MICROPARA MODULE 2 AND 3: MICROBIAL DIVERSITY, STRUCTURE, AND TAXONOMY

Cellular Microorganism

Organism that contains cells, either unicellular or multicellular.

Unicellular

Prokaryotes (Archaea, Bacteria, Cyanobacteria)

Multicellular

Eukaryotes (Algae, Fungi, Protozoa)

Acellular Microorganism

Organism that does not contain cell.

• Virus, viroids, prions

Prokaryotic Cell

• No true nucleus

• Ave size:

  • 0.2 - 2.0 diameter

  • 2 - 8 length

• Transverse binary fission

• Monomorphic or pleomorphic

Membrane-enclosed organelles - cytoskeleton

Prokaryotic Cell lacks ________-________ ____ and has no ___________

Archaea

• Means ancient

• Bacteria look identical microscopically to members of the Bacteria domain

Peptidoglycan

Archaea do not have ______________

Archaea

It has the the ability to grow in extreme environments

• Extreme temperatures: hot or cold

• Acidic or alkaline conditions

• Extreme salt concentration

Bacteria

• Single-celled prokaryote

• Comprised of specific shapes

• Multiply by binary fission

Prokaryote

A simple cell with a nucleoid region, surrounded by cytoplasm and a cell wall

Bacilli

Rod shaped

Cocci

Spherical shaped

Spirilla

Spiral shaped

• Glycocalyx

• Flagella

• Fimbriae

• Pili

Prokaryotic Cell Structure: Appendages

• Cell membrane

• Cytoplasm

• Chromosomes

• Ribosomes

• Inclusions

• Endospores (some)

Prokaryotic Cell Structure: Internal to the cell wall

Glycocalyx

The outer layer usually made up of bound polysaccharides on the cell surface and superifical layer of unbound proteoglycans and glycoproteins

Capsule

• Anti-phagocytic function

• Vaccine target

• attachment

Slime layer

• Glide or slide on surfaces

• Formation of biofilm

Flagella

Long, slender, threadlike, whip-like extension of certain cells or unicellular organisms used mainly for movement (others for signal transduction)

• Atrichous

• Monotrichous

• Lophotrichous

• Amphitrichous

• Peritrichous

Arrangements of Flagella:

Fimbriae

• Hair-like structures made of “pilin”

• Enable bacterial cell to adhere to surfaces

Pili

• Short, filamentous projection on a bacterial cell, used not for motility but for adhering to other bacterial cell (especially for mating) or to animal cells

• Joins bacterial cell for DNA transfer during conjugation

• “Sex pili”

Axial filaments

Flagella-like fibrils arising at the ends

Cell Wall

• Composed of peptidoglycan (murein)

  • N-acetylglucosamine (NAG)

  • N-acetylmuramic acid (NAM)

• Used to characterized bacteiral cells

Teichoic acid and lipoteichoic

Gram Positive

Lipoproteins, LPS, and phospholipid

Gram Negative

Gram Positive: Gram’s staining they retain crystal violet colour after the treatment with alcohol.

Gram Negative: Retain crystal violet after alcohol treatment and get decolourised (as the outer membrane containng phospholipids gets degraded and the violet dye passes our of the cells). They are counterstained with reddish safranin to observe under the microscope.

1. Staining

Gram Positive: ?

Gram Negative: ?

Gram Positive: Cell wall usually contains teichoic acid.

Gram Negative: Teichoic acid is absent in the cell wall.

2. Cell Wall

Gram Positive: ?

Gram Negative: ?

Gram Positive: Outer membrane in the cell wall is absent.

Gram Negative: Outer membrane, consisting of phospholipids and proteins, is found above the peptidoglycan.

a. Outer Membrane:

Gram Positive: ?

Gram Negative: ?

Gram Positive: Peptidoglycan in the cell wall is thicker. (20-80 n m), therefore, susceptibility to antibiotics (e.g., penicillin) that act upon the peptidoglycan is high. Pentaglycine links the two adjacent tetrapeptides in peptidoglycan.

Gram Negative: Peptidoglycan is comparatively quite thinner (8-12 nm) and thus, the susceptibility to penicillin-like antibiotics is low. Pentaglycine in peptidoglycan is absent. Pentaglycine in peptidoglycan is absent.

b, Peptidoglycan

Gram Positive: Cell wall has low lipid content

Gram Negative: Cell wall has high lipid because of the presence of outer membrane.

c. Lipid content

Gram Positive: ?

