Chapter 3

Ion table:

• Ca 2+ : Nerve impulse transmission and muscle contraction
• Na+ : Nerve impulse transmission and kidney function
• K+ : Nerve imoulse transmission and stomatal opening
• H+ : Catalysis of reactions and pH determination
• NH4 + : Production of nitrate ions by bactera
• NO3- : Nitrogen supply to plants for amino acid formation
• HCO3- : Maintennance of bloof pH
• Cl- : Balance positive charge of sodium and potassium ions in cells
• PO4 3- : Cell membrane formation, nucleic acid and ATP formation, bone formation
• OH- : Catalysis of reactions, pH determination

Carbohydrates contain carbon, hydrogen and oxygen. Lipids contain carbon, hydrogen and oxygen. Proteins contain carbon, hydrogen, nitrogen and sulfur. Nucleic acids contain carbon, hydrogen and phosphorous. 

Electrons are not always shared equally in a covalent bond, so one of the atoms may be more negative or positive depending on its electronegativity, shown by the δ + or δ -  and when this happens the molecule is said to be polar. Oxygen and hyrdogen are examples of elements that don't share atoms equally, so the OH bond is polar. Water therefore interacts with other water molecules to form hydrogen bonds where the slighty charged parts of the molecules are attracted to each other, which is what gives water molecules their unique properties. Water has an unusaully high boiling point so is a liquid at room temperature unlike carbon dioxide and oxygen which is due to the hydrogen bonds. When water freezes it runs to ice, which is less dence than its liquid state, this is because the hydrogen bonds fix slightly further away, producing a rigid open structure that allows ice to float. Water therefore has cohesive properties and moved as one mass, and this is what allows plants to draw water up their roots through capillary action, it is also adhesive and water molecules are attracted to other materials. 

Becuase water is a polar molecule, water acts as a solvent in which many solutes in an organism can be dissolved in, for example the cytosol is mainly water, it also acts as a medium for chemical reactions and helps transport dissolved compounds into and out of the cells. Water makes a very efficient transport medium as cohesiona dn adhesionmean it can easily be transported and also enables capillary action. Water also acts as a coolant helping to buffer temperature chamges during chemical reactions due to the large amount of energy needed to break hydrogen bonds, so it allows a constant temperature to be maintained, something neccessary for many cellular reactions. Water also provides a stable enviroment for organisms to live in, as it doesn't change temperature or state easily along with ice acting as an insulating layer for animals to live under

Carbohydrates are molecules that only contain the elements carbon, hydrogen and oxygen. A single unit is called a monosaccaride, for example glucose or ribose, and when two are linked they form disaccaride like lactose and sucrose, when more than two join they become a polysaccaride such as glycogen or starch.

Glucose is a hexose monosaccaride that has a six carbon ring structure, and two varients, alpha glucose, where the OH group on carbon 1 is LOWER, and beta glucose, where the OH group on carbon 1 is TOP. Glucose is soluble in water due to the hydrogen bonds between the hydroxyl groups and water and means it can dissolve in the cytosol of the cell. When two aplha glucose molecules are side by side, the two hydroxyl groups interact in a condensation reaction where bonds are broekn and reformed to make a covalent glycosidic bond on carbons 1 and 4 and a disaccaride is formed, with water as a by product, the new molecule is maltose.

Fructose and galactose are also hexose monosaccarides, galactose and glucose join to make lactose, commonly found in milk, pentose monosaccarides are sugars that have a five carbon ring structure,for example ribose. 

Manly alpha glucose molecules can be joind by glycosidic bonds to form two slighlt different polysaccarides known collectively as starch. One of the polysaccarides is called amylose which is formed entirely from 1-4 glycosidic bonds, the angle of the bond means that it twists to form a helix which is further stabilised by hydrogen bonding within the molecule. This makes it much more compact and less soluble than the glucose used to make it. Another type of starch is formed when glycosidic bonds form between carbon 1 and 6, this polysaccaride is called amylopectin that has many 1-4 glycosidic bonds but also some 1-6 ones, which gives it a branches structure. 

The functional equivalent of starch in plants and fungi is glycogen, which forms more branches than amylopectin whihc makes it very compact and that there are many free ends where glucose can be added or removed quickly so glucose demands can be met. 

