Topic 2

2 Explain how models such as the fluid mosaic model of cell membranes are interpretations of data used to develop scientific explanations of the structure and properties of cell membranes. Davson Danielli model proposed membrane consisted of phospholipid bilayer surrounded by 2 layers of protein. This was incorrect because it was unclear how proteins would permit membrane to change shape without bonds being broken Proteins are largely hydrophobic so it shouldnt be in contact with aqueous cytoplasm Number and type of proteins vary greatly between different cells. Evidence from freeze fracturing - split cell membranes between 2 lipid layers gives 3D image of surface Shows smooth surface with bumps sticking out Phospholipid bilayer is the structure accepted which consists of: Glycolipid - Carbohydrate chain attached to phospholipid bilayer. Involved in cell signaling and cell attachment Glycoprotein - Peripheral or Integral protein which carbohydrate chain attached. Involved in cell-to-cell recognition Cholesterol - Type of lipid. C27H46O. Controls fluidity of membrane. More cholesterol = less fluidity = less permeable. Keeps membranes stable at room temp, otherwise they would burst open. Integral Protein - Span whole width of the membrane. Many are glycoproteins Peripheral Proteins - Confined to inner and outer surface of membrane. If on extracellular side, mainly used for receptors to hormones and neurotransmitters and cell recognition . If on cytosolic side, used for cell signaling and chemical reactions. Can dissociate into the cytoplasm Channel Protein - Integral protein which helps diffuse substances that pass through the membrane alone but are vital for the cell Receptor Protein - Integral and peripheral proteins with binding sites for hormones and neurotransmitters. Can be used for enzymes catalysing reactions. Filamental Cytoskeleton - structure within the cytoplasm that helps it to keep its structure, protects the cell and allows locomotion Phospholipid - Main component of bilayer. Consists of a phosphate head and fatty acid tail. Phosphate head is hydrophilic and fatty acid tail is hydrophobic, therefore aqueous cytoplasm is kept outside the cell. Have a polar nature

3 Explain what is meant by osmosis in terms of the movement of free water molecules through a partially permeable membrane (consideration of water potential is not required). Osmosis is the net movement of free water molecules from area of high water concentration to area of low water concentration via a partially permeable membrane. Process by which cells exchange water with their environment Net movement is dependent on difference in water potential Isotonic - No net movement of water Hypertonic - Net movement of water out of a cell. In plants, cytoplasm pulls away from cell wall, cell becomes plasmolysed. In animals, cytoplasm pulls away from cell membrane and cell becomes crenated Hypotonic - Net movement of water into a cell. In plants, cytoplasm is pushing against cell wall, so the cell becomes turgid In animals, cytoplasm pushes against cell membrane and causes the cell to burst by lysis. This is because there is no protective cell wall, unlike plants.

4 Explain what is meant by passive transport (diffusion, facilitated diffusion), active transport (including the role of ATP), endocytosis and exocytosis and describe the involvement of carrier and channel proteins in membranetransport. Small and non-polar molecules (e.g. O2 and CO2) pass through easily As the molecules become larger, and increase in polarity, the membrane becomes less permeable Passive transport - The transport of substances without the use of energy in the form of ATP Active Transport - The transport of substances with the use of energy in the form of ATP Diffusion - The net movement of particles from an area of high concentration to an area of low concentration Facilitated diffusion - The net movement of particles (diffusion) down a concentration gradient via a channel or carrier protein. Specifically for ions. Active Transport - The net movement of particles (diffusion) against a concentration gradient (from low to high) with the use of ATP. For organic molecules and ions Endocytosis and Exocytosis involves the transport of substances within vesicles (bulk transport for large substances) In endocytosis, the vesicle will fuse with the cell surface membrane In exocytosis, the vesicle will pinch off the cell surface membrane

Give two differences between active transport and diffusion.

1. active transport is {against /eq}concentration gradient /eq ;2. active transport requires ATP /eq ;3. ref to involvement of (membrane) proteins inactive transport ;

5 Describe how membrane structure can be investigated practically, eg by the effect of alcohol concentration or temperature on membrane permeability.

