Biological MoleculesCarbohydrates

Carbohydrates include sugars, starch, glycogen and cellulose. There are Monosaccharides disaccharides and polysaccharides. Monosaccharides consist of 3 separate groups trioses pentoses and hexose's. These are all types of soluble reducing sugars with the exception of sucrose. Disaccharides are carbohydrates whose molecules are made of two monosaccharides linked together. E.g., glucose + glucose = maltose.

An example of a hexose (6carbons) molecule, (Glucose) in alpha (right) and beta (left) form. These ring forms are produced when a bond forms between the oxygen attached to carbon 5 and carbon 1.

An example of a disaccharide below in a condensation reaction

Aldehydes and ketones

Aldehydes are reducing agents. This means that aldose sugars are reducing agents, and are called reducing sugars. When a reducing agent reduces anotehr compound, the reducing agent is oxidised. Ketose sugars are not reducing agents but they react to form reducing agents in alkaline conditions used to test for reducing sugars. This means that Ketoses such as fructose are not as strong reducing agents as aldoses such as glucose. All monosaccharides as shown above are either aldoses or ketoses, this also applies to most disaccharides. Sucrose is the only exception.

Proteins

Proteins are polymers who's molecules are made from many amino acid molecules linked together. Examples of proteins can be seen in the form of enzymes, antibodies and haemoglobin.

3 groups

Amino group – NH2

Carboxyl group – COOH

R group – always different determining the amino acid.

Protein Structure

Primary Structure - Sequence of amino acids in a polypeptide chain.

Secondary Structure - Repeating three dimensional structure of the polypeptide backbone. The two common structures are alpha helix and beta strand.

Tertiary structure - the chain. The three dimensional shape of the polypeptide chain.

Quaternary structure - Many proteins or more polypeptide chains are bonded to make a complete molecules. Disulphide links and hydrogen bonds hold the chains together.

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). As shown below Triglycerides Triglyceride molecules are made from one molecule of glycerol linked to three fatty acids, glycerol is an alcohol. Fatty acids are organic acids also called carboxylic acids and always have a COOH group. By condensation this group combines with the - OH group of a glycerol molecule forming an Ester bond. Triglycerides functions are storage molecules, long chains of fat can be broken down for energy.

Bonds

Proteins – Hydrogen form between groups with dipoles (unevenly charged molecules). Ionic bonds forms between groups with opposite charges, disulphide links form between cysteine side chains. Peptide bonds join 2 peptides to make a dipeptide or more to make a poly peptide

Carbohydrates – Glycosidic bonds covalent and formed between c1 and c4, (1 – 4) bond.

Phospholipids and triglycerides are joined by ester bonds. A saturated fatty acid contains only single bonds between carbons. Unsaturated contain one or more double bonds between carbon atoms.

Introduction – What is a cell?A cell is a basic unit from which living organisms are made. All living organisms are made up of one or more cells. A cell is surrounded by a cell surface membrane, and contains a solution of proteins and other substances in water. This solution is called cytoplasm. Within this, there are many structures called organelles which make up the cell.

Most cell are very small, which can only be seen by using a microscope. However, some are big enough to be seen by the naked eye. Bacteria cells and many protoctists are made up of just one cell, and are known as unicellular organisms. Others, including all plants and animals are made up of many cells, and these are called multicellular organisms.

There are two main cells:

Eukaryotic

Prokaryotic

References:AQA AS Biology. Module 1: Molecule, Cells and Systems

www.biologymad.com

www.swarthmore/edu/NatSci/cpurrin1/posteradvice.htm

‘Tool Box’ AS Biology CD

Organelles

Cell wall – layer of tough cellulose fibrils which surround the plant cells. It allows cells to become turgid without bursting, maintaining the shape of a cell.Cell membrane – Thin boundary between cell and environment, controlling the passage of materials in and out of the cell. Proteins are also embedded within the membrane for cell recognition in the immune system.Nucleus – one of the main organelles found in all eukaryotic cells. Usually large, about 10цm in diameter, bounded by a large double membrane with many pores. It is the site of DNA, arranged in chromosomes which are responsible for the cell division and protein synthesis.Nucleolus – Darkly staining region found in the nucleus, which synthesizes ribosomes.Mitochondrion – Elongated with a smooth outer membrane, and a folded inner membrane, ranging from 1цm to 10цm in size, in the cytoplasm of the cell. Their function is the site of aerobic respiration, and most of the cell’s ATP is made here. The main use of ATP is for the process of photosynthesis.Chloroplast – Biconcave disc ‘lens shaped’ with many internal membranes. There are numerous in the cytoplasm, and use the ATP made for photosynthesis. Containing large amounts of chlorophyll, this is the pigment which colours the leaves and is the site of photosynthesis.Vacuole – Large central organelle in most plant cells, which is surrounded by a membrane called the tonoplast, full of fluid. Contains cell sap, and stores compounds like sucrose and sugar beet. Rough Endoplasmic Reticulum – This is an extensive membrane system with many cavities and tubes, with ribosomes attached. It is found throughout the cytoplasm, connected to the nuclear membrane. It transports system, collecting, storing, packaging and transporting proteins made on the ribosomes.Smooth Endoplasmic Reticulum – Membrane system with small cavities, and no ribosomes attached. Unlike the RER, it is only found in small patches in the cytoplasm, and synthesizes lipids and some steroids.Golgi body – Stack of flattened membranes, resembling stack of pancakes. The size varies, and is close to the RER. The function of this organelle is to receive vesicles from the RER and appears to modify chemicals before their secretion from the cell.Ribosome – Small and dense structure results in them being last out of the main organelles to be the last sediment, acting like a giant enzyme. In eukaryotic cells, they are large, 80s compared to 70s in a prokaryotic cell. Ribosomes are where the genetic code is used to build proteins, process called translation

Microscopy

The two main aspects of microscopy are magnification, and resolution

Magnification is a measure of enlargement, calculated by the eyepiece lens x the lens

Resolution refers to the detail seen

There are three main types of microscopes used to look at cells and their organelles. Each show a different level of resolution.

The light microscope uses lenses to focus a beam of light coming from the object, and the magnification and resolution are limited by the wavelength of light. This causes the magnification to be lower, only maximising x 1500, compared to x 500,000 for an electron microscope. Also the limited wavelength results in a lower resolving power, of 200 nm. This means that light microscopes cannot resolve objects closer than 200nm into two separate images.

Transmitting Electron microscopes use magnets to focus a beam of electrons onto the object, transmitting them trough. This means that sections have to be thin, and preparation is complex. The preparation process could result in artefacts, which appear on the specimen, that would not be there naturally in a living organism. However, the magnification level is much higher of x 500,000 with a resolution power of 1nm, making the observation very detailed.

In Scanning Electron microscopes the electron beam bounces off the surface of the object, allowing 3D objects to be seen in detail. Here, there is no need for a thin section of the specimen, making the preparation easier. Like the TEM, these microscopes have a high magnification and resolution, enabling better detailed objects to be seen.

Size and Scaling

1mm = 1000цm

1цm = 1000nm

Cells, Organelles and MicroscopesCarys Norman

Fig. 3. Photographs of mitochondria (top right), RER (bottom right) and nucleus and nucleolus (left)

Lysosomes - These are small membrane-bound vesicles formed from the RER containing 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. Before each division the centriole replicates itself and the two centrioles move to opposite ends of the cell, where they initiate the spindle that organises and separates the chromosomes (see module 2).

Undulipodium (Cilium and Flagellum) - This is a long flexible tail present in some cells and used for motility. It is an extension of the cytoplasm, surrounded by the cell membrane, and is full of microtubules and motor proteins so is capable of complex swimming movements. There are two kinds: flagella (no relation of the bacterial flagellum) are longer than the cell, and there are usually only one or two of them, while cilia 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.

Mesosome - A tightly-folded region of the cell membrane containing all the membrane-bound proteins required for respiration and photosynthesis. Can also be associated with the nucleoid.

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.

Cell Fractionation and CentrifugationThis is a process which extracts pure samples of a particular

organelle. The method is:1. This tissue is chopped up2. Add ice cold, isotonic which contains a buffer solution fluid.

Being ice cold will minimise enzyme reactions. The fluid must be isotonic to avoid distortion of organelles by water loss or gain, and a buffer solution will resist any changes in pH

3. Resulting mixture is centrifuged at high speed, which will increase the gravitational field, and the organelles will separate out according to density and shape. The first organelle to sediment out is the nuclei, followed by mitochondria and chloroplasts, then RER, plasma membrane and SER, finishing with ribosome's being the least dense.

Fig. 4.

Light microscope

Prokaryotic and Eukaryotic CellsEukaryotic cells have a ‘true nucleus’ referring to a large nucleus which contains linear DNA inside a membrane.

Plant, animal and fungi cells are all types of eukaryotic cells.

Under an optical or light microscope organelles within an animal cell which can be seen include;

Nucleus – a large circular organelle that contains DNA

Nucleolus – a dark feature inside the nucleus

Plasma membrane – very thin membrane surrounding the cell

Cytoplasm – ‘cell fluid’, containing different organelles which cannot be distinguished at this level of magnification.

Figure 1. Photograph from an electron micrograph of an eukaryotic cell, showing the different organelles.

Features of a prokaryotic cell:

Complex cell wall which is coarse, tough and made out of murein (protein)

Plasma membrane – main boundary between cell and the environment

Mesosomes – inner folding of the cell membrane, giving the cell a large surface area for the attachment of enzymes used in metabolic processes

Genetic material – found in the nucleoid, but there is no nuclear membrane. Have a single circular piece of DNA

Ribosomes – protein synthesis

Figure 2. Photograph of a prokaryotic cell taken from an electron micrograph, showing the different organelles.

IntroductionLife on Earth evolved in the water, and all life still depends on water. 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 four 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.

Biochemical Tests These five tests identify the main biologically important chemical compounds:

Starch (iodine test). To approximately 2 cm³ of test solution add two drops of iodine/potassium iodide solution. A blue-black colour indicates the presence of starch as a starch-polyiodide complex is formed. Starch is only slightly soluble in water, but the test works well in a suspension or as a solid.

