Microbiology Exam 3 CH 15, 21, 22, 23

Catabolic reaction

Break down complex biomolecules

Anabolic reaction

Build complex biomolecules

Amphibolic reaction

Participate in anabolic or catabolic reactions - cell regulation of enzymes

Biosynthesis (anabolism) requirements

Essential elements

Reduction

Energy

Essential elements

Energy

Coupling reaction to ATP hydrolysis, NADPH oxidation, or ion flow down a concentration gradient

Control of energy costs

Regulation

Genome loss/cooperation

Competition and predation

Fixation

Covalent incorporation of small molecules into larger biochemical material

Autotroph carbon use

CO2 is used as their sole or primary source

Requires lots of energy

4

Number of CO2 pathways in microbes

Reductive Pentose Phosphate Cycle (Calvin-Benson Cycle)

Preformed by oxygenic phototrophic bacteria, chloroplasts, Faculative anaerobes purple bacteria, and lithotrophic bacteria

Reductive Pentose Phosphate Cycle (Calvin-Benson Cycle)

Primary carbon fixation pathway for plants, algae, and photosynthetic bacteria

CO2 is reduced to form carbohydrates

CO2 + ribulose → RuBisCO

RuBisCO → 2 molecules of 3-PGA

3-PGA + ATP/NADPH → G3P

RuBisCO

enzyme catalyzes the first step of the reductive pentose phosphate cycle?

the three phases of the Calvin cycle?

1. Carbon fixation
2. Reduction
3. Regeneration of RuBP

Rubisco

Catalyzes the condensation of CO2 to ribulose 1,5-bisphosphate and the splitting of the unstable 6C intermediate into two 3C PGA molecules

Carboxysomes

protein-bound microcompartments found in many cyanobacteria and chemoautotrophic bacteria that concentrate CO₂ around RuBisCO to improve carbon fixation

RuBisCO and carbonic anhydrase

key enzymes are found inside carboxysomes

Carboxysomes function

increase the local concentration of CO₂ around RuBisCO, improving carbon fixation efficiency and reducing photorespiration

photorespiration

A wasteful process that occurs when RuBisCO binds O₂ instead of CO₂, reducing carbon fixation efficiency.

Reverse TCA cycle

a carbon fixation pathway used by some bacteria and archaea that fixes CO₂ into organic molecules by running the citric acid (TCA) cycle in reverse.

anaerobic and microaerophilic bacteria and archaea

microorganisms that use the Reverse TCA Cycle

Reverse TCA Cycle importance

It allows certain microorganisms to grow autotrophically by using CO₂ as their carbon source and inorganic chemicals as energy sources

Nitrogen Fixation

the process of converting atmospheric nitrogen gas (N₂) into ammonia (NH₃), a form of nitrogen that cells can use to make amino acids, proteins, and nucleic acids

Nitrogen assimilation

the process by which organisms incorporate ammonia (NH₃), ammonium (NH₄⁺), nitrate (NO₃⁻), or nitrite (NO₂⁻) into organic molecules such as amino acids and nucleotides.

How nitrogen assimilation differs from nitrogen fixation

• Nitrogen fixation: converts N₂ → NH₃

• Nitrogen assimilation: converts NH₃, NO₃⁻, or NO₂⁻ → organic nitrogen compounds

Nitrigenase

the enzyme complex responsible for nitrogen fixation, converting atmospheric nitrogen gas (N₂) into ammonia (NH₃)

28 ATP per N2

Amount of ATP consumed in nitrogen fixation

Oxygen's effect on nitrogenase

inhibits and can inactivate nitrogenase, so nitrogen-fixing organisms must protect the enzyme from exposure to O₂

Strategies for oxygenic environment

Protective Proteins

Temporal separation of photosynthesis

Specialized cellsà heterocysts

Barber-Bosch process

an industrial process that converts atmospheric nitrogen gas (N₂) and hydrogen gas (H₂) into ammonia (NH₃).

Conditions for Barber-Bosch Process

High temperature (~450°C), high pressure (~200 atm), and an iron catalyst.

Ammonia (NH₃)

the main product of the Haber-Bosch process

Microbial ecology

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.

Two ways to study microbes in environment

Culture based methods

Culture independent methods

Culture based methods

Isolate an organism using growth medium

Study its characteristics, capabilities, genomic content

Problems:

0.1-1% of all bacteria are currently culturable

The GREAT PLATE ANOMALY

The GREAT PLATE ANOMALY

the observation that only a small percentage of microorganisms seen in natural environments can be grown on laboratory culture media. Less than 1% can be cultured

Culture independent methods

techniques used to study microorganisms without growing them in the laboratory. They analyze microbial DNA, RNA, proteins, or other cellular components directly from environmental samples.