1. Cut piece of beetroot into 1cm3 cubes2. Place in distilled water overnight to remove any dye released on preparation. Then wash and blot dry. 3. Place 8 different boiling tubes of distilled water into 8 different water baths of varying temperatures 4. When water reaches temperature of corresponding water bath, place a 1cm3 into each boiling tube 5. Leave all test tubes for 30 mins6. Remove beetroot cube from each tube after and place dye solution from each boiling tubes in separate cuvettes7. Place each cuvette in colorimeter to measure % absorbance8. Use absorbance to calculate % transmission ( 100 - absorbance.)9. Increase in temp increases transmission/ absorbance due to membrane molecules gaining more heat energy.10. Vibrations caused large gaps in membrane due to denaturing of integral and peripheral proteins in membrane, leaving large pores for dye to leak out of. 11. Possible issues: Cutting accurately sized beetroot/ error in reading from colorimeter/ difficulty in maintaining temperature

Variables that both of these students must keep the same if their results are to be compared.

1. reference to pre-treatment e.g. rinsing method ; 2. {size / mass / surface area / volume / shape} of beetroot ; 3. beetroot storage conditions / eq ; 4. {same / type / species / eq} beetroot ; 5. {age of beetroot / storage time} ; 6. (incubation) time / eq ; 7. {volume / concentration / eq} of {water / solution}(added to beetroot) ; 8. pH ;

6 Describe the properties of gas exchange surfaces in living organisms (large surface area to volume ratio, thickness of surface, difference in concentration) and explain how the structure of the mammalian lung is adapted for rapid gaseous exchange.

Rate of diffusion is increased with: Temperature (more kinetic energy) Steep Concentration gradient (more collisions) Stirring/moving (more movement) Large Surface area to volume ratio Short diffusion pathway (distance) E.g site of gas exchange in mammals are the lungs Alveolar epithelium O2 diffuses out of the alveoli across the alveolar and capillary epithelium into the blood CO2 diffuses into the alveoli from the blood and is breathed out

suggest how gas exchange occurs in an amoeba.

1. (gas exchange) occurs through the {cell membrane / phospholipid bilayer} ; 2. idea that the membrane is thin ; 3. oxygen enters cell (from water) / eq ; 4. carbon dioxide leaves cell (into water) / eq ; 5. {O2 / oxygen / CO2 / carbon dioxide} are {small / non-polar} (molecules) ; 6. reference to diffusion ; 7. {reference to / description} (suitable) concentration gradient ; 8. reference to large surface area (to volume ratio) ;

7 Describe the basic structure of an amino acid (structures of specific amino acids are not required) and the formation of polypeptides and proteins (as amino acid monomers linked by peptide bonds in condensation reactions) and explain thesignificance of a proteins primary structure in determining its three-dimensional structure and properties (globular and fibrous proteins and types of bonds involved in three dimensional structure).

Residual group [R] varies within each amino acid Amino acids are joined together by peptide bonds These can formed through condensation reactions (removal of water) This produces a polypeptide chain This sequence of amino acids is the primary structure of a protein Amino acids are linked by hydrogen bonds, forming alpha- helices or eta pleated sheets and are the secondary structures The residual group in the amino acids, and the sequence of amino acids in the primary structure determine the bonding and folding of the 3D structure of a protein The 3D structure has hydrogen and ionic bonding with disulfide bridges It also has hydrophilic regions (on the outside) and hydrophobic regions (on the inside) Type of amino acid determines types of Residual group Globular proteins have a relatively high number of R groups Quaternary protein structures form when there is more than one polypeptide chain bonded together 3D structure of a protein determines its properties There are two types of protein: Globular and Fibrous

Globular Round and compact Chains are coiled so hydrophilic regions face outwards and hydrophobic regions face inwards Soluble -> easily transported in fluids e.g Haemoglobin in the blood

Fibrous Long coiled polypeptide chains forming a rope shape Held together by bonds (e.g. hydrogen, disulfide, ionic) makes it strong. Often found in supportive tissue e.g. Collagen, Keratin

8 Explain the mechanism of action and specificity of enzymes in terms of their three-dimensional structure and explain that enzymes are biological catalysts that reduce activation energy, catalysing a wide range of intracellular andextracellular reactions.

