Biology Unit 1

• Lungs allow rapid gas exchance between atmosphere and blood.
• Air drawin in via trachea due to low pressure, created by reib and diaphragm movement.
• Alveoli are sites of gas exchange

• Layer of mucus in tubes of gas exchange,.
• Any dust, debris or microroganisms enter airways trapped in the mucus removed by cilia that cover epithelial cells lining tubes.
• People with CF have drier mucus, cilia find it more difficult to remove.

• Two major effects on health.
• 1) Increases chance of lung infection.            2) Makes gas exchange less efficient.

• Form the outer surface of many animals including mammals.
• Line cavaities and tubes within the animal and cover srufaces of internal organs.

• Cells work together as a tissue known as epithelium.
• Consists of one or more layers of cells sitting on a basement membrane.
• Small intestine epithelial cells extend out from basement membrane.
• Column-shapred cells make up columnar epithelium.
• Free surface facing the intestine lumen, normally covered in microvilli which increases surface area.

• In trachea, bronchi and bronchioles there are ciliated epithelial cells with cilia on the free surface.
• Cilia beat and move substances along tube they line.
• ciliated columnar epithelium of gas exchange airways appears to be stratified, but in fact each cell in contact with basement membrane.
• Appears to have several layers because some cells have nucleus at the base of cells whils in others it is centre.
• Epithelium known as pseudostratified.

How sticky mucus increases the change of lung infections

• Microorganisms become trapped in mucus and lungs.
• Can cause illness- pathogens.
• Musucs normally moved by cilia into back of mouth cavity where either coughed out or swallowed, reducing risk of infection.
• Acid in the stomach kills most microorganisms that are swallowed.

• In CF mucus layer is so sticky that cilia cannot move the mucus.
• Mucus production still continues, airway build up layers of thickened mucus.
• Low levels of oxygen in the mucus, partly because oxygen diffuses slowly through it, partly because epithelial cells use up more oxygen in CF patients.
• Harmdful bacteria can thrive in anaerobic conditions.

• White blood cells fight infections within mucus but as they die they break down, releasing DNA which makes mucus even stickier.
• Repeated infections can eventually weaken the body's ability to fight pathogens, and cause damage to the structures of the gas exchange system.

• Gases such as oxygen cross walls of alveoli into blood system by diffusion.
• To supply enough oxygen to all the body's respiring cells, gas exchange must be rapidly.
• Fine structure of lungs helps maximise this.

How sticky mucus might affect gas exchange

• Sticky mucus layer in bronchioles of a person with cystic fibrosis tends to block narrow airways, preventing ventilation of alveoili below blockage.
• Reduces number of alveoli providing surface area for gas exchange.
• Blockages more likley to narrow ends of airways.
• Blockages will often allow air to pass when person breathes but not when they breath out, resulting in over inflation of the lung tissue beyong blockage.
• Can damage elasticity of the lungs.

• People with CF find it difficult to take part in physical excercise because gas exchange system cannot deliver enough oxygen to muscle cells.
• Oxygen needed for the chemical processes of aerobic respiration, which release the energy used to drive the contraction of the muscles during excerise.
• People with CF become short of breth when taking excercise, but it is beneficial.

• Proteins have wide range of functions in living things.
• Antobodies, enzymes and many hormones all protein molecukes.
• Various roteins make up muscles, ligaments, tendons and hair.
• Components of cell membranes.
• All proteins composed of same basic units: amino acids.
• 20 different amino acids that occur commonly.
• Plants can make all amino acids wheras animals can make only some. (62)

Primary Structure

• Two amino acids join in a condensation reaction to form a dipeptide, with a peptide bond forming between the two subunits.
• Process can be repeated to form polypeptide chains which may contain thousands of amino acids.
• Protein made up of one or more of polypeptide chains.
• Sequence of amino acids in polypeptide knowns as the primary structure of a protein.

Further Levels of Protein Structure

• Interactions between the amino acids in the polypeptide chains cause chain to twist and fold into 3 dimensional shape, the tertiary structure.

Secondary Structure

• The chain of amino acids may twist to form a-helix (shape like extended spring).
• Within helix, hydrogen bonds form between the C=O of the carboxylic acid and the -NH of the amine group of different amino acids, stabilising the shape.

• Several chains link together wiyh hydrogen bonds holding the parallel chains in an arrangement known as a B-pleated sheet.
• Within one protein molecule there may be sections with a-helices and other sections that contain B-pleated sheets.