Reducing Sugars (Benedict's test). All monosaccharides and most disaccharides (except sucrose) will reduce copper (II) sulphate, producing a precipitate of copper (I) oxide on heating, so they are called reducing sugars. Benedict’s reagent is an aqueous solution of copper (II) sulphate, sodium carbonate and sodium citrate. To approximately 2 cm³ of test solution add an equal quantity of Benedict’s reagent. Shake, and heat for a few minutes at 95°C in a water bath. A precipitate indicates reducing sugar. The colour and density of the precipitate gives an indication of the amount of reducing sugar present, so this test is semi-quantitative. The original pale blue colour means no reducing sugar, a green precipitate means relatively little sugar; a brown or red precipitate means progressively more sugar is present.

Non-reducing Sugars (Benedict's test). Sucrose is called a non-reducing sugar because it does not reduce copper sulphate, so there is no direct test for sucrose. However, if it is first hydrolysed (broken down) to its constituent monosaccharides (glucose and fructose), it will then give a positive Benedict's test. So sucrose is the only sugar that will give a negative Benedict's test before hydrolysis and a positive test afterwards. First test a sample for reducing sugars, to see if there are any present before hydrolysis. Then, using a separate sample, boil the test solution with dilute hydrochloric acid for a few minutes to hydrolyse the glycosidic bond. Neutralise the solution by gently adding small amounts of solid sodium hydrogen carbonate until it stops fizzing, then test as before for reducing sugars. Lipids (emulsion test). Lipids do not dissolve in water, but do dissolve in ethanol. This characteristic is used in the emulsion test. Do not start by dissolving the sample in water, but instead shake some of the test sample with about 4 cm³ of ethanol. Decant the liquid into a test tube of water, leaving any undissolved substances behind. If there are lipids dissolved in the ethanol, they will precipitate in the water, forming a cloudy white emulsion. The test can be improved by adding the dye Sudan III, which stains lipids red.

Protein (biuret test). To about 2 cm³ of test solution add an equal volume of biuret solution, down the side of the test tube. A blue ring forms at the surface of the solution, which disappears on shaking, and the solution turns lilac-purple, indicating protein. The colour is due to a complex between nitrogen atoms in the peptide chain and Cu2+ ions, so this is really a test for peptide bonds.

Carbohydrates 

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

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.

Disaccharides (double sugars)  Disaccharides are formed when two monosaccharides are joined together by a glycosidic bond. This reaction involves the formation of a molecule of water (H2O) when two glucose molecules join together to form the disaccharide maltose. This bond is between carbon 1 of one molecule and carbon 4 of the other molecule it is called a 1-4 glycosidic bond. A reaction, where H2O is formed, is called a condensation reaction. The reverse process, when bonds are broken by the addition of water is called a hydrolysis reaction.

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.

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.

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. 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. 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.

Tertiary Structure This is the compact globular structure formed by the folding up of a whole polypeptide chain. Every protein has a unique tertiary structure, which is responsible for its properties and function. For example the shape of the active site in an enzyme is due to its tertiary structure. The tertiary structure is held together by bonds between the R groups of the amino acids in the protein, and so depends on what the sequence of amino acids is. There are three kinds of bonds involved: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. So the secondary structure is due to backbone interactions and is thus largely independent of primary sequence, while tertiary structure is due to side chain interactions and thus depends on the amino acid sequence.

Quaternary Structure This structure is found in proteins containing more than one polypeptide chain, and simply means how the different polypeptide chains are arranged together. The individual polypeptide chains are usually globular, but can arrange themselves into a variety of quaternary shapes. This final three-dimensional shape of a protein can be classified as globular or fibrous.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.

Biochemistry – Biological molecules, their uses and their chemical testsChris Blackhall 12PK

LipidsLipids are a mixed group of hydrophobic compounds

composed of the elements carbon, hydrogen and oxygen.

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

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 CH2 units 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 togther with three

fatty acid molecules to form a triglyceride molecule:

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 each other. 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.

ProteinsProteins 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 ionised 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 (bwlow) , but this form never exists in solution, and therefore doesn't exist in living things.  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.

There are only 5 different groups that you need to know:•Glycine (Gly)•Alanine (Ala)•Valine (Val)•Leucine (Leu)•Isoleucine (Ile)

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. In a polypeptide there is always one end with a free amino (NH3) group, called the N-terminus, and one end with a free carboxyl (CO2) group, called the C-terminus. In a protein the polypeptide chain may be hundreds of amino acids long. Amino acid polymerisation to form polypeptides is part of protein synthesis.

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.

There are four kinds of protein structure:

Primary Structure This is just the sequence of amino acids in the polypeptide chain, so is not really a structure at all. However, the primary structure does determine the rest of the protein structure. Finding the primary structure of a protein is called protein sequencing, and the first protein to be sequenced was the protein hormone insulin. Secondary StructureThis is the most basic level of protein folding, and consists of a few basic motifs that are found in all proteins. The secondary structure is held together by hydrogen bonds between the carboxyl groups and the amino groups in the polypeptide backbone. The two most common secondary structure motifs are the a-helix and the b-sheet.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.

The b-sheet. The polypeptide chain zig-zags back and forward forming a sheet of antiparallel strands. Once again it is held together by hydrogen bonds.

Group name monomers polymers % dry mass Proteins amino acids polypeptides

50nucleic acids nucleotides polynucleotides 18

carbohydrates monosaccharides polysaccharides 15     

Group name components largest unit % dry mass lipids fatty acids + glycerolTriglycerides 10

Introduction

Organisms are mad from a huge variety of organic and inorganic compounds which can be classified into a few major types. The main organic molecules are carbohydrates, proteins, and lipids.

Carbohydrate, protein and lipid molecules are all based on the elements carbon, hydrogen and oxygen. Proteins also contain nitrogen and sometimes sulphur.

There is a huge variety of carbohydrates, proteins and lipids, but these are made from a small number of similar molecules. These building blocks are joined together by condensation reactions which link substances together and also produce water. Large organic molecules are broken down by the process of hydrolysis, which literally means splitting using water.

Carbohydrates Carbohydrates include sugars, starches, cellulose and glycogen. Carbohydrates always contain the elements carbon, hydrogen and oxygen, and can be divided into three categories according to size.

•Monosaccharides -Single sugars like glucose and fructose.

•Disaccharides –Double sugars like sucrose and maltose.

•Polysaccharides Multiple sugars like starch, glycogen and cellulose.

Both mono-and disaccharides are sugars and are sweet, white, water soluble solids. Polysaccharides are polymers of sugars and are neither sweet nor soluble. Polymers are long chain-like molecules made from similar units called monomers. The carbohydrates starch, glycogen and cellulose are polymers. Proteins are also polymers but lipids are not.

Monosaccharides The commonest monosaccharides is glucose which exists in two forms: α glucose and β glucose. The different forms affect the properties of the polymers that contain them.

DIAGRAM a and b

Fructose and galactose are also examples of monosaccharides. Both are isomers of glucose. This means that they contain the same atoms as glucose, but in slightly different arrangements to produce molecules with different shapes. The sugars ribose and deoxyribose, which give their names to RNA and DNA, are also monosaccharides.

The primary structure is the sequence of amino acids in the polypeptide. An example would be alanine-glycine-leucine-valine-glutamic acid.  •The secondary structure:Helix and Beta pleated sheet Secondary structure is joined together by hydrogen bonds.  •The tertiary structure :Different types of primary and secondary structures, this is known as a globular proteins. The globular structure is held together by hydrogen bonds, disulphide bonds, ionic bonds and hydrophilic internalisations.  •The Quaternary structure Some proteins contain more than one polypeptide chain (two or more polypeptides). The way in which these are linked is the quaternary structure. Collagen is a fibrous proteinHaemoglobin, a lobular protein, two a and b.  •Buirettes are used in a biochemical to show that the solution contains protein. •Amino acids have the ability to receive or donate protons •Amine group on the left with nitrogen •Carboxyl group on right with carbon

Lipids Lipids are a group of compounds that include fats oils and waxes. They all contain the elements carbon, hydrogen and oxygen. There are two types of lipid: triglycerides and phospholipids.

•Triglyceride The triglyceride are the familiar fats and oils. Triglyceride molecules are made from one molecule of glycerol linked to three fatty acids.

The Hydrocarbon chain of a fatty acid may contain many carbon atoms and they can be written in a lazy form can be represented in an R group or as below.

These atoms may all be joined by double bonds to make unsaturated fatty acids, or some may be joined by double bonds to make unsaturated fatty acids. Lipids which contain saturated fatty acids are usually solid at room temperature (fats), and those containing unsaturated fatty acids are usually liquid (oils).

Biological moleculesChris Kelly 12WH

South Bromsgrove High School, A Specialist Technology College, Bromsgrove, Worcestershire, B60 3NL

.

When these chains lie parallel to each other, many hydrogen bonds

form along the length so that the individual cellulose chains are bound

together into strong fibrils. These fibrils are glued together to form cell

walls.

Cellulose is the most abundant polysaccharide on earth, but most

animals cannot digest it because they do not possess the enzyme cellulase.

Proteins Are very important in living organism. Amino acids are the

monomers of a protein. Amino acids differ on the basis of their functional

group. e.g. Amine, Carboxyl, functional.

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

condensation polymerisation reaction. (Peptide bonds form between adjacent

amino acids. This is a condensation reaction).

The structure of proteins is complex and can be described at four level:

PrimarySecondaryTertiaryQuaternary

Disaccharides •The commonest examples of these double sugars are maltose, sucrose and lactose.•Maltose is formed from two glucose molecules. It is common in germinating seeds, where it is produced from the break down of starch.Sucrose is formed from a glucose and a fructose molecule. It is the main transport carbohydrate in plants and so is found in high concentration in phloem tissue.•Lactose is formed from a glucose and a galactose molecule. It is found in the milk mammals.

Polysaccharides There are three types of polysaccharides.•Starch•Glycogen•Cellulose These are all polymers, formed from hundreds or thousands of glucose units.

•Starch is the main storage material in plants. Storage compounds are insoluble and compact, but quickly available when needed. Starch is actually a mixture of two compounds, amylose and amylopectin. Amylose consists of single, unbranched chains of a glucose that form spirals. Amylopectin consists of branched chains of a glucose molecules.

-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.

Glycogen is the ain storage carbohydrate in mammals. It is a very similar in structure to amylopectin, but is even more branched and so can be built up and broken down even more quickly, matching the energy needs of mammals.

Cellulose strengthens plant cell walls. It is made only from β glucose molecules. The slight difference in structure between α glucose and β glucose means that, instead of forming a spiral, β glucose chains are long and straight.

