biology: Life's machinery

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BIOLOGY: LIFE’S MACHINERY

BIOL10009

SEMESTER ONE, 2021

BIOLOGICAL SCIENCES

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MODULE ONE: WHAT IS LIFE?

SUMMARY OF MODULE

Life is defined by Cellular Theory and the following criteria:

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Responds to the environment

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Ability to grow and change

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Independently reproduces

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Contains a metabolism

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Maintains homeostasis

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Passes traits onto offspring Life began 3.8 billion years ago on Earth. The earliest forms of evidence of life are

stromatolites – indentations on rocks caused by cyanobacteria.

Biomolecule Structure Purpose

Nucleic Acids Bonded via phosphodiester bonds between nucleotide monomers, polar/hydrophilic

Instructs cells on how to undergo protein synthesis

Proteins Bonded via peptide bonds between amino acid monomers, polar OR non-polar

Forms hormones, antibodies, enzymes, intercellular signals, pheromones, or structural components

Carbohydrates Bonded via glycosidic links between monosaccharide monomers, polar/hydrophilic

Primary source of energy for cellular respiration and acts as structural component in plants

Lipids Bonded via ester links between fatty acid chain monomers, non-

polar/hydrophobic

Stores energy, acts as a structural component for the cell membrane, aids in heat retention and buoyancy in water

Primary active transport involves pushing concentrated ions into the extracellular

environment, using ATP, to allow for a different species of ions that are concentrated intracellularly to enter the cell. Secondary active transport involves the transfer of large molecules that are mixed in with several smaller ions.

Prokaryotes Eukaryotes

Consist of the domains bacteria and archaea Consists of the domain eukarya

Evolved 3.8 billion years ago Evolved 2.1 billion years ago

Prokaryotic ribosomes are smaller, and are made up

of fewer rRNA strands/proteins Eukaryotic ribosomes are larger, and are made up of

more rRNA strands/proteins Single chromosome is circular. Chromosome is not

stored in a membrane-bound nucleus. Reproduction occurs via binary fission

Chromosomes are linear and wrapped around histone proteins. Reproduction occurs via mitosis or meiosis

Organelles consist of ribosomes, peptidoglycan wall,

capsule, cell membrane, cytosol, cilia, and flagella Organelles consist of the endomembrane system, mitochondria/chloroplasts, microbodies, cytosol and the cytoskeleton

Bacteria can form resting spores. Archaea cannot, and are commonly extremophiles

Eukaryotes cannot form resting spores and are most commonly not extremophiles

DNA Polymerase synthesises the leading strand of DNA in the 3’ to 5’ direction in a

linear fashion, however the lagging strand must be synthesised backwards (as synthesis

can only occur in 3’ to 5’ direction), through the synthesis of multiple small Okazaki

fragments.

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MODULE ONE: WHAT IS LIFE?

What exactly is life? This is perhaps the fundamental question of Biology. How do we know that something is alive? In this module, you will investigate the molecules and cellular structures that make up the world of living things

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DEFINING LIFE

Life is defined by seven different criteria that must be met:

❖ Responsiveness to the environment

❖ The ability to grow and change

❖ The ability to reproduce independently

❖ Have a metabolism and be able to breathe

❖ Maintain homeostasis

❖ Must be made of cells

❖ Pass traits onto offspring

Most biologists subscribe to a way of thinking in line with cellular theory, which states that the cell is the fundamental, smallest unit of life. Organisms must be made up of cells to be considered ‘alive’. Cellular theory also states that all cells come from pre-existing cells, and that all cells share a common ancestor.

Prions, viruses, and viroids do not meet these criteria. They are not able to reproduce independently of a host cell, they do not have metabolic processes and in the case of prions, are not made up of cells. Their status as living or non-living agents is still currently debated.

By mimicking the conditions of early earth for a period of 80 years, the Miller-Urey experiment found that many biological molecules can form on their own. All 20 essential amino acids, DNA/RNA bases, lipids, 3- and 6-carbon sugars and certain vitamins or coenzymes were observed within the experiment to have formed independently. As such, it is plausible that life was able to generate on Earth on its own. It is hypothesised that groups of lipids would naturally join via intermolecular forces to form proto-cells, and smaller molecules could diffuse into these proto-cells into an environment that would allow the production of bigger biomolecules. The energy needed for this production could easily come from lightning.

