A Level Notes

Biology Unit 1 page 1 AQA AS Biology Unit 1 Contents Specification Biological Molecules Cells Human Physiology Disease Appendices Chemical bonds Carbohydrates Lipids Proteins Biochemical Tests Enzymes Eukaryotic Cells Prokaryotic Cells Cell Fractionation Microscopy The Cell Membrane Movement across Cell Membranes Exchange The Gas Exchange System Lung Diseases The Heart Coronary Heart Disease The Digestive System Cholera Lifestyle and Disease Defence against Disease Immunisation Monoclonal Antibodies 1 – Mathematical Requirements 2– The Unit 1 Exam 2 4 6 8 10 16 17 24 28 30 31 35 37 44 46 50 54 58 0 67 68 72 80 81 83 86 These notes may be used freely by A level biology students and teachers, and they may be copied and edited. Please do not use these materials for commercial purposes. I would be interested to hear of any comments and corrections. Neil C Millar ([email protected] co. uk) Head of Biology, Heckmondwike Grammar School High Street, Heckmondwike, WF16 0AH July 2011 HGS Biology A-level notes NCM/7/11 AS Biology Unit 1 page 2 Biology Unit 1 Specification Biochemistry Biological Molecules Biological molecules such as carbohydrates and proteins are often polymers and are based on a small umber of chemical elements. • Proteins have a variety of functions within all living organisms. The general structure of an amino acid. Condensation and the formation of peptide bonds linking together amino acids to form polypeptides. The relationship between primary, secondary, tertiary and quaternary structure, and protein function.

• Monosaccharides are the basic molecular units (monomers) of which carbohydrates are composed. The structure of ? -glucose and the linking of ? glucose by glycosidic bonds formed by condensation to form maltose and starch. Sucrose is a disaccharide formed by condensation of glucose nd fructose. Lactose is a disaccharide formed by condensation of glucose and galactose. Glycerol and fatty acids combine by condensation to produce triglycerides. The R-group of a fatty acid may be saturated or unsaturated. In phospholipids, one of the fatty acids of a triglyceride is substituted by a phosphate group. Biochemical Tests Iodine/potassium iodide solution for starch. Benedict’s reagent for reducing sugars and non-reducing sugars. The biuret test for proteins. The emulsion test for lipids. Enzymes Enzymes as catalysts lowering activation energy through the formation of enzyme-substrate omplexes. The lock and key and induced fit models of enzyme action. Use the lock and key model to explain the properties of enzymes. Recognise its limitations and be able to explain why the induced fit model provides a better explanation of specific enzyme properties. The properties of enzymes relating to their tertiary structure. Description and explanation of the effects of temperature, competitive and non-competitive inhibitors, pH and substrate concentration. Investigate the effect of a specific variable on the rate of reaction of an enzyme-controlled reaction. Cell Biology Cells

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The appearance, ultrastructure and function of plasma membrane; microvilli; nucleus; mitochondria; lysosomes; ribosomes; endoplasmic reticulum and Golgi apparatus. Apply their knowledge of these features in explaining adaptations of other eukaryotic cells. HGS Biology A-level notes The structure of prokaryotic cells to include cell wall, plasma membrane, capsule, circular DNA, flagella and plasmid. Microscopes and Cell Fractionation The difference between magnification and resolution. The principles and limitations of transmission and scanning electron microscopes. Principles of cell ractionation and ultracentrifugation as used to separate cell components. Plasma Membranes The arrangement of phospholipids, proteins and carbohydrates in the fluid-mosaic model of membrane structure. Use the fluid mosaic model to explain appropriate properties of plasma membranes. • The role of carrier proteins and protein channels in facilitated diffusion. • Osmosis is a special case of diffusion in which water moves from a solution of higher water potential to a solution of lower water potential through a partially permeable membrane. Investigate the effect of solute concentration on the rate of uptake f water by plant issue. • The role of carrier proteins and the transfer of energy in the active transport of substances against a concentration gradient. Physiology Exchange Diffusion is the passive movement of substances down a concentration gradient. Surface area, difference in concentration and the thickness of the exchange surface affect the rate of diffusion. Gas Exchange System The gross structure of the human gas exchange system limited to the alveoli, bronchioles, bronchi, trachea and lungs. The essential features of the alveolar epithelium as a surface over which gas exchange takes place.