Beta cellulose is unable to join in the same way as alpha glucose, the only way they can join is if every alternate glucose molecules is upside down. This means that the polysacccaride is unable to coil or form branches, so a straight chain molecule called cellulose is formed. Cellulose molecules make hydrogen bonds with each other forming microfibrils, which join to make macrofibrils, which are insoluble and used to make cell walls once forming into fibres.

Lipids, commonly known as fats or oils, are molecules containing carbon, hydrogen and oxygen. Lipids are non polar molecules as the electrons in the outer p orbitals are evenly distributed, so there are no positive or negative regions within the molecules, and for this reason they are not soluble in water. Lipids are large complex molecules known as macromolecules which aren't built from repeating units. 

Triglycerides: A triglyceride is made by combing glycerol with three fatty acid chains, they react to from ester bonds as one is a carboxylic acid and the other an alcohol. The hydroxyl groups interact leading to the formation of 3 water molecules. The reaction is called esterfication, 3 water molecules can be supplied in the reverse rection when triglyceride's are broken down in a hydrolysis reaction. 

Fatty acid chains that have no double bonds are called saturated, which are usually solid. Those with double bonds are called unsaturated as it causes a kink or bend in the molecule so they cannot pack as closley together, making them liquid at room temperature. 

Phospholipids are modified triglycerides that contain an inorganic phosphorous ion (Pi) along with carbon, hydrogen and oxygen. Pi ions are found in the cytoplasm of all cells, they have extra electrons and are negatively charged, making them soluble in water. One of the fatty acid chains in a triglyceride is replaced with a Pi to mkae a phospolipids. They are unusual because, due to their length, they have a non polar tail which are repelled by water and are hydrophobic, the charged heads can interact with water, and are hydrophillic. As a result they will form a layer on the surface of water with the phosphate heads in the water and the fatty acid tails sticking out - they act as a surfactant. They can also form bilayers with a hydrophobic core, protected from the water by the hydrophillic heads. This is significant as it means they can be used to seperate aqueous environments in cells, and so can help to form membrane bound organelles. 

Sterols, steroid alcohols, are complex organic molecules that are based with a 4 carbon structure and a OH group at one end. This makes them hydrophillic but the rest of the molecule is hydrophobic. Cholesterol is an example of a sterol, which has an important role in the formation of cell membranes as it can position itself between the phospholipids adding stability and regulating their fluidity by keeping the membrane's fluid at low temperatures. 

Roles of lipids: Due to their non-polar nature, lipids have many biological roles such as membrane formation and the creation of hydrophobic barriers, hormone production, electrical insulation for impulse travel, waterproofing such as on plant leaves, triglycerides in particular can be stored under the skin and around vital organs and provide thermal insulation to reduce heat loss, cushioning to protect vital organs, and bouyancy for aquatic animals like whales. 

Lipids can be identified using an emulsion test, where a white emulsion will form on the top layer when you mix a sample with ethanol and then mix and shake it with water if a lipid is present. 

Benedict's test for reducing sugars: All monosaccarides and some disaccarides are reducing sugars, meaning they can donate electrons and reduce other molecules. To do this place the sample in a boiling tube after making it a liquid form , then add an equal volume of copper(II)sulfate (Benedict's), and heat themoxture gently in a water bath for 5 minutes. Reducing sugars will react with the blue Cu 2+ ions, reducing them to brick red Cu + ions, so a brick red precipitate is formed. Non reducing sugars dont react with Benedict's so will remain blue, indicating a negative result. If sucrose is boiled with dilute HCL it will give a positive result when warmed with Benedict's, because sucrose has been hydrolysed by the acid to glucose and fructose, which are both reducing sugars. 

Iodine test for starch: This can be used to determine the presence of starch, adding a few drops of iodine dissolved in alkali solution with cause it to change from yellow to purple/black if starch is present in the sample. 

Reagent strips can be manufactured to test for the presence of reducing sugars like glucose, the advantage beinf that you can use a colour coded chart to determine concentration. 

Peptides are polymers made of amino acid molecules, proteins consist of one or more polypeptides arranged in complex macromolecules. All amino acids have the same basic structure, variable R groups result in different amino acids. There are 20 commonly found in cells, 9 are essential and can only be obtained from what we eat, 5 are non essential as our bodies are able to make them from other amino acids, and 6 are conditionally essential as are only needed for infants and growing children. Amino acids join when the amine and carboxylic acids connected to the central carbon react. The R-groups are not involved in this point. The hydroxyl in the carboxylic acid group of one amino acid reacts with a hydrogen in the amine group of another amino acid. A peptide bond is formed between the amino acids and a dipeptide is formed. When many acids are joined by peptide bonds a polypeptide is formed which is catalysed by peptidyl transferase in ribosomes. The different R-groups are able to interact with each other forming different types of bonds whihc lead to long complex structures, the presence of different sequences of amino acids results in different shaped proteins being formed, which then determine the function of the organism. 

