sites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes CAPE Biology Unit 1 Study Notes Topics: Biological Molecules Cellular Ultrastructure Cell membrane and transport Enzymes Structure and function of Nucleic Acids Mitotic and Meiotic Cell Division Patterns of Inheritance Aspects of Genetic Engineering Variation and Natural Selection Asexual Reproduction and Vegetative Propagation Sexual Reproduction in flowering plants : Sexual Reproduction in Man SiSsserrerrenes hitps:oninefiphimis convhexgarknbtitp=1 anetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Units of measurement metre millimetre micrometre nanometre picometre L Biological Molecules Life on Earth evolved in the water, and all life stil depends on water. At least 80% of the mass of living organisms is water, and almost all the chemical reactions of life take place in aqueous solution. The other chemicals that make up living things are mostly organic macromolecules belonging to the four groups; proteins, nucleic acids, carbohydrates or lipids. These macromolecules are made up from specific monomers as shown in the table below. Between them these four groups make up 93% of the dry mass of living organisms, the remaining 7% comprising small organic molecules (like vitamins) and inorganic ions. m mm am. nm pm =im 10° m 0% m =10°m 10? m Group name monomers polymers Proteins amino acids polypeptides nucleic acids nucleotides Polynucleotides carbohydrates monosaccharides polysaccharides Group name ‘components Targestunit | _% dry mass lipids fatty acids + glycerol Triglycerides: 10 The first part of this unit is about each of these groups. We'll ook at each of these groups in detail, except nucleic acids, which are studied in module 2, hitps:oninefiphimis convhexgarknbtitp=1 anesites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Water Water is a polar covalent compound. Due to difference in electro-negativities of oxygen and hydrogen, one end of the water molecule bears a slight negative charge, while the other end beats a slight positive charge. This is called the dipolar nature of water. The positive end of one water molecule is attracted to the negative end of another water molecule. This force of attraction is called a hydrogen bond. Water has a number of important properties essential for life. Many of the properties below are due to the hydrogen bonds in water: Solvent. Because it is charged, water is a very good solvent. Charged or polar molecules such as salts, sugars, amino acids dissolve readily in water and so are called hydrophilic ("water loving"). Uncharged or non-polar molecules such as lipids do not dissolve so well in water and are called hydrophobic ("water hating”). Specific heat capacity. Water has a specific heat capacity of 4.2 J g* °C", which means that it takes 4.2 joules of energy to heat 1 g of water by 1°C. This is unusually high and This means that a lot of heat must be added / removed to change the temperature of water. This property of water prevents sudden Hydrogen bond fluctuations in temperature of organisms or aquatic environment. The gradual change in temperature gives organisms enough time to cope with the change. The high specific heat capacity also helps to resist temperature changes (maintain constant temperature). The density of pure water is 1g/em3.The density of water changes with temperature. Thus in aquatic habitats there will be layers of water with different densities. The differences in density cause the circulation of water and nutrients within the habitat, thus affecting the vertical distribution of organisms. Latent heat of vaporisation. Water requires a lot of energy to change state from a liquid into @ gas, and this is made use of as a cooling mechanism in animals (sweating and panting) and plants (transpiration). As water evaporates it extracts heat from around it, cooling the organism. Latent heat of fusion. Water also requires a lot of heat to change state from a solid to a liquid, and must loose a lot of heat to change state from a liquid to a solid. This means itis difficult to freeze water, so ice crystals are less likely to form inside cells. Density. Water has maximum density at 4° C. This means that the densest water (at 4°CAt this temperature, the expansion and the contraction of water cancel each other hitps:oninefiphimis convhexgarknbtitp=1 anesites, 1112 PM ‘CAPE Biology Unit 1 Study Notes ut.) will remain at the bottom of an aquatic habitat. This prevents aquatic habitats from freezing completely, so that aquatic organisms can survive at the bottom (unfrozen at 44°C). Surface tension is the property of a liquid which makes its surface behave like a stretched membrane, mainly caused due to hydrogen bonding between molecules (water).This is especially useful to some aquatic invertebrates that can skate or lay eggs on the water surface. Mosquito larvae also use the surface tension of water to cling to the surface and breathe air, through siphons. Surface tension decreases the ease with which gases dissolve into water. * Cohesion. Water molecules “stick together" due to their hydrogen bonds, so water has high cohesion. This explains why long columns of water can be sucked up tall trees by transpiration without breaking. It also explains surface tension, which allows small animals to walk on water. + Ionisation. When many salts dissolve in water they ionise into discrete positive and negative ions (e.g. NaCl Na* + CI). Many important biological molecules are weak acids, which also ionise in solution (e.g. acetic acid acetate: + H"). The names of the acid and ionised forms (acetic acid and acetate in this example) are often used loosely and interchangeably, which can cause confusion. You will come across many examples of two names referring to the same substance, e.g.: phosphoric acid and Phosphate, lactic acid and lactate, citric acid and citrate, pyruvic acid and pyruvate, aspartic acid and aspartate, etc. The ionised form is the one found in living cells. + pH. Water itself is partly ionised (HzO _H* + OH: ), so it is a source of protons (H* ions), and indeed many biochemical reactions are sensitive to pH (-logfH")). Pure water, cannot buffer changes in H* concentration, so is not a buffer and can easily be any pH, but the cytoplasms and tissue fluids of living organisms are usually well buffered at about neutral pH (pH 7-8). Practice questions 1. Water readily sticks to many other substances, a property called 1) cohesion 2) adhesion 3) polarity 4) hydrophobic bonding 2. Water striders are common insects that can skip across the surface of ponds and streams. This lifestyle is enabled by water's 1) cohesion and resulting surface tension 2) high specific heat 3) adhesion 4) none of the above hps:fontine.iphiri.comMhexgarknttip=t anetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Which best describes how charges are distributed on a water molecule? 1) The oxygen end is positive relative to the end with the two hydrogen atoms. 2) The oxygen end is negative relative to the end with the two hydrogen atoms. 3) The charge is neutral and equal throughout the molecule. 4) The oxygen end is neutral; one of the hydrogen atoms has a slight positive charge and the other hydrogen atom has a slight negative charge Relative to other substances, water tends to resist changes in temperature. Why? 1) Water is extremely dense, and like all dense materials, it can absorb a great deal of heat with a relatively small change in temperature. 2) Water is abundant. Large bodies of water resist changes in their temperature simply because they are massive objects. 3) Water is highly cohesive. Its molecules tend to resist increases in their motion. When water is heated, some of the energy is used to disturb the hydrogen bonds between neighboring molecules. 4) Water is highly adhesive. Pure water does not resist temperature change, but if water is bonded to other substances, molecules will tend to "stay put" and resist, increases in their motion Water is sometimes called the "universal solvent.” Is that acourate? 1) Certainly. Water's polar nature means that it can adhere to and dissolve all other substances. 2) Notatall, Only salts and carbohydrates can be dissolved in water. 3) _ For the most part. Water readily dissolves hydrophobic substances, but not hydrophilic ones. 4) For the most part. Water readily dissolves most substances, but not hydrophobic ones. Many mammals control their body temperature by sweating. Which property of water is most directly responsible for the ability of sweat to lower body temperature? 1) water's change in density when it condenses 2) water's ability to dissolve molecules in the air 3) the release of heat by the formation of hydrogen bonds 4) _ the absorption of heat by the breaking of hydrogen bonds 5) _ water's high surface tension The bonds that are broken when water vaporizes are 41)ionic bonds. 2) hydrogen bonds between water molecules. hitps:oninefiphimis convhexgarknbtitp=1 sitetsites, 1112 PM 10. "1 12. 13. ‘CAPE Biology Unit 1 Stuay Notes 3) covalent bonds between atoms within water molecules. 4) polar covalent bonds 5) nonpolar covalent bonds. Which of the following is a hydrophobic material? 1) paper 2) table salt 3) wax 4) sugar 5) pasta Water is a polar molecule. This means that - 1) the opposite ends of the molecule have opposite electrical charges 2) water molecules are linear, like a pole 3) water is one of the many hydrophobic molecules 4) the atoms in water have equal electronegativities 5) all of the above The partial charges on a water molecule ocour because of . 1) the unequal sharing of electrons between the hydrogen and the oxygen atoms of a water molecule 2) _ the achievement of a stable configuration by one atom of a bond but not by the other partner 3) covalent bonding 4) widespread ionization _5) the high electronegativity of hydrogen The tendency of water molecules to stay close to each other as a result of hydrogen bonding 1) provides the surface tension that allows leaves to float on water 2) iscalled cohesion 3) keeps water moving through the vessels in a tree trunk 4) acts to moderate temperature 5) all of the above Most of water's unique features (for example, its versatility as a solvent, ability to moderate temperature, and cohesive behavior) result from the fact that 1) hydrogen is the only element without any neutrons 2) — oxygen attracts electrons more than hydrogen does 3) oxygen has only one stable isotope, but hydrogen has three 4) _ oxygen has two unfilled electron shells 5) More than one of the above is correct. The ability of water molecules to form hydrogen bonds with other water molecules and water's abilty to dissolve substances that have charges or partial charges are 1) both caused by waters ability to form covalent bonds with hydrophobic substances 2) due to water's partial charges and low molecular mass, respectively hitps:oninefiphimis convhexgarknbtitp=1 anetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes 3) _ both caused by water's partial charges 4) _ both caused by water's two electron shells and the opposite spins of those shells 5) both due to water's low molecular mass 14. The phenomenon responsible for the maintenance of a column of water as it moves upward through a vessel is 1) cohesion 2) adhesion 3) surface tension 4) evaporation 5) heat of vaporization Carbohydrates Carbohydrates Carbohydrates contain only the elements carbon, hydrogen and oxygen. The group includes monomers, dimers and polymers, as shown in this diagram: Monossccerides inci Polysaceries i eg ghicosefrucose gg marone maltose eg, starch glycogen Monosaccharides Sipe suros al ‘nd mrin Monosaccharides (simple ‘sugars These all have the formula (CH2O)n, where n can be 3-7. The most common and important monosaccharide is glucose, which is a six-carbon or hexose sugar, so has the formula CeH12Os. Its structure is: Glucose forms a six-sided ring, although in three-dimensions it forms a structure that looks a bit ike a chair. The six carbon atoms are numbered as shown, so we can refer to individual ‘carbon atoms in the structure. In animals glucose i s the main transport sugar in the blood, and its concentration in the blood is carefully controlled. There are many isomers of glucose, with i, the same chemical formula (CsH:2Os), but different "“~j—" structural formulae. These isomers include alpha «+ glucose, beta glucose, fructose and galactose. iA, aN Common five-carbon, or pentose sugars (where n = 5, CsH1oOs) include ribose and deoxyribose (found in nucleic acids and ATP) and ribulose (which occurs in photosynthesis), pt gcse hitps:oninefiphimis convhexgarknbtitp=1 781sites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Disaccharides (double sugars) Disaccharides are formed when two monosaccharides are joined together by a glycosidic bond. The reaction involves the formation of a molecule of water (H:0): i ; 4. on 5 i iA Ni iA Ni wv Ni, eI inv meeIN Ik iv Ente Yd or re: This shows two glucose molecules joining together to form the disaccharide maltose. Because this bond is between carbon 1 of one molecule and carbon 4 of the other molecule itis called a 1-4 glycosidic bond. Bonds between other carbon atoms are possible, leading to different shapes, and branched chains. This kind of reaction, where HO is formed, is called a condensation reaction. The reverse process, when bonds are broken by the addition of water (e.g. in digestion), is called a hydrolysis reaction. Disaccharides In general: : polymerisation reactions are condensations, : breakdown reactions are hydrolyses There are three common disaccharides: Maltose (or malt sugar) is glucose 1-4 