The RNA world hypothesis is a theory that states that DNA was formed when RNA enzymes (ribozymes) aided RNA in self-replicating to become double-stranded. For a myriad of reasons, DNA was a more reliable information molecule than RNA, and so it replaced it as the core nucleic acid in most living organisms.

Meteorites (such as the Murchison meteorite) have been found to contain biomolecules on their surface; proteins that were found on asteroids had chemically different R groups on their amino acids, suggesting they were developed in different conditions to proteins from Earth.

This evidence forms the basis of panspermia – the theory that life on Earth began when extra- terrestrial unicellular organisms arrived from a meteorite that collided with the Earth, instead of life originating in situ.

As far as biologists have currently observed, all forms of life depend on water - it is the universal solvent, which allows chemical reactions to take place at the speed and magnitude necessary for sustaining life. Water cannot do this in solid or gaseous forms, and so planets must be within the habitable zone of their respective stellar systems (where water exists in its liquid form) if it is to develop life. As such, life can only have started on Earth after liquid water became available, roughly 4 billion years ago.

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The first evidence of life is suggested to be approximately 3.8 billion years old, found in the form of stromatolites, which were formed during the Proterozoic period. Stromatolites are specific patterns of layered rock formed by the movement of cyanobacteria, which still look the same. The oldest stromatolites are 3.5 billion years old. Many early life forms would not have fossilised due to the lack of hard structures and their microscopic nature, and so it is difficult to observe examples of organic life from this period.

MOLECULES OF LIFE Nucleic Acids

Biomacromolecules are composed primarily of carbon, hydrogen, nitrogen, and oxygen, with carbon being the absolute basis and backbone for most of such molecules. Carbon is significant as it can form up to four covalent bonds and is relatively chemically stable.

Biomolecules are also reliant on hydrogen bonding; the strongest form of intermolecular bonding between partially positive hydrogen and electronegative atoms of adjacent molecules (such as oxygen, fluorine, and nitrogen). Water undergoes hydrogen bonding and is polar.

The four main biomacromolecules consist of proteins, nucleic acids, lipids, and carbohydrates.

They make up approximately 30% of all biomass on Earth.

Nucleic acids consist of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), which are made up of nucleotide monomers - nitrogenous bases, attached to a sugar-phosphate backbone. Both DNA and RNA are non-branched, linear polynucleotides. Uracil, the nitrogenous base that replaces thymine in RNA, has one less methyl group than thymine.

Other than that, they are identical, and both are classified as pyrimidines (single ringed) along with cytosine, whereas guanine and adenine are purines (two ringed structure).

Figure One: Adenine nucleotide, consisting of deoxyribose sugar, phosphate group and adenine nitrogenous base. Visuals were made using https://molview.org/?cid=74049528, courtesy of Herman Bergwerf

The monomer for DNA is called a nucleotide – nucleotides are made up of a nitrogenous base, a molecule of deoxyribose sugar, and a phosphate group. Before the phosphate is added, a bonded nitrogenous base and pentose sugar make up a nucleoside. The pentose sugars deoxyribose (which makes up DNA) and ribose (which makes up RNA) only differ by one oxygen on carbon-2 of the five-membered ring.

When nucleotides join up to form nucleic acid polymers, phosphodiester bonds form between carbon 3’ atoms and phosphate groups in a condensation/dehydration reaction, which releases a water molecule in the process. Nucleotides are always added to the 3’ end of the growing strand

2𝐶 𝐻 𝑂 𝑃 → 𝐶 𝐻 𝑂 𝑃 + 𝐻 𝑂

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The final strand of DNA is coiled up around proteins called histones and then stored as chromosomes within the nucleus.

Proteins

DNA acts as the instructions for protein synthesis - the coding strand of DNA is read and transcribed by mRNA, which adds on complementary nucleotides in the 5’ to 3’ direction of the RNA strand, and the 3’ to 5’ direction of the DNA strand. The final RNA strand is identical to the template strand, other than the switch between thymine and uracil bases. This RNA strand travels to the ribosome where translation occurs. A polypeptide chain is built by amino acid monomers, brought by tRNA - RNA which has folded in on itself in order to form an appropriate 3D structure.