Enzymes speed up biological reactions The more concentrated a system is, the more collisions occur between molecules or ions of reacting substances The energy between these collisions has the potential to cause a metabolic reaction [Metabolic reaction - A molecule is combined with something else, split into smaller parts or change its shape] Metabolic reactions are reversible therefore they tend to run spontaneously towards a dynamic equilibrium Enzymes are globular proteins which speed up the rate at which the dynamic equilibrium in a reversible reaction is attained Enzymes are not used up in the reaction Enzymes either work for the forward or backward reaction Within a metabolic reaction, there is a minimum amount of energy required for the reaction to spontaneously take place. This is the activation energy Enzymes lower the activation energy

Enzymes have an active site specific to a particular substrate that it can chemically recognise, bind to and modify Early scientists believed in the lock and key model - where a substrate directly fits into the active site, forms an enzyme substrate complex, and the products detach from the active site However this was not accurate, since evidence showed that the substrate changed shape slightly to fit into the active site The Induced Fit Model showed that the substrate does not have to fit into the active site. The initial contact strains the bonds in the substrate, which makes them easier to break in the formation of new products In order for the reaction to be catalysed, the substrate must change its shape correctly at the right orientation for the reaction to occur

An enzyme's active site is determined by its 3D structure Each enzyme has a different 3D structure, therefore a different active site

Describe the structure of an enzyme.

1. ref to an enzyme as a protein ;2. ref to {3D / tertiary / globular} structure ;3. ref. to named bonds (holding structure inplace) ;4. between the R groups ;5. ref to active site ;6. idea of specificity of active site ;

Describe the three-dimensional (tertiary) structure of an enzyme

1. globular / eq ; 2. reference to active site ;3. reference to specific shape of active site ; 4. reference to {bonds /named bond / interaction / eq} between R groups ; 5. credit correctly named {bond/interaction} e.g. disulphide bond, hydrogen bonds, hydrophobic interactions (between R groups) ; Explain how the primary structure of an enzyme determines its three-dimensional (tertiary) structure and its properties.

1. (primary structure) {position / sequence / order /eq} of the {amino acids / R groups} / eq ; 2. idea that this determines the {positioning / type} of the {bonds / folding / eq} ; 3. determining the {shape / properties} of the active site / eq ; 4. idea of interaction of active sites and substrates e.g. enzyme substrate complex forms ; 5. idea of {polar / hydrophilic} on the outside of enzymes / {non polar / hydrophobic} on the inside / eq ; 6. reference to solubility ;

9 Describe how enzyme concentrations can affect the rates of reactions and how this can be investigated practically by measuring the initial rate of reaction.1. Set up a reaction where there is effervescence of a gas as a product (e.g. Hydrogen Peroxide and catalase)2. Therefore you can measure the volume of oxygen give off. 3. Connect a delivery tube connected to a bung of the solution of hydrogen peroxide and catalase to an upside down measuring cylinder4. This measuring cylinder must be upside down in water (to collect the oxygen)5. For the first minute, record the vol produced and divide by the time to give the initial rate of reaction 6. Repeat by increasing the concentration of catalase7. Controls: Vol of hydrogen peroxide, temperature, pH 8. Errors: Oxygen escapes from measuring cylinder whilst placing upside down, some oxygen diffuses into the water9. Explanation: As enzyme concentration increases, rate of reaction increases. 10. Increase in concentration, increases the number of active sites and probability of enzyme substrate complexes forming11. This lowers the activation energy of the reaction and speeds up the rate

Describe how this apparatus could be used to compare the catalase activity

1. reference to measuring volume of oxygen ; 2. suitable reference to time e.g. oxygen produced in unit time, time taken to produce same volume of oxygen ; 3. idea of measuring the initial rate of reaction ; 4. reference to controlled variable in relation to the mussel e.g. age, part of mussel, mass, surface area ; 5. reference to a controlled variable in relation to the experiment e.g. volume of hydrogen peroxide, temperature, concentration, pH ; 6. suitable reference to repeats ;

10 Describe the basic structure of mononucleotides (as a deoxyribose or ribose linked to a phosphate and a base, ie thymine, uracil, cytosine, adenine or guanine) and the structures of DNA and RNA (as polynucleotides composed ofmononucleotides linked through condensation reactions) and describe how complementary base pairing and the hydrogen bonding between two complementary strands are involved in the formation of the DNA double helix.