glucose. It is formed on digestion of starch by amylase, because this enzyme breaks starch down into two- +f glucose units. Brewing beer starts with malt, which it ei is a maltose solution made from germinated "| gh, semen 1 barley. Maltose is the structure shown above. tame hitps:oninefiphimis convhexgarknbtitp=1 artetsites, 1112 PM ‘CAPE Biology Unit 1 Study Notes Sucrose (or cane sugar) is glucose 1-2 fructose. It is common in plants because it is less reactive than glucose, and itis their main transport sugar. It is the common table sugar that you put in your tea. There are 12 Carbon atoms, 22 Hydrogen atoms, and 11 Oxygen atoms in each molecule of Sucrose. Sucrose is non reducing disaccharide of glucose and fructose. One Oxygen atom has a single bond and altached to ring of hexagon which has five Carbons and one Oxygen and another single bond of (same) Oxygen attached to the ring of pentagon which has four Carbons atom and one Oxygen atom. Take a moment to study the diagrams and identify the location of the numbered carbon atoms in each diagram. Lactose (or milk sugar) is galactose 1-4 glucose. It is found only in mammalian milk, and is the main source of energy for infant mammals. hps:fontine.iphiri.comMhexgarknttip=t snetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Polysaccharides Polysaccharides are long chains of many monosaccharides joined together by glycosidic bonds. There are three important polysaccharides: + Starch is the plant storage polysaccharide. It is insoluble and forms starch granules inside many plant cells. Being insoluble means starch does not change the water potential of cells, so does not cause the cells to take up water by osmosis (more on ‘osmosis later). It is not a pure substance, but is a mixture of amylose and amylopectin Amylose is simply poly-(1-4) glucose, so is a straight chain. In fact the chain is floppy, and it tends to coil up into a helix. Amylopectin is poly(1-4) glucose with about 4% (1- 6) branches. This gives it a more open molecular structure than amylose. Because it has more ends, it can be broken more quickly than amylose by amylase enzymes. Both amylose and amylopectin are broken down by the enzyme amylase into maltose, though at different rates. jh" och AL Ni IAL fr NI f~ION| Amylose ‘+ Glycogen is similar in structure to amylopectin. Itis poly (1-4) glucose with 9% (1-6) branches. Itis made by animals as their storage polysaccharide, and is found mainly in muscle and liver. Because itis so highly branched, it can be mobilised (broken down to glucose for energy) very quickly. 10 hitps:oninefiphimis convhexgarknbtitp=1 torresites, 1112 PM ‘CAPE Biology Unit 1 Study Notes Glycogen ae aan PANE TATE neces we ‘e Bg ‘t | aaa i (peacoat om Ws VND ay \o4 t4 pw ‘ty 0% NL Easy diagrams Amylose Amylopectin Glycogen + Cellulose is only found in plants, where it is the main component of cell walls. It is poly (1-4) glucose, but with a different isomer of glucose. Starch and glycogen contain a-glucose, in which the hydroxyl group on carbon 1 sticks down from the ring, while cellulose contains b-alucose, in which the hydroxyl group on carbon 1 sticks up. This means that in a chain alternate glucose molecules are inverted. "1 hps:fontine.iphiri.comMhexgarknttip=t antesites, 1112 PM ‘CAPE Biology Unit 1 Study Notes aldose ers $0004 aoe a @666-" This apparently tiny difference makes a huge difference in structure and properties. While the a1-4 glucose polymer in starch coils up to form granules, the 1-4 glucose polymer in cellulose forms straight chains. Hundreds of these chains are linked together by hydrogen bonds to form cellulose microfibrils. These microfibrils are very strong and rigid, and give strength to plant cells, and therefore to young plants and also to materials such as paper, cotton and cellotape. The b-glycosidic bond cannot be broken by amylase, but requires a specific cellulase ‘enzyme. The only organisms that possess a cellulase enzyme are bacteria, so herbivorous animals, like cows and termites whose diet is mainly cellulose, have mutualistic bacteria in their guts so that they can digest cellulose. Humans cannot digest cellulose, and it is referred toas fibre. 12 hps:fontine.iphiri.comMhexgarknttip=t ratesites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes * Other polysaccharides that you may come across include: © Chitin (poly glucose amine), found in fungal cell walls and the exoskeletons of insects. ‘Pectin (poly galactose uronate), found in plant cell walls. © Agar (poly galactose sulphate), found in algae and used to make agar plates. © Murein (a sugar-peptide polymer), found in bacterial cell walls. Lignin (a complex polymer), found in the walls of xylem cells, is the main component of wood. Proteins Proteins are the most complex and most diverse group of 400 Acid Sttugy, biological compounds. They have an astonishing range of > 1 re, different functions, as this list shows. i 0 HNC — Cama ‘structure .g. collagen (bone, cartilage, tendon), I So keratin (hair), actin (muscle) Hn eae e.g. amylase, pepsin, catalase, etc apa) a (210,000 others) transport e.g. haemoglobin (oxygen), transferrin (iron) pumps e.g. Na*K* pump in cell membranes motors e.g. myosin (muscle), kinesin (cilia) hormones e.g. insulin, glucagon receptors e.g. rhodopsin (light receptor in retina) antibodies e.g. immunoglobulins storage e.g. albumins in eggs and blood, caesin in milk blood clotting | e.g. thrombin, fibrin 13 hitps:oninefiphimis convhexgarknbtitp=1 tanetsites, 1112 PM ‘CAPE Biology Unit 1 Study Notes Proteins are made of amino acids. Amino acids are made of the five elements C HO N'S. The general structure of an amino acid molecule is shown on the right. There is a central carbon atom (called the “alpha carbon"), with four different chemical groups attached to +a hydrogen atom +a basic amino group an acidic carboxyl group +a variable "R" group (or side chain) Amino acids are so-called because they Effect OF Ph on Amino Acid Structure H 4 H have both amino groups and acid groups, which have opposite charges. At neutral pH (found in most living organisms), the groups 11 are ionised as shown above, so there isa positive charge at one end of the molecule R R and a negative charge at the other end. The %s¥y neutral pH low pH (acid) overall net charge on the molecule is charg charge=0 ——charge+1 therefore zero. A molecule like this, with both positive and negative charges is called a zwitterion. The charge on the amino acid changes with pH { ( H H H. H H. ~as WA Ny H. b H we, nts H oH H- b H | rok OF C. & ‘o-u oS ‘o® & ‘o® ion at low pH witterion ion at high pH? neutral pH There ate 20 different R groups, and so 20 different amino acids. Since each R group is slightly different, each amino acid has different properties, and this in turn means that proteins can have a wide range of properties. The following table shows the 20 different R groups, grouped by property, which gives an idea of the range of properties. You do not need to learn these, but it is interesting to see the different structures, and you should be familiar with the amino acid names. You may already have heard of some, such as the food additive monosodium glutamate, which is simply the sodium salt of the amino acid glutamate. Be careful not to confuse the names of amino acids with those of bases in DNA, 4 hps:fontine.iphiri.comMhexgarknttip=t tanssites, 1112 PM ‘CAPE Biology Unit 1 Study Notes such as cysteine (amino acid) and cytosine (base), threonine (amino acid) and thymine (base). There are 3-letter and 1-letter abbreviations for each amino acid. Polypeptides ‘Amino acids are joined together by peptide bonds. The reaction involves the formation of a molecule of water in another condensation polymerisation reaction: Sy-c—c / Wf When two amino acids join together a dipeptide is formed. Three amino acids form a tripeptide. Many amino acids form a polypeptide. e.g.: keratin which is found in finger nails and hair In a polypeptide there is always one end with a free amino (NHs) group, called the N= terminus, and one end with a free carboxyl (CO2) group, called the C-terminus. In a protein the polypeptide chain may be hundreds of amino acids long. Amino acid polymerisation to form polypeptides is part of protein synthesis. It takes place in ribosomes, and is special because it requires an RNA template. The sequence of amino acids in a polypeptide chain is determined by the sequence of the genetic code in DNA. Protein synthesis Protein Structure Polypeptides are just a string of amino acids, but they fold up to form the complex and well- defined three-dimensional structure of working proteins. To help to understand protein structure, it is broken down into four levels 15 hps:fontine.iphiri.comMhexgarknttip=t t5it6tsites, 1112 PM ‘CAPE Biology Unit 1 Study Notes Primary structure of a protein The primary structure is the sequence of amino acids in a polypeptide chain. This sequence is determined by the genetic code on DNA. The primary structure determines the secondary, tertiary or quaternary structure of a protein. Examples: NH, — Leucine — Valine — Isoleunine — Protine _ Gtutamine — Serine — Arginine — COOH COOH — Proline —Valine — Cystine — Protine— Glutamine — Arginine — Leucine — NH, The eventual shape and function of both polypeptide chains is going to be different. The secondary structure of proteins Within the long protein chains there are regions in which the chains are organised into regular structures known as alpha-helices (alpha- helixes) and beta-pleated sheets. These are the secondary structures in proteins. These secondary structures are held together by hydrogen bonds. These form as shown in the diagram between one of the lone pairs on an oxygen atom and the hydrogen attached to a nitrogen atom: The alpha-helix Lf rst t=] PN i 16 hps:fontine.iphiri.comMhexgarknttip=t teresites, 1112 PM ‘CAPE Biology Unit 1 Study Notes In an alpha-helix, the protein chain is coiled like a loosely-coiled spring. The "alpha" means that if you look down the length of the spring, the coiling is happening in a clockwise direction as it goes away from you. Notice that all the "R” groups are sticking out sideways from the main helix. Notice the regular arrangement of the hydrogen bonds. All the N-H groups are pointing upwards, and all the C=O groups pointing downwards. Each of them is involved in a hydrogen bond, Beta-pleated sheets In a beta-pleated sheet, the chains are folded so that they lie alongside each other. The next diagram shows what is known as an “anti-parallel” sheet. All that means is that next-door chains are heading in opposite directions. The folded chains are again held together by hydrogen bonds involving exactly the same groups as in the alpha-helix. 7 hps:fontine.iphiri.comMhexgarknttip=t tresites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes fahelix (B) Fig. 4.37 The c helix and 8 sheet secondary structures of protein molecules. ‘The R side chains bonded to c-carbons are numbered Tertiary structure of a protein Tertiary structure of a protein is the complex three - dimensional shape the polypeptide chain takes when the polypeptide helix ( secondary structure ) twists and folds around itself . The tertiary structure is maintained by Hydrogen bonds, disulphide bridges (covalent bonds) and ionic bonds between the R groups of amino acids. Hydrophobic interactions also help to maintain the shape of globular proteins (Eg: enzymes ). 18 hitps:oninefiphimis convhexgarknbtitp=1 tenetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Quaternary structure of a protein Quaternary structure is the linking together of two or more polypeptide chains. Examples:+ Haemoglobin consist of four polypeptide chains, Insulin consists of two polypeptide chains, Collagen consists of three polypeptides chains. Example: Keratin (in hairs, Nails and Skin) The specific three dimensional shape (secondary, tertiary, quaternary structure) of a protein is maintain by three types of chemical bonds between R groups of amino acids 1. Hydrogen bonds: Occur between some H atoms (having a slight positive charge) an ‘oxygen and nitrogen atoms (having a slight negative charge). Although these bonds are weak, the large number of bonds maintains the three dimensional shape. 