Archean Occurred from 3800 to 2500 mya
The time duration in which the first life was seen on Earth (not chemical evolution)
Special Archea Bacteria and anaerobic Eubacteria are seen that can harness energy by
breaking inorganic matter.
Proterozoic Occurred 2500 to 543 mya
Saw the rise of Eukaryotic cells
Phanerozoic Started 543 mya and continues to now.
Multicellular organisms appear and dominate
QUALITIES OF LIFE:
Self-Replicating Life from life with a genetic program
Metabolizing Capturing, processing and releasing chemical energy (food)
Self-regulating To be able to maintain an internal environment different from the external
To be able to balance the internal environment in a certain range (homeostasis)
Reproducing Creating another life from a living organism
Evolving Adapting and changing to the environment by generations.
Responding Sensing and interacting with the surrounding world.
Growth Increasing in size.
(Eu)bacteria Formerly heavily relied on morphology for classification (size, shape, mobility)
Currently classed in a chemical/genetic manner since many species share same morphs.
Nucleoid Region Nucleoid region of the bacteria contains the genetic material
Bacterial DNA is circular
Bacillus Bacteria Rod shaped bacteria
Generally large, gram positive, spore bearing, and forms colonies in chains.
Some of them have a flagella for mobility
E.g. bacillus anthracis causes anthrax
Coccal Bacteria Coccus bacteria are spherical
Can occur singly, in pairs, or in groups in cubicle packets/grape-like clusters
Generally non-motile (w/o flagella or cilia) and do not form spores
E.g. staphylococci and streptococci have pathogenic species.
Spirochete These are non-rigid and spiral shaped.
Bacteria Generally, they are gram negative, anaerobic and feed on dead organic matter.
Very common in sewers and polluted water; e.g. Treponema
Spirillum Spirilla are rigid and spiral shaped
Bacteria Generally, they are gram negative, aerobic and highly motile containing a flagella.
1 BACTERIA (CELL STRUCTURE):
In spite of the variation, they typically have a generic structure:
DNA is large and circular, found in a nucleoid region of the cell, with no nuclear envelope
Ribosomes Protein/rRNA structures that synthesizes protein from mRNA, in process of translation
They are very different in eukaryotes, bacteria, and Archea
Cell Wall Made up of peptidoglycan (exclusive to bacteria), meshwork of sugars and peptides.
(in plants cell walls are cellulose-based; in fungi, cell walls are chitin-based)
Periplasm Space in between 2 phospholipid bilayers of the gram negative cells.
Contains many proteins that serve diverse functions (antibiotic resistance, ETC, and other
Peptidoglycan Made of peptides and organic sugars.
Reacts with the Gram’s stain positively; thus, gram-positive bacteria have outer
Capsule Thick rigid gelatinous layer completely surrounding the cell wall of some bacteria
Protective function by making the bacteria harder to ingest by phagocytes
Gram positive Bacteria that are gram pos react to Gram’s stain, and contain thick peptidoglycan layer
Their cell boundary consists of:
o Cytoplasm | Plasma Memb. | Peptidoglycan | (Capsule) | Extracellular
They retain the first dye, appearing blue-black
See slide 36 and 37
Gram negative Acetone-alcohol washes out the violet dye, making the smear look red.
This is because their peptidoglycan layer is not as easily accessible
Their cell boundary consists of:
o Cytoplasm | Plasma Memb. | Peptidoglycan | outer memb. | Capsule | Extracellular
Gram neg. bacteria are generally vectors for diseases.
Bacterial Strictly a prokaryotic motor, as it evolved in a different manner than that of eukaryotes.
Flagella Is an example of a biological motor
Bacteria pump the protons into the region outside the memb. similar to ETC on mitos.
The proton pump opening is in the motor; as proton moves through it, the protein
changes shape, and ratchet against the motor, which starts/spins the flagellum
Flagellar hook Sharp bend just outside the cell surface (base of filament) allows axis of helix to point
directly away from the cell
Flagellar motor Motor that turns in response of a proton going down the bearing.
This is what turns the filament, producing propulsion.
This is thought to be a precursor to ATP synthase commonly found in mitochondria.
CELL WALL TYPES:
Cellulose: Organic compound made of polysaccharides, found in the cell walls of mainly plants & algae
Chitin: Long polymer composed of a derivative of N-containing glucose
Typically found in cell walls of fungi, exoskeletons of arthropods and radula of molluscs.
