ME&D Midterm 1

What are some common misconceptions about evolution?

That it is a hypothesis and not a theory. It uses facts to form an explaination

What are the best estimates for the age of the Universe and of planet Earth?

14 billion years; 4.5 Billion years

How was Earth different in its early years compared to now?

High levels of CO2, high temperatures, water, volcanic gases

What environmental conditions were thought to be necessary for the evolution of life on Earth?

Entry of essential elements (CHONPS), continual energy source, temp allowing for water formation

What is meant by the “emergent properties” of organic compounds?

unique chemistry that results from increasing complexity spontaneously under the right conditions

Describe the Miller-Urey experiments and what chemicals were produced

They tried to recreate early earth’s atmosphere, and amino acids/ nucelotide bases were produced.

What was likely wrong about the Miller-Urey concept of the early Earth’s atmosphere?

They used methane instead of CO2 which decreased the likeliness.

Give an example of a hypothesis about the evolution of life on Earth

RNA world, deep sea vents (where life originated), stromatolites (layers of solidified microbes).

Differentiate between the scientific terms hypothesis and theory

hypothesis is testible, theory uses facts and other information to generate an explanation and organize laws

What is an example of a self-replicating molecule that can catalyze reactions?

RNA

What is the oldest known evidence of life on Earth? What evidence indicates its biotic origin?

Stromatolites (microbial mats). Contain hopanoids and C13

Name the 3 major time periods in the Precambrian Era. What events distinguished each of these time periods?

Hadean: No life on earth

Archean: First recorded life on earth

Proterozoic: Oxygenation of the atmosphere and expansion of microbial life.

Give examples of natural selection, and of artificial selection, that Charles Darwin studied in his development of the Theory of Evolution

The galapagos finches, wolves/dogs

What are some characteristics of the hypothesized Last Universal Common Ancestor (LUCA) for all forms of life on Earth

Genetic code based on DNA, RNA intermediates, proteins, cell duplication and division

What system of organizing life on Earth was developed by the Swedish scientist Carl Linnaeus?

Binomial nomenclature and the three kingdoms

Describe the concept proposed in Lamarckian evolution

As the environment changes, the organism changes too (i.e giraffes necks get longer in their lifetime)

What are the five components to Charles Darwin’s Theory of Evolution?

1. Populations have variability

2. If populations are unchecked, they will grow exponentially

3. Some species are more successful than others

4. Organisms that can survive longer can reproduce more and leave more offspring

5. Over time, heritable changes will lead to one species becoming another

Define a monophyletic group of organisms

A common ancestor and all of it’s descendants

What is a molecular clock?

Temporal information that is contained in DNA sequences that can be used to measure genetic changes over time

Why is the 16S rRNA gene the most commonly used sequence for molecular phylogenetic analyses?

The small subunit rRNA is present in all domains of life, and has a conserved sequence, is likely not going to be HGT-ed.

Why are there specific domains that are highly conserved in the sequence of the 16S rRNA gene?

Any changes to the domains will be detrimental

Describe the process of generating a phylogenetic tree

line up sequences, modify values of genetic differences, compare using statistics

What is a bootstrap value?

The percentage of the time that a branching order appears after many calculations

Based on what evidence did Carl Woese propose the domain Archaea? What are the 3 Domains of life?

used rRNA to reclassify the tree of life into bacteria, archea, and eukarya

What does a rRNA-based tree that shows vertical inheritance not reveal about evolution that can sometimes be observed with protein-coding genes?

transmission can be horizontal too, genes can be passed between species

Define ortholog and paralog

Ortholog: Genes that have the same function but are from different species

Paralog: Genes that have a different functions have homology

How did the authors of “Insights into the phylogeny and coding potential of microbial dark matter” generate genome sequences from novel bacteria?

isolation of individual cells and whole genome sequencing of bacteria that can’t be cultured.

What is a Superphylum of bacteria? Give an example of a bacterial Superphylum

Multiple phyla with a common ancestor. Terrabacteria, Cyanobacteria

How were the bacteria in the Candidate Phya Radiation discovered?