IntroductionOrganisms are made of a huge variety of compounds. The main organic compounds are carbohydrates, proteins, lipids, and nucleic acids. I will write about these first three groups. The molecules of these groups are mainly made of Carbon, Oxygen and Hydrogen. There are many different lipids, proteins and carbohydrates, they are all made of a small number of simpler molecules joined together. The joining of these smaller molecules happens in a condensation reaction. In which H2O is produced. And the opposite can happen by adding water, this is called hydrolysis and is used to break large molecules into smaller ones. E.g. a disaccharide into two monosaccharides. But the first subject topic is lipids.

LipidsLipids are fats, oils and waxes. They are insoluble in water, this is because they have no dipoles and so no charges to attract water molecules. Lipids are made of Carbon oxygen and hydrogen. Most lipids are composed of compounds called triglycerides. Triglycerides are a glycerol bonded to three fatty acid chains. (see fig. 1)They are made from a special type of condensation reaction, called esterfication. Which forms ester bonds between the glycerol and fatty acid. (see fig. 2)

Fig. 1

CarbohydratesCarbohydrates are separated into three categories.Monosaccharides- one, single sugarDisaccharides- two, double sugarPolysaccharides- many, multiple sugars.

And sugars are separated into reducing sugars, and non-reducing sugars. Reducing sugars can donate electrons to other molecules, all monosaccharides, and some disaccharides are reducing sugars.

The Most common monosaccharide is glucose. There are two types of glucose, alpha ( and beta ( .Glucose is a hexose sugar, because it has a structure like a hexagon (see fig.3). The difference between Alpha and Beta glucose is the 1st and 4th carbons.

Fig. 3

ChromatographyChromatography is used to separate, then identify the individual chemicals in a mixture.

It works by drawing a line on a piece of chromatography paper (in pencil, because ink would run) called the origin. Then dropping a very small amount of liquid onto the origin. You then allow this spot to dry, then repeat the process about 4times, until you have a concentrated spot on the origin line. (see fig. 7) You then put the piece of paper into a solvent, but ensure the line of origin is above the solvent line.

Fig. 7

Biological MoleculesHolly Stockham

Biochemical testsThere are tests that you can do to find out what a substance contains. These tests are below:

Starch. Adding Iodine to the solution, if it turns blue/black it contains starch.

Protein. By adding biurets solution and heating up the solution gently you can see if it contains protein. A positive result would turn the solution lilac.

Lipids. You do the emulsion test, which is adding ethanol, shaking, then adding the solution to water. It is called the emulsion test because if the solution contains lipids a white emulsion will be formed.

Reducing sugars. Add Benedicts solution, then heat up to near boiling pt. the colour will go from Blue to green to yellow to orange to red. Depending how much reducing sugar it contains. (red containing the most reducing sugar.)

Non-reducing sugars. First you must add it to dilute HCL, which hydrolyses the non-reducing sugars to reducing sugars. Then it must be neutralised with NaHCO3, then there should be a positive result from the benedicts test (as above)

ReferencesAdvanced Biology by Jones and Jones.CGP AS-level BiologyCollins AQA AS BiologyBiology toolbox CD

Proteins Proteins are made from long chains of amino acids. (see fig. 5) And like lipids and carbohydrates, they are formed by condensation reactions, and broken down by hydrolysis. But the bonds between the amino acids, making the proteins are called peptide bonds (see Fig. 6).

Fig.5 An amino acid

Fig. 6

Solvent front

origin

Spot of pigment

The chemicals can then be identified comparing Rf values to a table of already known Rf values. The Rf value is calculated by this formula:

Rf value = Distance from origin to top of spot

Distance from origin to solvent front

(Note: The Rf Value will be between 0 and 1.)

But sometime the solvent doesn’t completely separate out all the chemicals properly, so you need to do two way chromatography. Where you turn the paper 90o and place it into another solvent. Which should completely separate out the chemicals.

glycerol

Fatty acid chain

Fig. 2

Ester bonds

triglyceride

Fatty acids can be saturated or unsaturated. The difference is that saturated fatty acids are completely “covered” in hydrogen, and they have no double bonds. Whereas unsaturated fatty acids have double bonds, and the capability to bond with more hydrogen. If an unsaturated lipid has more than one double bond it is called polyunsaturated. Saturated lipids are normally found in animals, and unsaturated, in plants.

There is another type of lipid, a phospholipid.

Phospholipids are used in cell membranes because they have a hydrophobic tail and hydrophilic head. So they control what can come in and out. The structure of a phospholipid varies from that of a triglyceride, but not by much. A phospholipid still has the same glycerol backbone as a triglyceride, only instead of having three fatty acid chains, it has two, and a phosphate group, which is ionised to attract water (that’s why the head is hydrophilic).

To break up a lipid you need to add water, hydrolysis. Which is normally done by adding a dilute acid, and heating it up. Then you get glycerol and chains of fatty acids again.

The main use of triglycerides in the body is as an energy source. They contain much more energy per gram than either carbohydrates or proteins. Triglycerides can be broken down and oxidised in respiration and the energy from them is used to make ATP.

Alpha glucose Beta Glucose

To form a Disaccharide you must join two monosaccharides together in a condensation reaction (see fig.4). The monosaccharides bond at carbon 1 and 4, creating a 1-4 glycosidic bond. And produce water. That creates a disaccharide, some key examples of disaccharides are maltose, sucrose, and lactose. Maltose is formed from two alpha glucose molecules, and is the sugar produced when starch is broken down.

To break a disaccharide into a monosaccharide/ break down a polysaccharide to a disaccharide you use hydrolysis, it basically means adding water. It reverses the condensation reaction, and is usually done by adding a warm dilute acid.

Polysaccharides are formed when 2 or more disaccharides join together.

The three main polysaccharides are:

Starch (amylose and amylopectin)

Amylose is a long unbranched chain, it’s compact, and is therefore good for storage.

Amylopectin is branched, which means it is easy to break down the side branches to get at the glucose.

Glycogen

It’s similar to amylopectin, only with a lot more side branches, so it looks a bit like a brush. This is good for quick energy release, as glycogen is stored in animals.

Cellulose

Is a straight chain, (a bit like a brick wall) with hydrogen bonds linking the chains together. This is good because it makes the structure strong, as it is used for cell wall. Also enzymes can’t break it, because they can’t reach the glycosidic bonds.

Fig. 4

Amine group

Functional group

Carboxyl group

The formation of a protein. Showing the peptide bond

The functional group is shown as “R” because it changes in different amino acids. For instance:

Amino Acid Functional Group

glycine H

alanine CH3

valine C3H7

isoleucine C4H9

leucine C4H9

The Primary structure of a protein is the order of the amino acids.

The Secondary structure is the shape e.g. beta pleated sheet or a helix.

The Tertiary structure is a globular protein. It’s made up of lots of helixes and beta pleated sheets. It's 3D, enzymes are globular proteins. Globular proteins are therefore affected by all the things you associate with enzymes, like temperature and pH. It is held together by many different bonds, like disulphide, hydrogen bonds, van der waals forces, and ionic bonds.

The Quaternary structure is 2 or more polypeptides, so a big group of globular proteins.

Beta pleated sheet

helix

Introduction- A cell is the basic unit from which all living organisms are made. Some cells are big enough to be seen with the naked eye, however most cells are microscopic and can only be seen with microscopes. Bacteria tend to have the smallest cells, around 0.5um across, whereas human cells are between 10um and 30um in diameter. Despite the variations in size, cells have certain features in common.

For further information

References –

www.biologymad.com

http://library.thinkquest.org

Collins AQA AS Biology Module 1: Molecules, cells and systems

Mary Jones and Geoff Jones Advanced Biology

Letts Biology Revision guide

Organelles

Organelles are small structures within cells that perform dedicated functions. As the name implies, you can think of organelles as small organs. Organelles were historically identified through the use of microscopy, and were also

identified through the use of cell fractionation. There are many different types of organelles: Eukaryotic cells contain:

Cell wall – A layer of tough cellulose fibrils (made of a variety of polysaccharides) that surrounds plant cells to give support and protection. The cell wall allows the cell to become turgid without bursting and maintains the shape of the cell. Cell membrane – A thin boundary around all cells and most organelles that controls what passes in and out of the cell. Proteins are embedded in the cell membrane and are also involved in cell recognition in the immune system. Nucleus – Large, usually round, bounded by double membrane with many pores. The most important part of the cell, controls growth, contains DNA, responsible for cell division, regulates metabolism and protein synthesis. Quite simply, the total control of the cell.Nucleolus – The darkly stained region in the nucleus that is involved with the synthesis of ribosomes. Mitochondrion – Usually round and elongated with a smooth outer membrane and a folded inner membrane. The mitochondria are contained in the cytoplasm of cells and are the site of aerobic respiration and where most of the cells ATP is produced.Chloroplast – A biconcave disc (the perfect compromise between a sphere and a disc) with many internal membranes. Chloroplasts are the site of photosynthesis as they contain the green pigment chlorophyll. Vacuole – A large central organelle in most plant cells, surrounded by a membrane called the tonoplast, full of fluid.

Vacuoles store compounds such as sucrose and the difference in water potential compared to the surrounding fluids enables the cell to produce turgor pressure. Rough endoplasmic reticulum (rough ER) – The extensive membrane system that has many cavities and tubes with ribosomes attached. Rough ER is found throughout the cytoplasm connected to nuclear membrane and acts as the transport system in the cytoplasm, collecting, storing, packaging and transporting the proteins made in the ribosomes. Smooth endoplasmic reticulum (smooth ER) – The membrane system with small cavities and no ribosomes, found in small patches in the cytoplasm. The smooth ER is involved in the synthesis of lipids and some steroids. Golgi body – A stack of flattened membrane discs found free in the cytoplasm near to the rough endoplasmic reticulum. The golgi body receives packages (vesicules) of protein from the rough endoplasmic reticulum and is involved in the synthesis and modifying of chemicals before their secretion from the cell. Ribosome – A small and dense structure that acts as an enzyme. The ribosome is attached to the rough endoplasmic reticulum or free in the cytoplasm and is where the genetic code is used to build protein (translation).

Prokaryotic cells only contain a cell membrane, cell wall, ribosomes, DNA and a cilia or a flagella (as shown previously).