The translation of RNA, built from a DNA template, allows for the synthesis of proteins; the most functionally diverse of all biomolecules (they act as enzymes, hormones, travel passages, antibodies, etc.). Proteins are three dimensional molecules, made up of a polypeptide chain which has been folded up to form a unique structure that relates to the protein’s function. Polypeptide chains are made up of amino acid monomers that are bonded together via covalent peptide bonds. All amino acids contain an amine group, a carboxyl group, and a variable R group attached to an α-Carbon. There are 20 different amino acids, each with a unique R group that is classified as polar, non-polar, acidic, or basic.

Carbohydrates

Carbohydrates, also known as polysaccharides or sugars, are the primary source of energy for most organisms. They also sometimes act as structural components, seen particularly through the presence of the polysaccharide cellulose in plant cell walls. All carbohydrates have the general formula (CH₂O)ₙ, where n is typically an integer between 3-8. The monomer for carbohydrates is called monosaccharides.

Monosaccharides bond together to form disaccharides and eventually polysaccharides via condensation polymerisation reactions that create glycosidic links between monomers. Three of the most common monosaccharides are glucose, galactose, and fructose, which all have the same chemical formula. They form the following disaccharides:

• Sucrose: α-Glucose and Fructose (α-1,2 glycosidic link)

• Maltose: α-Glucose and α-Glucose (α-1,4 glycosidic link)

• Lactose: β-Glucose and Galactose (β-1,4 glycosidic link)

Common polysaccharides consist of starch, chitin, cellulose, and glycogen. Starch is a plant polysaccharide that comes in two forms, a non-branched form, amylose, which consists of purely α-1,4 glycosidic links, and a branched form, amylopectin, in which there are branches attached via an α-1,6 glycosidic link. It is a source of energy for plants. In animals, fungi and bacteria, glycogen is used instead of starch. Glycogen is a highly branched molecule made up of α-glucose molecules.

Figure Two: Molecular structure of amylose (starch), made up of alpha glucose monomers (the oxygen in the glycosidic bonds point downwards). Image courtesy of Patricia Shapley, University of Illinois, 2012, http://butane.chem.uiuc.edu/pshapley/GenChem2/B10/2.html, accessed December 2021

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Cellulose is an abundant polysaccharide in the kingdom plantae; it makes up a large proportion of plant cell walls. They are made up of β-glucose molecules (in which the direction of oxygen in the glycosidic links alternates), which makes them very strong and indigestible. Cellulose consists of β-1,4 glycosidic linkages between monomers.

Fungi use chitin instead of cellulose, which is also

made up of β-glucose, however with acetyl groups (CH₃CHNH) attached to carbon-2, forming N-acetylglucosamine.

Figure Three: Molecular structure of cellulose, consisting of beta glucose monomers. Image sourced from https://www.123rf.com/clipart-vector/cellulose_structure.html?sti=o11b6nelvl2okrqx22|

Lipids

The final biomacromolecule classification is lipids, which are nonpolar and insoluble in water.

These molecules consist of a smaller proportion of oxygen compared to carbohydrates, which relates to their ability to store energy and combust.

Triglycerides are lipids composed of three fatty acid chains attached to a glycerol molecule via three ester links. Waxes, on the other hand, consist of two carbons attached via an ester bond, and two fatty acid chains attached to each carbon.

Lipids may be saturated, monounsaturated, or polyunsaturated depending on the number of double bonds within the fatty acid chains. Saturated fatty acids have no double bonds and thus have chains which are completely straight with strong intermolecular bonds. These fats have higher boiling points and are typically solid at room temperature. Monounsaturated fats contain one double bond and polyunsaturated contain multiple double bonds - each (cis) double bond forms a kink within the tail, and each kink weakens the strength of intermolecular bonds, which lowers the boiling point. As such, these lipids are more likely to be in liquid oil form at room temperature. Lipids are used as energy reserves or as blubber for warmth/buoyancy.

One form of lipids are phospholipids; two fatty acid tails attached to a glycerol, phosphate head and choline molecule. Unsaturated phospholipids are more fluid than saturated ones due to the weaker attraction between phospholipid molecules. The head of the phospholipid is hydrophilic while the tail is hydrophobic, meaning that when in an aqueous environment, lipids naturally form micelles (circular monolayer) or bilayer membranes. These membranes are semi-permeable. Non-polar, small, or uncharged molecules (such as water, gases, or small polar ions such as urea) can diffuse through such membranes. Other molecules require the assistance of protein channels or protein carriers to pass through the membrane.