Hydrogen bonds occur between the nitrogenous bases In DNA, Adenine to Thymine and Guanine to Cytosine This is called Complementary base pairing In RNA, Uracil replaces Thymine Mononucleotides are linked by condensation reactions This forms a DNA double helix

11 Describe DNA replication (including the role of DNA polymerase), and explain how Meselson and Stahls classic experiment provided new data that supported the accepted theory of replication of DNA and refuted competing theories.

DNA Replication Double helix unzips forming 2 separate strands Mononucleotides join to the exposed strands by complementary base pairing This forms 2 identical DNA strands

Three types of replication proposed before Meselson Stahl Experiment: Conservative - DNA strands were wrapped around histone proteins which allowed it to replicate Semi conservative - DNA helix could unzip and new templates could be copied from each side Dispersive - Split itself into multiple segments and then replicates itself

Meselson and Stahl Grew E.coli in Heavy Nitrogen (N15) and spun in centrifuge N15 would sink to the bottom of the test tube Grew E.coli in Light Nitrogen (N14) Combined with light nitrogen DNA of first generation, bacteria were hybrid half N15 and N14 Second generation formed 2 strands of N14 This shows that semi conservative replication is the method of DNA replication

12 Explain the nature of the genetic code (triplet code only; nonoverlappingand degenerate not required at AS).

Triplet code - 3 bases code for one amino acid 4 x 4 x 4 = 64 amino acids which meets the requirement of 20 amino acids that need to be coded for

13 Describe a gene as being a sequence of bases on a DNA molecule coding for a sequence of amino acids in a polypeptide chain.

Gene is a sequence of bases on a DNA molecule coding for a sequence of amino acids on a polypeptide chain

14 Outline the process of protein synthesis, including the role of transcription, translation, messenger RNA, transfer RNA and the template (antisense) DNA strand (details of the mechanism of protein synthesis on ribosomes are notrequired at AS).

Transcription Hydrogen bonds break between bases/ DNA Helix unwinds This is catalysed by DNA Helicase Forms 2 separate strands Free floating mono nucleotides containing ribose sugars attach to the exposed bases on the template strand Formation of phosphodiester bonds by condensation reaction During this Thymine replaces Uracil Catalysed by DNA ligase, the mRNA strand detaches from the template strand This mRNA strand is modified then leaves the nucleus via the nuclear envelope.

Translation The mRNA strand attaches to the ribosome binding site tRNA molecules carrying an anti codon and amino acid, join to the codon on the mRNA strand (by complementary base pairing) When the tRNA molecule detaches it leaves an amino acid behind. As the mRNA strand passes through the ribosome, more amino acids join together by peptide bonds This forms a polypeptide chain (primary structure of a protein) The start codon initiates translation The stop codon stops translation (UUG)

15 Explain how errors in DNA replication can give rise to mutations and explain how cystic fibrosis results from one of a number of possible gene mutations. Mutation is a change in the base sequence of DNA Point mutation - Change specific nucleotides (bases) Chromosomal mutation - Change in position of whole genes within a chromosome Whole chromosome - Chromosome is missing or duplicated (deletion, insertion, replication)

16 Explain the terms gene, allele, genotype, phenotype, recessive, dominant, homozygote and heterozygote, and explain monohybrid inheritance, including the interpretation of genetic pedigree diagrams, in the context of traits such ascystic fibrosis, albinism, thalassaemia, garden pea height and seed morphology. Allele - Version of a gene Genotype - Set of genes in an organism Phenotype - Set of characteristics of an organism as a result of its genotype and its interaction with the environment Recessive - Allele that does not affect the phenotype in the presence of dominant allele (requires two copies of allele) Dominant - Allele that always affects the phenotype (only require one copy of allele) Homozygote - Individual which possesses two copies of the same allele Heterozygote - Individual which possesses two different alleles Monohybrid Inheritance - The inheritance of one characteristic

1) Cystic Fibrosis Recessive Mutation in the CFTR protein Affects the lungs, digestive and reproductive systems

