Biology AS Topic 1

Cystic Fibrosis

1 in 25 are carriers of faulty CF allele.

CF = sticky mucus layer lining the tubes and ducts in the gas exchange, digestive and reproductive system.

People with CF have drier mucus than usual= stickier mucus layer that the cilia find hard to remove.

Sticky mucus increases chance of lung infection & makes gas exchange less efficient, particularly in later stages of disease.

Lungs allow rapid gas exchange between atmosphere and blood.

Air drawn into lungs via trachea due to low pressure in lungs- created by movement of ribs and diaphram.

Trachea divides into 2 bronchi- carrries air from each lung.

Each lung = tree-like system of tubes ending in narrow tubes, bronchioles, attached to tiny balloon-like alveoli.

Alveoli sites of gas exchange.

Usually layer of mucus which are produced by goblet cells in walls of airway. Dust, debris or microorganisms trapped.

Cilia beats to remove mucus- it covers epithelial cells.

Form the outer surface of many animals, line cavities and tubes cover the surface of the internal organs.

Cells work together (tissue known as epithelium) - consists of 1 or more layers of cells sitting on a basement membrane (protein fibres in a jelly matrix)

Several different types of epithelium: Squamous or Pavement, Ciliated and Columnar.

Pavement = in walls of alveoli and capillaries. The very thin flattened cells. Less than 0.2μm thick.

Columnar = in small intestine the cells extend out from the basement membrane. The free surface facing the intestine lumen is normally covered in microvilli, increases the surface area.

Ciliated = in trachea bronchi & bronchioles. Have cilia on free surface composed of several layers. Pseudistratified

Miccroorganisms trapped in the mucus in the lungs. They are pathogens (so can cause illness). With CF the mucus is so sticky that cilia cannot move the mucus. Mucus production still continues and the airways build up of thickened mucus.

Low levels of oxygen in mucus - because oxygen diffuses slowly through it and epithelial cells use up more oxygen in CF patients.

Harmful bacteria thrive in these anaerobic conditions.

WBC's fight the infections within mucus but as they die they break down, releasing DNAwhich makes mucus even stickier.

Repeated infections can weaken bodys ability to fight pathogens & cause damage to structures if gas exchange system.

Sticky mucus reduces gas exchange- Gases such as ox cross walls of alveoli into blood system by diffussion. To supply enogh ox to respiring cells gas exchange must be rapid.

Substances that diffuse into or out of a cell move down a concentration gradient (from high to low concentration).

The gradients are maintained by cell continuously using the substances absorbed by the cell continuously using the substances absorbed and producing waste. e.g ox diffusing into a cell is used for repiration which produces carbon dioxide.

The larger the organisim, the more exchange has to take place to meet the organism's needs. Larger multicellular organisms have more problems absorbing substances because of size of surface area compared to volume. surface area to volume ratio dividing total surface area by its volume.

Alveoli provide a large surface area for exchange of gases between the air and the blood. Venilation of the lungs ensures that the air in the alveoli is frequently refreshed- helps maintain a steep concentration gradient and maximise gas exchange across the walls of the alveoli.

Features of gas exchange surface: large surface area of alveoli, numerous capillaries around the alveoli, thin walls of the alveoli and capillaries meaning short distance between alveolar air and blood in capillaries.

The rate of diffusion is dependent on three properties of gas exchange: Surface area - rate of diffusion is directly proportional to the surface area. As surface area increases rate of diffusion increases. Concentration gradient - rate of diffusion is directly proportional to the difference in concentration across gas exchange surface, the greater the concentration gradient the faster the diffusion. Thickness of the gas exchange surface - rate of diffusion is inversely proportional to thickness of gas exchange surface, Thicker the surface slower the diffusion.

