All living things are made of cells, and cells are the smallest units that can be alive. Life on Earth is classified into five kingdoms, and they each have their own characteristic kind of cell. However the biggest division is between the cells of the prokaryote kingdom (the bacteria) and those of the other four kingdoms (animals, plants, fungi and protoctista), which are all eukaryotic cells. Prokaryotic cells are smaller and simpler than eukaryotic cells, and do not have a nucleus.

• Prokaryote = without a nucleus
• Eukaryote = with a nucleus

We’ll examine these two kinds of cell in detail, based on structures seen in electron micrographs (photos taken with an electron microscope). These show the individual organelles inside a cell.

Eukaryotic Cells

• Cytoplasm (or Cytosol). This is the solution within the cell membrane. It contains enzymes for metabolic reactions together with sugars, salts, amino acids, nucleotides and everything else needed for the cell to function.
• Nucleus. This is the largest organelle. Surrounded by a nuclear envelope, which is a double membrane with nuclear pores – large holes containing proteins that control the exit of substances such as RNA from the nucleus. The interior is called the nucleoplasm, which is full of chromatin- a DNA/protein complex containing the genes. During cell division the chromatin becomes condensed into discrete observable chromosomes. The nucleolus is a dark region of chromatin, involved in making ribosomes.
• Mitochondrion (pl. Mitochondria). This is a sausage-shaped organelle (8µm long), and is where aerobic respiration takes place in all eukaryotic cells. Mitochondria are surrounded by a double membrane: the outer membrane is simple, while the inner membrane is highly folded into cristae, which give it a large surface area. The space enclosed by the inner membrane is called the matrix, and contains small circular strands of DNA. The inner membrane is studded with stalked particles, which are the site of ATP synthesis.
• Chloroplast. Bigger and fatter than mitochondria, chloroplasts are where photosynthesis takes place, so are only found in photosynthetic organisms (plants and algae). Like mitochondria they are enclosed by a double membrane, but chloroplasts also have a third membrane called the thylakoid membrane. The thylakoid membrane is folded into thylakoid disks, which are then stacked into piles called grana. The space between the inner membrane and the thylakoid is called the stroma. The thylakoid membrane contains chlorophyll and stalked particles, and is the site of photosynthesis and ATP synthesis. Chloroplasts also contain starch grains, ribosomes and circular DNA.
• Ribosomes. These are the smallest and most numerous of the cell organelles, and are the sites of protein synthesis. They are composed of protein and RNA, and are manufactured in the nucleolus of the nucleus. Ribosomes are either found free in the cytoplasm, where they make proteins for the cell’s own use, or they are found attached to the rough endoplasmic reticulum, where they make proteins for export from the cell. They are often found in groups called polysomes. All eukaryotic ribosomes are of the larger, “80S”, type.
• Smooth Endoplasmic Reticulum (SER). Series of membrane channels involved in synthesising and transporting materials, mainly lipids, needed by the cell.
• Rough Endoplasmic Reticulum (RER). Similar to the SER, but studded with numerous ribosomes, which give it its rough appearance. The ribosomes synthesise proteins, which are processed in the RER (e.g. by enzymatically modifying the polypeptide chain, or adding carbohydrates), before being exported from the cell via the Golgi Body.
• Golgi Body (or Golgi Apparatus). Another series of flattened membrane vesicles, formed from the endoplasmic reticulum. Its job is to transport proteins from the RER to the cell membrane for export. Parts of the RER containing proteins fuse with one side of the Golgi body membranes, while at the other side small vesicles bud off and move towards the cell membrane, where they fuse, releasing their contents by exocytosis.
• Vacuoles. These are membrane-bound sacs containing water or dilute solutions of salts and other solutes. Most cells can have small vacuoles that are formed as required, but plant cells usually have one very large permanent vacuole that fills most of the cell, so that the cytoplasm (and everything else) forms a thin layer round the outside. Plant cell vacuoles are filled with cell sap, and are very important in keeping the cell rigid, or turgid. Some unicellular protoctists have feeding vacuoles for digesting food, or contractile vacuoles for expelling water.
• Lysosomes. These are small membrane-bound vesicles formed from the RER containing a cocktail of digestive enzymes. They are used to break down unwanted chemicals, toxins, organelles or even whole cells, so that the materials may be recycled. They can also fuse with a feeding vacuole to digest its contents.
• Cytoskeleton. This is a network of protein fibres extending throughout all eukaryotic cells, used for support, transport and motility. The cytoskeleton is attached to the cell membrane and gives the cell its shape, as well as holding all the organelles in position. There are three types of protein fibres (microfilaments, intermediate filaments and microtubules), and each has a corresponding motor protein that can move along the fibre carrying a cargo such as organelles, chromosomes or other cytoskeleton fibres. These motor proteins are responsible for such actions as: chromosome movement in mitosis, cytoplasm cleavage in cell division, cytoplasmic streaming in plant cells, cilia and flagella movements, cell crawling and even muscle contraction in animals.
• Centriole. This is a pair of short microtubules involved in cell division.
• Cilium and Flagellum. These are flexible tails present in some cells and used for motility. They are an extension of the cytoplasm, surrounded by the cell membrane, and are full of microtubules and motor proteins so are capable of complex swimming movements. There are two kinds: flagella (pl.) (no relation of the bacterial flagellum) are longer than the cell, and there are usually only one or two of them, while cilia (pl.) are identical in structure, but are much smaller and there are usually very many of them.
• Microvilli. These are small finger-like extensions of the cell membrane found in certain cells such as in the epithelial cells of the intestine and kidney, where they increase the surface area for absorption of materials. They are just visible under the light microscope as a brush border.
• Cell Membrane (or Plasma Membrane). This is a thin, flexible layer round the outside of all cells made of phospholipids and proteins. It separates the contents of the cell from the outside environment, and controls the entry and exit of materials. The membrane is examined in detail later.
• Cell Wall. This is a thick layer outside the cell membrane used to give a cell strength and rigidity. Cell walls consist of a network of fibres, which give strength but are freely permeable to solutes (unlike membranes). Plant cell walls are made mainly of cellulose, but can also contain hemicellulose, pectin, lignin and other polysaccharides. There are often channels through plant cell walls called plasmodesmata, which link the cytoplasms of adjacent cells. Fungal cell walls are made of chitin. Animal cells do not have a cell wall.

Prokaryotic Cells

• Cytoplasm. Contains all the enzymes needed for all metabolic reactions, since there are no organelles
• Ribosomes. The smaller (70 S) type.
• Nuclear Zone. The region of the cytoplasm that contains DNA. It is not surrounded by a nuclear membrane.
• DNA. Always circular, and not associated with any proteins to form chromatin.
• Plasmid. Small circles of DNA, used to exchange DNA between bacterial cells, and very useful for genetic engineering.
• Cell membrane. made of phospholipids and proteins, like eukaryotic membranes.
• Mesosome. A tightly-folded region of the cell membrane containing all the membrane-bound proteins required for respiration and photosynthesis.
• Cell Wall. Made of murein, which is a glycoprotein (i.e. a protein/carbohydrate complex). There are two kinds of cell wall, which can be distinguished by a Gram stain: Gram positive bacteria have a thick cell wall and stain purple, while Gram negative bacteria have a thin cell wall with an outer lipid layer and stain pink.
• Capsule (or Slime Layer). A thick polysaccharide layer outside of the cell wall. Used for sticking cells together, as a food reserve, as protection against desiccation and chemicals, and as protection against phagocytosis.
• Flagellum. A rigid rotating helical-shaped tail used for propulsion. The motor is embedded in the cell membrane and is driven by a H⁺ gradient across the membrane. Clockwise rotation drives the cell forwards, while anticlockwise rotation causes a chaotic spin. This is an example of a rotating motor in nature.

Summary of the Differences Between Prokaryotic and Eukaryotic Cells

Endosymbiosis

Prokaryotic cells are far older and more diverse than eukaryotic cells. Prokaryotic cells have probably been around for 3.5 billion years – 2.5 billion years longer than eukaryotic cells. It is thought that eukaryotic cell organelles like mitochondria and chloroplasts are derived from prokaryotic cells that became incorporated inside larger prokaryotic cells. This idea is called endosymbiosis, and is supported by these observations:

• organelles contain circular DNA, like bacteria cells.
• organelles contain 70S ribosomes, like bacteria cells.
• organelles have double membranes, as though a single-membrane cell had been engulfed and surrounded by a larger cell.

