Biology Aqa Notes

Module 2.1: Biological Molecules * State the functions of biological molecules in organisms
Carbohydrates – energy storage and supply, structure (in some organisms)
Proteins – Structure, transport, enzymes, antibodies, most hormones
Lipids – Membranes, energy supply, thermal insulation, protective layers/padding, electrical insulation in neurones, some hormones
Vitamins and minerals – From parts of some larger molecules and take part in some metabolic reactions, some act as coenzymes or active enzyme activators
Nucleic acids – information molecules, carry instructions for life
Water – Takes part in many reactions, support in plants, solvent/medium for most metabolic reactions, transport

* Define metabolism
Metabolism is the sum total of all the biochemical reactions taking place in the cells of an organism.

* Name the monomers and polymers of carbohydrates, proteins and nucleic acids. | Monomer | Polymer | Carbohydrates | Monosaccharides (simple sugars) | Polysaccharides | Proteins | Amino acids | Polypeptides and proteins | Nucleic Acids | Nucleotides | DNA and RNA |

* Describe the general features of condensation and hydrolysis reactions.
Condensation reactions link monomers together. The same reaction is repeated many times to make a polymer and is used to link subunits in lipid molecules.

In condensation reactions a water molecule is released, a covalent bond is formed and a larger molecule is formed by the bonding together of smaller molecules.

When a larger molecule splits this is called a hydrolysis reaction. In hydrolysis reactions a water molecule is used, a covalent bond is broken, smaller molecules are formed from splitting larger ones.

* State the structural difference between α and β glucose.
The two ring structures are virtually identical but the OH and H groups are either above or below the plane of carbon 1. In glucose the OH at carbon 1 is below the plane of the ring. In β glucose he OH at carbon 1 is above the plane of the ring.

* Describe the formation and breakage of glycosidic bonds in the synthesis and hydrolysis of a disaccharide.
A condensation reaction joins to monosaccharides together to form a disaccharide molecule. A covalent bonds called a glycosidic bond is formed. Water breaks the glycosidic bond in a hydrolysis reaction. A H and OH from each molecule is used to form water. When you break down large molecules in digestion which breaks the glycosidic bonds.

* Describe the molecular structure of alph-glucose as an example of a monosaccharide carbohydrate.
3- carbon monosaccharides are called triose sugars.
5-carbon monosaccharides are called pentose sugars
6-carbon monosaccharides are called hexose sugars. (Fructose and glucose).

* Explain how the structure of glucose relates to its functions in living organisms.
As the glycosidic bonds between glucose is covalently bonded which is a strong bond, a lot of energy is released when these bonds are broken so this is a good energy store. This energy can be used to make ATP which holds small packets of energy for use in cell processes.
Animals and plants can only break down glucose but cannot break down β glucose.

* Compare and contrast the structure and functions of amylose and cellulose. Amylose (in Starch) | Cellulose | Long, straight chained amylose molecules. Stored in chloroplasts and elsewhere in plant cell in membrane-bound starch grains. Starch can be broken down to glucose molecules which can be respired to release energy. Made of α glucose monomers. | Made of β glucose monomers which form a long, straight polymer called a cellulose chain found only in plants. These form fibres because they contain OH groups which H bond which also form bundles called microfibrils and then macrofibrils. This has great mechanical strength and when embedded in a polysaccharide glue of substance called pectins they form cell walls. |

* Describe the structure of glycogen
Glycogen or animal starch is made up of glucose. Glycogen differs from starch because the 1-4 linked glucose chains in glycogen are shorter and have more branched meaning that glycogen is more compact than starch and forms glycogen granules in animal cells.

* Explain how the structures of starch and glycogen related to their functions in living organisms.
They are both energy storage molecules. They don’t dissolve so the molecules don’t affect water potential of the cell. They hold glucose in their chains which can be broken off and used to provide glucose for respiration.

* Explain how the structure of cellulose relates to its function in living organisms.
Cell walls in plant cells give strength to cells supporting the plant. The macro fibril arrangement allows water to move in and out of the cells easily. The cell wall prevents cells from bursting and they become turgid instead. Macrofibril arrangement determines how the cells can grow or change shape (like guard cells that result in opening and closing of stomata as water moves in and out of the cell). Cells can be reinforced with other substances to provide extra support or to make it waterproof.

