Exam Review 3: Exam April 21/ Review April 16

Exam 3 Review
Know the Following:

Prokaryotes/Archaea/Eukaryotes
Anoxic- anaerobic and much hotter than the present Earth

Abiotic non-living syntheses that set the stage for the origin of life.

The first life forms may have been self-replicating RNAs (RNA life).

Autotrophy-Use of CO2 for metabolite

Chemolithotrophic-use of inorganic compounds for metabolites

The phylogeny of microorganisms is their evolutionary relationships

SSU (small subunit) RNA sequencing is synonymous with 16S or 18S sequencing.

Phylogenetic trees based on ribosomal RNA have now been prepared for all the major prokaryotic and eukaryotic groups. The amplification of the gene encoding 16S ribosomal RNA, sequencing it, and analyzing the sequence in reference to other sequences.

Bacterial taxonomy places emphasis on analyses of phenotypic properties of the organism.

Taxonomy: The science of classification.. Consists of two major subdisciplines, identification and nomenclature

Horizontal/Lateral Gene flow: Transduction, Conjugation, Transformation

Largest group: The Proteobacteria

Phenotypic
Gram stain
Morphology
Metabolism
Biochemical reactions

Genotypic
16rRNA:genes for 16S rRNA and related molecules are amplified, treated with one or more restriction enzymes, separated by electrophoresis and then probed with complementary rRNA.

The Archaea can be divided into four groups: the methanogens, the halophiles, the hyperthermophiles and the genus Thermoplasma

Found in: Soil, Mineral deposits, Aquatic areas, Volcanic areas, Animals

Archaeal cell walls do not contain muramic acid and D-amino acids, the building blocks of peptidoglycan.

The Archaeal membranes differ from Bacterial membranes in that they contain ether-linked lipids bonded to glycerol

The eukaryotic microbes: algae, fungi, slime moulds and protozoa.

Eukaryotic microorganisms differ from Bacteria and Archaea.
These differences include:
cell size
internal structure
genetic arrangement
evolutionary history.

Know Eukaryotic organelles
The endoplasmic reticulum
The golgi apparatus
Lysosomes
The peroxisome
3 energy organelles: mitochondria, hydrogenosome, chloroplast

The chloroplast is the site of photosynthetic energy production and CO2 fixation in eukaryotic phototrophs (algae).

Instead, chlorophyll and all other components needed for photosynthesis are located in a series of flattened membrane discs called thylakoids

Endosymbiosis

Microbiological Eukaryotes: Protozoa, flagellates, ciliates, sporozoa, fungi, slime moulds, algae

Genomics
Genes: A hereditary unit consisting of a sequence of DNA that occupies a specific location on a chromosome and determines a particular characteristic in an organism.

Genome: entire complement of genes

Sequencing: determining the total bases - that make up the DNA

Cloning vectors: A carrier, such as a bacterial plasmid or bacteriophage.

Genomic sequencing:
Reveals genes
Reveals functions of organism
Evolutionary history
Transcription and translation of genetic
information in the genome

An open reading frame or ORF is a portion of a prokaryotic organism's genome which contains a sequence of bases that could potentially encode a protein.

Bacterial Artificial Chromosomes
The use of the F plasmid to carry large amounts of chromosomal DNA

Yeast Artificial Chromosomes
Vectors which replicate in yeast like normal chromosomes but can carry large fragments of DNA

Shotgun techniques use random cloning and sequencing of relatively small genome fragments

Annotation: conversion of raw sequence data into a list of the genes present in the genome.

Bioinformatics: the use of computer tools to acquire, analyze, store, and access DNA and protein sequences

The purpose of genomics is to determine the number, sequence and function of genes in an organism

Gene families: genes that are related to other genes within the organism

Microarrays are genes or gene fragments attached to a solid support in a known pattern


Diversity
Photoautotrophs
Carbon source is carbon dioxide
Energy source is sunlight
Reduction of CO2 to organic compounds

Photoheterotrophs: Use organic carbon as their carbon source


Light-Dependent Reactions-Purpose: to produce ATP from light energy

Pigments:

Chlorophylls a and b
Bacteriochlorophyll
Carotenoids

Chlorophyll Pigment of oxygenic phototrophs.

Bacteriochlorophyll: the chlorophyll pigment of anoxygenic phototrophs.

Prokaryotes-No chloroplasts

Pigments are integrated into the internal membrane system

Carotenoids:
Most widespread accessory pigments
Hydrophobic pigments embedded in membrane
Photoprotective role: Quench toxic oxygen
Transfers energy to the reaction center which is used to make ATP

Antenna: chlorophyll molecules harvest light energy and transfer it on to reaction center of the pigments.

Exciton: mobile forms of energy (photons)
Pigments absorb light energy, give up electron, which enter electron transfer chains.
Water molecules split, ATP and NADH form, and oxygen is released

Anoxygenic Photosynthesis: Photosynthesis in which O2 is not produced

In oxygenic photosynthesis, water donates electrons to drive CO2 production, and oxygen is produced as a by-product.

