microbes

The Last Universal Common ancestor is known to be the origin to all life on earth. There i  large debate over what this was.

The Earth is 4.5 Billion years old - The oldest fossil records date back to 3.7 billion years ago.

Stromatolites - structures of layered rock formed by cyanobacteria

Biofilms - Layers of single cell bacteria

(these are all considered too complex to be the first organisms)

LUCA is agreed to contain the following things in order for it to create life.

1. Assumption of RNA/DNA (most likely RNA as it holds gene for modification)

2. Metabolism - ATP synthase (requires H+ gradient), enzymes with iron sulfur clusters (catalyst)

3. Compartment

4. Heat stable genes (faster reactions at higher temps)

5. Lipids and porous rock (needed for chemical gradient)

Genes organisms contain from LUCA are passed down in a direct line of inheritance. Our genes nowadays may not be directly inherited from LUCA as they may have been transferred horizontally by other organisms living over long periods of time.

• Water
• Uv light and lightening
• Concentration of products
• metals (for catalyst and enzyms)
• Compartments
• Concentration gradient (H+) (Metabolism)
• Stable environment

Miller Urey experiment (1952)

Used simple gases, ammonia, methane, hydrogen gas, and boiling water in the lab in an attempt to recreate the conditions that made LUCA. After leaving the chemical reaction for 1 week it turned pink and they discovered that they created ammino acids. These are an essential building block of life. PROVED THE BUILDING BLOCKS OF LIFE CAN BE NATURALLY OCCURING.

AMINO ACID --> MONOMER --> POLYMER

Charles darwin

• thearised that if a protein compound was concenived in a warm little pool with a concoction of suitable elements (light, heat, water, ammonas, electricity, phosphate salts) then that could create the origin of life.
• Some suitable places for thus would be Oceans, under water vents, thermal pools, meteor crates.

Volcanic chambers

• Could be the most likely place that a lipid membrane was first stabalised?
• bubble in volanic rock could lead to the formation of interconnected chambers 
• But were lipids needed at all? As the ion gradient in volcanic rock could provide the same role and supply metabolism via energy differences in compartments)

RNA 

• formed from monomers in nature - miller and urey proved ammino acids could be formed naturally.
• Act as catalysts (known as riozymes in this state)
• Ribosomes present in all cells and necessary for replication  - possible mixture of RNA and protein 

The theroy that life originated in space, or elsewhere in the solar system.

• Meteorites have been found to contain organic molecules
• Bacteria and tardigrades can survive in space
• Life did appear quickly after the last great bombardment

Domain bacteria

• single cell prokaryotes
• forming biofilms
• most diverse domain

Domain Archea

• diverse prokaryotes
• Only rcently gained their own domain
• few have been cultured in a lab setting
• an example is extremophiles

The Haekel tree (1866)

• based on observable differences between organisms
• Very simple
• placed phyla in the complete wrong order

The Whitake tree (1967)

• Placed prokaryotes at the btoom of the tree

Phylogentic tree (2016)

• the current agreed view of lifeforms, includes total diversirty represented by sequenced genomes
• contains the 3 domains Plant, fungi, animal
• Proaryotes dominate the tree
• DNA encoding ribosomal RNA (rRNA) used to detrmine phylogenetic reltionships.
• Makes the most sense in evolutionary terms, animals only evolved recently - they have the smallest branch.

Cell wall

• bacteria cell wall made of Peptidoglycan (polysaccharide)
• Gram +ve bacteria has a simple wall - multiple sheets of peptidoglycan (up to 90% of the wall)
• Gram -ve bacteria has two membranes (inner and outer)

(Periplasmic space sits inbertween these layers and contains peptidoglycan and proteins/enzymes)

• Archea cell wall made of Psuedomurein (polysaccharide)
• S layers interlocking protein and glycoporotein molecules

Cytoplasmic membrane

• Permeability barrier - sepereates cell from environment and enables homeostasis (transporting nutrients and waste in and out of cell

(Property of being hydrophobic and hydrophillic allows this permeability)

• proteins in the structure creates pores and channels so solute can be transported and controlled across the membrane.
• Protein anchor - holds proteins in place so reaction can occur (formed from layer of lipids)
• these proteins help to stabalise the structure of fluid lipids
• maintains a proton gradient - allows generation of energy

Inside the cell

• Nuceoid - contains main genetic information , double stranded DNA
• Cytoplasm - chemical reactions
• Plasmid - circualr loop of double stranded DNA containing genes
• Ribosomes - Translates mRNA into proteins in the cytoplasm
• Magnetosome - biominerlised particles of magnetite, imparting a magnetic dipole on the cell allowing it to orient itself in a megnetic field. This causes magneto taxis, the process of migrating along earths magnetic field lines.
• Gas vesicle - conical structure containing protein. The confer bouyancy so the cells can position themselves in regions of the water coloumn best suited for their metabolism.
• Endopsore - Highly differentiated dormant cells, functioning as survival structures that cn tolerate harsh conditions. (last resort of survival)
• Storage vesicle

outside cell

• Cell wall 
• cytoplasmic membrane
• flagella - thin appendages anchored into the cell, allowing it to push or pull itself through liquid.
• capsule - sticky coating of polysaccharides that stick to the cell wall and form a tight matrix that excludes small particles.
• pilli - filimentous structures made of protein that extend from the cell, allowing bacteria to stick to surfaces, other cells and biofilms.
• fimbria - short forms of pilli

Vertical gene transfer: Binary fission

• The main from of replication. Cell replicates genetic information and then divides into 2 daughter cells.
• Each daughter call has a copy of original DNA, half of cytoplasm, cell wall etc..