* Describe the structure of an amino acid
All have the same basic structure. There is an amino group at one end and an acid group at the other end with a carbon in between. The amino acids joined together give a repeating backbone. There are 20 types of naturally occurring amino acid but each has a different R group. Some are hydrophobic and some are hydrophilic.

* Describe the formation and breakage of peptide bonds in the synthesis and hydrolysis of dipeptides and polypeptides.
Condensation reactions between the acid groups of one amino acid and the amino groups of another amino acid forms a covalent bond known as a peptide bond. A water molecule is also produced. The new molecule made of two amino acids is called a dipeptide. This can be broken down in a hydrolysis reaction which needs a water molecule.

* Explain the term primary structure
Primary structure is the specific sequence of amino acids that make up a protein.

* Explain the term secondary structure with reference to hydrogen bonding
Formed when a chain of amino acid coils or folds to form an alpha helix or a beta pleated sheet. Hydrogen bonds hold the coils in place but many are formed so they give stability to the molecule.

* Explain the term tertiary structure with reference to hydrophobic and hydrophilic interactions, disulfide bonds and ionic interactions.
Further folding of the secondary structure and 3D shape is formed. Hormones rely on 3D shape for receptor molecules. Can be structural. Disulfide bonds have a very strong covalent bond. Ionic bonds are strong when oppositely charged amino acids are next to each other. Hydrogen bonds are found whenever charged groups are found close to hydrogen. Hydrophobic tend to be on the inside and hydrophilic tend to be on the outside of proteins. Heating this structure causes increase in kinetic energy causing bonds to break and breaking shape of molecule. (Enzyme denaturing).

* Explain the term quaternary structure with reference to the structure of haemoglobin.
More than one polypeptide subunit joined together. Only functions if all subunits are present. Haemoglobin is an example made of 4 sub-units. (2 alpha chains and 2 beta chains). They form a water soluble globular protein. A specialised part of each polypeptide (haem group) contains an iron ion. The oxygen molecule can bind to the heam group. One haemoglobin molecule can bind up to 4 oxygen molecules. The heam group is a prosthetic group.

* Describe the structure of a collagen molecule
Fibrous protein made up of 3 polypeptide chains wound round each other. Hydrogen bonds are formed between the chains giving strength. Then forms covalent bonds called cross-links next to other molecules. This results in a collagen fibril which joins together to make a collagen fibre. Collagen provides mechanical strength to many areas like the walls of arteries, tendons, bones, cartilage and cosmetic treatments.

* Compare the structure and function of haemoglobin and collagen Haemoglobin | Collagen | Globular protein | Fibrous protein | Soluble in water | Insoluble in water | Wide range of amino acid constituents in primary structure | Approximately 35% of the molecule’s primary structure is one type of amino acid (glycine) | Contains a prosthetic group – haem | Doesn’t contain a prosthetic group | Much of the molecule is wound into alpha helix structures. | Much of the molecule consists of left-handed helix structures. |

* State that lipids (fats and oils) are a range of biological molecules including triglycerides.
Functions of lipids: source of energy, energy storage, used in biological membranes, insulation, protection and some hormones. They are insoluble in water. Fatty acids, triglycerides and cholesterol are all examples of lipids. Fatty acids consist of a hydrocarbon chain and an acid group. They can be unsaturated or saturated. Many saturated fats are solid (animal lipids – lard) and many unsaturated fats are liquid like oils. Triglycerides are a glycerol molecules bonded to 3 fatty acid molecules. They are formed through condensation reactions and broken with hydrolysis reaction. The bond formed is an ester bond and they are insoluble in water (hydrophobic).

* Compare the structure of triglycerides and phospholipids.
Phospholipids are like triglycerides because they have a glycerol molecule and a fatty acid. However, the third fatty acid is not there and there is a phosphate group bonded to the OH instead. The phosphate head is hydrophilic but the hydrocarbon chain is hydrophobic.