Two separate light reaction center are involved, photosystems I and II.

Photosystem I resembles the system in anoxygenic photosynthesis. Photosystem II splits H2O to yield O2


Light Independent reactions:

Synthesis part of photosynthesis
Can proceed in the dark
Calvin-Benson cycle

Most phototrophic and other autotrophic organisms accomplish fixation of CO2 via the Calvin cycle, in which the enzyme ribulose bisphosphate carboxylase (RubisCO) plays a key role

Assimilative Metabolism: When an inorganic compound such as NO3, SO4 or CO2 is reduced for biosynthesis

Dissimilative metabolism : The reduced product is excreted into the environment

Phototrophic: obtains energy from light

Chemolithotrophic: oxidize inorganic compounds for energy(some facultative)

Chemoorganotrophic: obtains energy from the oxidation of organic compounds.

Autotrophic: use CO2 as nutrient source

Methanotrophs: use methane for energy

Decomposition: the breakdown of organisms, and the release of nutrients back into the environment.

Nitrogen Cycling: Plants rely on nitrogen from the soil and cannot acquire it from the gaseous nitrogen in the atmosphere.

Under anoxic conditions, organic matter is degraded principally to methane and carbon dioxide by syntrophic bacteria

The principal form of nitrogen on Earth is nitrogen gas (N2), which can be used as a nitrogen source only by the nitrogen-fixing bacteria.

Nitrogen fixation: the microbiological reduction of nitrogen to ammonia

Ammonia produced by nitrogen fixation or by ammonification from organic nitrogen compounds can be assimilated into organic matter.

Nitrification: The process by which ammonia is oxidized to nitrate

Denitrification: the microbial process by which nitrate is reduced to gaseous nitrogenous compounds (N2)

Methane is decomposed to ammonia

Utilization of sulfur and Iron as electron donors. Changes in soil or water content.

Microbial decomposition is the single largest source of CO2 released to the atmosphere.

Syntrophy: a metabolic process in which two or more organisms cooperate in the degradation of some compound.

The principal form of nitrogen on Earth is nitrogen gas (N2), which can be used as a nitrogen source only by the nitrogen-fixing bacteria.

Sulfate reduction is an important biogeochemical process

Bacterial reduction of ferric iron occurs in anoxic environments causes acid mine drainage.

Methods:
Enrichment culture: technique is a means of obtaining microorganisms from natural samples.

The Winogradsky column is a miniature anoxic ecosystem that can be used as a long-term source of bacteria for enrichment culture purposes

A pure culture can be obtained by conventional microbiological procedures, including streak plates, agar shakes, and dilution methods.

MPN: Most probable number: method of measuring the numbers of microbes in different media and conditions

DAPI is a general stain for identifying microorganisms in natural samples

The green fluorescent protein makes cells autofluorescent and is a means for tracking cells introduced into the environment.

Some stains can differentiate live versus dead cells-Viability stains.

Fluorescent antibodies that are specific for one or a small group of related cells can be prepared

Nucleic acid probes and PCR=highly specific


Microbial Ecology
Microbial ecology: how microorganisms interact with one another and their environment.


Guild: A microbial community which consist of metabolically related organisms.

Ecosystem: a community of organisms and their natural environment.

Biogeochemistry: the study of microbial energy transformations and biogeochemical processes that result in the recycling of elements.

Microenvironment: the place where the microorganism actually lives.

Oxic: the outer zones of a small soil particle containing O2

Anoxic: the center of a soil particle only a very short distance away which is completely anoxic (O2-free)

Biofilms are bacterial colonies, encased in slime, that form on surfaces. Biofilms can lead to damage as a result of the products excreted by the cells. Biofilm involves cell-to-cell communication (quorum sensing) COOPERATION

“A” horizon of soil : where most microbes exist.

The most important factor influencing microbial activity in surface soil is the availability of water
In deep soil (the subsurface environment), nutrient availability plays a major role.

Primary producers: Phototrophs in aquatic ecosystems

Marine waters have less nutrients for bacteria. Many use light to drive ATP synthesis.
Proteorhodopsin

Bacteria -oceanic surface waters
Archaea - deeper waters

Barophiles grow best under pressure.

Barotolerants can grow under elevated pressures but grow best at atmospheric pressures

Extreme barophiles: obtained from the greatest depths, require high pressure for growth.


Bioremediation: the cleanup of oil, toxic chemicals and pollutants by microbes.

Key microbial habitats on plants include the rhizoplane/rhizosphere(root) and the phyllosphere.

The plant provides the energy source needed by the root nodule bacteria, and the bacteria provide fixed nitrogen for the growth of the plant. The bacteria induce the formation of root nodules within which the nitrogen-fixing process occurs.