Bio 220 Exam 3

Rubisco

-consists of small (S) and large (L) subunits -catalyzes the condensation of CO2 to ribulose 1,5 bisphosphate, and the splitting of the unstable 6C intermediate into two 3 C PGA molecules -enzyme that is involved in carbon fixation -most abundant protein on the planet -normally housed in the structures called carboxzymes (polyihedtreal shaped structures in photosyntheic cells)

Which energy saving measure would be most "drastic" measure for the cell? A. Genome Reduction B. Competition /Secondary Metabolites C. Regulation

Genome Reduction

What do wastewater treatment plants have in common with wetland filtration (purification)? The type of wastewater treated is the same. The engineering designs and flow are similar. They depend on microbes to remove nitrogen and carbon. Chlorine is used to decontaminate pollutants. They are both continually aerated.

They depend on microbes to remove nitrogen and carbon.

What temperatures do you think pathogenesis related RNA thermometers (which would alter the microbes metabolism upon entering a human host) are set for

~99 F

Sigma H is the one involved in

high temperature responses

Which of the following is the most limiting element for marine phytoplankton? iron phosphorous sulfur hydrogen carbon

iron

Microbes participate in which step of wastewater treatment? preliminary tertiary primary every step secondary

secondary

Activator:

Region of DNA where activator proteins can bind

imbalance

inputs do NOT equal outputs

Steady state

inputs equal outputs

Important :

**-there are different layers of control or different levels of control -Some things that cover like almost everything. having to do with a cell, and that would be like circadian rhythms that some cells exhibit - then we have things like heat shock proteins that can the response to an elevated earn rapid increase in temperature would lead to sort of multiple pathways being coordinated at one time by the cell -We have operans; which related to a single process like lactose degradation; cell can control those individually. -A single gene; a cell can even control a single gene ***so they have all of these different sort of sized regulations that they can undertake depending on what what it is that we're talking about**

Enzymes couple synthetic reactions to reactions releasing energy

**Biosynthesis spends energy

Sigma Factors and Regulatory RNA

- a regulon is a set of genes and operons scattered around the chromosome with related functions -regulons are coordinately controlled by a single repressor or activator protein -but in many cases bacteria need to coordinately activate genes, operons, and regulons of seemingly disparate function that are needed for survival -one way to do this is to first regulate the synthesis or activity of the sigma factor that directs the expression of all those genes

The carbon cycle

-all food webs involve influx and efflux of carbon -the major carbon reservoirs are crust and the ocean -atmospheric reservoir is much smaller -the ocean absorbs a good part of the extra CO2 in the atmosphere -however, atmospheric CO2 continues to increase at a rate of about 2 ppm per year -the CO2 traps solar radiation as heat--a process known as the greenhouse effect

Chapter 10: Molecular Regulation

-bacteria are fighting for survival bacteria are able to: -sense changes in temperature, salinity, pH -respond to changes in nutrient concentrations -recognize the presence / abundance of other microbes of the same species as themselves and that can provide them certain advantages

Quorum Sensing

-hwaian bobtail squid -refers to the process where bacterial cells work together at high density's -important for a lot of pathogens bc say one pathogen cell got into your body and the cells that pathogens still sell started pumping out its toxin. // There's a really good chance that our immune system would identify that toxin find that single pathogen cell and wipe it out before it was really able to do any damage us or Take advantage of sort of the damage that it had caused and start growing rapidly or something would have that single pathogen cell was able to get in there and then start replicating, really stealthily And then once there was a certain number of those pathogens around then they all coordinated their production of toxin that could lead to a lot more damage and maybe overwhelm the, the host immune system and they have a better chance of doing that. So it's like a coordinated attack.

Why fix nitrogen ?

-it gives you a competitive advantage -It's that trick that you have that other organisms don't. And so if nitrogen, you know, if all the cells are sort of hanging around in the lake waiting for some nitrogen to appear. -They're not able to do anything until that nitrogen shows up because they need it to make proteins or whatever. But you have the trick that you can make your own. -And so that's going to allow you to grow and occupy more space and multiply. When those other cells are sort of stuck hanging around and not able to do it right. So it does cost a lot of energy, but it's worth it if it allows you to outcompete your part, your competitors.

