Exam 3 Flashcards
Define science
Experimental, hypothesis-driven investigation of phenomena to elucidate (1) patterns in nature and (2) the processes governing the formation, maintenance, and changing of those patterns
What are the three parts of a scientific statement?
Cause -> Verb -> Effect
Where do Psychrophiles thrive?
Temperatures below 25*C
Where do Mesophiles thrive?
Temperatures between 20 and 35*C
Where do Thermophilies thrive?
Temperatures between 40 and 80*C (These were the bacteria present on early earth)
Where do Hyperthermophiles thrive?
Temperatures above 80*C
How can certain bacteria survive extreme heat?
Saturated fat membrane lipids, enzymes modified to be more stable at higher temperatures, and more GC content in DNA
Define Halotolerant organisms
do not mind salt
Define Halophilic organisms
thrive with 3% salt
Define Extreme Halophiles
thrive with 15+% (above saturation level of water)
Describe the ability of halophiles to counter salt
Salt pulls water out of the cell, halophiles counter this with organic solutes
Gram positive organisms tend to be more halotolerant
Define obligate aerobes
Must have O2 to use as terminal electron carrier
Define facultative aerobes
Can use O2 or anaerobic pathways
Define microaerophiles
Require O2 levels between 2-10%
Define obligate anaerobes
Killed by O2
Define tolerant anaerobes
Can survive O2, do not use it for energy
What tool can we use to determine the optimum oxygen levels for a particular microorganism? What would those look like for each organism?
Tubes with resazurin (pink=O2, clear=no) And thioglycate agar can be used to determine the optimum oxygen levels for a particular microorganism
Obligate Aerobe grow on top, Facultative Aerobe clusters near the top, Microaerophile have a high band, Obligate Anaerobes grow on the bottom, and Tolerant Aerobes grow evenly throughout
What are the components of Chlorophyll?
Porphyrin (rings), with magnesium and lipid side chains
What are the subtypes of Chlorophyll?
Chlorophyll a - plants, algae, cyanobacteria - red and blue
Chlorophyll b - plants, algae, cyanobacteria - red and blue
Bacteriochlorophyll a - infrared
What is the benefit of different absorption spectra among chlorophyll sub types?
Allows for more flexibility of light used, less competition.
What is the photosynthetic reaction center?
Complex of proteins and pigments that together execute photosynthesis.
Define Photophosphorylation
Conversion of light energy to chemical energy
What is a photoautotroph?
An autotroph that is also a phototroph. Most phototrophs are autotrophs.
How do phototrophs convert light energy into chemical energy?
Via proton motive force- use an electron transport chain and chemiosmosis
What are the two major classes of photophosphorylation?
Anoxygenic (cyclic photophospohrylation) and Oxygenic
What is the electron source in anoxygenic photosynthesis?
H2S and organic compounds
What is the electron source used for in anoxygenic photosynthesis?
to transfer between reaction center and electron transport chain (light to P870)
How is P870 as an electron donor?
Can be either a strong or a poor donor, depending on if it is excited by light energy
What is anoxygenic photosynthesis also known as? Why?
Cyclic photophosphorylation. The electrons travel in a cycle and the chlorophyll both receives and donates an electron.
Describe the process of Cylic photophosphorylation
Light excites the chlorophyll (P870, etc) → other chlorophylls → quinones → Q pool → cytochromes → back to chlorophyll
What is the goal of Cylic photophosphorylation?
Generates PMF (proton motor force) and recycles electrons
What generates the PMF in Cyclic photophosphorylation?
Electron transfer from quinones to cytochromes
What can Quinones carry? What can cytochromes carry?
Quinones carry both H+/e-, cytochromes carry only e-
What type of organisms employ anoxygenic photosynthesis?
Purple non-sulfur, purple sulfur, and green sulfur bacteria
What is the electron source in oxygenic photosynthesis?
H2O
What types of organisms employ Oxygenic photosynthesis?
Plants, algae and cyanobacteria
What are the mechanisms behind oxygenic photosynthesis?
2 distinct, interconnected photosystems (I and II) -> non-cyclic
Differentiate between photosystem I and II
Photosystem II (P680) generates ATP, Photosystem I (P700) generates NADPH
Describe the “Z” scheme of electron flow employed by oxygenic photosynthesis
Starts at Photosystem II (P680)
Electrons go from H2O → P680 → Pheophytin → Quinone → Cytochrome bf → Plastocyanin
Plastocyanin transfers electrons to Photosystem I (P700).
P700 → Carrier → reduces Ferredoxin → Flavoprotein→ reduce NAD(P)+
Ferredoxin can also donate back to the Cytochrome bf to create the cyclic electron flow
What type of photosynthesis do cyanobacteria employ?
Oxygenic
What type of pigments does Cyanobacteria have?