Cell fractionation –

Cell fractionation is a process which allows scientists to extract pure samples of a particular organelle. Cell fractionation is a combination of various methods used to separate a cell’s organelles and components. There are two phases of cell fractionation: homogenization and centrifugation. Homogenization is the process of breaking open the cells. Cells are broken apart by chemicals, enzymes, or sound waves. Some scientists even force the cells through small spaces at high pressure to break them apart. Centrifugation is the isolation of the cell organelles.

The tissue is chopped up and when the cells are broken apart substances that would normally be kept separate by membranes mix together and can begin to react, so a fluid is added to prevent this which is ice cold, contains a buffer and isotonic. The mixture is then put in a homogeniser (blender) to break up the cells. The resulting mixture is then centrifuged at high speed. The spinning greatly increases the gravitational field, and the organelles separate out according to density and shape. The first most heaviest organelle to sediment out is the nuclei. The remaining fluid, the supernatant, is poured off the centrifuged again to collect other organelles. The order that organelles sediment is: nuclei, mitochondria, chloroplasts (if using plant preparations), rough endoplasmic reticulum, plasma membranes, smooth endoplasmic reticulum and finally ribosomes.

Prokaryotic and eukaryotic cells, organelles and microscopy.Sarah Townsend

South Bromsgrove High School

Microscopy

There are two main concepts in microscopy and these are resolution and magnification. Resolution is the ability to distinguish between two clear dots. Magnification is how much bigger a sample appears to be than it is in real life. Light microscope - This microscope uses light to see and magnify objects. The light rays are focused on to a transparent specimen by condenser rays. The rays pass through the specimen and are focused

Prokaryotic Cell – (From the Greek meaning ‘before nuclei’ – the DNA is not enclosed by a membrane). All bacteria and cyanobacteria (blue –green algae) are prokaryotes as they lack a membrane – bound nucleus. They are usually smaller than eukaryotic cells and are similar in size to a mitochondrion or a chloroplast. In fact, they probably were prokaryotic cells which came to live inside the larger eukaryotic cells millions of years ago. They have few internal organs that are distinguishable. All prokaryotic cells are surrounded by a cell wall. However this is different from

Figure 1. A prokaryotic cell taken from an electron micrograph

a plant cell wall because it contains different polysaccharides. Instead they contain peptidoglycans which are made up of molecules in which peptides and sugars are combined. The cell walls are very strong and important because they prevent the cell from bursting when the cell absorbs water and help to protect against invasion by viruses. Many prokaryotic cells have a thick layer of jelly surrounding them called a capsule which is made of polysaccharides and protects from viruses and antibodies. Beneath the cell wall is a cell surface membrane that is made up of a phospholipid bilayer and the cytoplasm that contains ribosomes that are approximately 20 nm in diameter. The DNA is not chromosomal but in a circular loop called a plasmid. Some contain a flagellum which is used for movement. They divide by binary fission and have three major shapes: rod, spherical and spiral.

Figure 2. A eukaryotic cell taken from an electron micrograph.

Eukaryotic cell – (From the Greek meaning ‘truly nuclear’ – the larger nucleus contains the DNA inside a membrane). Organisms with complex cells are eukaryotes and are found in plants, animals and fungi. They can be easily distinguished through a membrane bound nucleus (nuclear envelope) and contain membrane bound structures (organelles). The organelles such as the mitrochondrion or chloroplast are there to perform metabollic functions and energy conversion. Other organelles provide structural support and cellular motility. They are generally much larger than prokaryotic cells. Not all eukaryotic cells contain cell walls, only plant cells, not animals cells. The plant cell wall contains pectin, hemicellulose and cellulose (different from a prokaryotic cell). The DNA is linear (chromosomal), complex, organised into chromosomes and combined with histone proteins. They divide by replication

(making copies of themselves). The eukaryotic cell is clearly developed from a prokaryotic cell. This is because eukaryotes formed through the merger of prokaryotes, which predate them in the fossil record by some 2 billion years.

again by two more lenses – the objective lens and the eyepiece lens. These two lenses produce a magnified image. As many specimens are colourless and nearly transparent, stains are used to make different parts of the specimen show up clearly. Some stains can be added to living cells, but others must be ‘fixed’ by adding a chemical known as a fixative. These chemicals react with substances such as proteins in the cell, making them insoluble and so anchoring them in position. The cells are killed when the fixative is added. Stains may be added either before or after the fixing process. So long as the specimen is thin enough to allow light to pass through,

Figure 3. A light microscope

they can be used to see major organelles such as the nucleus or mitochondrion. The fluorescent light microscope is the most common and widely used light microscope. This microscope is used to visualise stained cells with fluorescent dyes. However, limitations occur as the microscope can not see beyond 200 nm resolution and x1500 magnification due to the long wavelength of light dissipating if the light is refracted too far. They are relatively cheap. Electron microscope - This microscope uses electrons to see instead of light. They are focused using electromagnets rather than glass lenses. As electrons are easily stopped by air molecules, the space inside must be a vacuum. As our eyes do not respond to electrons, the electrons are allowed to hit a fluorescent screen which emits visible light where the electrons hit. Electrons cannot penetrate materials as well as light, so specimens must be much thinner. This places great limitations on what can be viewed, in particular it is not possible to look at living material, all specimens musty be dead. Specimens are stained using heavy metal ions such as lead or osmium and are taken up by particular parts of the cells. Atoms of these ions have large, positively charged nuclei which scatter electrons rather than letting them pass straight through. These

Figure 4. An electron microscope

electrons therefore do not arrive on the screen, so leaving a dark area in the image. The structures in a cell which have taken up these heavy metal stains therefore appear dark. Scanning electron microscopes work in a very different way. The electrons do not pass through the specimen but are reflected off its surface. Scanning electron microscopes are used to provide three dimensional images of surfaces. Because the wavelength of electrons are shorter than light, they have a resolution of 1nm and a magnification of x500000. However, they are very expensive.

Figure 5. cell fractionation

Introduction

There are two main types of cells, Eukaryotic and Prokaryotic. They are very different and contain different organelles which help them to do their specific jobs. An Organelle is a discrete structure of a cell with specialized functions. They are similar to the organs in a body because they are vital in the survival of the cell.

There are many ways to identify organelles such as microscopy which can be done using different microscopes to give different resolutions and better images. Cell fractionation can also be used as it is a method of splitting up the cell so that all the different organelles are separate.

There are two different types of microscopes, light and electron with there being two more different types of electron microscopes. Transition and Scanning which both do different jobs and see different things along with the light microscope.

MicroscopyThere are two different types of Microscopes, Light and Electron microscopes they or both very different with there also being two different types of electron microscopes.

Light Microscopes are is a very simple microscope with not a very high resolution or magnification. Resolution being the ability to distinguish between two points on an image and Magnification being how much bigger a sample appears to under the microscope.

The resolving power of a microscope is limited by the wavelength of light which is 400 to 600 mm for visible light. To improve the resolving power of a light microscope a shorter wavelength of light is need that is why some microscopes have blue filters as blue has the shortest wavelength of visible light.

Light microscopes cost between £100 and £500 compared to the cost of an electron microscope which is over £1,000,000. They are cheep to operate as well as being small and portable. The samples are simple and easy to prepare with little damage done to the samples during this process. A vacuum is not required unlike in the electron microscopes meaning that the specimen has to be dead. The natural colour is maintained in a light microscope even though stains are often needed to make the cells visible but the maximum magnification is only up to 2000 times.

Electron microscopes are much more advanced as they have a magnification of over 500,000 times. They use an electron beam which is very expensive and can damage the specimens which also must be stained with an electron dense chemical.

Electron microscopes can also be split into Scanning electron microscopes and Transmission electron microscopes. Scanning electron microscopes pas the scanning beam over the surface of the specimen and electrons reflect of it as it has been coated in heavy metals. The reflected electron beams are focused on a florescent screen to make up the image which is linked to a computer to make the image clearer. It is similar to echo location.

Transmission electro microscopes pas a beam of electrons through the thin specimen and focusing the image on a screen or film. The TEM is very big, expensive and not very clear.

Cells and Microscopy

By Abby Pask

Eukaryotic CellsEukaryotic cells are the larger of the two types of cell and can be more than 10µm in diameter. They have a true nucleus and contain many organelles that can either be double or single. This makes them very complex cells which have a number or different jobs.

The genetics of a Eukaryotic cell is made up of linear DNA and is associated with proteins to form chromatin. It has a true nucleus which means it has a nuclear envelope and is one of the main difference between a eukaryotic cell and a Prokaryotic cell. Another main difference is the number of ribosome's in the cell with the eukaryotic cell having a large number (80S)

The cells walls are made up of either chitin in fungi or cellulose in plants but animal cells do not have a cell wall

Figure 1. This is a basic diagram of a eukaryotic cell with all the main organelles that it contains including the nucleus and the endoplasmic reticulum

Figure 2. These two photos are different eukaryotic cells that have been magnified using a microscope. The main recognisable organelles have been labels

Prokaryotic Cells

Prokaryotic cells are much smaller than Eukaryotic cells being less than 5µm in diameter. They have smaller ribosome's (70s) and less organelles which are all not membrane bound. The genetics of a prokaryotic are also very different as there is circular DNA and no proteins. There is no true nucleus which means that the DNA is free to move within the cytoplasm.The cell walls are made from Glycoprotein's or other polysaccharides, but not cellulose or chitin as these are found in Eukaryotic cells.Prokaryotic cells include bacteria and blue-green algae as they are very small and not very complex

Figure 3. This is a basic diagram of a Prokaryotic cell with all the main organelles that it contains including the ribosome's and the Nucleoid

Figure 4. This is a prokaryotic cell seen through a microscope it shows the cell wall and cell membrane which outline the cell.

OrganellesThere are many different Organelles with many different functionsEukaryotic cellsNucleus- Where DNA is kept and where RNA is transcribed

Ribosome's- The site of protein synthesis, where RNA is translated into proteinsMitochondria- The site or aerobic respiration

Chloroplasts- the site of photosynthesisEndoplasmic reticulum- There are two types the rough ER and the smooth ER. The ER is the transport network for molecules targeted for certain modifications and specific final destinations.

Golgi Apparatus- The ‘post box’ of the cell as it modifies molecules and packages them into small membrane bound sacs called vesicles.

