LIPIDS - CAPE U1

Lipids 

Lipids are a mixed group of hydrophobic compounds composed of the elements carbon, hydrogen and oxygen.

Structure:

􀀀glycerol (3C alcohol) + fatty acid

􀀀fatty acid = long HC “tail” with carboxyl (COOH) group “head

Triglycerides 

􀀀3 fatty acids linked to glycerol

􀀀ester linkage = between OH & COOH

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

Glycerol is a small, 3-carbon molecule with three alcohol 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 CH₂units long, but it is always an even number because of the way fatty acids are made. The hydrocarbon chain is sometimes called an R group, so the formula of a fatty acid can be written as R-COO^-.

• 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 together with three fatty acid molecules to form a triglyceride molecule, in another condensation polymerisation reaction: see animation formation of triglycerides

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 thay 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 facting the water and the hydrophobic tails facing eachother. This is called a micelle.
Alternatively, they may form a double-layeredphospholipid 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.

Terpenes

Terpenes are small hydrophobic molecules found mainly in plants. They include vitamin A, carotene and plant oils such as geraniol, camphor and menthol.

CAPE 1 - Carbohydrates

Carbohydrates  

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

Review Table

Monosaccharides (simple sugars) 

These all have the formula (CH₂O)_n, where n can be 3-7. The most common and important monosaccharide is glucose, which is a six-carbon or hexose sugar, so has the formula C₆H₁₂O₆. Its structure is:

a-glucose (used to make starch and glycogen)	or more simply
b-glucose (used to make cellulose)

 Glucose forms a six-sided ring, although in three-dimensions it forms a structure that looks a bit like a chair. 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 isomers of glucose, with the same chemical formula (C₆H₁₂O₆), but different structural formulae. These isomers include fructose and galactose.

Common five-carbon, or pentose sugars (where n = 5, C₅H₁₀O₅) include ribose and deoxyribose (found in nucleic acids and ATP) and ribulose (which occurs in photosynthesis).

Disaccharides (double sugars) 

Disaccharides are formed when two monosaccharides are joined together by a glycosidic bond. The reaction involves the formation of a molecule of water (H₂O) and is known as dehydration or condensation: 

see animation: dehydration or condensation of monosaccharides

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. Bonds between other carbon atoms are possible, leading to different shapes, and branched chains.

This kind of reaction, where H₂O 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. 

see animation:hydrolysis of carbohydrates (di- and polysaccharides 

In general:

polymerisation reactions are condensations breakdown reactions are hydrolyses

 There are three common disaccharides:

• Maltose (or malt sugar) is glucose 1-4 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 1-2 fructose. It is common in plants because it is less reactive than glucose, and it is their main transport sugar. It is the common table sugar that you put in your tea.
• Lactose (or milk sugar) is galactose 1-4 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. Starch and glycogen contain a-glucose, in which the hydroxyl group on carbon 1 sticks down from the ring, while cellulose contains b-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 b14 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 and also to materials such as paper, cotton and sellotape.

The b-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.

Chitin - (poly glucose amine), found in fungal cell walls and the exoskeletons of insects. The structure resembles that of cellulose, except that the hydroxyl groups on C# 2 have been replaced by acetylamino groups. 

• Other polysaccharides that you may come across include:
• .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.
  
  

CAPE 2 - Photosynthesis: Structure of the leaf, Photophosphorylation & The Calvin Cycle

The structure of leaf

¢In flowering plants, the major photosynthetic organ is the leaf.

¢ The functions of a leaf are best achieved by containing chlorophyll, absorbing carbon dioxide (and disposing of oxygen) and have a water and solute supply/transport route.

¢has a large surface area and arrangement such that it can absorb as much light as possible.

Shape and position

¢Large surface area of the lamina

¢Large surface area-to-volume ratio for maximum exposure to light and efficient gas exchange

¢Arrangement of leaves (leaf mosaic) helps the plant to absorb as much light as possible

¢Blade held at right angles to incident light

¢Thinness minimises diffusion pathway for gaseous exchange

Stomata

¢many stomata in the lower epidermis, which are pores in the epidermis through which gaseous exchange occurs.

¢Each stomata is bounded by two guard cells, and

¢changes in the turgidity of theses guard cells cause them to change shape

¢so that they open and close the pore. If the guard cells gain water, the pore is open, and vice-versa.

Mesophyll

¢main site of photosynthesis - have many more chloroplasts than spongy mesophylls, and also have several adaptions to maximise photosynthetic efficiency;

¢Large Vacuole - Restricts chloroplasts to a layer near the outside of the cell where they can be reached by light more easily.