The Cell Membrane

The cell membrane (or plasma membrane) surrounds all living cells. It controls how substances can move in and out of the cell and is responsible for many other properties of the cell as well. The membranes that surround the nucleus and other organelles are almost identical to the cell membrane. Membranes are composed of phospholipids, proteins and carbohydrates arranged in a fluid mosaic structure, as shown in this diagram.

The phospholipids form a thin, flexible sheet, while the proteins “float” in the phospholipid sheet like icebergs, and the carbohydrates extend out from the proteins.

The phospholipids are arranged in a bilayer, with their polar, hydrophilic phosphate heads facing outwards, and their non-polar, hydrophobic fatty acid tails facing each other in the middle of the bilayer. This hydrophobic layer acts as a barrier to all but the smallest molecules, effectively isolating the two sides of the membrane. Different kinds of membranes can contain phospholipids with different fatty acids, affecting the strength and flexibility of the membrane, and animal cell membranes also contain cholesterol linking the fatty acids together and so stabilising and strengthening the membrane.

The proteins usually span from one side of the phospholipid bilayer to the other (intrinsic proteins), but can also sit on one of the surfaces (extrinsic proteins). They can slide around the membrane very quickly and collide with each other, but can never flip from one side to the other. The proteins have hydrophilic amino acids in contact with the water on the outside of membranes, and hydrophobic amino acids in contact with the fatty chains inside the membrane. Proteins comprise about 50% of the mass of membranes, and are responsible for most of the membrane’s properties.

• Proteins that span the membrane are usually involved in transporting substances across the membrane (more details below).
• Proteins on the inside surface of cell membranes are often attached to the cytoskeleton and are involved in maintaining the cell’s shape, or in cell motility. They may also be enzymes, catalysing reactions in the cytoplasm.
• Proteins on the outside surface of cell membranes can act as receptors by having a specific binding site where hormones or other chemicals can bind. This binding then triggers other events in the cell. They may also be involved in cell signalling and cell recognition, or they may be enzymes, such as maltase in the small intestine (more in digestion).

The carbohydrates are found on the outer surface of all eukaryotic cell membranes, and are usually attached to the membrane proteins. Proteins with carbohydrates attached are called glycoproteins. The carbohydrates are short polysaccharides composed of a variety of different monosaccharides, and form a cell coat or glycocalyx outside the cell membrane. The glycocalyx is involved in protection and cell recognition, and antigens such as the ABO antigens on blood cells are usually cell-surface glycoproteins.

Remember that a membrane is not just a lipid bilayer, but comprises the lipid, protein and carbohydrate parts.

Transport Across The Membrane

Cell membranes are a barrier to most substances, and this property allows materials to be concentrated inside cells, excluded from cells, or simply separated from the outside environment. This is compartmentalization is essential for life, as it enables reactions to take place that would otherwise be impossible. Eukaryotic cells can also compartmentalize materials inside organelles. Obviously materials need to be able to enter and leave cells, and there are five main methods by which substances can move across a cell membrane:

• 1. Simple Diffusion
• 2. Osmosis
• 3. Facilitated Diffusion
• 4. Active Transport
• 5. Vesicles

1. Simple Diffusion

A few substances can diffuse directly through the lipid bilayer part of the membrane. The only substances that can do this are lipid-soluble molecules such as steroids, or very small molecules, such as H₂O, O₂ and CO₂. For these molecules the membrane is no barrier at all. Since lipid diffusion is (obviously) a passive diffusion process, no energy is involved and substances can only move down their concentration gradient. Lipid diffusion cannot be controlled by the cell, in the sense of being switched on or off.

2. Osmosis

Osmosis is the diffusion of water across a membrane. It is in fact just normal lipid diffusion, but since water is so important and so abundant in cells (its concentration is about 50 M), the diffusion of water has its own name – osmosis. The contents of cells are essentially solutions of numerous different solutes, and the more concentrated the solution, the more solute molecules there are in a given volume, so the fewer water molecules there are. Water molecules can diffuse freely across a membrane, but always down their concentration gradient, so water therefore diffuses from a dilute to a concentrated solution.

Water Potential. Osmosis can be quantified using water potential, so we can calculate which way water will move, and how fast. Water potential (Y, the Greek letter psi, pronounced “sy”) is a measure of the water molecule potential for movement in a solution. It is measured in units of pressure (Pa, or usually kPa), and the rule is that water always moves by osmosis from less negative to more negative water potential (in other words it’s a bit like gravity potential or electrical potential). 100% pure water has Y = 0, which is the highest possible water potential, so all solutions have Y < 0 (i.e. a negative number), and you cannot get Y > 0.

Cells and Osmosis. The concentration (or OP) of the solution that surrounds a cell will affect the state of the cell, due to osmosis. There are three possible concentrations of solution to consider:

• Isotonic solution a solution of equal OP (or concentration) to a cell
• Hypertonic solution a solution of higher OP (or concentration) than a cell
• Hypotonic solution a solution of lower OP (or concentration) than a cell
• The effects of these solutions on cells are shown in this diagram:

The diagram below shows what happens when 2 fresh raw eggs with their shells removed with acid are placed into sucrose solution (hypertonic) and distilled water (hypotonic). Water enters the egg in water (endosmosis) causing it to swell and water leaves the egg in sucrose causing it to shrink (exosmosis).

These are problems that living cells face all the time. For example:

• Simple animal cells (protozoans) in fresh water habitats are surrounded by a hypotonic solution and constantly need to expel water using contractile vacuoles to prevent swelling and lysis.
• Cells in marine environments are surrounded by a hypertonic solution, and must actively pump ions into their cells to reduce their water potential and so reduce water loss by osmosis.
• Young non-woody plants rely on cell turgor for their support, and without enough water they wilt. Plants take up water through their root hair cells by osmosis, and must actively pump ions into their cells to keep them hypertonic compared to the soil. This is particularly difficult for plants rooted in salt water.

3. Facilitated Diffusion.

Facilitated diffusion is the transport of substances across a membrane by a trans-membrane protein molecule. The transport proteins tend to be specific for one molecule (a bit like enzymes), so substances can only cross a membrane if it contains the appropriate protein. As the name suggests, this is a passive diffusion process, so no energy is involved and substances can only move down their concentration gradient. There are two kinds of transport protein:

• Channel Proteins form a water-filled pore or channel in the membrane. This allows charged substances (usually ions) to diffuse across membranes. Most channels can be gated (opened or closed), allowing the cell to control the entry and exit of ions.
• Carrier Proteins have a binding site for a specific solute and constantly flip between two states so that the site is alternately open to opposite sides of the membrane. The substance will bind on the side where it at a high concentration and be released where it is at a low concentration.

The rate of diffusion of a substance across a membrane increases as its concentration gradient increases, but whereas lipid diffusion shows a linear relationship, facilitated diffusion has a curved relationship with a maximum rate. This is due to the rate being limited by the number of transport proteins.

4. Active Transport (or Pumping).

Active transport is the pumping of substances across a membrane by a trans-membrane protein pump molecule. The protein binds a molecule of the substance to be transported on one side of the membrane, changes shape, and releases it on the other side. The proteins are highly specific, so there is a different protein pump for each molecule to be transported. The protein pumps are also ATPase enzymes, since they catalyse the splitting of ATP into ADP + phosphate (Pi), and use the energy released to change shape and pump the molecule. Pumping is therefore an active process, and is the only transport mechanism that can transport substances up their concentration gradient.

The Na⁺K⁺ Pump. This transport protein is present in the cell membranes of all animal cells and is the most abundant and important of all membrane pumps. We look at it in more detail in module 4 (A2 course)

5. Vesicles

The processes described so far only apply to small molecules. Large molecules (such as proteins, polysaccharides and nucleotides) and even whole cells are moved in and out of cells by using membrane vesicles.

Endocytosis is the transport of materials into a cell. Materials are enclosed by a fold of the cell membrane, which then pinches shut to form a closed vesicle. Strictly speaking the material has not yet crossed the membrane, so it is usually digested and the small product molecules are absorbed by the methods above. When the materials and the vesicles are small (such as a protein molecule) the process is known as pinocytosis (cell drinking), and if the materials are large (such as a white blood cell ingesting a bacterial cell) the process is known as phagocytosis (cell eating).

Exocytosis is the transport of materials out of a cell. It is the exact reverse of endocytosis. Materials to be exported must first be enclosed in a membrane vesicle, usually from the RER and Golgi Body. Hormones and digestive enzymes are secreted by exocytosis from the secretory cells of the intestine and endocrine glands.

