B1.1 - Cell structures

B1.1.1 - Plant and animal cells

Types of cell

Differences between plant cells and animal cells

Plant cells have three main subcellular differences, as they produce their own food and are unable to move their whole body from place to place.

• Chloroplast - They contain chlorophyll, which captures the energy from the sun due to its green colour, and stores is as ATP. This is then used in photosynthesis and they are the only green parts of the cell.

• Vacuole - This is a watery sack of dissolved sugars and salts in the middle of the cell. This helps to keep the cell ridged, which keeps the plant upright.

• Cell wall - It is made of a tough fibre called cellulose and it surrounds the cell, helping to keep it supported and protected.

B1.1.2 - Bacterial cells

What is bacteria?

Bacteria are the smallest living cells at 1μm! For this reason, they require a very powerful microscope to be seen. On an agar plate, the dots are colonies of bacteria. Each colony can be made up of millions of individual bacteria. Bacteria are unicellular organisms - this means that each cell can carry out the seven life processes independently: movement, respiration, sensitivity, growth, reproduction, excretion and nutrition. Therefore, bacteria are prokaryotic cells.

Examples of prokaryotic cells

Most prokaryotes are bacteria. Here are some examples:

• Escherichia coli or E.Coli - This causes food poisoning.

• Streptococcuss - This causes sore throats.

• Streptomyces - This is found in soil.

B.1.1.3 - Light microscopy

What is a light microscope?

Light gets passed through an object placed on a slide on the stage, then through the objective lens and the eyepiece lens. This magnifies the object, allowing you to see small structures in detail.

How can you observe cells through a light microscope

• Move the stage to its lowest position.

• Select the lowest magnification objective lens.

• Place the slide with the cells onto the stage and hold down with the clips.

• Raise the stage as high as it will go without it touching the lens.

• Lower the stage slowly using the coarse focus knob until you see the cells (they will normally be blurry)

• Turn the fine focus knob slowly until the object comes into clear focus.

Once the cells have been focussed on a low magnification, to focus on a higher magnification (to see the cells in greater detail) switch to a higher magnification lens but keep the stag in the same place. Use the fine focus knob to bring the object into clear focus again.

Magnification

To calculate the total magnification, use this formula:

Total magnification = eyepiece lens magnification x objective lens magnification

Why stain cells?

Scientists use stains on cells because many cells are colourless. The stain may highlight the whole cell or just certain subcellular structures, making it easier to observe.

Examples of some common stains are:

1. Methylene blue - this makes it easier to see the nucleus of an animal cell

2. iodine - this makes it easier to see the plant cell nucleus as it stains starch

crystal violet - this stains bacterial cell walls.

How to apply a stain.

1. Place the cells on a glass slide.

2. Add one drop of stain.

3. Place a coverslip on top.

4. Tap the coverslip lightly with a pencil to remove air bubbles.

B1.1.4 - Electron microscopy

What is an electron microscope?

The resolution of a microscope is defined as the smallest distance between two points that can be seen as separate entities. Structures smaller that 0.2 micrometres cannot be seen with a light microscope.

Electron microscopes were developed during the 1930s and use high-energy electrons rather than light (hence the name) to produce an image. They allow scientists to see in greater detail than ever before, such as the detail within subcellular structures, such as chloroplasts.

The two types of electron microscope are:

1. Transmission electron microscopes (TEM) - produce the most magnified images by a beam of electrons being passed through a very thin slice of a sample.

2. Scanning electron microscope (SEM) - produce a 3D image of a surface by the bean of electron being sent across the surface of a specimen, which are then collected to form an image.

Comparing microscopes: light vs electron

B1.2 - What happens in cells?

B1.2.1 - DNA

What does DNA look like?

DNA is stored in the nucleus of every cell. Long molecules of DNA are called chromosomes. Most people have 46 chromosomes in each cell, half which are inherited from your mother, and half from your father. Most people’s DNA is unique - apart from identical twins and clones.

DNA is arranged into short sections that code for a specific characteristic, such as eye colour. These are called genes.

The code that a gene contains causes specific proteins to be made that determine the cells function. An example of this would be haemoglobin, which binds to oxygen, allowing red blood cells to transport it around the body.

