Biology Teach Yourself Series Topic 3: Chemical Nature of the Cell

Transcription

1 Biology Teach Yourself Series Topic 3: Chemical Nature of the Cell A: Level 14, 474 Flinders Street Melbourne VIC 3000 T: W: tssm.com.au E: TSSM 2013 Page 1 of 19

2 Contents Chemical nature of the Cell 3 Organic compounds 3 As it appears in Unit 1 3 Carbohydrates.3 As it appears in Unit 1 3 Lipids..4 As it appears in Unit 1 4 Proteins...5 As it appears in Unit 1 5 Nucleic acids.6 As it appears in Unit 1 6 Review questions 6 Proteins...9 As it appears in Unit 3 9 Nucleic acids 11 As it appears in Unit Metabolic pathways.12 As it appears in Unit The proteome 13 As it appears in Unit TSSM 2013 Page 2 of 19

3 Chemical Nature of the Cell 99% of all life is composed chemicals made up of carbon (C), hydrogen (H), oxygen (O) and nitrogen (N). The major groups of compounds located in cells are carbohydrates, lipids, proteins and nucleic acids. These carbon-based compounds are all organic compounds and are all made up of elements carbon, hydrogen and oxygen. Some also contain the elements nitrogen, phosphorus and sulfur. Organic Compounds As it appears in Unit 1 Organic compounds are frequently large molecules (polymers) that are composed of smaller sub units bonded together. These sub units are referred to as monomers, which when bound together through polymerisation to form polymers. Carbohydrates As it appears in Unit 1 Carbohydrates are the most common organic molecule. They contain the elements carbon, hydrogen and oxygen, which in simple carbohydrates occur in a ratio of 1:2:1 such as glucose C 6 H 12 O 6. Simple carbohydrates are referred to as either monosaccharides (one sugar) or disaccharides (two sugars). When many monosaccharides are bonded together, they form polysaccharides or complex carbohydrates such as starch and glycogen. Monosaccharide Disaccharide Polysaccharide TSSM 2013 Page 3 of 19

4 Common functions of carbohydrates include: Cellular respiration substrate: e.g. glucose Energy Storage: e.g. glycogen in animals or starch in plants Structural support: e.g. cellulose in plants or chitin in arthropods Cellular communication: e.g. glycoproteins act as receptors Lipids As it appears in Unit 1 Lipids include fats and oils, which are hydrophobic. Phospholipids are a major component of plasma membranes, which separate the cell s internal environment from the external environment. Lipids comprise carbon, hydrogen and oxygen, however, they are found in different proportions to carbohydrates. Lipids contain a much smaller proportion of oxygen and a higher proportion of hydrogen. This enables lipids to be a better form of energy storage than carbohydrates because the bond between carbon and hydrogen is a high energy bond. Lipids are made up of two different molecules, fatty acids and glycerol. A common form of lipid is a triglyceride, which contains one glycerol with three fatty acids attached. Triglyceride Common functions of lipids include: Material transport Structural: the plasma membrane is made up of phospholipids Thermal insulation: blubber provides animals such as whales with insulation Electrical insulation: the myelin sheath surrounding neurons is made up of lipids Waterproofing: water runs off waxy surfaces Homeostasis: steroids are lipid based hormones Buoyancy: Fats float, animals with high fat content in their tissues float more easily TSSM 2013 Page 4 of 19

5 Proteins As it appears in Unit 1 Proteins are polymers composed of sub-units called amino acids. The amino acids are held together by peptide bonds, which is why proteins as sometimes referred to as polypeptides. All proteins contain carbon, hydrogen, oxygen and nitrogen, and they can also contain sulfur as well as phosphorus and other elements. Amino acids all have the same basic structure: a central carbon atom that is bound to a hydrogen atom, a carboxyl acid group (COOH), an amine group (NH 2 ) and a variable R group. It is the R group that differentiates one amino acid from another. Common roles of proteins include: Defence: Antibodies provide a defence against infectious organisms Material transport: Protein carriers and protein channels facilitate the entry and exit of large water soluble substances. Catalysis: enzymes are proteins which catalyse chemical reactions Homeostasis: the majority of hormones are protein based TSSM 2013 Page 5 of 19