Prokaryotic Cells Vacuole- transport and storing nutrients, metabolites, and waste products.Cytoplasm- contains all the enzymes needed for metabolic reactionsNucleoid- The region of the cytoplasm that contains DNA Meosome- A tightly folded region of the cell membrane containing proteins required for respiration and photosynthesis.Capsule- A thick polysaccharide layer outside of the cell wall used for protection and a food reserve.Flagellum- A rigid rotating helical shaped tail used for propulsion.Both types of CellsCell Membrane- Made of phospholipids and proteins which is used for protection and transport.Cell Wall- Keeps a cell rigid and gives protection.

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.

RECAP OF LIPIDSWhat's the difference between a phospholipids and triglyceride Molecule? 

Triglycerides are the familiar fats and oils. The molecules are made

from one molecule of glycerol linked to three fatty acids. Glycerol is

an alcohol. Fatty acids are organic acids (also called carboxylic acids)

and also have a -COOH group. BY condensation, this group combines

with the -OH group of a glycerol molecule, forming an ester bond.

Because triglycerides are fat, they acts as a storage molecule. Phospholipids have two fatty acids and a phosphate molecule

attaches where as a triglyceride molecule only has three fatty acid

chains. There function is to form membranes.

Biochemical testsThese five tests identify the main biologically important

chemical compounds. For each test take a small amount of the substance

to test, and shake it in water in a test tube. If the sample is a piece of

food, then grind it with some water in a pestle and mortar to break up

the cells and release the cell contents. Many of these compounds

are insoluble, but the tests work just as well on a fine suspension.

Starch (iodine test). To approximately 2 cm³ of test solution add two

drops of iodine/potassium iodide solution. A blue-black colour indicates the presence of starch as a starch-polyiodide complex

is formed.

Reducing Sugars (Benedict's test). To approximately 2 cm³ of test

solution add an equal quantity of Benedict’s reagent. Shake, and heat

for a few minutes at 95°C in a water bath. A precipitate indicates

reducing sugar. The colour and density of the precipitate gives an

indication of the amount of reducing sugar present, so this test is semi-

quantitative. A blue colour means no reducing sugar, a green precipitate means relatively little sugar; a brown or red

precipitate means progressively more sugar is present.  Non-reducing Sugars (Benedict's test). Using a separate

sample, boil the test solution with dilute hydrochloric acid for a few minutes

to hydrolyse the glycosidic bond. Neutralise the solution by gently adding small amounts of solid sodium hydrogen carbonate until

it stops fizzing, then test as before for reducing sugars.

Biological moleculesChris Kelly 12WH

South Bromsgrove High School, A Specialist Technology College, Bromsgrove, Worcestershire, B60 3NL

.

Lipids (emulsion test). Lipids do not dissolve in water, but do dissolve

in ethanol. This characteristic is used in the emulsion test. Do not start

by dissolving the sample in water, but instead shake some of the test

sample with about 4 cm³ of ethanol. Decant the liquid into a test tube

of water, leaving any undissolved substances behind. If there are lipids

dissolved in the ethanol, they will precipitate in the water, forming a

cloudy white emulsion. The test can be improved by adding the dye

Sudan III, which stains lipids red.

Protein (biuret test). To about 2 cm³ of test solution add an equal

volume of biuret solution, down the side of the test tube. A blue ring forms at the surface of the solution, which disappears on

shaking, and the solution turns lilac-purple, indicating protein.

ConclusionBiochemistry is a particularly difficult area in biology as it is

split up into different sections. For example you have to remember the

types, function and importance carbohydrates-monosaccharides, disaccharides and polysaccharides and proteins, Lipids and biochemical tests.

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, 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-.

Saturated or unsaturated

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).

These fatty acids are joined by a condensation reaction however in this

reaction it is known as ESTERIFICATION and an ESTER bond is

formed.

With three branches three ester bonds can form so three fatty acids can

bond so therefore it is called a triglyceride. Is first molecule of a fatty

acid  

Acknowledgments

Literature cited

For further information

Introduction

The cell is the basic functioning unit of organisms in which chemical reactions take place. These reactions involve energy release needed to support life and build structures. Organisms consist of one or more cells and these can be seen with microscopes which enables sub-cellular units called organelles become visible. Each organelle has been researched to help us understand more about the processes of life. To see a virtual cell you can visit www.life.uiuc.edu/plantbio/cell

Prokaryotic and Eukaryotic cellsOrganisms can be classified into two groups, prokaryotic and eukaryotic to their cellular structure.

Eukaryotic cells A eukaryote is an organism with a complex cell or cells, in which the genetic informationis organized into a membrane- bound nucleus or nuclei. This type of cell comprises of animals,plants and fungi- which are mostly multi cellular. Also, eukaryotic cells are generally much larger than prokaryotic cells and have a variety of internal membranes and structures, called organelles and the DNA in this structure is divided into several bundles called chromosomes.

Prokaryotic cells The prokaryotic kingdom consists of only bacteria which means they have no nucleus. Overall, prokaryotic cells are less complicated than eukaryotic cells and are considered to have evolved earlier.

Microscopic measurementIt is sometimes necessary to measure microscopic structure such as; for cures to diseases or for research. There are two instruments needed for this process, a graticule and stage micrometer.

Measurement technique:

•Put a graticule into the eyepiece of a microscope

•Look through the eyepiece lens and the graticule line can be seen

•Put a stage micrometer on the microscope stage

•Look through the eyepiece lens

•Line up the ruled line of the graticule with the ruled line of the stage micrometer

•Calibrate the eyepiece by finding out the number of eyepiece unit (e.u.) is equal to one stage unit (s.u.); each is 0.01mm

•Take away the stage micrometer and replace it with a specimen

•Measure the dimensions of the specimen in terms of eyepiece units

MagnificationMicroscopes magnify the image of a specimen to enable the human eye to see minute objects that are not visible to the naked eye. Resolution of a microscope = the ability to distinguish between two objects (dots) as separate entities. Magnification = is the measurement of enlargement

The magnification of an object can be calculated using this equation:

observed size

Magnification = actual size

Cells and MicroscopyHeather Bradley

Artefacts:When microscope specimens are prepared there are often several chemical and physical

procedures.Often the material is dead so changes from the living specimen are expected. Microscopic

materialshould be analysed with care because there may have been some artificial change in the

material duringpreparation. These are artefacts; structures alien to the material which should not be

interpreted as partof the specimen.

Acknowledgements:• www.biologymad.co.uk• Collins AQA Biology book• Letts AS Biology book• www.wikepedia.co.uk

Organelles

Mitochondria:

These consist of an outer membrane enclosing a semi-fluid matrix. Throughout the membrane matrix is a an internal membrane, folded into cristae. The cristae and matrix contain enzymes which enable this organelle to carry out aerobic respiration, which release energy in the form of ATP for use within the cell.

Nucleus This controls all cellular activity using coding instructions which are, located in the cell to make specific proteins. RNA is produced in the nucleus pores.

Present in both animal and plant cells

Cell membrane

This covers the outside of a cell and consists of a bilayer of phospholipids interspersed with proteins. It separates the cell from the outside environment, gives protection and allows the diffusion of substances into and out of the cell.

Cytoplasm

This is a semi-fluid medium that is present in all cells and many ions are dissolved within the substance and many chemical reactions occur here.

Endoplastic reticulum

This can be in the form of rough endoplastic reticulum (RER) which consist of ribosomes on the outer layer or smooth endoplastic reticulum (SER) without ribosomes. The RER is a transport system throughout the cytoplasm that collects, stores, packages and transports the proteins made on the ribosomes. The SER synthesises lipids and some steroids.

Ribosomes

These are situated on the rough endoplastic reticulum and consist of a small and dense structure and acts as a giant enzyme. They are around 20nm and the building of proteins occurs here.

Golgi body

These are a series of flattened sacs, each separated from the cytoplasm by a membrane. The Golgi body is a packaging system where important chemicals become wrapped, forming vesicles. The vesicles become detached from the main Golgi sacs, enabling the isolation of chemicals from each other in the cytoplasm. This organelle aids the production and secretion of many proteins, carbohydrates and glycoproteins.

Lysosomes

These are specialised vesicles because they contain digestive enzymes. These have the ability to break down proteins and lipids.

Centrioles

There are two short cylinders in a cell which contain microtubules. Their function is to aid cell division.

Present only in plant cells

Cell wall

Around the cell membrane in a plant cell is a cell wall. This provides the cell with rigidity and allows many substances to be imported and exported by the cell, creating an effect hydrostatic skeleton. When the cell has a maximum amount of water content, it has maximum strength, and is said to be turgid.

Chloroplasts

These enable the plant to photosynthesise which produces energy due to the presence of chlorophyll in the chloroplasts within the cell.

Vacuole

This is a large central organelle in most plant cells and is a semi-fluid substance. It stores compounds such as sucrose and water potential enables the cell to gain turgor pressure when osmosis into the vacuole occurs.

Prokaryotic cell Eukaryotic cell

Size 0.1-10µm in diameter (small cell) 10-100µm diameter, much greater volume (large cell)

Site of nuclear material DNA free in cytoplasm DNA inside distinct membrane- bound nucleus

Organisation of nuclear material DNA is circular, not attached to histones DNA is linear, attached to histones (organising proteins) and condenses inot visible chromosomes before cell division

Cell division By binary fission By mitosis or meiosis

Ribosomes

Internal structure

Cell walls

Small – around 70s

Very few organelles

Complex and always present

Larger- around 80s

Complex membrane systems and many organelles

Present in plants and fungi but not in animals and their structure is relatively simple

O

A M

There are two types of microscopes

ELECTRON MICROSCOPESThe use of a beam of electrons ‘illuminates’ the specimen instead of using an electromagnetic radiation microscope. Electrons act like waves so can easily be produced, focused by using electromagnets and detected using a phosphor screen or photographic screen.

LIGHT MICROSCOPESThis type of microscope uses white light to illuminate a specimen. The light is focused onto the specimen by

a condensing lens. The specimen is placed on a microscope slide which is clipped onto a platform,

known as a stage. The image is viewed via an eyepiece or ocular lens.

Transmission electron microscope

•Works much like a light microscope

•Transmits a beam of electrons through a thin specimen and then focusing the electrons to form an image on a screen or on film.

•This is the most commonly used

•Has the best resolution

Scanning electron microscope

•Scans a fine beam of electrons on to a specimen and collects the electrons scattered by the surface

•Poorer resolution

•Gives excellent 3-D images of the surface

Light MicroscopeAdvantages:

•Easy to set up

•Not as expensive as Electron microscopes

•Specimens can be living

•Resolving power is high(200nm)

•Preparation of specimens is usually complex

Disadvantages:

• Maximum magnification is low (x 1500)

•Cannot resolve objects closer than 200nm into two separate images.