Culture independent method examples

• DNA sequencing

• 16S rRNA gene analysis

• Metagenomics

• PCR (Polymerase Chain Reaction)

• Fluorescence in situ hybridization (FISH)

16S rRNA gene based analysis

a culture-independent method that identifies and classifies bacteria by analyzing the gene that encodes the 16S ribosomal RNA (rRNA) component of the small ribosomal subunit

The 16S rRNA gene is found in all bacteria and contains both conserved and variable regions, making it useful for identification and classification.

Metagenomics

the analysis of all genetic material recovered directly from an environmental sample, allowing scientists to study entire microbial communities.

Contigs

continuous DNA sequences formed by assembling overlapping DNA fragments obtained during genome sequencing. They help scientists reconstruct the DNA sequence of an organism's genome from many smaller sequence read and help identify organisms and analyze microbial communities.

Scaffolds

larger DNA assemblies made by linking together contigs in the correct order and orientation, even if gaps remain between them.They help researchers reconstruct larger portions of a genome when complete continuous sequences cannot be obtained.

Functional annotation

the process of identifying the biological function of genes, proteins, or DNA sequences found during genome sequencing.

Provides:

Enzyme function

Metabolic pathways

Antibiotic resistance genes

Virulence factors

Cellular processes

the difference between structural and functional annotation

• Structural annotation: Identifies genes and genomic features.

• Functional annotation: Predicts the biological role of those genes

Transcriptomics

the study of all RNA molecules (the transcriptome) produced by a cell, organism, or microbial community at a specific time and under specific conditions.It reveals which genes are actively being expressed and how cells respond to environmental conditions.

transcriptome

the complete set of RNA transcripts (especially mRNA) produced from the genome at a given time

FISH

a culture-independent technique that uses fluorescently labeled DNA or RNA probes to detect and identify specific microorganisms directly in a sample.

Biogeochemistry

the study of how biological, geological, and chemical processes interact to cycle elements through the environment.

Major elements recycled

C, O,

N, H, P, S

Minor (trace) elements

Fe, Mg, Cu, Zn

Box model

simplified diagram used to represent the storage and movement of matter (such as carbon, nitrogen, or phosphorus) between different reservoirs, called boxes.

What the boxes represent in a box model

• Atmosphere

• Oceans

• Soil

• Sediments

• Living organisms

What the arrows represent in a box modeL

the fluxes, or rates at which materials move between reservoirs.

Residence time

the average amount of time an element or molecule remains in a particular reservoir (box) before leaving it.

Amount in Reservoir ÷ Rate of Output

Steady state

a condition in which the amount of a substance in a reservoir remains constant because the rate of input equals the rate of output.

The reservoir size remains constant over time, even though materials are continuously entering and leaving.

Carbon cycle

the movement of carbon between the atmosphere, oceans, soil, rocks, and living organisms through biological, chemical, and geological processes.

50%, 1%

Phytoplankton accounts for this percentage of global photosynthesis and this about of global plant mass

Temperature

Growth is dependent on what

Lower pH

More CO2

Coccolithophores

microscopic marine algae (phytoplankton) that produce calcium carbonate (CaCO₃) plates called coccoliths. They remove CO₂ from seawater through photosynthesis and incorporate carbon into both organic matter and calcium carbonate shells.

Coccoliths

protective plates made of calcium carbonate (CaCO₃) that surround coccolithophore cells.

Nitrogen cycle

the movement and transformation of nitrogen between the atmosphere, soil, water, and living organisms through biological and chemical processes.

Eutrophication

the excessive enrichment of water with nutrients, especially nitrogen and phosphorus, leading to rapid growth of algae and aquatic microorganisms.

Eutrophication and oxygen depletion

When algae die, decomposer bacteria break them down and consume large amounts of dissolved oxygen, creating hypoxic (low-oxygen) conditions.

Major effects of eutrophication

• Algal blooms

• Oxygen depletion

• Fish kills

• Reduced water quality

• Loss of biodiversity

Iron cycle

the movement and transformation of iron between different oxidation states, primarily ferrous iron (Fe²⁺) and ferric iron (Fe³⁺), through biological and chemical processes in the environment.

Microbiome

the community of microorganisms (bacteria, archaea, fungi, viruses, and protists) and their genetic material living in a particular environment.

Human microbiome project

a research initiative launched by the National Institutes of Health (NIH) to identify and characterize the microorganisms that live on and in the human body. They used

• 16S rRNA gene sequencing

• Metagenomics

• Culture-independent methods

HMP phase one findings

1. Healthy humans harbor diverse microbial communities at different body sites.

2. Different body sites have distinct microbiomes (gut, mouth, skin, nose, and vagina each contain different microorganisms).