Oxygen is problematic to N-fixation

-needs to occur in a reducing environment (anaerobic) -Strategies to deal with Oxygenic environment 1. Protective Proteins 2. Temporal separation of photosynthesis 3.Specailaized cells --> heterocysts (which allow the nitrogen to occur in a physically different space than where photosynthesis is occuring)

Haber-Bosch process

-synthetically produces NH4 -450 million tons annually -1-2% of the WORLD energy supply goes to running this process -Responsible for massive increase in farm productivity and also "dead zones" in various parts of the ocean or lakes -synthetic or man made way to produce ammonium -makes tons and tons of fertilizer per year -originally invented to get around the fact that Germany t could not acquire their typical nitrates from South America because the United States had blocked sort of their supply line. So they want to inventing this process.

Nitrogen Fixation

-takes N2 gas and using those electrons from the NADPH and lots of ATPS to hydrogenate that nitrogen so you wind up with 2 molecules of ammonia after you have fixed this nitrogen ; the enzyme involved in this process is called nitrogenase -the amount of energy that is required to fix one molecule of nitrogen gas is 28 ATPs and that is almost equal to the amount of energy you get from one molecule of glucose -in living cells nitrogen fixation is an enormously energy-intensive process -the mechanism is largely conserved across species N2 + 8H+ + 8e- (from NADPH (3 ATP/2 e-)) + 16 ATP----> 2NH3 + H2 +16 ADP +16 Pi -16 ATP + 12 ATP equal about 28 ATPs are consumed per Nitrogen fixed

Paradigm of the Lactose Operon

-the lactose utilization lacZYA operon of Escherichia coli was the first gene regulatory system described

cells have preferences for different types of Metabolites or different molecules

1. In catabolite repression, an operon enabling the catabolism of one nutrient is represented by the presence of a more favorable nutrient (commonly glucose) ex. e coli growing on glc before growing on lactose dioxin growth curve (first part of the growth curve the cell is growing on glc and then only after the glc runs out does it start growing on lactose) 2. The biphasic curve of culture growing on two carbon sources is often called diauxic growth

The Calvin cycle is not the only pathway that fixes carbon dioxide... there are three others

1. Reverse TCA cycle: arrows in diff direction than normal TCA because its running in the opposite direction; 2. Acetyl-COA Pathway 3. 3- Hydroxypropionate Cycle

How many ATP equivalents are used in the enzymatic conversion of N2 to NH3? 16 64 28 None; only GTP is used. 48

28

How many turns of the Calvin cycle does it take to feed one molecule of glyceraldehyde-3-phosphate into the biosynthesis of glucose? 1 6 2 5 3

3

Why do you think there are large annual fluctuations of [CO2]?

Changes in the seasons

20 Amino Acids required for life and we can only produce 11! Where do we get the other 9? A. Diet B. Microbiome C. Both

Both

Which of the following is NOT true about quorum sensing in bacteria? A. It involves the production of AHLs B. It involves the detection/binding of AHLs C. High AHL concentration DO NOT result in coordinated gene expression D. High AHL concentrations DO result in coordinated gene expression

C. High AHL concentration DO NOT result in coordinated gene expression

Two strains of E. coli were developed, each of which overproduced an amino acid, either histidine or tryptophan. When grown together in medium with adequate amino acids, they grew but did not associate with each other. When these strains were grown together in medium without histidine and tryptophan, they grew and formed ________ in order to ________. A. carboxysomes; share the excess of the two amino acids B. carboxysomes; provide ATP to each other to make the missing amino acids C. nanotubes; share the excess of the two amino acids D. nanotubes provide ATP to each other to make the missing amino acids E. heterocysts; share the excess of the two amino acids

C. nanotubes; share the excess of the two amino acids

The ________ pathway is utilized for carbon fixation in chloroplasts and cyanobacteria. acetyl-CoA Calvin cycle reverse TCA cycle glycolosis 3-hydroxypropionate cycle

Calvin cycle

several different pathways in microbes that go about fixing carbon dioxide. The main one that we talked about was the Calvin cycle We talked about how energy intensive that is it uses lots of ATP and and adpH. That nadpH was, you know, produced previously when we talked about metabolism or catabolism that nadpH is that electron carrier that's earmarked for biosynthesis.