Peptidoglycan: Polymer of sugars/amino acids that form the cell wall of bacteria (but not archea)
Gram + bacteria have a thicker peptidoglycan layer than the gram – bacteria.
Its role is to provide structural strength to counteract osmotic pressure, but doesn’t have
bacteria its shape.
2 BACTERIA (REPRODUCTION):
Binary Fission Simple reproduction process in which the cell cleaves close to the middle as it finishes up
As the cell separates, each genome copy is anchored at the plasma membrane.
Bacteria can only reproduce asexually, since they have no genetic
In this form of reproduction, variation only comes about from mutation
Circular Piece of genome that is circular in shape, and as a result does not need telomeres.
Genome It is found mostly in the nucleoid region of bacteria and prokaryotes.
This genome is copied as a result of binary fission.
Daughter Cell A parent cell divides into 2 daughter cells; each with a copy of the parental genome
Mutation A random change of nucleotide sequence in the genome that can potentially cause it and
all its derivative cells to be different in appearance or function from normal.
Conjugation Transfer of genetic material between 2 bacterial cells by direct cell to cell contact
Typically, plasmids are used in genetic material transfer.
Conjugation plays a huge role in bacterial variation and bacterial genome diversity
Filamentous projection on a bacterial cell used for adhering to other bacteria
Can bring the bacteria towards what the Pilli Bridge is attached to.
Also significant as it is the bridge by which plasmids are transferred in conjugation.
Plasmid Fragments of circular DNA found in the cytosol of the bacteria.
Plasmids have to ability to merge with the circular DNA in the nucleoid region.
In this case, during conjugation, the entire genome up to the plasmid copy is transferred
to the recipient gene; the bacteria will express genes that are not native to it.
+ - For conjugation to occur, the 2 bacterium do not have to the same species. +
F and F Bacterium that can provide plasmid copies to other bacterium are known as F cells.
F cells copy and transfer the plasmid genes to F cells; those without that gene.
Transformation The ability of bacteria to uptake free DNA from the extracellular and incorporate it into
its own genetic material.
Transformation allows bacteria to uptake the DNA and tests them for beneficiality.
This process began 2.8 bya, and increases variation within bacteria.
If the uptake is successful (e.g. allows them to metabolize new things, or produce certain
proteins), then it will survive and pass it on to its future derivatives.
If the DNA is deleterious (i.e. poisonous to the bacteria), then it will kill itself, or it will
store it in a separate membrane as toxins for predators.
This is possible since the genetic material is universal to all life; species aren’t a factor.
They can only pick up DNA from the same domain, so it can’t take stuff up from
Any process by which an organism incorporates genetic material from another organism
Transfer without being its offspring.
This includes Transformation, Transduction and Conjugation.
Transduction Transduction is a very rare method to increase variation.
Bacteriophages hijack the living bacterial cells to replicate their genes.
After they replicate, they burst the cell in a lytic process and release the next gen. virus.
The bacterial genome is destroyed/digested in the process.
In extremely rare cases, some bacterial genome survive and is locked in the viral capsid
Then this virus containing bacterial genome will transfer it to other bacteria, increasing
its variation. There is also a potential for the viral DNA to combine with the bacterial DNA
Bacteriophage Viruses that invade bacteria and use them as their host. They insert their genetic
material into that of bacteria, essentially taking over its central control.
Host produces everything that is needed to make new viruses, their genes and capsid.
If bacterial genes survive, they also move into a capsid for transduction to occur.
3 Pathogen Infectious biological agent (bacteria, viruses, prions, virions, and funi)
Penicillin Anti-microbial agent (antibiotic) derived by penicillium fungi
First drug that was effective against many bacterial strains since it inhibits a specific
enzyme (DD-transpeptidase) which links peptidoglycans together, causing it to lyse.
Antibiotic Antibiotics are a chemical (natural or synthetic) that kills/inhibits growth of bacteria and
Resistance micro-organisms, usually by destroying the cell wall or interfering with its metabolism.
Antibiotic resistance occurs when a micro-organism contains a gene (plasmid) that can
negate the effects of the antibiotic.
Redox Pairs: An electron donor and its corresponding oxidized form (e.g. NADH and NAD+)
Oxidation: Increase of charge as a species loses one or more electrons.