The combination of genes in an organism controls how an it functions and its appearance.

What is the structure of DNA?

DNA is made up of two strands, which are joined together by bases, and is twisted together to form a shape known as a double helix.

DNA is made up of lots of smaller units called nucleotides which are joined together, making it a polymer.

Each nucleotide is made of a sugar called deoxyribose, a phosphate group and a base. The bonds between the bases are what holds the two strands of DNA together.

There are four different types of nucleotide in DNA and each one contains a different base. The four bases are adenine, guanine, thymine, cytosine. They can be referred to by the first letter of their name, so adenine as A etc.

How do the bases in DNA bond?

To hold the strands on DNA together, one strand bonds with a base on the other strand. These bases are always complementary and bond in the same formation, hence they are called complementary base pairings. The complementary base pairings are displayed below:

• adenine always bonds with thymine (A-T)

• cytosine always bonds with guanine (C-G)

B1.2.2 - Transcription and translation

How is a copy of DNA made?

DNA is too big to leave the nucleus of a cell. Therefore, a copy of it has to be made that is small enough to leave the nucleus. This copy is called messenger RNA (mRNA), and is like a single strand of DNA.

mRNA is produced in a process called transcription. The DNA around a gene unzips, so that both strands are separated. One of these DNA strands acts as a template for the mRNA. Complementary bases attach to the strand being copied. For example cytosine (C) attaches to guanine (G), which forms a strand of mRNA. There is no tyrosine (T) in mRNA, so a base called uracil (U) binds with adenine (A) instead.

When all the bases have been successfully paired, the mRNA detaches itself from the DNA template. The DNA then zips itself back up.

The mRNA is small enough to move out of the nucleus. It moves to the cytoplasm in a cell, where it attaches to ribosomes. This is where the protein will be made.

How is a protein made?

Proteins are made from amino acids. The order of nucleotides in the DNA determines the type and order of amino acids, and the type and order of amino acids determines the type of protein made.

When the mRNA attaches to a ribosome, the process of translation begins. A new protein is made during translation. Here the nucleotide sequence is interpreted and a new protein is made.

1. The ribosome reads the nucleotides on the amino acid in groups of 3 - this is called a codon. Each codon codes for a specific amino acid.

2. The ribosome continues to read the codon code, adding more and more amino acids.

3. The amino acids form bonds and join together in a chain. This is a protein.

Each type of protein folds in a different way, due to the different amino acids; each sequence of amino acids determines how the protein will fold. The different shapes are important for protein function. Enzymes and hormones are all examples of different types of protein.

B1.2.3 - Enzymes

What are enzymes?

Enzymes are a type of protein. They can be used to speed up a reaction without being used themselves. This means that once a reaction is finished, they can be used to catalyse the same type of reaction again.

Enzymes are involved in many different reactions, such as:

• They break down larger molecules into smaller ones (such as in digestion).

• They make larger molecules out of smaller ones (such as in protein synthesis).

What do enzymes look like?

Enzymes are made up of folded amino acids. Like all proteins, the way they are folded is incredibly important, as this forms the active site of the enzyme.

The molecules bind to the enzyme at the active site. The molecule that binds to the enzyme is called the substrate.

Do enzymes bind to all molecules?

Enzymes only bind with specific molecules that fit exactly into the active site. The lock and key hypothesis describes the enzyme like a lock, and the substrate as a key. Only one type of key will fit into the lock correctly.

When the enzyme binds to the correct substrate, the reaction happens quickly and the products are released from the enzyme. The enzyme can either build a larger molecule out of smaller substrates, or a smaller molecule out of larger substrates. Once this reaction is complete, the enzyme is ready to catalyse another reaction.

Enzymes that are used to build large molecules from smaller ones:

Enzymes are used to break down larger molecules into smaller ones:

B1.2.4 - Enzyme reactions

What factors affect enzymes?

The rate of a reaction with enzymes is dependant on a number of factors, three of which are:

• Temperature

• pH

• Concentration of enzymes to substrate

The conditions at which an enzyme works best are known as the optimum conditions.