Electron microscope:

Advantages:

•Magnifies over 500,000 times

•High depth of focus

•Field of view good

•High resolution 0.2µm

Disadvantages:

•Expensive to buy (over £1 million)

• Expensive to maintain

•Large in size

•Vacuum is required

•Specimens are dead so distorts object for viewing

•Images in black and white

CentrifugationCell fractionation is a process which allows scientists to extract pure samples of a particular organelle, e.g.

the mitochondria, for study. This is the process that is called centrifugation:

1. The tissue is chopped up. When cells are broken apart, substances that would normally be kept separate inside the cell mix together and can begin to react, interfering with further study. To prevent this from happening three conditions are included where cells are kept:

• Cool at around 5°C ( this slows down the inevitable destruction by the cells’ own enzymes

• In an isotonic solution, equal concentration of substances inside and outside the cell membrane (this ensures that the organelles are not damaged by osmosis and can still function)

• At a specific pH by a buffer solution (organelles can still function as they are kept at suitable conditions.)

2. The mixture is placed in a homogeniser (blender) to break up the cells.

3. The resulting mixture is centrifuged at high speed. The spinning greatly increases the gravitational field, and the organelles separate out according to their density, it will be in this order;

Nuclei

Mitochondria

Rough Endoplastic reticulum

Plasma membrane

Smooth Endoplastic reticulum

Golgi apparatus

Densest

Least dense

More information can be found on the website www.biologymad.co.uk and www.biologymodel.co.uk

More information can be found on organelles and microscopy on;

• www.wikipedia.co.uk

• www.exam.net.co.uk

• www.ASguru.co.uk (bbc.co.uk/bitesizerevision)

• www.biology.arizona.edu/cell_bio/_cell_bio.html

Graticule

Stage micrometer

Eukaryotic cells contain:

Plant cells Animal cells

-Cell surface membranes - cell surface membrane

-Cell wall - ribosomes

-Ribosomes - endoplastic reticulum

-Endoplastic reticulum - Golgi apparatus

-Golgi apparatus - microtubules

-Micotubules - mitochondria

-Mitochondria - true nucleus envelope

-True nucleus with envelope - DNA several linear areas

-DNA with linear molecules

Eukaryotic cells don’t contain:

Plant cells Animal cells

-Lysosomes - Cell wall

-Rarely contain cilia and

flagella

Prokaryotic cells contain:•Cell surface membrane•Cell wall•Ribosomes, about 20nm in diameter•Cilia and flagella•DNA- single circular moleculeProkaryotic cells contain:•Endoplastic reticulum•Golgi body•Microtubules•Mitochondria•True nucleus with envelope Conclusion

Overall, the topic of cells and organelles is quite detailed and thorough revision needs to be acquired in order to understand the topic fully. Microscopes allow you to see a working cell and its’ organelles ,so that research into their function and how they were formed on the earth and hoe they have developed into the specimens they are today. This poster should be informative and with extra websites to visit on the page you should find useful facts and ideas about organelles, their function, where they are in the cell and how to see they through a microscope.

www.thinkquest.co.uk would be a suitable website to visit to support this knowledge on eukaryotic and prokaryotic cells

Prokaryotic Cell:without a true nucleus found in bacterial cells.

Features of the Cell

Complex cell wall: a tough coarse mesh made of the protein murein. Allows cells to become turgid without bursting and is important in maintaining the shape of the cell.

Plasma membrane: a phospholipid bilayer which controls what passes in and put of cells. Only allows small polar water soluble molecules to diffuse through due to the polar heads of the phospholipids which repel non polar molecules. Contains embedded proteins for the transportation of larger molecules and for the recognition of cell.

Mesosomes: Are inner foldings of cell membranes to give a large SA, they also contain the proteins and enzymes involved in respiration and in a eukaryote cells case photosynthesis.

Genetic Material: isn't found in a membrane bound nucleus but in the nuclear zone which is a region of cytoplasm that contains DNA. It also contains plasmid which are smaller circles of DNA that carry beneficial genes rather than vital and are used for the carrying of genes between cells. The DNA is always circular and not associated with proteins to make chromatin.

Ribosomes the smaller 70S type: these are the site of protein synthesis.

Cytoplasm: contains all enzymes required for metabolic reactions as……..

THERE ARE NO MEMBRANE BOUND ORGANEELS IN PROKARYOITIC CELLS

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 the only known example of a rotating motor in nature.

Capsule: an outer layer of cell which prevents the cell form drying out . It is also used as a food reserve, for sticking cells together and protecting the cell against digestion form other cells digestive enzymes.

Cell Ultra-structure and Microscopy

Esme IngramEukaryotic Cell:with a true nucleus –

membrane bound nucleus-found in animal,plant and fungi cells.

Chloroplast

The site of photosynthesis and are biconcave disc shaped with lots of internal membranes allowing a bigger surface area. Contains thykaloids which are phospholipid bilayers that have chlorophyll molecules embedded in them . These chlorophyll molecules absorb light energy then transfer it to other protein molecules which generate ATP.Thykaloids form stacks called graenum which greatly increases the efficiency of light dependent reactions by capturing most of the light that enters the cell.

Vacuole•A large membrane surrounded tonoplast filled with fluid of substances in in solution in water. It is used as a food reserve and can be as a feeding vacuole for digesting food. It is also used for expelling water as a it is contractile. Its main function in plants is structure and support, it’s difference in water potential compared with that outside of the cell enables cell to produce turgor pressure- which helps it maintain its shape.

Mitiochondrion• The site of aerobic respiration where ATP is made. It is surrounded by a double membrane the outer being thin and permeable whilst the inner is tightly folded into cristae which give it a large surface area. The very inside of the cell is the matrix which contains enzymes for early stages of respiration and DNA controlling respiration. The inner membrane is studded with stalked particles which are the site of TP synthesis.

Golgi BodyIt is a stack of curved cristanea which are found free in the cytoplasm. It synthesises and modifies protein before secretion form cell.Has vesicles entering and exiting it which contain newly synthesised proteins and have broken off RER

They travel towards golgi and fuse with its convex face.

Proteins are finished off + packaged-ready for exportation form cell

Proteins are transported in vesicles which break form golgi body

They fuse with cell surface membrane and release contents to outside

The vesicle become incorporated into cell membrane

RibosomesIn the eukaryotes they are of the larger 80S type. They are a small and dense structure and act as giant enzyme. They are either suspended in cytoplasm where they make protein for cells use or attached to ER where the proteins are for exportation. They are where the genetic code is used to build protein because a ribosome binds to a length of RNA and the info’ encoded in the RNA is used to assemble the correct order of amino acids in a protein. They are made of one large and one small subunit.

CytoskeletonNetwork of protein fibres used for strength, support and motility it is attached to cell membrane and helps hold cell in shape as well as organelles in place. There are three types of protein fibres (microfilaments, intermediate filaments and microtubules), and each has a motor protein that can move along the fibre carrying a cargo These motor proteins are responsible for cilia and flagella movements.

Endoplasmic ReticulumThere are two kinds of ER which are smooth ER and rough ER.It is a system of membranes running through the cytoplasm of the cell , the membranes enclose spaces called cristernae which form an interconnecting channel throughout cytoplasm. RER has ribosomes attached which are involved in protein synthesis. The cisternae break into small vesicles and travel to golgi body.

The Nucleus

•In a eukaryotic cell the nucleus bound by a double membrane, this isolates DNA kept inside it from other reactions in the cell to prevent it from damage.

•The nucleus contains a nucleolus which is a dark region where ribosome synthesis takes place.

•The ribosomes leave the nucleus form through the nuclear pores before being assembled into complete ribosomes as the outer membrane (part of nuclear envelope- phospholipid bilayer) links with ER.

•The nucleus contains nuclear plasma which contains chromatin a DNA1:protien2 complex which contains genes and is involved in cell division.

Other Eukaryote Features

•Cytoplasm:enzyme containing solution inside of the cell.

• Lysosomes: small membrane bound vesicles formed on RER containing enzymes, they are used to break down waste products.

•Centriole: pair of short microtubules involved in cell division.

•Undulipodium (Cilium and Flagellum): a long flexible tail present in some cells and used for motility

•Microvilli: finger like extensions of cell which increase surface area for maximum absorption.

Cell Centrifugation

The process which enables us to extract pure samples of an organelle based on the order of the sedimentation(density)

1. The tissue is chopped up and added to an ice cold, isotonic and buffer containing solution.

2. The mixture is put in a blender to break up cells.

3. It is then centrifuged at high speeds , and due to the increase in gravitational filed the organelles separate out according to density, the nuclei are always first.

MicroscopyMagnification: a measurement of how far we can expand and see the object, so it is a measure of enlargement. Overall magnification = Objective lens x Eyepiece lens

Resolution:the ability to distinguish between two dots.

The Light Microscope

Light rays are transmitted through specimen and two lenses

The objective lens (set of 3) provides the initial magnification of the image in the range of X4-X40

The eyepiece lens (top)is used to further magnify the image and focus it on the retina

Limitations of the light microscope: light is limited by its long wavelength so has a lower resolving power than electron microscopes, it only takes a small amount of power before it dissipates.

Real Size(ųm)=(observed size X 100)/magnification

Limitations of Electron Microscopes

•Specimens must be fixed in plastic, dead and viewed in a vacuum.

•Specimen can be damaged by electrons or by an electron dense chemical used to stain them

Comparing Them-table taken form www.biologymad,comLight Microscope Electron Microscope

Cheap to purchase (£100 – 500) Expensive to buy (over £ 1 000 000).

Cheap to operate.Cheap to operate. Expensive to produce electron beam.

Small and portable. Large and requires special rooms.

Simple and easy sample preparation. Lengthy and complex sample prep.

Material rarely distorted by preparation.Preparation distorts material.

Vacuum is not required. Vacuum is required.

Natural colour of sample maintained. All images in black and white.

Magnifies objects only up to 2000 timesMagnifies over 500 000 times.

Specimens can be living or dead Specimens are dead, as they must be fixed in plastic and viewed in a vacuum

Stains are often needed to make the cells visibleThe electron beam can damage specimens and they must be stained with an electron-dense chemical (usually heavy metals like osmium, lead or gold).