2) Albinism Recessive Mutation in protein for melanin synthesis Stops melanocytes from producing melanin

3) Thalassaemia Recessive Mutation in gene coding for alpha haem Causes slow haemoglobin production

4) Garden Pea Height Controlled by a single gene with 2 alleles Allele for tall plants is dominant (T) Allele for small plants is recessive (t) 5) Seed Morphology Controlled by a single gene with two alleles Allele for smooth seeds is dominant (S) Allele for wrinkled seeds is recessive (s)

17 Explain how the expression of a gene mutation in people with cystic fibrosis impairs the functioning of the gaseous exchange, digestive and reproductive systems.

CFTR protein present in apical membranes (in epithelial cells) Affects reproductive, digestive and respiratory systems

1. CFTR protein is a pump to actively transport Cl- ions out of the cell 2. This prevents Na+ from entering the cell 3. Water remains outside of the cell by osmosis

Respiratory Cilia lining the airways cannot move because mucus is viscous Leads to mucus buildup Gas exchange cannot take place in the area below the blockage Surface area available is reduced, reducing the efficiency of gas exchange This causes breathing problems More prone to lung infections because mucus containing microbes cannot be removed

Digestive Tube connecting pancreas to intestine becomes blocked with viscous mucus Prevents digestive enzymes produced by pancreas from reaching small intestine Reduces ability to digest food fewer nutrients absorbed Mucus can cause cysts to form in pancreas, inhibiting the production of enzymes Mucus lining of the small intestine is abnormally thick

Reproductive In men Vas Deferens becomes blocked or is missing, so sperm from the testicles cannot reach the penis In women, cervical mucus prevent sperm from reaching the egg reduces motility of the sperm

18 Describe the principles of gene therapy and distinguish between somatic and germ line therapy.

Principles: Cells are removed from the patient In lab, virus is modified so it cannot reproduce A gene is inserted into the virus (Genetic engineering) The altered virus is mixed with cells from the patient The cells from the patent become genetically altered The altered cells are injected into the patient (e.g bone marrow) The genetically altered cells produce the desired protein or hormone Treatment must be repeated Somatic therapy Change alleles in body cell Added to cells most affected by disorder Germ line therapy Changes to alleles in sex cells Cells of offspring will be affected and wont suffer from the disease If disorder is recessive, add a working dominant allele If disorder is dominant silence allle by sticking DNA in the middle of it Types of vectors: Liposome (spheres made of lipid), Plasmids (rings of bacterial DNA, modified viruses (that can accept human DNA)zx

19 Explain the uses of genetic screening: identification of carriers, preimplantation genetic diagnosis and prenatal testing (amniocentesis and chorionic villus sampling) and discuss the implications of prenatal genetic screening.

Used for identifying a carrier (before pregnancy) Carried out by a taking a blood sample and looking at the chromosomes to see if the patient is a carrier

Preimplantation genetic diagnosis requires IVF Remove cell from zygote before placing in mother Check DNA/genome to see if it carries the gene for the disease Prenatal screening Amniocentesis - Withdrawal of a tiny sample of amniotic fluid within the membrane sac (amnion) surrounding the fetus. (15-16 weeks) Chorionic Villus Sampling (CVS) - Withdraw fluid containing cells from the membrane sac (chorionic villi) surrounding the amnion (8-12 weeks) Implications PGD allows couples to test embryos before implantation (so only embryos without the allele may be implanted) PGD reduces chance of babies being born with genetic disorders Prenatal screening allows parents to make informed decisions and decide whether they will have the child or have an abortion Prenatal screening allows parents to prepare for the future care of the child and arrange any medical treatment which can start as soon as the child is born.

20 Identify and discuss the social and ethical issues related to genetic screening from a range of ethical viewpoints

Social Tests arent always 100% accurate - could give false positives and negatives Other genetic abnormalities may be found Prenatal testing increases the risk of miscarriage Results of genetic tests may be given to employers or insurance companies - leading to genetic discrimination Ethical Unethical to abort a fetus because it has a genetic disorder Used to find out other characteristics - concern over people in the future selecting embryos for desired characteristics (designer babies)