BIOLOGY

Introduction

1.   Knowledge and comprehension of biological facts, ideas and opinions

2. Appropriate use of knowledge – application, analysis and interpretation, synthesis and evaluation

3. Experimental skills such as manipulation, measurement, observation, recording, reporting, presentation and planning, and designing of experiments.

Biology, bio (life) and logy (study), is the study of all living things. It draws on other natural sciences such as physics and chemistry, to better understand the functions and reactions of these living things. The environment is also an important factor as it often affects the lives of these living things.

Biology encompasses the study of genetics, evolution, and all the functions of living organism. It has many parts and may be broken up into practical and theoretical biology.

Practical Biology

This encompasses the medical sciences, breeding sciences(this is used widely in the horse racing industry to gain desired traits) and experimental biology.

Theoretical Biology

This includes taxonomy (the classification of living things), ecology (the study of populations and their environments), biochemistry (the study of the chemistry of organisms) and microbiology (the study of micro-organisms).

Taxonomy

All living things (organisms) have seven characteristics in common. They all:

1. Reproduce- produce an offspring (organism of its own kind)

2. Feed/need nutrients- make their own food (plants), or consume readymade food as a source of energy

3. Respire- release energy from food with the aid/use of oxygen

4. Grow- increase in size by getting taller or wider

5. Excrete- get rid of unwanted substances

6. Move- plants move parts of themselves while animals often move from place to place

7. Sensitive- plants and animals react to changes in the environment.

Although all organisms have these characteristics, there are differences amongst them that enable them to be classified differently.

Biological classification was originated in the work of the Swedish naturalist Carolus Linnaeus, where classifications were done based on shared physical characteristics. The science of classifying into ordered systems that indicate a natural relationship is known as taxonomy. Taxonomy involves the naming of organisms and placing these organisms into relevant groups based on their similarities. The taxonomic classifications are as follows:

- Kingdom

- Phyla (Phylum)

- Class

- Order

- Family

- Genera (genus)

- Species

example

The list above is in the order of the largest (kingdom) to the smallest (individual species). The kingdom is the most general (broad) classification, while species is the most specific means of classifying an organism.

The scientific name of any organism is called the binomial name. For example, humans have a binomial name of Homo sapiens. You will notice the binomial name can be broken down into two names:  a genus name followed by a species name.  Hence the binomial name indicates the species and genus to which the organism belongs.

The basic criterion for an organism to belong to the same species is the ability to interbreed. If two organisms of different species try to breed then there will not be any offspring or the offspring will be sterile. An example of this is when a horse (Equus caballus) tries to mate with a donkey (Equus assinus).

You may be wondering why we classify. The answer is simple; it brings order and makes life easier. There is however no single perfect classification system and as we learn more about organisms our original classification is modified.  For example:  a small child may classify all four legged organisms  as dogs, but over time as the child learns and grows he/she will notice that there are similarities and differences within the group of four legged animals, and will  develop a  better system of classification. This is similar to what biologists have done over many years.

Recap

1. The science of classification is called taxonomy.

2. Various species are located and classified in an ecosystem.

3. Species are a group of closely related organisms that are able to interbreed and produce fertile offspring.

4. All living things display seven characteristics (life processes).

Ecology Symbiosis: Mutualism, Commensalism and Parasitism The Ecosystem Feeding Relationships Food Chain and Food Webs

Symbiosis: Mutualism, Commensalism and Parasitism

The species in an ecosystem will interact in different ways. These interactions may have positive, neutral or negative impacts on the species involved.

The term symbiosis can be used to broadly refer to these types of relationships as it directly translates to mean living together (sym: with; bio: life).

Symbiosis is the ecological relationship between two or more organisms living closely together with some form of feeding relationship involved. The three main symbiotic relationships are:

- Mutualism, where both organisms benefit.

- Commensalism, where one organism benefits while the other organism is not harmed.