3. Microbiomes vary greatly between individuals, but healthy people can still be healthy despite these differences.

4. Microbial genes greatly outnumber human genes, providing many additional metabolic capabilities.

5. The microbiome plays important roles in digestion, metabolism, immune function, and protection against pathogens

HMP phase two findings

Changes in the microbiome were linked to changes in human health and disease, showing that both microbial activity and host responses are important in disease development.

What are they doing and how do they affect health?

Microbe acquisition

the process by which an organism obtains microorganisms that become part of its microbiome.

Hygiene hypothesis

reduced exposure to microorganisms during early childhood may increase the risk of developing allergies, asthma, and autoimmune diseases because the immune system does not receive enough stimulation to develop properly.

Skin

Difficult to colonize

10^12 microbes in moist areas

Mostly gram positive

Oral and nasal cavities

• Initially infant's mouth is colonized with:

• Nonpathogenic Neisseria (Gram-negative cocci)

• Streptococcus, Lactobacillus (Gram-positive rods)

• As teeth emerge, other different bacteria start growing:

• Prevotella; Fusobacterium: between gums and teeth

• Streptococcus mutans: tooth enamel

• Nasopharynx and oropharynx are populated b taphylococcus aureus and S. epidermidis

• Also by harmless streptococci

Respiratory tract

• The lungs and trachea were previously thought to be sterile.

• The ciliated mucous lining of the trachea, bronchi, and bronchioles makes up the mucociliary escalator.

• Sweeps foreign particles up and out of the lung

Mucociliary escalator

a defense mechanism of the respiratory tract in which mucus traps microbes and particles, and cilia move the mucus upward toward the throat where it can be swallowed or expelled.

Stomach

• Stomach has very high acidity.

• Few microbes survive.

• Helicobacter pylori

• Survives at pH 1

• Burrows into protective mucus

• Causes gastric ulcers

• 

Hypochlorydia

Decrease in stomach acidity

Hypochlorydia cause

malnourishment

Intestine

• The intestine contains 101'-1013 bacteria/gm of feces.

• Ratio of 1,000 anaerobes: 1 facultative organism

• Infant intestines are initially colonized by large numbers of

E. coli that quickly generate a reducing environment.

• This supports growths of strict anaerobic species-mainly Bifidobacterium, Bacteroides, and Clostridium.

• Approximately 1500 bacterial species and a few methanogenic archaea comprise the intestinal microbiome.

Microbe benefit

• Protect against pathogens (competitive exclusion)

• Aid in digestion

• Produce vitamins (such as vitamin K and some B vitamins)

• Help develop and regulate the immune system

• Contribute to normal body functions

Microbia harm

• Cause opportunistic infections

• Become harmful if it enters the wrong body site

• Contribute to dysbiosis (microbial imbalance)

• Cause disease in immunocompromised individuals

Containment breaches

The accidental penetration of certain organisms beyond a site of colonization can cause infections.

Bacteremia

the presence of bacteria in the bloodstream

Disrupted balance

Emotional stress, a change in diet, or antibiotic

therapy can alter gut microbiome balance.

The resultant dysbiosis can lead to poor digestion or

inflammatory bowel disease (IBD).

Dysbiosis

imbalance or disruption of the normal microbiota that can negatively affect health.

Gnotobiotic mice

laboratory mice in which all microorganisms are known. They are either germ-free (contain no microorganisms) or colonized with a defined set of known microbes.

Obesity and Dysbiosis

Microbiota can influence obesity in two major ways.

- Harvesting of energy from ingested foods

- Triggering of intestinal inflammation

§ The metabolic versatility of intestinal microbes allows

them to digest many foods that we cannot.

- In the process, these microbes produce short-chain

fatty acids (SCFAs) that our cells use in many ways.

- Numerous investigations suggest that the amounts

and ratios of these SCFAs influence obesity.

Probiotic

foods or supplements that contain

live microorganisms intended to maintain or

improve the "good" bacteria (normal microflora) in

the body.

Prebiotic

foods (typically high-fiber foods)

that act as food for human microflora.

Fecal transplantation

• Fights diseases like recurrent C. difficile infections.

• Approximately 90% success rate!

BOD

the amount of dissolved oxygen required by microorganisms to break down organic matter in water.

a higher BOD.

A higher concentration of organic substances in an environment leads to

the oxygen minimum zone

Which zone is generated when costal sediments bring nutrients to the middle layers of the ocean, sandwiched between the upper and lower oxygenated layers?

photosynthesis

Which of the following decreases the amount of carbon dioxide in the atmosphere?

secondary

Microbes participate in which step of wastewater treatment?

They depend on microbes to remove nitrogen and carbon.

What do wastewater treatment plants have in common with wetland filtration (purification)?

the atmosphere.

The predominant source of nitrogen on Earth is

the Haber process

Which of these is involved in commercial chemical fertilizer production?

iron

Which of the following is the most limiting element for marine phytoplankton?