• A polypeptide chain often bends and folds to produce a precise 3 dimensional shape.
• Chemical bonds and hydrophobic interactions between T groups maintain this final tertiary structure of the protein.
• An R group is polar when the sharing of the electrons when it is not quite even.
• Polar R groups attract other polar molecules, like water and are hydrophilic (water attracting)
• Non-polar groups are hydrophobic (water-repelling).
• Hydrophobic R groups are arranged so they face the inside of the protein, excluding water from the centre of the molecule.

• A protein may be made up of several polypeptide chains held together.
• EG: Haemoglobin, the protein found in red blood cells that carried oxygen, is made up of 4 polypeptide chains and held together in a quaternary structure.
• Only proteins with several polypeptide chains have a quaternary structure.
• Single chain proteins stop at the tertiary level.

Conjugated Proteins

• Some proteins have another chemical group associated with their polypeptide chains.
• EG: Polypeptide chains make up myoglobin is associated with iron-containing group.

• Proteins can be divided into two distinct groups: globular/fibrous.

Globular

• The polypeptide chain is folded into a compact spherical shape.
• These proteins are soluble due to the hydrophilic side chains that project from the outisde of the molecules and therefore important in metabolic reactions.
• Enzymes are globular proteins.
• Their 3 dimensional shape is crucial to their ability to form enzyme substrate complexes and catalyse reactions within cells.

• 3 dimensional shapes of globular proteins are critical to their roles in binding to other substances.
• EG: Transport proteins within membrances and the oxygen-transport pigments haemoglobin (red blood cells) and myyoglobin (muscle cells).
• Antibodies are also globular and rely on their precise shapes to bind to the microorganisms that enter our bodies.

• Fibrous proteins do not fold up into a ball shape but remain as long chains.
• Several polypeptides chains can be cross-linked for additional strength.
• These insoluble proteins are importatn structural molecules.

Fibrous Proteins

• Keratin in hair/skin and collagen in the skin/tendons/bones/cartilate and blood vessels.

• Collagen is made up of three polypeptide chains that wind around each other to form a rope-like strand held together by hydrogen bonds between the chains.
• Each strand cross-links to other strands to produce a molecule with tremendous strength.

Phospholipid Bilayer

• CF caused by a faulty transport protein in the surface membranes of epithelial cells.
• Bilayer-basic structure is two layers of phopholipids.
• In phospholipid there are only two fatty acids; a negatively charged phosphate group replaces the third fatty acid.

• Phosphate head of the molecule is polar; one end is slightly positive and the rest is slightly negative.
• Makes the phosphate head attract other polar moelcules, like warer, and it si therefore hydrophilic (water-attracting).
• Fatty acid tails are non-polar, hydophobic (water-repelling).
• Fats and water don't mix, so when phospholipids are added to water they arrange themselces into spherical clusters called micelles or form a bilayer.
• The bilayer is favoured by phospholipids because the two fatty acids are too bulky to fit into the interior of a micelle.

• Formation of bilayers by phospholipids is of critical biological importance.
• Lipid bilayer will tend to close itself so that there are no edges with exposed hydrocarbon chains, forming compartments.

• Cells are filled with a watery or aqueous cytoplasm and are surrounded by aqueous tissue fluid.
• Cell surface membrane phospholipids tend to adopt their most stable arrangement themselves, whis is bilayer.
• Arrangement avoids the hydrophobic fatty acid tails having any contact with water on either side of the membrane but ensures the hydrophilic phosphate heads are in contact with water.

• Cell surface also contains proteins, chloestoerol, glycoproteins (protein molecules with polysaccharides attached) and glycolipids (lipid molecules with polysaccharides attached).
• Proteins span the membrane.
• Other proteins are found within the inner layer or only within the outer layer.
• Membrane proteins have hydrophobic areas and these are positioned within the membrane bilayer.

• Thought some of the proteins are fixed within the membrane, but others are not and can move around in the fluid phospholipid bilayer. 
• Arrangements known as the fluid mosaic model of membrane structure.

• Most widely acccepted membrain model until 197-s was a three-layer protein-lipid sanwich based on the evidence of the elextron micrographs in which the dark outer layer were thought to be proteins and the lighter region lipid.
• However, protein-liid sandwich does not allow hydrophilic phosphate heads to be in contact with water, not does it allow the non-polar hydrophobic amino acids on the outside of the membrane proteins to be kept away from water.
• Considerationn of how lipidsbehaved in water, forming a bilyaer because it is the most stable arrangements, was used to refine the model
• Interpretation of the slectron micrograph evidence changed to support the new model of the membrane structure.
• Phosphate heads are more electron dense and show up as darker edges to the membran, with the tails forming lighter inner part of sandwich.