- Parasitism, where one organism benefits and causes harm to the other organism.

Mutualism

This is a beneficial relationship to both partners of different species living together. For example a bee and a pollinating flower. The bee gains nectar from the flower for survival, as it uses the bee to carry its pollen to other flowers. So both organisms living together benefit from their existence.

Commensalism

The association of two or more partners living together, where only one benefits from the partnership and the other remains unharmed.  An example of this is the relationship between a sea anemone with and a clown fish. The anemone travels with the fish on route to its destination and the fish remains unharmed.

Parasitism

Parasites are completely dependent on a host for survival. The relationship is beneficial to one, and harmful to the other.  Parasites may live outside or inside a host; they are called ectoparasites (the prefix ecto means outside) and endoparasites (theprefix endo means inside). An example of the endoparasite is the tapeworms which live in the digestive systems of its host. Examples of ectoparasites are ticks and lice.

The Ecosystem

An ecosystem is a system formed from the interaction between all the organisms living in a specific area, as well as the interactions these organisms have with the non-living components of their environment, such as air, soil, water and sunlight. In other words, an ecosystem consists of a community (all the species in a habitat) and its environment.

Each organism within an ecosystem has a specific role to play. The term niche is used to describe the status/function/role of an organism within its environment and community.

Both environmental factors as well as the organisms in an ecosystem are susceptible to change. The organisms may change so significantly that the environment is no longer suitable for their existence. This may lead to new organisms occupying that space. This change in the plant and animal community, which is usually gradual, is referred to as succession.

The species found in an ecosystem are often very dependent on each other for survival as energy usually flows through the ecosystem from one organism to the other.

Hence, we are able to arrive at food chains and food webs after studying ecosystems.

Feeding Relationships

Energy is contained within organic molecules produced by autotrophs (organisms that make their own food) – such as plants. These energy rich organic molecules are made by autotrophs through the process of photosynthesis. Because these autotrophs are able to make their own food, they are called producers. These producers provide food (material and energy) to heterotrophic organisms (organisms that cannot make their own food), such as animals. These animals may then be eaten by other animals transferring their energy to the next.

This chain continues as each preceding animal is eaten. This chain is called a food chain. A food chain may be defined as a simple diagram that shows the flow of energy from one organism to another in the form of food. Each stage of the food chain or each feeding level of the chain is called the trophic level.

The first level of the food chain is known as the (primary) producer and is in most cases a plant e.g. grass, cabbage etc. Animals (consumers) that eat plants (feed on the primary producer) are called primary consumers. Organisms that feed on the primary consumers are secondary consumers. Those that feed on secondary consumers are called tertiary consumers. Quaternary consumers then feed on tertiary consumers.

Examples of food chains:

Animals that feed on plants ONLY are known as herbivores.

Animals that feed on meat (animals) ONLY are known as carnivores.

Animals that feed on both plants and animals are called omnivores.

Organisms called saprophytes are also found within the food chain, and they serve as decomposers of living organism. A decomposer is an organism that breaks down dead or decaying organisms. In breaking down dead organisms, decomposers recycle nutrients found in dead organisms as well as help with the eradication of waste material. The two most common examples are bacteria and fungi.

Bacteria mostly decompose meat and waste from carnivores, while fungi preferentially break down the remains of fruits and vegetables. Decomposition of dead organisms is important to other members of an ecosystem, as the decomposer often releases substances that are useful to the organisms that are still alive.

NOTE:

1. Food chains are diagrams so they should be constructed with a pencil.

2. The arrows in a food chain always go across (left to right), never up and never down.

Food Chain and Food Webs

Within an actual ecosystem the feeding relations are more complex than simple food chains. This is because tertiary consumers may also feed on primary consumers and secondary consumers. There is also selective feeding among consumers. For example, secondary consumers may not consume all primary consumers and primary consumers may not consume all types of producers.  In the food chains containing omnivores such as humans that feed on consumers and producers, then this chain may become more complex. As a result of this complexity, feeding relationships are represented by food webs rather than food chains.

