BIOL 211 Midterm #3

Myococcus xanthus

A soil bacterium that secretes CaCO3 under specific conditions in a process called biomineralization.

Biomineralization

The natural process by which living organisms—including bacteria, fungi, plants, and animals—produce, deposit, or retain inorganic minerals.

Metabolites

Compounds produced by microorganisms through metabolic pathways (ex. antibiotics)

Bioprospecting

The process of looking for valuable metabolites in the natural environment.

What microorganism of industrial importance produces citric acid as a metabolite?

Aspergillus niger

When did Pfizer create a large scale production of citric acid from Aspergillus niger?

By 1929

When was it discovered that Aspergillus niger produced citric acid?

1917

Why is finding metabolites with industrial importance difficult?

They are produced in small amounts

Microorganisms tightly regulate their metabolism to prevent over production

What are two processes in which microbes regulate metabolism?

Induction and repression turning gene expression on and off

Primary metabolites

Immediate products of metabolism and are directly involved in the normal growth of an organism

Secondary metabolite

Organic compounds that are not directly required for basic growth, development, or reproduction

Synthesized near the end of growth or in a stationary phase

What are the steps to get a process from a laboratory flask to an industrial fermenter?

Laboratory flask - laboratory fermenter - pilot plant fermenter - industrial fermenter

Which genus of soil bacteria have proven to be especially adept at producing valuable antibiotics"?

Streptomyces

What are 5 examples of Streptomyces and closely related soil bacteria species that produce antibiotics?

erythromycin, streptomycin, tetracycline, vancomycin, and rifampin

What nutrients are used to commercially produce antibiotics in large fermenters?

Sugary-molasses substances with a combination of proteins and vitamins

What are two examples of steroid hormones?

Progesterone

Cortisone

How are steroid hormones commercially produced?

Providing an appropriate microorganism with a commonly available sterol compound that it converts into a medically valuable hormone

Bioconversion for hormones

Minor chemical alterations by specific bacterial or fungal species can result in the production of medically valuable steroid hormones at a small fraction of the cost and labor of obtaining the hormone from other sources.

What two example organisms are crucial for the conversion of cholesterol into estradiol?

Arthobacter simplex

Myobacterium

Define extremozymes and provide an example

Enzymes produced by microorganisms usually found in extreme enviornments

Ex. TAQ polymerase

Biopesticides

Proteins produced by specific bacteria that are toxic to insects

Give an example organism of a biopesticide

Bacillus thuringiensis and moth larvae

What organism is especially effective as a biopesticide against mosquito larvae?

Bacillus thuringiensis israelensis

Nanotechnology

Technology or the use of materials at an extremely small scale

Ex. bacteria and detecting humidity

Bioremediation

The use of living organisms to degrade environmental contaminants.

What organisms are the most promising for bioremediation?

Non-fastidious organisms

Ex. Pseudomonas species

What is special about spices in microbiology and history?

They contain antimicrobial compounds that can prevent food spoilage.

In depth, explain the four mechanisms commonly used to preserve foods

1) Chemical processing (explain)

2) Biological processing (explain)

3) Physical processing (explain)

4) Non-thermal processing (UV, irridation)

Volatile compounds

Chemicals that easily change from a liquid or solid into a gas and enter the air. Because they evaporate easily, they can often be detected by smell.

Zymomans mobilis

Gram - rod shaped bacteria known for efficiently converting sugars into ethanol

The Sumerians were among the first to brew beer.

Saccharomyces cerevisiae

“Brewer’s yeast”

Used in bread making

Describe the conditions of early earth

Very hot, very little oxygen, no ozone layer (intense UV radiation), very abundant in hydrogen gas

How does the atmosphere of early earth compare to the atmosphere today?

Early earth had a “reducing atmosphere” which made the synthesis of biological molecules common and set the stage for early life

Today the atmosphere is “oxidizing” - digestion is more likely

Other than hydrogen what molecules were common in early earth’s atmosphere?

Ammonia, methane and water vapor

What test determined that inorganic materials could be assembled and react to form biological molecules in the conditions of early earth?

