Biological Systems

Biology

The science of life that aims to understand the living world.

Empiricism

Knowledge derived from experience and sensory evidence, rather than innate ideas.

Hypothesis

A tentative explanation that is testable and falsifiable.

Theory

A general, verifiable principle that explains many observations, broader in scope than a hypothesis.

Emergent Properties

New properties that emerge at each level of biological organization that did not exist at the preceding level.

Abiogenesis

The hypothesis suggesting that life can spontaneously form from non-living material under specific early Earth conditions.

• Inorganic molecules → small organic molecules → macromolecules → proto-cell

Miller-Urey Experiment

A 1953 experiment that simulated early Earth conditions and demonstrated that organic molecules could form from inorganic compounds.

Panspermia

The hypothesis that life did not originate on Earth but was brought here from another planet.

Phospholipid

A type of fatty acid that forms the basis of cell membranes, characterized by a hydrophilic head and hydrophobic tails.

RNA

A nucleic acid that likely preceded DNA and has both information storage and catalytic properties.

What is theme 1?

Organisation

• Molecule → organelle → cell → tissue → organ → organism → population → community → ecosystem → biosphere

What is theme 2?

Information

• DNA stores information that is passed down from adult cell to progeny

What is theme 3?

Energy and matter

• Producers and consumers

• Chemicals taken from soil and air by plants → transferred to the organisms that eat the plants → decomposers break down

What is theme 4?

Interaction

• Everyone has a role that influences others

• Parasitism, egg fertilisation, predator vs prey, deforestation

What is theme 5?

Evolution

• Descent with modification (genetic variation)

Conditions of Early Earth

Atmosphere of methane, hydrogen, carbon dioxide, water vapour, ammonia, lightning strikes

Four main organic molecules?

• Amino acids → protein

• Nucleotides → nucleic acid

• Simple sugars → carbohydrates

• Fatty acids → lipids

Why is reproduction a vital characteristic of life?

• All organisms must be able to store + retrieve biological information to make copies of themselves

Steps of making a self-replicating proto-cell?

1. Enough energy + starting material → small organic molecules

2. Join into macromolecules like RNA that can self replicate

3. Wrap in protective phospholipid membrane

The Central Dogma

DNA → RNA → Protein

Transcription

DNA is transcribed to RNA by an enzyme called RNA polymerase which copies the 3’-5’ strand of DNA

Translation

An mRNA molecule associates with a ribosome (rRNA) and codons are interpreted by tRNA which transfers the correct amino acid to the growing polypeptide chain

The Central Dogma to evolution

Changes to protein structure can cause functional changes within cells/organisms. Protein structure is encoded by genes (DNA) which is inherited from parent to offspring, meaning changes at the DNA level are responsible for evolution of organisms

Evolution

A change in allele frequency in a population over time

Allele

A variant form of a gene

Natural selection

Individuals that have certain heritable traits survive and reproduce at a higher rate than other individuals because of those traits

Darwin’s observations

Members of a population often vary in their inherited traits

All species produce more offspring than the environment can support + many fail to survive or reproduce

Darwin’s conclusion

Species evolve over time as they adapt to their environment - descent with modification. All life is related and has a common ancestor

Modification at a genetic level

Errors in DNA replication where a single nucleotide base is changed, inserted or deleted from a DNA or RNA sequence of an organism’s genome, causing a mutation

Evidence supporting the Theory of Evolution

• Observations

• Fossil records

• Homology

Homology

Shared similarities between species that were inherited from a common ancestor

Natural selection mechanism

Survival of the fittest leading to adaptation

Genetic drift mechanism

Random process or chance events create bottleneck and founder effects

Gene flow

Result of migration / external source

Microevolution

Descent with modification is based on gradual change

Macroevolution

A set of highly conserved genes organize the body as it develops and mutations that cause changes in the spatial expressions of these genes can cause dramatic changes

3 types of rocks

• Igneous

• Sedimentary

• Metamorphic

Fossilization

Carcass is buried in mud and silt, soft tissue decomposes and leaves bones and shell, sediment builds up and hardens into rock

The deeper a fossil is in the strata ..