A food web may be defined as a series of interconnecting food chains that shows the feeding patterns amongst organisms in a habitat/ecosystem/community.

Just as food chains, food webs have trophic levels. The lowest level which consists of the producers is the first trophic level. Going up the web, the trophic levels increase as the complexity of the organisms and their feeding patterns also increase.

DIAGRAM OF A TERRESTRIAL FOOD WEB

In the web shown above, there are several food chains present. Because of the commonalities amongst the chains, they can be joined at some point to show the complex feeding patterns of the organisms. There are three trophic levels in the web constructed.

1. The first trophic level consists of the seeds and leaves.2. The second trophic level comprises of squirrel, iguana, grasshopper and caterpillar.3. Ocelot, broad-winged hawk and fly catcher are all on the third and final trophic level of the food web.

NOTE:

1. The arrows point towards the organisms that are higher up the food chain. The arrows should be drawn with a ruler, never curved and the arrow-head should not be shaded.

2. Food webs are diagrams so they should be constructed with a pencil. They should also have a title.

3. In this instance, an exception is made concerning crossing lines as this is sometimes unavoidable in food webs.

Nutrient Cycles

Carbon Cycle Nitrogen Cycle

Carbon Cycle

THE CARBON CYCLE

With light energy from the sun along with the presence of chlorophyll, water and carbon dioxide are used by plants to create carbohydrates via photosynthesis.

Through the process of respiration, living organisms (plants and animals) utilize oxygen in order to convert food into energy; carbon dioxide is released by this process.

Plants may be eaten by animals or later die and decompose to become fossil fuel. Fossil fuels formed from the decomposition of plants and animals are later burned to provide energy returning carbon dioxide to the atmosphere.

Carbon is transferred up the food chain from the producers (plants, which create carbohydrates via photosynthesis), to varying levels of consumers.

Carbon may also be used in the formation of carbonated rocks, a process known as chemical combination. When these rocks are broken down, they release carbon dioxide back into the atmosphere. This process is known as weathering.

Summary:

The processes that require carbon dioxide are photosynthesis and chemical combination.

The processes that release carbon dioxide/carbon are respiration, weathering and combustion.

The Nitrogen Cycle

The Nitrogen cycle

Lightning reacts with nitrogen gas in the atmosphere to form nitrogen dioxide. This nitrogen dioxide (NO2) is then partly dissolved in water during rainfall to form nitric acid. When the rainfall hits the ground, nitrates are formed which are then absorbed by the roots of plants.

Nitrogen fixing bacteria (present on the root nodules of leguminous plants) converts nitrogen in the atmosphere to ammonium salts through a process call ammonification. Ammonification is also done by decomposers (saprophytes) which convert dead plants and animals as well as faecal matter into ammonium salts. The ammonium salts are then converted into nitrates by nitrifying bacteria. This process is known as nitrification.

Some of the nitrates present in the soil are absorbed by plants. These nitrates in the plants are eaten by animals. The animals in turn release faecal matter and eventually die and decompose, returning nitrates to the soil. The addition of fertilizers to the soil also produces soil nitrates.

The nitrates in the soil can also be converted into nitrogen gas by denitrifying bacteria present in the soil. This process is called denitrification. The nitrogen is returned to the atmosphere and the cycle continues.

Diffusion

Diffusion occurs in everyday life. For example, whenever someone sprays perfume you will eventually smell it across the room. This is an instance of diffusion.

Diffusion is correctly defined as the movement of particles from a region of high concentration (many particles in a small area) to a region of low concentration (few particles in a small area). When the particles are released in the surroundings, they randomly move until there is an even distribution of the particles throughout.

DIAGRAM SHOWING THE DIFFUSION OF PARTICLES

Diffusion is mostly seen in liquids and with gases. This is because solid particles are held together very closely and cannot move very far. When molecules can move freely, they tend to spread themselves out as evenly as possible.