Stanley Miller - had two chambers, one was the ocean the other was atmosphere

The ocean boiled so water vapor was released into the atmosphere

After, the molecules were subject to artificial lighting and days after numerous compounds had been synthesized including amino acids

What is another hypothesis on the origins of life other than Miller’s"?

That life began in deep ocean vents where heated water and minerals, along with reduced compounds provided an environment were life could arise.

Ribozymes

RNA molecules that can act as enzymes

What is the RNA world hypothesis?

That RNA was once the genetic material that early life relied on. DNA stores information but cannot catalyze the replication of the information, RNA can with the discovery of ribozymes.

Liposomes

Phospholipids exposed to water create a spherical shape, this was thought to have been the formation of the first cell when incorporated with self replicating RNA

What is hypothesized about the switch from an RNA to DNA world?

That the switch occurred before the divergence of the three kingdoms (bacteria, archea and eukarya) because all of these organisms use DNA

Stromatolites

Layered sedimentary rock created over time from microorganisms, specifically cyanobacteria

Through what process were chloroplasts and mitochondria “created”?

Endosymbiosis

Symbiosis

A relationship between two organisms that is mutually beneficial

How did mitochondria and chloroplasts evolve?

When aerobic prokaryotes developed a symbiotic relationship with primitive anaerobic eukaryotic cells

Later, some developed chloroplasts allowing them to perform photosynthesis

Did chloroplasts or mitochondria evolve first?

Mitochondria - present in all eukaryotic cells

It is believed that eukaryotes evolved from what type of ancestor?

An archean ancestor

Lokiarchaeota

An organism that provides an evolutionary bridge between archea and eukarya (gene analysis)

List the advantages to multicellularity

More cells = larger organisms (protection)

Better homeostasis

Less genetic mutations

More diverse, more complex, more biological processes can occur at once

What are the advantages of being unicellular?

More rapid replication

Can adapt quickly and populate in favorable conditions

What were most likely the earliest viruses?

Bacteriphages

What are the three hypothesis of how viruses evolved?

1) Regressive - gradually lost their genetic material and ability to live on their own without a host (ex. Rickettsia prove that they can lose genetic material)

2) Escaped-gene - fragments of nucleic acids escaped and developed the ability to duplicate independently of the cell (evidence came from transposons in retroviruses)

3) Coevolved with the rest of life - viruses evolved alongside cellular forms of life and ultimately developed into obligate parasites of these early cells

What were Charles Darwin’s two main points about evolution?

He proposed that the organisms alive today descended from ancestral species

He suggested a mechanism by which such descent could occur (natural selection)

What 5 things are needed for natural selection according to Charles Darwin?

1) Exponential reproduction

2) Limited resources

3) Genetic variation

4) Survival of the fittest

5) Gradual population change

Artificial selection

A process by which humans (not natural factors) choose which plants/animals reproduce based on favorable traits

What is a specific example of antibiotic resistance?

Vancomycin - many bacteria strains have adapted to change the amino acids used to structure their cell walls which prevent the antibiotic from binding to it destroy it - today it is useless against many bacteria

How does Vancomycin work in normal bacterial cells vs mutated ones?

Cell wall is made out of thick peptidoglycan with alternating NAG and NAM sugars, attached to each is a short amino acid chain that helps connect them

The antibiotic attaches the the amino acid chain which covers where the sugars attach and destorys cell wall construction (cell weakens and can burst)

In a mutated cell with resistance, the amino acid ending is changed and Vancomycin cannot bind to destroy the cell wall

Virulence

The capability of an organism to cause disease

How might virulence of an organism differ between populations?

Population exposed frequently to the pathogen - lower virulence

Population not exposed to the pathogen - high virulence when infected

Red Queen hypothesis

The continual selection pressure imposed by pathogens on their hosts favors genetic diversity in the host.

One prominent way to obtain genetic diversity is through sexual reproduction

Ecology

The study of how living things interact with each other and the environment

Trophic level

The position of an organism in the food chain

What happens to decomposers in cold/dry enviornments?

They are scarce or slow-growing

Why do plants grow slowly in dry/cold enviornments?

Due to reduced decomposer activity, fewer nutrients recycled to promote plant growth

Why does the biomass of producers way outweigh that of consumers?