Calvin cycle

Which of the following oxygenic phototrophs are believed to have generate the majority of oxygen gas in Earth's atmosphere? purple bacteria Chloroflexus Cyanobacteria Chlorobium Clostridium

Cyanobacteria

Which of the following can be used to make a vaccine? A. DNA B. Protein C. Attenuated virus D. RNA E. All of the above

E. All of the above

In contrast to catabolism, biosynthesis always requires E phosphorous. A energy. B glucose. C the TCA cycle. D nitrogen gas.

Energy

Jupiter's moon ________ is a candidate for extraterrestrial life due to its subsurface oceans. Io Mimas Europa Deimos Titan

Europa

Which of the following is NOT true regarding food webs in ecosystems? Primary producers assimilate minerals into biomass. Primary producers absorb energy from outside the ecosystem. Grazers convert 10% of carbon back to carbon dioxide. Consumers convert 90% of biomass carbon to atmospheric CO2. All energy gained by an ecosystem is eventually lost as heat.

Grazers convert 10% of carbon back to carbon dioxide.

If I wanted to identify if bacteria in a sample were actively degrading toluene I could use:

Metatransciptomics

Which of the following is NOT correct regarding nitrogen assimilation into biomass? It is expensive, requiring reducing energy and ATP. It is easy for living organisms to assimilate nitrogen due to its great stability. Nitrogen forms must be fully reduced to NH3. Only bacteria and archaea can assimilate elemental nitrogen. Different oxidation states of nitrogen require different amounts of reducing energy.

It is easy for living organisms to assimilate nitrogen due to its great stability.

Immunity from infection by a pathogen a second time is provided by ? A. Innate Immune System B. Helper T- Cells C. Memory Cells

Memory cells

If I wanted to see which bacteria had the potential to degrade cellulose I could use:

Metagenomics

Microbial Ecology: chapter 21

Microbial ecology is the ecology of microorganisms; their relationship with one another and with their environment . It concerns the three major domains of life.. Eukaryota, Archaea and Bacteria- as well as viruses

Operator:

Region of DNA sequence where repressor proteins can bind

Which abundant oxygenic phototroph accounts for half the ocean's photosynthesis? Vibrio cholerae. Symbiodinium. Rhizobium. Trichodesmium. Prochlorococcus.

Prochlorococcus.

What is a region of DNA upstream of a gene that is needed for transcription initiation?

Promoter

Metatranscriptomics is the study of ________ obtained from an environmental community. lipids DNA proteins RNA organisms

RNA

The genomic and energetic costs of biosynthesis lead microbes to evolve several strategies to control these cost:

Regulation : cells are in control of what molecules or what proteins are being produced at a given time right what pathways are being conducted Genome loss/ cooperation: the actual loss of genetic information from the cell if the cell is able to get a molecule from another organism. Competition and Predation (Secondary Products): the production of secondary metabolites to kill off other organisms that then they can scavenge those products for

Based on this graph of these bacterial communities is more diverse?

Soil-1

Catabolite repression of lactose by glucose results in the cell being more efficient ?

True

Sensing the External Environment

Two-component signal transduction systems sense the external environment (monitors what is going on outside of the cell) Sensor Kinase in the cell membrane: -binds to environmental signal -Activates itself via phosphorylation -y shaped protein Response regulator in the cytoplasm: -takes phosphate from sensor -binds chromosome -alters transcription rate for several genes Sensor Kinase: part of it extends into the extracellular space and part of it is intracellular and so there's all different types of The sensor kinases out there that recognize all different types of environmental cues, things like salinity pH different types of nutrient concentrations. And so when they sense whatever it is that they're targeted to sense They sort of have a confirmation or change where they wind up having some ATP right that ATP acts or acts upon this response regulator. The second part of the signal transduction system and then that interacts with the with the DNA and whether or not that gene gets enhanced transcription or reduced transcription.

