Good Solvent - Water molecules attracted to ions and polar molecules - Used in blood, xylem and phloem for transport.
High Specific Heat Capacity - Lots of energy needed to break the hydrogen bonds - Helps prevent changes in body temperature.
High Latent Heat of Vaporisation - Lots of thermal energy needed to change water molecules to vapour - Used as a coolent.
High Cohesion - Hydrogen bonds 'stick' molecules together - Helps in xylem.
Can be Reactive - Water reacts with other substances - Used in hydrolysis reactions and in photosynthesis.
Incompressibility - Outside pressure cannot force water into a smaller space - Makes hydrostatic skeleton for some animals.
Monomers and Polymers
Monomer - The smaller sub-units which make up a macromolecule.
Macromolecule - A biological molecule which is made up of monomers.
Polysaccharide - Glucose monomer, C H O, Eg Starch, Glycogen, Cellulose.
Proteins - Amino Acid monomer, C H O N S, Eg Haemoglobin, Collagen, Enzymes.
Lipids - Glycerol, Fatty Acids monomers, C H O, Eg Triglycerides.
Phospholipids - Glycerol, Fatty Acid and Phosphate monomers, C H O P N.
Nucleic Acids - Nucleotide monomers, C H O N P, Eg DNA and RNA.
Monomers are joined together by Covalent Bonds formed in condenstion reactions,a dn are broken in hydrolysis reactions.
Macromolecules made up of chains of Amino Acids.
Different Amino Acids have different residual froups (R Groups).
Single chain of Amino Acids is a polypeptide.
A,A's have Peptide Bonds between them to form a polypeptide.
The peptide bond forms between an Amine Group and a Carboxylic Acid Group. When peptide bond forms water is eliminated, which is a condensation reaction.
Properties of proteins depends on R Groups. Some are charged (polar) and interact with water, some are not charged (hydrophobic).
R Groups determine the shape of the Active Site of an enzyme.
Primary Structure - Its Amino Acid sequence, determined by gene that codes for polypeptide.
Secondary Structure - Folding of polypeptide to either alpha helix, or beta pleated sheet, which are stabalised by hydrogen bonds.
Tertiary Structure - Further folding of polypeptide to give a more complex 3D shape. Stabalised by following bonds:
Hydrogen Bonds between polar groups anywhere on polypeptide.
Disulfide Bonds (covalent) between sulphur containing R groups and aminio acid cysteine.
Ionic Bonds between R Groups.
Hydrophobic interactions between non-polar R groups.
Globular and Fibrous Proteins
Globular - Folded into complex 3D shapes, Eg Haemoglobin.
Fibrous - Have linear 3D shapes and are insoluble, Eg Collagen.
Four Polypeptides, 2 of each alpha- or beta-globin. In middle of each polypeptide if haem group, flat and circular with atom of iron at the centre. H Group combines loosely with 1 O2 molecule. Has Quaternary Structure as more than 2 polypeptides, which are Hydrogen bonds and Ionic bonds.
Three identical polypeptide chains wound together to form a triple helix. Every third A.A is glycine (smallest R Group). Polypeptides sequences staggered so glycine found at every position so can pack closely and form many H Bonds. Adjacent molecules of collagen form covalent bonds between R Groups. Gives collagen great strength.
Made up of Carbon, Hydrogen and Oxygen, in the ratio Cx(H2O)y. Eg Glucose
Monosaccharides - Simplest form of carbohydrate which cant be broken down to further sugars by hydrolysis.Trioses - 3 Carbon atoms (glyceraldehydes), pentoses - 5 Carbon atoms (ribose and deoxyribose) and Hexoses - 6 Carbon atoms (Glucose).
Glucose - Two types alpha-glucose and beta-glucose. Differ because of position Hydroxyl group (-OH) around carbon atom 1. A-G has -OH below Carbon1, B-G has -OH above Carbon1.
Glycosidic Bond - Forms when condensation reaction as Oxygen atom acts as a 'Bridge' between monomers, and the reaction releases a water molecule. These make polysaccharides and Disaccharides.
Disaccharides - Two monomers joined together by glycosidic bonds. Eg Maltose which oxygen links carbon1 on A-G to carbon 4 on A-G. Sucrose is glucose and fructose linked. Disaccharides can be hydrolysed by extra and intracellular enzymes which catalyse the breakdown of glycosidic bond by adding water.
