Biology (Mr Foxton)

Covalent bonds- is when atoms share electrons with other atoms, resulting in the outermost shell being filled and it becomes strongly bonded with another atom (drawn with a single line).

Hydrogen bonds- a weak intercation which happens wherever molecules contain a slightly negatively charged atom bonded to a slightly positively charged hydrogen atom (drawn with a dotted line showing dipoles). The molecule can be described as polar.

Reactions:

A condensation reaction- occurs when two molecules are joined together with the removal of water.                                                                                                                                              

A hydrolysis reaction- occurs when a molecule is split into two smaller molecules with the addition of water.

Types of molecules:

Monomers- a small molecule which binds to many other odentical molecules to form a polymer. (Monosaccharides, amino acids & nucleotides)

Polymers- a large molecule made from many smaller molecules called monomers. (Polysaccharides, polypeptides/proteins & DNA/RNA)

• Liquid: water molecules continually break & make hydrogen bonds, making it difficult to leave the liquid phase. Water also has low viscosity, so it can flow easily. (Provides habitats e.g. rivers / major component in tissues / reaction & transport medium).
• Density: water becomes more dense as it gets colder to 4 degrees celsius. From 4 to freezing point water molecules align so it is less dense than liquid water. (Aquatic organisms have a stable environment / bodies of water are insulated in winter).
• Solvent: water is polar so water molecules are attracted to postive and negative parts of solutes. The water molecules cluster around the charged part of solute molecules or ions, dissolving them in the soution. (Molecules & ions can move and react and be transported).
• Cohesion and surface tension: hydrogen bonding pulls water molecules together- cohesion. They are all bonded to molecules beneath them, so water can resist a force applied to it- surface tension. ( columns of water can be pulled up vascular tissue/ insects can walk on water).
• High specific heat capacity and high latent heat of vaporisation: water molecules are held tight togehter, so a lot of heat energy is needed to increase kinetic energy & make water evaporate. So it does not heat up or cool down easily. (Stable temperature for enzyme-controlled reactions/ mammals cooled sweat evaporates).
• Reactant: its role as a reactant is extermely important for phtoosynthesis, hydrolysis, digestion and synthesis of large biological molecules.

Carbohydrates- a group of molecules containing C, H & O, they are ' hydrates carbon' because for every carbon atom there are two hydrogen atoms & one oxygen atom. They act as a source of energy (glucose), a store of energy (starch & glycogen) and structural units (cellulose & chitin).

• Monosaccharides: they are the simplest carbohydrates , soluble in water & sweet. Important as a source of energy as they contain many carbon-hydrogen bonds. (Hexoses- 6c, pentose- 5c & triose- 3c). Triose and tetrose sugars exist as straight chains, others are in a ring or cyclic form. 
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• Disaccharides: are sweet, soluble & formed when two monosacchairdes join together by a condensation reaction, forming a glycosidic bond.
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• a-glucose + a-glucose -> maltose,  a-glucose + fructose -> sucrose , B-galactose + a-glucose -> lactose , B-glucose + B-glucose -> cellobiose

Polysaccharides- are polymers of monosaccharides. By joining lots of glucose units you can create an energy store. Glucose releases energy tof orm ATP (glucose + oxygen -> carbon dioxide + water)

• Starch: is the energy store in plants, comprising of amylose and amylopectin.
  
• Amylose- a long chain of a-glucose molecules, with 1->4 glycosidic bonds. It coils into a spiral shape with hydrogen bonds holding the strcture. Hydroxyl groups on carbon 2 are in the inside of the coil, so it is less soluble maintaining structure. It is compact & chain can be hydrolysed quickly, releasing energy.
  
• Amylopectin- branched a-glucose units with 1->4 and 1->6 gylcosidic bonds. It coils into a spiral shape held with hydrogen bonds & branches emerging from the spiral. Brached chains are more compact, but also the branches can be hydrolysed easily.
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• Glycogen: is the energy store in animals. Has many branches with 1->4 & 1->6 glycosidic bonds. The 1->4 bonded chains are smaller, so it had less tendency to coil & has more branches. Its more compact, and is easier to remobe monomer units.
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Cellulose: is found in plants, forming cell walls. It is tough, insoluble and fibrous. It is made form B-glucose, and when joining them together by a condensation reaction each molecule most be rotated 180 degrees. Formin 1->4 glycosidic bonds and giving additional strength to prvemt the chain spiralling. The hydroxyl group on carbon 2 sticks out, enabling hydrgoen bonds to be formed between chains.

