Prelim 3 Biog1440 Flashcards
Symbiosis
The living together between organisms
-Interactions and possible co-evolution with associates microbes that allows some biological exchanges
Mutualism
Ex. bees and flowers
Species A, benefits
Species B, benefits
Commensalism
Ex. barnacles sticking and feeding out of whales
Species A, benefits
Species B, neutral
Parasitism
Ex. parasites
Species A, benefits
Species B, costs
Endosymbionts
microbes that reside within the body or cells of an organism
ex. wolbachia is a reproductive aprastie of insects and nematodes
ex. mitochondria and chloroplast
Lynn Margulis endosymbiosis theory
The eukaryotic cell could arise from a symbiotic union of primitive prokaryotic cells. This states that you start with two microbes and they engage in such a tight symbiosis that it leads to a eukaryotic cell.
Symbiogenesis
Mitochondria and chloroplasts evolved from certain bacteria engulfed by primitive cells
Microbiota
The ecological community of microorganisms associated with a host
ex. the skin microbiota
- The gut microbiota is not endosymbiotic, because the gut lumen is not “inside the body”
Rhizobacteria
They occupy the rhizosphere. Could either:
- Stay on the surface of the root.
- They are endophytic. They live between the cells of host plant tissues and form root nodules
Rhizobacteria depend on…
Nutrients secreted by plant cells, in return, they help to enhance plant growth by
- Producing chemicals (or some nutrients) that stimulate plant growth
- Producing antibiotics that eliminate bad microbes and protect the plant from disease/infection
- Absorbing toxic metals or increasing nutrient availability
The nitrogen cycle
Transforms nitrogen gas into nitrogen containing compounds that can be uptaken by the roots of the plants
- Nitrifying bacteria generate NO3- from NH4+
- The nitrifying bacteria takes the ammonium and generates nitrate. Nitrate will be the favored form of nitrogen that will be absorbed by the root alongside some ammonia.
Nitrogen fixing bacteria
Use nitrogen and generate ammonia (NH3) that will become ammonium (NH4+)
Ammonifying bacteria
Some additional bacteria can also generate some ammonium from a different source. They use decomposition products from the soil and generate some ammonium
Denitrifying bacteria
Takes nitrate and actually generates nitrogen (N2). So they do not help with the growth of the plant but would oppose it.
Rhizobia
Endosymbionts of legumes. Along a legume’s roots are swellings called nodules, composed of plant cells colonized
Nodules
Root tissue but mostly filled with some of the Rhizobia bacteria
Relationship between rhizobia and plants
The plant obains fixed nitrogen from Rhizobium, and Rhizobium obtains sugar and anaerobic environment
Development of nitrogen-fixing root nodules
Chemical dialogue between root cells (flavonoids) and Rhizobia (Nod factors)
To initiate the dialogue once a plant wants or needs to engage in symbiosis with Rhizobia, it will secrete some compounds called flavanoids (which are pigments) and those pigments will be synthesized and diffuse in the ground. If there is Rhizobia in the ground, they will bind and recognize the flavanoids. In response, they will produce proteins, NOD factors, that diffuse back towards the root. When the root receives some of those bacterial derived NOD factors, the roots will modulate the activity, their shape, and somehow follow the trail of the NOD factor a finds a microbe to internalize it
Where does Rhizobia attach?
The root hair which causes them to deform, grow, find and attach to microbes so it will enter those threads and colonize the roots. They grow within the root to develop these nodules.
Microbes in the human microbiota include species from each major domain:
- Bacteria ex. proteobacteria, cyanobacteria
- Archaea ex. crenarchaeota “extremophile”
- Eukarya ex. Fungi, yeast, plants, animals
Microbiota cannot be
Cultured
New solutions to microbiota investigation
Next generation sequencing: does NOT require culturing
Metagenomics: sequence-based analysis of genome of entire microbial communities, does not require culturing
Principal Component Analysis (PCA) Graph
Regroups together the different type of microbial community that look more alike
Microbiota is most abundant in the
GI tract. The large intestine is the preferred site. Over 70% if all bacteria are in the colon.