Primary structure - this is the sequence in which the amino acids are joined, and is directed by information carried by the DNA, the particular amino acid sequence will influence how the polypeptide folds to give the protein's final shape, which in turn will determine its function.

Secondary structure - the oxygen, hydrogen and nitrogen atoms of the basic repeating structure interact, causing hydrogen bonds to form, pulling the the chain into a coil shape called an alpha helix. Polypeptide chains can also lie parallel to each other joined by hydrogen bonds forming sheet like structures, called a beta pleated sheet. Secondary structure is a result of hydrogen bonds depening on the specific amino acid sequence.

Tertiary structure - this is the folding of the protein into its final shape, the coiling or folding of the protein causes R-groups of different amino acids closer together so they can interact, causing further folding in these regions. There can be hydrophobic/hydrophillic interactions between polar R-groups, hydrogen bonds, ionic bonds between oppositely charged R-groups, and disulfide bonds between R-groups that contain sulfur form strong covalent bonds.

Quaternary structure - this results in the association of 2 or more induvidual proteins called subunits, same interactions as tertiary structure except their between different protein molecules. The protein subunits can be different or identical, enzymes often consist of two identical subunits. Haemoglobin has 4 made of two sets of two identical subunits. 

Proteins are assembled in aqueous environments so the way in which the R-groups fold also depends on whether they are hydrophobic or hydrophillic, as the hydrophillic ones will be on the outside.

Proteases are enzymes that catalyse the opposite reaction of forming peptide bonds through hydrolysis, reforming the carboxlic acid and amine groups. 

Peptide bonds form violt coloured complexes with copper ions in alkaline solutions, so this can be used as an identification test for proteins.

Globular proteins are compact, water soluble and usually roughly spherical, and form when tertiary structure determines that hydrophobic R-groups are kept away from the aqueous environment, so the proteins can interact with water. This solubility is very important as they are involved in immunity, muscle contraction and homeostasis.

Insulin - this is a globular protein that is involved in the regulation of blood glucose concentration, hormones are transported in the bloodstream so have to be soluble and have to fit into specific receptors so have to have specific shapes. 

Conjugated proteins are globular proteins that contain a non-protein component called a prosthetic group, lipids or carbohydates can combine with proteins and so can metal ions derived from vitamins.

Haemoglobin - This is a red oxygen carrying pigment that has two alpha and two beta subunits, each of which contains a prosthetic Fe 2+ ion that allows them to reversibly bind to oxygen.

Catalase - this is a quaternary protein enzyme containing 4 Fe 2_ groups that allow it to interact with hydrogen peroxide and speed up its breakdown, as it is a common by product of metabolism but is toxic to cells.

Fibrous proteins are formed from long insoluble molecules due to a high proportion of amino acids with hydrophobic R-groups in their primary structures, they usually contain a limited number of amino acids and have quite repetitive sequences, leading to organised structures that tend to make strong, long molecules that aren't folded into complex 3D shapes.

Keratin: This is a group of fibrous proteins present om hair skin and nails, it has lots of disulfide bonds, varying amounts determining flexibility, keratin forms strong, inflexible insoluble materials due to high amounts of the amino acid, cysteine.

Elastin: This is a fibrous protein found in elastic fibres which are present in the walls of the blood vessels and in the alveoli of the lungs - they give these structures the flexibility to expand when needed. Elastin is made by linking many soluble tropoelastin protein molecules to make a very large, insoluble, stable, crossed linked structure. Tropoelastin molecules are able to stretch and recoil without breaking which have alternate hydrophobic and lysein rich areas, elastin is made when multiple tropoelastin molecules aggregate as a result of interactions between the hydrophobic areas, and the structure is stabilised by cross linkong covalent bonds between the lyseine amino acids, whilst maintaining flexibility.