6 Nucleic Acids As it appears in Unit 1 There are two types of nucleic acid: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Both are comprised of long chains of subunits called nucleotides. Each nucleotide contains a sugar (deoxyribose in DNA or ribose in RNA) molecule, a phosphate molecule and a nitrogen base. The sugar and phosphate parts are identical in each nucleotide. There are four different types of nucleotides because there are four different types of nitrogen bases. The four nitrogen bases are adenine, thymine, cytosine and guanine, which are designated by the letters A, T, C and G. Nucleic acids contain the elements carbon, hydrogen, oxygen, nitrogen and phosphorous. S G C A T A T G C Review Questions 1. What is the name for the chain of molecules that comprise a protein? 2. Complete the table below. Organic Molecule Monomers Glycogen Chitin Amino acids Deoxyribonucleic Acid TSSM 2013 Page 6 of 19

7 3. Element Relative composition of four organic molecules (arbitrary units) Molecule A Molecule B Molecule C Molecule D Carbon Hydrogen Oxygen Nitrogen Phosphorous a. Which of the organic molecules above represents a nucleic acid? How can you tell? b. Where in a cell would you be most likely to find high concentrations of molecule B? c. If an individual was suffering from hyperglycemia (high blood sugar levels), which organic molecule would they be likely to have in very high concentrations? 4. The formula that represents a protein is compound A. C 8 H 12 O 2 B. C 8 H 11 PNO 7 C. C 3 H 6 O 3 D. C 12 H 16 N 18 O A polysaccharide made by animal cells is A. Starch. B. DNA C. Glycogen. D. Cellulose. TSSM 2013 Page 7 of 19

8 6. The following diagram represents which organic monomer? P S A. Amino acid B. Nucleic acid C. Fatty acid D. Nucleotide N TSSM 2013 Page 8 of 19

9 Proteins As it appears in Unit 3 Nearly every process that a cell undertakes relies on proteins, which are a focus of Unit 3 Biology. Proteins have four levels of structure: primary, secondary, tertiary and quaternary. A protein s primary structure is determined by the order of amino acids that make up the protein. A change to a single amino acid will alter the shape of the protein and accordingly its function. Primary structure: Sequence of amino acids A protein s secondary structure relates to the way that the protein coils and folds as hydrogen bonds form between amino acids. Tight coils are referred to as α-helices while the folds in a protein are referred to as β-sheets. Secondary structure: Beta sheet and alpha helix TSSM 2013 Page 9 of 19

10 A protein s tertiary structure relates to the bonds that form between the R groups of different amino acids causing the protein to further twist and fold. These twists and folds are held in place by hydrogen, ionic and disulfide bonds that form between the R groups. The tertiary structure is directly related to the function of the protein. Tertiary structure: the overall shape of a single polypeptide When two or more polypeptide chains interact they form a quaternary protein. Haemoglobin is a quaternary protein as it is comprised of four polypeptide chains. A range of hydrogen, ionic and covalent bonds hold the polypeptide chains together and control the shape of the molecule. Quarternary structure: in this case the protein is made up of 4 polypeptide chains Proteins carry out a wide range of roles within an organism, from being involved in controlling metabolic pathways to helping to provide structure (e.g. keratin and collagen) to assisting functionality (e.g. enzymes) to transportation (e.g. haemoglobin). TSSM 2013 Page 10 of 19