-When 60 to 70 cellulose chains are bound together, they form microfibrilis. And a bundle of microfibrilis (400) form macrofibrils whih are embedded in pectins.

Cellulose is an excellent material in plant cell walls because:

• microfibrilis and marcofibrils have very high tensile strength, due to hydrogen & glycosidic bonds, supporting the plant.
• macrofibrils run in all directions, criss-crossing the wall for extra strength, mineral ions can pass in & out aswell and can make cell wall waterproof.
• it is difficult to digest cellulose because the bonds are less easy to break
• it prevent cells form bursting when they are turgid
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Lipids- a group of substances that are soluble in alcohol & contain large amounts of carbon and hydrogen.

• Triglycerides: it consists of one glycerol molecule bonded to 3 fatty acids. There is a condensation reaction between the -COOH group of the fatty acod and thr -OH group of glycerol forming an ester bond. (Glycerol- alcohol, fatty acids- have a carboxyl group attached to a hydrocarbon tail
• Funtion of triglycerides: energy source (ester bonds hydrolysed generate ATP), energy store (insoluble in water), insulation (heat and electrical insulator), buoyancy (fat is less dense than water) & protection ( fat around organs).
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• Phospholipids: molecule consisting of glycerol, 2 fatty acids & a phosphate group. There is a condensation reaction between the OH group of a phosphoric acid molecule & one of three -OH groups of a  glycerol molecule forming an ester bond. When they are surrounded by water the phosphate group has a negative charge making it polar, but fatty acids are non-polar. Form phospholipid bilayer (hydrophilic head, hydrophobic tail) , selectively permeable.
• Cholesterol: is a steroid alcohol ( type of lipid) consisting of 4 carbon-based rings. It is a small hydrophobic molecule, sitting in the hydrophobic part of the bilayer. Regulates fluidity and is made in the liver of animals. 

Proteins: are large polymers comprised of long chains of amino acids. They form structural components of animals, adopt specific shapes e.g enzymes/ antibodies/ hormones & act as carriers.

• Amino acids: monomers of all proteins, they all have the same basic structure. Each have an amino group (-NH2) , carboxyl group (-COOH) & a variant/ R group. Amino acids are joined together by peptide bonds (covalent bonds).
• Primary structure- the sequence of amino acids found in a molecule, there are 20 different types of amino acids.
• Secondary structure- the coiling (a-helix) & folding (B-pleated sheet) of an amino acid chain, resulting in hydrogen bond formation in different parts of the chain. Hydrogen bonds are weak but form stable structures.
• Tertiary structure- the overall 3d shape of a protein molecule, its shape arises due to interactions.
  
• Quaternary structure- protein structure where a protein consists of more than one polypeptide chain.
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• Hydrogen bonds
• Ionic bonds: they can form between positive & negative R groups
• Disulfide links: the R group e.g cysteine contains sulfur, strong covelant bonds form between two sulfur R groups
• Hydrophobic & hydrophilic interactions: Hydrophobic R groups in the centre. Hydrophilic R groups on outside.

Fibrous Proteins: has a relatively long thin structure, insoluble in water & metabolically inactive, often have structural roles.

• Collagen- provides mechanical strength (good tensile strength & prevents pulling forces), is in different tissues e.g. skin & blood vessel walls (prevent arterys bursting). The polypeptides are made from glycine, proline & alanine that wind to make a triple helix.
  
• Keratin- is rich in cysteine & lots of disulfide bridges making it strong. Provides mechanical protection & impermeable barrier.
• Elastin- cross-linking & coiling make the structure strong & extensible, found in living things that stretch e.g. skin.
  

Globular Proteins: has molecules of a relatively spherical shape, which are soluble in water & often have metabolic roles.