Reduction Reduction of charge by gaining one or more electrons.
Cellular *stepwise oxidation vs. direct burning/combustion.
Respiration: Process by which glucose is oxidized for a gradual transfer of energy from glucose to the cell
Glucose is split into 2 3C molecules during glycolysis and moves to the Kreb’s cycle
Role of O 2s to accept free electrons and combine them with H to make water.
Anaerobic: These are organisms that live/thrive without requiring oxygen.
Many other metabolic processes are used to acquire energy, like fermentation of glucose
Mainly comprised of bacteria; humans are capable of anaerobic for only short time periods
ATP yield is significantly lower than aerobic, but process is 2.5x faster.
Fermentation: Anaerobic process by which energy is produced by the oxidation of an organic compound
(glucose) by using electron acceptors without the use of Oxygen.
Product of fermentation is ethanol and CO in2yeast.
Crucial process in anaerobic resp. as it allows for the regeneration of NAD+ by accepting
electrons from NADH
In humans, fermentation produces lactic acid, where pyruvate acid is reduced by NADH.
Aerobic: Aerobic organisms live and thrive in oxygenated environments
These guys require oxygen to oxidize glucose in the cellular resp.
Animals, fungi, and some bacteria adopt aerobic resp. methods.
Multicellular organisms must overcome problems associated with a large V to SA ratio
One way to deal with this to create body cavities to increase SA (e.g. lungs)
Electron Donor: Chemicals that donates an electron to another chemical; a.ka. reducing agent
Electron Receptor: Chemicals that accept a free electron; a.k.a. oxidizing agent
Electron Transport Organic process in which an electron is moved from highly reducing products of the citric
Chain: cycle (NADH and FADH2) down a chain of enzymes/proteins inside of a plasma membrane
to a highly oxidizing dioxygen. When this high energy moves across the proteins/enzymes,
protons are pumped out of the inner space, to be used for ATP synthase.
The proton gradient across the membrane makes protons more likely to enter the memb.
As the Hydrogen moves in through ATP synthase, ATP is generated. The H then combines
with Oxygen, the final electron acceptor to make water. This process is 40% efficient.
Proton Gradient Occurs when there is a greater concentration of protons on one side of a membrane
compared to the other. This increases the tendency for the protons to diffuse through.
ATP Synthase Important enzyme which provides energy to the cell by ATP synthesis.
Imbedded in phospholipid bilayer and has 2 subunits: top one rotates when a proton passes
it, creating energy required to bind a phosphate to an ADP molecule.
There is evidence that it originated from mechanism that powers bacterial flagella.
Autotroph: Organism that produce complex C molecules (organics) from inorganic CO 2
They are capable of producing their own food and organic building blocks.
Includes plants and algaes, and reduce atmospheric CO in 2he process.
They receive energy from inorganic sources such as sunlight
Photo trophs One of the only 2 metabolic pathway (other is chemoorganoheterotroph) that moved on to
They make their own organic compound by reducing inorganic CO using2solar energy.
These include plants and algae.
Chemo organo An organism that uses organic compounds as their source of energy.
trophs This includes all animals and fungi and most heterotrophs (chemolithotrophs are exception
as they use inorganic compounds as energy)
Organic chemicals that are used for energy include glucose, lipids and acetates.
Chemo litho An organism that uses an inorganic electron donor to acquire its energy
The compound is oxidized to remove a high energy electron which ultimately produces ATP
E.g. Nitrifying bacteria (uses NH3to make NO a3d an electron) and Iron bacteria (Fe to
In aerobic bacteria, the electron acceptor can be oxygen
Plays an important role in withering rocks to establish an ecosystem
Heterotrophic: Organisms that consume their C compounds from other organisms
Includes all carnivores (single and multi-cells); they move to consume prey
Photo Organisms that use light for energy but must acquire their C source from elsewhere
heterotrophs Source includes other organisms or the environment as they can’t use CO 2
Chemo organo One of the only 2 metabolic pathways (other being phototrophs) that moved to
heterotrophs multicellular life.
Organisms that acquire their energy through breaking of C bonds in organic substances,
which originated from another organism (as food)
These are predominantly animals and fungi.