Gram Negative: ?

Gram Positive: Periplasmic space is absent.

Gram Negative: A periplasmic space is present between outer membrane and plasma membran.e

Periplasmic space

Gram Positive: ?

Gram Negative: ?

Gram Positive: Flagella, if present contain two rings in the basal body.

Gram Negative: Flagella, if present, have four rings in basal body.

3. Flagella

Gram Positive: ?

Gram Negative: ?

Gram Positive: These bacteria are mostly spore-forming

Gram Negative: They are generally non-sporous

Spores

Gram Positive: ?

Gram Negative: ?

Gram Positive: Pili over the cell surface are absent.

Gram Negative: Some G- bacteria have pili (made up of protein pilin) over the cell wall that elp in conjugation with other cell and attachment with some substratum or with other cells in aggregates

Pili

Gram Positive: ?

Gram Negative: ?

Plasmid

Contains extra-chromosomal DNA which carry genes that confer protective trait that may be duplicated and passed on to an offspring.

Ribosomes

A minute particle composed of protein and ribonucleic acid (RNA) that serves as the site of protein synthesis.

Inclusions

An abnormal structure in cell nucleus or cytoplasm having chracteristic staining properties.

Endospore

Bacteria undergo sporulation during exposure to harsh conditions

Bacteria: Prokaryotic

Archaea: Prokaryotic

Eukarya: Eukarya

Cell Type

Bacteria: ?

Archaea: ?

Eukarya: ?

Bacteria: Single, circular

Archaea: Single, circular

Eukarya: Several, linear

Chromosome

Bacteria: ?

Archaea: ?

Eukarya: ?

Bacteria: 70S

Archaea: 70S but structure is more similar to 80S

Eukarya: 80S

Types of ribosome

Bacteria: ?

Archaea: ?

Eukarya: ?

Bacteria: +

Archaea: +

Eukarya: +

Contains unique ribosomal RNA signature sequence:

Bacteria: ?

Archaea: ?

Eukarya: ?

Bacteria: 1

Archaea: 3

Number of shared sequences shared with Eukarya -

Bacteria: ?

Archaea: ?

Bacteria: -

Archaea: +

Protein Synthesis similar to Eukarya

Bacteria: ?

Archaea: ?

Bacteria: +

Archaea: -

Eukarya: -

Presence of peptidoglycan in cell wall

Bacteria: ?

Archaea: ?

Eukarya: ?

Bacteria: Fatty acids with ester linkages

Archaea: Long chain, branched hydrocarbons with ester linkages

Eukarya: Fatty acids with ester linkages

Cell Membrane lipids

Bacteria: ?

Archaea: ?

Eukarya: ?

Bacteria: -

Archaea: -

Eukarya: +

Sterols in membrane

Bacteria: ?

Archaea: ?

Eukarya: ?

Eukaryotic Cell (Eukaryotes)

All members of the living world except the prokaryotes are considered __________

• They are single celled and multi-celled

• Contain basic organelles: cell membrane, cytoplasm, nucleus

• Membrane bound “true” nucleus

• Mitosis/meiosis

• Examples: Algae, Fungi, Protozoa

10 - 30 um

Average size of Eukaryotic Cell

Algae

Photosynthetic eukaryotes with a wide variety of shapes that occur in most habitats, ranging from marine and freshwater to dese sands and from hot boiling springs to snow and ice belonging to Kingdom Protista.

• Small, single-celled forms (filamentous) to most complex multicellular forms.

• They are not plants, they are more plantlike than protozoa. They lack true roots, stems, and leaves.

• They have important role in balancing the environment.

• Examples: Chlamydomonas, Spirogyra, Rhodymenia

Fungi

Can be single celled or very complex multicellular organisms.

• Found in just about any habitat but most live on the land, mainly in soil or on plant material rather than in sea or fresh water.

• Decomposers grow in the soil or on dead plant matter where they play an important role in the cycling of carbon and other elements.

• Examples: Yeast and Molds

Protozoa

• Are single celled organisms. They come in many different shapes and sizes ranging from an Amoeba which can change its shape to Paramecium with its fixed shape and complex structure.