• Haemoglobin- the quaternary structure is made up of 4 polypeptides; 2 a-globin chains, 2 B-globin chains & 4 haem groups. Each of the globin chains have their own tertiary structure of many bonds (specific shape). The haem group is its prosthetic group (a non-protein component forming a permenant part of the protein molecule), it contains the iron ion. In sickle cell anaemia a mutation resulting in non-polar B-polypeptide makes it less soluble, carrying less oxygen.
  
• Insulin- made up of 2 polypeptide chains, with a section of a-helix & B-pleated sheet. Both chains fold into a tertiary structure joined by disulfide link, with hydrophilic R groups on the outside so soluble, bind to glycoprotein receptors.
  
• Pepsin- made up of single polypeptide chain of 327 amino acids, folding into a symmetrical tertiary structure, has 43 acidic R groups, so stable in stomach conditions.

• Testing for carbohydrates (starch- iodine test): add iodine solution (potassium iodide) to sample, if starch present colour change from yellow-brown to blue-black. (Iodine form triiodide ion slipping in amylose helix causing colour change).
• Testing for reducing sugars (Benedicts test/ reagent test strips): heat a reducing sugar with benedicts solution ( alkaline copper 2 sulfate), there is a colour change from blue-> green-> yellow-> orange-red. (Copper ions are reduced formin red-orange copper oxide).
  
• Testing for non-reducing sugars (Benedicts test): test a sample for reducing sugars, take a seperate sample & boil it with hydrochloric acid to hydrolyse sucrose to glucose & fructose. Cool the soultion & use sodium hydrogencarbonate to neutralise it. Test for reducing sugars again, positive result orange-red colour change.
• Testing for lipids (emulsion test): take a sample & mix thoroughly with ethanol, filter and pour solution in water. A cloudly white emulsion indicates presence of lipids.
  
• Testing for proteins (the biuret test): add biuret A (sodium hydroxide) & then biuret B (copper sulphate). The coulour changes from light blue to lilac if protein present. (Colour formed between nitrgoen atoms and Cu2+ ions)

• Colorimeter- it works by shining light through a sample. You use a centrifuge to seperate the precipitate & excess benedicts solution & place in a cuvette. The colorimeter tells you the % of transmission, telling glucose concentration.

Nucleotides: are biological molecules consisting of a 5-carbon sugar, a phosphate group (more than 1 phosphate group- phosphorlayted nucleotides) & nitrogenous base. They form the monomers of nucleic acids, DNA (deoxyribose pentose sugar) & RNA (ribose pentose sugar). The nitrogenous base is linked to carbon 1, phosphate group linked to carbon 3 or 5 of the suagr. Covalent bonds are formed by condensation reactions (Phosphodiester bond- phosphate & sugar).

DNA: There is purines (2 rings-adenine or guanine) & pyrimidines (1 ring-thymine or cytosine). Adenine + thymine (2 hydrogen bonds), Gunaine + cytosine (1 hydrogen bond). They pair together giving stability.

Double helix: shape of DNA molecule, due to the coiling of the two sugar-phosphate backbone strands into a right-handed spiral configuration. 'The antiparallel sugar-phosphate backbones' 5' to 3' direction.

RNA: the nitrogenous base is uracil, which is a pyrimidine replacing thymine. The polynucleotide is usually single-stranded & shorter. There are three forms messanger / transfer / ribosomal RNA.

Semi-conservative replication: results in 2 new molecules, each of which contains one old strand & one new strand, conserves the old strand.

1) The DNA unwinds, the double helix is untwisted a bit at a time, catalysed by a gyrase enzyme. The strands unzip & hydrogen bonds are broken, catalysed by DNA helicase.

2) Free phosphorylated nucleotides, present in the nucleoplasm are bonded to the exposed bases. The enzyme DNA polymerase, catalyses the addition of new nucleotide bases in 5' to 3' direction.

3) The leading strand is synthesised continuously, the lagging strand is in fragments that are lated catalysed by ligase enzymes. 

4) Hydrolysis of the activated nucleotides to release the extra phophate groups supplies the energu tp make phosphodiester bonds between the sugar residue and phospahte group of the next.