Chlorophyll a and phycobilins
Describe the types of Phycobilins. How are they arranged and what is this arrangement called?
Phycobilins = phycoerythrin (blue) and phycocyanin (red)
Arranged in antenna like complexes - phycobilisomes to help gather light
Composition influenced by light
Cyanobacteria are responsible for what percent of CO2 fixation in aquatic environments?
50%
Describe the environment that cyanobacteria normally dwell in
Cyanobacteria are widely dispersed (fresh water, marine water, hot springs, deserts). They are found on and in rocks (they have a role in erosion protection)
What is the role of nitrogen fixation for cyanobacteria?
Many cyanobacteria employ nitrogen fixation, often in symbiosis with plants.
Define Scytonemin
Pigment that protects Cyanobacteria from UV damage
Define Cyanophycin
Only known nitrogen storage molecule, a polymer of aspartic acid and arginine
What are the negative qualities of Cyanobacteria?
Nuisance blooms in freshwater, produce potentially lethal toxins, odor and taste problems in drinking water.
Describe the use of temporal separation by certain species of Cyanobacteria
can fix N2 in presence of O2 using temporal separation, fix N2 at night and photosynthesize at day
oxygen damages the N2 generating mechanisms
What is a baeocyte?
a reproductive cell that grows to a large size while replicating its DNA over and over until it quickly splits into many cells
What does it mean to divide in a single plane?
Filaments are chains of cells that form when the plane division is fixed resulting in a 1D colony (grow in strings, may also mean only one direction)
What is a heterocyst?
larger thick walled cells found in the filaments of certain cyanobacteria that fix nitrogen alongside vegetative cells that undergo photosynthesis
What are subcultures? What can they allow?
Subcultures are where samples are taken from a saturated culture and placed into a new environment with more resources, can allow two populations of bacteria to diverge
Define Pan Genome
All genes present in all populations of a species
Individuals can survive loss of function if:
if others in the population still provide that function
What are the four ways Diversity can arise?
Random mutations,
Selective Pressures/Natural Selection,
Genetic Drift (Different populations arising from sampling variation),
Horizontal gene Transfer (Transformation, conjugation, or transduction)
How do mutations arise?
Spontaneously, not as a physiological response
How do you determine the minimum number of generations between two species and their most recent common ancestor?
Fewer differences → more recent common ancestor # of differences / 2 = min # of generations (one mutation per, no back mutations)
Describe Chronometers/Molecular Clocks
A technique that uses the mutation rate of nucleic acids or proteins to figure out the time since divergence between the two organisms
What do all organisms have that serve as scaffolding for their ribosomes? What does this mean?
rRNA.
Since it is serving the same function, it will have many conserved regions.
Lets us know about the 3 domains of life
How are Phylogenetic trees created?
Align Sequences → Produce a Distance Matrix (differences from each organism to the others) → Create A Tree
Enzymes that help bacteria survive oxygen
superoxide dismutase, catalase, and peroxidase
Winogradsky column
Top has high levels of oxygen and low levels of sulfur, bottom is opp
Cyanobacteria → Purple Nonsulfur Bacteria → Purple Sulfur Bacteria → Green Sulfur Bacteria → (Sulfate producers)
What are akinetes?
Enveloped, thick-walled dormant cell that is resistant to cold and desiccation
resting spores
What are hormogonia?
a portion of filament in some cyanobacteria that becomes detached and reproduces by cell division
fragmented filaments
Describe the flucuation experiment by delbruck and luria that demostrated that mutations occur spontaneously, not as a result of selective pressure
Resistance is random and passed to offspring, not a physiological response to a bactericide
One large flask that is plated 20 times will produce similar numbers of resistant bacteria
One large flask that is subcultured into 20 different cultures will produce a varied number of resistant bacteria per plate
Why is 16S rRNA used to study evolution?
In every living thing
Made of conserved sequences (both broad and specific) and variable sequences
Conserved sequences are used to design primers to amplify DNA so it can be sequenced and compared with others to create phylogenetic trees
The variable sequences = areas where changes can accumulate
Very large sequence, lot of room for changes t
Describe bacterial growth with a single sugar
Lag Phase → Log Phase → Stationary (→ Death)
Describe diauxic bacterial growth
Lag → Log → Stationary → Slower Log Phase → Stationary (→ Death)
First stationary phase -> 𝜷-galactosidase is produced, concentration
increases before leveling off
Concentration of first sugar remains steady until first log phase
Concentration of the second sugar remains steady until the second log phase
How can the concentration of sugar enzymes be monitored?
using substrates that produce a color when cleaved by 𝜷-galactosidase
How can you stop the production of an enzyme?
Turn of transcription, turn off translation, destroy with proteases, do not activate with phosphorylation or methylation