Metagenomics

What can they do? portrays functional potential of microbiome gene content bacteria, archaea, fungi and viruses human/host background

Operons:

a collection of genes arranged in tandem that are transcribed into a single RNA, under control of a single promoter(red arrow)

A higher concentration of organic substances in an environment leads to a lower BOD. methanogenesis. oligotrophy. increased photosynthesis. a higher BOD.

a higher BOD

Which of the following molecules is a key substrate for many biosynthetic products and also links glycolysis with the TCA cycle? A. malate B. acetyl-CoA C. citrate D. succinate E. oxaloacetate

acetyl-CoA

Parasitism

an intimate association where one partners benefits, while harming a specific host (tapeworms)

Synergism:

an optional cooperation where both species benefit, but can grow independently -some gut bacteria

The high biological oxygen demand that accompanies algal blooms in eutrophic lakes ultimately increases the level of ________ conditions in the water column. oxygenic aerobic anoxic thermophilic oligotrophic

anoxic

The predominant source of nitrogen on Earth is the mantle. the deep ocean. the atmosphere. the upper ocean. freshwater.

atmosphere

Residence time

avg time in a reservior

term fixation in general just sort of refers to taking an inorganic molecule like carbon dioxide or nitrogen gas and incorporating that into biomass and to do those both of those processes requires lots of energy.

carbon fixation

Biosynthesis is the building of complex biomolecules, also known as anabolism the reverse of catabolism

chapter 15

Reservoir

compartment sources and sinks as elements cycle from sources to sinks, microbial metabolism generates a series of redox changes

building things cost alot of ..

energy

What does functional annotation in metagenomic analysis involve? determining the number of species in the sample calculating the %G+C in the metagenome finding homologs or recurring peptide motifs that infer the function of the sequence making contigs and scaffolds and assembling the sequence analyzing the RNA sequences to see what was transcribe

finding homologs or recurring peptide motifs that infer the function of the sequence

One mechanism by which microorganisms minimize biosynthetic energy cost is A. genome loss and cooperation. B. reducing agents such as NADPH. C. lithoautotrophy. D. denitrification. E. carbon dioxide fixation.

genome loss and cooperation.

The enzyme nitrogenase is inhibited by oxygen. Which of the following does NOT protect nitrogenase from oxygen? special thick-walled cells (heterocysts) in filamentous cyanobacteria, such as Anabaena growth under anaerobic conditions temporal separation of nitrogen fixation (at night) and photosynthesis (during the day) in some species of cyanobacteria growth under aerobic conditions special nitrogenase-protecting proteins in Azotobacter species

growth under aerobic conditions

Are the compounds measured in this graph steady state or imbalance?

imbalance

Industrial nitrogen fixation is achieved through the Haber process? in which N2 is reduced catalytically by H2 at ambient temperature. in which N2 is hydrogenated by CH4 at extreme temperature and pressure. in which nitrate and nitrite are chemically converted to NH at ambient temperature. which requires little energy. which is carried out by purified enzymes in a reactor.

in which N2 is hydrogenated by CH4 at extreme temperature and pressure.

Flux

movement of element in/out of a reservior

The algal and fungal interaction within a lichen are best described as mutualism. amensalism. synergism. parasitism. commensalism.

mutualism

The ________ is a set of conditions, including its habitat, resources, and relations with other species of the ecosystem, that enable an organism to grow and reproduce. benthos metagenome environment resource requirement niche

niche

they would prefer to break down glucose before they ever started breaking down lactose glucose is very easily. Put right into the like glycoysis and that whole sort of, you know, the TC cycle and central metabolism lactose requires a couple of extra steps before the products of Lactose can be put into like glycolyis and central metabolism. So the cell in an effort to be more efficient with choose if it was given the choice to break down glucose. Or to take up glucose before ever worrying about growing on lactose.

notes

Lakes that have dilute concentrations of nutrients are termed eutrophic. oligotrophic. syntrophic. atrophic. aphotic.

oligotrophic.