Sometimes materials can pass straight through cells without ever making contact with the cytoplasm by being taken in by endocytosis at one end of a cell and passing out by exocytosis at the other end.

BIOCHEMISTRY

At least 80% of the mass of living organisms is water, and almost all the chemical reactions of life take place in aqueous solution. The other chemicals that make up living things are mostly organic macromolecules belonging to the 4 groups proteins, nucleic acids, carbohydrates or lipids. These macromolecules are made up from specific monomers as shown in the table below. Between them these four groups make up 93% of the dry mass of living organisms, the remaining 7% comprising small organic molecules (like vitamins) and inorganic ions.

The first part of this unit is about each of these groups. We’ll look at each of these groups in detail, except nucleic acids, which are studied in module 2.

WATER

Water molecules are charged, with the oxygen atom being slightly negative and the hydrogen atoms being slightly positive. These opposite charges attract each other, forming hydrogen bonds. These are weak, long distance bonds that are very common and very important in biology.

Water has a number of important properties essential for life. Many of the properties below are due to the hydrogen bonds in water.

• Solvent. Because it is charged, water is a very good solvent. Charged or polar molecules such as salts, sugars and amino acids dissolve readily in water and so are called hydrophilic (“water loving”). Uncharged or non-polar molecules such as lipids do not dissolve so well in water and are called hydrophobic (“water hating”).
• Specific heat capacity. Water has a specific heat capacity of 4.2 J g^-1 °C^-1, which means that it takes 4.2 joules of energy to heat 1 g of water by 1°C. This is unusually high and it means that water does not change temperature very easily. This minimizes fluctuations in temperature inside cells, and it also means that sea temperature is remarkably constant.
• Latent heat of evaporation. Water requires a lot of energy to change state from a liquid into a gas, and this is made use of as a cooling mechanism in animals (sweating and panting) and plants (transpiration). As water evaporates it extracts heat from around it, cooling the organism.
• Density. Water is unique in that the solid state (ice) is less dense that the liquid state, so ice floats on water. As the air temperature cools, bodies of water freeze from the surface, forming a layer of ice with liquid water underneath. This allows aquatic ecosystems to exist even in sub-zero temperatures.
• Cohesion. Water molecules “stick together” due to their hydrogen bonds, so water has high cohesion. This explains why long columns of water can be sucked up tall trees by transpiration without breaking. It also explains surface tension, which allows small animals to walk on water.
• Ionization. When many salts dissolve in water they ionize into discrete positive and negative ions (e.g. NaCl Na⁺ + Cl^-). Many important biological molecules are weak acids, which also ionize in solution (e.g. acetic acid acetate^- + H⁺). The names of the acid and ionized forms (acetic acid and acetate in this example) are often used loosely and interchangeably, which can cause confusion. You will come across many examples of two names referring to the same substance, e.g.: phosphoric acid and phosphate, lactic acid and lactate, citric acid and citrate, pyruvic acid and pyruvate, aspartic acid and aspartate, etc. The ionized form is the one found in living cells.
• pH. Water itself is partly ionized (H₂O H⁺ + OH^- ), so it is a source of protons (H⁺ ions), and indeed many biochemical reactions are sensitive to pH (-log[H⁺]). Pure water cannot buffer changes in H⁺ concentration, so is not a buffer and can easily be any pH, but the cytoplasms and tissue fluids of living organisms are usually well buffered at about neutral pH (pH 7-8).

CARBOHYDRATES

Carbohydrates contain only the elements carbon, hydrogen and oxygen. The group includes monomers, dimers and polymers, as shown in this diagram:

Monosaccharides

All have the formula (CH₂O)_n, where n is between 3 and 7. The most common & important monosaccharide is glucose, which is a six-carbon sugar. It’s formula is C₆H₁₂O₆ and its structure is shown below

or more simply

Glucose forms a six-sided ring. The six carbon atoms are numbered as shown, so we can refer to individual carbon atoms in the structure. In animals glucose is the main transport sugar in the blood, and its concentration in the blood is carefully controlled.

There are many monosaccharides, with the same chemical formula (C₆H₁₂O₆), but different structural formulae. These include fructose and galactose.

Common five-carbon sugars (where n = 5, C₅H₁₀O₅) include ribose and deoxyribose (found in nucleic acids and ATP).

Disaccharides

Disaccharides are formed when two monosaccharides are joined together by a glycosidic bond. The reaction involves the formation of a molecule of water (H₂O):

This shows two glucose molecules joining together to form the disaccharide maltose. Because this bond is between carbon 1 of one molecule and carbon 4 of the other molecule it is called a 1-4 glycosidic bond. This kind of reaction, where water is formed, is called a condensation reaction. The reverse process, when bonds are broken by the addition of water (e.g. in digestion), is called a hydrolysis reaction.

• polymerisation reactions are condensation reactions
• breakdown reactions are hydrolysis reactions

There are three common disaccharides:

• Maltose (or malt sugar) is glucose & glucose. It is formed on digestion of starch by amylase, because this enzyme breaks starch down into two-glucose units. Brewing beer starts with malt, which is a maltose solution made from germinated barley. Maltose is the structure shown above.
• Sucrose (or cane sugar) is glucose & fructose. It is common in plants because it is less reactive than glucose, and it is their main transport sugar. It’s the common table sugar that you put in tea.
• Lactose (or milk sugar) is galactose & glucose. It is found only in mammalian milk, and is the main source of energy for infant mammals.

Polysaccharides

Polysaccharides are long chains of many monosaccharides joined together by glycosidic bonds. There are three important polysaccharides:

Starch is the plant storage polysaccharide. It is insoluble and forms starch granules inside many plant cells. Being insoluble means starch does not change the water potential of cells, so does not cause the cells to take up water by osmosis (more on osmosis later). It is not a pure substance, but is a mixture of amylose and amylopectin.

Amylose is simply poly-(1-4) glucose, so is a straight chain. In fact the chain is floppy, and it tends to coil up into a helix.
Amylopectin is poly(1-4) glucose with about 4% (1-6) branches. This gives it a more open molecular structure than amylose. Because it has more ends, it can be broken more quickly than amylose by amylase enzymes.

Both amylose and amylopectin are broken down by the enzyme amylase into maltose, though at different rates.

Glycogen is similar in structure to amylopectin. It is poly (1-4) glucose with 9% (1-6) branches. It is made by animals as their storage polysaccharide, and is found mainly in muscle and liver. Because it is so highly branched, it can be mobilised (broken down to glucose for energy) very quickly.

Cellulose is only found in plants, where it is the main component of cell walls. It is poly (1-4) glucose, but with a different isomer of glucose. Cellulose contains beta-glucose, in which the hydroxyl group on carbon 1 sticks up. This means that in a chain alternate glucose molecules are inverted.

This apparently tiny difference makes a huge difference in structure and properties. While the a1-4 glucose polymer in starch coils up to form granules, the beta1-4 glucose polymer in cellulose forms straight chains. Hundreds of these chains are linked together by hydrogen bonds to form cellulose microfibrils. These microfibrils are very strong and rigid, and give strength to plant cells, and therefore to young plants.

The beta-glycosidic bond cannot be broken by amylase, but requires a specific cellulase enzyme. The only organisms that possess a cellulase enzyme are bacteria, so herbivorous animals, like cows and termites whose diet is mainly cellulose, have mutualistic bacteria in their guts so that they can digest cellulose. Humans cannot digest cellulose, and it is referred to as fibre.

Other polysaccharides that you may come across include:

• Chitin (poly glucose amine), found in fungal cell walls and the exoskeletons of insects.
• Pectin (poly galactose uronate), found in plant cell walls.
• Agar (poly galactose sulphate), found in algae and used to make agar plates.
• Murein (a sugar-peptide polymer), found in bacterial cell walls.
• Lignin (a complex polymer), found in the walls of xylem cells, is the main component of wood.

LIPIDS

Lipids are a mixed group of hydrophobic compounds composed of the elements carbon, hydrogen and oxygen. They contain fats and oils (fats are solid at room temperature, whereas oils are liquid)

Triglycerides

Triglycerides are commonly called fats or oils. They are made of glycerol and fatty acids.

Glycerol is a small, 3-carbon molecule with three hydroxyl groups.
Fatty acids are long molecules with a polar, hydrophilic end and a non-polar, hydrophobic “tail”. The hydrocarbon chain can be from 14 to 22 CH2 units long. The hydrocarbon chain is sometimes called an R group, so the formula of a fatty acid can be written as R-COOH.