Electron Microscopes:This uses a beam of electrons in order to illuminate the specimen. A beam of electrons has an effective wavelength of less than 1 nm, so can be used to resolve small cellular ultra structure.

Transmission Electron Microscope

Electrons are produced from a tungsten filament at top of evacuated column

The specimen either absorbs or transmits electrons

Condensed lens focuses electrons onto specimen

Objective and projector lenses magnify and focus image onto fluorescent screen

Scanning Electron Microscope

Tungsten filament at the top of an evacuated column produces electrons

Condenser lenses focus beams of electrons

Objective lenses magnifies the beam of electrons

And electrons are reflected of the specimen and collected in the form of an image on screen.

.

Prokaryotic Cells Eukaryotic cells  

small cells (< 5 mm) larger cells (> 10 mm)

always unicellular often multicellular

no nucleus or any membrane-bound organelles, such as mitochondria

always have nucleus and other membrane-bound organelles

DNA is circular, without proteins

DNA is linear and associated with proteins to form chromatin

ribosomes are small (70S)

ribosomes are large (80S)

no cytoskeleton always has a cytoskeleton

motility by rigid rotating flagellum made of flagellin

motility by flexible waving undulipodium, made of tubulin

cell division is by binary fission

cell division is by mitosis or meiosis

reproduction is always asexual

reproduction is asexual or sexual

huge variety of metabolic pathways

common metabolic pathways

This table was taken form www.biologymad.com

Endosymbiosis

The theory that prokaryotic cells were around a lot longer than eukaryotic cells and that in fact eukaryotic cell organelles like nuclei derived from prokaryotic cells that became incorporated inside larger prokaryotic cells.

It is supported by evidence such as;

•Organelles contain circular bacteria-plasmids-like bacterial cells.

•They also contain 70S ribosomes like bacteria cells.

•Also the double membranes of organelles imply that a single membrane was engulfed and surrounded by a larger cell.

Comparing the Two Cells

Jonathan Stevens

Module One: Biological Molecules

Lipids, Proteins and Carbohydrates

Introduction:

In the following poster I will go into detail of many things to do with biological molecules, the main aspects I will go into detail are carbohydrates, lipids and proteins. I will show the structures of the molecules and the types of bonding and how they join and get broken down. I will state the chemical tests for the certain types of molecules and what too look for to see If the substance contains the specific type of molecule. I will the state and explains the functions of proteins and etc.

Carbohydrates:

There are 3 main types of carbohydrates and they are polysaccharides, monosaccharide and disaccharides. All carbohydrates contain 3 elements these

elements are carbon, hydrogen and oxygen.

Monosaccharide:

A monosaccharide is a single sugar this is a molecule of sugar in its smallest form, an example of this is glucose, glucose is a sugar which our body uses, there are two types of glucose there is alpha and beta, the structures of these molecules differ, they are as follows:

Alpha Beta

Glucose can join together to form long chains which are polysaccharides, the first stage of the joining is when two glucoses join to become a disaccharide the glucoses can join up in different orders and this makes different disaccharides for example alpha plus alpha. The process of joining is between carbon one and carbon four, they join by a glycosilic bond, reaction gives out water and it is called a condensation reaction. The glycosilic bond can also be broken they are broken, they are broken down by adding it with acid, this reaction adds water to the molecule which rejoins the two glucoses, this reaction is a called hydrolosis. The test for monosaccharide is to add benedict's solution to the substance which is at near boiling, if the substance contains monosaccharide the benedict's solution will change to a green – red solution.

Disaccharides:

Disaccharides are two monosaccharide joined together, they are joined by condensation reaction. The test for disaccharides is as follows, add hydrochloric acid to the solution which is at near boiling, then add benedict's solution to the solution and if the benedict's solution changes to a green to red colour.

Polysaccharides:

These are massive chains of monosaccharide and disaccharides an example of this is starch which make up bigger molecules.

Lipids: Lipids all contain a glycerol backbone which looks as follows:

Lipids contain a fattys acid and this has a carboxyl this is shown below, the zig zaged line represents a long hydrocarbon chain, the chain can be saturated or unsaturated.

A fatty acid joins to a glycerol backbone they join by esterficationthis is a condensation reaction and releases water. A glycerol backbone can join up to three things on its 3 branches, one example it can make is a triglyceride, this is when a glycerol backbone joins to three fatty acids.

Esterfication

A fatty acid is hydrophobic this means it doesn’t like to react with water this is because the water will breaks the bonds between the glycerol and the fatty acid because if you add water you are adding back hydrogen's, and why do they share hydrogen's if they could have one each. The glycerol head is hydrophilic which means it is water loving.

Proteins: Proteins are a key part of the body they have many functions these functions are: ~for enzymes~anti-bodies~actin & myosin which make muscles contract~used to make tissues~blood clotting involve many proteins~gives strength to hair and nails

Proteins are made up of amino acids and each amino acid has three groups these groups are amino group, functional group and the carboxyl group, a diagram of this is below:

The functional group can join to different molecules these molecules make up different proteins and amino acids which have different jobs, examples of these are below:

Proteins and amino acids have many structures and these structures are:

Primary structure this is the order of the amino acids

Secondary structure: this structure is when the long strand of amino acids either curve into a helix or the create a beta pleated sheets, the helix and sheets are joined together by hydrogen bonds.

Tertiary structure: the third structure is when the helix’s and sheets join together to form a globular protein this big structure is also known as a enzyme, the big structure is joined together by many bonds these bonds are:di-sulphide, hydrogen, Ionic, Hydrophobic, Van der Waals

Quartary structure: this structure is when gobular proteins join together to make bigger structures this structure can join together to make a well known structure which is a red blood cell.

IntroductionAll living things are made up of one (unicellular) or more cells (multicellular), they are the smallest units that can be alive. Every cell possesses internal coded instructions to control cell activities and development they also have the ability to continue life by some sort of cell division. The biggest division in cells is that of prokaryotic and eukaryotic. Such differences in the divisions are listed below.

Prokaryotic and Eukaryotic cells

Prokaryotic

Has a cell membrane

Has a cell wall

Has ribosomes which are small

Has no endoplasmic reticulum

Has no golgi apparatus

Has no mitochondria

Has no true nucleus with envelope

DNA is circular

May have flagellum for motility

Asexual reproduction

Always unicellular

Small cells

No cytoskeleton

Binary fusion (cell division)

Variety of metabolic paths

Cell fractionation and centrifugationThis means separating different parts and organelles of a cell, so that they can be studied in detail. The

step by step procedure is;

1. Chop up the tissue, by doing so you are mixing substances together you need to prevent this by adding a ice cold (minimise enzyme reaction), isotonic (avoid distortion of organelles) and buffer (resist changes in ph) solution.

2. Put mixture into homogeniser to break up the cells 3. Mixture is centrifuged at high speed, the spinning increases gravitational field and consequently

organelles separate according to density4. The remaining fluid (the supernatant) is poured off and centrifuged again to collect other organelles.

The order of sedimentation and density is;1. Nuclei2. Mitochondria3. Rough ER4. Plasma membranes and Smooth ER5. Ribosomes

Microscopes Magnification – is the measure of enlargement Magnification = size of image

Size of specimen

Resolution - refers to the detail visible and the limit of the resolution depends on the wavelength, shorter wavelengths give the best resolution.

Light microscope – Light rays are focused on to a transparent specimen by a condenser lens. The rays pass through the specimen and are focused again by two more lenses – the objective lens and the eyepiece lens. Light microscopes haven’t got a high enough resolution and the wavelength of light is limited. Advantages are that; it is small, no vacuum is required and that samples can be living or dead.

Electron microscopes – Beam of electrons is transmitted through the material. This means that sections have to be thin and the preparation is complex, it also has to be a vacuum. Advantages of the electron microscope are that; it has a bigger resolution than that of a light microscope, the scanning electron microscope shows 3D image, there is a better quality and a higher depth of focus. However they are very big and expensive and have a limited field of view.

The process of a scanning electron microscope is• Pass a beam of electrons over the surface of the specimen

in the form of a ‘scanning’ beam.• Electrons are reflected off the surface of the specimen as it

has been previously coated in heavy metals.• It is these reflected electron beams that are focussed of the

fluorescent screen in order to make up the image. 

Process of transmission electron microscope where you pass a beam of electrons through the specimen. The electrons that pass through the specimen are detected on a fluorescent screen on which the image is displayed.  

Biological Cells Lauren Boast

Organelles – Cells contain several types of organelle which are contained in the cytoplasm. An organelle is a subunit of the cell designed to carry out its own specific function separate from all the other activities going on in the cell.

Nucleus – Controls all cellular activity using coded instructions located in DNA, this DNA allows the nucleus to make specific proteins. The nucleus is surrounded by a nuclear envelope which has nuclear pores. The interior is called the nucleoplasm, which is full of chromatin and the nucleolus is a dark region of chromatin, involved in making ribosomes.Mitochondria – Consists of an outer membrane and an internal membrane folded into cristae. The cristae contain enzymes which enable mitochondria to carry out respiration.Ribosomes –Smallest and the most numerous of organelles they aid in the manufacture of proteins and are the place where amino acids are bonded together. They are often found in groups called polysomes.Endoplasmic Reticulum – found as either Rough ER (with ribosomes) or smooth ER (without ribosomes). Smooth ER is a series of membrane channels involved in synthesising and transporting materials. The ribosomes, which are studded onto the Rough ER synthesise proteins.Golgi body – A packaging system where important chemicals become membrane wrapped. It also aids in the production and secretion of many proteins, carbohydrates and glycoprotein’sLysosomes – Specialised vesicles that contain digestive enzyme and they are used to break down unwanted chemicals, toxins, organelles or even whole cells, so that the materials may be recycledCell wall – Provide a rigid support for the cell and are made mainly of celluloseChloroplasts - Enable the plant to photosynthesise, the chloroplasts have a triple membrane. In the third membrane, the thylakoid membrane, is chlorophyll and other photosynthetic pigments arranged in photosystems, together with stalked particles, and it is the site of photosynthesis and ATP synthesis. Chloroplasts also contain starch grains, ribosomes and circular DNA.Vacuole – Large space in plant cell that contains chemicals such as glucose and mineral ions in water. Plant cell vacuoles are filled with cell sap, and are very important in keeping the cell rigid, or turgidCell membrane – Separates cell from outside environment and controls what enters and leaves the cell. It is made of phospholipids and proteins

Eukaryotic

Has a cell membrane

Plant cells have a cell wall animal cells don’t

Has large ribosomes

Has an endoplasmic reticulum

Had a golgi apparatus

Has mitochondria

Has a true nucleus with envelope

DNA is linear

Undulipodium for motility

Sexual or asexual

Reproduction

Often multicellular

Large cells

Cytoskeleton

Mitosis or meiosis

Common metabolic paths

Scanning electron microscope

Transmission electron microscope

References

www.biologymad.com

Advanced Biology – pgs 49 -72

AQA AS biology spec A – 4 – 11

Letts revise AS 33 - 34

Cells- IntroductionAll living things are made of cells, and cells are the smallest things that can be alive. Life on Earth is classified into five parts, 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.Eukaryote = ‘true nucleus’, meaning there is a large nucleus which contains the cells DNA inside the membrane.Prokaryote = ‘before the nucleus’ meaning the DNA is not enclosed by a membrane.