Refers to Thickness of the gas exchange surface.

rate of diffusion = Surface area x difference in concentration

thickness of the gas exchanage surface

The large surface area of the alveoli, the steep concentraion gradient between the albeolar air and the blood and the thin walls of the alveoli and capillaries combine to ensure rapid diffusion across the gas exchange surface.

Sticky mucus on bronchioles block narrow airways. preventing ventillation of the alveoli below the blockage. Reduces number of alveoli providing surface area frp gas exchange.

Blockages more likely at narrow ends of airways - will often allow air to pass when the person breathes in but not when they breathe out = over inflation of the lung tissue beyond the blockage, can damage elasticity of lungs.

CF patients find it difficult to take part in exercise because gas exchange system cannot deliver enough ox to muscles. People with CF become short of breath when taking exercise but exercise is benificial to them.

Mucus on surface of epithelial cells is sticky because it contains less water than normal. Reduced water level due to abnormal salt and water transport across cell surface membranescaused by faulty transport protein in the membrane.

Proteins wide range of functions - antibodies, enzymes and many hormones are all protein molecules. Proteins make up - muscles, liaments, tendons and hair. & have important functions within the membrane. Composed of amino acids - 20 different amino acids occur in proteins. Amino acids that animals have to obtain in their diet are known as essential amino acids.Each amino acid has a different side chain called residual or R group.

Refer to 2.6 and 2.7 for general structures and condensation reaction forming dipeptide.

Primary structure : two amino acids join in a condensation reaction to form a dipeptide, with a peptide bond forming between the two 'subunits'. A protein is made up of one or more of these polypeptide chains = primary structure of a protein.

Primary structure : two amino acids join in a condensation reaction to form a dipeptide, with a peptide bond forming between the two 'subunits'. A protein is made up of one or more of these polypeptide chains = primary structure of a protein.

Further levels of protein structures : interactions between the amino acids in polypeptide chain cause chain to twist and fold into 3D shape. Lengths of the chain may first coil into <!-- /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0cm; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman";} @page Section1 {size:595.3pt 841.9pt; margin:72.0pt 90.0pt 72.0pt 90.0pt; mso-header-margin:35.4pt; mso-footer-margin:35.4pt; mso-paper-source:0;} div.Section1 {page:Section1;} -->

α-helices or come together in β-pleated sheets = secondary structure, the chain folding into 3D = tertiary structure.

Secondary structure - chain of amino acids may twist to form an α-helix shaped like a spring. In helix- hydrogen bonds form between the C=O and -NH of the amine group stabilising the shape.Within one protein there may be sections with α-helices and others with β-pleated sheets.

Tertiary and quaternary structures - polypeptide chain often bends and folds to produce a precise 3D shape. chemical bonds & hydrophobic interactions between R groups maintain tertiary structure of prot. R group = polar, sharing of the electrons within it is not quite even. Polar R groups attract other polar molecules therefore hydrophillic (water attracting). Non-polar groups are hydrophobic (water repelling). Non-polar , hydrophobic R groups are arranged so they face inside of protein - excluding water from centre of the molecule.

A protein may be made up of several polypeptide chains held together.

Proteins can be divided into two groups: globular and fibrous proteins.

Globular proteins: polypeptide chain is folded into a compact spherical shape. These proteins = soluble due to hydrophillic side chains that project from outside of moles = important in metabollic reactions. Enzymes = globular proteins. 3D shape = critical to roles in binding to other substances e.g transport proteins within membranes and ox transport pigments in haemoglobin & myoglobin.

Fibrous proteins = do not fold up into a ball shape but remain as long chains - can be made stronger if cross linked with multiple chains. Insoluble proteins = important structural molecules. Keratin in skin, hair, collegen, tendons, bones, cartilage and blood vessel walls are fibrous proteins.

CF caused by a faulty transport protein in the surface membranes of epithelial cells.

Bilayer = 7nm wide. Basic structure is two layers of phospholipids. In a phospholipid there are only two fatty acids; a negetively charged phosphate group replaces the 3rd fatty acid.