The exchange of gases in the lungs. The mechanism of breathing. Pulmonary ventilation as the product of tidal volume and ventilation rate. Lung Diseases The course of infection, symptoms and transmission of pulmonary tuberculosis. The effects of fibrosis, asthma and emphysema on lung function. Explain the symptoms of diseases and conditions affecting the lungs in terms of gas exchange and respiration. Interpret data relating to the effects of pollution and smoking on the incidence of lung disease. Analyse and interpret data associated with specific risk factors and the incidence of lung disease.

NCM/7/11 AS Biology Unit 1 Heart Heart structure and function. The gross structure of the human heart and its associated blood vessels in relation to function. Myogenic stimulation of the heart and transmission of a subsequent wave of electrical activity. Roles of the sinoatrial node (SAN), atrioventricular node (AVN) and bundle of His. Pressure and volume changes and associated valve movements during the cardiac cycle. Candidates should be able to analyse and interpret data relating to pressure and volume changes during the cardiac cycle. Cardiac output as the product of heart rate and stroke volume.

Investigate the effect of a specific variable on human heart rate or pulse rate. Coronary Heart Disease Atheroma as the presence of fatty material within the walls of arteries. The link between atheroma and the increased risk of aneurysm and thrombosis. Myocardial infarction and its cause in terms of an interruption to the blood flow to heart muscle. Risk factors associated with coronary heart disease: diet, blood cholesterol, cigarette smoking and high blood pressure. Describe and explain data relating to the relationship between specific risk factors and the incidence of coronary heart disease.

Digestive System The gross structure of the human digestive system limited to oesophagus, stomach, small and large intestines and rectum. The glands associated with this system limited to the salivary glands and the pancreas. The structure of an epithelial cell from the small intestine as seen with an optical microscope. Digestion is the process in which large molecules are hydrolysed by enzymes to produce smaller molecules that can be absorbed and assimilated. The role of salivary and pancreatic amylases in the digestion of starch and of maltase located in the intestinal epithelium.

Digestion of disaccharides by sucrase and lactase. Absorption of the products of carbohydrate digestion. The roles of diffusion, active transport and co-transport involving sodium ions. The role of microvilli in increasing surface area. Lactose intolerance. Cholera The cholera bacterium as an example of a prokaryotic organism. Cholera bacteria produce toxins that increase secretion of chloride ions into the lumen of the intestine. This results in severe diarrhoea. The use of oral rehydration solutions (ORS) in the treatment of diarrhoeal diseases. Discuss the applications and mplications of science in developing improved oral rehydration solutions; and ethical issues associated HGS Biology A-level notes page 3 with trialling improved oral rehydration solutions on humans. Disease Lifestyle and Disease Disease may be caused by infectious pathogens or may reflect the effects of lifestyle. • Pathogens include bacteria, viruses and fungi. Disease can result from pathogenic microorganisms penetrating any of an organism’s interfaces with the environment. These interfaces include the digestive and gas-exchange systems. Pathogens cause disease by damaging the cells of the host and by producing oxins. • Lifestyle can affect human health. Specific risk factors are associated with cancer and coronary heart disease. Changes in lifestyle may also be associated with a reduced risk of contracting these conditions. Analyse and interpret data associated with specific risk factors and the incidence of disease. Recognise correlations and causal relationships. Defence against Disease Mammalian blood possesses a number of defensive functions. Phagocytosis and the role of lysosomes and lysosomal enzymes in the subsequent destruction of ingested pathogens. Definition of antigen and antibody.