How does temperature affect enzyme controlled reactions?

The higher the temperature, the faster the reaction - the particles gain more kinetic energy and make more collisions.

When the temperature becomes too high, the shape of the amino acids changes, and so the active site of the enzyme is denatured. This means that the substrate can no longer fit into the active site of the enzymes and so the reactions cannot take place. Once an enzyme has denatured, it is thought to be irreversible.

How does pH affect enzyme controlled reactions?

Enzymes have their own optimum pH. If the pH is changed, it could cause the amino acids to unfold, thus changing the shape of the active site. The enzyme has now denatured, and the rates of reaction have slowed. Here are two graphs showing the optimum pH of two different enzymes found in the body (pepsin and pancreatic amylase):

How does the concentration of substrate to enzymes/enzymes to substrate affect enzyme-controlled reactions?

The higher the amount of substrate molecules, the faster the rate of reaction. But when there is a certain substrate concentration, the rate of reaction has reached its maximum as all the enzymes are bound to substrate molecules. This means that increasing the number of substrate molecules further will not increase the rate of reaction.

The higher the concentration of enzymes, the faster the reaction. However, if no new substrate molecules are added, the reaction will eventually stop.

B1.3 - Respiration

B1.3.1 - Carbohydrates, proteins and lipids

Why do you need food?

The nutrients in food are used for many different body functions. For example, foods rich in fats and carbohydrates provide your body with energy to move and stay alive. Foods rich in protein are used for the growth and repair of body tissues. Small amounts of vitamins and minerals are essential to remain healthy.

The more active you are, the more food you need. Chemical reactions in the cells transfers energy from the chemical stores in food. The rate at which this is done is called metabolic rate. The higher the metabolic rate, the more food needs to be consumed.

What are carbohydrates?

Some carbohydrates are polymers, which means they consist of many carbohydrate monomers, such as sugars. Some of the different types of sugars are:

• sucrose - used in cakes

• lactose - found in milk

Starch is an example of a carbohydrate polymer. It is synthesised from glucose monomers. Plants often convert glucose into starch. Starch is a chemical energy store.

What are proteins?

Proteins are polymers that are made from amino acids. There are about 20 different types of amino acid. The order of the amino acids determines which protein is synthesised. Protein is broken down by protease enzymes into its amino acid components.

What are lipids?

Lipids are fats and oils that we eat. They are used by mammals as a store of energy, but also by animals as a form of insulation and to help with buoyancy. Lipids are synthesised from three fatty acid molecules and a glycerol molecule. Lipids are broken down in your small intestine into fatty acids and glycerol by the enzyme lipase.

Once food molecules have been fully digested into the components (glucose, fatty acids, glycerol and amino acids), they travel in the bloodstream around the body to the cells that need them.

B1.3.2 - Aerobic respiration

What is respiration?

Our bodies are continuously transferring energy to make us move, grow, keep warm and keep our heart beating to name a few. This energy is created by reacting the glucose from the food we eat and the oxygen we breathe in, which is transported through to the cells in our blood, in a process called aerobic respiration.

Aerobic respiration results in the transfer of energy from the energy store in glucose to the chemical energy store in the cell, called adenosine triphosphate (ATP). ATP is used by all living organisms.

What happens to the energy?

ATP produced during respiration is used for:

• the synthesis of larger molecules from smaller ones to make new cell material. For example, plants use sugars, nitrates and other nutrients to make amino acids, which can then be used in the synthesis of proteins.

• movement. ATP contracts the muscles and enables the organism to move.

• staying warm. When the surrounding environment is colder than the organism, the body performs respiration at a faster rate, creating more energy by heating and thus enabling them to keep their body at a constant temperature.

Where does respiration occur?

Aerobic respiration is occurring constantly in both plant and animal cells, providing the cell with a constant supply of energy. Respiration occurs in the mitochondria of a cell, with each chemical reaction being controlled by a specific enzyme.

Most cells contain mitochondria, but the number of mitochondria tells you how active the cell is. For example, muscle cells transfer lots of energy, so they have many mitochondria.