Phosphate head of molecules is polar; on end is slightly positive and the rest is slightly negetive = makes the phosphate head attract other polar molecules like water = hydrophillic. The fatty acid tails are non-polar therefore hydrophobic. When water is added to phospholipids they arrange themselves to avoid contact between hydrophobic tails - spherical clusters called micelles or form a bilayer. Bilayer is favoured by phospholipids because two fatty acids are too bulky to fit into interior of micelle. A lipid bilayer will close on itself so that there are no edges with exposed hydrocarbon chains, thus forming compartments.

Cells contain watery/aqueous cytoplasm and are surrounded by aqueous tissue fluid.

Contains: proteins, cholesterol, glycoproteins (protein molecules with polysaccharides attached) and glycolipids (lipids molecules with polysaccharides attached). Other proteins are found only within the inner layer or only within the outer layer. Membrane proteins have hydrophobic areas and these are positioned within the membrane bilayer.

Some of the proteins are fixed and some can move aroundin the fluid phospholipid bilayer = fluid mosaic model

Evidence for fluid mosaic model: Protein lipid sandwich model and freeze fracture of membranes

Diffusion = movement of molecules or ions from a region where they are at a higher concentration to a lower concentration. Diffusion continues until equilibrium, when evenly spread. Small uncharged particles diffuse across cell membrane passing between lipid moles as they move down the concentration gradient. Small moles like ox and carbon dioxide can diffuse rapidly across the cell membrane.

Hydrophillic moles and ions are larger than carbon dioxide molecules and cannot diffuse through the bilayer - their hydrophillic tails provide an impenetrable barrier to them. Instead they cross the membrane with the aid of proteins in facilitated diffusion. They may diffuse through water-filled pores within channel proteins that span the membrane.

Each type of channel protein has a specific shape that permits passage of only one type of mole/ion. Some channels can be opened or closed depending on precense or absence of a signal = a specific molecule like a hormone. The channels are called gated channels.

Proteins in facdiff are not just simple channels but carrier proteins. The ion/mole binds onto a specific site on the protein. The protein changes shape then ion/mole crosses membrane. the movement can be either way depending on concentration of the membrane. Moles move from high-low concentration due to more binding to carrier proteins on the side of the membrane where the concentration is higher.

Diffusion is sometimes called passive transport, 'passive' refers to the fact that no metabolic energy is needed for transport.

Osmosis = movement of water moles from a solution with lower concentration of solute to one with a higher through a partially permeable membrane.

Osmosis is due to the random movement of water moles across the membrane and is a particular type of diffusion.

The presence of partially permeable membrane prevents movement of some moles. The solute cannot cross the membrane but free water moles can diffuse through it to achieve equilibrium

look at figure 2.21

If substances need to be moved across a membrane against a concentration gradient then energy is required. Specific carriers are also needed. The energy comes from respiration and is supplied by the energy transfer molecule ATP. The substance to be transported binds to the carrier protein - substance released on other side of protein.

Active transport or pumping of substances across membranes occurs in every cell.

Sometimes very large moles or particles need to be transported across cell surface membranes. Achieved by = exocytosis and endocytosis, which rely on the fluid of the nature of the membrane.

Exocytosis is the release of substances, usually proteins or polysaccharides, from the cell as vesicles (small membrane-bound sacs) fuse with the cell membrane. For example, insulin is released into the blood by exocytosis. Neurotransmitters are also released this way from nerve endings.

Endocytosis is the reverse process: substances are taken into the cell by the creation of a vesicle. Part of the cell membrane engulfs the solid or liquid material to be transported. In some cases the substance to be absorbed attaches to a receptor in the membrane and is then absorbed by endocytosis.