Diffusion not only occurs in everyday life within the environment, it also occurs within the bodies of living organisms.

Examples:

-The oxygen and nutrients from a mother is transported across the placenta via diffusion to the foetus during pregnancy.

-Carbon dioxide needed for photosynthesis is diffused from the atmosphere into plants through pores called the stomata.

Many other instances of diffusion occur in both plants and animals.  The rate at which diffusion occurs depends on the concentration gradient. The concentration gradient is the gradual

difference in concentration between two regions. The greater the difference in the concentration, the steeper the concentration gradient and the faster diffusion will occur faster.

Space 1                       Space 2

000                             00000000

Space 3                       Space 4

00                               0000

Diffusion will occur faster from space 2 to space 1 than from space 4 to space 3.

Activity

Fill a container with water and leave it to stand. Place some dye in the container of water, as shown above and leave for about 10 minutes. What do you think will be seen after the time has passed?

Osmosis

Osmosis is defined as the movement of solvent particles (usually water) from a region of high concentration to a region of low concentration through a partially permeable membrane. It is often regarded as a form of diffusion in which only water molecules move. So, water moves from an area where it is in high concentration (abundant), to an area where it is in low concentration (less abundant) until both areas have the same concentration of water.

Consider the diagram below where large solute particles are unable to pass through the membrane, it only allows water to pass through. Osmosis occurs until there is an equal concentration on either side (until equilibrium is met).

The Figure above shows Osmosis.

The arrows represent the direction in which water molecules will move across the semi-permeable membrane.

Water has a natural tendency to move from a place where it is in higher concentration to a region where it is of a lower concentration. This tendency is measured as the water potential. Osmosis can be loosely defined as the movement of water molecules from a region of higher water potential to a region of lower water potential. Pure water has the highest water potential. The presence of solute particles (dissolved particles) will reduce the water potential. Because of this, the more solute particles that are present, the lower the water potential of the solution.

How Osmosis applies to Organisms

Cell membranes are often compared with a Visking tube as they only allow certain substances to pass through them. This is termed as selective permeability or partially permeable.

The body is made up of approximately 70% water. The cytoplasm of cells contains a lot of this water. This means that a lot of osmosis occurs within the body as the concentration of the cytoplasm may vary from time to time. Different solutions will have different effects on red blood cells as it regards to osmosis. A hypotonic solution has higher water concentration than the contents of the cell. A hypertonic solution has a lower water concentration than the cell contents.

Osmosis and animal cells

Because animal cells have no cell wall, they are not strong enough to withstand the pressure caused from swelling. Water therefore moves by osmosis into the cell and the cell becomes

swollen and bursts, dispersing the cell contents when the cell is exposed to a hypotonic solution. The bursting of a cell is called lysis of the cell. In a hypertonic solution, water will leave the cell and enter the surrounding solution. In this case, the cell will most likely shrink and become shrivel (flaccid). An isotonic solution has equal concentration of water outside and inside the cell so there is no net movement of water. The cell remains normal.

Osmosis and plant cells

In the case of plants, many prefer the water concentration being greater outside the plant. Unlike an animal cell, plant cells have a cell wall. This means that the plants cell will become turgid in hypotonic solution, but will not burst as water moves in the plant. As water moves in the plant and the concentration of water in the plant gets greater, eventually equilibrium is reached (equal concentration of water inside and outside the cell). After this point, any water coming in the plant cell is released at an equal rate thereby achieving an osmotic balance. This water movement inside plants is essential for building pressure, called turgid pressure. Turgidity is important in plants as it helps them to stay upright and keeps the leaves firm. In a highly concentrated solution, plant cells will become shrivelled. If the surrounding solution is highly concentrated, plasmolysis will occur. Plasmolysis occurs when the cell membrane surrounding the cytoplasm shrinks further and further away from the cell wall. This often results in the death of the cell as the cell membrane usually gets damaged while it gets torn away from the cell wall.