Collagen: This is another fibrous protein which is a connective tissue found in skin, tendons and ligaments that is made by combining three polypeptide chains wound around each other to form a triple helix structure. Every third amino acid in the chains is glycine, and its small size allows the three protein molecules to form a closely packed triple helix, and many hydrogen bonds form between the polypeptide chains forming long quaternary proteins with staggered ends which allow proteins to join the ends to form tropocollagen fibrils which can cross link to form strong fibres. Collagen also has high amounts of the amino acids proline and hydroxyproline that have repelling r-groups which increase stability. Collagen fibres can aggregate in ligaments and tendons to make large mesh bundles.

 Nucleic acids contain the elements carbon, oxygen, nitrogen and phosphorous, they are large polymers formed from singular nucleotides, each of which contain a pentose monosaccaride with five carbons, an inorganic phosphate group that is negatively charged, and a nitrogeneous base. Nucleotides are linked together by condensation reactions to form a polynucleotide polymer, the phosphate group on the fith carbon of the sugar forms a covalent bond with the hydroxyl OH group at the third carbon of an adjacent nucleotide to form a phosphodiester bond, these bonds form a sugar-phosphate backbone with a base attached to each sugar, these bonds are broken by hydrolysis.

DNA: Deoxyribonucleic acid contains deoxyribise and one of 4 different bases per nucleotide, Pyrimidines which are smaller, have a single ring structure, thymine and cytosine, which bind to Purines which have a larger double ring structure, adenine and cytosine. A DNA molecule consists of two polynucleotide chains coiled into a helix, which are held together by hydrogen bonds between the bases, and has two parallel strands which run in opposite directions so the bases can bind - antiparallel. The pairing between the bases allows DNA to be copied and transcribed. Complementary base pairing is where adenine and thymine form two hydrogen bonds and always join with each other, and cyosine and gaunine form three hydrogen bonds to alwyas bind together. This means DNA alwyas has the same amount of all the bases and has a constant structure.

Ribonucleic acid plays an essential role in the transfer of genetic information from the DNA to the proteins that make up the enzymes and tissues of the body, as DNA is a very long molecule which is unable to leave the nucleus. So instead a short section of DNA that corresponds to a single gene is transcribed onto a short mRNA molecule. RNA differs as the sugar is just ribose, and the thymine base is replaced with uracil, which can withstand the composition of the cytoplasm, and base pairing rules still apply, and they are formed in the same way. The RNA polymers are very small and can leave the nucleus and travel to the ribisomes, the site of protein synthesis. After this the RNA molecules are degraded in the cytoplasm and the phosphodiester bonds are hydrolysed and the nucleotides are released to be reused. 

DNA can be exracted by grindinfg up a sample and mixing it with detergent, adding salt to break hydorgen bonds between DNA and water, adding protease to break down proteins associated with the DNA, adding ethanol that will cause the DNA to precipitate out of solution.

When a cell prepares to divide, the two strands of DNA divide to act as a template for another two strands to be made, this is through the process of semi conservative replication, as once the two strands have seperated as a result of breaking the hydrogen bonds between the bases, free DNA nucelotides pair with their complementary bases which have been exposed, and then hydrogen bonds are reformed. In this was two new molecules of DNA have been made where each consists of one old strand and one new strand, so the mechanism is semi conservative. DNA replication is controlled by enzymes. The unwinding of the DNA strands of the double helix is carried out by the enzyme, DNA helicase, which travels along the backbone catalysing the reverse reactions that cause the hydrogen bonds between the base pairs to break. Free nucleotides pair with the newly exposed bases on the template strands as the unzipping continues, and then DNA polymerase catalyses the formation of phosphodiester bonds between the nucleotides, and then the hydrogen bonds reform. DNA polymerase always moves along the template strand in the same way as it binds to the OH on the third carbon and travels towards the 5th carbon. As DNA only unzips in one direction, DNA polymerase has to replicate each each of the template strands in opposite directions, the strand unzipped from the 3rd carbon end cna be continuously replicated and is called the leading strand - undergoes continous replication. With the other strand it to wait till a section has been unzipped to then work backwards, and results in DNA being produced in Okazaki fragments which are then joined, this is the lagging strand and undergoes discontinous replication.