2. tonic bonds: Occur between - COOH groups and — NH2 groups found in the R groups. They are stronger than H bonds, but can be broken by changes in pH and temperature 3. Disulphide bonds: Some amino acids, like cysteine and methionine contain sulphur atoms in the Rgroups. Disulphide bonds can form between sulphur atoms of amino acids that are close together. These bonds are Ntedrorhnctte Itorec ites: strong and. contibute to L rea sn the strength of structural {nd van dor Waals proteins like collagen. PR oy, ees They are also useful in 6 Hie oth ieee linking the two polypeptide Hydrogen # “et chains of insulin together. bend Note: E08 Eon, sss cH, Hydrophilic and hydrophobic CH Disulfide bridge interactions also help to maintain | the shape of globular proteins in water (solution). The ° hydrophobic (water hating) parts —CH,—CH,-CH,—CH, -NHJ#IEO-C—cH,— ‘of the polypeptide chain face nee away from water by folding inwards. The hydrophilic parts of the chain remain on the surface of the globular structure. ee 19 hitps:oninefiphimis convhexgarknbtitp=1 tortetsites, 1112 PM ‘CAPE Biology Unit 1 Study Notes Insulin is a globular protein. It is made up of two polypeptide chains which are linked to each other by two disulphide bridges (bonds) - Quatemary structure. Chain A has 21 amino acids and Chain B has 30 amino acids. Insulin has a three dimensional structure consisting of 3 helices and 3 conserved disulfide bridges. A The polypeptide chains are highly twisted (tertiary structure) and rolled up in to a globule when dissolved in water (hydrophobic interactions). Collagen is a fibrous protein. It is made up of three polypeptide chains (quaternary structure) each CWRBALLPOL. polypeptide chain is twisted to form a helix. The three polypeptide helices wind around each other like a rope with three strands. Hydrogen bonds hold the three strands in place. This makes collagen very stable, insoluble, flexible, but inelastic. Collagen is found mainly in tendons and bones. Each helix has a regular, repeating pattern of amino acids in the sequence of gly-pro- X, where gly stands for the amino acid glycine, pro stands for the amino acid proline and X stands for any other amino acid. Short segments at the end of collagen chains contain an amino acid called hydroxylysine. These amino acids form cross-links that stabilize the side- by-side packing of collagen chains, creating fibrils. Fibrils are extremely strong, even when significantly stretched. This strength is important to their function of connecting muscles to bones, where they must withstand enormous forces. ui Lipids are a mixed group of hydrophobic compounds composed of the elements carbon, hydrogen and oxygen. pide complex ‘imple Triglcendes Phospholipids Waxes Steroids Terpenes Triglycerides Triglycerides are commonly called fats or oils. They are made of glycerol and fatty acids. Glycerol is a small, 3-carbon molecule with three alcohol groups. non oa On On bu hps:fontine.iphiri.comMhexgarknttip=t zanersites, 1112 PM ‘CAPE Biology Unit 1 Study Notes Fatty acids are long molecules with a a polar, hydrophilic end and a non- | = =—~ polar, hydrophobic “all. TRE 1” crc cane . hydrocarbon chain can be from 14. \_ pet to 22 CH2 units long, butitis always ~~~~__ an even number because of the way fatty acids are made. The hydrocarbon chain is sometimes called an R group, so the formula of a fatty acid can be written as R-COO”. r rio ty B HHH If there are no C=C double bonds in the hydrocarbon chain, then it saturated with hydrogen). These fatty acids form straight chi melting point. i a saturated fatty acid , and have a high If there are C=C double bonds or triple bonds in the hydrocarbon 4+ 5 chain, then it is an unsaturated“, fatty_acid (ie. unsaturated with gf hydrogen). These fatty acids form bent chains, and have a low melting point. Fatty acids with more than one double bond are called poly-unsaturated fatty acids (PUFAS). One molecule of xe Qo H glycerol joins cH—(CH, } COOH HO+C-H cH—(CH,)- So-CH + HO together with three fatty acid molecules to I forma ce CooH HOFF H CH—(CH) 0-H triglyceride ° molecule, in another condensation polymerisation reaction (CH, CoH HO H— cl (CH) —CO~ bet Triglycerides are insoluble in water. They are used for storage, insulation and protection in fatty tissue (or adipose tissue) found under the skin (sub-cutaneous) or surrounding organs. They yield more energy per unit mass than other compounds so are good for energy 2 hps:fontine.iphiri.comMhexgarknttip=t austsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes storage. Carbohydrates can be mobilised more quickly, and glycogen is stored in muscles and liver for immediate energy requirements. + Triglycerides containing saturated fatty acids have a high melting point and tend to be found in warm-blooded animals. At room temperature they are solids (fats), e.g. butter, lard, * Triglycerides containing unsaturated fatty acids have a low melting point and tend to be found in cold-blooded animals and plants. At room temperature they are liquids (oils), eg. fish oil, vegetable oils, Phospholipids Phospholipids have a similar structure to triglycerides, but with a phosphate group in” -_— place of one fatty acid ___ parry ac tans Hs Wop chain. There may also. ~~ cH CH) -C-OC-H be other groups vu attached tothe phosphate. Phospholipids have a polar hydrophilic "head (the negatively-charged phosphate group) and two non-polar hydrophobic "tails" (the fatty acid chains). This mixture of properties is fundamental to biology, for phospholipids are the main components of cell membranes. ILYCEROL When mixed with water, phospholipids form droplet spheres with the hydrophilic heads facing the water and the hydrophobic tails facing each other. This is called a micelle, Alternatively, they may form a double-layered phospholipid bilayer. This traps a compartment of water in the middle separated from the external water by the hydrophobic sphere. This naturally-occurring structure is called a liposome, and is similar to a membrane surrounding a cell. hitps:oninefiphimis convhexgarknbtitp=1 zanesites, 1112 PM ‘CAPE Biology Unit 1 Study Notes FATTY ACIDCHAINS hpi) Bilayer Waxes Waxes are formed from fatty acids and long-chain alcohols. They are commonly found wherever waterproofing is needed, such as in leaf cuticles, insect exoskeletons, birds' feathers and mammals’ fur. Steroids Steroids are small hydrophobic molecules found mainly in animals. They include: cholesterol, which is found in animals cell membranes to increase stiffness + bile salts, which help to emulsify dietary fats + steroid hormones such as testosterone, oestrogen, progesterone and cortisol * vitamin D, which aids Ca®* uptake by bones. Terpenes Terpenes are small hydrophobic molecules found mainly in plants. They include vitamin A, carotene and plant oils such as geraniol, camphor and menthol, 23 hps:fontine.iphiri.comMhexgarknttip=t aanersites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Biochemical Tests These five tests identify the main biologically important chemical compounds. For each test take a small amount of the substance to test, and shake it in water in a test tube. If the ‘sample is a piece of food, then grind it with some water in a pestle and mortar to break up the cells and release the cell contents. Many of these compounds are insoluble, but the tests work just as well on a fine suspension. + Starch (iodine test). To approximately 2 cm® of test solution add two drops of iodine/potassium iodide solution. A blue-black colour indicates the presence of starch as a starch-polyiodide complex is formed. Starch is only slightly soluble in water, but the test works well ina suspension or as a solid. * Reducing Sugars (Benedict's test). All monosaccharides and most disaccharides (except sucrose) will reduce copper (I) sulphate, producing a precipitate of copper (|) oxide on heating, so they are called reducing sugars. Benedict's reagent is an aqueous solution of copper (II) sulphate, sodium carbonate and sodium citrate. To approximately 2 cm* of test solution add an equal quantity of Benedict's reagent. Shake, and heat for a few minutes at 95°C in a water bath. A precipitate indicates reducing sugar. The colour and density of the precipitate gives an indication of the amount of reducing sugar present, so this test is semi-quantitative. The original pale blue colour means no reducing sugar, a green precipitate means relatively little sugar; a brown or red precipitate means progressively more sugar is present. + Non-reducing Sugars (Benedict's test). Sucrose is called a non-reducing sugar because it does not reduce copper sulphate, so there is no direct test for sucrose. However, if it is first hydrolysed (broken down) to its constituent monosaccharides (glucose and fructose), it will then give a positive Benedict's test. So sucrose is the only sugar that will give a negative Benedict's test before hydrolysis and a positive test afterwards. First test a sample for reducing sugars, to see if there are any present before hydrolysis. Then, using a separate sample, boil the test solution with dilute hydrochloric acid for a few minutes to hydrolyse the glycosidic bond. Neutralise the solution by gently adding small amounts of solid sodium hydrogen carbonate until it stops fizzing, then test as before for reducing sugars. + Lipids (emulsion test). Lipids do not dissolve in water, but do dissolve in ethanol. This characteristic is used in the emulsion test. Do not start by dissolving the sample in water, but instead shake some of the test sample with about 4 om? of ethanol. Decant the liquid into a test tube of water, leaving any undissolved substances behind. If there are lipids dissolved in the ethanol, they will precipitate in the water, forming a cloudy white emulsion. The test can be improved by adding the dye Sudan Ill, which stains lipids red 24 hitps:oninefiphimis convhexgarknbtitp=1 2ainetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Protein (biuret test). To about 2 cm? of test solution add an equal volume of biuret solution, down the side of the test tube. A blue ring forms at the surface of the solution, which disappears on shaking, and the solution tums lilac-purple, indicating protein. The colour is due to a complex between nitrogen atoms in the peptide chain and Cu2* ions, S0 this is really a test for peptide bonds Practice questions Multiple-Choice Questions 1) 2) 3) 4) For this pair of items, choose the option that best describes their relationship. (i) The number of alpha glucose 1-4 linkages in cellulose (ii) The number of alpha glucose 1-4 linkages in starch A) Item (A) is greater than item (B). B) Item (A) is less than item (8). C) Item (A) is exactly or very approximately equal to item (B). D) Item (A) may stand in more than one of the above relations to item (B). For this pair of items, choose the option that best describes their relationship. (i) The probability of finding chitin in fungal cell walls (ii) The probability of finding chitin in arthropod exoskeletons AA) Item (A) is greater than item (B). B) Item (A) is less than item (B). C) Item (A) is exactly or very approximately equal to item (B). D) Item (A) may stand in more than one of the above relations to item (B). For this pair of items, choose the option that best describes their relationship. (i) The number of cis double bonds in saturated fatty acids (ii) The number of cis double bonds in unsaturated fatty acids A) Item (A) is greater than item (B). B) Item (A) is less than item (B). C) Item (A) is exactly or very approximately equal to item (B) D) Item (A) may stand in more than one of the above relations to item (B). For this pair of items, choose the option that best describes their relationship. (i) The probability that amino acids with nonpolar side chains are hydrophobic. (ii) The probability that amino acids with side chains containing a carboxyl group are hydrophobic. AA) Item (A) is greater than item (B). _B) Item (A) is less than item (B). C) Item (A) is exactly or very approximately equal to item (B). D) Item (A) may stand in more than one of the above relations to item (B). 25 hitps:oninefiphimis convhexgarknbtitp=1 2snetsites, 1112 PM 5) 6) i) 8) 9) 10) 11) 12) ‘CAPE Biology Unit 1 Stuay Notes Which of the following is not a polymer? A) glucose B) starch C) cellulose D) chitin What is the chemical mechanism by which cells make polymers from monomers? A) phosphodiester linkages B) hydrolysis C) dehydration reactions D) ionic bonding of monomers E) the formation of disulfide bridges between monomers Which of the following polymers contain nitrogen? A) starch B) glycogen C) cellulose D) chitin What is a triacylglycerol? A) a protein with tertiary structure B) a lipid made with three fatty acids and glycerol C)a lipid that makes up much of the plasma membrane D) a molecule formed from three alcohols by dehydration reactions The tertiary structure of a protein is the A) bonding together of several polypeptide chains by weak bonds. B) order in which amino acids are joined in a polypeptide chain. C) unique three-dimensional shape of the fully folded polypeptide. D) organization of a polypeptide chain into an a helix or B pleated sheet. Altering which of the following levels of structural organization could change the function of a protein? ‘A) secondary B)tertiary C) quaternary D) all of the above Avocados are fruit that contain large amounts of lipid (i) Describe how you would use a biochemical test to show that an avocado contains lipid. (2 marks) (ii) Describe how a phospholipid molecule is different from a triglyceride molecule. (1 mark) The diagram shows part of a cellulose molecule. hitps:oninefiphimis convhexgarknbtitp=1 zenersites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes (i) What type of bond is bond X?.(1 mark) (ii) Cellulose is found in plant cell walls. Bond X has an important role in the function of cellulose. Explain this role.(2 marks) Magnification and Resolution Magnification of the microscope is how much bigger a sample appears to be under the microscope than itis in real life. Overall magnification = Objective lens x Eyepiece lens (note magnification of a diagram is size of diagramisize of specimen) Resolution is the ability to distinguish between two points on an image. The resolution of an image is limited by the wavelength of radiation used to view the sample. This is because when objects in the specimen are much smaller than the wavelength of the radiation being used, they do not interrupt the waves, and so are not detected. The wavelength of light (min. ~ violet is 400m) is much larger than the wavelength of electrons, so the resolution of the light microscope is a lot lower. The actual resolution is often half the size of the wavelength of radiation used. Thus, for the light microscope the maximum resolution is about 200nm. In other words, if two objects in the specimen are closer than 200nm in real life, then they will only show up as one object on the image. Using a microscope with a more powerful magnification will not increase this resolution any further. It will increase the size of the image, but objects closer than 200nm will still only be seen as one point. LIGHT MICROSCOPE ELECTRON MICROSCOPE Resolution 200nm. Resolution 0.2 nm Cheap to operate. [Expensive to produce electron beam. [Small and portable. Large and requires special rooms. [Simple and easy sample preparation. _|Lengthy and complex sample prep. Material rarely distorted by preparation. _ [Preparation distorts material. [vacuums notreauied. —____|Vacuur required Natural colour of sample maintained. [All images in black and white. Magnifies objects only up to 2000 times _|Magnifies over 500 000 times ar hitps:oninefiphimis convhexgarknbtitp=1 ametsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Practice Questions 1. Explain the difference between magnification and resolving power (resolution) with respect to microscopy? 