¢Cylindrical Arrangement - They are arranged at right angles to the upper epidermis, reducing the number of light-absorbing cross walls preventing light from reaching the chloroplasts. This also allows long-narrow air spaces between them, providing a large surface area for gaseous exchange.

¢Thin cell walls - to allow gases to more easily diffuse through them.

Vascular System

¢Supplies water and mineral salts (xylem)

¢Removes products of photosynthesis (phloem)

¢As supporting skeleton together with lignified collenchyma and sclerenchyma

Chloroplasts: The Sites of Photosynthesis in Plants

¢In eukaryotes, photosynthesis takes place in organelles called chloroplasts.

¢Approximately 3 – 10 µm in diameter and are visible with a light microscope

¢Surrounded by two membranes, which form the chloroplast envelope.

¢Contain chlorophyll and other photosynthetic pigments located on a system of membranes

¢The membranes run through a ground substance called stroma.

¢The membrane system is the site of the light-dependent reactions in photosynthesis.

¢The membranes are covered with chlorophyll and other pigments, enzymes and electron carriers.

¢The system contains of many flattened, fluid-filled sacs called thylakoids which form stacks called grana.

¢The stroma is the site of the light independent reactions of photosynthesis.

¢The structure is gel-like containing soluble enzymes for the Calvin cycle and other chemicals such as sugars and organic acids.

Trapping Light Energy

¢Light energy is trapped by photosynthetic pigments

¢Different pigments absorb different wavelengths of light.

¢The photosynthetic pigments of higher plants form two groups: chlorophylls and carotenoids.

A Photosystem: A Reaction Center Associated with Light-Harvesting Complexes

¢ A photosystem

—Is composed of a reaction center surrounded by a number of light-harvesting complexes

¢ The light-harvesting complexes

—Consist of pigment molecules bound to particular proteins

—Funnel the energy of photons of light to the reaction center

¢ When a reaction-center chlorophyll molecule absorbs energy

—One of its electrons gets bumped up to a primary electron acceptor

Light-dependent reactions - Photophosphorylation

CLICK HERE FOR: Cyclic and Noncyclic Photophosphorylation animation

¢Include ATP synthesis in photophosphorylation and photolysis to give hydrogen ions

¢The hydrogen ions combine with a carrier molecule NADP to make reduced NADP

¢Photophosphorylation of ADP to ATP can be cyclic or non-cyclic depending on the pattern of electron flow.

¢NADP - nicotinamide adenine dinucleotide phosphate.

—It is a coenzyme that serves as an electron carrier in a number of reactions, being alternately oxidised.

¢NADPH – reduced nicotinamide adenine dinucleotide phosphate (NADP) carrying electrons and bonded with a hydrogen (H) ion; the reduced form of NADP.

Non-cyclic Photophosphorylation

Chemiosmosis

CLICK HERE FOR: Chemiosmosis animation

The Light Independent Reaction: Cyclic Photophophorylation - Cyclic Electron Flow

¢Occurs under certain conditions

—. Photoexcited electrons take an alternative path

—. Only photosystem I is used

—. Only ATP is produced

The Calvin cycle uses ATP and NADPH to convert CO2 to sugar

CLICK HERE FOR: Calvin Cycle animation

¢The Calvin cycle

—Is similar to the citric acid cycle

—Occurs in the stroma

¢The Calvin cycle has three phases

—Carbon fixation

—Reduction

—Regeneration of the CO2 acceptor

Photorespiration:

¢Concept 10.4: Alternative mechanisms of carbon fixation have evolved in hot, arid climates

¢On hot, dry days, plants close their stomata

—Conserving water but limiting access to CO2

—Causing oxygen to build up

¢In photorespiration

—O2 substitutes for CO2 in the active site of the enzyme rubisco

—The photosynthetic rate is reduced

C4 & CAM Plants

¢C4 plants minimize the cost of photorespiration

—By incorporating CO2 into four carbon compounds in mesophyll cells

¢These four carbon compounds

—Are exported to bundle sheath cells, where they release CO2 used in the Calvin cycle

¢CAM plants

—Open their stomata at night, incorporating CO2 into organic acids

¢During the day, the stomata close

—And the CO2 is released from the organic acids for use in the Calvin cycle

CAPE 1 - Water: Properties

PROPERTIES OF WATER

CLICK HERE FOR: tutorial on properties on water

CLICK HERE FOR: salt vs. sugar dissolving in water animation

CLICK HERE FOR VIDEO ON: Cohesion and Adhesion

 CLICK HERE FOR ANIMATION: interactions in the phases of water