Active Transport

Protein channels and carriers form pores within the cell membrane that allow for the transfer of molecules that cannot passively diffuse through. These proteins are involved in both active and facilitated transport. When molecules need to pass through the plasma membrane against the concentration gradient, active transport, which requires ATP, is used instead of facilitated diffusion. There are two forms of active transport: primary and secondary.

In primary active transport, ions that are high in concentration extracellularly are pushed out of the cell to allow for the uptake of ions which are concentrated intracellularly

For example, three sodium ions are pushed out and two potassium ions are brought in.

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This creates a build-up of negative charge inside the cell as positively charged ions are lost.

The negative charge can then be fixed by secondary active transport, which uses extracellular positive ions to push through large, non-charged molecules into the cell, thus returning the charge to normal and allowing the transport of larger molecules

For example, sodium ions re-enter the cell, pushing a large glucose molecule along with it.

Secondary active transport does not require ATP; however, it requires the products of primary active transport which does require ATP.

Figure Four: Diagram of primary active transport (left) and secondary active transport (right). Image courtesy of GuyHowto.com, https://www.guyhowto.com/active-transport-definition-process/

PROKARYOTIC LIFE Origination of prokaryotes

Prokaryotes are a classification of life that describe cells with no membrane bound nucleus or specialised organelles. They are typically small compared to eukaryotic life; 1 - 10µm versus 10 - 100µm. Furthermore, they are far older than eukaryotes, as seen from their metabolic simplicity. Although prokaryotes are simple, this does not correlate with their degree of diversity or how much they have evolved since their origination. Prokaryotes are often far more evolved than eukaryote equivalents.

Prokaryotic life arose approximately 3.7 billion years ago, with eukaryotic life arising approximately 1.5 billion years later. Stromatolite fossils act as the earliest evidence for life, and they come from ancient prokaryotes. Photosynthetic cyanobacteria, which evolved from early proto cells that formed into prokaryotes, increased the concentration of O₂ in the atmosphere through photosynthetic conversion of CO₂, which was high in concentration in the early Earth atmosphere. Due to the increase in atmospheric oxygen concentration, ozone, O₃, was also soon synthesised through abiotic reactions. This molecule formed a protective layer in the Earth’s atmosphere called the ozone layer, which would protect future terrestrial life forms from the Sun’s carcinogenic UV rays. The increase in oxygen gas allowed for the rapid evolution and diversification of life that occurred during the Cambrian explosion. The addition of oxygen into the atmosphere is known as the “great oxygenation event”. Conditions of early Earth included the following:

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❖ Low concentrations of oxygen gas

❖ High concentrations of carbon dioxide

❖ High concentrations of ammonia

❖ High concentrations of methane

❖ Intense UV radiation hitting the Earth’s surface

As such, early life evolved to work around these conditions – photosynthesis was anaerobic due to the lack of oxygen reactant, and most life remained under Earth’s oceans to avoid being affected by the Sun’s deadly radiation.

Morphology and Physiology of Prokaryotes

Bacteria have three outer layers: the capsule, the cell wall, and the plasma membrane. The cell wall in prokaryotes is made up of a different molecule than the cell wall in plants. Plant cell walls are made up of cellulose, whereas bacterial cell walls are made up of a protein called peptidoglycan. Peptidoglycan is more prominent in gram positive than gram negative bacteria.

Figure Five: Prokaryotic cell diagram. Image sourced from https://www.shutterstock.com/search/prokaryotic+cell

A unique feature of bacteria is the ability to form resting spores; a phenomenon in which bacteria produce cocoons when nutrients are low, or the environment is not favourable. Once they have entered these cocoons, they enter a state of rest. Certain spores can be opened after extremely long periods of time, up to 250 million years with their bacterial inhabitants still alive - these immortal spores are called endospores. Endospores are more common in gram positive bacteria than gram negative bacteria, and they are resistant to UV light. The possibility of these endospores is in fact an argument in favour of the possibility of panspermia, as these endospores might be able to persist in the vast coldness of space for long periods of time.

Prokaryotes can replicate very fast compared to eukaryotic cells, due to their minimal DNA.

They can replicate every 20 minutes via binary fission. Due to the magnitude of bacteria populations, it can be assumed that less DNA is a positive selection pressure for their evolution.