The older it is

Radiocarbon dating

Amount of time it takes carbon-14 to decay to half the amount a living-organism once had in the body

Fossil record documents

The great changes in the types of organisms on Earth at different points in time and that many were unlike what is alive today and that even though they were once common, are now extinct

4 main eons

Hadean

Archaean

Proterozoic

Phanerozoic

7 key events in the evolution of life on Earth

1. Prokaryotes

2. Atmospheric oxygen

3. Single-cell eukaryotes

4. Multicellular eukaryotes

5. Animals

6. Colonisation of land

7. Appearance of humans

First single-cell organism

Appearance of the first proto-cell 4.1-3.8 billion YA

Atmospheric oxygen

Appearance of photosynthesis caused an oxygen holocaust that decimated many bacteria 2.7 - 2.4 billion YA

First eukaryotes

Endosymbiosis between bacteria and first cells 1.8 billion YA

Multicellularity

Larger and more complex cells largely increased diversity and potential 1.8 - 1.2 billion YA

Appearance of animals

Animals like sponges first appeared 700 million YA followed by the Cambrian explosion 540 million YA

Colonisation of land

Small organisms 1 billion YA and then larger organisms like plants, fungi and animals 500 million YA

Appearance of humans

Primates > hominidae > homo > h. sapiens 300 000 YA

Evolutionary radiations

Many key events associated with increases in taxonomic diversity caused by elevated speciation rates

Cretaceous mass extinction

Largest mass extinction event with at least 70% of all life forms eradicated 65 MYA

Adaptive radiations

Mass extinctions lead to many available ecological niches that survivors can exploit once conditions stabilise

Four macromolecules

Carbohydrates, proteins, nucleic acids, lipids

Polymers

Long chains of monomer subunits

Monomer

Molecule that covalently bonds with others to form polymer chain

Dehydration reaction

Synthesizing a polymer by removing a water molecule to form a new bond

Hydrolysis

Breaking down a polymer by adding a water molecule to break a bond

Carbohydrate types

Monosaccharides and polysaccharides

Lipid types

Fats, phospholipids, steroids

Nucleic acid types

DNA and RNA

Nucleotide structure

Phosphate group attaches to a sugar and a nitrogenous base

Nucleotide alphabet of bases

DNA: C, T, A, G

RNA: C, U, A , G

Polynucleotide

Nucleic acids bonded by a phosphodiester bond and attach to a sugar-phosphate backbone

Base complementarity

A-T, G-C : percentage of A-T is the same, likewise G-C

Strand directionality

Two complementary strands run antiparallel: 5’ to 3’ strand of one is opposite to 3’ to 5’ strand

DNA sequence

Linear order of bases in a gene → amino acid sequence of a protein → protein structure → protein function

Chromosomes

Arrangement of copies of all genes in strands

DNA replication

1. Double helix unravels 2. Free bases bond complementary bases on og template strands 3. Polymerisation connects bases together, forming two new daughter strands

RNA exists as signal strands

Pyrimidines: C, U

Purines: A, G

Role of RNA

RNA copies the message of DNA and transports it to the site of protein production by messenger RNA (mRNA)

Protein functions

Enzymes, defense against pathogens, storage, transport across cell membranes, hormones, receptors for cell-signaling, contractile/motor, structure

Peptide bond

Bond between two amino acids

Polypeptides

Chain of amino acids formed of a backbone and side chains

Protein

One or more polypeptides

Amino Acid structure

Amino group attached to a side chain (R group) and a carboxyl group by alpha-carbon

Levels of protein structure

1. Primary structure: linear polypeptide chain

2. Secondary structure: a-helix and b-pleated sheets are segments due to hydrogen bonds

3. Tertiary structure: main 3D shapes from interactions between R-group

4. Quaternary structure: interaction between protein subunits

AA sequence ..

Determines structure to determine protein

Denaturation

Protein structures can unravel due to extreme environmental conditions leading to loss of structure and therefore function

Carbohydrates

• Have a carbonyl group and multiple hydroxyl group

• Polymers of simple sugars

• Energy and structure

Lipids

Mostly of hydrocarbons, are hydrophobic

• Energy storage, membranes, hormones

Phylogeny

Evolutionary history of a species

Systematics

Classification of organisms and the determination of their evolutionary history

Monophyletic (clade) tree

An ancestral species and all of its descendants

Paraphyletic tree

An ancestral species and some, but not all of its descendants

Polyphyletic tree

Most recent common ancestor is not part of the group

Dear King Phillip Came Over For Good Soup

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

Domains of life

Bacteria, Archaea, Eukarya

Kingdoms of Domain Eukarya

Fungi, Plants, Protists, Animalia

Determining the timespan of a phylogenetic tree

Fossil records and molecular clock

Convergent evolution

Evolution of similar features in species of different lineage due to similar environmental pressures not shared ancestry

Outgroup

Baseline comparison for the group of interest to determine which traits are ancestral and which are derived