• They live in a wide variety of moist habitats including fresh water, marine environments, and the soil.

• Some are parasitic, which means they live in other plants and animals including humans where they cause disease.

Plasmodium

Causes malaria. They are motile and can move by means of flagella, cilia, and amoeboid movement.

Ribosomes

Function: Protein synthesis

Present in Prokaryote and Eukaryotes

Cytoskeleton

Function: Shape, support, endocytosis in eukaryotes

Present in some prokaryotes and all eukaryotes

Centrosome

Function: Role in mitosis, cytokinesis, Flagella and cilia formation in animal cells

Absent in Prokaryotes

Present in Animals (Eukaryotes)

Nucleus

Function: Contains DNA and is the control center

Absent in Prokaryotes

Present in All Eukaryotes

Endoplasmic Reticulum

Function: Transport nutrients within cell, lipid synthesis (EUK; contains ribosomes make proteins)

Absent in Prokaryotes

Present in All Eukaryotes

Golgi Apparatus

Function: Exocytosis, secretion, protein packaging

Absent in Prokaryotes

Present in Some Eukaryotes

Lysosomes

Function: Breakdown nutrients, self destruct aged or bad cells

Absent in Prokaryotes

Present in Some Eukaryotes

Peroxisomes

Function: Neutralization of toxins

Absent in Prokaryotes

Present in Some Eukaryotes

Vacuoles

Function: Storage and maintain hydrostatic equilibrium.

Absent in Prokaryotes

Present in Some Eukaryotes

Vesicles

Function: Storage, digestion, transport

Absent in Prokaryotes

Present in All Eukaryotes

Mitochondria

Function: Aerobic ATP Production

Absent in Prokaryotes

Present in Most Eukaryotes

Chloroplasts

Function: Photosynthesis

Absent in Prokaryotes

Present in Plants, algae, and some protozoa.

Acellular Structure

Without cell parts

Virus

• Considered acellular, non-living, obligate intracellular parasite

• Made up of a core containing DNA or RNa surrounded by a protein coat

• Can reproduce only by using the cellular mechanism of another cell

• Often considered the parasites of microbial world

Viroids

• Very small, circular RNA (may appear linear), and infectious in plants. They do not contain a capsid.

• The only human disease known to be caused by a viroid is hepatitis D; in this case the viroid is enclosed in a hepatitis B virus capsule.

Prions

• Contain only protein

• Causative agent for some neurodegenerative diseases in humans and animals

Eukaryotes

• Typically larger

• Compartmentalized by membrane-bounded sacs or organelles

• Contain a nucleus with multiple chromosomes

• Divide by complex process of mitosis

Prokaryote

• Typically smaller

• Not compartmentalized

• Do not have a nucleus

• Divide by binary fission

Prokaryotes Nuclear Properties

• An organized nucleus is absent

• Single, circular, coiled, naked DNA found to be associated with any histone, non-histone proteins, lies in the cytoplasm

• Nuclear envelope, nucleoplasm and nucleolus are absent

• DNA is attached with mesosome that is an invagination of the cell membrane.

Eukaryotes Nuclear Properties

• A well-organized nucleus

• Many linear, coiled DNA molecules associated with histones and non-histones histones.

• Nuclear membrane, nucleoplasm, nucleolus are present.

Prokaryotes Cytoplasmic Properties

• Cell organelles like mitochondria, chloroplast, endoplasmic reticulum, Golgi apparatus, central vacuole, etc, are not found in the cells in some prokaryotes, gas vacuoles are found that provide buoyancy and help in floating of the cells in aquatic environment

• Respirator enzymes and other components are found in the cell membrane

• In photosynthetic prokaryotes, the photosynthetic components are found in the membranous sacs or tubers, called thylakoids.

Eukaryotes Cytoplasmic Properties

• Cell organelles, mitochondria, chloroplasts, endoplasmic reticulum, Golgi apparatus, central vacuoles, etc are present

• Double membrane bound mitochondria are meant for aerobic respiration

• Double membrane bound chloroplasts with grana and stromal thylakoids perform the photosynthesis in photosynthetic eukaryotes.

Microtubules

Prokaryotes: Microtubules and microfilaments are absent.

