another redox pair. Good Energy sources are at the top, they are the reduced members of the pairs

When half reactions are paired, the electrons will move DOWN the tower

THE GREATER THE FALL, THE GREATER THE ENERGY YIELD

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9
Q

If the reduction potential of a half reduction is MORE POSTIVE…

A

Ie further down the table, the compound becomes a better electron acceptor

Good electron acceptors are the oxidized forms near the bottom of the table…. O2, NO3-

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10
Q

Energy rich compounds that conserve energy in microbial metabolism

A

From Mort energy storage to least…

Phosphoenolpyruvate, bisphosphoglycerate, acetyl phosphate, ATP, ADP
Acetyl CoA

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11
Q

What are the two ways to produce ATP in a chemotroph?

A
  1. substrate level phosphorylation,
  2. oxidative phosphorylation
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12
Q

Substrate level phosphorylation

A

Direct capture of energy

ATP is synthesized directly during catabolism of an energy substrate (like glucose)

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13
Q

Oxidative phosphorylation

A

Energy from catabolism is stored in an intermediate form –> the proton motive force (Pmf) and the pmf is then used to generate ATP

Which steps of aerobic respiration are definted as oxidative phosphorylation?

ETC, ATP formation via F1F0 ATPase

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14
Q

photophosphorylation

A

when light is used to form the proton motive force (pmf)

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15
Q

aerobic respiration

A

When O2 is the terminal electron acceptor for energy generation, the organism is doing this

Steps involved in aerobic respiration:
Glycolysis (Embden Meyerhof Pathway)
Krebs Cycle
ETC
ATP formation via F1F0 ATPase

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16
Q

anaerobic respiration

A

When an organism uses a terminal electron acceptor other than O2 ( Fe3+, NO3-, SO4 2-)

energy yields are lower than aerobic respiration (O2 is at the bottom of the table - nothing is better)

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17
Q

Fermentation

A

is when the energy substrate is both the redox donor and the redox acceptor

(the product is a rearrangement of the substrate into a lower energy state)

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18
Q

How many ATP are generated per/glucose in aerobic respiration?

A

38 ATP per glucose, 17 per pyruvate

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19
Q

What occurs in respiration?

A

redox reactions take place with an energy source (like glucose), the reductant, and an external terminal electron acceptor (or oxidant) like O2, NO3- Fe3+, etc

terminal electron acceptors are usually inorganic molecules. The best ones are those at the bottom of the redox table with very positive redox potentials

ATP is formed by both substrate level phosphorylation and by oxidative phosphorylation. q

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20
Q

In fermentation

A

THe organic compounds are both the electron donor (energy source) and the terminal electron acceptor. There is no added terminal electron acceptor.

Products incl: acetic acid, ethanol, lactic acid, H2

Nad+ accepts electrons. In needs to be regenerated (ie NADH –> Nad_+) by transferring the electrons to an organic waste compound (pyruvate)

ATP in fermentations is solely produced by SLP

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21
Q

How is ATP generated in fermentations?

A

ATP in fermentations is solely produced by SLP

No terminal electron acceptor –> no oxidative level phosphorylation

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22
Q

What are the major electron acceptors after O2?

A

NO3- (nitrate), Fe3+ (ferric iron), SO4 2-(sulfate), and CO2

IN THAT ORDER

Not as many protons are pumped into the periplasm - doesnt generate as much of a proton motive force and thus less ATP is generated

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23
Q

Electrons for cell growth

A

They are the reducing power for reducing carbon during anabolism
-they can be obtained from the energy source (for chemotrophs who get energy from chemical compounds) or some other chemical like H20 or H2S for phototrophs

Usually preserved in the form of NADH

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24
Q

What is the order of bacteria in a Winogradsky Column from top to bottom?

A

Cyanobacteria (photosynthetic guild)
Heterotrophic bacteria
Iron Oxidizing bacteria
Purple non-sulfur bacteria
Purple sulfur bacteria
Green sulfur bacteria
Sulfate-reducing bacteria

CHIPPGS

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25
Q

Energy and carbon and electron source of cyanobacteria

A

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

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26
Q

Energy, chemical, and electron source of: heterotrophic bacteria?

A

Energy Source: organics (organotrophs) (ie cyanobacteria)
Carbon source: organics (heterotrophs)
electron source: organics

redox acceptor = O2

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27
Q

Energy, chemical, and electron source of: Iron-oxidizing bacteria

A

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

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28
Q

Energy, chemical, and electron source of: purple non-sulfur bacteria

A

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

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29
Q

Energy, chemical, and electron source of: Purple Sulfur bacteria

A

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

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30
Q

Energy, chemical, and electron source of: green sulfur bacteria

A

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

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31
Q

Energy, chemical, and electron source of: sulfate reducing bacteria

A

Energy Source: Organics (Heterotroph)
Carbon source: Organics (Organotroph)
electron source: Organics

Redox acceptor: sulfate –> source of H2S for the above guilds

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32
Q

________ organisms are the foundation of the carbon cycle

A

autotrophic

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33
Q

What are the dominant photoautotrophic organisms of aquatic environments

A

microbes (bacteria and algae)

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34
Q

autotrophs

A

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

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35
Q

Respiration

A

Breaking down organic material - oxidizing it to CO2 - heterotrophy

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36
Q

How do plants and eukaryotic organisms fix CO2?