Eukaryotic Cells

Prokaryotic Cells

Organelles…

Cytoplasm (or Cytosol). This is the solution within the cell membrane. It contains enzymes for glycolysis (part of respiration) and other 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 and ribosomes from the nucleus. The nucleolus is a dark region of chromatin, involved in making ribosomesMitochondrion. 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 and quite permeable, while the inner membrane is highly folded into cristae, which give it a large surface area.Chloroplast. Bigger and fatter than mitochondria, chloroplasts are where photosynthesis takes place, so are only found in photosynthetic organisms (plants and algae).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.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, 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.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.Lysosomes. These are small membrane-bound vesicles formed from the RER containing a cocktail of digestive enzymes.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 filamentsMicrovilli. 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.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.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).Mesosome. A tightly-folded region of the cell membrane containing all the membrane-bound proteins required for respiration and photosynthesis. Can also be associated with the nucleoid. Capsule (or Slime Layer). A thick polysaccharide layer outside of the cell wall, like the glycocalyx of eukaryotes. Used for sticking cells together, as a food reserve, as protection against desiccation and chemicals, and as protection against phagocytosis.

MagnificationMagnification is the number of times larger and image is than the specimen. For example, if a cell is 10um in diameter, and a microscope produces an image of it which is 1000um in diameter, then the microscope has magnified the specimen 100 times.

Magnification= size of image

size of specimen

The magnification produced by a light microscope depends on the strengths of the objective lens and the eyepiece lens. If you are using a x40 objective lens and x10 eyepiece lens, then your specimen is being magnified 400 times. There is no limit to the amount a light microscope can magnify. By putting in stronger lenses, or more lenses, you could produce a huge image several metres across. But the image would not be at all clear, and you wouldn’t be able to see any more detail than before. This is because the resolution of a light microscope is limited.

ResolutionResolution is the degree of detail which can be seen. The limit of resolution of a microscope is the minimum distance by which two points can be separated and still seen as two separate points and not one fuzzy one. Newspaper photographs, for example, have a rather poor resolution, being made up of quite large dots which you can see with the naked eye. This limits the amount of detail which you can see. Compare this with a good quality photograph with a higher resolution (smaller dots).

The limit of resolution depends on the wavelength of light. The resolution limit is about 0.45 times the wavelength. Shorter wavelengths give the best (smallest) resolution. The shortest wavelength light which we can see is blue light, which has a wavelength of about 450 nm. This gives a resolution of about 0.45 x 450nm, which is close to 200 nm. Any objects smaller than this, or any points less than 200nm apart, will either be invisible or appear as blurs.

Electron beams, however, have a much shorter wavelength than light, so much better resolutions can be achieved. Electron microscopes have a maximum resolution around 400 times better than that of light microscopes, being able to separate objects as little as 0.5nm apart.

Overall: Magnification is how much bigger a sample appears to be under the microscope than it is in real life.Overall magnification = Objective lens x Eyepiece lens- Resolution is the ability to distinguish between two points on an image i.e. the amount of detail- The resolution of an image is limited by the wavelength of radiation used to view the sample. - This is because when objects in the specimen are much smaller than the wavelength of the radiation being used, they do not interrupt the waves, and so are not detected. - The wavelength of light is much larger than the wavelength of electrons, so the resolution of the light microscope is a lot lower. - Using a microscope with a more powerful magnification will not increase this resolution any further. It will increase the size of the image, but objects closer than 200nm will still only be seen as one point.

Laura Griffin 12C

MicroscopyLight Microscopes- Light rays are focused on to a transparent specimen by a condenser lens. The rays pass through the specimen and are focused again by two more lenses- the objective lens and the eyepiece lens. These two lenses produce a magnified image. As many biological specimens are colourless and nearly transparent, stains are often used to make different parts show up clearly. Stains usually colour a particular part of a cell; iodine solution, for example, colours starch grains blue- black. Some stains, such as methylene blue or iodine solution, can be added to living cells. In other cases, the specimen is ‘fixed’ by adding a chemical such as acetic acid or alcohol, known as a fixative. These chemicals react with substances such as proteins or nucleic acids in the structures in the cell, making them insoluble and so anchoring them in position. The cells are killed when the fixative is added. Stains may be added either before or after the fixing process. So long as the specimen is thin enough to allow light to pass through, there are no limitations on what you can look at using a light microscope. Living, moving organisms such as protoctists can be watched, or you can look at a permanent stained preparation of a thin section through a piece of human tissue.

Electron Microscopes- Have the general same principles as that of a light microscope except that beams of electrons are used instead of beams of light. They are focussed using electromagnets rather than glass lenses. As electrons are easily stopped by air molecules, the space inside an electron microscope must be a vacuum. As our eyes do not respond to electrons, the electrons are allowed to hit a fluorescent screen which emits visible light where the electrons hit.Electrons cannot penetrate materials as well as light rays can, so specimens for viewing in an electron microscope must be much thinner than those used in a light microscope. This, and the fact that the specimen has to be placed in a vacuum, places great limitations on what can be viewed using an electron microscope. In particular, it is not usually possible to look at living material. As in a light microscopes, materials are stained. Heavy metal ions, such as lead, are added to the specimen and are taken up by particular parts of the cells.There are two kinds of electron microscope. The transmission electron microscope (TEM) works much like a light microscope, transmitting a beam of electrons through a thin specimen and then focusing the electrons to form an image on a screen or on film. This is the most common form of electron microscope and has the best resolution. The scanning electron microscope (SEM) scans a fine beam of electron onto a specimen and collects the electrons scattered by the surface. This has poorer resolution, but gives excellent 3-dimentional images of surfaces.TEM…• Pass a beam of electrons through the specimen. The electrons that pass through the specimen are detected on a fluorescent screen on which the image is displayed.• Thin sections of specimen are needed for transmission electron microscopy as the electrons have to pass through the specimen for the image to be produced.• This is the most common form of electron microscope and has the best resolution SEM…• Pass a beam of electrons over the surface of the specimen in the form of a ‘scanning’ beam.• Electrons are reflected off the surface of the specimen as it has been previously coated in heavy metals.• It is these reflected electron beams that are focused of the fluorescent screen in order to make up the image. • Larger, thicker structures can thus be seen under the SEM as the electrons do not have to pass through the sample in order to form the image. This gives excellent 3-dimensional images of surfaces• However the resolution of the SEM is lower than that of the TEM.

Eukaryotic cells are both multi cellular and unicellular. Eukaryotic cells are larger than prokaryotic cells by a thousand times by volume. They have a variety and membranes and structures (organelles) and a cytoskeleton.

The bacterial cell wall is complex. The basic structure is a tough mesh made from a protein called murein. The plasma membrane (cell membrane) has the same structure in both prokaryotes and eukaryotes. However, bacterial cells do not contain membrane- bound organelles such as mitochondria, but they do have mesosomes which are inner foldings of the cell membrane that give a larger surface area for the attachment of enzymes involved in metabolic processes, e.g. respiration.

The genetic material differs from that of a eukaryotic cell. Bacteria have a single, circular piece of DNA. This is found in a region known as the nucleoid, but there is no nuclear membrane. Ribosome's are the sites of protein synthesis as in eukaryotic cells, but bacterial ribosome's are smaller than those in eukaryotic cells.The bacterial flagellum is a whip- like structure that rotates to produce movement, allowing some bacteria to move towards or away from stimuli. Not all bacteria have flagella and some bacteria may have more than one. There are plasmids which occur throughout the cytoplasm. These are tiny circles of DNA that are separate from the main circle of DNA. They carry genes which are beneficial rather than vital e.g. for antibiotic resistance, and they can be transferred between bacterial cells. Plasmids are of great interest to genetic engineers as they can be used as carriers of genes between cells.Some bacteria have a capsule which is a layer of slime outside the cell wall. The capsule can have several functions. For example, it can stop the cell from drying out or protect against digestion by a host’s digestive enzymes.

Animal Cells:when seen under an optical or light microscope, most animal cells possess…- Nucleus, large circular organelle containing DNA.- Nucleolus, a dark feature inside the nucleus.- Plasma Membrane, very thin membrane surrounding the cell.- Cytoplasm, literally ‘cell fluid’, containing many different organelles which cannot be distinguished at this level of magnification.

Plant Cells:Plant cells usually include the nucleus, nucleolus, plasma membrane and cytoplasm seen in animal cells, they also contain…- Cell wall, tough layer of cellulose surrounding the cell.- vacuole, a large membrane- bound organelle in the middle of most plant cells, which contains a fluid called sap.- Chloroplasts, contain chlorophyll and are the site of photosynthesis.

Cell Fractionation and Centrifugation:Cell fractionation is the process which allows scientists to extract pure samples of a specific organelle. The tissue is chopped up, e.g. a leaf, when cells are broken apart, the substances begin to react. This interferes with the study so a fluid is added. This fluid is ice cold to minimise enzyme reactions, is isotonic to avoid distortion of organelles and contains a buffer to resist any changes in PH. The mixture is then put in a homogeniser (blender) to break up the cells. This mixture is centrifuged at high speed, the organelles separate out depending on density and to some extent shape. The first organelle to sediment out is the nuclei, then the remaining fluid, the supernatant, is poured off and centrifuged again to collect other organelles. The order of sedimentation is:- Nuclei- Mitochondria and chloroplasts- Rough ER- Plasma membrane and smooth ER, then lastly the ribosomes.