 Evidence- E.coli was grown for 14 generations in a medium containing the heavy isotope of nitrogen (15N) & then transferred some of the bacteria into a lighter medium (14N) & replicated once. The replication shows two bands - one heavy & one light, showing semi-conservative replication.

Mutations: during the replication process there are enzymes that proof read & edit out incorrect nucleotides, reducing the rate of mutations.

DNA codes for polypeptides:

• Gene- a length of DNA that codes for a polypeptide or for legnth of RNA that is involved in regualting gene expression.
  
• Genetic code- is universal , degenerate & non-overlapping.

Transcription- the process of making messanger RNA from a DNA template

• A gene unwinds & unzips, by gyrate enzyme. Hydrogen bonds between complementary nucleotide bases break by DNA helicase.
• The enzyme RNA polymerase catatlyses the formation of temporary hydrogen bonds between RNA nucleotides & their complementary unpaired DNA bases, the template strand. The RNA strand is the coded strand.
• The mRNA then passes out of the nucleus, through the nuclear enverlope and attaches to a ribosome.

Ribosomes: are made in the nucleolus in 2 smaller subunits, they pass out seperately through pores in the nuclear enverlope & come togehter 9ribosomal RNA & protein) to form the ribosome.

Translation- formation of a protein, at ribosomes, by assembling amino acida into a particular sequence according to the coded instructions of the mRNA.

• tRNA (made in the nucleolus) bring the amino acids & find their place when the anticodon binds by temporary hydrogen bonds to the complementary codon in the mRNA molecule. Peptide bonds form between adjacent amino acids, ATP is needed. Components can by recycled.

Enzymes: are biological catalysts (remain unchanged) because they speed up metabolic reactions in living organisms. A small amount of catalyst can catalyse the conversion of a large number of substrate molecules into product molecules- the number of reactions that an enzyme molecule can catalyse per second is the turnover number. Enzymes are more specific than chemical catalysts, due to the fact they dont produce unwanted by-products & rarely ake mistakes.

• Enzyme-substrate complex- formed by temporary binding of the enzyme and substrate molecules during an enzyme-catalysed reaction, by non-covalent forces.
  
• Enzyme-product complex- enzyme with product molecules in its active site, the 2 are joined by non-covalent forces.
• Metabolites- the reactants, intermediates & products
  
• Catabolic reaction- metabolites are broken down into smaller molecules & releases energy
  
• Anabolic reaction- energy is used to synthesise lerger molecules from smaller ones

Active site: indented area on the surface of an enzyme molecule, with a shape that is complementary to the shape of a substrate molecule.  It consists of 6 to 10 amino acids & its tertiary structure is crucial. 

• Intracellular enzymes- enzymes that work inside of cells. Extracellular enzymes- enzymes that work outside of cells.

Cofactors: a substance that is present to ensure that an enzyme-catalysed reaction takes place at the appropriate rate. Prosthetic groups (permanently bound by covalent bonds), co-substrates (bind with the substrate to fit in active site) & coenzymes (small organic non-protein molecules bind temporarily to the active site of the enzyme).

The lock and key hypothesis: the enzymes active site gives it  a shape that is complementary to that of the substrate molecule.

The lock is the enzymes active site, and the key is the substrate molecule.

-The substrate molecules and enzyme molecules each have kinetic energy and are constantly moving, if a substrate molecule successfully collides then an enzyme-substrate complex forms.

-The substrate molecules are either broken down or built up forming an enzyme-product complex

The induced-fit hypothesis: the active site is not a rigid structure, but the presence of a substrate molecule in it induces a shape change giving it a good fit.

-The active site still has a complementary shape to the substrate molecule. But on the binding the subtle changes of the side chains (R groups) of the amino acids gives a precise conformation that exactly fits the substrate molecule, binding more effectively 

-An enzyme-substrate is formed and non-covalent bonds bind the substrate molecule to its active site and when they are converted an enzyme-product complex forms. 

-As the product molecules have a slightly different shape they detach and the enzyme molecule is now free to catalyse another reaction.