11 Nucleic Acids As it appears in Unit 3 Nucleic acids are also vitally important to the functioning of an organism as they contain the instructions for the production of proteins. There are two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). There are a number of differences between the two. DNA contains a deoxyribose sugar, whilst RNA contains a ribose sugar that has one more oxygen atom. DNA contains the nitrogenous base thymine whilst RNA contains the base uracil. DNA is usually double stranded and RNA is single stranded. Nucleotides bind together in what is called a 5 to 3 direction to form long polymers. This simply means that the phosphate group is attached to the 5 carbon of the sugar, which binds to the hydroxyl group (OH) of the next nucleotide, and the OH group is attached to the 3 carbon of its sugar. The bond that forms between the two nucleotides is referred to as a phosphodiester bond. In the process of polymerisation, the hydrogen from the sugar and the hydroxyl from the phosphate are removed as a water molecule in a process known as condensation. P 5 end 3 end S G C A T A T G C 3 end 5 end TSSM 2013 Page 11 of 19

12 Metabolic Pathways As it appears in Unit 3 Commonly a number of enzymes are used in a sequence to convert a substrate into one or more products. The chain of reactions is called a metabolic pathway. The existence of metabolic pathways is one reason why we study the proteome as proteins generally don't act in isolation. A metabolic pathway is a series of enzyme catalysed reactions that occur within a cell. They usually involve a step by step modification of a specific substance in order to produce a specific chemical. However, if there is one problem with the pathway then the final product will not be produced, unless the substance produced by the "missing link" reaction is supplied. The diagram below shows how the bread mould Neurospora produces arginine through a metabolic pathway involving several enzymes. If gene B is defective then there is no production of enzyme B, however, arginine can still be produced if the organism is supplied with citrulline as it is the substrate for enzyme C. This is because the reaction that converts citrulline into arginine is not defective. Gene A Gene B Gene C Enzyme A Enzyme B Enzyme C Raw materials Ornithine Citrulline Arginine TSSM 2013 Page 12 of 19

13 The Proteome As it appears in Unit 3 The proteome is the set of proteins produced by a cell. Proteomics is the study of the structure and function of proteins as well as the way they function and interact with each other. We study the proteome as proteins do not normally function in isolation from each other - they tend to work together. Although the each cell contains the same genetic information, the proteome tends to be different in each cell e.g. a skin cell would not manufacture insulin nor would a bone cell produce salivary amylase. One of the reasons for the study of proteomics is to improve our ability to diagnose and treat disease. We may be able to improve gene regulation or produce desired proteins. Another reason for the study of proteomics is to develop the ability to create designer (designed) drugs. If we can establish the shape of harmful substance or disease causing substance (antigen), then we may be able to create a molecule (antibody) that will bind to it and inactivate it. Examples of this include: Relenza: A drug designed to bind to neuraminidase on the surface of some influenza viruses. Glivec: A drug being developed to treat myeloid leukemia. A particular pathway is activated in this condition which leads to an uncontrolled replication of white blood cells, glivec is designed to block this pathway, preventing proliferation and therefore preventing the condition. Remicade: A drug designed to treat autoimmune diseases such as arthritis. Review Questions 7. Outline the importance of a protein s tertiary structure. TSSM 2013 Page 13 of 19

14 8. Explain how the quaternary structure of a protein is formed. 9. An unknown substance was taken from an organism. Following chromatographic analysis, it was discovered to contain carbon, hydrogen and oxygen in approximately a 2:2:1 ration. What type of organic compound is this substance likely to be? 10. a. A β-sheet is what type of protein structure? b. Outline the effect of breaking the disulfide bonds on nuclease function. c. Name the sub units that bind to form nuclease. 11. Many organic molecules occur as polymers, large molecules of smaller units joined together. Which of the following is an example of a polymer? A. Proteins composed of nucleic acids B. Starch composed of fatty acids C. Glycogen composed of nucleotides D. Chitin composed of monosaccharides 12. Which of the following is not a difference between DNA and RNA? A. DNA contains the base thymine and RNA contains the base uracil B. The sugar in RNA contains one less oxygen than the sugar in DNA C. DNA is generally double stranded while RNA is single stranded D. None of the above TSSM 2013 Page 14 of 19