GI Microbiota is dominated by 2 phyla
Firmicutes and Bacteriodetes
Bacteria increase in abundance and diversity…
From proximal to distal GI tract
Stomach –> Duodenum –> Jejunum –> Ileum –> Colon
Change in gut microbiota can possible explain…
Disease/infection. This seems like more correlation than causation.
Key functions of the gut microbiota
The gut microbiota is central to intestinal homeostasis and physiology (ability to keep physiological constants steady)
1) Immunity:
- Prevents colonization by pathogens. This means it protects from invading pathogens.
- It educates the immune system (gut, skin, lungs). Without the gut microbes, your immune system would not develop properly. Stabilizes out bar
- Stabilizes gut barrier function (decreases leakage). Prevents gut leakage by making sure the gut epithelium is sealed and nothing from the gut lumen can leak into circulation
2) Metabolic Role:
- Caloric salvage: Ex of B.theta which produces 226 glycoside hydrolases compared to your own 80 glycoside hydrolase. Therefore, these microbes process food and interact with gut digestion and contribute
- Produces short chain fatty acids (SCFAs, colonic fermentation) –> These are food for some cells in your body which are produced by microbiota
- Produces Vitamin K and folate (Vit B) – huge metabolic role
3) Chemical modulator:
- Participates in drug metabolism (activation or catabolism) –> medical drugs can be activated or the catabolism can be regulated by the presence of microbes. Depending on your microbes, the drug may differ from patient to patient
- Deconjugated bile acids (alteration of community –> bile acid malabsorption)
Gut brain axis
The idea that the gut is actually the second most neuron rich organ in the body & its in constant communication with the brain. It’s been proposed that microbes hosted in your gut can use that gut brain axis to influence the function of your brain.
Ways the gut communicates with the brain
- The HPA axis (hormonal axis), means hormones initiated by the brain can influence the gut and therefore, the microbes that they host, On top of that, the brain, through neurons (innervation), can directly influence physiology. (the microbiota is affected by our experiences –> hormonal axis, innervation)
- Microbes in your gut will synthesize neurotransmitters (they also synthesize SCFAs) that can modulate brain cells activity (in turn, microbes send chemical signals, including neurotransmitters, SCFAs, affecting memory, emotions, behavior)
Are our microbiotas the same?
Each individual has their own distinct pattern of microbial. For an individual, their fecal microbiota remains remarkably stable over a person’s lifetime.
-Genetics, diet, immune system affect microbiota
Where do we get our microbiota from?
-Initial exposure occurs during passage through birth canal.
- Then the gut microbiota develops influence by mother and diet (ex. breastfeeding)
- Up to 3 years of age, bacterial abundance and diversity increase (mostly in the first year)
- After that, final bacterial abundance is reached at around 1 years old
Effects of maternal exposures on gut microbiota
- Antisepsis
- Antibiotics
- Diet
- Genetics
- C-section
Dysbiosis
Microbial imbalance of the body
–> if suddenly, the diversity of microbes in your gut changes, generally decreases, and some specific microbes that are normally not abundant become abundant or some that are abundant become non-abundant, this is dysbiosis
O2 Gas
Required for aerobic life, but can also inactivate key enzymes in metabolism; animals rely on O2 carrier proteins (hemoglobin, myoglobin)
O2 is highly reactive (oxidant that accepts electrons)
N2 Gas
Is abundant, but not bioavailable except for a few select organisms that have nitrogenase (a very O2 sensitive enzyme)
CO2 Gas
Enters biomass by photosynthesis and is an important waste product from aerobic respiration
CO2 chemistry in water
Dominated by its reversible hydration to carbonic acid (catalyzed by carbonic anhydrase)
Pasteur Point
(~0.2%) Facultative cells switch from anaerobic to aerobic metabolism
What two things could aerobic organisms do when faced with Low O2 (below Pasteur Point)
- Evolved terminal oxidases with high O2 affinity (bo & bd types
- Turn to more ancient type of metabolism (Fermentation and Alternative electron acceptors)
E.Coli for low O2
- Under most aerobic conditions, the BO type is used, which has a high affinity for oxygen.
