BioSec: Text: Unit 1: Setting the Stage

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Light and Life

The book starts out talking about Monet, the French impressionist painter, and the reason why his later paintings lacked light blue, and appeared to be toned towards red-yellow. This was due to a physical ailment of cataracts. The opaqueness of a cataract affected lens causes it to absorb certain wavelengths of light.

The way in which you see the world is affected by biological processes. The way in which you view a computer is similar – an operating system on a machine is effectively a map to the internal workings of the machine. It gives you a perspective view of how to interact and process information stored within a computer.

The Physical Nature of Light

Light functions: Light is a source of energy that sustains life. Light provides organisms with information about the physical world.

Photosynthesis – biological process to create energy rich molecules (algae)

Light is defined as the portion of the electromagnetic spectrum that humans can detect with their eyes. It is hard to characterize because it although it can be described as a wave it also behaves like a stream of energy particles. When light interacts with matter three things can happen – it can be reflected off of the object, transmitted through the object or absorbed by the object. Absorption occurs when the energy of a photon is transferred to the electron of the pigment molecule. Pigments are molecules that can absorb photons of light – each differ in the wavelengths that they can absorb. The feature critical to light absorption is a region where carbon atoms are covalently bonded with alternating single and double bonds (conjugated system) which results in the delocalization of electrons. A single photon results in the excitation of one and only one, electron in the pigment molecule and secondly the energy of the photon must match the energy difference between the ground state and one of the excited states in order for the photon to be absorbed.

Why is cholorophyll green in color? The color of a pigment is determined by the wavelengths of light it cannot absorb.

Photosynthesis sustains almost all life – uses the energy in sunlight to build sugar molecules from carbon dioxide and water – releasing oxygen as a by-product.

Light as a Source of Energy

The excited electron state is a source of potential energy that can be used to do work. This energy is used to synthesize energy rich compounds (NADPH and ATP) which are used to convert CO2 into carbohydrates. Other biological molecules such as lipids, proteins, and nucleic acids from simple building blocks found in the environment.

Light as a Source of Information

Organisms use light to sense their environment. Not every person – and not every species sees the world in the same way. Rhodopsin - the most common photoreceptor found in nature – mystery as to why – perhaps it developed very early in the evolution of life consists of a protein called opsin that binds a single pigment molecule called retinal absorption of a photon causes the retinal pigment to change shape – causing chain reaction - alteration of protein, intracellular ion concentrations and electrical signals which are then sent to the brain even things without eyes can sense light direction and intensity eye – can be defined as the organ animals use to sense light – what distinguishes the eye from an eyespot of an invertibrate is the vision process – requires not only an eye but also a brain or simple nervous system that interprets signals sent from the eye

image forming eyes come in two varieties: compound eyes and single lens eyes -

compound eyes can be found in insects and crustaceans – hundreds to thousands of ommatidia units fitted closely together – each one samples only a small part of the visual field. Enables even slight motion detection.

Lens eyes (camera) – light enters through the transparent cornea – a lens concentrates the light and a layer of photoreceptors at the back of the eye, the retina – records the image.

Darwin proposed that the eye as it exists in humans and other animals did not appear suddenly but evolved by variation (mutation) and natural selection over time from a simple, primitive eye.

Any application during it's development life cycle evolves to hopefully become better at the task it was designed to perform. Not only programs, but operating systems, and hardware are selected and chosen by respective audiences somewhat based upon the usability, and performance of the system.

Computer scientists not only program, but attempt to imitate life in many ways as well. Robots were initially designed to perform specific tasks, but have evolved over time to complete more interesting behaviours. Sensors are designed to provide input in a variety of different ways to affect the behaviour of a robot. Cameras and photocells detect light. Touch screens, keyboards and mice provide the ability to provide stimuli.

“An optically refined eye is no good unless the brain of the organism improves at the same time, allowing for more advanced neural processing of the information being sent by the optic nerve.”

This makes me think of the case for an older camera driver for a newer model of video camera which is 1080 p enabled technically, but due to the old driver it can only process a lower resolution.

What can computer scientists learn from certain biological processes – don't throw out the old to replace with the new (as generally this type of thing doesn't work). Change can happen a lot but it doesn't completely waste what has already been created.

Light can Damage Biological Molecules

Light is a form of energy that has the potential to damage biological molecules both directly and indirectly. All organisms have developed mechanisms to help prevent or repair damage once it occurs. Carotenoids are accessory pigments that protect the photosynthetic apparatus from high light levels by absorbing extra light and converting the energy to heat.