* Explain how the structure of triglyceride, phospholipid and cholesterol molecules relates to their functions in living organisms. Lipid | Structure | Main role | Other features | Triglyceride | Glycerol plus 3 fatty acids | Compact energy store, insoluble in water so doesn’t affect water potential. | Stored as fat, which also has thermal insulation and protective properties | Phospholipid | Glycerol plus 2 fatty acids and a phosphate group | Forms a molecule that is part hydrophobic, part hydrophilic, ideal for basis of cell surface membranes. | Phosphate group may have carbohydrate parts attached – these glycolipids are involved in cell signalling. | Cholesterol | 4 carbon-based ring structures joined together | Forms a small, thin molecule that fits into the lipid bi layer giving strength and stability | Used to form steroid hormones. |

* Describe how hydrogen bonding occurs between water molecules.
Two hydrogen atoms are bonded to one oxygen atom covalently. The oxygen has a greater pull on the shared electrons so pulls them away from the hydrogen. This make the hydrogen slightly positively charged and the oxygen slightly negatively charged. Because all water molecules are like this they attract each other. So the negative oxygen in one molecule with attract a positive hydrogen in another. This allows hydrogen bonding to occur.

* Relate this, and other properties of water, to the roles of water in living organisms Property | Importance | Examples | Solvent | Metabolic processes depend on chemicals being able to react in a solution | 70-95% of cytoplasm is water. Dissolved chemicals take part in processes like reparation and photosynthesis in living organisms. | Liquid | Movement of materials around organisms, in calls and in multi-cellular organisms. | Blood in aminals and vascular tissues in plants use water for transport medium. | Cohesion | Water molecules stick to each other creating surface tension which makes long thin water columns very strong and difficult to break. | Transport of water in xylem relies of this in the transpiration stream. Small organisms may make use of this by walking on water. | Freezing | Water freezes forming ice on the surface allowing water underneath to be insulated. | Organisms such as polar bears live on floating ice. Aquatic organisms are not killed when temperatures fall. | Thermal stability | Large bodies of water have constant temperatures. Evaporation of water can cool surfaces. | Oceans provide a stable environment of temperature. Land-based organisms use evaporation as a cooling mechanism. | Metabolic | Water is a reactant in some chemical processes. | Used in hydrolysis reactions and in the process of photosynthesis. |

* Describe how to carry out chemical tests to identify the presence of proteins, carbohydrates and lipids. Testing for | Description | Result (colour change) | Starch | Add a few drops of iodine solution | Brown to blue/black | Reducing sugar | Add Benedict’s solution and heat to 80°C in a water bath. | Blue to orange-red | Non-reducing sugar | If reducing sugar test is negative, boil with hydrochloric acid, cool and neutralise with sodium hydrocarbonate solution or sodium carbonate solution; repeat Benedict’s test. | Blue to orange-red (on second test) | Protein | Add biuret reagent | Blue to lilac | Lipid | Add ethanol to extract (dissolve) lipid and pour alcohol into water in another test tube | White emulsion forms near top of water. |

* Describe how the concentration of glucose in a solution may be estimated by using colour comparison.
Glucose is reducing sugars so we carry out the Benedict’s test which forms and orange-red precipitate. The more glucose there is the more precipitate will be formed and the more of the Benedict’s solution will be used up. Filter the precipitate out and then measure the concentration of the remaining solution. This can be done using a colorimeter. It shines a light through the sample and will give a reading of how much light has passed through. The more copper sulphate that is used up in the Benedict’s test the more the light will be transmitted. Assay techniques are often used to compare measurements with known samples sot hat quantitative measurements can be made.

* State that DNA and RNA are polynucleotides, double stranded and single stranded respectively, made up of nucleotides containing the bases adenine, thymine, cytosine and guanine.
DNA stands for deoxyribosenucleic acid. A nucleotide consists of a phosphate group, one organic nitrogenous base and one sugar molecule. These are joined by covalent bonds to form one nucleotide. The four nucleotides are adenine, thymine, cytosine and guanine. (Uracil is in RNA) A condensation reaction between nucleotides joins them together. Chains of nucleotides are called nucleic acids. There are purines which have 2 ring structures which are adenine and guanine and there are pyrimidines which are one ring structure which are all the rest.

