Midterm 2-1 Flashcards
Anabolism
Energy-requiring metabolic reactions
Synthesis new cell material
The building of polymers - connecting of smaller units to generate larger units
What does a cell need to grow?
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)
Heterotrophs vs Autotrophs
HETEROTROPHS - Obtain their carbon from organic compounds
AUTOTROPHS - obtain their carbon from CO2
What does reduction of carbon mean?
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)
Do catabolic pathways use up or generate free energy?
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
Is the electron donor reduced or oxidized?
Loses electrons so it is oxidized
IS the electron acceptor reduced or oxidized?
It is reduced because it gains electrons
If the reduction potential of a half reduction is MORE NEGATIVE…
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
If the reduction potential of a half reduction is MORE POSTIVE…
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-
Energy rich compounds that conserve energy in microbial metabolism
From Mort energy storage to least…
Phosphoenolpyruvate, bisphosphoglycerate, acetyl phosphate, ATP, ADP
Acetyl CoA
What are the two ways to produce ATP in a chemotroph?
- substrate level phosphorylation,
- oxidative phosphorylation
Substrate level phosphorylation
Direct capture of energy
ATP is synthesized directly during catabolism of an energy substrate (like glucose)
Oxidative phosphorylation
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
photophosphorylation
when light is used to form the proton motive force (pmf)
aerobic respiration
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
anaerobic respiration
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)
Fermentation
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)
How many ATP are generated per/glucose in aerobic respiration?
38 ATP per glucose, 17 per pyruvate
What occurs in respiration?
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
In fermentation
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
How is ATP generated in fermentations?
ATP in fermentations is solely produced by SLP
No terminal electron acceptor –> no oxidative level phosphorylation
What are the major electron acceptors after O2?
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
Electrons for cell growth
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
What is the order of bacteria in a Winogradsky Column from top to bottom?
Cyanobacteria (photosynthetic guild)
Heterotrophic bacteria
Iron Oxidizing bacteria
Purple non-sulfur bacteria
Purple sulfur bacteria
Green sulfur bacteria
Sulfate-reducing bacteria
CHIPPGS
Energy and carbon and electron source of cyanobacteria
Energy Source: light (phototroph)
Carbon source: CO2 (autotroph)
electron source: H2O - produced oxygen
Energy, chemical, and electron source of: heterotrophic bacteria?
Energy Source: organics (organotrophs) (ie cyanobacteria)
Carbon source: organics (heterotrophs)
electron source: organics
redox acceptor = O2
Energy, chemical, and electron source of: Iron-oxidizing bacteria
Energy Source: Fe2+ from a lower guild (lithotroph)
Carbon source: CO2 (autotroph)
electron source: Fe2+
redox acceptor = oxygen
Energy, chemical, and electron source of: purple non-sulfur bacteria
Energy Source: H2S (lithotroph)
Carbon source: organics OR CO2
electron source: H2S
Redox acceptor = F3+ or O2
Energy, chemical, and electron source of: Purple Sulfur bacteria
Energy Source: light (phototrophs)
Carbon source: Co2 (autotrophs)
electron source: H2S (produces sulfate)
Energy, chemical, and electron source of: green sulfur bacteria
Energy Source: light (phototroph)
Carbon source: CO2 (autotroph)
electron source: H2S (produces sulfate)
Energy, chemical, and electron source of: sulfate reducing bacteria
Energy Source: Organics (Heterotroph)
Carbon source: Organics (Organotroph)
electron source: Organics
Redox acceptor: sulfate –> source of H2S for the above guilds
________ organisms are the foundation of the carbon cycle
autotrophic
What are the dominant photoautotrophic organisms of aquatic environments
microbes (bacteria and algae)
autotrophs
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
Respiration
Breaking down organic material - oxidizing it to CO2 - heterotrophy
How do plants and eukaryotic organisms fix CO2?
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
Oxygenic photosynthesis
When electrons in photoautotrophs come from water
Anoxygenic photosynthesis
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
methanotrophy
COnverts methane to CO2 (in an oxic environment)
methanogenesis
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
pedogram
10^12g
Nitrification
NH4+ –> NO3-
NH4+ –> NO2-
ammonium to nitrate or nitrite
denitrification
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
nitrogen fixation
important for nutrition
nitrogen gas to ammonia
ONLY CARRIED OUT BY BACTERIA
ammonification
organic nitrogen to ammonium
degradation of organic matter done by heterotrophs
Anammox
nitrite + ammonium –> nitrogen gas
NO2- + NH3 or NH4+ –> N2
anaerobic ammonia oxidation
Why can denitrification be detrimental to the atmosphere?