Question: Plants unable to synthesize carotenoids turn white when exposed to light because the chlorophyll becomes oxidized and the light harvesting capabilities destroyed – (what about mushrooms – is this the same for fungus (plant or animal)?)

Melanin is a pigment that absorbs UV radiation. Melanin in cells prevents light from damaging the DNA in skin cells that is linked with cancer by preventing the destruction of B vitamin folate. Melanin cannot completely filter out all light rays because vitamin d is necessary for proper bone development.

Melanin is the “firewall” of light entering our bodies. A firewall being a device or set of devices designed to permit or deny network transmissions based on a set of rules used to protect networks from unauthorized access while permitting legitimate traffic. /ref{}

Role of Light in Ecology and Behaviour

circadian rythyms nightly backups nightly software updates / system upgrades controlled by an internal clock – there are a lot of computational processes controlled by internal clock devices normal operational behaviour – versus abnormal operational behaviour – logins that occur in the middle of the night to specific accounts

DNA replication only occurs at night. <- highly sensitive processing occurs nightly in order to avoid serious damaging errors.

Hormone – melatonin – secreted from the brain in order to control sleep wake cycles as it's synthesis is active at night.

Camouflage – works when an animal is indistinguishable to another in its current environment.

Separating the message from the noise. Microdots. Cryptography. (Ideas that come to mind within this context.)

Story of the industrial revolution moths – reminded me of the mac laptops in the classroom – one university professor noted that a certain year, there were many different types of laptops and one or two macs, and the following year it was all macs. (can't find the reference right now) now due to the emergence of better security (ahem - supposidely) on Windows 7, will the variety go back to the way that it was?

Using Color as signals – warnings / error messages – The effective ones are different colors or make different sounds when they occur. So many high tech security companies focus their marketing also around these stark contrast colors – Symantec Yellow / Black – Black / White / Red – McAfee – Avast Orange / Black – Norton Orange / Yellow / Black

Life in the Dark

Even blind animals need to set their biological clocks to a circadian rythym. (Blind mole rat / Mexican cavefish)

Organisms Making their own Light: Bioluminescence

This is a process by which the pigment transfers energy from an electron to a photon to assume a grounded state. This reaction in nature is highly efficient in order to ensure less heat production within an organism.

Most bioluminescence is found under the sea, and less on land animals – most often found at great depths, but also in algae / bacterial blooms near the surface. One great mystery surrounding this phenomenon is bioluminescent mushrooms.

Origins of Life

What is Life?

The types of atoms and molecules found in living things is the same as those found in non living forms of matter. Living cells also obey the same fundamental laws of chemistry and physics as does the non living particles. Biochemical reactions that take place although complex are only modifications of reactions that take place by non living materials.

All forms of life share a set of attributes:

display order (cell fundamental unit – arranged in a highly ordered pattern) harness and utilize energy (acquire energy and use it to maintain state) reproduce (make more copies) respond to stimuli (adjust structure, function or behaviour according to environment) exhibit homeostasis (functions to maintain constant internal conditions) growth and development (increase their size) evolve (change over the course of generations to adapt to their environment)

Viruses are not alive because the lack the mechanisms required to produce proteins, and instead rely on highjacking the processes of a living cell to accomplish their replication.

3 Tenets of Cell Theory 1. Organisms are composed of one or more cells.

Single celled organisms are capable of carrying out all living activities. Multi-cellular organisms compartmentalize – that is, the activities are divided among groups of specialized cells.

2. The cell is the smallest unit that has the properties of life. 3. Cells arise only from growth and division of pre-existing cells.

The Chemical Origins of Life

The key building blocks of life – nucleic acids and proteins – are not individually synthesized molecules called monomers – they are macromolecules built up from large numbers of subunit monomers coming together to produce polymers. The synthesis of proteins and nucleic acids require protein-based catalysts (enzymes).

Clay – consists of very thin layers of minerals separated by thin layers of water. Present in evaporating tidal pools. The layered structure absorbs ions and organic molecules and promotes interactions (example: condensation).

Protobionts – first cells – abiotically produced organic molecules surrounded by a membrane.

The Origins of Information and Metabolism

Critical events necessary for life development: one to store, replicate and translate information for protein synthesis and the other to develop metabolic pathways to capture and harness energy for life functions (metabolism).

Deoxyribonucleic acid (DNA) is a large double stranded, helical molecule that contains a unique alphabet that provides the instructions necessary for assembling many components of a cell organism from simpler molecules. DNA is copied onto molecules of a related substance (RNA) which is used to direct the production of proteins. Any changes to DNA are what contribute to evolutionary change over generations.