* State that DNA is a double stranded polynucleotide
DNA is a long chain polymer of nucleotide monomers (polynucleotide). When the two strands come together like a ladder there forms a sugar-phosphate backbone. Hydrogen bonds are formed between the bases on the opposite sides.

* Describe how a DNA molecule is formed by hydrogen bonding between complementary bade pairs on two anti-parallel strands.
Adenine pairs up with Thymine and forms 2 hydrogen bonds between them whereas cytosine and guanine form 3 hydrogen bonds between them. The antiparallel chains (running in opposite directions) twist because of this forming a double helix.

* Explain how twisting of the DNA molecule produces a double helix shape
The two strands of DNA are anti-parallel with the sugars pointing in opposite directions. This makes the twisting structure of DNA and it also twists into a double helix shape.

* Outline how DNA replicates semi-conservatively, with reference to the role DNA polymerase
The DNA replication takes place in the interphase stage of the cell cycle. In order for this to happen the double helix must be untwisted, the hydrogen bonds need to be broken between the pairs and DNA needs to be unzipped, free DNA nucleotides are H bonded onto exposed bases and covalent bonds are formed between the phosphate of one nucleotide to another to make a backbone. This is semi-conservative replication.

* State that a gene is a sequence of DNA nucleotides that codes for a polypeptide
DNA is a sequence of nucleotides which contain the instructions to code for the amino acids in a protein. A gene is a length of DNA that codes for one or more polypeptides.

* Outline the roles of DNA and RNA in the cells of living organisms.
DNA codes for the amino acid sequence in a protein. RNA reads the DNA to make the polypeptides (which made the protein). There are three types of RNA. mRNA is messenger where a strand complementary to the DNA molecule I made out of the template strand, which is the copy of the coding strand. rRNA is ribosomal and found in ribosomes. tRNA carries amino acids to the ribosomes where they are bonded together to from polypeptides.

* State that enzymes are globular proteins with a specific tertiary structure
Globular protein is a tertiary structure and the hydrophobic amino acid R groups are on the inside of the protein while the hydrophilic amino acid R groups are on the outside of the structure. Enzymes are globular which are generally soluble in water, they act as catalysts, they are specific, contain an active site and their activity is affected by temperature and pH. Their active site is a very specific shape because it is maintained by the tertiary structure and it can only catalyse specific substrates.

* State that enzymes catalyse metabolic reactions in living organisms
Metabolism can be described as enzyme-driven. Each of the processes for forming or breaking a glycosidic/ester/peptide bond needs at least one specific enzyme in order to catalyse the reaction. The process of protein synthesis, digestion, and respiration also require enzymes. Each catalyses a specific reaction in the sequence of events that make up the process. Enzymes end in –ase.

* State that enzyme action may be extracellular or intracellular
Organisms use digestion which involves the breaking down of bonds (glycosidic/peptide and ester) inside their bodies and passes through and internal digestive system. Other organisms secrete enzymes outside themselves onto the food source and then the enzymes digest the molecules into their monomers which the organisms take in and use.
Many enzymes in digestive systems are extracellular as they are released from the cells that make them into digestive spaces. In intracellular enzymes the action takes part inside the cell.

* Describe the mechanism of enzyme action with reference to specificity, active site, lock and key and induced fit hypothesis.
Enzymes break down the bonds inside a molecule. They have a specifically shaped active site which is complementary to the shape of the substrate. This is called the lock and key because the substrate fits into the active site and is then held in place so the reaction can take place. The induced fit hypothesis says that as a substrate molecule collides with the active site, the active site changes shape to fit more closely around the substrate. This change in enxyme shape destabalised the substrate moelcule so the reaction can occur more easily and the products are now formed which are a different shape so move away from the active site. The enzyme can now catalyse the same reaction with another molecule.

* Explain what is meant by enzyme-substrate complex and enzyme – product complex.
The enzyme-substrate complex is when the active site hold the substrate molecule in place because the charged groups on the substrate and the active site are found near eachother. The enxyme-product complex is when the reaction has taken place and the products are formed which are complementary in shape to the active site.

* Describe how enzymes lower the activation energy of a reaction.
They lower the activation energy needed because the active site induces a fit to the substrate molecule which strains the substrate. This then requires less energy to break the bonds in this molecule than normally.