• If there are no C=C double bonds in the hydrocarbon chain, then it is a saturated fatty acid (i.e. saturated with hydrogen). These fatty acids form straight chains, and have a high melting point.

• If there are C=C double bonds in the hydrocarbon chain, then it is an unsaturated fatty acid (i.e. unsaturated with hydrogen). These fatty acids form bent chains, and have a low melting point. Fatty acids with more than one double bond are called poly-unsaturated fatty acids (PUFAs).

One molecule of glycerol joins togther with three fatty acid molecules to form a triglyceride molecule, in another condensation polymerisation reaction:

Triglycerides are insoluble in water. They are used for storage, insulation and protection in fatty tissue (or adipose tissue) found under the skin (sub-cutaneous) or surrounding organs. They yield more energy per unit mass than other compounds so are good for energy storage. Carbohydrates can be mobilised more quickly, and glycogen is stored in muscles and liver for immediate energy requirements.

• Triglycerides containing saturated fatty acids have a high melting point and tend to be found in warm-blooded animals. At room temperature they are solids (fats), e.g. butter, lard.
• Triglycerides containing unsaturated fatty acids have a low melting point and tend to be found in cold-blooded animals and plants. At room temperature they are liquids (oils), e.g. fish oil, vegetable oils.

Phospholipids

Phospholipids have a similar structure to triglycerides, but with a phosphate group in place of one fatty acid chain. There may also be other groups attached to the phosphate. Phospholipids have a polar hydrophilic “head” (the negatively-charged phosphate group) and two non-polar hydrophobic “tails” (the fatty acid chains). This mixture of properties is fundamental to biology, for phospholipids are the main components of cell membranes.

When mixed with water, phospholipids form droplet spheres with the hydrophilic heads facing the water and the hydrophobic tails facing each other. This is called a micelle.
Alternatively, they may form a double-layered phospholipid bilayer. This traps a compartment of water in the middle separated from the external water by the hydrophobic sphere. This naturally-occurring structure is called a liposome, and is similar to a membrane surrounding a cell.

Waxes

Waxes are formed from fatty acids and long-chain alcohols. They are commonly found wherever waterproofing is needed, such as in leaf cuticles, insect exoskeletons, birds’ feathers and mammals’ fur.

Steroids

Steroids are small hydrophobic molecules found mainly in animals. They include:

• cholesterol, which is found in animals cell membranes to increase stiffness
• bile salts, which help to emulsify dietary fats
• steroid hormones such as testosterone, oestrogen, progesterone and cortisol
• vitamin D, which aids Ca²⁺ uptake by bones.

PROTEINS

Proteins are the most complex and most diverse group of biological compounds. They have an astonishing range of different functions, as this list shows.

• structure e.g. collagen (bone, cartilage, tendon), keratin (hair), actin (muscle)
• enzymes e.g. amylase, pepsin, catalase, etc (>10,000 others)
• transport e.g. haemoglobin (oxygen), transferrin (iron)
• pumps e.g. Na⁺K⁺ pump in cell membranes
• motors e.g. myosin (muscle), kinesin (cilia)
• hormones e.g. insulin, glucagon
• receptors e.g. rhodopsin (light receptor in retina)
• antibodies e.g. immunoglobulins
• storage e.g. albumins in eggs and blood, caesin in milk
• blood clotting e.g. thrombin, fibrin
• lubrication e.g. glycoproteins in synovial fluid
• toxins e.g. diphtheria toxin
• antifreeze e.g. glycoproteins in arctic flea
• and many more!

Proteins are made of amino acids. Amino acids are made of the five elements C H O N S. The general structure of an amino acid molecule is shown on the right. There is a central carbon atom (called the “alpha carbon”), with four different chemical groups attached to it:

• a hydrogen atom
• a basic amino group
• an acidic carboxyl group
• a variable “R” group (or side chain)

Amino acids are so-called because they have both amino groups and acid groups, which have opposite charges. At neutral pH (found in most living organisms), the groups are ionized as shown above, so there is a positive charge at one end of the molecule and a negative charge at the other end. The overall net charge on the molecule is therefore zero. A molecule like this, with both positive and negative charges is called a zwitterion. The charge on the amino acid changes with pH:

low pH (acid)	neutral pH	high pH (alkali)
charge = +1	charge = 0	charge = -1

It is these changes in charge with pH that explain the effect of pH on enzymes. A solid, crystallised amino acid has the uncharged structure

however this form never exists in solution, and therefore doesn’t exist in living things (although it is the form usually given in textbooks).

There are 20 different R groups, and so 20 different amino acids. Since each R group is slightly different, each amino acid has different properties, and this in turn means that proteins can have a wide range of properties. The following table shows the 20 different R groups, grouped by property, which gives an idea of the range of properties. You do not need to learn these, but it is interesting to see the different structures, and you should be familiar with the amino acid names. You may already have heard of some, such as the food additive monosodium glutamate, which is simply the sodium salt of the amino acid glutamate. Be careful not to confuse the names of amino acids with those of bases in DNA, such as cysteine (amino acid) and cytosine (base), threonine (amino acid) and thymine (base). There are 3-letter and 1-letter abbreviations for each amino acid.

The Twenty Amino Acid R-Groups (for interest only no knowledge required)
	Simple R groups		Basic R groups
Glycine Gly G		Lysine Lys K
Alanine Ala A		Arginine Arg R
Valine Val V		Histidine His H
Leucine Leu L		Asparagine Asn N
Isoleucine Ile I		Glutamine Gln Q
	Hydroxyl R groups		Acidic R groups
Serine Ser S		Aspartate Asp D
Threonine Thr T		Glutamate Glu E
	Sulphur R groups		Ringed R groups
Cysteine Cys C		Phenylalanine Phe F
Methionine Met M		Tyrosine Tyr Y
	Cyclic R group
Proline Pro P		Tryptophan Trp W

Polypeptides

Amino acids are joined together by peptide bonds. The reaction involves the formation of a molecule of water in another condensation polymerisation reaction:

When two amino acids join together a dipeptide is formed. Three amino acids form a tripeptide. Many amino acids form a polypeptide. e.g.:

⁺NH₃-Gly — Pro — His — Leu — Tyr — Ser — Trp — Asp — Lys — Cys-COO^-

In a polypeptide there is always one end with a free amino (NH₂) (NH₃ in solution) group, called the N-terminus, and one end with a free carboxyl (COOH) (COO in solution)  group, called the C-terminus.

Protein Structure

Polypeptides are just a string of amino acids, but they fold up to form the complex and well-defined three-dimensional structure of working proteins. To help to understand protein structure, it is broken down into four levels:

1. Primary Structure

2. Secondary Structure

The a-helix. The polypeptide chain is wound round to form a helix. It is held together by hydrogen bonds running parallel with the long helical axis. There are so many hydrogen bonds that this is a very stable and strong structure. Helices are common structures throughout biology.
The b-sheet. The polypeptide chain zig-zags back and forward forming a sheet. Once again it is held together by hydrogen bonds.

3. Tertiary Structure

• hydrogen bonds, which are weak.
• ionic bonds between R-groups with positive or negative charges, which are quite strong.
• sulphur bridges – covalent S-S bonds between two cysteine amino acids, which are strong.

4. Quaternary Structure

Haemoglobin, the oxygen-carrying protein in red blood cells, consists of four globular subunits arranged in a tetrahedral (pyramid) structure. Each subunit contains one iron atom and can bind one molecule of oxygen.

These four structures are not real stages in the formation of a protein, but are simply a convenient classification that scientists invented to help them to understand proteins. In fact proteins fold into all these structures at the same time, as they are synthesised.

The final three-dimensional shape of a protein can be classified as globular or fibrous.

globular structure

fibrous (or filamentous) structure

The vast majority of proteins are globular, including enzymes, membrane proteins, receptors, storage proteins, etc. Fibrous proteins look like ropes and tend to have structural roles such as collagen (bone), keratin (hair), tubulin (cytoskeleton) and actin (muscle). They are usually composed of many polypeptide chains. A few proteins have both structures: the muscle protein myosin has a long fibrous tail and a globular head, which acts as an enzyme.