They are too small to get filtered out, so theyre genomes were isolated from entire genomic communities

How is a culture-dependent approach to study bacteria a biased method?

there are many organisms that cannot be cultured, so genes should be looked at too

In which kind of environment do you find many prokaryotic species that are at the root of the Tree of Life?

Thermophiles/ extremophiles

Describe the metabolism and habitat of species within the phylum Aquifex

Fix CO2 and get energy from inorganic chemical sources. Live in hot anaerobic environments

From what source have a large % of genes been laterally transferred to the genome of Aquifex species?

HGT

Describe the metabolism and habitat of species within the phylum Thermus-Deinococcus

Hot, heterotrophs,

What is an example of a thermal-stable enzyme isolated from a member of the phylum Thermus-Deinococcus? For what purpose is this enzyme used?

Taq polymerase, PCR

Give an example of a highly radiation-resistant bacterium (genus and species) that is in the phylum Thermus-Deinococcus? Indicate three ways by which this bacterium can resistant high radiation levels.

Deinococus radiodurans

1. multiple copies of DNA

2. Rapid DNA reapir system

3. Antioxidant enzymes

What does the electron transport system generate?

ATP/ energy

How is ATP generated in a cell?

Proton motive force

Energy yielding reactions involve movement of electrons from a

reduced state to an oxidated state

Define organotrophy, lithotrophy, and phototrophy

Organitrophy: organic electron donors and either electron acceptors

Lithotrophy: inorganic electron donors and either electron acceptors

Phototrophy: light capture and splitting of H2S/H2O

Define autotrophy and heterotrophy

Autotrophy: Getting carbon from yourself

Heterotrophy: Getting carbon from other sources

What is the reduction potential?

tendency of a molecule to accept electrons

What are some alternatives to oxygen as a TEA?

Nitrate, sulfate

Give some examples of fermentation products important in foods/beverages

Acetone, acetic acid, ethanol

What is an electron donor and a TEA used by methanogens?

CO2 is the TEA and methane is the donor

What are starting & ending compounds in nitrogen oxidation? sulfur oxidation?

Nitrate to N gas

Sulfate to H2S gas

The use of molecular hydrogen by microbes could help in what applied way?

bioremeiation of contaminated water

Describe the process by which bacteriorhodopsins yield energy from sunlight

A photon gets absorbed by retinal and then generates A PMF

In what microbe and in which habitat would you find bacteriorhodopsins?

Archea, in halophilic environments

What compound absorbs light energy in photosynthesis?

chlorophyll

What are the different components of a Photolytic electron transport system?

Antenna system, reaction center complex (PS), electron transport system, energy carriers

What is made more efficient by thylakoid membranes?

light aborption

What is a source of electrons for Photosystem I? Photosystem II? Z pathway?

PSI: H2S

PSII: Bacteriochlorophyll

Z: Water

What form of energy is produced by PSI?

NADPH

What form of energy is generated from photosystem II?

ATP

What is the energy product of the Z pathway?

ATP and NADPH

For each photosystem type, name a microbe that uses this for photosynthesis

PSI: Green sulfur bacteria

PSII: Nonsulfur bacteria

Z Pathway:cyanobacteria

What is a unique photosynthetic structure present in Chloroflexi species?

Z pathway

In the Z pathway which photosystem results in the production of O2?

PSII

What protein unites the 2 photosystems in the Z pathway?

Plastocyanin

What is a functional difference between the chlorophyll types found in photosynthetic bacteria? What selective advantage could this provide bacteria?

What light they can absorb, allows bacteria to coexist and absorb different light

What are the light and dark reactions?

Light is photosynthesis, dark is CBB

What wavelengths of light do the Cyanobacteria absorb

400nm

List the 6 bacterial phyla that include some phototrophic members

Firmicutes, Chloroflexi, Chlorobi, Proteobacteria, Cyanobacteria, Acidobacteria

What are the 3 essential stages of the Calvin cycle?

Fixation: CO2 to 3PG using RuBisCO

Reduction: 3PG to G3P

Regeneration: RuBP remade

The earliest stromatolites formed on Earth were likely formed by _______

anoxigenic photosynthetic bacteria (cyanobacteria)

How were Cyanobacteria previously described? What Superphylum are they in?