6 2. — Suggest an explanation for the Specimens having to be viewed in a vacuum in an electron microscope.2 3. The diagram shows a drawing of a mammalian cell (a) What is the actual diameter of the cell? 2 (b) What is the magnification? 2 Tom 28 hitps:oninefiphimis convhexgarknbtitp=1 zanesites, 1112 PM ‘CAPE Biology Unit 1 Study Notes 2. Cellular Ultrastructure All living things are made of cells, and cells are the smallest units that can be alive. Life on Earth is classified into five kingdoms, and they each have their own characteristic kind of cell However the biggest division is between the cells of the prokaryote kingdom (the bacteria) and those of the other four kingdoms (animals, plants, fungi and protoctista), which are all ‘eukaryotic cells. Prokaryotic cells are smaller and simpler than eukaryotic cells, and do not have a nucleus. Prokaryote = “before carrier bag" ie. without a nucleus Eukaryote= “good carrier bag" ‘ie. with a nucleus Eukaryotic Cells. cell wall cell membrane Golgi vesicles Golgi ribosome apparatus smooth ER chloroplast (no ribosomes) vacuole nucleolus —] membrane nucleus rough ER (endoplasmic. raphide reticulum) crystal druse large central crystal vacuole amyloplast mitochondrion {starch grain) cytoplasm © em. armatrong 2001 Plant cell 29 hps:fontine.iphiri.comMhexgarknttip=t zanersites, 1112 PM ‘CAPE Biology Unit 1 Study Notes pinocytotic vesicle mitochondrion lysosome Golgi ae apparatus nucleolus rough ER (endoplasmic reticular) nucleus smooth ER (no ribosomes) centrioles (2) Each composed of 9 microtubule triplets. microtubules cell (plasma ell (plasma) __sp\ cytoplasm ribosome ©EM Armstrong 2001 Animal cell sCytoplasm (or Cytosol). This is the solution within the cell membrane. It contains enzymes for glycolysis (part of respiration) and other metabolic reactions together with sugars, salts, amino acids, nucleotides and everything else needed for the cell to function. sNucleus. This is the largest organelle. Surrounded by a nuclear envelope, which is a double membrane with nuclear pores - large holes containing proteins that control the exit of substances such as RNA and ribosomes from the nucleus. The interior is called the nucleoplasm, which is full of chromatin- a DNA/protein complex in a 1:2 ratio containing the genes. During cell division the chromatin becomes condensed into discrete observable chromosomes. The nucleolus is a dark region of chromatin, involved in making ribosomes. hps:fontine.iphiri.comMhexgarknttip=t sonstsites, 1112 PM ‘CAPE Biology Unit 1 Study Notes ‘Mitochondrion (pl. Mitochondria). This is a sausage-shaped organelle (Sum long), and is where aerobic respiration takes place in all cummin eukaryotic cells. Mitochondria are surrounded Sn by a double membrane: the outer membrane sare is simple and quite permeable, while the inner membrane is highly folded into cristae, which give it a large surface area. The space enclosed by the inner membrane is called the mitochondrial matrix, andcontains small circular strands of DNA. The inner membrane is studded with stalked particles, which are the site of ATP synthesis ‘Chloroplast. Bigger and fatter than mitochondria, chloroplasts. are where photosynthesis takes place, so are only found in photosynthetic organisms (plants and algae). Like mitochondria they are enclosed by a double membrane, but chloroplasts also have a third membrane called the thylakoid membrane. The thylakoid membrane is folded into thylakoid disks, which are then stacked into piles called grana. The space between the inner membrane and the thylakoid is called the stroma. The thylakoid membrane contains chlorophyll and other photosynthetic pigments arranged in photosystems, together with stalked particles, and is the site of photosynthesis and ATP synthesis. Chloroplasts also contain starch grains, ribosomes and circular DNA. *Rough Endoplasmic Reticulum (RER). Similar to the SER, but studded with numerous ribosomes, which give it its rough appearance. The ribosomes synthesise proteins, which are processed in the RER (e.g. by enzymatically modifying the polypeptide chain, or adding carbohydrates), before being exported from the cell via the Golgi Body. *Golgi Body (or Golgi Apparatus). Another series of flattened membrane vesicles, formed from the endoplasmic reticulum. Its job is to transport proteins from the RER to the cell membrane for export. Parts of the RER containing proteins fuse with one side of the Golgi body membranes, while at the other side small vesicles bud off and move towards the cell membrane, where they fuse, releasing their contents by exocytosis, *Vacuoles. These are membrane-bound sacs containing water or dilute solutions of salts and other solutes. Most cells can have small vacuoles that are formed as required, but plant 31 hps:fontine.iphiri.comMhexgarknttip=t aunetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes cells usually have one very large permanent vacuole that fills most of the cell, so that the cytoplasm (and everything else) forms a thin layer round the outside. Plant cell vacuoles are filed with cell sap, and are very important in keeping the cell rigid, or turgid. Some unicellular protoctists have feeding vacuoles for digesting food, or contractile vacuoles for expelling water. +Ribosomes. These are the smallest and most numerous of the cell organelles, and are the sites of protein synthesis. They are composed of protein and RNA, and are manufactured in the nucleolus of the nucleus. Ribosomes are either found free in the cytoplasm, where they make proteins for the cell's own use, or they are found attached to the rough endoplasmic reticulum, where they make proteins for export from the cell. They are often found in groups called polysomes. All eukaryotic ribosomes are of the larger, "80S", type. “Smooth Endoplasmic Reticulum (SER). Series of membrane channels involved in synthesising and transporting materials, mainly lipids, needed by the cell. sLysosomes. These are small membrane-bound vesicles formed from the RER containing a cocktail of digestive enzymes. They are used to break down unwanted chemicals, toxins, organelles or even whole cells, so that the materials may be recycled. They can also fuse with a feeding vacuole to digest its contents. *Cytoskeleton. This is a network of protein fibre s extending throughout all eukaryotic cells, used for support, transport and motility. The cytoskeleton is attached to the cell membrane and gives the ceil its shape, as well as holding all the organelles in position. There are three types of protein fibres (microfilaments, intermediate filaments and microtubules), and each has a corresponding motor protein that can move along the fibre carrying a cargo such as. organelles, chromosomes or other cytoskeleton fibres. These motor proteins are responsible for such actions as: chromosome movement in mitosis, cytoplasm cleavage in cell division, cytoplasmic streaming in plant cells, cilia and flagella movements, cell crawling and even muscle contraction in animals. *Undulipodium (Cilium and Flagellum). This is a long flexible tail present in some cells and used for motility. Itis an extension of the cytoplasm, surrounded by the cell membrane, and is full of microtubules and motor proteins so is capable of complex swimming movements There are two kinds: flagella (no relation of the bacterial flagellum) are longer than the cell, and there are usually only one or two of them, while cilia are identical in structure, but are much smaller and there are usually very many of them. ‘Microvilli. These are small finger-like extensions of the cell membrane found in certain cells ‘such as in the epithelial cells of the intestine and kidney, where they increase the surface 32 hitps:oninefiphimis convhexgarknbtitp=1 sanetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes area for absorption of materials. They are just visible under the light microscope as a brush border. Cell Membrane (or Plasma Membrane). This is a thin, flexible layer round the outside of all cells made of phospholipids and proteins. It separates the contents of the cell from the outside environment, and controls the entry and exit of materials. The membrane is examined in detail later. *Cell Wall. This is a thick layer outside the cell membrane used to give a cell strength and rigidity. Cell walls consist of a network of fibres, which give strength but are freely permeable to solutes (unlike membranes). A wickerwork basket is a good analogy. Plant cell walls are made mainly of cellulose, but can also contain hemicellulose, pectin, lignin and other polysaccharides. They are built up in three layers called the primary cell wall, the secondary cell wall and the middle lamella. There are often channels through plant cell walls called plasmodesmata, which link the cytoplasms of adjacent cells. Fungal cell walls are made of chitin (poly-glucosamine). Animal cells do not have a cell wall, though they do have a layer of carbohydrate outside the cell membrane called the cell coat, or glycocalyx Prokaryotic Cells + Cytoplasm. Contains all the enzymes needed for all metabolic reactions, since there are no organelles + Ribosomes. The smaller (70 S) type. 2 + Nucleoid (or Nuclear Zone). The region of the tcleod cytoplasm that contains DNA. It is not surrounded x — by a nuclear membrane. TH Pree + DNA. Always circular, and not associated with any all wal proteins to form chromatin. ‘ll membrane + Plasmid. Small circles of DNA, used to exchange DNA between bacterial cells, and very useful for genetic engineering. + Cell_membrane. made of phospholipids and proteins, like eukaryotic membranes. + Mesosome. A tightly-folded region of the cell membrane containing all the membrane-bound proteins required for respiration and photosynthesis. Can also be associated with the nucleoia, pillus Mlagella Z 33 hitps:oninefiphimis convhexgarknbtitp=1 sanesites, 1112 PM ‘CAPE Biology Unit 1 Study Notes Cell Wall. Made of murein (not cellulose), which is a glycoprotein (ie. a protein/carbohydrate complex, also called peptidoglycan). There are two kinds of cell wall, which can be distinguished by a Gram stain: Gram positive bacteria have a thick cell wall and stain purple, while Gram negative bacteria have a thin cell wall with an outer lipid layer and stain pink. Capsule (or Slime Layer). A thick polysaccharide layer outside of the cell wall, like the glycocalyx of eukaryotes. Used for sticking cells together, as a food reserve, as protection against desiccation and chemicals, and as protection against phagocytosis. Flagellum. A rigid rotating helical-shaped tail used for propulsion. The motor is ‘embedded in the cell membrane and is driven by a H+ gradient across the membrane. Clockwise rotation drives the cell forwards, while anticlockwise rotation causes a chaotic spin. This is the only known example of a rotating motor in nature. Summary of the Differences between Prokaryotic and Eukaryotic Cells Prokaryotic Celis Eukaryotic cells ‘small cells (< 5 mm) larger cells (> 10 mm) ‘always unicellular often multicellular no nucleus or any membrane-bound organelles, such as mitochondria always have nucleus and other membrane- bound organelles DNA is circular, without proteins DNA is linear and associated with proteins to form chromatin ribosomes are small (70S) ribosomes are large (80S) no cytoskeleton always has a cytoskeleton motility by rigid rotating flagellum made of fiagellin motility by flexible waving undulipodium, made of tubulin cell division is by binary fission cell division is by mitosis or meiosis reproduction is always asexual reproduction is asexual or sexual huge variety of metabolic pathways ‘common metabolic pathways hps:fontine.iphiri.comMhexgarknttip=t aanetsites, 1112 PM Endosymbiosis Prokaryotic cells are far older and more diverse than eukaryotic cells. Prokaryotic cells have probably been around for 3.5 billion years, while eukaryotic cells arose only about 1 billion years ago. It is thought that eukaryotic cell organelles like nuclei, mitochondria and chloroplasts are derived from prokaryotic cells that became incorporated inside larger prokaryotic cells. This idea is called endosymbiosis, and is supported by these observations: ‘organelles contain circular DNA, like bacteria cells. scontain 70S ribosomes, like bacteria cells. ‘organelles have double membranes, as though a ‘CAPE Biology Unit 1 Study Notes -Q-P Large bacterium will engulf and digest smaller bacteria via a food vacuole and lysosomes ‘fa mutation allows the small bacteria inside the larger host bacteria If the smaller bacteri it may produce more ATP than itcan use be engulfed but not digestd it ms a effecent producer of ATP _slucose could be absorbed from the host and used to make ATP andthe excess used by the host, _;: a AadditionalATP gives host ell an adv reproduces more often via binary fatcesndsaceprotonochoodra also beefs alo reproduces wore ole ad passes the new host cells single-membrane cell had been engulfed and surrounded by a larger cell. organelles reproduce by binary fission, like bacteria. organelles are very like some bacteria that are alive today. Organization of cells 1. Tissue: A group of similar cells united to perform a specific function. A part of an organism consisting of an aggregate of cells having a similar structure and function. the mammalian skin is a good example of a tissue ,all skin cells are of the same type performing a similar function in this case protection of internal structures. 