In a short-day plant growing in a home garden, which of the following causes phytochrome to switch from one form to

( )Red and far-red light
( )Sunlight
( )Gibberellin
( )The dark period

Growth and Plant Hormones

- Plant Biology

Growth

All living organisms begin in the same form: as a single cell. That cell will divide and the resulting cells will continue dividing and differentiate into cells with various roles to carry out within the organism. This is life and plants are no different. Plant growth can be determinate or indeterminate, meaning some plants will have a cycle of growth then a cessation of growth, breakdown of tissues and then death (think of a radish plant or a tomato plant) while others (think of a giant cedar tree) will grow and remain active for hundreds of years. A tomato plant is fairly predictable and is said to have determinate growth, while the cedar tree has indeterminate growing potential. Development refers to the growth and differentiation of cells into tissues, organs and organ systems. This again all begins with a single cell.

Plant Growth Regulators and Enzymes

Genetic information directs the synthesis and development of enzymes which are critical in all metabolic process within the plant. Most enzymes are proteins in some form or another, are produced in very minute quantities and are produced on site—meaning they are not transported from one part of the organism to another. Genetic information also regulates the production of hormones, which will be addressed shortly. The major difference is that hormones are transported from one part of the plant to another as needed. Vitamins vital in the activation of enzymes and are produced in the cytoplasm and membranes of plant cells. Animals and humans utilize plants in order to provide some vitamin resources. In general, hormone and vitamin effects are similar and are difficult to distinguish in plants, and both are referred to in general as plant growth regulators.

Plant Hormones

The growth and development of a plant are influenced by genetic factors, external environmental factors, and chemical hormones inside the plant. Plants respond to many environmental factors such as light, gravity, water, inorganic nutrients, and temperature.

Groups of Hormones

Plant hormones are chemical messengers that affect a plant’s ability to respond to its environment. Hormones are organic compounds that are effective at very low concentration; they are usually synthesized in one part of the plant and are transported to another location.  They interact with specific target tissues to cause physiological responses, such as growth or fruit ripening. Each response is often the result of two or more hormones acting together.

Because hormones stimulate or inhibit plant growth, many botanists also refer to them as plant growth regulators. Many hormones can be synthesized in the laboratory, increasing the quantity of hormones available for commercial applications. Botanists recognize five major groups of hormones: auxins, gibberellins, ethylene, cytokinins, and abscisic acid.

Auxins

Auxins are hormones involved in plant-cell elongation, apical dominance, and rooting. A well known natural auxin is indoleacetic acid, or IAA which is produced in the apical meristem of the shoot. Developing seeds produce IAA, which stimulates the development of a fleshy fruit.  For example, the removal of seeds from a strawberry prevents the fruit from enlarging. The application of IAA after removing the seeds causes the fruit to enlarge normally.  IAA is produced in actively growing shoot tips and developing fruit, and it is involved in elongation. Before a cell can elongate, the cell wall must become less rigid so that it can expand. IAA triggers an increase in the plasticity, or stretchability, of cell walls, allowing elongation to occur.

Synthetic Auxins

Chemists have synthesized several inexpensive compounds similar in structure to IAA. Synthetic auxins, like naphthalene acetic acid, of NAA, are used extensively to promote root formation on stem and leaf cuttings. Gardeners often spray auxins on tomato plants to increase the number of fruits on each plant. When NAA is sprayed on young fruits of apple and olive trees, some of the fruits drop off so that the remaining fruits grow larger. When NAA is sprayed directly on maturing fruits, such as apples, pears and citrus fruits, several weeks before they are ready        to be picked; NAA prevents the fruits from dropping off the trees before they are mature. The fact that auxins can have opposite effects, causing fruit to drop or preventing fruit from dropping, illustrates an important point. The effects of a hormone on a plant often depend on the stage of the plant’s development.

NAA is used to prevent the undesirable sprouting of stems from the base of ornamental trees. As previously discussed, stems contain a lateral bud at the base of each leaf. IN many stems, these buds fail to sprout as long as the plant’s shoot tip is still intact.  The inhibition of lateral buds by the presence of the shoot tip is called apical dominance. If the shoot tip of a plant is removed, the lateral buds       begin to grow. If IAA or NAA is applied to the cut tip of the stem, the lateral buds remain dormant.  This adaptation is manipulated to cultivate beautiful ornamental trees. NAA is used commercially to prevent buds from sprouting on potatoes during storage.

Another important synthetic auxin is 2,4-D, which is an herbicide, or weed killer. It selectively kills dicots, such as dandelions and pigweed, without injuring    monocots, such as lawn grasses and cereal crops. Given our major dependence on             cereals for food; 2,4-D has been of great value to agriculture. A mixture of 2, 4-D         and another auxin, called Agent Orange, was used to destroy foliage in the jungles of Vietnam. A non-auxin contaminant in Agent Orange has caused severe health problems in many people who were exposed to it.

Gibberellins

In the 1920′s scientists in Japan discovered that a substance produced by the fungus Gibberella caused fungus-infected plants to grow abnormally tall. The substance, named gibberellin, was later found to be produced in small quantities by plants themselves. It has many effects on a plant, but primarily stimulates elongation growth. Spraying a plant with gibberellins will usually cause the plant to grow to a larger than expected height, i.e. greater than normal.

Like auxins, gibberellins are a class of hormones that have important commercial applications. Almost all seedless grapes are sprayed with gibberellins to increase the size of the fruit and the distance between fruits on the stems.  Beer makers use gibberellins to increase the alcohol content of beer by increasing the amount of sugar produced in the malting process. Gibberellins are also used to treat seeds of some food crops because they will break seed dormancy and promote uniform germination.

Ethylene

The hormone ethylene is responsible for the ripening of fruits. Unlike the other four classes of plant hormones, ethylene is a gas at room temperature. Ethylene gas diffuses easily through the air from one plant to another. The saying “One bad apple spoils the barrel” has its basis in the effects of ethylene gas.  One rotting apple will produce ethylene gas, which stimulates nearby apples to ripen and eventually spoil because of over ripening.

Ethylene is usually applied in a solution of ethephon, a synthetic chemical that breaks down and releases ethylene gas. It is used to ripen bananas, honeydew melons and tomatoes. Oranges, lemons, and grapefruits often remain green when they are ripe. Although the fruit tastes good, consumers often will not buy them, because oranges are supposed to be orange, right? The application of ethylene to green citrus fruit causes the development of desirable citrus colors, such as orange and yellow.  In some plant species, ethylene promotes abscission, which is the detachment of leaves, flowers, or fruits from a plant. Cherries and walnuts are harvested with mechanical tree shakers. Ethylene  treatment increases the number of fruits that fall to the ground when the trees are shaken. Leaf abscission is also an adaptive advantage for the plant. Dead, damaged or infected leaves drop to the ground rather than shading healthy leaves or spreading disease. The plant can minimize water loss in the winter, when the water in the plant is often frozen.

Cytokinins

Cytokinins promote cell division in plants. Produced in the developing shoots, roots, fruits and seeds of a plant, cytokinins are very important in the culturing of plant tissues in the laboratory.  A high ratio of auxins to cytokinins in a tissue-culture medium stimulates root formation. A low ratio promotes shoot formation. Cytokinins are also used to promote lateral bud growth in flowering plants.

Abscisic Acid

Abscisic acid, or ABA, generally inhibits other hormones, such as the auxin IAA. It was originally thought to promote abscission, hence its name. Botanists now know that ethylene in the main abscission hormone. ABA helps to bring about dormancy in a plant’s buds and maintains dormancy in its seeds. ABA causes the closure of a plant’s stomata in response to drought. Water stressed leaves produce large amounts of ABA, which triggers potassium ions to be transported out of the guard cells. This causes stomata to close, and water is held in the leaf. It is too costly to synthesize ABA for commercial agriculture use.

Other Growth Regulators

Many growth regulators are widely used on ornamental plants. These substances do not fit into any of the five classes of hormones. For example, utility companies all over the country often apply growth retardants, chemicals that prevent plant growth, to trees in order to prevent them from interfering with overhead utility lines. If is less expensive to apply these chemicals than to prune the trees, not to mention safer for the utility workers. Also, azalea growers sometimes apply a chemical to the terminal buds rather than hand-pruning them. Scientists are still searching for a hormone to slow the growth of lawn grass so that it doesn’t have to be mowed so often.

Plant movements

Plants appear immobile because they are usually rooted in one place. However, time lapse photography reveals that parts of plants frequently move. Most plants move too slowly for the passerby to notice. Plants move in response to several environmental stimuli such as: light, gravity and mechanical disturbances. These movements fall into two groups: tropisms and nastic movements.