Group of RNA molecules called ribozymes can catalyze reactions on precursor RNA molecules that lead to their own synthesis and on related RNA molecules. (single stranded molecules that can bend into specialized shapes) A single type of molecule could serve as both a carrier of information and a catalyst.

Selection may have favored DNA for the following advantages over RNA: Each strand is chemically more stable – due to the presence of the sugar deoxyribose instead of ribose. Base uracil found in RNA was replaced by thymine which allows for the detection of a damaged cytosine DNA is double stranded – in the case of a mutation / error – the complementary strand can be used to repair the damaged strand.

Early Life

The earliest conclusive evidence of life are fossilized remains of structures called stromatolites – a type of layered rock that is formed when microorganisms bind particles of sediment together to form thin sheets.

Panspermia – hypothesis that forms of life are present in outer space and may have seeded early Earth. Although life is complex it arose very quickly after the formation of the Earth. (The window for the development of life is very narrow) life is more resilient than previously thought, and could survive for years in space. (Extremophiles which are mostly prokaryotes can thrive under harsh conditions of temperature, pressure and nutrients and might be able to survive in a dormant state in interstellar space.)

prokaryotic and eukaryotic cells are the two fundamental cell types all forms of life are based from. Prokaryotic organsims exist in two domains: bacteria and Archaea.

Prokaryotic cells lack a nucleus (eukaryotic cells have a nucleus). All cells share fundamental features: - permeable plasma membrane (to separate external environment from cytoplasm (consisting of cytosol – mostly water, salts and various organic molecules, and structural features within the cell, including organelles)) – the membrane contains protein complexes that allow controlled transport of materials into and out of the cell. In photosynthetic prokaryotic cells the plasma membrane is the site of photosynthetic electron transport chains which harvest light energy for the synthesis of energy rich molecules. In eukaryotes mitochondria and chloroplasts perform energy transduction.

Prokaryotic cells have a nucleiod (central region) instead of a nucleus which is where the DNA of this organism is stored. They are 10 times smaller than a eukaryotic cell. They appear deceptively simple, as they are metabolically flexible which means they are able to use a variety of substances as energy and carbon sources to synthesize almost all of their required organic molecules from simple inorganic raw materials.

Where did oxygen come from? - Cyanobacteria could harness the electrons from water and when it split the water, Oxygen was a byproduct. The rise in oxygen in the atmosphere led to the evolution of prokaryotic cells. These cells were able to undergo aerobic respiration where energy is extracted from food molecules where oxygen acts as the final electron acceptor. Aerobic respiration enabled organisms to extract larger amounts of energy from food molecules than respiration that does not include oxygen. This was a key factor in the development of eukaryotic cells.

Eukaryotic Cells

Distinguished characteristics that separate eukaryotic cells from prokaryotic cells: separation of DNA and cytoplasm by nuclear envelope membrane bound compartments with specialized functions (mitochondria, chloroplasts, endoplasmic reticulum, Golgi complex, etc) highly specialized motor proteins that move cells and internal cell parts.

Membranes are connected directly or indirectly by vesicles – small membrane bound compartments that transfer substances between parts of the system. ER and Golgi complex serve the following functions: synthesis and modification of proteins protein transport into membranes or outside of the cell synthesis of lipids detoxification of harmful compounds Endoplasmic Reticulum – ER – extensive interconnected network of membranous channels and vesicles – each vesicle is formed by a single membrane that surrounds an enclosed space called the lumen. Rough er – ribosomes stud outer surface – destined for plasma membrane or release outside the cell smooth er – lipid production

Golgi complex – stack of flattened membranous sacs located between the rough er and the plasma membrane that recieves and chemically modifies proteins made in the ER transported to the complex by vesicles.

Secretory vesicles release their contents to the exterior of the cell by exocitosis. Vesicles may also absorb molecules from outside the cell using endocitosis.

Established theory of endosymbiosis states that prokaryotic ancestors of modern mitochondria and chloroplasts were engulfed by larger prokaryotic cells forming a mutually advantageous relationship called symbiosis. Mitochondria carry out aerobic respiration. Chloroplasts are thought to derive from endosymbiotic events involving cyanobacteria. Since cyanobacteria perform oxygenic photosynthesis – the host cell can easily supply the H20 necessary to drive photosynthesis. Only plants and algae have both mitochondria and chloroplasts.

The shape and internal organization of each type of cell are maintained by it's cytoskeleton (an interconnected system of protein fibers and tubes that extend throughout the cytoplasm). Three structural elements: microtubules (microscopic hollow tubes), intermediate filaments (fibres that occur singly, in parallel bundles and in interlinked networks) and microfilaments (thin fibres that consist of two rows of protein subunits wound around each other in a long spiral).