2. — Organ: A natural part or structure in an animal or a plant, capable of performing some special action (termed its function), which is essential to the life or well-being of the hps:fontine.iphiri.comMhexgarknttip=t 36 asnersites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes whole; as, the heart, lungs, etc, are organs of animals; the root, stem, foliage, etc, are organs of plants. In animals the organs are generally made up of several tissues, one of which usually predominates, and determines the principal function of the organ. Groups of organs. constitute systems. The stem of a dicot can be considered to be an organ since the xylem and phloem tissues form the transport network within the stem and epidermal tissue prevents loss of the transported substances Practice questions 4 To enter or leave a cell, substances must pass through a. a microtubule. b. the Golgi apparatus. c. a ribosome. d. the plasma membrane, You would expect a celll with an extensive Golgi apparatus to a, make a lot of ATP. b. secrete a lot of material. c. move actively. d. perform photosynthesis, Which of the following correctly matches an organelle with its function? a. mitochondrion . . . photosynthesis b. nucleus .... cellular respiration . central vacuole . . . storage d. ribosome . . . manufacture of lipids Of the following organelles, which group is involved in manufacturing substances needed by the cell? a. lysosome, vacuole, ribosome. ribosome, rough ER, smooth ER ©. vacuole, rough ER, smooth ER d. smooth ER, ribosome, vacuole A researcher made an interesting observation about a protein made by the rough ER and eventually used to build a cell's plasma membrane. The protein in the membrane was actually slightly different from the protein made in the ER. The protein was probably changed in the a. Golgi apparatus. b. smooth ER. c. mitochondrion. d. nucleus. The electron microscope has been particularly useful in studying bacteria, because a. electrons can penetrate tough bacterial cell walls. b. bacteria are so small. c. with few organelles present, bacteria are distinguished by differences in individual macromolecules. _d, their organelles are small and tightly packed together hitps:oninefiphimis convhexgarknbtitp=1 sanesites, 1112 PM 10. "1 12. 13. 14, 15. 16. 17. 18. 19, 20. ‘CAPE Biology Unit 1 Stuay Notes Which of the following clues would tell you whether a cell is prokaryotic or eukaryotic? a. the presence or absence of a rigid cell wall b. whether or not the cell is partitioned by internal membranes c. the presence or absence of ribosomes d. whether or not the cell carries out cellular metabolism Sara would like to film the movement of chromosomes during cell division. Her best choice for a microscope would be a a. light microscope, because of its resolving power. b. transmission electron microscope, because of its magnifying power. _c. scanning electron microscope, because the specimen is alive. d. light microscope, because the specimen is alive. A plant cell was grown in a test tube containing radioactive nucleotides, the parts from which DNA is built. Later examination of the cell showed the radioactivity to be concentrated in the a. rough ER. b. peroxisome. c. smooth ER. d. nucleus The bacterial cell surface structure is formed of : a.cell wall b.capsule c.cytoplasmic membrane d.all of the above What are the differences between prokaryotic and eukaryotic cells? Describe the structure and function of the nucleus and its components. Describe differences between rough and smooth endoplasmic reticulum. What are lysosomes and how do they function for the cell or body? Explain how they function in a tadpole losing its tal List the components involved in the production of a protein and explain the relationships of the components. Describe the types of vacuoles present and explain how their functions differ. Explain the role of peroxiosomes. Describe the structure of a ribosome and explain why prokaryotic cells also have them. Explain why there is a double membrane structure and the inner membrane is highly folded in both the mitochondria and chloroplast. Give the relationship between these 2 organelles. Include which types of cells contain them, Explain the meaning of the term tissue. 37 hitps:oninefiphimis convhexgarknbtitp=1 ametsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes 4 Cell membrane and transport ‘Channel protein Phospholipid —— Cholesterol Intergral protein x ) -Glycolipid Receptor protein N—_————. Giycoprotein Carbohydrate Peripheral protein Carrier protein Carrier protein The Structure of the Cell Membrane Structure The cell surface membrane is approximately 7.5nm thick and consists of a bilayer of lipids along with a highly variable component of protein. Some of these proteins are embedded in the surface of the membrane whilst others (intrinsic proteins) span the entire width of the membrane. This is known as the fluid mosaic model Lipids ‘There are three types of lipid in the cell surface membrane. 1. Phospholipids - which make up 75% of the lipid. Phospholipids are amphipathic molecules - this means that they have a dual nature in that one end of the phospholipids (the phosphate group) is hydrophilic (water-loving and polar) whilst the other end of the phospholipid (the fatty acid chains) is hydrophobic and non-polar. The phospholipid bilayer forms spontaneously with the non-polar fatty acid chains facing inwards towards each other and the polar phosphate groups facing outwards into the extra-cellular fluid and the inside of the cell (both of which are water-based environments). The interaction between the hydrophobic. and hydrophilic ends helps give the membrane stability and it is also these lipids which give the membrane selective permeability. Lipid soluble (hydrophobic) molecules easily pass hitps:oninefiphimis convhexgarknbtitp=1 sanesites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes through the membrane by diffusion whilst hydrophilic substances cannot diffuse through; instead they cross the membrane via water-filled pores or channels in intrinsic proteins. 2. Glycolipids - which make up 5% of membrane lipids. Glycolipids occur on the external surface of the cell surface membrane and the carbohydrate portion of the glycolipid extends into the intercellular space and is called a glycocalyx. These are important in cell-to-cell recognition. 3. Cholesterol - a steroid which makes up 20% of lipids in animal membranes but is rarely found in plant cell membranes. All lipids can move sideways (laterally) within the membrane and exchange position with each other. This gives the membrane fluidity which is essential in processes such as phagocytosis. The degree of fluidity of cell surface membranes is determined by: 1. The length of the fatty acid side chains (the longer the chains, the lower the fluidity). 2. The proportion of the fatty acids which are saturated (the higher the percentage of saturated fats, the lower the fluidity), 3. The steroid content (the higher the steroid content, the lower the fluidity). Proteins Intrinsic proteins - those which span the entire membrane - are usually glycoproteins. They have four main functions: 1, Toactas channels. By maintaining very different concentrations of ions on either side of the membrane, the cell surface membrane maintains an electrochemical gradient between the inside and outside of the cell which is essential for the efficient functioning of, for example, the sodium/potassium pump. 2. Transporters. For example, some proteins are able to identify and attach to specific substances such as nutrients, neurotransmitters or hormones. 3. Receptors. Some proteins recognise and bind to target molecules such as hormones. For example, the surface membrane of cells in the collecting duct of the kidney recognise and respond to ADH 4, Enzymes. For example, ATPase. As in lipids, intrinsic proteins have a hydrophobic and hydrophilic region and the interaction between these regions confers stability on the membrane. Extrinsic proteins are embedded in, but do not span, the membrane and many have a carbohydrate portion (glycocalyx) which extends into the intercellular space. 39 hitps:oninefiphimis convhexgarknbtitp=1 ganetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Movement across Cell Membranes Cell membranes are a barrier to most substances, and this property allows materials to be concentrated inside cells, excluded from cells, or simply separated from the outside environment. This is compartmentalisation is essential for life, as it enables reactions to take place that would otherwise be impossible. Eukaryotic cells can also compartmentalise materials inside organelles. Obviously materials need to be able to enter and leave cells, and there are five main methods by which substances can move across a cell membrane: 1. Lipid Diffusion 2. Osmosis 3. Passive Transport 4. Active Transport 5. Vesicles 1. Lipid Diffusion (or Simple Diffusion) ‘A few substances can diffuse directly through the lipid bilayer part of the membrane. The only substances that can do this are lipid-soluble molecules such as steroids, or very small molecules, such as H2O, O2 and CO>. For these molecules the membrane is no barrier at all Since lipid diffusion is (obviously) a passive diffusion process, no energy is involved and substances can only move down their concentration gradient. Lipid diffusion cannot be controlled by the cell 2. Osmosis Osmosis is the diffusion of water across a membrane. It is in fact just normal lipid diffusion, but since water is so important and so abundant in cells (its concentration is about 50 M), the diffusion of water has its own name - osmosis. The contents of cells are essentially solutions of numerous different solutes, and the more concentrated the solution, the more solute molecules there are in a given volume, so the fewer water molecules there are. Water molecules can diffuse freely across a membrane, but always down their concentration gradient, so water therefore diffuses from a dilute to a concentrated solution. hitps:oninefiphimis convhexgarknbtitp=1 aonetsites, 1112 PM ‘CAPE Biology Unit 1 Study Notes Water Potential Water Potential, Osmosis can be quantified using water potential, so we can calculate which way water will move, and how fast. Water potential (Y, the Greek letter psi, pronounced "sy") is simply the effective concentration of water. It is measured in units of pressure (Pa, or usually kPa), and the rule is that water always “falls” from a high to a low water potential (in other words it's a bit like gravity potential or electrical potential). 100% pure water has Y =0, which is the highest possible water potential, so all solutions have <0, and you cannot get ? > 0 A solution of high water potential thas a high concentration of water and a low concentration of solute More molecules of water are in contact, ‘with the selectively permeable membrane in solution A this leads to More water molecules ‘crossing into solution B, therefore water moves from high water potential to lower water potential Osmotic Pressure (OP). Osmotic pressure is the pressure applied by a solution to prevent the inward flow of water across a semi permeable membrane the pressure is caused by the concentration of solvents in the solution. OP is in effect the opposite of water potential and solutions with high water potential have low osmotic pressures and vice versa. Cells and Osmosis. The concentration (or OP) of the solution that surrounds a cell will affect the state of the cell, due to osmosis. There are three possible concentrations of solution to consider: + [sotonic solution a solution of equal OP (or concentration) to a cell Hypertonic solution a solution of higher OP (or concentration) than a cell TT hps:fontine.iphiri.comMhexgarknttip=t austsites, 1112 PM 42 ‘CAPE Biology Unit 1 Stuay Notes Hypotonic solution a solution of lower OP (or concentration) than a cell Simple animal cells (protozoans) in fresh water habitats are surrounded by a hypotonic solution and constantly need to expel water using contractile vacuoles to prevent swelling and lysis. Cells in marine environments are surrounded by a hypertonic solution, and must actively pump ions into their cells to reduce their water potential and so reduce water loss by osmosis. Young non-woody plants rely on cell turgor for their support, and without enough water they wilt. Plants take up water through their root hair cells by osmosis, and must actively pump ions into their cells to keep them hypertonic compared to the soil This is particularly difficult for plants rooted in salt water. hitps:oninefiphimis convhexgarknbtitp=1 aanetsites, 1112 PM ‘CAPE Biology Unit 1 Study Notes Effect of tonicity on animal cells cal egiteane cell bursts due to 2 > ERS mm twekosi oll I volumes of water move in and out of thecell therefore cell has no net gain