Lecture 1.2: Microbial Physiology and Metabolism

What are the six macroelements required as components of carbohydrates, lipids, proteins, and nucleic acids?

$C$, $O$, $N$, $H$, $S$, and $P$

Which four macroelements exist as cations and function as enzyme cofactors?

$K$, $Ca$, $Mg$, and $Fe$

List the trace elements required in smaller amounts by microorganisms.

$Mn$, $Zn$, $Co$, $Mb$, $Ni$, and $Cu$

What is the primary role of trace elements in microbial physiology?

They are mainly needed as cofactors of enzymes

What is the energy source for Phototrophs?

Light

What is the energy source for Chemotrophs?

Oxidation of organic or inorganic compounds

Why do organisms need sources of reducing equivalents?

For the electron transport chain, oxidation-reduction reactions, and biosynthesis in autotrophs

What is the source of reducing equivalents for Lithotrophs?

Reduced inorganic molecules

What is the source of reducing equivalents for Organotrophs?

Organic molecules

What is the main or only source of carbon for Autotrophs?

$$CO_2$$

What is the carbon source for Heterotrophs?

Reduced, preformed organic molecules

Define the energy, electron, and carbon source for Photolithotrophic autotrophy.

Light energy, inorganic electron donor, and $CO_2$ carbon source

Define the energy, electron, and carbon source for Photoorganotrophic heterotrophy.

Light energy, organic electron donor, and organic carbon source

Define the energy, electron, and carbon source for Chemolithotrophic autotrophy.

Chemical energy source, inorganic electron donor, and $CO_2$ carbon source

Define the energy, electron, and carbon source for Chemoorganotrophic heterotrophy.

Chemical energy source, organic electron donor, and organic carbon source

Which nutritional type includes all pathogens?

Chemoorganotrophic heterotrophy

What are the common sources of nitrogen ($N$ source) for microbes?

Amino acids, ammonia, nitrate ($NO_3^-$) converted to ammonia, and $N_2$

What is the inorganic source of phosphorus ($P$ source)?

Inorganic phosphate ($PO_4^{3-}$)

What are the common sources of sulfur ($S$ source)?

Sulfate ($SO_4^{2-}$) and reduced sulfur (e.g., cysteine)

What are growth factors?

Small organic molecules like amino acids, purines, pyrimidines, and vitamins

How do strict aerobes perform respiration?

They perform aerobic respiration only

What is the final electron acceptor for strict aerobes and what is it reduced to?

Oxygen ($O_2$), which is reduced to $H_2O$

What are the two potential final electron acceptors for strict anaerobes?

An inorganic molecule (for anaerobic respiration) or an organic molecule (for fermentation)

Provide two examples of inorganic final electron acceptors used in anaerobic respiration.

Nitrate ($NO_3^-$) and $Fe^{3+}$

What are two examples of final electron acceptors in fermentation and their reduced products?

Pyruvate (reduced to lactate) and acetyl-CoA (reduced to ethanol)

What describes the metabolic capability of facultative anaerobes?

They can perform both respiration and fermentation

Which group of bacteria are considered the most medically relevant?

Facultative anaerobes

In the E. coli respiratory chain, which branch is active during low aeration or the stationary phase?

Cytochrome d branch

Name the components shown within the Cytochrome d branch of E. coli.

$b558$, $595$, and $d$

In the E. coli respiratory chain, which branch is active during high aeration or the log phase?

Cytochrome o branch

Name the components shown within the Cytochrome o branch of E. coli.

$b582$, $o$, and $Cu^{2+}$

Where is the NADH dehydrogenase located in the E. coli respiratory chain diagram?

Inside the cell

What is the mobile electron carrier between NADH dehydrogenase and the cytochrome branches in the E. coli diagram?

Q (ubiquinone)

What molecule is oxidized by NADH dehydrogenase in E. coli?

$NADH + H^+$ into $NAD^+$

In the mouth, what are the characteristics of Streptococcus spp.?

Gram positive, cocci, facultative anaerobes

In the mouth, what are the characteristics of Peptostreptococcus spp.?

Gram positive, cocci, strict anaerobes

In the mouth, what are the characteristics of Actinomyces spp.?

Gram positive, rods, strict/facultative anaerobes

In the mouth, what are the characteristics of Lactobacillus spp.?

Gram positive, rods, facultative anaerobes

In the mouth, what are the characteristics of Veillonella spp.?

Gram negative, cocci, strict anaerobes

What are the nutritional characteristics of Aggregatibacter spp. and Capnocytophaga spp.?

They are rods and capnophilic

What gram classification and oxygen response do Porphyromonas spp., Prevotella spp., and Fusobacterium spp. share?

Gram negative, strict anaerobes

What is the morphology and oxygen response of Spirochetes in the mouth?

Spirals and strict anaerobes

In nutrient uptake, what is the direction of movement for facilitated diffusion?

From higher concentration to lower concentration

What is the energy requirement for facilitated diffusion?

No energy requirement

What are permeases?

Carrier proteins embedded in the plasma membrane involved in nutrient uptake

How is the uptake in facilitated diffusion driven internally?