Polysaccharides - More than 2 monomers joined together by glycosidic bonds.
Starch - Main energy store in plants. Made of amylose and amylopectin.
Amylose - single, unbranched polymer, insolube, polymer of glucoses joined by alpha-1,4-glycosidic bonds.
Amylopectin - branched chain so can be hydrolysed to release glucose, branches of alpha-1,6-glycosidic bonds.
Glycogen - Animals polymerise alpha-glucose to make glycogen which is even more branched than amylose but same bonds.
Cellulose - Polymer of beta-glucose, alternate glucose turned 180degrees, so straight chained, -OH groups projecting make hydrogen bonds with adjacent cellulose molecules, much stronger than starch ideal for cell walls, in bundles known as microfibrils which are layed down in cell walls in different directions to give added strength.
Made of mainly carbon and hydrogen atoms and a few oxygen atoms, so hydrophobic and less dense than water. Triglycerides (fats and oils) and phospholipids made up of glycerol (3-carbon compound which each C has -OH group which can react with FA and form ester bonds) and fatty acids (Long-chain hydrocarbon molecules, each has carboxyl group whic racts with -OH on glycerol, can very as length of hydrocarbon chain and number of double C=C bonds).
Triglycerides - Made of 3-FA chains and glycerol molecule. Condensation reaction, has Ester bonds, can be Saturated (single bonds + solid at rtp) or Unsaturated (double bonds + liquid at rtp). Monounsaturated has 1 double bond, Polyunsaturated has 2 or more DB. Used in animals and plants for energy store, thermal insulators, buoyancy and protection
Phospholipids - Similar to TG but 1 FA replaced by Phosphate group. PG hydrophillic so soluble in water, but FA hydrophobic so insoluble so overall form bilayers.
Cholesterol - Made of 4 hydrocarbon rings and hydrocarbon tail (non-polar) and -OH (polar) Arranged in bilayers and intreacts to control membrane fluidity.
Testing for Biological Molecules
Test for Starch - Add iodine, positive = blue/black negative = orange/brown. Iodine binds to centre of amylose helox, changing its colour.
Test for Reducing Sugars - 1cm3 of solution in test tube, add same vol of Benedicts solution (Blue), boil/heat to 80degreesC, Postive = colour changes from blue to green to yellow to red. Negative = no change in colour.
Test for non-reducing Sugars - Add sveral drops of dilute HCl to 2cm3 of test solution, boil in water bath for a few minutes, cool test tube and add alkali, carry out benedicts test as above. Positive means non-reducing, Negative means no reducing or non-reducing.
Test for Proteins - 1cm3 of test solution to test tube, add 1cm3 of biuret solution (copper sulfate and sodium hydroxide), Positive = violet colour, Negative = non change so blue.
Test for Lipids - crush test material and test tube with ethanol, filter ethanol into second test tube and add water, do not mix ethanol, Postive = milky emulsion forming.
DNA - Deoxyribonucleic Acid - A, G, C and T - sugar deoxyribose
RNA - Ribonucleic Acid - A, G, C and U - sugar ribose
Made of chains of nucleotides which make polynucleotides, joined by covalent bonds between phosphate and sugar molecules to form a 'backbone'.
Nucleotide - Made of pentose sugar (5 Carbon Atoms), Phosphate, Nitrogenous Base.
Bases - Purines (Adenine and Guanine, double ring of carbon and Nitrogen atoms) and Pyramidines (Thymine, Cytosine and Uracil, single ring...).
DNA is a Double Helix - Made of 2 polynuecleotides held togther by H bonds, arranged so Purine is opposite Pyramidine (A:T, G:C), A+T have 2 H bonds, G+C have 3 H bonds, the two polynucleotides are antiparallel.
DNA is stable info is stored for a long time, large molecule stores lots of info, two polynucleotides act as template for synthesis of new polynucleotide during replication.
Half the parent DNA molecule is passed onto the daughter molecule.
1) Double helix unwinds, DNA 'unzips' so H bonds between polynucleotides are broken.
2) Polynucleotides act as templates for assembly of nucleotides.
3) Free nucleotides, made in cytoplasm, move towards the exposed bases of DNA.
4) Base pairing occurs and H bonds form between complementary bases.
5) Enzyme DNA polymerase forms covalent bonds between free nucleotides attached to each template.
6) Two daughter DNA molecules form seperate double helices.