Tropisms

A tropism is a plant movement that is determined by the direction of an environmental stimulus. Movement toward an environmental stimulus is called a positive tropism, and movement away from a stimulus is called a negative tropism. Each kind of tropism is named for its stimulus. For example, a plant movement in response to light coming from one particular direction is called a phototropism. The shoot tips of a plant that grow toward the light source are positively phototropic.

Phototropism

Phototropism, as mentioned, is illustrated by the movement of sprouts in relation to light source direction. Light causes the hormone auxin to move tot he shaded side of the shoot. The auxin causes the cells on the shaded side to elongate more than the cells on the illuminated side. As a result, the shoot bends toward the light and exhibits positive phototropism. In some plant stems, phototropism is not caused by auxin presence or movement. In these instances, light causes the production of a growth inhibitor on the illuminated side of the shoot. Negative phototropism is sometimes seen in vines that climb on flat walls where coiling tendrils have nothing to coil around. These vines have stem tips that grow away from the light, or better put, toward the wall. This brings adventitious roots or adhesive discs in contact with the wall on which they can cling and climb.

Solar tracking is the motion of leaves or flowers as the follow the suns’ movement across the sky. By continuously facing toward a light source, moving or not, the plant maximizes the light available for photosynthesis.

Thigmotropism

Thigmotropism is a plant growth response to touching a solid object. Tendrils and stems of vines, such as morning glories, coil when they touch an object. Thigmotropism allows some vines to climb other plants or objects, thus increasing its chance of intercepting light for photosynthesis. It is thought that an auxin and ethylene are involved in this response.

Gravitropism

Gravitropism is a plant growth response to gravity. A root usually grows downward and a stem usually grows upward; that is, roots are positively gravitropic and stems are negatively gravitropic. Like phototropism, gravitropism appears to be regulated by auxins. One hypothesis proposes that when a seedling is placed horizontally, auxins accumulate along the lower sides of the root and the stem. This concentration of auxins stimulates cell elongation along the lower side of the stem, and the stem grows upward. A similar concentration of auxins inhibits cell elongation in the lower side of the root, and thus the root grows downward.

Chemotropism

Chemotropism is a plant growth response to a chemical. After a flower is pollinated, a pollen tube grows down through the stigma and style and enters the ovule through the micropyle. The growth of the pollen tube in response to chemicals produced by the ovule is an excellent example of chemotropism.

Nastic Movements

Plant movements that occur in response to environmental stimuli, but that are independent of the direction of the stimuli are called nastic movements. These movements are regulated by changes in water pressure in certain plant cells.

Thigmonastic Movements

Thigmonastic movements are a type of nastic movements that occur in response to touching or shaking a plant. Many thigmonasties involve rapid plant movements, such as the closing of the leaf trap of a Venus flytrap plant or the folding of a plant’s leaves in response to being touched. Some leaves of sensitive plants will fold within a few seconds after being touched. This movement is caused by the rapid loss of turgor pressure (water pressure) in certain cells, a process similar to that which occurs in guard cells in order to close stomata. Physical stimulation of the plant leaf causes potassium ions to be pumped out of the cells at the base of the leaflets and petioles. Water then moves out of the cells by osmosis. As the cells shrink, the plant leaves move. It is believed that the folding of a plant’s leaves in response to touch is to discourage insect feeding.

In addition, thigmonastic movements help prevent water loss in plants. When the wind blows across a plant, the rate of transpiration is increased. If the leaves of a plant fold in response to the “touch” of the wind, water loss is reduced.

Nyctinastic Movements

Nyctinastic movements are plant movements in response to the daily cycle of light and dark. Nyctinastic movements involve the same type of osmotic mechanism as thigmonastic movements, but the changes in turgor pressure are more gradual. Nyctinastic movements occur in many plants. Examples of plants that demonstrate these movements include honeylocust trees, silk trees and bean plants. The prayer plant gets its name from the fact that its leaf blades are vertical at night, resembling praying hands. During the day, however, the leaf blades are positioned horizontally. Carolus Linnaeus planted a “flower clock” made of different species of plants with nyctinastic movements. The movements of each plant species occurred at a specific time of day when the light was right for the plant.

Seasonal Responses

In nontropical areas, plant responses are strongly influenced by seasonal changes. For example, many trees shed their leaves in the fall, and most plants flower only at certain times of the year. Plants are able to sense seasonal changes. Although temperature changes are involved in some case and to certain degrees, plants mark the seasons primarily by sensing changes in night length.

Photoperiodism

A plant’s response to changes in the length of days and nights is called photoperiodism. Photoperiodism affects many plant processes, including the formation of storage organs and bud dormancy. However, the most studied photoperiodic process is flowering. Some plants require a particular night length to flower. In other species, a particular night length merely makes a plant flower sooner than it otherwise would.

Critical Night Length

It has been discovered that the important factor in flowering is the amount of darkness, or night length, that a plant receives. Each plant species has its own specific requirements for darkness, called the critical night length. Although it is now understood that night length, and not day length, regulates flowering, the terms short-day plant and long-day plant are still used. A short-day plant flowers when the days are short and the nights are long. Conversely, a long-day plant flowers when the days are long and the nights are short compared to the requirements of another plant.

Responding to Day Length and Night Length

Plants can be divided into three groups, depending on their response tot he photoperiod, which again acts a season indicator.

One group, called day-neutral plants (DNPs) are not affected by day length. Examples of DNPs for flowering include tomatoes, dandelions, roses, corn, cotton and beans.

Short-day plants (SDPs) flower in the spring of fall, when the day length is short. For example ragweed flowers when the days are shorter than 14 hours and poinsettias flower when the days are shorter than 12 hours. Chrysanthemums, goldenrods, and soybeans are SDPs for flowering.

Long-day plants (LDPs) flower when the days are long, usually in summer. For example, wheat flowers only when the days are longer than 10 hours. Radishes, asters, petunias, and beets are LDPs for flowering.

Phytochrome Regulation in Plants

Plants monitor changes in day length with a bluish, light-sensitive protein pigment called phytochrome. Phytochrome exists in two forms, based on the wavelength of the light that it absorbs. It is generally produced in meristematic tissues in very minute amounts. The two stable forms can be converted to each other by absorbing light. P_red (P_r) which absorbs red light and P_far-red (P_fr) which absorbs far-red light. In the daylight more P_r is converted to P_fr (the active form) than vice versa. P_fr will convert back to P_r over several hours in the dark where it would be stable indefinitely. The conversion in light is almost instantaneous. The phytochrome mechanism is what transforms the crook in the hypocotyls of the emerging seedling into a straight stalk. Stem elongation appears to be inhibited by P_fr. However, if light levels are low, the shaded stems of a tree for example, more far-red light will reach them and cause the conversion to P_r which lowers inhibition and allows the stems to grow longer and out from under the shade.

Tutorials » Plant Biology » Growth and Plant Hormones

Growth and Plant Hormones

- Plant Biology

Resources for Teaching and Learning Biology

General Biology
Nature of Science
Evolution

General Biology:

• ActionBioscience.org features issues-based articles written by prominent scientists, accompanying lesson ideas, and related teaching resources for high school and undergraduate biology educators. 
• AAAS Science NetLinks is a guide to standards-based Internet experiences for students.  
• BiosciEdNet.org provides a searchable database of resources from BEN Collaborative partner organizations such as AIBS, Ecological Society of America, American Society for Microbiology, and Botanical Society of America.
• BioQUEST Curriculum Consortium promotes curriculum innovation by serving a national role as a networking resource for individuals to share, distribute, and enhance cooperation among on-going and future biology education development projects.
• Biological Sciences Curriculum Study develops and supports the implementation of innovative science education curriculum for students in kindergarten through college.
• Project Kaleidoscope is a leading advocate for building and sustaining strong undergraduate programs in the fields of science, technology, engineering, and mathematics.
• National Academies’ Subject Hub for Education provides numerous resources and publications on the latest research in teaching and learning.
• National Science Teachers Association,a professional society for science teachers, provides professional development opportunities and teaching resources.
• National Association of Biology Teachers, a professional society for biology educators, offers an annual professional development conference and monthly publication.