Flagella are long hairlike structures that project from the cell surface and function in cell movement.

“The internet is a series of Tubes” - unknown origin -

Structures that perform the same function but do not share a common evolutionary history are said to be analogous. If they do share history, they are homologous.

Division of labour – some cells specialize in harnessing energy – others for the motility of the organism. Cells no longer needed to be independent.

Selection, Biodiversity, and Biosphere

Air travel can affect the spread of viruses such as influenza A which kills 500000 people a year. Since H3N2 was first reported in 1968 – it has undergone periods of relative stasis lasting 3 to 8 years followed by rapid changes. WHO has the opportunity to monitor the situation in East and SE Asia allowing vaccines to be developed against the most threatening strains.


Measured as the number of species of organisms, and reflects the reality that life exists from the ocean floor to the atmosphere. Other than taxonomic categories organisms are grouped based on how they obtain carbon.

Autotroph – self nourishing – synthesize organic carbon molecules using inorganic carbon (C02) heterotrophs – they obtain carbon from organic molecules, either from living hosts or from organic molecules in the products, wastes or remains of dead organisms. Chemotrophs – chemical nourishment – obtain energy by oxidizing inorganic or organic substances phototrophs – obtain energy from light

chemoautotrophs – bacteria and archeans; not found in eukaryotes chemoheterotrophs – found in some bacteria and archeans, also in proteins, fungi, animals, and plants photoautotrophs – photosynthetic bacteria – in some proteins and some plants photoheterotrophs – found in some photosynthetic bacteria


Occurs when some force or phenomenon affects the survival of individual organisms, when a large population is exposed to a lethal factor and only resistant individuals survive to reproduce. If resistance is inherited, then the offspring of survivors will be resistant. If the resistant population is able to reproduce quickly, there is the potential for explosive growth of a population of individuals immune to the lethal factor. Key factors – selective force and capacity for explosive population growth.

User interface adoption and product availability. (Economic comparison?)


Defined as a gradual change in the characteristics of a population of organisms over time, and can be a result of selection. Explains both the unity and diversity of life: all organisms alive today descended from a common ancestor – why all organisms share features such as the use of ATP (adenosine triphosphate) as a cellular energy source, DNA (deoxyribonucleic acid) as genetic material, and plasma membranes composed of lipid bilayers. Darwin's central ideas to the theory of evolution by natural selection: individual organisms in a population vary in many heritable traits. Any population has the potential to produce far more offspring than the environment can support. Competition for limited resources means that only some individuals can survive. Individuals may have traits that give them an advantage in their local environment; these are more likely to survive and reproduce. These individuals pass on favorable traits to their offspring

Adaptive Radiation – these occur when an evolutionary breakthrough allows diversification of life.

The appearance of oxygenetic photosynthesis increased the concentrations of oxygen which led to aerobic respiration and the ozone layer, which allowed organisms to colonize terrestrial environments by blocking harmful (UV) rays. Changes caused by an increase in atmospheric oxygen triggered an extraordinary diversification of life.

Islands are seen as showcases of evolution – Hawaii, New Zealand, Madagascar, Mauritius, Galapagos Islands – also island populations of animals and plants can be vulnerable to extinction. (negative impact of humans on biodiversity)

Terrestrial animals used nontoxic excretory products (urea, uric acid), whereas aquatic ones still relied heavily on ammonia.

The Biosphere

The area occupied by life on Earth. The various physical environments and their different abiotic factors (sunlight, temperature, humidity, wind speed, cloud cover and rainfall) influence the evolution and diversity of organisms.

Climate – weather conditions prevailing over an extended period of time.

Biotic Factors

Cumulative Impact on Biotic and Abiotic Factors

Energy and Enzymes

Energy and the Laws of Thermodynamics

Free Energy and Spontaneous Reactions

The Energy Currency of the Cell: ATP

The Role of Enzymes in Biological Reactions

Conditions and Factors that Affect Enzyme Activity


Energy and Enzymes:

Catalyst called enzymes speed up the rates of reaction without the need for an increase in temperature.

Phosphatases: A group of enzymes catalyze the removal of phosphates groups from a range of molecules.

Energy: The capacity to do work e.g build a protein from a group of amino acids or pump sucrose across a cell membrane.

First law of thermodynamics: Energy can be transformed from one place to another, but it cannot be created or destroyed.

Second law of thermodynamics: The total disorder (entropy) of a system and its surroundings always increases.

It takes energy to maintain low entropy or the “orderness” of things.

Cells are always breaking down and new ones are always being created by the synthesis of a huge array of proteins, carbohydrates and lipid molecules.