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)
assimilatory reduction
assimilatory reduction of inorganic compounds is done to use the reduced compounds as nutrients in biosynthesis
USING SOMETHING AS A NUTRIENT
dissimilitory reduction
dissimilitory reduction of inorganic compounds is their use in anaerobic respiration
using inorganic compounds as a terminal electron acceptor
What is the difference between anaerobic respiration and lithotrophy?
Anaerobic repiration involved the reduction of oxidised inorganic compounds as terminal electron acceptors
lithotrophy involves the oxidation of reduced organic compounds for energy ***
Lithotrophy involves the _______ of ________ inorganic compounds for energy
Lithotrophy involves the oxidation of reduced inorganic compounds for energy
lithotrophic sulfide oxidation
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
phototrophic sulfide oxidation
ie phototrophic purple sulfur
anaoxygenic photosynthesis –> energy comes from light but electrons come from H2S
(In oxygenic phototrophs they comes from H2O)
What enzyme do some bacteria have that allow them to fix nitrogen?
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
What does the bacteria get from the plant in the N2 fixing symbioses?
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
bacteroid
is the bacteria - the symbiotic unit inside the plant cell - the membrane is called the bacteroid membrane once it is engulfed
Leghemoglobin (Lb)
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
In Hfr conjugation
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
F’
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.
Transposition
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
what is the extracellular state of a virus called?
a virion. This is the infectious form of the virus.
The intracellular state of a virus is
not infectious in nature. Replicating genome
In a lab it can be used to unnaturally infect something
Possible shapes/ structures of virions?
Helical, icosahedral (20 sides, efficient), complex (non-symmetrical)
capsid
All viruses have a capsid, a protein coat that surrounds genomic material. It is composed of capsomeres
plaque forming units
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
bacteriophage
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
Viral one-step growth curve
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
What kind of phage undergoes a lytic infection?
A virulent phage
Bacteriophage T4
Class: l
linear dsDNA
Infects Ecoli host by attaching to lipid polysaccharides
What do early genes of T4 express?
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.
is mRNA positive or negative strand
positive! plus sense configuration
plus sense mRNA/strand
Which classes of viruses are DNA viruses?
l, ll, Vll
Which classes of viruses are RNA viruses?
lll, lV, V, Vl
Class l Viruses
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
Class ll Viruses
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
Class lll viruses
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)
Class lV Viruses
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
Class V Viruses
ssRNA (-) genomes
Rabies, influenza
RNA replicase synthesizes (+) RNA strands (mRNA)
RNA replicase uses (+) RNA as a template for (-) RNA to synthesize the genome
Class Vl Viruses
ssRNA (+) retroviruses
HIV
Reverse transcriptase synthesizes dsDNA
The negative sense DNA strand is then used as a template to synthesize mRNA and genome
Class Vll Viruses
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
Poliovirus
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
lysogen
A host with integrated viral DNA
prophage
viral DNA that is integrated into the host genome
provirus
A viral genome which integrates into a eukaryotic genome
Lamda adsorption and later
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)
What is teh lamda repressor gene?
cl
IF the lamda repressor gene (cl) is expressed upon penetration….
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!
IF the cro repressor gene (cro) is expressed upon penetration,
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
What are the sequences that allow viral genome to integrate into host genome?
att sequences. Attachment sites.
Both the host and lamda contain att sequences
like insertion sequences, share short stretches of homology
Where does lamda integrase nick for DNA integration?
Nicks at the att sites
DNA ligase helps to insert.
lamda DNA replication
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.
Does generalized transduction occur during a lytic or lysogenic infection?
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
What type of phage can be involved with specialized transduction?
Occurs during a lysogenic infection by a temperate phage.
lysogenic infection
Infection cycle of a temperate phage - can do lytic or lysogenic
Specialized transduction
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.
Gene transfer agents
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
Eukaryotic Viruses
many viruses are specific to certain tissues
3 differences between eukaryotic viruses and phage?
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.
4 possible outcomes of infection
- Cell lysis (most common)
- Latent infection (viral genome becomes a provirus)
- Persistent infection (virion leave the host by budding out the cell membrane - this doesn’t kill the cell but the cell remains infected)
- Transformation (infection can result in cancer if DNA is integrated such that it disrupts cell cycle genes)
Plant viruses
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.