Respiration transfers energy to the surroundings through heating. This means that respiration is an exothermic reaction, as it gives off heat. This is shown when a person may become hot after they have finished exercising.

B1.3.3 - Anaerobic respiration

How do you respire without oxygen?

During exercise, your muscles need an increased supply of blood and oxygen to keep supplying energy. This results in an increased breathing rate and heart beat. Despite these efforts, the body cannot keep up with the demand for oxygen.

Your body can transfer energy without oxygen for short periods of time, through a process called anaerobic respiration. This involves the converting of glucose to form energy and lactic acid.

In this reaction, glucose is not broken down completely, so poisonous lactic acid is formed.

Why do we normally respire aerobically?

There are two main reasons why the body normally respires aerobically:

• In aerobic respiration, the glucose molecule is fully broken down, whereas in anaerobic respiration it is not. This means that aerobic respiration produces more ATP molecules per glucose molecule that anaerobic respiration, resulting in a higher yield.

• The lactic acid produced during anaerobic respiration can cause cramp. When the build-up gets too high, the muscle cells stop contacting, which is known as fatigue.

After you have finished exercising, you still breathe heavily. This is because more oxygen is needed to break down the lactic acid. This oxygen is called the oxygen debt.

Do other organisms perform anaerobic respiration?

Animals also use anaerobic respiration when they need to transfer energy quickly, for example when there is a predator-prey chase. It also takes place in places where there is no oxygen available, for example in the roots of plants in waterlogged soils. However, in plants, instead of lactic acid being produced, ethanol and carbon dioxide are produced. This is also known as fermentation, and is used in lots of food products, from bread to alcohol.

B1.4 - Photosynthesis

B1.4.1 - Photosynthesis

What is photosynthesis?

In order to make food, plants have to have:

• carbon dioxide. This diffuses into the plant through the stomata from the air.

• water. This enters through the root hair cells in the roots through osmosis.

These products react to make glucose, which is used as an energy source for plants. Oxygen is also produced, and some is used by the plant for respiration, but the rest is released into the atmosphere.

Where does photosynthesis occur?

Photosynthesis occurs in the plant’s chloroplasts, which are found mainly in the leaf. This means that most photosynthesis happens in the leaf, but a small amount also occurs in the stem of the plant.

The leaves and stems of a plant are green because they contain the pigment chlorophyll in their chloroplasts. Light transfers energy from the sun to the chlorophyll, where the carbon dioxide and water react together to make glucose. Glucose stores energy in its chemical bonds. The two main stages in a photosynthesis reaction are:

1. The energy transferred from the light splits water into hydrogen and oxygen ions. This is the light-dependant stage.

2. Carbon dioxide gas combines with the hydrogen ions to form glucose. This is the light independent stage.

Photosynthesis is an example of an endothermic reaction, which means that energy must be transferred from the surroundings to keep it going.

Biological terms

Photosynthesis: Using light to make a new substance.

Phototropism: Growing towards the light

Photometer: An instrument for measuring light intensity.

Photoconductive: A material whose resistance decreases when it absorbs light.

What happens to the glucose produced?

Some of the glucose is used immediately by the plant through respiration. Other glucose molecules are converted into other forms of sugar. Here are some other forms of sugar, their structure and their uses.

• Fructose - found in high quantities in fruit.

• Sucrose - found in high quantities in stems, such as sugar cane. It is made up of one molecule of glucose and one molecule of fructose and is the form that glucose is transported around the plant.

Glucose that is not needed straight away is converted into starch. Starch is insoluble and so can be used to provide a store of energy when the plant is no longer photosynthesising, for example for respiration at night.

Plants are not only made of sugars and starch though. Chemical reactions make proteins, cellulose and fats from sugars and other substances.

B1.4.2 - Photosynthesis experiments

How can you test for starch?

An experiment to show the importance of light, carbon dioxide and chlorophyll for photosynthesis would involve testing for starch, as a plant converts any glucose it has not used immediately into starch for storage.

Here is how to carry out the experiment for a test for starch.

1. Take a leaf and drop it into boiling water for one minute to kill and preserve it.

2. Drop the leaf into boiling ethanol to remove the chlorophyll from the leaf. The leaf should turn white. Use a water bath instead of a Bunsen burner to heat the ethanol as it is flammable.