Antibody structure and the formation of an antigen-antibody complex. The essential difference between humoral and cellular responses as shown by B cells and T cells. The role of plasma cells and memory cells in producing a secondary response. The effects of antigenic variabilty in the influenza virus and other pathogens on immunity. Vaccines and monoclonal antibodies The use of vaccines to provide protection for individuals and populations against disease. The use of monoclonal antibodies in enabling the targeting of specific substances and cells. Evaluate methodology, evidence and data relating to he use of vaccines and monoclonal antibodies. Discuss ethical issues associated with the use of vaccines and monoclonal antibodies. Explain the role of the scientific community in validating new knowledge about vaccines and monoclonal antibodies thus ensuring integrity. Discuss the ways in which society uses scientific knowledge relating to vaccines and monoclonal antibodies to inform decision-making. NCM/7/11 AS Biology Unit 1 page 4 Biological Molecules Living things are made up of thousands and thousands of different chemicals. These chemicals are called organic because they contain the element carbon.

In science organic compounds contain carbon–carbon bonds, while inorganic compounds don’t. There are four important types of organic molecules found in living organisms: carbohydrates, lipids, proteins, and nucleic acids (DNA). These molecules are mostly polymers, very large molecules made up from very many small molecules, called monomers. 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. Group name Elements Monomers Polymers % dry mass of a cell Carbohydrates CHO monosaccharides polysaccharides 5 Lipids CHOP fatty acids + glycerol* triglycerides* 10 Proteins CHONS amino acids polypeptides 50 Nucleic acids CHONP nucleotides polynucleotides 18 * Triglycerides are not polymers, since they are formed from just four molecules, not many (see p8). We’ll study carbohydrates, lipids and proteins in detail now, and we’ll look at nucleic acids (DNA) in unit 2. Chemical Bonds In biochemistry there are two important types of chemical bond: the covalent bond and the hydrogen bond. Covalent bonds are strong. They are the main bonds holding the atoms together in H the organic molecules in living organisms.

Because they are strong, covalent bonds don’t break or form spontaneously at the temperatures found in living cells. So in H C H biology covalent bonds are always made or broken by the action of enzymes. Covalent bonds are represented by solid lines in chemical structures. H covalent bonds Hydrogen bonds are much weaker. They are formed between an atom (usually hydrogen) with a slight positive charge (denoted ? +) and an atom (usually oxygen or nitrogen) with a slight negative charge (denoted ? –). Because hydrogen bonds are weak they can break and form spontaneously at the temperatures found in – CO ?+ HN hydrogen bond living cells without needing enzymes. Hydrogen bonds are represented by dotted lines in chemical structures. HGS Biology A-level notes NCM/7/11 AS Biology Unit 1 page 5 Water Life on Earth evolved in the water, and all life still depends on water. At least 80% of the total mass of living organisms is water. Water molecules are charged, with the oxygen atom being slightly negative (? -) and the hydrogen atoms being slightly positive (? +). These opposite charges attract each other, forming hydrogen bonds that bind water molecules loosely together.

H ? + H ? + covalent bonds O H ? + H ?- ?+ H hydrogen bonds O ? – H O O H H Because it is charged, water is a very good solvent, and almost all the chemical reactions of life take place in aqueous solution. • 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”). Many important biological molecules ionise when they dissolve (e. g. acetic acid acetate- + H+), so the ames 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. 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. HGS Biology A-level notes NCM/7/11 AS Biology Unit 1 page 6 Carbohydrates Carbohydrates contain only the elements carbon, hydrogen and oxygen. The group includes monomers, dimers and polymers, as shown in this diagram: Carbohydrates Sugars Monosaccharides (monomers) Disaccharides (dimers) Polysaccharides (polymers) e. g. glucose, fructose, galactose e. g. sucrose, maltose, lactose e. g. starch, cellulose, glycogen Monosaccharides 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 C6H12O6. Its structure is: OH HCH C H O O H H C OH H C HO C H HO or more simply C OH OH OH Glucose Glucose forms a six-sided ring, although in three-dimensions it forms a structure that looks a bit like a chair. In animals glucose is the main transport sugar in the blood, and its concentration in the blood is carefully controlled. There are many isomers of glucose, with the same chemical formula (C6H12O6), but different structural formulae. These isomers include galactose and fructose: O O HO

OH HO Galactose Fructose Common five-carbon, or pentose sugars (where n = 5, C5H10O5) include ribose and deoxyribose (found in nucleic acids and ATP, see unit 2) and ribulose (which occurs in photosynthesis). Three-carbon, or triose sugars (where n = 3, C3H6O3) are also found in respiration and photosynthesis (see unit 4). HGS Biology A-level notes NCM/7/11 AS Biology Unit 1 page 7 Disaccharides Disaccharides are formed when two monosaccharides are joined together by a glycosidic bond (C–O–C). The reaction involves the formation of a molecule of water (H2O): O HO O OH HO O OH O H 2O O HO OH glycosidic bond