Flagella, an organelle which aids in movement of bacteria, are only made up of one protein, called flagellin. In comparison, eukaryotic flagella are composed of 200-300 different proteins.

Prokaryotic ribosomes are smaller and simpler than eukaryotic ribosomes.

❖ Prokaryotic ribosomes are made up of 55 proteins and 3 rRNA strands, with a mass of 2.3 MDa (mega Daltons), and subunits of 30s + 50s = 70s (S = svedberg units)

❖ Eukaryotic ribosomes are made up of 80 proteins and 4 rRNA strands, with a mass of 3.3 MDa, and subunits of 40s + 60s = 80s

Due to their differences, prokaryotic ribosomes are a common target of antibiotics – these drugs aim to inhibit protein production by attacking ribosomes. The protein products synthesised by ribosomes are essential to bacterial function.

Because bacterial DNA is circular, prokaryotic cells go through a slightly different replication process than eukaryotic cells. The circular chromosome binds to the plasma membrane, replicates, and then the two copies slide away from each other, allowing the plasma membrane to split in two. There are no organelles that need doubling, and only one chromosome, so this process is relatively simple, and less costly in terms of energy. Bacterial DNA also mutates at a much faster rate, due to the faster rate of spontaneous mutation, and thus they are much more functionally and genetically diverse.

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There are two domains of prokaryotes: bacteria and archaea. Archaea are more closely related to the third domain of life, eukarya, despite being very morphologically similar to bacteria. Archaea are similar to eukarya in terms of transcription/translation processes, using methionine as the starting protein and the use of RNA polymerases. Furthermore, archaea lack a peptidoglycan wall that is characteristic of bacterial cells. Archaea are not pathogenic and do not form resting spores.

Archaea are typically extremophiles; often acidophilic, thermophilic or both. They can withstand extreme temperatures and pH while maintaining homeostasis. They can survive in environments without oxygen by combining carbon dioxide and hydrogen gas.

Prokaryotes have multiple uses and functions within modern day society - some strains are pathogenic, while others form a part of the normal flora of the digestive system. They are also used for recycling and breaking down sewage, fixing nitrogen gas in the atmosphere into ammonia for plants, and producing insulin and other hormones needed by those with autoimmune disorders/hormone deficiencies.

EUKARYOTIC LIFE Eukarya Characteristics

Eukaryotic cells are far greater than prokaryotic cells in size and complexity. Compared to the differences between bacteria and archaea, there is not much difference in the morphology or genetics between plant and animal cells. Eukaryotes are roughly 2.1 billion years old and were likely to have started as jellyfish like organisms, which do not fossilize well due to their lack of hard bony structures.

The control centre of the eukaryotic cell is the nucleus, surrounded by the nuclear envelope.

This envelope contains nuclear pores that are 50 nm in diameter, created by transmembrane proteins separating the membrane. The nucleus contains all DNA except mtDNA and chromosomal/plastid DNA. Within the nucleus is the nucleolus; the subregion containing ribosomal genes, allowing for the creation of ribosomes that occurs via a phenomenon known as ribosomal biogenesis.

DNA is wound tightly around histone proteins, which pack together to form chromosomes.

Histones are positively charged to neutralise the negative charge of DNA, allowing it to be condensed to chromosomal form. A nucleosome is a subunit of DNA that consists of eight histones, in which DNA is wrapped around each twice. When DNA is wound tightly into chromosomes, it's called heterochromatin, and when it opens and unwinds to be transcribed, it is called euchromatin. When DNA is in its heterochromatin form, it cannot be transcribed, thus this is a form of transcriptional regulation.

Mitochondria have two membranes, an outer membrane, and an inner membrane which projects into the intra-organelle environment. These inner projections are known as cristae. In between the two membranes is the intermembrane space, and the fluid within mitochondria is called the mitochondrial matrix. Cellular respiration takes place within the mitochondria, and so appropriate protein complexes such as ATP synthase, are embedded into the surface of the cristae.

Chloroplasts are present within plant cells, either as a singular organelle or as a population.

Like mitochondria, chloroplasts also have two membranes, the inner membrane making up the lamellae and thylakoids where the compound chlorophyll is kept. Also contained in chloroplasts is stroma, the cytoplasm of the chloroplast, and the amyloplast, a vacuole

biology: Life's machinery