By the intracellular use of the compound

Give the example provided for facilitated diffusion uptake.

Conversion of glycerol to glycerol-3-P

What defines group translocation in nutrient uptake?

Transported substances are chemically altered during the process

What energy source is used in group translocation (PTS)?

The phosphate bond in phosphoenolpyruvate (PEP)

Explain the phosphate transfer in the PEP-PTS system.

Phosphate from PEP is transferred to several protein intermediates and eventually linked to the transported substance

Name a common substance transported via group translocation.

Some sugars

What is the primary characteristic of active transport regarding the state of the substance?

The substance remains unchanged by the transport process

What is used to drive the accumulation of a substance against a gradient in active transport?

Energy

What force is used by ion-driven transport systems?

Proton motive force (gradient of protons)

How is the proton motive force created for active transport?

By ATP hydrolysis or oxidation of reduced compounds ($NADH$)

What is the difference between symport and antiport in active transport?

Symport moves substances in the same direction as the favorable gradient; antiport moves them in the opposite direction

Name the common substances transferred via active transport.

Amino acids

What is a characteristic common to facilitated diffusion, group translocation, and active transport carriers?

They can be saturated

How do binding protein dependent transport systems function?

They use membrane proteins to form a channel and drive substances through using ATP hydrolysis

What common substances are transferred by binding protein dependent transport systems?

Sugars and amino acids

Why is the uptake of ferric iron difficult for microorganisms?

Ferric iron is very insoluble

What molecules do microorganisms use to aid in the uptake of ferric iron?

Siderophores

Describe the process of iron uptake involving siderophores.

Siderophore complexes with ferric ion; the complex is then transported into the cell

On how many organic compounds can E. coli grow to obtain carbon and energy?

More than 30 different organic compounds

How many compounds can Pseudomonas use for growth?

Several hundred compounds

What are nutritionally fastidious organisms?

Organisms with complex needs that can only grow in association with the human body or in complex media like blood agar

Provide two examples of nutritionally fastidious bacteria.

Staphylococci and Streptococci

What is Chlamydia classified as regarding its nutritional/growth needs?

An obligate intracellular parasite

What is the state of microbial growth in the real world compared to the laboratory?

Suboptimal with variable growth rates

How do stress responses affect a host even when bacteria are not growing?

By causing damage via immunogenic toxin production

What do some bacteria do when they stop growth due to unfavorable conditions?

They sporulate

What are the two major results of metabolic regulation in bacteria?

Pathways can be switched on and off, or turned up and down

What are the two primary ways metabolic control is established?

Control of enzyme activity and control of the number of enzyme molecules

Where do regulatory molecules bind on an enzyme in allosteric regulation?

The allosteric site

What is the nature of the binding between regulatory molecules and allosteric sites?

Noncovalent and reversible

What do positive effectors do in allosteric regulation?

Increase enzyme activity

What do negative effectors do in allosteric regulation?

Decrease enzyme activity

List two ways allosteric effector molecules act on an enzyme.

Change affinity of enzyme for substrate or change $V_{max}$

What is the purpose of the attenuator region in mRNA?

It is used in control of the number of enzyme molecules (attenuation)

What does most of the mRNA code for in pathways controlled by attenuation?

Enzymes of a particular metabolic pathway

In catabolic pathways, what is the process of initiating transcription called?

Gene induction

What molecule is the inducer for the gene for $\beta$-galactosidase in the Lac operon?

Allolactose

In the Lac operon, what happens to the repressor protein when allolactose binds?

The repressor becomes inactive

What occurs when the Lac repressor is inactive?

Transcription proceeds as RNA polymerase can move

What occurs in the Lac operon when the repressor is active and bound to the operator?

Transcription is stopped

In anabolic pathways, what is the process of stopping transcription called?

Gene repression

What molecule is required to activate an inactive repressor in anabolic pathways?

A corepressor

What is the result when an active repressor (repressor + corepressor) binds to the regulatory region?

Genes are not transcribed

In the context of transcription initiation, what does the abbreviation 'Reg.' represent?

Regulatory region/gene

What does 'PO' represent in the transcription control diagrams?

Promoter-Operator

True or False: The number of enzyme molecules can be controlled through regulation of enzyme synthesis.

True

Which macroelement is specifically linked to the term 'cations' and general enzyme cofactor roles?

$K$, $Ca$, $Mg$, and $Fe$

What is the difference between a macroelement and a trace element?

Macroelements are required in larger amounts; trace elements are required in smaller amounts

What is the specific oxidizing event used by Chemotrophs to get energy?

Oxidation of organic or inorganic compounds

Where do autotrophs specifically get their $\text{H/electrons}$ for biosynthesis?

From $CO_2$ (indirectly via reducing equivalents)

Define a 'Lithotroph'.

An organism that uses reduced inorganic molecules as a source of reducing equivalents

Define an 'Organotroph'.

An organism that uses organic molecules as a source of reducing equivalents

What carbon source do Chemolithotrophic autotrophs use?

$$CO_2$$

What energy source do Chemoorganotrophic heterotrophs use?

Chemical energy source

What is the inorganic source of sulfur for microbes?

Sulfate ($SO_4^{2-}$)