Transcription - DNA 'unzips' along length of gene so enzyme RNA polymerase can match free RNA nucleotides to form molecule which is complementary to template polynucleotide. Follows rules of base pairing. Each triplet of mRNA codes for a specific amino acid.
Movement of mRNA to ribosomes - mRNA moves from chromosome to a ribosome in the cytoplasm by passing through nucleus and through nuclear pore on nuclear envelope.
Amino Acid Activation - Enzymes attatch amino acids to their specific tRNA molecule which gets energy from ATP.
Translation - mRNA binds to ribosome. Two places on ribosome where tRNA molecule can attatch. The ribosome 'reads' the sequence of bases on mRNA and tRNA occupy the two spaces at a time and the amino acids form a peptide bond. So ribosome puts the amino acids together in the sequence dictated by the triplets, and when translated the mRNA a polypeptide is released. It either goes to the cytosol to be used, or it goes to golgi apparatus to be modified, packaged and put into a vesicle.
Enzymes are biological catalysts made of protein.
Some enzymes speed up catabolic reactions (molecules broken down), or they speed up anabolic reactions (molecules are built up).
Enzymes are Globular Proteins (increases rates of reactions), and has a specific Tertiary Structure (so they are specific to reaction).
Intracellular Enzymes - Work inside cells, catalysing processes which are generally multi-step processed (photosynthesis).
Extracellular Enzymes - Work outside cells, catalysing hydrolysis reactions.
Lock-and-Key Hypothesis - A substrate molecule may fit into the enzymes active site and are held in there for a short time which forms an enzyme-substrate complex. Then the reaction happens and a product is formed and the enzyme-substrate complex dissociates to realease the product. Substrate molecules have a shape which is complementary to the shape of the active site.
Induced-Fit Hypothesis - Enzyme changes shape to mould itself around the substrate molecule. R groups of the polypeptide forming the active site move to form temporary bonds with the substrate.
The active site of an enzyme decreases the activation energy of the enzyme so that the substrate has enough energy to react.
Factors Effecting Enzyme Activity
pH - When the pH changes from the optimum the shape of the enzyme changes and the affinity of the substrate for the active site decreases.Change of pH means change in concentration of H+ ions, which cancels out the charge on the R groups and tertiary structure changes, so active site looses its specific shape.
Temperature - If low temperature, there will be slow reaction as theres little kinetic energy. So as the temp increases more kinetic energy is given to the substrate and enzyme so reaction rate increases. Once you go past the optimum temperature, the high temperature causes the bonds which hold the tertiary structure together to break, the tertiary structure changes, so the shape of the active site changes. The enzyme is denatured.
Substrate Concentration - Rate of reaction increases as substrate concentration increases, substarte conc. is the limiting factor, as at a certain point all the active sites are filled and the enzyme concentration is limited so rate of reaction stops increasing.
Enzyme Concentration - Rate of reaction increases as the concentration of enzyme increases, no limiting factor as the substrate can be used again.
Experiment Measuring Rate of Reaction
Increasing Product - Measure the activity of catalase in breaking down hydrogen peroxide. Rate of reaction is determined by measuring how much oxygen is collected at intervals of time. As reaction proceeds less oxygen is produced as less substrate available, so reaction quickest at beginning when lots of substrate available.
Decreasing Substrate - Break down of starch to maltose using amylase, samples are taken form the reaction mixture and are tested with iodine solution. At start plenty of starch in reaction mixture, but later theres not much starch so iodine does not turn blue.
Cofactor - A non-protein component of an enzyme which can be organic or inorganic and is required my enzymes to carry a reaction out.
Coenzyme - An organic cofactor where many are involved in energy transfer reactions like photosynthesis and respiration.
Competitive Inhibitor - Molecular shape is similar to subtrate so it fits into active site, which slows the rate of reaction as substrate can't get in. Eg statins which compete with cholesterol.
Non-Competitive Inhibitor - Molecule which binds to part of enzyme which is not active site and changes the enzyme's tertiary shape, so changes shape of active site, so substrate cannot fit and so slows the rate of reaction. Eg potassium cyanide which binds to haem which is part of enzyme cytochrome oxidase.
Diet and Food Production
Balanced Diet - Having all the components of the diet in correct quantities.
Unbalanced Diet - Not having the correct amount of each component of diet.
This means that an unbalanced diet will lead to malnutrition as you will not get enough of certain nutrients, and way to many of other nutrients.