Eukaryotes: The cytoplasm contains a network of microtubules and microfilaments that are made up of proteins and function as the cytoskeleton.

Centrioles

Prokaryote: Centrioles are absent

Eukaryotes: In animal and motile cells a pair of centrioles, arranged right angles to each other and consisting of microtubules, are found at one side of the nucleus that produce spindle fibers during cell division.

Ribosomes

Prokaryotes: 70 S type

Eukaryotes: Ribosomes are of 80S type in the cytoplasm whereas, the cell organelles have generally 70S type of ribosomes.

Cytoplastic movement

Prokaryotes: Cyclosis is absent

Eukaryotes: Cyclosis, the cytoplasmic streaming, is present in eukaryotic cells that helps in the homogenous distribution of various components and movement of organelles.

Cell Wall

Prokaryotes: Absent

Eukaryotes: Cell wall, if present, has different composition in different eukaryotes, e.g. cellulose, hemicellulose, pectin, chitin (in fungi), etc

Flagella

Prokaryotes: In motile prokaryotes flagella, if present, are single-stranded consisting of flagellin protein. Here, the flagellum is not enveloped within any membrane.

Eukaryotes: n motile cells flagella, if present, are 11- stranded (9+2 arrangement) in the shaft portion and 9-stranded (9+0 arrangement) in the basal portion, where each strand is made up of α and β- tubulin proteins. Moreover, the flagellum is enveloped in a membrane.

Cell Division

Prokaryotes: Mitosis and meiosis are absent and the cell divides by simple binary fission method in which the DNA replicates into two that are equally distributed into two daughter cells with the help of mesosome, as the spindles are absent

Eukaryotes: Cell divides by mitosis and for sexual reproduction by meiosis, where the spindle fibres help in the separation of chromosomes into the daughter cells.

Protein Synthesis

Prokaryotes:

(i) Transcription (DNA to mRNA rRNA or tRNA) and translation (mRNA to protein) occur simultaneously in the cytoplasm.

(ii) During transcription, a gene in DNA leads to the formation of mRNA where the number ofnucleotides is exactly same as in the corresponding gene in the DNA.

Eukaryotes:

(i) Here, the transcription occurs in the nucleus, whereas, the translation in the cytoplasm.

(ii) In eukaryotes many genes in DNA are split genes containing exons and introns, where the transcription leads to the production of RnRNA that is quite longer than the actual mRNA. Thus, the mRNA is produced after the processing of HnRNA where the intervening introns and other unwanted nucleotide sequences from the 5′ and 3′ ends are removed. Moreover, a cap of 5-methyl guonasine at the 5′ end and a tail of poly A at the 3′ end of mRNA is also added

Sexual reproduction

Prokaryotes: True sexual reproduction is lacking, as gametes are not formed in these organisms. Though, some kind of parasexuality through transformation, conjugation or transduction may occur that involves exchange of some genetic material

Eukaryotes: Sexually reproducing eukaryotes produce gametes that unite to form the zygote (true sexual reproduction).

Cell Division

The process by which a parent cell divides into two or more daughter cells

• Usually occurs as part of a larger cell cycle

Haploid and Diploid

2 genetic states

Haploid

One copy of chromosome
in humans, n = 23

in humans, gametes (sperm & ova)

Diploid

Two copies of chromosome

in humans, n = 46

in humans, all body cells are _ found in skin, blood, and muscle cells also known as somatic cells.

Mitosis

The chromosomes condense, divide, and are separated into two sets, one for each daughter cell.

Meiosis I

Homologous chromosomes segregate into separate cells, changing the genetic state from diploid to haploid.

Meiosis II

The two haploid cells divide to form a total of four haploid cells callled gametes.

Taxonomy

The way of identifying different organisms, classifying them into categories, and naming them. All organisms, both living and extinct, are classified into distinct groups with other similar organisms and given a scientific name.

Hierarchical classification

One way to help scientists understand, categorize and organize the diversity of life. In this manner, it minimizes confusion and provide reliable means of identifying and naming an organism.

Taxis

arrangement or order

Momos

law

nemein

means to distribute or govern

Taxonomy

The science of biological classification

Taxa or Taxon

A group or level of classification or hierarchy categorized at different levels