Nature of Science:

• Evolution and the Nature of Science Institute. The Institute provides lessons designed to improve the teaching of evolution by incorporating evolutionary thinking in the context of a more complete understanding of modern scientific thinking. 
• Learn History and Nature of Science. Describes a series of articles published in NSTA journals which focus on how to teach the history and nature of science.
• The Nature of Science. Published by the Royal Society of Chemistry, LearnNet provides a variety of activities designed to look at different aspects of the nature of science and teach investigative skills.
• Nature of Science standards. What students should know and be able to do, from Benchmarks for Science Literacy, AAAS Project 2061
• PBS Evolution: What is the nature of science? This online lesson accompanying the PBS series explores how the scientific process helps develop our understanding of the natural world.
• Reshaping their views: Science as liberal arts. Discusses strategies for professors to use in general-education courses to encourage students to learn more about the nature of science and scientific inquiry, by Judith Bramble in New Directions for Teaching and Learning, Volume 2005, Issue 103, p. 51-60, Fall 2005, Wiley Periodicals, Inc.
• Symposium on the nature of science. Beyond Creationism: A reporter’s eye view of the world in collision (video). J. Madeleine Nash, Senior Correspondent, TIME Magazine.
• Teaching about Evolution and the Nature of Science 1998 book from National Academies Press.
• Understanding Science. An accessible and free web-based resource that accurately communicates what science is and how it really works, includes an interactive representation of the process of science. 
  
• Using iMovie to Teach History and the Nature of Scientific Inquiry. Great Scientific Debates on Apple Learning Interchange

Evolution:

• ActionBioscience.org – Evolution. All of the articles and interviews on evolution, published in AIBS’s online education resource.
• AIBS Evolution Initiatives. A description of the activities AIBS engages in to support the teaching of evolution and communicating the nature of science.
• Evolution and the Fossil Record. 2001. From the American Geological Institute and the Paleontological Society.
• The Evolution Project. PBS website, television series, and teaching resources.
• Evolution Resources from the National Academies. All of the Academies resources for learning and teaching evolution, including books, reports, definitions, legal issues, and upcoming events.
• National Center for Science Education. A non-profit membership organization committed to defending the teaching of evolution in public schools.
• National Evolutionary Synthesis Center. Evolutionary biology resources for educators, students, scientists, and the general public.
• Science, Evolution, and Creationism. This 2008 book, published by the National Academies Press, explains the methods of science, examines the scientific evidence in support of biological evolution, and evaluates alternative perspectives.
• The Society for the Study of Evolution. A comprehensive listing of general resources, evolution societies, and teaching resources.
  
• “Teaching about Evolution: Old Controversy, New Challenges” (PDF, 100k) A 2001 article written by Rodger Bybee, Biological Sciences Curriculum Study, recipient of the 2001 AIBS Education Award. Published by AIBS in BioScience, April 2001.
• Understanding Evolution. From the University of California, Museum of Paleontology, a one-stop source for information on evolution, with teaching resources.

BREAST EXAMINATION

Anatomy: The breast is made up of milk producing glands that are arranged into units known as lobules. These glands are connected via a series of ducts that ultimately join up to form a common drainage path, terminating at the nipple. The nipple is surrounded by a ring of pigmented tissue known as the areola. Fibro-elastic and fatty tissue provide support for the rest of the structure and allow the breast to maintain its distinctive shape. The breast lies on top of the pectoral muscle, which in turn rests on the thoracic cage. Rough boundaries of the breast are as follows:

1. Superior aspect of the breast is bounded by the clavicle
2. Inferiorly by the inframamary crease (“bra line”)
3. Medially by the sternum
4. Laterally by the axilla

Each breast contains a network of lymphatic tissue, ~ 90% of which drain into a lymph node group found in the ipsilateral axilla. The remaining 10% drain into the Internal Thoracic nodes, which are located beneath the sternum (not accessible by exam). Lymph drainage pathways are important in the setting of breast cancer, as this is usually the first site of spread (see below). For obvious reasons (i.e., milk production) woman have significantly more breast tissue then men. 

Assorted images of the breast–NIH  

Basic breast anatomy and info on breast cancer, The cancer council Victoria, Australia. 

Why and when should a breast examination be performed? 

In the asymptomatic patient: The asymptomatic breast exam is generally performed only on women. This is because diseases of the breast, in particular cancer, occur far more commonly in women then men. Malignancies generally originate in either the glandular tissues that secrete milk or in the ductal structures that transport it to the nipple. 

Examination can be done by the clinician (Clinical Breast Exam – CBE) or patient (Self Breast Exam – SBE). Those performed by the clinician are usually done on an annual basis, beginning at the age of 40, which coincides with time of increased risk for development of breast cancer. Other major breast cancer risk factors include: prior history of breast ca, family history in 1st degree relative (particularly if at a young age), increasing patient age and features that result in prolonged/uninterrupted exposure to estrogen (e.g. early age at onset menstruation, never having been pregnant, older age at first pregnancy, older age at menopause). SBE is often recommended on a monthly-to-every-few-months basis. 

Interestingly, while both SBE and CBE are part of routine clinical care, there are no studies that demonstrate that either of these techniques, when performed as stand-alone examinations, actually improves clinical outcomes (i.e. detects cancer at an earlier stage, demonstrating positive impact on cancer related morbidity or mortality). In contrast, mammography (performed with or without CBE), has a strong body of evidence to support its routine use as a screening tool for early detection of malignancy. 

In the symptomatic patient: The goal of the examination in the setting of symptoms is to better characterize the abnormality, identify underlying etiology, and direct additional evaluation and treatment. Breast related symptoms may include any of the following:

• Discrete masses detected by the patient, often concerning for malignancy
• Pain, which can be associated with a number of processes including: cyclical in a menstruating women (reflecting transient hormone induced changes in the breast tissue), occasionally malignancies.
• Unusual nipple discharge, which may include:
  • Blood, concerning for malignancy
  • Milk when not pregnant. Suggestive inappropriate Prolactin secretion from the pituitary – may also be induced by certain medications
  • Other
• Discoloration or change in the quality of the skin:
  • Redness suggests infection or inflammation – in the post partum patient, this is often due to mastitis, a diffuse inflammatory condition caused by congestion from inadequately expressed milk.
  • “Peau d’orange” quality – an “Orange Peel” like texture that’s caused by an uncommon, aggressive inflammatory malignancy

If a mass or other abnormality is identified, it’s location can be described as being in one of 4 quadrants (left upper, left lower, right upper, right lower) of the breast. Alternatively, it can be described relative to it’s position, imagining a clock face were superimposed on the breast. 

It’s worth noting that breast symptoms may be caused by diseases elsewhere in the body. For example, as mentioned above, inappropriate milk production may be due to a pituitary tumor secreting Prolactin. Or breast development in men may signify underlying liver disease. Given this, breast symptoms may merit careful history and evaluation of other organ systems. As symptoms can occur in male or female patients (though overall, female >>> male), evaluation is indicated in either sex patient who presents with breast concerns. 

Examination in Detail

Getting Started

1. Carefully explain what you are going to do – and why.
2. Room should be a comfortable temperature.
3. Patient should be in a gown – all undergarments (bras, shirts, etc) should be removed.
4. Have the patient remove their arms from the sleeves of the gown – though keep both breasts covered by laying the garment on top of their chest. Alternatively, the patient may put on the gown so that it opens in the front, which may make exposing one breast at a time a bit easier.
5. Patient should be lying flat on the table – It may help to have them place hand on side to be examined behind their head, allowing easier access to breast and axilla.
6. Uncover only the breast that you are going to examine.
7. Observe the breast, looking for evidence of skin or nipple dimpling/retraction, discoloration, obvious masses or asymmetry.
8. Observing the breasts while the patient sits up may increase your ability to detect asymmetry or other surface abnormalities, particularly if the person has large breasts.

Palpation of the Breast and Axilla: The goal of this exam is to examine the breast in a systematic fashion, such that all of the tissue is palpated. 3 methods are described below. The accuracy of the exam is increased by allowing adequate time. This will vary with breast size. Specifically, it will take more time to carefully evaluate larger breasts. Regardless of the method used to assure that the breast is examined in its entirety, palpation technique should be as follows:

Palpation Technique in Detail

1. Use the pads of the middle 3 fingers of one hand.
2. Press downward using a circular motion.
3. Apply steady pressure, pushing down to the level of the chest wall. Apply enough pressure to palpate to 3 levels of depth: first superficial, then medium, and then deep/to the level of the chest wall.
4. Make sure to palpate the nipple and areolar regions.

What precisely are you trying to identify? Normal breasts have a lumpy consistency, created by the mix of lobular, ductal and supporting tissue. The CBE (as mentioned above) is largely performed to identify masses consistent with malignancy. Most lumps are benign (e.g. fibroadenomas, cysts). Masses of concern tend to have the following characteristics: Feel different from the rest of the breast tissue (aka “dominant mass”), firmness, irregular/hard to define borders, fixed/stuck to adjacent tissue – and increase in size over time. As breast density decreases with age (lobular tissue replaced by fat), it is easier to identify masses in older patients.