Chemo litho Organisms that use inorganic substances to produce ATP, but must acquire their C sources
from another organism (e.g. colourless sulphur bacteria)
Lithotrophs Any organism that use inorganic substrates and transforms them into their reducing form
for biosynthesis or used in aerobic/anaerobic respiration to oxidize the NADH to NAD+
Exclusively seen in prokaryotes (bacteria and archea)
E.g. Nitrobacters, Acidithiobacillus, Ferrooxidans (using Iron)
Prokaryotes: Includes all unicellular organisms that lack a nucleus
This includes archea, bacteria, as well as cyanobacteria.
One of the longest living domains on Earth and also the first ones to arrive; most diverse.
Archea Bacteria: Single cell organisms that resembles a bacteria, but is different due to their genome
They arose in the Archean Eon, and have survived to this day in extreme conditions.
They have a very unique metabolic pathway, to be able to use Sulphur compounds for food.
Extremophiles: Property of Archea bacteria to be able to live in extreme conditions
They have not changed for bya’s, and have thought to have lived through mass extinctions
Part of reason why they are so resistant: highly branched, rigid plasma memb. doesn’t break
5 Thermophiles: Archea that can withstand high temperatures (45 to 122ºC)
Typically found in hot springs and hydrothermal vents. E.g. Thermos Aquatis
Methanogens: Archea that produce CH as4a metabolic by product, from living in non-oxygenated areas
E.g. methanoberibacter Smithii, found in human guts to help digestion of polysaccharides.
Halophiles: Extremophillic archea that can surive and thrive in very high salinity
E.g. halobacterium halobium.
(Eu)bacteria: Single celled organisms that are fairly uniform in morphology since developed 3.8 bya
they are the most abundant and varied organism on Earth
They do not contain double membrane organelles inside their cytoplasm.
Cyanobacteria: The first phototrophs on Earth, the first organisms to convert light and inorganic CO i2to
usable organic matter (food or structural components)
Also responsible for oxidation of minerals in ocean, O r2ch atmosphere and ozone layer.
A.k.a blue-green algae, that are primitive ancestor of plants and eukaryote algae.
Photosynthesis: Process by which light is converted into energy that cells use to make food/building blocks
This is achieved by the use of photosynthetic pigments to capture photons of light.
Takes inorganic CO a2d water as the reactants to produce glucose and O . 2
Stromatolite: Layers of sedimentary rock made by biofilms secreted by cyanobacteria.
One forms a layer, and when it dies, another one forms a lay on top of it.
Provides some of the most ancient records of life on Earth.
One of the 5 kingdoms in the Linnaean classification system
Includes unicellular organisms without a nucleus.
Includes the domain of bacteria and archea, but exludes cyanobacteria (its plantae)
Nitrogen Very important role of diazotroph bacteria.
Fixation: They are the only living creatures that can integrate atmospheric N into organic compounds
This N containing organics makes it way to plants and the rest of the ecosystem.
Living Fossils: The fact that some of the living bacteria resemble bacteria found in fossils bya’s old.
We can study the anatomy of these “living fossils” to speculate the origins of bacterial cells.
Eukarya: Domain consisting of all eukaryote organisms including protists, fungi, animals and plants.
Eukaryotes An organism with genetic material contained within a distinct nucleus.
6 PROTEROZOIC EON
Proterozoic: Started about 2.5 bya and ended about 542 mya.
This eon saw the rise of the eukaryotes and protists.
ENDOSYMBIOSIS AND ORIGINS OF THE NUCLEAR ENVELOPE
Nuclear Memb. that surrounds and protects the genetic material of the cell.
Envelope: Origins lie in the invagination of the plasma memb of the cell, creating a membrane around DNA
Provides a customized area in which genetic material occur at maximum efficiency.
Separates events like DNA replication and transcription from the rest of the cell.
Endomembrane Refers to the different membranes that are suspended in the cytoplasm within eukaryotes.
System: They are membranes that divide structural or functional units of the cell (organelles)
Structures of the endomembrane system include nuclear envelope, rER, sER, golgi, etc.
Plays an important role in transport, protection, and selective permeability.
Histone Proteins found in the nuclei of eukaryote cells, used in DNA packaging.
They are used to package DNA, making it more compact and easier to store.
They are highly alkaline, and combine easily with nucleic acid
Endosymbiosis: Process by which smaller bacteria entered a bigger bac