Many times the movement of ions requires movement against a concentration gradient, this is called active transport. Energy is used because substances must be moved against their natural tendency to diffuse in the opposite direction. Many times plants (roots) require more minerals from their surroundings although they have a greater concentration of minerals inside their cells already. This movement of ions is called active transport.

Introduction to Plant Nutrition

All living things feed/need nourishment. In a previous lesson, you learnt that plants are producers, and producers make their own food. This food is in the form of a sugar (often glucose). Sugars are made during a process called photosynthesis from carbon dioxide and water. The end products, organic compounds, are composed from the simple inorganic compounds water and carbon dioxide. In order for the reaction to take place energy comes from light (usually the sun) and is stored within the sugar which is an energy-rich molecule.

The two raw materials required for photosynthesis are acquired by different means. Carbon dioxide is absorbed by the leaves while water is obtained by the roots from the soil.

Photosynthesis occurs inside special organelles called chloroplasts. This organelle is found in all green plants and is located mainly in the leaves; hence photosynthesis takes place mainly in the leaves. The conversion of light energy to chemical energy is done by the chloroplast.

Many different kinds of sugars may be made during photosynthesis, but glucose (C6H12O6) is the one that is usually made. The glucose is dissolved and transported throughout the plant via vascular tissues called phloem. This dissolved glucose may be stored for later use or converted into a myriad of products such as different sugars, starch, pectin, lignin and many more.

The whole process of photosynthesis involves two stages: the light dependent stage and the light independent stage.

Light Dependent Stage

Also referred to as the light reactions, this stage of photosynthesis occurs on the thylakoid membrane of the chloroplast.

In the light dependent stage or light reactions, light from the sun is absorbed by the chlorophyll of the plant. The light energy is used to split the water molecule (H2O) into hydrogen and oxygen (photolysis).

(Remember that carbon dioxide and water are used to make the sugars produced by photosynthesis.)

 

The equation used to depict photolysis is:

(oxygen is given off as a by-product)

 

The energy produced in the light stage is used to produce ATP (adenosine tri-phosphate). ATP is a high-energy molecule that stores energy for later use. The oxygen that is given off is released from the plants. This is why it is said that plants use CO2 and release O2 during the process of photosynthesis.

 

The hydrogen produced is attached to NADP (nicotinamide adenine dinucleotide phosphate) to form NADPH, where H signifies the hydrogen atom. Hence NADPH is used to store and transport Hydrogen for the light independent stages (dark reaction). NADPH is therefore referred to as an electron carrier as it only transports the hydrogen electron from one place to another.

Dark Reaction

These reactions occur without light but can occur with light as well. This stage of photosynthesis is also known as the Calvin Cycle or the dark reactions.  

The Carbon-fixation reaction occurs at this stage. This reaction uses the energy (in the form of ATP) produced from the light stage to provide the energy needed to combine the hydrogen (also produced from the light stage) with carbon dioxide to form glucose (C6H12O6). Several enzymes are used in the process of converting CO2 to carbohydrates. The overall process is represented by the equation below:

Word equation for overall reaction:

Chemical equation for overall equation:

Recall:

-Carbon dioxide is obtained from the air by the leaves of the plant via diffusion.

-Water is obtained by the leaf cells from the plant’s transport systems.

-Sunlight is absorbed by the chlorophyll in the leaves and supplies the light energy needed for the process.

-Carbohydrates that are produced is mainly glucose and is transported throughout the plant and later produces starch. Oxygen is merely a by-product.

Factors Affecting Photosynthesis

During the process of photosynthesis, there are certain factors that alter (speed it up or slow it down) the rate at which the process is carried out. Three major factors that will be discussed are light intensity, carbon dioxide concentration, and temperature.