E + S -> ESC -> EPC -> E + P

Effect of temperature- at an enzymes optimum temperature, the enzyme & substrate molecules will gain kinetic energy & move faster, will increase the rate os successful collisions. Therefore the formation of ES complexes increases rate of reaction to its maximum. Increasing temperature also makes the molecule vibrate, this may break some weak hydrogen or ionic bond, this changes the proteins tertiary structure & rate of reaction decreaaes making it denatured.

Effect of pH- (a buffer resists changes in pH) Small changes of pH wither side of the optimum pH slow the rate of reaction because the active site is disrupted. Excess hydrogen ions will interfere with hydrogen bonds & ionic forces so the active site shape changes. Increasing concentration of hydrogen ions will alter charges of the active site. Extreme pH's may be permenantely changed.

Effect of substrate concentration- as substrate is added & its concentration is increased, the rate of reaction increases as more ES complexes can form as there are mor collisions. Substrate concentration is a limiting factor because all the enzymes active sites are occupied.

Effect of enzyme concentration- as enzyme concentration is increases more active sites on the enzymes become available & there are more successful collisions. The enzyme concentration is a limiting factor until the substrate concentration is fixed or limiting. The initial rate of reaction is its maximum.

• Competitive inhibition: where the inhibitor molecule is a similiar shape to the substrate molecule & it competes with the active site, blocking the active site. The amount of inhibitor depends on the concentration of substrate.
• Non-competitive inhibition: when the inhibitor binds to the allosteric site changing the active site shape.

Pathogen: a microorganism that causes disease, they live in host taking their nutrition.

• Bacteria: belong to the kingdom Prokaryote. There cells are smaller, but can reproduce rapidly & once in the host they can multiply quickly. Their presence can cause disease by damaging cells or releasing waste products/ toxins. 
• Tuberculosis- a disese that affects many parts of the body, killing cells & tissues, affects lungs 
• Bacterial meningitis- infection of the meninges, membranes become swollen affecting brain and nerves 
• Ring rot (in plants)- ring of decay in the vascualr tissue of a potato tuber or tomato
• Fungi: can send senf out specialised reproductive hyphae, which grow to the surface of the skin & release spores. 
• Black sigatoka (bananas)- causes leaf spots reducing yield
• Ringworm (cattle)- growth of fungus in skin with spore cases erupting & causing a rash
• Athlete's foot (humans)- growth under skin of feet
• Viruses: invade cells & take over the genetic machinery & other organelles, the host cells eventually bursts, realeasing many new viruses to infect healthy cells
• HIV/AIDS- attacks in the immune system (human immunodeficiency virus)
• Influenza- attacks respiratory system, causing muscle pains & headaches
• Tobacco mosaic virus- casuses mottling & discolouration of leaves
• Protoctista: cause harm by entering host cells & feeding on the contents as they grow
• Blight (tomatoes & potatoes)- affects both leaves & potato tubers
• Malaria- parasite in the blood , causes headaches & fevers maybe death/coma 

Transmission: passing a pathogen from an infected individual to an unaffected individual

Animal-

Direct transmission- passing a pathogen from host to new host with no intermediary.

Such as physical contact, like touching a person infected or contaminated surfaces (HIV, ringworm, athletes foot) & oral transmission, like eating contaminated food (Cholera, food poisoning) & droplet infection pathogen in the air (Tuberculosis, Influenza) & transmission of spores. Can be prevented by: hygiene, less overcrowding, better diet & sterilising equipment.

Indirect transmission- passing a pathogen from host to new host via a vector.For example, Plasmodium parasite that causes malaria enters the human host via a bite from a female Anopheles mosquito.

Plant-

Direct transmission- pathogens are present in the soil & will infect plants by enetering the roots & spores may be carried in the wind (airborne transmission)

Indirect transmission- spores or bacteria may become attached to a burrowing insect, such as a beetle, which attacks a plant carrying a disease

Disease and climate- warmer conditions make bacteria & fungi reproduce more quickly.

Physical defences (Passive defences): 

• Cellulose cell wall & lignin thickening of cell walls- acts as a barrier & lignin is waterproof
• Waxy cuticles- prevent water collecting on the cell surfaces, which could contain pathogens
• Stomatal closure- stops pathogens enetering
• Callose (large polysaccharide)- deposited in sieve tubes, stops pathogens spreading
• Tylose formation- balloon swelling projection filling the xylem, stopping pathogens spreading

Chemical defences (Passive defences):

• Bark contains a variety of chemical defences (tannins in bark). Many chemicals are not produced until the plant detects an infection as it requires energy.