This shows two glucose molecules joining together to form the disaccharide maltose. This kind of reaction, where two molecules combine into one bigger molecule, is called a condensation reaction. The reverse process, where a large molecule is broken into smaller ones by reacting with water, is called a hydrolysis reaction. In general: • polymerisation reactions are condensations • breakdown reactions are hydrolyses There are three common disaccharides: Maltose (or malt sugar) is glucose–glucose. It is formed on digestion O of starch by amylase, because this enzyme breaks starch down into two-glucose units.

Brewing beer starts with malt, which is a maltose O Glucose Glucose O HO OH solution made from germinated barley. Sucrose (or cane sugar) is glucose–fructose. It is common in plants O because it is less reactive than glucose, and it is their main transport sugar. It is the common table sugar that you put in your tea. Glucose O O HO Fructose O Lactose (or milk sugar) is galactose–glucose. It is found only in mammalian milk, and is the main source of energy for infant O HO O Galactose Glucose OH mammals. Polysaccharides Polysaccharides are chains of many glucose monomers (often 1000s) joined ogether by glycosidic bonds. Starch, glycogen and cellulose are polysaccharides. They will be studied in unit 2. HGS Biology A-level notes NCM/7/11 AS Biology Unit 1 page 8 Lipids Lipids are a mixed group of hydrophobic compounds composed of the elements carbon, hydrogen, oxygen and sometime phosphorus (CHOP). The most common lipids are triglycerides and phospholipids. Triglycerides Triglycerides, or triacylglycerols, are made of glycerol and fatty acids. H three alcohol (OH) groups. H H HC Glycerol is a small, 3-carbon molecule with C C H OH OH OH Carboxyl acid group Hydrocarbon chain (14-22 carbon atoms)

Fatty acids are long molecules made of a nonpolar hydrocarbon chain with a polar carboxyl H H H H H H acid group at one end. The hydrocarbon chain HC C C C C C can be from 14 to 22 CH2 units long. Because H H H H H H C O OH the length of the hydrocarbon chain can vary it is sometimes called an R group, so the formula or CH3 — (CH2)n — COOH of a fatty acid can be written as R-COOH. or R — COOH One molecule of glycerol joins together with three fatty acid molecules by ester bonds to form a triglyceride molecule, in another condensation polymerisation reaction: 3 fatty acid molecules R R R O C O C O C 1 glycerol olecule 1 triglyceride molecule H OH HO C H R OH HO C H R OH HO C H R O C O C O C 3 water molecules H O C H O C H O C H H 3 H2O H 3 ester bonds Triglycerides are commonly known as fats or oils, and 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. When oxidised triglycerides yield more energy per unit mass than other compounds so are good for energy storage. However, triglycerides can’t be mobilised quickly since they are so insoluble, so are no good for quick energy requirements.

Tissues that need energy quickly (like muscles) instead store carbohydrates like glycogen. HGS Biology A-level notes NCM/7/11 AS Biology Unit 1 page 9 • If the fatty acid chains in a triglyceride have no C=C double bonds, then they are called saturated fatty acids (i. e. saturated with hydrogen). Triglycerides with 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, H H H H C C C C H H H H saturated lard. • If the fatty acid chains in a triglyceride do have C=C double bonds they are called unsaturated fatty acids (i. . unsaturated with hydrogen). Fatty acids with more than one double bond are called poly-unsaturated fatty acids (PUFAs). Triglycerides with unsaturated fatty acids have a low melting point and tend to be found in cold-blooded animals and plants. At room temperature they are H H H H C C C C H H unsaturated liquids (oils), e. g. fish oil, vegetable oils. An “omega number” is sometimes used to denote the position of a double bond, e. g. omega-3 fatty acids. Phospholipids Phospholipids have a similar structure to triglycerides, but with a phosphate group in place of one fatty acid chain.