Because 90% of energy between trophic levels is lost as heat, only 10% moves on (need more producers to continue the chain)

Biomass

The collective mass of any population or community in a particular location

Define microbial ecology

The study of microorganisms and how they interact with each other and their environment, as well as larger animals and hosts

What is the environment of microbes called?

Microenviroments - the area immediately surrounding a microorganism

How can microbes influence entire communities?

Through their activities in microenvironments - may influence the surrounding area and other organisms

Where do many microbes live?

In biofilms

Biofilms

Bacterial cells encased in a layer of polysaccharides (even fungi are found in biofilms)

What is one medical and one non-medical effect of biofilms?

Antibiotics struggle penetrate biofilms (resistance)

Corrode vessels of ships, increase drag and fuel costs

Biofilms in pipes block flow of materials

What is a good aspect of biofilms?

Bioremediation often relies on biofilms

What does soil harbor?

Rich microbial communities that are always changing due to geological and biological processes

What part of soil is the most nutrient dense?

Topsoil (because microorganism break down matter and release nutrients)

What is the pattern in organic material in layers of soil?

From top soil down matter gets less organic - less microbial activity takes place, oxygen levels also decrease

What is an adaptation of soil microorganisms to continue living even in dry conditions?

Endospore formation

What happens when soil becomes waterlogged?

Oxygen levels drop and fungi cannot grow as well, fungi also produce spores

What type of microorganisms are soil microbes?

Mesophiles (live in temps between 20-50 degrees C)

What soil microorganism can handle changes in pH?

Fungi - some grow exceptionally well in acidic environments because there is less competition from bacteria

Rhizosphere

The soil environment immediately surrounding the roots

What is an example of how the rhizosphere provides a mutualistic relationship between microorganisms and plants?

Biofilm formation on the roots of plants which allow microbes to gain amino acids and nutrients from the plant

In turn, the microbes convert minerals into a form that can be absorbed by the plant

What are mutually beneficial relationships between fungi and plants referred to as?

Mycorrhizal associations - often rely on plants as partners for phosphorus and nitrogen exchanges for sugars

Lichens

A symbiotic relationship between algae and fungi - produce organic materials via photosynthesis during short summer (in winter enter dormancy)

What are some of earth’s oldest inhabitants?

Linchens

Unlike in terrestrial environments where plants are the main producers, what are the main producers in water?

Microorganisms - mainly algae and cyanobacteria, make up phytoplankton

Thermocline

Sharp demarcation in temperature between the upper, warmer layers and deeper, colder layers in a body of water

What is the oxygen level like below the thermocline in a body of water?

Much lower because there is very little mixing between the different “layers”

How do oxygen levels change in a body of water depending on the season?

Typically, below the thermocline oxygen levels are much lower, but during autumn the surface cools quickly and sinks, mixing in with deeper water which provides the deeper levels with increased oxygen

How do lakes switch from anaerobic and aerobic during the year?

Lake bottom is anaerobic during the summer and aerobic during the winter

Oligotrophs

Organisms that can prosper and survive where others would starve

Eutrophs

Well nourished microorganism that require high nutrient environments

Where are most microorganisms found in moving water?

In biofilms attached to rocks

What causes algal blooms?

Water pollution, overflow of organic materials into bodies of water (increased phosphate)

Eutrophication

The addition of excess nutrients to aquatic ecosystems, along with the subsequent ecological problems

What zone of the ocean is most nutrient-rich?

Littoral zone (greenish-blue zone)

What zone of the ocean is poor in nutrients? What organisms live there?

Pelagic zone, archea live here (deep blue zone)

Barotolerant organisms

Pressure-adapted organisms (hydrostatic pressure)

What is a red-tide bloom and why does it occur?

A type of harmful algae bloom

Dinoflagelletes live in coastal waters in low concentrations but warm conditions can trigger rapid division, they release toxins that paralyze fish and other marine animals

Humans can be infected through nuerotoxins in the air or eating affected shellfish

Exobiology

The study of life beyond earth

Water found on mars

Europa orbiting Jupiter of interest

How do chemoautotrophic organisms gain energy?

They fix carbon dioxide into biological molecules (chemical energy)