and neither shrinks nor swells. Effect of tonicity on plant cells ¢_j— e+ ))— a SS ~ ‘equal volumes of water move in and out of thecell therefore the cell has no net gain and neither shrinks nor swells 43 hps:fontine.iphiri.comMhexgarknttip=t agitetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Passive Transport (or Facilitated Diffusion) Passive transport is the transport of substances across a 1 membrane by a trans-membrane protein molecule. The transport Bea proteins tend to be specific for one molecule (a bit ike enzymes), so substances can only cross a membrane if it contains the : appropriate protein. As the name suggests, this is a passive diffusion process, so no energy is involved and substances can only move down their concentration gradient. There are two kinds of transport protein: = Channel Proteins form a water-filled pore or channel in the membrane. This allows charged substances (usually ions) to diffuse across membranes. Most channels can be gated (opened or closed), allowing the cell to control the entry and exit of ions. «Carrier Proteins have a binding site for a specific solute and constantly fip between two states so that the site is alternately open to opposite sides of the membrane. The substance will bind on the side where it at a high concentration and be released where itis at a low concentration. Active Transport (or Pumping). poopebledie nan be coe pedi Active transport is the pumping of substances across a membrane by a trans-membrane protein pump molecule. The protein binds a molecule of the substance to be transported on one side of the membrane, changes shape, and releases it on the other side. The proteins are highly specific, so there is a different protein pump for each molecule to be transported. The protein pumps are also ATPase enzymes, since they catalyse the splitting of ATP — ‘ADP + phosphate (Pi), and use the energy released to change shape and pump the molecule. Pumping is therefore an active process, and is the only transport mechanism that can transport substances up their concentration gradient. The Na*k* Pump. This transport protein is present in the cell membranes of all animal cells and is the most abundant and important of all membrane pumps. The Na*k* pump is a complex pump, simultaneously psec e/a \ a hitps:oninefiphimis convhexgarknbtitp=1 aanetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes pumping three sodium ions out of the cell and two potassium ions into the cell for each molecule of ATP split. This means that, apart from moving ions around, it also generates a potential difference across the cell membrane. This is called the membrane potential, and all animal cells have it. It varies from 20 to 200 mV, but and is always negative inside the cell. In most cells the Na*K* pump runs continuously and uses 30% of all the cell's energy (70% in nerve cells). The rate of diffusion of a substance across a membrane increases as its concentration gradient increases, but whereas lipid diffusion shows a linear relationship, facilitated diffusion has a curved relationship with a maximum rate. This is due to the rate being limited by the number of transport proteins. The rate of active transport also increases with concentration gradient, but most importantly it has a high rate even when there is no concentration difference across the membrane. Active transport stops if cellular respiration stops, since there is no energy. Vesicles The processes described so far only apply to small molecules. Large molecules (such as proteins, polysaccharides and nucleotides) and even whole cells are moved in and ut of cells by using membrane vesicles. Endocytosis is the transport of materials into a cell. Materials are enclosed by a fold of the cell membrane, which then pinches shut to form a closed vesicle. Strictly speaking the material has not yet crossed the membrane, so it is usually digested and the small product molecules are absorbed by the methods above. When the materials and the vesicles are small (such as a protein molecule) the process is known as pinooytosis (cell drinking), and if the materials are large (such as a white blood cell ingesting a bacterial cell) the process is known as phagocytosis (cell eating). Exocytosis is the transport of materials out of a cell. itis the exact reverse of endocytosis. Materials to be exported must first be enclosed in a membrane vesicle, usually from the RER and Golgi Body. Hormones and digestive enzymes are secreted by exocytosis from the secretory cells of the intestine and endocrine glands. Sometimes materials can pass straight through cells without ever making contact with the cytoplasm by being taken in by endocytosis at one end of a cell and passing out by exocytosis at the other end. 45 hitps:oninefiphimis convhexgarknbtitp=1 asnetsites, 1112 PM ‘CAPE Biology Unit 1 Study Notes ‘ll membrane andthe parof the mebrane in Coote with he oie ‘errs and ese tof the cal vesicle megs with te © Cellmenbraeivaginats to palin soi particle ‘The ivaginaton pinches oft form a esc iside the ell ‘esc formed by gol body ‘mov tote cell membrane Exocytosis, Endocytosis(phagocytosis) ‘The imagination inks of 0 Ferma wesc niet el Cell membranenvagites vopulinligds Endocytosis(pinocytosis ‘Summary of Membrane Transport Method Uses energy __| Uses proteins _| Specific Controllable Lipid Diffusion N N N N Osmosis N N Y N Passive N Y Y Y Transport Active Transport | Y Y y y Vesicles yY N y y 46 hps:fontine.iphiri.comMhexgarknttip=t asnetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Practice questions 1. Which of these is part of the cell membrane? a. triglycerides b. phospholipids c, ATP d. more than one of these 2. How do fat-soluble molecules normally get into a cell? a. they dissolve in the fat layers of the membrane and enter the cell by diffusion b. they pass through protein pores in the cell membrane ©. they are absorbed by phagocytosis _d. they never get in 3. The phospholipids are unusual molecules because: a. they have hydrophilic regions _b. they have hydrophobic regions «. they are triglycerides d. both A and B 4. Which of the following statements best describes the "fluid mosaic mode!" of the structure of the cell membrane? a. two layers of protein with lipid layers between the protein layers b. two layers of lipid with proteins between the lipid layers . a double layer of lipid molecules with protein molecules suspended in the layer d. A single layer of protein on the outside and a single layer of lipids on the inside 5. The movement of chloride ions from an area where chloride is concentrated to an area where chloride is less concentrated is which of these? a. diffusionb. active transport c. osmosis d. exocytosis 6. _Ifacell has a solute concentration of 0.07% which of the solutions would be hypotonic to the cell? a. 0.01% solute b. 0.1% solute c. 1% solute d. 10% solute 7. Which of the following is necessary in order for osmosis to occur? a. a permeable membrane b. a semi-permeable membrane ¢. an isotonic solution d. ATP 8. Which of these are passive transport mechanisms? a. osmosis b. diffusion c. phagocytosis d. both A and B 9. The sodium-potassium pump (which carries sodium out of a cell and potassium into a cell) is an example of: a. active transport b. endocytosis c. exocytosis d. passive transport 47 hitps:oninefiphimis convhexgarknbtitp=1 ametsites, 1112 PM 10. 1. 12. 13. ‘CAPE Biology Unit 1 Study Notes The process of a cell engulfing a solid object is: a. phagocytosis b. exocytosis c. pinocytosis d. diffusion Accel contains 3% salt and 97% water. How would the cell respond when placed into the following solutions? a. distilled water- __b. 10% salt solution Why are both passive and active transport processes important in cell membranes? Fig. 2.1 represents the structure of a plasma (cell surface) membrane. (2) () Name molecules A, B and F. In your answer you should spell the names of the molecules correctly. [3] (b) (i) Describe the structure of molecule A. [2] (ii) State one function of molecule C. [1] (©) Molecule D is a glycoprotein. This molecule consists of a protein embedded in the membrane with a branched carbohydrate chain projecting out from the surface of the cell. Outline three roles of glycoproteins in membranes. [3] hps:fontine.iphiri.comMhexgarknttip=t aartetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes 4. Enzymes Enzymes are biological catalysts. There are about 40,000 different enzymes in human cells, each controlling a different chemical reaction. They increase the rate of reactions by a factor of between 10° to 10'? times, allowing the chemical reactions that make life possible to take place at normal temperatures. They were discovered in fermenting yeast in 1900 by Buchner, and the name enzyme means “in yeast’. As well as catalysing all the metabolic reactions of cells (such as respiration, photosynthesis and digestion), they also act as motors, membrane pumps and receptors. Enzyme Structure Enzymes are proteins, and their function is determined by their complex structure. The reaction takes place in a small part of the enzyme called the active site, while the rest of the protein acts as “scaffolding”. This is shown in this diagram of a molecule of the enzyme amylase, with a short length of starch being digested in its active site. The amino acids around the active site attach to the substrate molecule and hold it in position while the reaction takes place. This makes the enzyme specific for one reaction only, as other molecules won't fit into the active site Many enzymes need cofactors (or coenzymes) to work properly. These can be metal ions (such as Fe®, Mg, Cu") or organic molecules (such as haem, biotin, FAD, NAD or coenzyme A). Many of these are derived from dietary vitamins, which is why they are so important. The complete active enzyme with its cofactor is called a holoenzyme, while just the protein part without its cofactor is called the apoenzyme. There are three ways of thinking about enzyme catalysis. They all describe the same process, though in different ways, and you should know about each of them. 1. Reaction Mechanism In any chemical reaction, a substrate (S) is converted into a product (P): SD P (There may be more than one cc "™™% substrate and more than one +3]—- fa— ts product, but that doesn't matter here.) In an enzyme-catalysed Enzyme Substrate Enzyme-Substrate Enzyme Product reaction, the substrate first comes binds to the active site of the enzyme to form an enzyme-substrate (ES) complex, then the substrate is converted into product while attached to the enzyme, and finally the product is released. This mechanism can be shown as: 49 hitps:oninefiphimis convhexgarknbtitp=1 aanetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes The enzyme is then free to start again. The end result is the same (SDP), but a different route is taken, so that the S DP reaction as such never takes place. In by-passing this step, the reaction can be made to happen much more quickly. 2. Molecule Geometry The substrate molecule fits into the active site of the ‘enzyme molecule like a key fitting into a lock (in fact it is sometimes called a lock and key mechanism). Once there, the enzyme changes shape slightly, distorting the molecule in the active site, and making it more likely to change into the product. For i final energy content of products example if a bond in the substrate is to be broken, that bond might be reaction progress stretched by the enzyme, making it more likely to break. Alternatively the enzyme can make the local conditions inside the active site quite different from those outside (such as pH, water concentration, charge), so that the reaction is more likely to happen. It's a bit more complicated than that though. Although enzymes can change the speed of a chemical reaction, they cannot change its direction, otherwise they could make “impossible” reactions happen and break the laws of thermodynamics. So an enzyme can just as easily tum a product into a substrate as turn a substrate into a product, depending on which way the reaction would go anyway. In fact the active site doesn't really fit the substrate (or the product) at all, but instead fits a sort of half-way house, called the transition state. When a substrate (or product) molecule binds, the active site changes shape and fits itself around the molecule, distorting it into forming the transition state, and so speeding up the reaction. This is sometimes called the induced fit mechanism. 