Extremophiles and Microbial Growth Factors

Extremophiles

Organisms that thrive in extreme environmental conditions, such as high temperatures, high salinity, extreme pH, or high pressure.

Extremozymes

Enzymes contained in extremophiles that are useful in industrial and medical applications.

PCR

Polymerase chain reaction, a method that requires heat-resistant DNA polymerases like Taq polymerase for DNA amplification.

Taq polymerase

A heat-resistant DNA polymerase derived from Thermus aquaticus, essential for PCR.

Biogeochemical cycles

Processes that extremophiles play crucial roles in, contributing to environmental cleanup (bioremediation).

Temperature

One of the parameters defining a microbial growth environment, optimal ranges for microbial enzymes.

pH

The acidity or alkalinity of the environment, a parameter defining microbial growth.

Osmotic Pressure

The concentration of solutes affecting water availability, a parameter defining microbial growth.

Oxygen Levels

Determines aerobic or anaerobic metabolism, a parameter defining microbial growth.

Nutrient Availability

Essential elements like carbon, nitrogen, and phosphorus that define microbial growth environments.

Pressure

A parameter defining microbial growth, where some microbes thrive under extreme pressure (barophiles).

Psychrophiles

Microbes that thrive in cold temperatures (0-20°C).

Mesophiles

Microbes that prefer moderate temperatures (20-45°C).

Thermophiles

Microbes that grow in high temperatures (45-80°C).

Hyperthermophiles

Microbes that survive in extreme heat (>80°C).

Acidophiles

Microbes that grow in acidic environments (pH <5.5).

Neutrophiles

Microbes that prefer neutral pH (6.5-7.5).

Alkaliphiles

Microbes that thrive in basic environments (pH >8.5).

Obligate Aerobes

Microbes that require oxygen for growth.

Facultative Anaerobes

Microbes that can grow with or without oxygen.

Obligate Anaerobes

Microbes that cannot tolerate oxygen.

Aerotolerant Anaerobes

Microbes that ignore oxygen and grow without it.

Microaerophiles

Microbes that require low oxygen levels.

Halophiles

Microbes that thrive in high salt concentrations.

Osmotolerant

Microbes that can tolerate high solute concentrations.

Barophiles

Microbes that grow under high pressure.

Water Activity (awa_w)

Measures the availability of water for microbial use, affected by solute concentration, humidity, and temperature changes.

Compatible solutes

Substances like proline and trehalose that cells synthesize or import to balance internal water pressure.

H+ ions

Influence enzyme activity, protein structure, and membrane stability.

pH changes

Drastic pH changes can denature proteins, disrupt metabolic processes, and alter nutrient transport.

Acidophiles

Acidophiles pump out excess H+ ions or use proton pumps to maintain internal pH.

Alkaliphiles

Alkaliphiles use Na+/H+ antiporters to regulate internal pH by exchanging sodium ions for protons.

Oxygen Tolerance

Just because an organism can live in an oxygenated environment does not mean it uses oxygen for growth.

Anaerobes

Some anaerobes can use oxygen as an electron acceptor under certain conditions, while obligate anaerobes cannot tolerate oxygen at all.

Nutrient Exhaustion Response

When nutrients are depleted, cells may enter a dormant state, slow down metabolism, or switch to alternative nutrient sources.

Physical Methods of Microbial Growth Control

Includes heat (autoclaving, pasteurization), radiation (UV, gamma rays), filtration, and desiccation.

Chemical Methods of Microbial Growth Control

Includes disinfectants (kill microbes on surfaces), antiseptics (kill microbes on living tissue), and antibiotics (target bacterial cells selectively).

D-Value

The D-value is the time required to reduce a microbial population by 90% at a given temperature.

Microbial Competition

Microbes prevent the growth of others by producing antibiotics, secreting bacteriocins, competing for nutrients, and altering the environment.

Bacterial Genomes

Bacterial genomes are typically single, circular chromosomes, double-stranded DNA, and supercoiled for compact storage.

Plasmids

Plasmids are small, circular, extrachromosomal DNA molecules found in some bacteria.

Restriction Enzymes

Cut DNA at specific sequences for cloning and analysis.

Gel Electrophoresis

Separates DNA fragments by size using an electric field.