A

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

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37
Q

Oxygenic photosynthesis

A

When electrons in photoautotrophs come from water

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38
Q

Anoxygenic photosynthesis

A

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

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39
Q

methanotrophy

A

COnverts methane to CO2 (in an oxic environment)

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40
Q

methanogenesis

A

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

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41
Q

pedogram

A

10^12g

42
Q

Nitrification

A

NH4+ –> NO3-
NH4+ –> NO2-

ammonium to nitrate or nitrite

43
Q

denitrification

A

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

44
Q

nitrogen fixation

A

important for nutrition
nitrogen gas to ammonia

ONLY CARRIED OUT BY BACTERIA

45
Q

ammonification

A

organic nitrogen to ammonium

degradation of organic matter done by heterotrophs

46
Q

Anammox

A

nitrite + ammonium –> nitrogen gas

NO2- + NH3 or NH4+ –> N2

anaerobic ammonia oxidation

47
Q

Why can denitrification be detrimental to the atmosphere?

A

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)

48
Q

assimilatory reduction

A

assimilatory reduction of inorganic compounds is done to use the reduced compounds as nutrients in biosynthesis

USING SOMETHING AS A NUTRIENT

49
Q

dissimilitory reduction

A

dissimilitory reduction of inorganic compounds is their use in anaerobic respiration

using inorganic compounds as a terminal electron acceptor

50
Q

What is the difference between anaerobic respiration and lithotrophy?

A

Anaerobic repiration involved the reduction of oxidised inorganic compounds as terminal electron acceptors

lithotrophy involves the oxidation of reduced organic compounds for energy ***

51
Q

Lithotrophy involves the _______ of ________ inorganic compounds for energy

A

Lithotrophy involves the oxidation of reduced inorganic compounds for energy

52
Q

lithotrophic sulfide oxidation

A

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

53
Q

phototrophic sulfide oxidation

A

ie phototrophic purple sulfur

anaoxygenic photosynthesis –> energy comes from light but electrons come from H2S

(In oxygenic phototrophs they comes from H2O)

54
Q

What enzyme do some bacteria have that allow them to fix nitrogen?

A

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

55
Q

What does the bacteria get from the plant in the N2 fixing symbioses?

A

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

56
Q

bacteroid

A

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

57
Q

Leghemoglobin (Lb)

A

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

58
Q

In Hfr conjugation

A

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

59
Q

F’

A

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.

60
Q

Transposition

A

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

61
Q

what is the extracellular state of a virus called?

A

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

62
Q

The intracellular state of a virus is

A

not infectious in nature. Replicating genome

In a lab it can be used to unnaturally infect something

63
Q

Possible shapes/ structures of virions?

A

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

64
Q

capsid

A

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

65
Q

plaque forming units

A

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

66
Q

bacteriophage

A

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

67
Q

Viral one-step growth curve

A

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

68
Q

What kind of phage undergoes a lytic infection?

A

A virulent phage

69
Q

Bacteriophage T4

A

Class: l

linear dsDNA

Infects Ecoli host by attaching to lipid polysaccharides

70
Q

What do early genes of T4 express?

A

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.

71
Q

is mRNA positive or negative strand

A

positive! plus sense configuration

plus sense mRNA/strand

72
Q

Which classes of viruses are DNA viruses?

A

l, ll, Vll

73
Q

Which classes of viruses are RNA viruses?

A

lll, lV, V, Vl

74
Q

Class l Viruses

A

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

75
Q

Class ll Viruses

A

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

76
Q

Class lll viruses

A

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)

77
Q

Class lV Viruses

A

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

78
Q

Class V Viruses

A

ssRNA (-) genomes

Rabies, influenza

RNA replicase synthesizes (+) RNA strands (mRNA)
RNA replicase uses (+) RNA as a template for (-) RNA to synthesize the genome

79
Q

Class Vl Viruses

A

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

80
Q

Class Vll Viruses

A

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

81
Q

Poliovirus

A

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

82
Q

lysogen

A

A host with integrated viral DNA

83
Q

prophage

A

viral DNA that is integrated into the host genome

84
Q

provirus

A

A viral genome which integrates into a eukaryotic genome

85
Q

Lamda adsorption and later

A

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)

86
Q

What is teh lamda repressor gene?

A

cl

87
Q

IF the lamda repressor gene (cl) is expressed upon penetration….

A

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!

88
Q

IF the cro repressor gene (cro) is expressed upon penetration,

A

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

89
Q

What are the sequences that allow viral genome to integrate into host genome?

A

att sequences. Attachment sites.
Both the host and lamda contain att sequences

like insertion sequences, share short stretches of homology

90
Q

Where does lamda integrase nick for DNA integration?

A

Nicks at the att sites

DNA ligase helps to insert.

91
Q

lamda DNA replication

A

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.

92
Q

Does generalized transduction occur during a lytic or lysogenic infection?

A

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

93
Q

What type of phage can be involved with specialized transduction?

A

Occurs during a lysogenic infection by a temperate phage.

94
Q

lysogenic infection

A

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

95
Q

Specialized transduction

A

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.

96
Q

Gene transfer agents

A

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

97
Q

Eukaryotic Viruses

A

many viruses are specific to certain tissues

98
Q

3 differences between eukaryotic viruses and phage?

A

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.

99
Q

4 possible outcomes of infection

A
  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)
100
Q

Plant viruses

A

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.

CMMB 343 (8 decks)

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