Sequences of bases are not always matched exactly and errors can occur randomly or spontaneously and result to a change in the sequences, called a mutation. DNA is contained within the cells of all organisms, and code for specific amino acid chains that are used as a blueprint for the synthesis of all tissues. The instructions that DNA carries are contained in the sequence of bases along the chain, the code is a simple triplet that is made of three bases, called a codon, each of which codes for an amino acid. A section of DNA that contains the complete sequence for an entire protein is called a gene. The genetic code is universal, all organisms use it. The base code is degenerate, which means that as there are only 20 amino acids but much more codons, that many amino acids can be coded for by more than one codon. This includes one specific one, methionine which always comes at the start of a gene, signalling the start of a new sequence, having a single start codon ensures that the codons are read in frame, so the code doesn't overlap. There also three stop codons that signal the end of a sequence.

In eukaryotic cells, DNA is contained within a double membrane called the nuclear envelope that encloses the nucleus, and protects the DNA from being damaged in the cytoplasm. Protein synthesis occurs in the cytoplasm at ribosomes, but the DNA molecule is too large to leave the nucleus, so the base sequence of genes has to be copied and transported to the rough ER through the process of transcription, which produces a shorter molecule of RNA. First the section of DNA that contains the gene unwinds under the control of DNA helicase. Only one of the two strands of DNA contains the code for the protein to be synthesised. This is the sense strand and runs from the 5th carbon to the third. The other strand which runs in the opposite direction is the antisense strand which acts as a template strand, so that the complementary RNA strand formed carries the same base sequence as the sense strand. Free RNA nucleotides will base pair with complementary bases exposed on the antisense strand when the DNA unzips, with the exception if uracil binding to adenine. Phosphodiester bonds are formed by the enzyme RNA polymerase. Transcription stops at the end of the gene and the completed short strand of RNA is called messenger RNA. The mRNA  then detaches from the DNA template leaves the nucleus through the nuclear pore and the double helix reforms. The mRNA travels to a ribosome in the cytoplasm for the next stage in protein synthesis. 

In eukaryotic cells, ribosomes are made up of two subunits, one large and one small, which are composed of almost equal amounts of the ribosomal RNA, which is important in maintaining the structural stability of the protein synthesis sequence. After leaving the nucleus the mRNA binds to a specific site on the small subunit, which holds it in position whilst it is translated into a sequence of amino acids. Transfer RNA is another form of RNA and is composed of a strand of RNA folded in a way that three bases, called the anitcodon, are at one end of the molecule. This anitcodon will bind to a complementary codon on mRNA following normal base pairing rules. Each tRNA molecule has a specific anticodon and a specific amino acid corresponding to the codon on the mRNA. When the tRNA anitcodons bind to the codons along the mRNA, the amino acids are brought together in the correct sequence to form the primary structure of the protein. Amino acids are added one at a time to the polypeptide chain. A tRNA with the complementary anticodon will bind to the mRNA start codon, and another will bind to next codon, and the two amino acids are bound by peptidyl transferase, an ezyme component of the ribosome which forms a peptide bond between the two amino acids. The ribosome then moves along the mRNA releasing the first tRNA and the second becoming the first, this process is repeated and amino acids are added to the chain one by one. The polypeptide chain will then fold inot its secondary and tertiary shape and then ot will undergo further modifications at the golgi apparatus. Many ribosomes can follow the mRNA behind the first, so multiple identical polypeptides can be made at once.

Cells require energy for synthesis, transport and movement, adenine triphosphate molecules can supply this energy. An ATP molecule is composed of a nitrogeneous base, a pentose monosaccaride, and three phosphate groups. Energy is needed to break bonds and is released when bonds are fromed. A small amount of energy is needed to break the fairly weak bond holding the last phosphate group in ATP. However a large amount of energy is released when the liberated Pi undergoes reactions to form inorganic molecules, and releases approximately 30.7 kJmol-1. As water is involved in the removal of the phosphate group, this is another example of a hydrolysis reaction, ATP is hydrolysed into adenine diphosphate (ADP) and a phosphate ion, releasing energy. The instability of the phopsphate bonds in ATP mean it is not a good long term energy store. Fats and carbohydrates are much better energy stores. The energy released from the breakdown of these is used to reattach Pi to ADP to form ATP - phosphorylation. The interconversion of ADP to ATP is happening constantly, and so ATP is a good immediate energy store. The propertoes of ATP give it its ideal function: It is small so can move easily in and out of cells, it is water soluble so can be present in aqueous environments, it contains bonds with intermdeiate energy, which is large enough to be useful for cellular reactions but not so large that energy is wasted as heat, it releases energy in small quantities suitable for cellular needs, and it is easily regenerated.