 

Light Intensity (Sunlight)

 

The graph above shows how the rate of photosynthesis may be coupled with the available light (sunlight).

 

Effect of light intensity on the rate of photosynthesis

Photosynthesis is dependent on light from the sun; as the light intensity increases, the rate of photosynthesis increases at a similar rate. Overtime the rate of photosynthesis falls off and begins to level off as other factors become limiting, in other words, there is a point at which no

further addition of light will benefit the plant and the rate of photosynthesis now becomes dependent on other factors. This is called light saturation and is usually reached at 10000 lux.

 

Carbon dioxide concentration

Carbon dioxide is needed to make sugars. Carbon dioxide concentration in the atmosphere is about 0.03% but an increase in the percentage of carbon dioxide available in the air will result in an increase in the rate of photosynthesis. There is also a point where any further increase in carbon dioxide concentration will not lead to an increase in the rate of photosynthesis.

TemperatureTo some extent both the day and night reactions of photosynthesis are enzyme controlled and therefore temperature sensitive. As with all enzyme controlled reactions there is an optimum temperature. The effect of temperature on enzyme controlled reactions is shown in the next section.

Other factors that may affect photosynthesis include:

-Chlorophyll concentration

-Water

-Pollution

-The stomata on leaves (whether they are open or closed)

Investigating Photosynthesis

Several experiments may be carried out to test what substances/conditions are necessary for photosynthesis to take place. Tests may also be done to verify the use of carbon dioxide and water in the photosynthetic process. To confirm the products, additional tests may also be done.

In testing for the substances/conditions necessary, experiments may be done in controlled environments where only the substance being tested for is lacking. If the substance missing is indeed essential for the photosynthetic process, there will be some hindrance to the process. However, if the condition/substance is unnecessary, photosynthesis will occur regardless of the absence of that particular condition/substance.

If tests are being carried out to determine whether a leaf photosynthesizes, the leaves have to be de-starched before experimentation. This can be done by leaving the leaves in a very dark area for at least 24 hours. The iodine test can then be performed to verify the absence of starch in the leaf.

In a previous lesson, it was said that plants photosynthesize to make sugars, mostly glucose. This glucose is often converted to starch. Hence, leaves can be tested for starch as a means of proving that the leaf is photosynthetic. Iodine solution is used for the starch test and a positive result is indicated by a blue-black colour after iodine has been added to the leaf.

Note:

It is important that leaves being tested for starch are boiled and de-colourised before testing is done.

The Leaf

Being the main food-making organ in plants, leaves are often green in colour as they contain a lot of chlorophyll. The veins seen on a leaf are used to support the leaf. In these veins, there are vascular bundles which contain xylem vessels as well as phloem which carry substances to and

from the leaf. The diagram below shows what is seen when the cross-section of a leaf is viewed under a microscope.

TRANSVERSE SECTION THROUGH PART OF A LEAF

 

Functions of parts of the leaf

Epidermis- protects the inner layers of cells in the leaf. It does not contain chloroplasts. The cells of the upper epidermis often secretes a waxy substance (cuticle) that stops water from evaporating from the leaf. Sometimes a cuticle is present on the under-side of the leaf.

 

Stomata- singular stoma, these are small holes on the leaf that are surrounded by guard cells. These holes open or close depending on the position of the guard cells which are ‘sausage shaped’. The guard cells contain chloroplasts.

 

Mesophyll- these cells make up the middle layer of the leaf. (meso- middle, phyll- leaf). These cells all contain chlorophyll.

-Palisade layer- these cells are closer to the top of the leaf and are arranged like a fence/ palisade.

-Spongy layer- these cells are below the palisades and are more round and arranged loosely with air spaces between them.

 

Vascular bundle- this makes up the vein in a leaf. It consists of xylem vessels and phloem tubes.

-Xylem vessels- these carry water around the plant

-Phloem tubes- carries food around the plant that has been made by the leaf