Free energy: The portion of a system’s energy that is available to do work.

Spontaneous reactions:

1- Reactions tend to be spontaneous if the products have less potential energy than the reactants.

2- Reactions tend to be spontaneous when the products are less ordered than the reactants.

3- Change in free energy indicated whether a reaction is spontaneous. The free energy change as the system goes from initial to final states is the sum of the changes in the energy content and entropy.

Point of chemical equilibrium: a state in which reaction does not stop but rather a state in which the rate of the forward reaction equals the rate of the backward reactions.

The change in free energy of life is always negative as organisms constantly take in energy-rich molecules and use them to do work. Organisms reach equilibrium only when they die.

Exergonic reaction: A reaction that releases free energy. Products contain less free energy than the reactants

Endergonic reaction: The products contain more free energy than the reactants.The reactants involved in the reaction need to gain free energy from the surroundings to form products of the reaction. Catabolic pathway: Energy is released by the breakdown of complex molecules to simpler compounds e.g. cellular respiration

Anabolic pathway: Energy is consumed to build complex molecules from more simple ones. e.g. photosynthesis.

Cells supplies energy to drive endergonic reactions using ATP (adenosine triphosphate)

ATP contains free enegry from high energy phosphate bonds.

Removal of one or two of the three phosphate groups is a spontaneous reaction that relieves the repulsion of the negatively charged phosphate groups and releases large amounts of free energy.

The breakdown of ATP is a hydrolysis reaction and results in the formation of ADP (adenosine diphosphate) and a molecule of inorganic phosphate.

Hydrolysis of ATP produces free energy (heat).

How do living cells link the hydrolysis of ATP to an endergonic reaction such that the energy is not wasted as heat?: Energy coupling: An enzyme brings ATP and the reactant molecule into close association.

Energy in carbohydrates, fats and proteins consumed in food is used in the energy requiring endergonic process that combines ADP and Pi.

The continued breakdown and resynthesis of ATP is called the ATP cycle.

A spontaneous reaction does not mean that it proceeds rapidly.

Activation Energy: initial energy required to start a reaction and tranform molecules into transition state where bonds are stable and are ready to be broken.

Enzymes act as a catalyst by lowering the activation energy required by molecules in reactants to start a reaction.

Enzymes speed-up the rate of spontaneous exergonic reactions.

Enzymes do not supply free energy to the reaction.

Three main mechanisms in which an Enzyme lowers activation Energy:

1- Bringing the reacting molecules together

2- Exposing the reactant molecule to altered charge environments that promote catalysis

3- Changing the shape of a substrate molecule

Temperature and pH levels have a significant effect on enzyme activity and thus the reaction rates. The optimum pH level for an enzyme depends on the pH level of its environment. If Temperature becomes too high the enzyme of denatured.

As the enzyme concentration increases the rate of catalysis increases.

Competitive Enzyme inhibition: enzyme inhibitors bind to the enzyme’s active site

Non-competitive inhibitors: enzyme inhibitors bind to a location on the enzyme other than the active site.

Enzyme inhibition is important to the cell since it controls the presence of multiple active enzymes at the same time. (allosteric regulation).

Feedback inhibition provides a mechanism to prevent the wasting of cell’s energy. If the concentration of the inhibitor increases the enzyme action is inhibited, if the concentration of the inhibitor decreases, the enzyme is activated.

Membranes and Transport

An overview of the Structure of Membranes

The Lipid Fabric of a Membrane

Membrane Proteins

Passive Membrane Transport

Active Membrane Transport

Exocytosis and Endocytosis

Cellular Respiration

The Chemical Basis of Cellular Respiration


Cellular respiration allows organism to uses energy that is stored in chemical bonds of glucose (transferring electrons). This energy is then used to create ATP.

Redox reactions are a set of reactions that partially or completely transfer electrons. The reason they are called redox reactions is because they always occur in pairs – one oxidation and one reduction. The oxidation reaction is the reaction that releases an electron (increases in oxidation state). While the reduction reaction is the reaction that accepts this electron (decreases in oxidation state).

I think that redox reaction is extremely important and we see it almost everywhere. We use a battery for almost everything when we need a portable power source and it is an excellent example of redox reactions.

Cellular Respiration: An Overview


Pyruvate Oxidation and the Citric Acid Cycle

Electron Transport and Chemiosmosis

The Efficiency and Regulation of Cellular Respiration

Oxygen and Cellular Respiration


Photosynthesis: An Overview

The Photosynthetic Apparatus

The Light Reactions

The Calvin Cycle

Photorespiration and CO2-Concentrating Mechanisms