Active defences:

• Cell walls become thickened and strengthened with additional cellulose
• Deposition of callose
• Oxidative bursts producing highly reactive oxygen molecules that can damage cells
• Necrosis- deliberate cell suicide (Canker)

The skin: the main primary defence, the outer layer is covered in epidermis & it consists of layers of cells (keratinocytes). The keratinised layer of dead cells acta as an effective barrier to pathogens.

Blood clotting and skin repair: many clotting factors are released from the platelets from the damaged tissue, activating an enzyme cascade. Once the clot has formed it dries out & forms a scab. As the new skin is completes, the scab will be released.

Mucous membranes: the airways, lungs & digestive system is protected by mucous membranes. The epithelial layer contains mucus-secreting cells called goblet cells. In airways, the mucus lines the passages & traps pathogens. The ciliated cells have cilia, which move the mucus to the top of the trachea, where it is swallowed & destroyed.

Coughing & Sneezing: the sudden expulsion of air will carry with it the microorganisms causing the irritation.

Inflammation: histamine a cell signalling substance is released. Its main effect is vasodilation, making the capilary walls more permeable to white blood cells & some proteins. They then enter the tissue fluid, leading to an increase production of tissue fluid causing swelling. Excess fluid is drained into the lymphatic system.

• Eyes are protected by antibodies & enymes in tear fluid ( lysosomes)
• The ear canal is lined with wax, which traps pathogens

Secondary defences: are used to combat pathogens that have entered the body. When a pathogen enters the body, it is recognised as foreign by the chemical markers on its outer membrane (antigens/ opsonins)

Phagocytes: the first line of secondary defence is phagocytosis- specialised cells in blood & tissue fluid engluf & digest pathogens

• Neutrophils- a type of white blood cell that engulfs foreign matter & traps it in a large vacuole (phagosome) which fuses with lysosomes to digest the foreign matter. They are manufactured in the bone marrow, short-lived & are released in large numbers.
• Macrophages- are larger cells manufactured in the bone marrow & travel in the blood as monocytes. Many are found in lymph nodes where they mature into macrophages (dendritic cells- found in peripheral tissues). Maacrophages initiate the specific response and engulfs the pathogen, to become an antigen-presenting cell.

Active immunity: 

• The anitgen presenting cell moves around the body where it comes into contact with specific cells that activate the full immune response, the T lymphocytes & B lymphocytes.
• Activation of the B an T cells is called clonal selection. The whole reponse is coordinates by hormone-linke chemcials called cytokines.

The specific immune response: involves B lymphocytes & T lymphocytes (white blood cells with a large nucleus & specialised receptors), that produce antibodies. The antibodies are specific proteins that attach to pathogenic antigens.

Cell signalling is achieved by the release of hormone-like chemicals. macrophages release monokines attracting neutrophils & stimulate B cells to differentiate and release antibodies. T cells & macrophages release interleukins, which stimulate clonal expansion & differentiation of B & t cells.

• T helper cells- release cytokines that stimulate B cells to develop & stimulate phagocytosis
• T killer cells- which attack & kill host-body cells that display the foreign antigen
• T memory cell- which provide long-term immunity
• T regulator cells- shut down the immune reponse after the pathogen has been successfully removed.
• B cells develop into 2 types of cells: plasma cells (circulate in the blood & release antibodies) & B memory cells (remain in the body for a number of years & act as the immunological memory).

Antibodies: they are Y shaped & have two distinct regions & they consist of four polypeptide chains. They have variable region with a specific shape to the shape of the antigen & a constant region for easy binding of phagocytic cells. Disulfide bridges hold heavy and light polpeptides togther & hinge region to allow flexibility so more grip.]

• Opsonins: binding sites for phagocytic cells. Aggultinins: 'cross-link' pathogens. Anti-toxins: make toxins harmless.
• Secondary immune response- due to memory cells it is quick enough to prevent symptoms not showing.