3. _ Enzymes allow many chemical reactions to occur within the homeostasis constraints of alliving system. Enzymes funetion as organic catalysts. A catalyst is a chemical involved in, but not changed by, a chemical reaction. Many enzymes function by lowering the activation energy of reactions. By bringing the reactants closer together, chemical bonds may be weakened and reactions will proceed faster than without the catalyst. The use of enzymes hitps:oninefiphimis convhexgarknbtitp=1 sonesites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes ‘can lower the activation energy of a reaction (E).Enzymes can act rapidly, as in the case of carbonic anhydrase (enzymes Enzymes typically end in the -ase suffix), which causes the chemicals to react 107 times faster than without the enzyme present. Carbonic anhydrase speeds up the transfer of carbon dioxide from cells to the blood. There are over 2000 known enzymes, each of which is involved with one specific chemical reaction. Enzymes are substrate specific. The enzyme peptidase (which breaks peptide bonds in proteins) will not work on starch (which is broken down by human-produced amylase in the mouth). For ‘example, for the catalase reaction (2H,02 —» 2H,0 + O2) the activation energy is 86 kJ mol" with no catalyst, 62 kJ mol" with an inorganic catalyst of iron filings, and just 1 kJ mol" in the presence of the enzyme catalase. The activation energy is actually the energy required to form the transition state, so enzymes lower the activation energy by stabilising the transition state, and they do this by changing the conditions within the active site of the enzyme. So the three ideas above are really three ways of describing the same process. Factors that Affect the Rate of Enzyme Reactions 1. Temperature Ontinen emp Enzymes have an optimum temperature at which they work fastest. For mammalian enzymes this is about 40°C, but there are enzymes that work best at very different temperatures, e.g. enzymes from the arctic snow flea work at -10°C, and enzymes from thermophilic bacteria work at 90°C. Enzyme activity Up to the optimum temperature the rate increases geometrically with temperature (i.e. it's a curve, not a SS straight line). The rate increases because the enzyme and Tempers substrate molecules both have more kinetic energy so collide more often, and also because more molecules have sufficient energy to overcome the (greatly reduced) activation energy. The increase in rate with temperature can be quantified as a Qro, which is the relative increase for a 10°C rise in temperature. Qro is usually 2-3 for enzyme-catalysed reactions (ie. the rate doubles every 10°C) and usually less than 2 for non-enzyme reactions. The rate is not zero at 0°C, so enzymes still work in the fridge (and food still goes off), but they work slowly. Enzymes can rate attemp (t +10)°C ‘even work in ice, though the rate is extremely slow due to | Qj) = ————~ —__— the very slow diffusion of enzyme and substrate molecules through the ice lattice. rate at temp °C 51 hitps:oninefiphimis convhexgarknbtitp=1 sitetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Above the optimum temperature the rate decreases as more and more of the enzyme molecules denature. The thermal energy breaks the hydrogen bonds holding the secondary and tertiary structure of the enzyme together, so the sencn enzyme (and especially the active site) loses its shape to ri become a random coil. The substrate can no longer bind, ana A and the reaction is no longer catalysed. At very high "™#* temperatures this is imeversible. Remember that only the weak hydrogen bonds are broken at these mild temperatures; to break strong covalent bonds you need to boil in concentrated acid for many hours. Tw 2° Ph Enzymes have an optimum pH at which they work fastest. For most enzymes this is about pH 7-8 (physiological pH of most cells), but a few enzymes can work at extreme pH, such as protease enzymes in animal stomachs, which have an optimum of pH 1. The pH affects the charge of the amino acids at the active site, so the properties of the active site change and the substrate can no longer bind. For example a carboxyl acid R groups will be uncharged a low pH (COOH), but charged at high pH (COO). 3. Enzyme concentration As the enzyme concentration increases the rate of the reaction increases linearly, because there are more enzyme molecules available to catalyse the reaction. At very high enzyme concentration the substrate concentration may become rate-limiting, so the rate stops increasing. Normally enzymes are present in cells in rather low concentrations. 4. Substrate concentration The rate of an enzyme-catalysed reaction shows a curved dependence on substrate concentration. As the 7 substrate concentration increases, the rate increases because more substrate molecules can collide with ima enzyme molecules, so more reactions will take place. "#4 At higher concentrations the enzyme molecules become saturated with substrate, so there are few free enzyme molecules, so adding more substrate doesn't . make much difference (though it will increase the rate ‘si cnn of E-S collisions). 52 hitps:oninefiphimis convhexgarknbtitp=1 sanetsites, 1112 PM ‘CAPE Biology Unit 1 Study Notes The maximum rate at infinite substrate concentration is called Vmax, and the substrate concentration that give a rate of half Vmax is called Kus. These quantities are useful for characterising an enzyme. A good enzyme has a high Vmax and a low Ku 5. Covalent modification The Serpe i activity of some enzymes is controlled by nme stating vaste ste other enzymes, which modify the protein ary? chain by cutting it, or adding a phosphate or methyl group. This modification can +>— » tum an inactive enzyme into an active enzyme (or vice versa), and this is used to control many metabolic enzymes and Ete to switch on enzymes in the gut (see later) e.g. hydrochloric acid in stomach® G-— Eat activates pepsin® activates rennin i 6. Inhibitors Inhibitors inhibit the activity of enzymes, reducing the rate of their reactions. They are found naturally, but are also used artificially as drugs, pesticides and research tools. There are two kinds of inhibitors. a) A competitive inhibitor Sinan molecule has a similar ‘"” structure to the normal shine aoe ES -@—-E= and it can fit into the il active site of the al enzyme. It therefore competes with the € = G Gp me substrate for the active site, so the reaction is slower. Competitive inhibitors increase Ky for the enzyme, but have no effect on Vex, SO the rate can approach a normal rate if the substrate concentration is increased high enough. The sulphonamide anti-bacterial drugs are competitive inhibitors. Pros 53 hps:fontine.iphiri.comMhexgarknttip=t santsites, 1112 PM ‘CAPE Biology Unit 1 Study Notes b) A non-competitive inhibitor molecule is quite different in structure from the substrate molecule and does not fit into the active site. It binds to another part of the enzyme molecule, changing the shape of the whole enzyme, including the active site, so that it can no longer bind substrate molecules, Non- competitive inhibitors therefore simply reduce the amount of active enzyme (just ‘like decreasing the enzyme ts £ Nonconpestive ihibior concentration), so they decrease Vas, but have no effect on Ki weakly and can be washed out are sometimes called reversi that bind tightly and cannot be washed out are called imeversibl —“S-t: — ¢€ OB worries Active ie anges tape Inhibitors that bind fairly hibitors, while those cyanide, heavy metal ions and some insecticides are all non-competitive inhibitors. 7. Allosteric Effectors The activity of some ‘enzymes is controlled by certain molecules binding to a specific regulatory (or allosteric) site on the enzyme, distinct from the active site. Different molecules can inhibit or activate the enzyme, allowing sophisticated control of the rate. Only a few enzymes can do this, and they are often at the start of a long biochemical pathway. They are generally activated by the substrate of the pathway and inhibited by the product of the pathway, thus only tuming the pathway on when it is needed hps:fontine.iphiri.comMhexgarknttip=t eased atv se santsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Feedback Inhibition If the product of a series of enzymatic reactions, e.g., an amino acid, begins to accumulate within the cell, it may specifically inhibit the action of the first enzyme involved in its synthesis (red bar). Thus further production of the enzyme is halted. First committed step End RRR ian Practice questions 1. An enzyme is generally named by adding ___ to the end of the name of the a) "-ose". cell in which it is found — b) "-ase". cell in which it is found c) "ose". substrate d)"-ase". substrate e) "-ase". coenzyme 2. Which statement describes the currently accepted theory of how an enzyme and its substrate fit together? a) As the product is released, the enzyme breaks down. b) The enzyme is like a key that fits into the substrate, which is like a lock. c) The active site is permanently changed by its interaction with the substrate. d) As the substrate binds to the enzyme, the shape of the enzyme site changes to accommodate the reaction. 3. Which statement is Not true about the effects of various conditions on the activity of an enzyme? a) Higher temperatures generally increase the activity of an enzyme up to a point. b) Above a certain range of temperatures, the protein of an enzyme is denatured. ) A change in pH can cause an enzyme to be inactivated. d) An enzyme's activity is generally reduced by an increase in substrate concentration. 4, Which statement is Not true about enzyme inhibition? a) In competitive inhibition, the inhibitor binds to the active site of the enzyme. b) In noncompetitive inhibition, the inhibitor binds to the allosteric site of the substrate. c) Most inhibitors act in a reversible fashion. d) All of the above statements are true. 55 hitps:oninefiphimis convhexgarknbtitp=1 ssnatsites, 1112 PM 10. ‘CAPE Biology Unit 1 Stuay Notes The active site of an enzyme a) is similar to that of any other enzyme. b) is the part of the enzyme where its substrate can fit. ) can be used over and over again. d) Both B and C are correct. An allosteric site on an enzyme is a) the same as the active site. b) where ATP attaches and gives up its energy. c) often involved in feedback inhibition. d) All of these are correct. A student conducts an experiment to test the efficiency of a certain enzyme. Which would probably not result in a change in the enzyme's efficiency? a) Bringing the temperature of the experimental setup from 20 degrees C to 50 degrees C. b) Adding an acidic solution to the setup. _c) Adding more substrate but not enzyme. d) Placing the substrate and enzyme in a container with double the capacity. Which of the following statements about enzymes is Not True? a) Competitive inhibitors act away from the active site. b) Allosteric inhibitors act away from the active site. c) Competitive inhibitors usually resemble the substrate. d) Noncompetitive inhibitors are allosteric inhibitors. In noncompetitive inhibition, the allosteric inhibitor a) attaches to the active site, preventing the substrate from attaching there. b) attaches to the substrate, preventing it from attaching to the active site c) changes the pH of the environment, thus preventing enzyme-substrate complex formation. 4d) attaches to the enzyme at a site away from the active site, altering the shape of the enzyme. Which of the following statements is Not True about all enzymes? a)are proteins. _b) lower the activation energy of reactions. c) operate at the same optimum pH. 4) can be identified because their names end in - ase. hitps:oninefiphimis convhexgarknbtitp=1 sonstsites, 1112 PM ‘CAPE Biology Unit 1 Study Notes 11. Lysozyme is an enzyme found in many places within the human body. It consists of a single polypeptide folded into a complex shape. Fig. 3.1 shows a ribbon model of lysozyme, (a) With reference to Fig. 3.1, state the name given to the level of organisation shown, (i) by the whole polypeptide [1] (ii) at region X.. [1] (b) Name the part of the enzyme where the reaction occurs... [1] 87 hps:fontine.iphiri.comMhexgarknttip=t srnetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes 5. Structure and function of Nucleic Acids DNA DNA and its close relative RNA are perhaps the most important molecules in biology. They contains the instructions that make every single living organism on the planet, and yet it is only in the past 50 years that we have begun to understand them. DNA stands for deoxyribonucleic acid and RNA for ribonucleic acid, and they are called nucleic acids because they are weak acids, first found in the nuclei of cells. They are polymers, composed of monomers called nucleotides. Nucleotides Nucleotides have three parts to them * a phosphate aroup(PO?), which is negatively mossgponenate charged, and gives nucleic acids their acidic rr 1 properties. onosprote—€ * a pentose sugar, which has 5 carbon atoms in it. By uae convention the carbon atoms are numbered as shown to distinguish them from the carbon atoms in the base. If carbon 2 has a hydroxyl group attached (as shown), Pnesoroaigaty_ then the sugar is ribose, found in RNA. If the carbon 2 just has a hydrogen atom attached instead, then the sugar is deoxyribose, found in DNA * a nitrogenous base. There are five different bases (and you don't need to know their structures), but they all contain the elements carbon, hydrogen, oxygen and nitrogen. The bases are usually known by there first letters only, so you don't need to lear the full names. The base thymine is found in DNA only and the base uracil is found in RNA only, so there are only four different bases present at a time in one nucleic acid molecule. Base: Adenine(A) Cytosine (C) Guanine (G)_Thymine (T) Uracil (U) hitps:oninefiphimis convhexgarknbtitp=1 sanesites, 1112 PM ‘CAPE Biology Unit 1 Study Notes The nitrogenous bases are of two kinds: 1. Purines: bases with a double ring structure. Eg: Adenine and Guanine 2. Pyrimidines: bases with a single ring structure. Eg: cytosine, uracil, thymine (PYCUT) Nucleotide Polymerisation ara Nucleotides polymerise by forming bonds between carbon 3 of the sugar and an oxygen atom of the phosphate. This is a condensation polymerisation reaction. The bases do not take part in the polymerisation, so there is a sugar-phosphate backbone with the bases extending off it. This means that the nucleotides can join together in any order along the chain, Many nucleotides form a polynucleotide. A polynucleotide has a free phosphate group at one end and a free OH group at the other end. Structure of DNA The three-dimensional structure of DNA was discovered in the 1950's by Watson and Crick. The main