Horizontal gene transfer (or lateral)

• Transfer of genetic information between cells. not inherited.
• Transformation is a process of horizontal gene transfer where some bacteria take up foreign genetic material from the environment (Naked DNA).

Conjugation (Via Pili)

• Plasmid is passed and copied from one prokaryotic cell to another
• A single stranded piece of plasmid is passed to the recipient.
  
• The recipient cell synthesises a new DNA strand
• Both cells end up with a double stranded copy of the plasmid DNA.

Transduction via virus

• A virus can copy its own DNA and inadvertently pick up DNA from its host cell.
• Very rarely this DNA can be inserted into the DNA of the next host to be infected and is therefore a form of horizontal gene transfer.

Areas with no available water

Places above 130 degrees (this includes certain depths of the crust layer in the earth)

e.g molten rock, earths crust, magma

Organisms that can survive extreem conditions - Extremophiles

• Hottest (hyperthermophile) - 80 degrees
• Coldest (Psychrophile) - -20 degrees
• Highest pH (Hyperalkaliphile) - 12.5 pH
• Lowest pH (Hyperacidophile) - 0 pH
• Highest pressure (Hyper piezophile/ Hyperbarophile) - 11 Mpa

1. First cells divided imperfectly

2. This caused random mutations, detrimental ones died off, beneficial ones outcompeted.

3. Different niches in the environment formed, gene populatiobs evolved into seperate species suited to their own habitat.

4. Comunities know as biofilms/microbial mats formed, shown in fossil records 3.5 billion years ago (fibrae. pilli, and capsules attatched to each other)

+ OF BIOFILMS

• Community structure prevents detachment from a favourable environment.
• Saftey in numbers, protected from the environment
• Large availability of trapped nutrients
• Sharing of nutrients and enzymes with neighbour cells.

• Used as a survivial startegy
• Cooperation is mostly beneficial
• Can be taken advantage of - cheaters are any cells using public goods without giving anything back.

The black queen hypothesis

In a community organisms will lose genes over time by relying on others in the community to continue to provide them (damaging symbiosis)

Nutritional modes

Photoautotroph - energy from light, Carbon from CO2

Chemoautotroph - Energy from inorganic chemicals, Carbon from CO2

Photoheterotroph - Energy from light, carbon from organic compounds

Chemoheterotroph - Energy and carbon from organic compounds

Reaching depths of 5Km below continental surface, over 10Km under the sea surface

Reaches an end once tenperatures hit 120 degrees, beginning the molten core

• Mostly microbrial life ound within - Bacteria, Archae, eukaryotes
• Contains 1/10 - 1/3 of the total global biomass (70% of all prokaryotes)
• (diversity equal to that above ground)
• (Makes up almost 50% of all life on earth)
• 30 Peta grams of carbon

Microbes living here have very slow metabolism and growth rate - Estimated to divide once every 1000 years

EMERGED 1.7 BILLION YEARS AGO

step 1 -

• 2 billion years ago, prokaryote cell had increased metabolism due to increased oxygen
• This caused major increase of energy, cell then absorbs more food and more energy from the food it finds.
• As a result, gentic material increases in size and more membrane space is needed for the ribosomes to stick to.
• This caused the plasms membrane of the ancestral prokarypote to fold in. This allowed more space so more ribosomal reactions could occur.
• Cell eventually becomes more complex  - leading to formation of endoplasmic reticulum, nuclear envelope, and nucleus.

Step 2 -

• Larger ancestral prokaryote engulfed the aerobic heterotrophic prokaryote (cyanobacteria)
• This became mitochondria, the ancestral heterotrophic eukaryote was was create.

Step 3 - 

• Ancestral heterotrophic eukaryote then engulfed a photosynthetic prokaryote (cyanobacteria)
• This led to the eukaryote containing all of the previous organelles as well as a plastid
• = Ancestral photosynethic eukaryote (precursor to all living orgainsms)

If one eukaryotic cell goes into an another, u would expect to see 2 nuclei.

There is evidence that chloroplasts of some algae are not derived from 1st endosymbiosis

Later in evolutionary history algae were taken up by other eukaryotic cells to create cells within cells.

• mitochondria and chloroplasts contain their own DNA  - closed circular like that found in bacteria
• Mitochodrial DNA in the nucleus resembles bacterial gene sequences 
• 70S ribosomes are found in mitochondria and chloroplasts (eukaryote ribosomes are 80S)
• Phylogeney of RNA fits early endosymbiosis
• Mitochondria divide by binary fission

scale - 10-1000x larger that prokaryote

Known as chimeras - genes are from more than one organism

Membrane bound nucleus contains: Chromosomes, Diploid, Histone protein

Folded internal memebranes contain: Endoplastic reticulum, Gogo complex

Membrane bound organelles: Mitochondria in animals, Mitochondria and chloroplasts in plants

Archaeplastida

Rhizaria

Chromalveolata

Excavata

Amboebozoa

Opisthokonta

Rhodophytes - Red algae

Chlorophyted - green algae

Glaucophytes

Chlorarachniophyta

Foraminifera

Radiolarians

Oomycetes 'egg fungi'

Diatoms

Chrysophytes 'Gold (brown) algae'

Ciliates

Dinoflagellates

Apicomplexans

Diplomonads

Parabasalids

Kinetoplastids

Euglenid

Gymnamoebas

Entamoebas

Slime molds

Fungi