Polymerase Chain Reaction (PCR)

Amplifies specific DNA sequences using heat-stable polymerases.

DNA Sequencing

Determines nucleotide sequences for genetic and forensic studies.

RNA Polymerase

Enzyme responsible for synthesizing RNA from a DNA template.

Sigma Factors

Direct RNA polymerase to specific promoter sequences to initiate transcription.

Transcription Process

DNA is transcribed into RNA, which is used to synthesize proteins.

Ribosomes & tRNA

Assemble amino acids into proteins.

Translation Process

mRNA is translated into proteins.

Protein Folding & Modification

Chaperones assist folding, and modifications like phosphorylation regulate function.

Protein Secretion

Uses pathways such as Sec and TAT systems.

Protein Degradation

Misfolded proteins are broken down by proteases (e.g., Lon, Clp in bacteria).

Bioinformatics

Identifies genes and their functions from DNA sequences.

Genetic Code

The set of codons that specify amino acids.

Differences Between DNA and RNA

Includes differences in sugar, strands, bases, stability, and function.

DNA Polymerase

Enzyme that mediates DNA replication.

RNA Polymerases

Enzymes that mediate transcription.

Start Codon

Start site for translation, typically AUG.

Stop Codon

Termination sequence that signals the end of translation.

Cellular Location of DNA

Located in the nucleus (eukaryotes) and cytoplasm (prokaryotes).

Final Product of Replication

Two daughter DNA strands (semi-conservative).

Final Product of Transcription

mRNA, tRNA, or rRNA (single stranded).

Final Product of Translation

Functional proteins.

DNA Supercoiling

Refers to the twisting of the DNA helix to fit inside the bacterial cell.

Topoisomerases

Enzymes that manage DNA supercoiling.

Type I topoisomerases

Cut one strand to relieve supercoils.

Type II topoisomerases

Cut both strands and introduce negative supercoils.

DNA gyrase

A type II topoisomerase that introduces negative supercoils.

Fluoroquinolones

Drugs that inhibit bacterial DNA gyrase, preventing supercoiling and replication.

Initiation

The process where DNA unwinds at the origin (oriC).

Elongation

The phase where DNA polymerase III synthesizes new strands.

Termination

The point where replication ends at the termination (ter) site.

DnaA

A protein that binds to oriC to initiate replication.

Methylation of GATC sites

A process that ensures timing control of replication initiation.

SeqA protein

Prevents premature initiation of DNA replication.

Clamp loader

Loads the sliding clamp onto DNA.

Primase

Synthesizes RNA primers for DNA replication.

DNA helicase (DnaB)

Unwinds DNA during replication.

Helicase loader (DnaC)

Loads DnaB onto DNA.

DNA proofreading

DNA polymerase III has 3' → 5' exonuclease activity to correct errors.

Leading strand

Synthesized continuously during DNA replication.

Lagging strand

Synthesized in Okazaki fragments during DNA replication.

DNA ligase

Seals gaps between Okazaki fragments.

Catenanes

Interlinked bacterial chromosomes formed after replication.

Topoisomerase IV

Resolves catenanes to separate chromosomes.

XerCD recombinase

System that resolves chromosome dimers at the dif site.

Rolling-circle replication

Used by plasmids and some viruses to produce a continuous single-stranded DNA.

Bidirectional replication

Used for bacterial chromosomes, where replication proceeds in both directions from oriC.

Handcuffing

A mechanism used by plasmids to prevent over-replication by binding two plasmid molecules together.

Primary chromosome

Contains essential genes.

Secondary chromosome

Smaller, carries some essential genes but arose from a plasmid.

Plasmid

Extrachromosomal, non-essential DNA.

Metagenome

The collective genome of a microbial community.

Single-cell genomics

Preferred when studying rare or unculturable microbes, analyzes one cell at a time.

Open Reading Frame (ORF)

A sequence of DNA that has the potential to be translated into a protein.

Start Codon

A start codon (AUG in most cases).

Stop Codon

A stop codon (UAA, UAG, or UGA).

DNA Sequence Alignment

The process of arranging DNA sequences to identify regions of similarity.

Homologous Genes

Genes that share an evolutionary relationship.