* Describe and explain the affect of temperature changes on enzyme activity.
Temperature increase increases the kinetic energy of both the substrate and enzyme molecules. This will increase the number of collisions which will also increase the rate of reaction.
However if the temperature is too high the kinetic energy makes the bonds in the molecule vibrate and break the weaker bonds like H bonds. These bonds hold the tertairy structure in place and the rate of reaction will decrease because the 3D shape of the enzyme (hence its active site) will change shape which means that it cannot function and will denature. The temperature at which the enzyme works best at is called the optimum temperature.

* Describe and explain the effects of pH changes on enzyme activity pH is the measure of H+ ions in a soulution. Many of the enzymes bonds are hydrogen and ionic bonds which hold the 3D shape of the enzyme together. H+ ions can interfere with these bonds which means that increasing the amount of hydrogen ions can alter the tertairy structure of the enzyme molecule because it alters the charges around the active site. All enzymes have an optimum pH where the shape of the active site bests fits the substrate moelcule. The location of particular enzymes affect their optimum pH like Pepsin in the digestive system can work at lower (more acidic) pH than other enzymes.

* Describe and explain the effects of enzyme concentration and substrate concentration on enzyme activty.
As the concentration of the substrate increases, collisions between enzyme and substrate occur more often which increases the reaction rate. However if it is increased further there will be a point where it reaches a max value because all the active sites are occupied at all times.
As the enzyme concentration increases more active sites are avaliable so more enzyme-substrate complexes can form and reaction rate increases. There will be a point where all the substrate moelcules are occupying the active sites and the reaction rate is the max possible for the fixed substrate concentration. Limiting factors are factors when if all other conditions are kept constat, increasing the concentration of that factor alone will increase the reaction rate.

* Explain the effects of competitive and non-competitive inhibitor on the rate of enxyme controlled reactions, with reference to both reversible and non-reversible inhibitors.
Competitive inhibitors have a similar shape to the substrate molecule and can also occupy the active site but because it is not identical the products are not produced. These work because when the inhibitor is in the active site the substrate cannot occupy it. So the reaction rate slows down. The levels of inhibiton depend on the concetrations of inhibitor and substrate. Non-competitve inhibitors don’t compete with substrate molecules. They attarch to the enzyme molecule and distort their tertairy structure (active site) decreasing the rate of reaction. Competitive inhibitors are not permanent and can be decribed as reversible. Many non-competitive inhibitors are permanent which is irreverible and leave the enzymes denatured.

* Explain the importance of cofactors and coenzymes in enzyme-controlled reactions.
Cofactores are substances which ensure that enzyme-controlled reactions take place at an appropriate rate. A type of cofactor is an enzyme.
Conenzymes are organic, non-protein molecules which are not permanent and bond to the active site. They can bind before or at the same time as the substrate molecule. They can take part in the reaction and be changed like the substrate. They can be recycled to take part in the reaction again. The role of coenzymes is often to carry chemical groups between enzymes so that they link together the enzyme-controlled reactions that need to take place in a sequence.
Coenzymes that are a permanent part of an enzyme molecule are called prothestic groups. They contribute to the final 3D shape and to other properties like charges in a molecule.
Certain ions can increase the reaction rate. They can combine with the enzyme or substrate to make the enzyme-substrate complex form more easy. Amylase catalyses the breakdown of strach to maltose.

* State that metabolic poisons may be enzyme inhibitors, and describe the action of one named poison.
May posions inhibit overactive enzymes in the body. Potassium cyanide inhibits cell respiration and is a non-competitive inhibitor for a respiratory enzyme called cytochrome oxidase. Inhibition can decrease the use of oxygen so ATP cannot be made, than the organsim can only respire anaerobically which leads to a build up of lactic acid.

* State that some medicinal drugs work by inhibiting the activity of enzymes.
Antibiotics can kill or inhibit the growth of MOs. Penicillin forms cross-links in the bacterial cell wall of some bacteria so the mall of growing bacteria are not made so baterial reproduction is halted. Antibiotic resistance is because there might be an individual with a mutation with altered enzymes. These enzymes may be capabile of inactivating antibiotics.