The cells that line the airways produce mucus. People who dont have CF=amount of water in the mucus continuously regulated to maintain a constant viscosity (stickiness) of the muc. It must be runny enough to be moved by the beating cilia but not so runny that floods the airway.This regulation of the water content of the mucus is achieved by the transport of sodium ions and chloride ions across the epithelial cells. Water then follows the ions because of osmosis.

EXCESS WATER IN THE MUCUS

Excess water in the mucus: if the mucus layer contains too much water its detected by the membranes of cells lining airways (epithelial). Carrier proteins in the basal membranes of ep cells actively pump sodium ions out of the cells. The concentration of sodium ions in cell falls, setting up a concentration gradient across the apical membrane (membrane facing airway). Sodium ions diffuse down this concentration gradient- the ions pass into the cell by facilitated diffusion through sodium channels in apical membrane.The raised concentration of Na in tissue fluid creates a potential difference between this tis flu and mucus on ap mem side. Tis flu now contains more positively charged ions than does the mucus- creates electrical gradient between tis and muc- this then causes negetively charged chloride ions to diffuse out of muc into the tis flu via gaps between ep cells. -The elevated Na+ and Cl- concentrations in tissue fluid draw water out of cell by osmosis across basal membrane into tissue fluid. the water loss increases overall solute concentration within cell. Water is then drawn out of the mucus by osmosis across apical membrane and into cells (because solute concentration is higher within cell then in mucus. Having too much water in mucus = normal because cilia are continuously moving mucus along airways. Movement of mucus from numerous small bronchiole branches into fewer larger bronchiol means that water must be removed to reduce volume of mucus to avoid airways flooding.

When there is too little water in mucus, chloride ions are transported across basal membrane into ep cells. Creates a concentration gradient across apical membrane, with concentration of chloride ions being higher inside than out. At same time CF transmembrane regulatory (CFTR) protein channels (type of gated channel) open. Cl ions diffuse out of the cell through the CFTR channels down this concentration gradient into the mucus. Open- CFTR channels block (close) sodium ion channels in the apical membrane.

When there is too little water in mucus, chloride ions are transported across basal membrane into ep cells. Creates a concentration gradient across apical membrane, with concentration of chloride ions being higher inside than out. At same time CF transmembrane regulatory (CFTR) protein channels (type of gated channel) open. Cl ions diffuse out of the cell through the CFTR channels down this concentration gradient into the mucus. Open- CFTR channels block (close) sodium ion channels in the apical membrane...

CF not regulate water in mucus- CF patients = have CFTR protein missing or it does not function correctly. When there is too little water in the mucus, Cl- cant be secreted across apical membrane = no blockage of epithelial sodium ion channels. Since Na+ channels are always open, there is continual Na+ absorption by epithelial cells. Raisdd level of Na+ = draws chloride ions and water out of mucus into the cells- makes mucus more vicious- makes harder for beating cilia to move it so mucus is not effectively cleared up and out of lungs. Sticky mucus builds up in airways- becomes infected with bacteria causing airway inflammation and damage.

CF patients have difficulty maintaining body mass cause of problems with digestion and absorption nutrients. Also have high basal metabolic rates.

Poor appetites - have to eat more than most people including high energy food- to obtain nutrients & energy. Require 120-140% of recommended daily intake. Take food supplements that contain digestive enzymes- to help break down large food enzymes.

Chemical breakdown of food moles & absorption of soluble products into bloodstream occurs in small intestine. Glands secrete digestive enzymes into lumen of the gut- where act as catalysts to speed up extracellular breakdown of foodmoles. Wide range of enzymes are produced by exocrine glands outside the gut. Enzymes also built into membranes of gut wall. Groups of pancreatic cells produce enzymes that help down in breakdown of carbs proteins and lipids. The digestive enzymes are delivered to gut in pancreatic juice released through pancreatic duct.In a CF patient pancreatic duct becomes blocked by sticky mucus, impairing the release of digestive enzymes. the lower the concentration of enzymes in si= reduce rate of digestion. Food is not fully digested- not all the nutrients absorbed. Malabsorption Syndrome. Cysts of hard damaged or fibroused tissue...p77

Enzyme function depends on protein three dimensional structure

Enzymes = globular proteins that act as biological catalysts- speed up chem reactions. They have an active site- may be a small part of large molecule protein. Only a few amino acids can be directly involved in active site.