There may also be other groups attached to the phosphate. Phospholipids have a polar hydrophilic “head” (the negatively-charged phosphate group) and two non-polar hydrophobic “tails” (the fatty acid chains). glycerol H H fatty acid fatty acid R R O C O C C O O C C hydrophobic tails phosphate hydrophilic head H O OPO O H or H This mixture of properties is fundamental to biology, for phospholipids are the main components of cell membranes. When mixed with water, phospholipids form droplet spheres with a double-layered phospholipid bilayer. The hydrophilic heads facing the water and the hydrophobic tails facing each other.

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 (see p35). phospholipid bilayer HGS Biology A-level notes aqueous compartment NCM/7/11 AS Biology Unit 1 page 10 Proteins Proteins are the most complex and most diverse group of biological compounds. They have an astonishing range of different functions, as this list shows. structure e. g. collagen (bone, cartilage, tendon), keratin (hair), actin (muscle) enzymes e. g. amylase, pepsin, catalase, etc (>10,000 others) ransport 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 lubrication e. g. glycoproteins in synovial fluid toxins e. g. cholera toxin antifreeze e. g. glycoproteins in arctic flea and many more! Amino Acids Proteins are made of amino acids. Amino hydrogen acids are made of the five elements C H O N S.

Amino acids are so-called because they contain both an amino group and an acid group. The general structure of an amino acid molecule is shown on the right. There is a central carbon atom (called amino group H H H N C? C R O OH carboxy acid group the “alpha carbon”, C? ), with four different chemical groups attached to it: 1. a hydrogen atom R group + 2. a basic amino group (NH2 or NH3 ) 3. an acidic carboxyl group (COOH or COO-) 4. a variable “R” group (or side chain) HGS Biology A-level notes NCM/7/11 AS Biology Unit 1 page 11 There are 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 table on page xx 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. 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: H H N H O C? C R H H N OH H O C? C R H H H C? C H N R N OH O H C? C R O H2 O OH peptide bond When two amino acids join together a dipeptide is formed. Three amino acids form a tripeptide. Many amino acids form a polypeptide. e. g. : N-terminus C-terminus H2N-Gly — Pro — His — Leu — Tyr — Ser — Trp — Asp — Lys — Cys-COOH In a polypeptide there is always one end with a free amino (NH2) group, called the N-terminus, and one end with a free carboxyl (COOH) group, called the C-terminus.

In a protein the polypeptide chain may be many 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 bases in DNA. Protein synthesis is studied in detail in unit 5. HGS Biology A-level notes NCM/7/11 AS Biology Unit 1 page 12 Protein Structure Polypeptides are just strings of amino acids, but they fold up and combine to form the complex and welldefined three-dimensional structure of working proteins.

To help to understand protein structure, it is broken down into four levels: 1. Primary Structure This is just the sequence of amino acids in the polypeptide chain, so is not really a structure at all. However, the primary structure does determine the rest of the protein structure. 2. Secondary Structure This is the most basic level of protein folding, and consists of a few basic motifs that are found in almost all proteins. The secondary structure is held together by hydrogen bonds between the carboxyl groups and the amino groups in the ?- ?+ CO HN hydrogen bond polypeptide backbone.

The two most common secondary structure motifs are the ? -helix and the ? -sheet. The ? -helix. The polypeptide chain is wound round to form a helix. It is held together by hydrogen bonds running parallel with the long helical axis. There are so many hydrogen bonds that this is a very stable and strong structure. Do not confuse the ? -helix of proteins with the polypeptide backbone N C? C=O H-N hydrogen bonds C? H-N C=O C=O H-N C? C? C=O C? H-N H-N C=O famous double helix of DNA – helices are common structures throughout biology. H The ? -sheet. The polypeptide chain zig-zags back

H H N C? C N C? C N H O O O O O H H H H H NH C? and forward forming a sheet of antiparallel strands. H Once again it is held together by hydrogen bonds. H C? C N C? C N C? C N C C? N C C? N C C? N C C? N C C? N O O O H H H N C? C N C? C N O O H CO H C? C O O HGS Biology A-level notes O C? C N C? C N C? C O O O NCM/7/11 AS Biology Unit 1 page 13 3. Tertiary Structure This is the compact globular structure formed by the folding up of a whole polypeptide chain. Every protein has a unique tertiary structure, which is responsible for its properties and function.