15 13. The protein pepsin is derived from a parent molecule, pepsinogen. Cell organelles that are essential for the production of pepsinogen include A. Ribosomes B. Microtubules C. Endoplasmic Reticulum D. Golgi Apparatus 14. Dietary Protein Digested to Phenylalanin e Phenylalanine hydroxylase produced No phenylalanine hydroxylase No tyrosinase Tyrosin e Tyrosinase produced Phenylketonuria Albinism Melanin Brain damage if not under dietary management Lack of pigment in skin, eyes, hair: pale appearance Variations in depth/ shade of skin, hair and eye colour a. Based on the information above, outline the importance of phenylalanine hydroxylase and tyrosinase in normal body functioning. TSSM 2013 Page 15 of 19

16 b. If an individual was unable to produce tyrosinase describe what would happen to them and provide reasons why? TSSM 2013 Page 16 of 19

17 Solutions to Review Questions 1. Answer: Polypeptide Explanation: A protein is comprised of a chain of amino acids held together by peptide bonds. 2. Answer: 3. Organic Molecule Glycogen Chitin Protein Deoxyribonucleic Acid a. Answer: D Monomers Monosaccharides Monosaccharides Amino acids Nucleotides Explanation: D is the only molecule that contains phosphorous, which is present in nucleic acids. b. Answer: Plasma membrane Explanation: The plasma membrane is primarily composed of a phospholipid bilayer so lipids would be found in very high concentrations. c. Answer: Molecule A Explanation: People that suffer from hyperglycemia have high levels of sugar. As molecule A contains carbon, hydrogen and oxygen in a ratio of 1:2:1, which means that it is a carbohydrate. 4. Answer: D Explanation: D is a protein as it contains carbon, hydrogen, oxygen and nitrogen but does not contain phosphorous, which would make it a nucleic acid. 5. Answer: C Explanation: Glycogen is an energy storage molecule in animals. 6. Answer: D Explanation: As this monomer contains a phosphorous group, a sugar and a nitrogenous base therefore it must be a nucleic acid. 7. Answer: Proteins require a specific shape so that they can carry out their function. The protein s tertiary structure forms an active site that binds with its target site or receptor. Without this specific structure it would not be able to carry out its function. TSSM 2013 Page 17 of 19

18 8. Answer: The quaternary structure of a protein relates to the interaction of two or more polypeptides that give the protein molecule its final shape. 9. Answer: Lipid Explanation: Like carbohydrates, lipids always contain the elements carbon, hydrogen and oxygen but in different proportions, lipids comprise a much smaller proportion of oxygen than carbohydrates. 10. a. Answer: Secondary Structure Explanation: A β-sheet is part of a protein s secondary structure as its shape is formed by the creation of hydrogen bonds between the individual amino acids. b. Answer: It would decrease the rate at which nuclease would be able to catalyse the breakdown of nucleic acids into nucleotides. Explanation: As nuclease is an enzyme, any alteration of its tertiary structure will change the shape of its active site, which will reduce its ability to carry out its required function. c. Answer: Amino acids Explanation: Amino acids bind together using peptide bonds to form a polypeptide or protein. As nuclease is a protein its sub units are amino acids. 11. Answer: D Explanation: Chitin is a complex carbohydrate or polysaccharide which is formed when multiple monosaccharides binds together. 12. Answer: B Explanation: RNA comprises a ribose sugar which contains one less sugar than DNA s deoxyribose sugar, not one more. 13. Answer: A Explanation: Both pepsin and pepsinogen are enzymes, which are proteins. Proteins are synthesized in the ribosomes. 14. a. Answer: Phenylalanine hydroxylase and tyrosinase are enzymes, which catalyse the breakdown of phenylalanine and tyrosine. Both phenylalanine and tyrosine are involved in metabolic pathways that result in the production of the skin pigment melanin. If either of these enzymes is missing, there is a reduced amount of melanin produced. Without phenylalanine hydroxylase, phenylalanine builds up, which can cause brain damage. The absence of tyrosinase leads to albinism. TSSM 2013 Page 18 of 19

19 b. Answer: They would suffer from albinism as they would not be able to produce melanin as they lack tyrosinase. This would mean that they would be unable to convert tyrosine into melanin. There would also be a buildup of tyrosine. TSSM 2013 Page 19 of 19