Lock-and-key theory- a single molecule with a complementary shape or more than one that together have a complementary shape fit in active site. these substrate moles form temporary bonds with amino acids of the active site to produce enzyme substrate complex. The enzyme holds to substrate mole in a way it reacts more easily. When reaction has taken place products released leaving enzyme unchanged.

Induced fit theory- the active site is often flexible. When a substrate enters the active site enzyme moles change shape slightly fitting more closely aound substrate. like a person putting on a wetsuit. only a specific substrate will induce the change in shape of an enzymes activite site.

Activation energy - to convert substrates into products bonds must change both within and between molecules. breaking chemical bonds requires energy whilst energy is released when bonds form. energy needed to break bonds and start a reaction = Activation energy. without an enzyme, heating a substrate would provide this energy. The heat energy aggitates atoms within moles and moles become unstable- reaction can then proceed. in cells = enzymes reduce amount of energy needed to bring about a reaction- allows reaction to occur without raising temp of cell.

The attraction of oppositely charged groups distort the shape of the subsrates and assist in breaking of bonds or in formation of new bonds. Enzymes catalyse many different types of reactions, some occuring inside cells, (intracellular) others in tissue fluid, blood or aqueous solutions (extracellular reactions) Sometimes large substrate molecules will be broken down into smaller units in catabolic reactions. Other enzymes catalyse anabolic (building up) reactions.

Enzymes=globular proteins,active site allows binding with specific substrates, catalyse reactions, reduce activation energy so chem reaction takes place, doesnt alter the end-product/nature of reaction&remain unchanged&bind with another substrate mole.

Rate of reaction- measured by determining the quantity of substrate used or quantity of product formed in a given time. If we mix a fixed quantity of enzyme and substrae, at first reaction will be quick, however as substrate is used up there are fewer substrate moles to bind with the enzyme & reaction slows down and eventually stops (no further increase in product occurs). intitial rate of reaction = slope of reaction.

En & sub affecting rate of reaction- the initial rate of reaction is directly proportional to the enzyme concentration because the more enzyme that is present th greater the number of active sites that are availible to form enzyme substrate complexes. The increase in rate will continue in this linear fashion assuming that there is an excess of substrate. At high substrate concentration it is the enzye concentration that limits the rate of reaction. Every active site is occupied and substrate molecules cannot enter an active site until one becomes free again.

CF can cause severe problems in the reproductory system. Females have a reduced chance of becoming pregnant because a mucus plug develops in the cervix, which stops sperm from reaching the egg. Males lack the vas deferens (sperm duct) on both sides which means sperm cannot leave the testes. Where the vas deferens is present it can become partially blocked by a thick sticky mucus layer, means fewer sperm are present in each ejaculate.Unusually salty sweat is one of the first signs that a baby may have CF

Cystic fibrosis is caused by a mutation in the DNA that carries the instructions for making the CFTR protein.

DNA is found in every cell nucleus. It contains the genetic code which dictates all the inheritance characteristics of an organism. Does this by controlling the manufacture of proteins, your protiens coded for by DNA, are what make you unique. They play a vital role in giving you the unique characteristics that mean you are not the same as everyone else.

Gene and genome- a gene is a sequence of bases on a DNA molecule coding for a sequence of amino acids in a polypeptide chain. Each chromosome found in the cell nucleus contains a large amount of DNA and carries numerous genes. Genes make up only a fraction of the total length of DNA in the chromosomes; the job of the remainder of the DNA is not fully known. Together all the genes in an individual (or species) are known as a genome.