Commensalism

one partner benefits and the other is unaffected Vulture and lion

Amensalism

one partner is harmed, and the other is unaffected (walking across the lawn)

Two component signal transduction systems allow a cell to measure conditions ? the cell, while regulatory proteins allow the cell to monitor conditions ? the cell

outside; inside

Nitrogenase is sensitive to

oxygen so needs to occur in an anaerobic environment

Which of the following fix CO2 as their sole carbon source? organotrophs and iron oxidizers heterotrophs and methanogens photoheterotrophs and chemotrophs methanogens and phototrophs photoautotrophs and lithoautotrophs

photoautotrophs and lithoautotrophs

Which of the following decreases the amount of carbon dioxide in the atmosphere? burning of logs anaerobic fermentation microbial decomposition of logs aerobic respiration photosynthesis

photosynthesis

Which of the following are most likely to be found in the upper 200 m of the open ocean? barophiles phototrophs psychrophiles methanogens thermophiles

phototrophs

Promoter:

region of DNA just upstream of a gene. This region is needed for transcription initiation (binding of RNA polymerase and initiate transcription)

usually have a regulatory protein that is expressed off of a diff promoter

regulatory protein will bind to the regulatory sequence and either block or enhance transcription of the target genes that are downstream of it

Which of the following organisms forms a specific mutualistic association with legumes? rhizobia morels agrobacteria Vibrio sp. E. coli

rhizobia

Which term represents the region of soil influenced by plant roots? stele rhizoplane cortex rhizosphere root cap

rhizosphere

Thousands of species of microbes in the cow ________ ferment and break down plant material to small particles. rumen reticulum stomach intestine omasum

rumen

The term "metagenome" was coined by Jo Handelsman and colleagues in 1998 to refer to shotgun cloning. screening of libraries for the expression of genes. the DNA sequence obtained directly from a mixture of genomes. the DNA sequence taken directly from a colony. all uncultured organisms from a community.

the DNA sequence obtained directly from a mixture of genomes.

Which of these is involved in commercial chemical fertilizer production? lightning strikes nitrification the Haber process denitrification cellular nitrogen fixation

the Haber process

Which zone is generated when costal sediments bring nutrients to the middle layers of the ocean, sandwiched between the upper and lower oxygenated layers? the deep oxycline the oxygen minimum zone the upwelling zone the upper oxycline the benthos

the oxygen minimum zone

Which techique:

the spatial layout of a biofilm and how the different microbes are ordered in that biofilm which technique we use ???? answer: fluorescence in situ hybridization see how things are aligned in the sample

Tryptophan The tryptophan biosynthetic pathway in E coli and repression of the tryptophan operon

uses a repressor protein when repressor protein is not active it is called an Aporepressor when it has its corepressor bound to it is called a holorepressor the holrepressor is going to block the transcription of those genes the corepressor of biosynthetic operons like for tryptophan or other amino acids that co repressor is the product that operon so tryptophan ; tryptophan serves as the corepressor of the tryptophan operon

Culturing methods often detect organisms that may be rare in the environment but prevail when nutrients appear. What are these typically called? weed organisms OTUs protists microbial dark matter rhizobia

weed organisms

Metatranscriptomics

what are they doing? describes active gene expression elucidates the active members bacteria, archaea, fungi, viruses human/host background

16 s amplicon based approach

who is there descriptive view of microbiome diversity assess the general composition of the microbiota economical and therefore scale to large projects bacterial, archaeal, fungal diversity complex bacterial communities

Eolian sources of iron in marine systems are due to: precipitation of Fe3+ by OH- or PO43-. phytoplankton consumers. iron-oxidizing bacteria. wind-borne dust from dry land. reduction of Fe3+ by anaerobic respiration.

wind borne dust from dry land