Coronary Heart Disease - CHD is high in some countries which eat large quantities of animal fats which are rich in saturated fatty acids. Countries where low amounts of animal fats are consumed, there is low amounts of CHD.
Blood Cholesterol - Lipoproteins transport cholesterol. LDL's deliver cholesterol to tissues from liver (bad) and HDL's deliver choleserol to liver from tissues (good).
Low Density Lipoproteins - Tend to deposit the cholesterol in the wall of arteries which accumilates and form plaques. This causes atherosclerosis where the wall of the artery enlarged by the plaque, the lumen is narrowed and it resitricts the blood flow. It also roughens the lining of the wall which increases the chances of blood clots forming.
Food Production and Preservation
Autotrophs - Use external source of energy to make their food. These are producers (first) in the food chain.
Heterotrophs - Organisms which take in complex molecules to act as their source of energy.
Human diet depends on plants as it makes all the other levels of the food chain.
Selective Breeding - Individuals who show the desired feature are chosen to breed together so these characteristics are passed on through their genes. A plant breeder may breed a high-yielding plant but is suseptible to fungal disease, and breed this with a low-yielding plant which is resistant to the disease, to then get a high-yielding plant which is resistant to the fungal disease. This takes many years.
Fertilisers - Restore soils fertility to increase the crop yields. Organic is from wastes of animals and plants and atificial is made from chemicals. Plants need nitrate to make amino acids, magnesium ions to mae chlorophyll, potassium ions as enzyme cofactors for guard cells and phosphate ions to make DNA and RNA.
Food Production and Preservation Continued
Different types of Pesticides:
Herbicides - applied before crop germinates to kill weeds which compete
Fungicides - applied if weather conditions make it likely that crop infected by fungi.
Insecticides - appplied when insect pests reach a level that they cause an economic loss
Microorganisms can make food using biological processes.
Bacteria makes yoghurt and cheese, and yeast makes alcohol and bread.
Advantages - Grow quickly giving high yields and fast production. Factories use up less land and can use waste material in process, no ethical issues.
Disadvantages - Microorganisms are subject to infection, production vessels can be contaminated by competitors, purification before entring human food chain is expensive.
Food contaminated by microorganisms that act as decomposers.
Food preservation techniques used to help prevent food spoilage.
Salting - Removes water by osmosis.
Pickling - Ethanoic acid gives low pH so enzymes are denatured.
Heat Treatment - Pasturisation which kills pathogens, heated to 71.7 degrees for 15secs, or 135 degrees for at least 1 second.
Freezing - Water is forzen so nto available for organisms and enzymes are inactive.
Irradiation - X-rays kill bacteria by breaking bonds in proteins and DNA.
Health and Disease
Health - The state of complete physical, mental and social wellbeing, which is more than just the absence of disease.
Disease - The absence of health.
Parasites - Organisms which live in or on a host, obtain their nourishment from their host.
Pathogens - Parasites that invade the body, multiply in tissues and cause disease.
Malaria - Pathogen is Plasmodium and has insect vector of female Anopheles mosquito.
TB - Pathogen is Mycobacterium Tuberculosis, or Mycobacterium Bovis, tansmits from airborne droplets of water.
HIV/AIDS - Human Immunodeficiency Virus, transmitted from unprotected sex, infected blood, sharing of hypodermic needles.
Global Impact of Infectious Diseases
Malaria - Widely distributed throughout tropics and sub-tropics. More than 500mill people become ill with it each year, mosquitoes resistant to insecticides, plasmodium is resistant to drugs. Control measures - Sleep in nets to prevent mosquitoes biting.
TB - Spread worldwide, 1/3 of human population carry the bacterium but many it is inactive, more likely to spread in poverty-stricken and overcrowded conditions. Control meaures - cured by long course of antibiotics, BCG vaccine against it not very effective.
HIV/AIDS - 39.5mill people living with it, TB is an opportunistic disease associated with HIV. Control measures - use condoms, health education abotu safer sex, blood donations screened for HIV, blood donations heat treated fo kill viruses, needle exchange schemes.
The Immune System
Primary Defences - Prevent pathogens from entering tissues.
They are - The epidermis, layers of dead skin cells containing fibrous protein keratin. Mucus secreted by epithelial lining of airways, digestive systems and reproductive system to trap bacteria. Ciliated cells in airway to move mucus to mouth. HCl secreted by stomach lining to kill most organisms
If pathogens get passed these barriers, the next line of defence is formed by 5 groups of cells.