Three Methods for systematic examination of the breast:

Method 1 – Vertical strips:

1. In this technique, you are breaking the breast into a series of vertical strips, each of which is evaluated sequentially, moving lateral to medial.
2. Start at the clavicle, adjacent to the axilla.
3. Move your hand down in a vertical line until you’ve reached the area below the breast. Actual palpation technique is as described above.
4. Then move a bit more medially, and examine while traveling up towards the top of the breast.
5. When you reach the clavicle, move medially and repeat until you’ve evaluated the entire breast.
6. There is a “tail” of breast tissue that extends from the lateral aspect of the structure towards the axilla. Make sure that you palpate this region as well.

Method 2 – Pie or Radial Spoke Pattern:

1. Imagine that the breast is broken into a series of pie-type slices, with the nipple at the center.
2. Start at the nipple, working outwards toward the periphery of the slice that you’re examining. Move your hands a few centimeters along each time.
3. When you are clearly no longer over the breast, move to the next slice
4. Make sure that you palpate the “tail” of the breast as described above.

Method 3 – Circular Pattern:

1. Start at the nipple.
2. Work along in circular fashion, moving in a spiral towards the periphery.
3. Make sure that you palpate the “tail” of the breast as described in above.

Following direct palpation of the breast, the axillary region should be palpated. This is because the axillary lymph nodes are usually the first site of spread in the setting of breast cancer. While this is of greatest importance when you identify a concerning mass in the breast itself, include the axilla in all of your breast exams. To examine, proceed as follows:

1. It may help to have the patient lower their arm so it is next to their side, as when the hand is behind their head, the axillary skin is taught and perhaps more difficult to palpate thru.
2. Gently move the arm 20-30 cm away from the patient’s body, so that you can gain access to the axillary region.
3. Direct the finger tips of the examining hand (it’s a bit easier to use your L hand when examining the R breast, and vice versa) toward the top of the axilla.
4. Then push the palmar aspect of the hand towards the chest wall. You are trying to identify any abnormal nodules/lumps that could represent axillary adenopathy. In addition, you may be able to trap the nodes between your hand and the chest wall, which can then be better characterized.
5. Most women will not have palpable axillary lymph nodes. If you do feel discrete masses, make note of: firmness, quantity and degree of mobility. In general, malignancy is associated with: firmness, increased quantity, adherence to each other and/or the chest wall.
6. Recognize that adenopathy may not be due to breast disease. For example, infections of the hand can cause acute, painful axillary adenopathy. Similarly, systemic diseases (e.g. lymphoma, sarcoidosis) may also cause lymph node enlargement. Thus, as with all other aspects of the exam, history and findings in other regions are of great importance.

The other breast is then examined. 

Additional aspects of the exam that can be performed:

1. Assessment of nipple discharge: If the patient reports unusual discharge from the nipple, gently palpate the breast near the nipple, with a goal of trying to express and examine any abnormal fluid. Bloody discharge is particularly concerning for cancer. Most discharge, however, will be secondary to benign conditions.
2. Puckering/Dimpling: This can suggest an underlying mass which is distorting the skin above it. In this setting, careful palpation around the dimpling is often revealing. In addition, if it’s unclear if there is dimpling or asymmetry, observe the breasts while the patient sits up (with hands placed on hips). This may help clarify differences between the 2 sides and accentuate asymmetry.
3. Nipple Retraction: This is concerning for a mass growing underneath the nipple. In this case, carefully palpate the tissue around and underneath the nipple. 
4. Redness/Pain: Suggestive of inflammation and/or infection. Carefully note the extent of redness as well as temperature differences. Assess for any focal swelling or fluctuance that might suggest underlying abscess.

Pitfalls and Problem Areas: 

1. Examining women with large breasts: In this setting, it can be technically challenging to assure that you’ve done a thorough examination of all the tissue. In order to minimize error there no special “tricks.” Instead, rely on basic exam principles, in particular: Take your time – may take 3 or minutes to examine each breast! Be thorough and ordered, covering all areas of the breast sequentially.
2. Careful evaluation of masses: There are many anecdotes relating to missed diagnoses of breast cancer. I recognize that all masses do not represent malignancy. In fact, most are benign (e.g. secondary to fibro-cystic changes, cysts, transient changes that vary with time of the menstrual cycle, etc). An array of thoughtful reviews have been written that describe the appropriate evaluation of abnormal findings. Specifically: when to evaluate with ultrasound, when to consider aspiration, when to consider biopsy, when to re-evaluate at a different point in the menstrual cycle (greatest amount of swelling is usually immediately prior to menstruation), when to refer, etc.. The comments which follow are not meant to contradict this information. Nor are they particularly applicable to those with clear expertise in the appropriate evaluation of abnormal exam findings.What follows is directed to the more novice examiner:
   • If you clearly identify a discrete mass, consider it to be malignant until proven otherwise. In general, determination of final diagnosis requires a biopsy.
   • A dominant breast mass that does not have a corresponding abnormality on Mammogram (i.e. “normal mammo”) should still be considered malignant until proven otherwise. This is because not all malignancies generate mammographic findings.
   • While uncommon, breast cancer can occur in men. Thus, discrete masses should be appropriately evaluated.
   • Breast cancer can occur in young women (20s and 30s) �thus worrisome masses in this population should be appropriately evaluated.
   • If you have any concerns or uncertainty re any exam finding, seek input from someone with appropriate experience and training.
3. Pay very careful attention to any mass that the patient brings to your attention. Women who are good self-examiners can often detect subtle/early changes concerning for malignancy that an examiner may have difficulty identifying.

Assorted basic information about breast cancer, NIH site. 

More information about breast cancer, NCI Site 

Gail Model for calculating breast CA risk – NCI

This information was tagged from http://meded.ucsd.edu/clinicalmed/breast.htm#Anatomy and is copyrighted by its original owner. Content is not owned or is an originality of Easysemester.com

Aerodynamics
What makes a paper airplane fly? Air — the stuff that’s all around you. Hold your hand in front of your body with your palm facing sideways so that your thumb is on top and your pinkie is facing the floor. Swing your hand back and forth. Do you feel the air? Now turn your palm so it is parallel to the ground and swing it back and forth again, like you’re slicing it through the air. You can still feel the air, but your hand is able to move through it more smoothly than when your hand was turned up at a right angle. How easily an airplane moves through the air, or its aerodynamics, is the first consideration in making an airplane fly for a long distance.

Drag & Gravity
Planes that push a lot of air, like your hand did when it was facing the side, are said to have a lot of “drag,” or resistance, to moving through the air. If you want your plane to fly as far as possible, you want a plane with as little drag as possible. A second force that planes need to overcome is “gravity.” You need to keep your plane’s weight to a minimum to help fight against gravity’s pull to the ground.

Thrust & Lift
“Thrust” and “lift” are two other forces that help your plane make a long flight. Thrust is the forward movement of the plane. The initial thrust comes from the muscles of the “pilot” as the paper airplane is launched. After this, paper airplanes are really gliders, converting altitude to forward motion.

Lift comes when the air below the airplane wing is pushing up harder than the air above it is pushing down. It is this difference in pressure that enables the plane to fly. Pressure can be reduced on a wing’s surface by making the air move over it more quickly. The wings of a plane are curved so that the air moves more quickly over the top of the wing, resulting in an upward push, or lift, on the wing.

The Four Forces in Balance
Long flights come when these four forces — drag, gravity, thrust, and lift — are balanced. Some planes (like darts) are meant to be thrown with a lot of force. Because darts don’t have a lot of drag and lift, they depend on extra thrust to overcome gravity. Long distance fliers are often built with this same design. Planes that are built to spend a long time in the air usually have a lot of lift but little thrust. These planes fly a slow and gentle flight.

ADDITIONAL LINKS:

http://www.allstar.fiu.edu/aero/fltmidfly.htm

You are to give 30 mg. of Inderal. The available dosage strength is a scored 60mg. tablet. What amount will you give?

Here is the correct answer:
1/2 tablets

this is because formula is DOCTORS ORDER/ AVAILABLE AMOUNT X D

Dr order was 30mg

available was 60 so apply formula and there si your answer

30
———————————-
60 = .5 tablets

2. Azulfidine 1.5 g has been ordered every twelve hours. The available tablets are 500 mg each. What amount will you give?