- However, if the oxygen levels fall much below the Pastuer point, E.Coli can make alternative types of terminal oxidase (an alternate complex IV) with a significantly higher affinity for molecular O2 and the abolity to bind oxygen even when it’s in the low level (BD-type)
- If oxygen levels fall even further, E.Coli can turn to alternative electron acceptors such as nitrate or fermentation
Efficient mechanisms to bring O2 to tissues
- Oxygen carrier (proteins)
- Human respiration: mitochondrial O2 tension is just above Pasteur Point
O2 Concentration throughout the body
- O2 is highest at the lung (source) but drops dramatically at the mitochondria (sink)
- In the tissues, oxygen is being so rapidly consumed and it can only be brought to the tissues so rapidly by the arterial blood in the capillaries that the steady-state level of oxygen in the tissues is perhaps 20%
Incomplete Reduction of O2 (list the partially reduced species or ROS)
When oxygen is a substrate for reduction to water, partially reduced intermediates can escape
-Superoxide anions
-Hydrogen peroxide
-Hydroxyl radical
These can damage many molecular components, known as oxidative stress
Hydroxyl Radical
When hydrogen peroxide reacts with metals. These reactive species will damage proteins and lipids and contribute to various pathologies
Reactive Oxygen Species (ROS) and Oxidative Damage
Important contributors to many pathologies (often Fe II reacting or other metal cofactors in enzymes)
How do cells protect themselves from ROS?
- Respiratory Shields: The ability of the electron transport chain to efficiently consume oxygen (eukarya have this in the ETC and bacteria have this at the plasma membrane)
- O2 Binding Proteins: Proteins that bind oxygen to allow oxygen sensitive enzymes to function (plants use leghemoglobin to protect O2 sensitive nitrogenase in symbiotic bacteria)
- Detoxification: One important mechanism to protect enzymes against inactivation by ROS is to enzymatically remove these from the cell
- -> superoxide dismutase: removes superoxide, converting it into oxygen and hydrogen peroxide
- -> hydrogen peroxide is removed by catalase and peroxidases
- Avoidance: One strategy is to hide or avoid oxygen by living exclusively in anaerobic environments
Antioxidant enzymes
Superoxide dismutase, catalase, peroxidases. The function of antioxidant is not to remove oxidants entirely, but instead to keep them at an optimum level
Diazotrophs
Organisms that can use N2 gas as a source of nitrogen
Nitrogen fixation is (energy)
Energetically costly! Nitrogenase uses 16 ATP molecules as a source of energy and an input of 8 electrons. It produces 2 ammonia. (NH3)
Microbes can perform this at room temperature
N2+8e- +8H+ —> 2NH3 + H2
nitrogenase
(16 ATP)
Haber Bosch
Nitrogen can be released with a molecular hydrogen to generate ammonia. Requires temp of 400 degrees centigrade and over 400 atmospheres (pressure)
N2+3H2 —> 2NH3
Process for industrial fertilizer production and has been touted as the technological advance that has had the most impact on the modern world, driving the Green Revolution and fueling population growth.
How does nitrogenase assimilate nitrogen gas into ammonia?
Involves a very large complex of proteins, the nitrogenase and these proteins contain a lot of iron molybdenum co-factors, & iron sulfur clusters.
They are involved in the transfer of electrons into the nitrogen
Leghemoglobin
Made by plants to buffer O2 low enough to allow nitrogenase to function, but now so low to stop respiration in plant cells
Hemoglobin
Made by animals to carry O2 through circulation
Myoglobin
Made by animals to store O2 in muscles
Anabaena
Another way in which bacteria can protect their nitrogenase from oxygen is by separating the process of oxygenic photosynthesis from nitrogen fixation
- Heterocyst (specialized N2 fixing cells) only perform respiration and nitrogen fixation (not oxygenic photosynthesis)
- Neighboring cells do oxygenic photosynthesis, thereby making sugars that can feed the heterocyst
Heterocyst
Specialized N2 fixing cells that only perform respiration and nitrogen fixation (not oxygenic photosynthesis). They respire to get energy and fix nitrogen. They share that fixed nitrogen, in the form of ammonia, with the neighboring vegetative cells.