• Experiments show that there were 3 types of protein, those that could be dissociated from membran easily by increasing ionic strength 

• More phospholipids containing unsaturated fatty acids there are present in the membrane, the more fluid it is.
• The kinks in the hydrocarbon tails of the unsaturated phospholipids prevent them from packing closely together, so mor emovement is possible.
• Chlolesterol reduces the fluidity of the membrane by preventing movement of phospholipids.

• Different types of protein are found within the membrane, each type having a specific function.
• Some functions as enzymes, others as carriers and channel proteins involved in the transport of substances in and out of cells.
• Glycoproteins and glycolipids have important roles in cell to cell recognition and as receptors.

For  a cell to function correctly it needs to be able to control transport across its surface membrane. Molecules and ion move across membranes by:

• Diffusion
• Osmosis
• Active Transport
• Exocytis
• Endocytis

• Diffusion is the net movement of molecules and ions from a regions where they are at a higher concentration to a region of their lower concentration.
• Diffusion will continue until equilibrium, when the substance is evenly spread throughout the whole volume.
• Small uncharged particles diffuse across the cell memebrane, passing between the lipid molecules as they move down the concentration gradient.
• Small molecules like oxygen and carbon dioxide can diffuse rapidly across the cell membrane.
• Carbon dioxide is polar but its small size allows rapid diffusion.

• Hydrophilic molecules and ions that are larger than carbon dioxide cannot simply diffuse through bilayer.
• Insoluble in lipids, the hydrophobic tails of the phospholipids providing and impenetrable barrier to them.
• Instead they cross the membrane with the aid of proteins in a process called facilitated diffusion.
• May diffuse through water-filled pores within channel proteins that span the membrane.
• Different channel proteins for transporting different molecules.
• Each type of channel protein has a specific shape that permits the passage of only one particular type of ion or molecule.
• Some challes can be opened or closed depending on the presence or abscence of a signal, which could be a specific molecule, like a hormone, or a change in potential difference (voltage) across the membrane.
• These channels are called gated channels. 

• Some proteins play role in facilitated diffusion, not just simple channels but are carrier proteins.
• Ion or molecule indsonto a specific site on the proten.
• Protein changes chape and the ion or molecule crosses membrane.
• Movement can occur in either direction with the net movement being dependent on the concentration difference across the membrane.
• Molecules move from high to low concentration due to more frequent binding to carrier proteins on the side of the membrane where the concentration is higher.

• Diffusion is sometimes called passive transport.
• Passive here refers to the fact no metabolic energy is needed for the transport. 

• Net movement of water molecules from a solution with lower concentration of solute to a solution with a higher concentration of solute through a partially permeable membrane.

• Osmosis random movement of water molecules across the membrane.
• Solute molecules are present, water molecules from hydrogen bonds with them and this reduces movement of water molecules.
• More solute present there are fewer water molecules free to collide with and move across the membrane.

• With unrestricted movement of the molecules there will be diffusion of both solute and water in both directions until equilibrium is achieved.

• Presence of partially permeable membrane prevents movement of some molecules.
• Solute cannot cross the membrane but free water molecules can dffuse through the membrane to achive equilibrium.
• Water moves from left to right, where there aremore free water molecules to where there is a lower concentration of free water molecules.

• Substances need to be moved across membrane against a concentration gradient (low concentration to high concentration) then energy is required.
• Like facilitated diffusion, specific carrier proteins are needed.
• Energy comes from respiration and supplied by energy transfer molecule ATP.
• Substance to be transported binds to the carrier protein.
• Energy from ATP causes changes shape of carrier protein causing substance released on other side of membrane.

• Active transport or pumping of substances across membranes occurs in every cell.
• EG: Transport of ions across epithelial cells.

• Very large molecules or particles need to be transported across cell surface membranes.
• Achieved by exocytosis and endocytosis which rely on the fluid nature of the membrane.

• Exocytosis is release of substances, usually proteins or polysaccharides from the cell as vesicles (small membran bound sacs) fuse with the cell membrane.
• EG: Insulin (hormone produced by pancreas) is relased into blood by exocytosis.

• Endocytosis is the reverse process.
• Substances are taken into a cell by the creation of a vesicle.
• Part of cell membrane engulfs solid or liquid material to be transported.
• Some cases the substance to be absorbed attached to a receptor in the membrane and is then absorbed by endocytosis.
• How chloesterol is taken up into cells.
• White blood cells ingest bacteria and other foreign particles by endocytosis.