3. Wash the leaf with water to remove the ethanol and to soften the leaf. Lay the leaf out on a white tile.

4. Drop some iodine solution onto the leaf. If starch is present, the iodine on the leaf should turn from yellow-brown to a blue-black colour.

If a plant is unable to photosynthesise, it will not be able to produce starch, therefore, a good way of testing if photosynthesis is to test for starch levels in a leaf. Before carrying out many photosynthesis experiments, the leaf will need to be de-starched. This is done by leaving the plant in a dark place for a minimum of 24 hours. This means the plant cannot photosynthesise and is forced to use up the starch that has been stored in the leaf. If the above experiment had been done with a de-starched leaf, the iodine would have remained yellow-brown.

How can you prove chlorophyll is needed for photosynthesis?

Variegated leaves only have chlorophyll in some areas of the leaf. This is why parts of the leaf are white, while other parts are green. To prove that chlorophyll is needed for photosynthesis, take a de-starched variegated leaf and place it in the sunlight for several hours. Repeat the above experiment to find out where the starch has been produced.

How can you prove light is needed for photosynthesis?

Below is a method to prove that light is needed for photosynthesis.

1. Take a de-starched plant leaf and cover a small section with tin foil or black card. This ensures that no sun can reach this part of the plant.

2. Place the leaf in sunlight for several hours.

3. Remove the card from the leaf and test the leaf for the presence of starch. The part covered by the card should remain with no starch present, whereas the part exposed to light should have starch present.

How can you prove carbon dioxide is needed for photosynthesis?

1. Take a de-starched plant and place it inside a polythene bag. Make sure the bag is sealed so that no gas exchange can occur.

2. Place a pot of soda lime inside the polythene bag with the plant. Soda lime absorbs carbon dioxide and water vapour.

3. Place the plant in sunlight for several hours.

4. Test the leaves for the presence of starch.

How can you prove oxygen is given off during photosynthesis?

1. Fill a beaker three-quarters of the way with water. Place a piece of pondweed in the beaker and cover with an upside-down funnel.

2. Fill a test tube with water. Place it upside-down over the tip of the funnel, ensuring not to let any air enter.

3. Place the apparatus in the light for maximum photosynthesis.

4. When a full tube of gas has been collected, place a glowing splint inside the test tube. As oxygen was produced, the glowing splint should relight.

B1.4.3 - Factors affecting photosynthesis

Which factors affect the rate of photosynthesis?

The limiting factors that affect the rate of photosynthesis are light intensity, concentration of carbon dioxide and temperature. If the quantity of any of these factors changes, the rate of photosynthesis is impacted.

The rate of photosynthesis can be found by measuring the amount of products (oxygen and glucose) formed. Glucose is used to create new cells, so the rate of photosynthesis made can be found by the increase in a plant’s biomass.

How does light intensity affect the rate of photosynthesis?

The higher the light intensity, the faster the rate of photosynthesis, until the maximum rate of photosynthesis has been reached or something else becomes the limiting factor. In very low light intensities or complete darkness, there is no photosynthesis.

How does carbon dioxide affect the rate of photosynthesis?

Carbon dioxide is one of the reactants for photosynthesis, but there is only about 0.04% carbon dioxide in our atmosphere. This means that carbon dioxide is almost always the limiting factor in the outside world, however, in a lab, carbon dioxide levels can be controlled more effectively. For example, farmers artificially increase the levels of carbon dioxide in greenhouses so that plants can photosynthesise more.

How does temperature affect the rate of photosynthesis?

Photosynthesis is a series of reactions that are controlled by enzymes. If the temperature rises too high, the enzymes will denature and the reaction will stop. Likewise, if the temperature is too low, the enzymes will slow down and the reaction will eventually stop.

B1.4.4 - Interaction of limiting factors

How can you investigate the rate of photosynthesis?

One way to measure the rate of photosynthesis is by using Elodea (pondweed). The rate of photosynthesis can be measured by the amount of oxygen produced in a set amount of time. The number of bubbles produced per minute is the rate of photosynthesis.