Separation in Time: Crocosphaera Watsonii
This small unicellular cyanobacterium separates nitrogen fixation and carbon fixation in time
-During daylight hours, this organism is a phototroph: uses photosynthesis to fix carbon dioxide into sugars and produces oxygen
- At night, it shuts down its photosynthesis pathways and activates nitrogen fixation (because it isn’t actively producing O2, it isn’t poisoning its own nitrogenase)
A benefit of separating these processes through time is that it allows Crocosphaera Watsonii to share iron which is scarce in surface oceans (iron in enzymes for photosynthesis during the day and actively degrades these large photosynthetic complexes to release that iron and build nitrogenase)
–> energy from sun
Environmental penalties of Haber Bosch
- Consumption of fossil fuels
- Prodigious production of greenhouse gases
- Spoiling of watersheds, by fertilizer run-off (e.g. algal bloom)
Carboxylation: productive
Rubisco catalyzes the carboxylation of ribulose bisphosphate (the initial CO2 incorporation step we consider in the first step of the Calvin Cycle)
Oxygenation: non-productive
Rubsico can also be inhibited by oxygen and it can be an oxidase. But when rubisco acts an an oxidase, there is no net incorporation of carbon into the cell. So this inhibits carbon dioxide production.
Formula for CO2 in aqueous solution
CO2 + H20 –> H2CO3 (carbonic acid) –> H+ + HCO3 (bicarbonate) –> H+ _ CO32- (carbonate)
Carbon-Concentrating Mechanisms
Cells that are performing carbon dioxide fixation through photosynthesis often rely on CCMs. These allow these cells to perform carbon dioxide fixation with much greater efficiency.
- Carbonic Anhydrase (CA)
- Active transport of bicarbonate
- Morphological CCM (cyanobacteria have carboxysomes & algae have pyrenoids)
- Biochemical CCM (capture of CO2 by PEP carboxylase, C4 plants (a spatial mechanism), CAM plants (a temporal mechanism).
Why do we need CCM?
- Rubisco is an unusually slow enzyme with a low affinity for CO2
(even at atmospheric levels of carbon dioxide, rubisco functions at only 35% if its catalytic capacity) - High concentration of O2 competes with CO2
-CO2 solubility in H2O is dominated by chemistry
Carboxysomes
High concentrations of rubisco contained in these symmetrical protein shells
Cyanobacteria concentrate rubisco in these
What occurs in the carboxysomes?
The high concentration of rubisco is coupled with the presence of carbonic anhydrase such that as bicarbonate ion diffuses in, it is rapidly converted into CO2 gas -> CO2 gas is captured by rubisco to be fixed into carbon`
Algae CCM
Rather than encasing their carbonic anhydrase in a protein shell, they use structures called pyrenoids where there is a starch layer that concentrates the carbonic anhydrase and rubisco in these structures
C4 plants
Spatial separation of steps- In C4 plants, carbon fixation occurs in different types of cells (mesophyll & bundle-sheath cells)
C3 plants take carbon dioxide and directly incorporates it into rubisco during the day.
CAM plants
Temporal separation of steps- In CAM plants, carbon fixation & Calvin Cycle occur in the same cell at different times
Solution concentration is determined by
Pressure of each gas (Partial Pressure)
Solubility is determined by
-The gas CO2>>O2>N2 -Temperature -Pressure (Henry's Law) -Salinity
As temperature increases…
Oxygen solubility decreases
As salinity increases…
gas composition decreases (including oxygen)
Gas availability decreases…
With decreasing pressure
Why do we need carrier proteins?
To overcome the limited solubility of oxygen in water. Proteins that contain cofactors (such as the heme group in hemoglobin) that have central metal ions
Hemoglobin uses __ to bind oxygen
Uses iron
Hemocyanin uses __ to bind oxygen
Two copper ions
Hemocyanin
Bind O2 between two copper ions. They float free in the ‘hemolymph”
- Used by mollusks and arthropods