Anoxygenic photosynthetic bacteria, Terrabacteria

Name 2 internal structures within Cyanobacteria, and describe their shape and function

Carboxysomes: helps with carbon fixation

Heterocysts: Nitrogen fixation

What are some environmental contributions and problems associated with the growth of Cyanobacteria?

They can cause toxin production in the water, cause off taste in the water

Describe the 3 differentiated cell types of some Cyanobacteria and indicate any phenotype associated with each cell type

1. Vegetative: Actively growing

2. Heterocyst: Specialized N fixation cells

3. Akinete: Thick walled dormant cell (capsule)

Subsection 1 cyanobacteria

Unicellular and coccoid, no heterocysts or akinetes

Subsection II cyanobacteria

Form colonial structures, no heterocysts/akinetes

Subsection III cyanobacteria

Filamentous cyanobacteria, no akinetes/heterocysts

Subsection IV

Multicellular filaments that have akinetes and heterocysts

Subsection V cyanobacteria

More complex branching, heterocysts and akinetes

How is cellular differentiation regulated in some Cyanobacteria species?

HetR protein helps with heterocyst formation

What is the evidence for the Cyanobacterial origin of the chloroplast?

Chloroplasts have their own DNA, there are genome regions that resemble bacteria, ribosomes are similar, photosynthetic pigments simolar

Give three examples of DNA plasticity.

Regulation of gene expression, mutation, gene transfer

Why do some genes have different mutation rates than other genes?

High selective pressure

transition mutation

purine to purine / py to py

Transversion mutation

Purine to pyrimidine

Give three examples of mutagens. For each of your examples, what is the mechanism by which the mutagen damages DNA?

Chemical agents: replace nucleotides

Radiation: Dimers

xRays: break the DNA

Describe the Ames test for determining if a chemical is a mutagen. Why might a chemical giving a positive Ames test not actually cause mutations in humans?

Grown of a plate where if many colonies grow, it is a mutagen. Sometimes the dose is so high needed to be dangerous

What are the 3 different mechanisms of horizontal genetic transfer?

conjugation (pili), transformation (environmental), transduction (phage)

For transformation, describe each step in the process

Introduction, uptake, and expression of foreign DNA

What are the contstraints of transformation

some species are not compentent to take up DNA, some bacteria have species recogition sequences that help with uptake of DNA

Describe the experiments conducted by Dr. Frederick Griffith that first demonstrated transformation

Modifed strains of bacteria to have or not have capsules, then killed off the encapsulated ones. The remaining cells expressed encapsulation.

Give an example of lysogenic conversion, listing the bacterial species, its phage, the gene product produced in the bacteria and the disease that is caused

Phages that are able to increase the virulence of a bacterial host.

S. pyogenes, scarlet fever

In the specific case of Vibrio cholerae, what is the toxin that induces the disease cholera and where are the genes that encode the toxin present?

Cholera toxin, found in the CTX phage

Describe one mechanism by which bacteria can resist the effects of an antibiotic

congjugation, HGT

What is the only form of gene transfer where the donor survives?

Conjugation- direct contact between cells

Give an example of inter-domain horizontal genetic transfer

Mitochondrial/ chroloplast endosymbiosis

What is an example of interdomain lateral gene transfer?

Wolbachia infect the reproduction system of many insects

What is the eukaryotic definition of a species? Why is this not relevant to prokaryotes?

individuals that are capable of interbreeding, prokaryotes reproduce asexually

Give an example of three characteristics of a microorganism that could be used to develop a dichotomous key. Why is this not 100% reliable as a method of identifying microorganisms?

Gram stain, width of cell, etc. Based of morphology

Determination of the average nucleotide identity (ANI) is now a primary method used to determine whether 2 microorganisms are the same species. The ANI is determined for _______ genes and a value greater than or equal to ___% indicates that 2 microorganisms are the same species.

orthologous genes, 95%

What is the class and Phylum of bacteria in which the closest known relative of mitochondria is most closely related to

Rikettsailes

What genus of bacteria, known to be intracellular pathogens, were identified as being the closest living relatives to mitochondria?

Rikettsia prowazekki

How were bacteria within the Oceanic Mitochondrial Affiliate Clade discovered to be the closest relatives of mitochondria so far?

through phylogenetic and genetic studies of marine bacteria