features of the structure are: * DNA is double-stranded, so there are two polynucleotide stands alongside each other. The strands are antiparallel, i.e. they run in opposite directions. * The two strands are wound round each other to form a double helix. ‘* The two strands are joined together by hydrogen bonds between the bases. The bases therefore form base pairs, which are like rungs of a ladder. * The base pairs are specific. A only binds to T (and T with A), and C only binds to G (and G with C). These are called complementary base pairs. This means that whatever the sequence of bases along one strand, the sequence of bases on the other strand must be complementary to it. (Incidentally, complementary, which means matching, is different from complimentary, which means being nice.) 59 hps:fontine.iphiri.comMhexgarknttip=t santsites, 1112 PM ‘CAPE Biology Unit 1 Study Notes Function of DNA DNA is the genetic material, and genes are made of DNA. DNA therefore has two essential functions: replication and expression. * Replication means that the DNA, with all its genes, must be copied every time a cell divides. * Expression means that the genes on DNA must control characteristics. A gene was traditionally defined as a factor that controls a particular characteristic (such as flower colour), but a much more precise definition is that a gene is a section of DNA that codes for a particular protein. Characteristics are controlled by genes through the proteins they code for, like this: a shape and sequences 4, sequence of siticn. ee oftbases STINE amino acids —Heterminesy function Arana chetecteistios in DNA in polypeptide - of cel (eg. enzyme) Expression can be split into two parts: transcription (making RNA) and translation (making proteins). These two functions are summarised in this diagram (called the central doama of genetics). No one knows exactly how many genes we humans have to control all our characteristics, the latest estimates are 60-80,000. The sum total of all the genes in an organism is called the genome. Amazingly, genes only seem to comprise about 2% of the DNA in a cell. The majority of the DNA does not form genes and doesn't seem to do anything. The purpose of this junk DNA remains a mystery! hps:fontine.iphiri.comMhexgarknttip=t conesites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes RNA RNA js a nucleic acid like DNA, but with 4 differences:;RNA has the sugar ribose instead of deoxyribose;RNA has the base uracil instead of thymine;RNA is usually single stranded;RNA is usually shorter than DNA Messenger RNA (mRNA) mRNA carries the "message" that codes for a particular protein from the nucleus (where the DNA master copy is) to the cytoplasm (where proteins are synthesised). It is single stranded and just long enough to contain one gene only. It has a short lifetime and is degraded soon after it is used. Ribosomal RNA (rRNA) FRNA, together with proteins, form ribosomes, which are the site of mRNA transtation and protein synthesis. Ribosomes have two subunits, small and large, and are assembled in the hucleolus of the nucleus and exported into the cytoplasm. Transfer RNA (tRNA) {RNA is an ‘adapter’ that matches amino acids to their codon = {RNA is only about 80 nucleotides long, and it folds up by complementary base pairing to form a looped clover-leaf structure. At one end of the molecule there is always the base sequence ‘ACC, where the amino acid binds. On the middle loop there is a triplet nucleotide sequence called the anticodon. There are 64 different tRNA molecules, each with a different anticodon sequence ‘complementary to the 64 different codons. The amino acids are attached to their tRNA molecule by specific enzymes. These are highly specific, so that each amino acid is attached to a tRNA siete adapter with the appropriate anticodon 61 hitps:oninefiphimis convhexgarknbtitp=1 eutetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes A DNA RNA Bases, Deoxyribonucleic aia Ribonucleic acid Image adapted from: National Human Genome Research Institute, 62 hitps:oninefiphimis convhexgarknbtitp=1 canstsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Differences between RNA and DNA DNA, BNA LA Drm Y Ky (ibnnclele acd} (ory ribomcae aid) ™ | oe recy! thymidine - ‘single doable DNA is a long polymer with a RNA is a polymer with a ribose and Bases & deoxyribose and phosphate backbone phosphate backbone and four Sugars: and ourdifferent bases: adenine, _ different bases: adenine, guanine, guanine, cytosine and thymine cytosine, and uracil 1.Found in nucleus and cytoplasm 2.sugar is ribose. 3. Bases are AU.CG The helix geometry of RNA is of A- Form. RNA strands are continually made, broken down and reused. RNA is more resistant to damage by Ultra- violet rays. 1.Found in nucleus 2. sugars deoxyribose 3. Bases are A,T,C,G The helix geometry of DNA is of B- Form. DNA is completely protected by Unique the body i.e. the body destroys Features: enzymes that cleave DNA. DNA can be damaged by exposure to Ultra-violet rays Deoxyribose sugar in DNAjs less Ribose sugar is more reactive reactive because of C-H bonds. Stable because of C-OH (hydroxy!) bonds. in alkaline conditions. DNA has smaller Not stable in alkaline conditions. RNA Difference: Stability: grooves where the damaging enzyme on the other hand has larger grooves can attach which makes it harder for which makes it easier to be attacked the enzyme to attack DNA. by enzymes. Pairing of | A-T(Adenine-Thymine), G-C(Guanine- A-U(Adenine-Uracil), G-C(Guanine- Bases: Cytosine) Cytosine) Predominant Typically a double- stranded molecule A single-stranded molecule in most of 63 hitps:oninefiphimis convhexgarknbtitp=1 canstsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes Structure: with along chain of nucleotides: its biological roles and has a shorter chain of nucleotides Stands for: Deoxyribo Nucleic Acid RiboNucleic Acid The main job of RNA is to transfer the genetic code need for the creation of Medium of long-term storage and _proteins from the nucleus to the transmission of genetic information _ ribosome. This process prevents the DNA from having to leave the nucleus, so it stays safe. Job/Role: ‘The sequence of bases on DNA codes for the sequence of amino acids in proteins. But there are 20 different amino acids and only 4 different bases, so the bases are read in groups of 3. This gives 4° or 64 combinations, more than enough to code for 20 amino acids. A group of three bases coding for an amino acid is called a codon, and the meaning of each of the 64 codons is called the genetic code. There are several interesting points from this code: * The code is degenerate, i.e. there is often more than one codon for an amino acid. The degeneracy is on the third base of the codon, which is therefore less important than the others, + One codon means "start" ie. the start of the gene sequence. It is AUG. + Three codons mean "stop" i.e. the end of the gene sequence. They do not code for amino acids. * The code is only read in one direction along the mRNA molecule. Replication - DNA Synthe: DNA is copied, or replicated, before every cell division, so that one identical copy can go to each daughter cell. The method of DNA replication is obvious from its structure: the double helix unzips and two new strands are built up by complementary base-pairing onto the two old strand. Replication starts at a specific sequence on the DNA molecule called the replication origin, 1. An enzyme unwinds and unzips DNA, breaking the hydrogen bonds that join the base pairs, and forming two separate strands. 2. The new DNA is built up from the four nucleotides (A, C, G and T) that are abundant in the nucleoplasm. 3. These nucleotides attach themselves to the bases on the old strands by complementary base pairing. Where there is a T base, only an A nucleotide will bind, and so on. hitps:oninefiphimis convhexgarknbtitp=1 anessites, 1112 PM ‘CAPE Biology Unit 1 Study Notes 4. The enzyme DNA polymerase joins the new nucleotides to each other by strong covalent bonds, forming the sugar-phosphate backbone. In addition to catalyzing the formation of Hydrogen bonds between complementary bases on the template and newly synthesized strands, DNA polymerase also catalyzes the reaction between the 5’ phosphate on an incoming nucleotide and the free 3' OH on the growing polynucleotide. As a result, the new DNA strands can grow only in the 5° to 3' direction, 5. Awinding enzyme winds the new strands up to form double helices. 6. The two new molecules are identical to the old molecule 65 hps:fontine.iphiri.comMhexgarknttip=t esethps:fontine.iphiri.comMhexgarknttip=tsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes DNA polymerase enzymes are only able to join the phosphate group at the 5' carbon of a new nucleotide to the hydroxyl (OH) group of the 3' carbon of a nucleotide already in the chain. As a result, DNA can only be synthesized in a 5' to 3' direction while copying a parent strand running in a 3' to 5' direction. Remember as mentioned above, each DNA strand has two ends. The 5' end of the DNA is the one with the terminal phosphate group on the 5' carbon of the deoxyribose; the 3' end is the one with a terminal hydroxyl (OH) group DNA replication can take a few hours, and in fact this limits the speed of cell division. One reason bacteria can reproduce so fast is that they have a relatively small amount of DNA. This replication mechanism is sometimes called semi-conservative replication, because each new DNA molecule contains one new strand and one old strand. The Genetic Code tte v € x é UW Phensaine [UB sere [VAY wone ad Oras U y [We Premiainne | vec seine [UNC Twoone | ucc Owteme |C Win tecne Ue Sete [UM So ver soo | Woe_tecne ee Sete |e Se vee _Twptnton [6 eu lecine cau Prone [cay wane cou arene |v fl [ee tenne ccc pro exc wntane ere wenne fe | in eine co rime [et Game [aa Aemme | | BL | cue tescine Cc Proline | CAG_Glutamine | C56 Avgnine | ‘Au olewcne Ae) Teenie [aad aspwasne | Gd Seine [Uv 14 | Ate toluene | Ace Teenie | ne apace | ace Seine fe fin totwce | en Tweonine [Aaa tyne | en trgnine | AvG_Metionine St | AoG_Teonine | 6 tyne | G_Argine_[ GW Vine eT g | ou vnc ce Aunne | ne Aipweened [eee Grime fe Gin eine GA Aonne |G Giromencd | Gea Gyeme [A Gic_teine ce_Annne |e _Guome nod [Gee _Gyine [6 ‘Wonpolar aliphatic Polar, uncharged Aromatic Posttvely charged Negatively charged Transcription - RNA Synthesis DNA never leaves the nucleus, but proteins are synthesised in the cytoplasm, so a copy of each gene is made to carry the "message" from the nucleus to the cytoplasm. This copy is mRNA, and the process of copying is called transcription. 67 hitps:oninefiphimis convhexgarknbtitp=1 ernetsites, 1112 PM ‘CAPE Biology Unit 1 Study Notes Fee mlotis bind complementary To ghe exposed bases one sense stand [A Fre mihotides move jot expose arson Zp eticase ups he double Stand da ata specie oi ‘There ae fe milous ne tteewsonamattiasagethe [OWE sit nn pe 9 Matar mma movin the ‘Stopaom whee wantin ses > 1. The start of each gene on DNA is marked by a special sequence of bases. 2, The RNA molecule is built up from the four ribose nucleotides (A, C, G and U) in the nucleoplasm. The nucleotides attach themselves to the bases on the DNA by complementary base pairing, just as in DNA replication. However, only one strand of RNA is made. The DNA stand that is copied is called the template or sense strand because it contains the sequence of bases that codes for a protein. The other strand is just a complimentary copy, and is called the non-template or antisense strand. toform sing tandems molecule hps:fontine.iphiri.comMhexgarknttip=t eanetsites, 1112 PM ‘CAPE Biology Unit 1 Stuay Notes ‘The new nucleotides are joined to each other by strong covalent bonds by the enzyme RNA polymerase. Only about 8 base pairs remain attached at a time, since the mRNA molecule peels off from the DNA as it is made. A winding enzyme rewinds the DNA. The initial mRNA, or primary transcript, contains many regions that are not needed as part of the protein code. These are called introns (for interruption sequences), while the parts that are needed are called exons (for expressed sequences). All eukaryotic genes have introns, and they are usually longer than the exons. The introns ‘are cut out using Spliceosomes and the exons are spliced together by enzymes The result is a shorter mature RNA containing only exons. The introns are broken down. ‘The mRNA diffuses out of the nucleus through a nuclear pore into the cytoplasm. Translation - Protein Synthesis 1 A ribosome attaches to the mRNA at an initiation codon (AUG). The ribosome encloses two codons. met-tRNA diffuses to the ribosome and attaches to the mRNA initiation codon by complementary base pairing. The next amino acid-tRNA attaches to the adjacent mRNA codon (leu in this case). The bond between the amino acid and the tRNA is cut and a peptide bond is formed between the two amino acids. The ribosome moves along one codon so that a new amino acid-tRNA can attach. The free RNA molecule leaves to collect another amino acid. The cycle repeats from step 3. The polypeptide chain elongates one amino acid at a time, and peels away from the ribosome, folding up into a protein as it goes. This continues for hundreds of amino acids until a stop codon is reached, when the ribosome falls apart, releasing the finished protein A single piece of mRNA can be translated by many ribosomes simultaneously; so many protein molecules can be made from one mRNA molecule. A group of ribosomes all attached to one piece of mRNA is called a polysome. 69 hitps:oninefiphimis convhexgarknbtitp=1 canes