DNA is one type of nucleic acid = deoxyribonucleic acid. it is a long chain molecule made of many units called nucleotides and mononucleotides.

A mononucleotide contians three molecules linked together by condensation reactions: deoxyribose (5carbon sugar), phosphate group and an organic base containing nitrogen. Mononu... are also linked together by condensation reactions between sugar of one nucleotide and phosphate of the next one. producing a chain of polynucleotide. Nitrogen base is the only part of nucleotide thats variable. 4 bases= adenine, cytosine, guanine and thymine.

DNA = 2 strands of nucleotides twisted round eachother to make a double helix. Sugars & phosphates form 'backbone' and are on the outside. 2 strands that run in opposite directions = antiparallel strands & held together by hydrogen bonds between pairs of bases.

Adenine only pairs with thymine and cytosine only pairs with guanine. The key to this pairing is in the structure of the bases and the bonding between them. Bases A&G both have a 2ring structure, whereas C&T only have 1ring. The bases pair so that there are effectively 3 rings forming each 'rung' of the DNA molecule. The shape and chem structure of bases dictates how many H bonds each one can form& determines AT with 2 Hbonds, and CG with 3bonds. Bases A&T and bases C&G are referred to as complementary base pairs.

CF gene = in chromosome 7. It instructs cell to make the CFTR protein that forms the transmembrane chloride channel.

The triplet code - is the code carried by DNA is (three base). Each adjacent group of 3 bases codes for an amino acid. Several triplets code for the same amino acid; others are start signals or stop signals (called chain terminators).

From DNA -> Proteins- DNA is in the nucleus, and proteins are made in the cytoplasm. DNA cant pass through the membranes surrounding the nucleus into the cytoplasm. So a 'copy' of DNA is made. This 'copy' is not made from DNA but from another type of nucleic acid called ribonucleic acid, RNA. RNA canleave the nucleus carrying the info to the cytoplasm where it is used in the manufacture of proteins.

Difference between RNA & DNA- RNA = a single strand made of a string of RNA nucleotides; similar in structure to DNA nucle.. except they contain ribose sugar and not deoxyribose. Also in RNA nucs the base uracil replaces thymine so RNA doesnt contain T.

3 types of RNA involved in protein synthesis; messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA).

PS has 2 stages- 1st occurs in nucleus, 2nd in cytoplasm.

1 Transcription- DNA double helix unwinds & Hbonds between the base break, allowing 2 strands to partly seperate. The template strand is used in the production of a mRNA mole- built from free RNA nucs which line up alongside the DNA template strand. Because of complementary base pairing the order of bases on DNA exactly determine the order of bases on RNA- every triplet code on DNA gives rise to a complementary codon on mRNA. Template strand = antisense strand because once transcribed makes an mRNA mole as the same base sequence as DNA coding strand (sense strand). Process of synthesising involves a number of enzymes such as- RNA polymerase. Completed mRNA leaves the nucleus through a pore in the nucleur envelope and enters the cytoplasm.

2 Translation takes place on ribosomes- they are small organelles made of ribosomal RNA & protein. Ribosomes are found free in the cytoplasm or attached to endoplasmic reticulum, a system of flattened membrane bound sacs. A transfer RNA mole carrying an amino acid mole has three bases called an anticodon & they pair with complementary bases on the mRNA codon. Then the amino acids that the tRNA carry join by means of peptide bonds.

A protein mole- made up of 50-2000 amino acids. Sequence of amino acids, primary structure, detremines the 3D structure and properties of protein.

Mistake in translation can produce mRNA with inncorrect codons.

DNA replication- double helix unwinds, H bonds between bases break, free DNA nucs line up next to each DNA strand & Hbonds form between complementary bases. Enzyme DNA polymerase links adjacent nucs to form a complementary strand.

Semi-conservative replication

Sickle cell anaemia = a mutation in the gene that codes for one of the polypeptide chains in haemogoblin.