VIRUSES & ORIGIN OF CELLS

Outline the conditions on early earth/prebiotic

1. High temperature/UV radiation

2. No oxygen/reducing atmosphere (carbon dioxoide, ammonia, methane, hydrogen gas PRESENT) - volcanic activity/no ozone layer

3. Liquid environment/water vapour

Outline the evidence for origin of carbon compounds

1. Electrical spark

2. Reducing gases/ no oxygen

3. Water vapour

Organic compounds (amino acids/peptide/nucleotides/fatty acids)

Outline the theories for the origin of compounds

MILLER & UREY:

• Recreated conditions of prebiotic earth

• Synthesised carbon compounds from inorganic compounds

OPARIN & HALDANE:

• Theorised primordial soup

Outline the cell theory in greater detail

1. all living things are made of cells

2. Cells are the basic unit of life

3. Cells arise/come from other cells

Cells are the smallest units of self-sustaining life

Outline the spontaneous origin of cells

1. Synthesis of simple organic molecules/monomers

2. Assembly of these molecules into polymers/proteins (RNA, phospholipids and proteins, enzymes)

3. Chemical reactions were accelerated by catalytic molecules

4. Origin of self-replicating molecules (RNA) — self replicating, catalytic molecule which can be used as a genetic molecule

5. Packaging of molecules into membranes

Discuss the challenges of explaining origin of Miller Urey (spontaneous origin of cells)

Miller Urey COULD: prove that formation of oroganic compounds from inorganic molecule could occur under prebiotic conditions

Millery Urey COULDNT: prove that it did occur this way

LIMITATIONS:

1. Higher concentrations of gases (low concentration of methane prebiotic vs high concentrations used in the apparatus)

2. Only electrical spark in the apparatus — but carbon dioxide, ammonia and water require nuclear and UV radiation

3. In water, amino acids remain as monomers — prebiotic soup requires water

4. Difficulty synthesising nucleotides without specific compounds like cyanamide, cyanoacetylene, glycoaldehyde and glyceraldehyde.

Outline the alternate origins of cells

1. Protocell first

• Cell like compartments formed and gained genetic material later

• Cells can split to form new cells

2. Metabolism first

• Chemical reactions can develop independently

• System would evolve to include genetic material and membranes

3. Gene first

• Spontaneous generation of genetic material

• RNA could evolve to include metabolism and membranes

Outline overarching challenges in testing the theories of origin of cells

1. hypothesis and theories must be testable/repeatable

2. Not possible to replicate conditions of prebiotic earth

3. Fossil evidence of cells not possible

Outline the formation of phospholipid molecules

1. Protocells formed from fatty acids — stable compounds and could have accumulated

2. Condensation of fatty acids with glycerol to form triglycerides

3. Phosphorylation to form a simple phospholipid

4. Monolayer formation when a small amount of lipids are placed in water

5. Polar region associates with water, non-polar region orients upwards

Outline the spontaneous formation of vesicles

1. Coalescence of fatty acids — phospholipids into spherical bilayers

2. Fatty acid molecules are amphipathic (polar end is hydrophilic and attracted to water, non-polar end is hydrophobic with hydrophobic interactions)

3. Microspheres/small vesicles form spontaneously when fatty acids are mixed with water

Outline the evidence for the first genetic material & its evolution

RNA is presumed to be the first as it is self-replicating and catalytic

EVIDENCE:

1. Ribose is formed from primordial soup/Miller Urey experimentation

2. Ribose is required for deoxyribose formation

3. RNA can form spontaneously from RNA nucleotides

4. RNA is self-replicating

5. Ribozymes in ribosomes catalyse reactions that form peptide bonds

EVOLUTION:

1. Leads to DNA as the genetic material — more stable and enzymes as the catalytic molecules

2. RNA produced both proteins and DNA

Outline the fossil and molecular evidence for the last universal common ancestor (LUCA)

FOSSIL EVIDENCE:

1. Common ancestor is the most recent species from which two species evolved

2. Species will share characteristics with common ancestor

3. More shared characteristics → more closely related the species are/more recent common ancestor

4. Peradactyl limb is a homologous structure — similiar structrure, different functions

5. Perdactyl limb is an example of divergent evolution due to adaption to different environments & selective pressures

MOLECULAR EVIDENCE:

1. Shared molecular sequences of DNA (cytochrome C) or hemoglobin (polypeptide sequences)

2. Shared biochemistry — same bases in DNA and amino acids

3. Universal genetic code

4. Shared genes in archaebacteria and eubacteria that originated from LUCA

5. All life on earth evolved from a common ancestor from LUCA

Discuss the approaches to estimate dates of the first living cells and the last universal common ancestor

DNA/Protein Evidence:

1. DNA mutates at a constant rate/molecular clock over time

   • Can determine the time of divergence from the common ancestor

   • Estimates of the branching can be determines based on the number of mutations between the species

2. Proteins and amino acid sequences can also be used

3. Predictability of DNA base changes/mutation rates suggest evolutionary timelines

4. The greater the differences, the longer the time span since the two species had a common ancestor

5. Molecular clock can determine when the first living cells and the last universal common ancestor existed

FOSSIL EVIDENCE:

1. Mineralised structures (bones, bacteria)

2. Radioactive carbon dating and location can determine the age of the fossil

3. Location (lower strata) can identify older fossils, more ancient life

Discuss the evidence for the evolution of LUCA near hydrothermal vents

1. LUCA was a single celled autotrophic microbe with a RNA genome 2.5 - 3.5 billion years ago

2. Evolved in the deep ocean in alkaline hydrothermal vents

3. Hydrothermal vents have higher temperatures and gases which provide energy for the formation of complex carbon compounds

4. Anaerobic(no oxygen near hydrothermal vents) & Chemoautotrophic (so used energy from oxidation of inorganic compounds)

5. Fossilised microorganisms/bacteria rocks called stromatolites

   • Structures of hematite (iron (III) oxide formed are similar to those produced by modern bacteria)

   • Cancerous compounds and carbonate suggests the formation of organic compounds with similar metabolic processes/chemosynthetic reactions

   • Genetic and amino acid sequence analysis suggests they share a common ancestor (were anaerobic, chemautotrophic, thermophilic, converted nitrogen to ammonia)

Outline the challenge in explaining the spontaneous origin of cells

Pastur used a swan neck flask 
1. Curved to trap microbes/dust, whilst still allowing air
2. Boiled/sterilised nutrient medium removed micro-organism s
3. Over time, sterilised borth remained clear with no growth of micro-organisms 
4. Flask was exposed to air/dsut by tipping/cracking the glass -- then turned cloudy (microorgansims grew) 

Outline the structural features common to viruses

1. Capsid (outer protein coat) for attachment proteins

2. Nucleic acids (DNA/RNA) as genetic material

   • Linear/circular

   • Single/double strand

3. No cytoplasm — very few enzymes

4. Very small (20-300nm)

5. Non-living — obligate parasites

   • Fixed size

   • Acellular/not made of cells

   • No metabolism

   • Cannot reproduce independently

Outline the diversity of structure in viruses

1. Unlike living organisms that share a common ancestor, viruses are diverse

2. Features evolved from convergent evolution (different ancestor, similar environmental pressure)

Viruses vary in:

1. Size (20-300nm)

2. Shape (Polyhederal, spherical, helical, complex)

3. Genes (4-200/300 genes)

4. Method of replication (in cytoplasm/nucleus)

5. Structure of capsid (icosahedral/spiral)

6. Enveloped (lipid membrane)/non-envoloped

7. Nucleic acids (RNA/DNA)

   • Single stranded RNA can replicate positive/negative sense RNA

   • Retroviruses use reverse transcriptase enzyme copy RNA into double stranded DNA

Outline the enveloping/non-enveloping of viruses — as a means of diversity

ENVELOPED (HIV, corona, influenze):

1. Phospholipids from host membranes (plasma/internal)

2. Glycoproteins from virus bind to host membrane receptors

NON-ENVELOPED (Bacterophage, polio): Infect bacteria of plant cells

Outline the lytic cycle

1. The virus/phage reproduces using the host machinery and bursts out of the host cell, killing it

2. Viruses attach to receptors on the host cell using glycoproteins

3. Virus injects nucleic acid

4. Viral nucleic acid is transcribed and mRNA is translated to produce viral particles

5. Envelope of the virus comes from the membranes of the host cell

Outline the lysogenic cycle

1. The virus infects a cell and the viral DNA becomes integrated into the host genome

2. Phage particles are formed with both viral and bacterial DNA

3. Lysogenic cycles allow for incorporation of new genes into the bacteria, increasing adaptation and evolution

Define a prophage and lysogen

PROPHAGE: viral DNA incorporated into host DNA

LYSOGEN: A host cell with viral DNA

Outline temperate phages

1. Viruses that can adopt either a lytic or lysogenic reproductive cycle

2. A change in the environment (UV radiation/chemicals) can trigger a switch

How do you determine whether a virus enters the lytic/or lysogenic cycle?

Use the multiplicity of infection (MOI)

MOI = (# of infectious virus particles) divided by (# of target cells present)

Outline the different hypotheses & evidence for the origins of viruses

CELL FIRST - ESCAPE THEORY:

1. Viruses arose from genetic materials (DNA/RNA) that gained the ability to move between cells

2. E: Transposons (repetitive DNA sequences) that can move between cells

3. E: These genetic elements became surrounded by an outer boundary forming a virus particle

CELL FIRST - REGRESSIVE/REDUCTION THEORY:

1. Viruses are remnants of cellular organisms/were once small cells that became parasites of larger cells (mutualism)

2. E: Bacteria have lost the ability to peform metabolic processes and are parastiic

3. E: Over time, the cellular structures that were no longer needed were shed, leaving behind jsut the viral structures

VIRUS FIRST THEORY:

1. Viruses evolved before the host cell

2. E: During evolution, we expect simpler organisms to give rise to more complex organsims

3. Simple nature of virus particles indicates viruses evolved first

What is the evidence that viruses evolved from a common ancestor/multiple origins of evolution

COMMON ANCESTOR:

1. Simple structure

2. Common genetic code

3. Similar structure (capsid, nucleic acids)

MULTIPLE ORIGINS OF EVOLUTION:

1. Diversity of viruses!

Outline the rapid evolution in viruses

EVOLUTION:

1. Occurs over generations: viruses can replicate in an hour

2. Requires genetic variation: RNA has higher mutation rates + viruses don’t correct replication errors

3. Requires selective pressure: High selective pressure because organisms have evolved mechanisms to kill viruses