Neutrophil - Blood and Tissues - Phagocytosis
Macrophage - Tissues - Phagocytosis
B Lymphocyte - Blood and Lymph Nodes - Production of anitbodies
T helper Lymphocyte - Blood and Lymph Nodes - Stimulate B lymphocyte to divide and to produce antibodies, stimulate phagocytosis
T killer Lymphocyte - Blood and Lymph Nodes - Destroy cells infected with viruses
The Immune System
Immune Response - The body's reaction to a foreign antigen.
Antigen - Molecules found on the surface of cells.
Antibody - An immunoglobulin, Y-shaped protein on the surface of B cells that is secreted into the blood or lymph in response to an antigenic stimulus, Protein molecules released by the immune system in response to a foreign ntigen that can neutralise them.
The Immune Response
Four main stages:-
Phagocytes (Ph) engulf Pathogens(P) - Ph recognises antigens on P. Cytoplasm of Ph moves round P engulfing it. P is now contained in a Phagocytic Vacuole (PhV) in cytoplasm of Ph. A lysosome fuses with the PhV, the enzymes break down the P. The Ph then presents the P's antigens, sticks the antigens on its surface to activate other immune system cells.
Phagocytes Activate T Lymphocytes (TL) - A TL is another type of white blood cell. Their surface is covered with receptors (R). The R's bind to antigens presented by Ph. Each TL has a different receptor on its surface. When R on surface of TL meets a complementary antigen it binds to it, so each TL will bind to a different antigen. This activates TL, it divides and differentiates into different types of TL that carry out different functions. Some activated TL release substances to activate B Lyphocytes (BL). Some attach to antigens on a P and kill the cell. Some become Memory Cells (MC).
The Immune Response Continued
TL Activate B, which divide into Plasma Cells (PC) - BL are another type of white blood cell. They are covered with proteins called antibodies. Antibodies bind to antigens to form an antigen-antibody complex. Each BL has a different shaped antibody on its surface. When the antibody on the surface of a BL meets a complementary shaped antigen it binds to it, so each BL will bind to a different antigen. This, together with substances released from TL activates the BL, which is cell signalling. The activated BL divides by mitosis into PC and MC.
PC Make more Antibodies to a specific Antigen - PC are clones of the BL, they secrete loads of the antibody specific to the antigen into the blood. These antibodies will bind to the antigens on the surface of the P to form lots of antigen-antibody complexes.
Structure of Antibodies - Variable region of antibody form the antigen binding sites. The shape of the VR is complementary to a particular antigen, this area differs between antibodies. The hinge region allows flexibility when the antibody binds to the antigen. The constant regions allow binding to receptors on immune system cells, which is the same in all antibodies. Disulfide bridges hold the polypeptide chains together.
The Immune Response Continued
Antibodies help to clear infection by - Agglutinating Pathogens - each antibody has 2 binding sites, so an antibody can bind to 2 P at the same time - so P become clumped together. Ph can then bind to antibodies and phagocytose a lot of P all at once. Neutralising Toxins - antibodies can bind to the toxins produced by P. This prevents the toxins from affecting human cells, so toxins are neutralised, Toxin-antibody complexes are also phagocytosed. Preventing the P binding to human cells - when antibodies bind to the antigens on P they may block the cell surface receptors that the P need to bind to the host cells. This means the P can't attach to or infect the host cells.
Primary Response is Slow - When a P enters the body for the 1st time the antigens on its surface activate the immune system (primary response). The PR is slow because there aren't many BL that can make the antibody needed to bind to it. The body will produce enough of the right antibody to overcome the infection. Whilst the infected person will show symptoms. After being exposed to the antigen both TL and BL produce MC, which remain in the body for a long time. Memory TL remember the specific antigen and will recognise it a second time round. Memory BL record the specific antibodies needed to bind to the antigen. The person is now immune, their immune system now has the ability to respong quickly to a 2nd infection.
The Immune Response Continued
The Secondary Response is Faster - If the same P enters the body again the immune system will produce a quicker, stronger immune response (secondary response). Memory BL divide into PC that produce the right antibody to the antigen. Memory TL divide into the correct type of TL to kill the cell carrying the antigen. The SR often gets rid of the P before you begin to show symptoms