For example the shape of the active site in an enzyme is due to its tertiary structure. The tertiary structure is held together by bonds between the R groups of the amino acids in the protein, and so depends on what the sequence of amino acids is. These bonds include weak hydrogen bonds and sulphur bridges covalent S–S bonds between two cysteine amino acids, which are much stronger. So the secondary structure is due to backbone interactions and is thus largely independent of primary sequence, while tertiary structure is due to side chain interactions and thus depends on the amino acid sequence. . Quaternary Structure Almost all working proteins are actually composed of more than one polypeptide chain, and the quaternary -S Haemoglobin consists of four chains arranged in a tetrahedral (pyramid) structure. -S-S- -S – structure is the arrangement of the different chains. There are a huge variety of quaternary structures e. g. : Antibodies comprise four chains arranged in a Y-shape. Collagen consists of three chains in a triple helix structure. The enzyme ATP synthase is composed of 22 chains forming a rotating motor. HGS Biology A-level notes Actin consists of hundreds of globular chains rranged in a long double helix. NCM/7/11 AS Biology Unit 1 page 14 These four structures are not real stages in the formation of a protein, but are simply a convenient classification that scientists invented to help them to understand proteins. In fact proteins fold into all these structures at the same time, as they are synthesised. The final three-dimensional shape of a protein can be classified as globular or fibrous. Globular Proteins Fibrous (or Filamentous) Proteins The vast majority of proteins are globular, i. e. they Fibrous proteins are long and thin, like ropes. They have a compact, ball-shaped structure.

This group tend to have structural roles, such as collagen includes enzymes, membrane proteins, receptors (bone), keratin (hair), tubulin (cytoskeleton) and and storage proteins. The diagram below shows a actin (muscle). They are always composed of many typical globular enzyme molecule. It has been drawn polypeptide chains. This diagram shows part of a to highlight the different secondary structures. molecule of collagen, which is found in bone and cartilage. ? helix ? sheet A few proteins have both structures: for example the muscle protein myosin has a long fibrous tail and a globular head, which acts as an enzyme (see unit 4).

Protein Denaturing Since the secondary, tertiary and quaternary structures are largely held together by hydrogen bonds, the three-dimensional structure of proteins is lost if the hydrogen bonds break. The polypeptide chain just folds up into a random coil and the protein loses its function. This is called denaturing, and happens at temperatures above about 50°C or at very low or high pH. Covalent bonds are not broken under these conditions, so the primary structure is maintained (as are sulphur bridges). HGS Biology A-level notes NCM/7/11 AS Biology Unit 1 page 15

The Twenty Amino Acid R-Groups Simple R groups Basic R groups Glycine Gly G H Lysine Lys K CH2 CH2 CH2 CH2 NH+ 3 Alanine Ala A C H3 Arginine Arg R CH2 CH2 CH2 NH C Valine Val V CH3 CH CH3 Histidine His H CH3 CH CH3 CH Isoleucine Ile I CH2 CH2 N CH O Asparagine Asn N CH3 CH2 C Glutamine Gln Q CH3 CH2 CH2 NH2 O C NH2 Hydroxyl R groups Serine Ser S CH 2 CH Threonine Thr T Acidic R groups O Aspartate Asp D OH CH3 CH2 CH2 Glutamate Glu E OH CH2 C C OH O OH Sulphur R groups Cysteine Cys C CH 2 SH Methionine Met M CH2 CH2 Ringed R groups Phenylalanine Phe F S CH3 CH2

Tyrosine Tyr Y CH2 Cyclic R group CH2 COOH Proline Pro P H CH2 NH HGS Biology A-level notes C? + NH2 C NH CH2 Leucine Leu L CH NH2 Tryptophan Trp W OH CH CH NH CH2 CH2 NCM/7/11 AS Biology Unit 1 page 16 Biochemical Tests These five tests identify the main biologically-important chemical compounds. For each test take a small sample of the substance to test and, if it isn’t already a solution, grind it with some water 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.

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