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Ch1~the chemical nature of cells


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Unit 3 Biology VCE
Supports 'Nature Of Biology' textbook

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Ch1~the chemical nature of cells

  1. 1. The Chemical Nature of Cells Chapter 1 Unit 3 Biology ~ 2011
  2. 2. KEY KNOWLEDGE The Chemical Nature of Cells <ul><li>By the end of this chapter, you should: </li></ul><ul><ul><li>Enhance your knowledge & understanding of the synthesis of biomacromolecules such as polysaccharides, lipids, proteins and nucleic acids. </li></ul></ul><ul><ul><li>Enhance your knowledge & understanding of the structure & function of nucleic acids. </li></ul></ul><ul><ul><li>Understand the structural diversity of proteins & how this diversity relates to the variety of functions that proteins carry out in living organisms </li></ul></ul><ul><ul><li>Develop an understanding of the concept of the proteome of an individual or a cell. </li></ul></ul>
  3. 3. The Chemical Basis of Life <ul><li>All cells are composed of atoms and molecules which interact in thousands of simultaneous chemical reactions. </li></ul><ul><li>Organisms are composed of chemicals that react with each other and with the substances in the environment. </li></ul>
  4. 4. Biochemistry <ul><li>The study of the chemicals involved in living organisms is called ‘biochemistry’. </li></ul><ul><li>Investigations in biochemistry allow for the development of pharmaceuticals, vaccines and improvements in medical diagnoses. </li></ul><ul><li>GENOMICS & PROTEOMICS are two recent fields of science dealing with the study DNA and proteins. </li></ul><ul><li>All the data that is gathered needs to be collated, analysed and stored in a systematic way. Thus the field of BIOINFORMATICS has been developed. </li></ul>
  5. 5. Bioinformatics
  6. 6. Biomolecules <ul><li>Living things are made from the following major groups of biological molecules: </li></ul><ul><ul><li>Proteins </li></ul></ul><ul><ul><li>Nucleic Acids </li></ul></ul><ul><ul><li>Carbohydrates </li></ul></ul><ul><ul><li>Lipids </li></ul></ul><ul><li>Cells require these molecules for survival. </li></ul><ul><li>They are an integral part to the structure & function of the cell. </li></ul>
  7. 7. Polar vs Non-Polar <ul><li>POLAR : this is when the molecule has an unequal distribution of electrons resulting in an overall negative charge at one end and an overall positive charge at the other. </li></ul><ul><li>NON-POLAR : molecules with an equal distribution of charge. </li></ul><ul><li>The polarity of the molecule will affect its interaction within the cell, for example a polar molecule can dissolve in water. </li></ul>
  8. 8. WATER ~ why is it so important? <ul><li>ALL known life forms require water to survive </li></ul><ul><li>75% - 85% of a cell’s weight is water </li></ul><ul><li>Almost all substances and chemical reactions of biological significance require water. </li></ul><ul><li>Cells are constantly bathed by a watery solution </li></ul><ul><li>Water is essential for the cycling of matter between the living & non-living parts of ecosystems. </li></ul>
  9. 9. Chemical Properties of Water <ul><li>H 2 O </li></ul><ul><li>Water can exist as a solid (ice), a gas (steam) or as a liquid </li></ul><ul><li>Water molecules are highly polar. </li></ul><ul><li>The oxygen part of the molecule is negative so it is attracted to the positive end of other water molecules. </li></ul><ul><li>Water molecules join together by HYDROGEN BONDING </li></ul><ul><li>Hydrogen bonds involve the bonding between a hydrogen atom on one molecule and the negative atom of another molecule or element </li></ul>
  10. 10. Water: the versatile solvent <ul><li>The polarity of water molecules allows substances to dissolve in it. </li></ul><ul><li>This ability is due to the water molecules interacting with other charged particles </li></ul><ul><li>HYDROPHILIC : Polar molecules can form hydrogen bonds with polar molecules of water and so they dissolve ( water loving ). </li></ul><ul><li>HYDROPHOBIC : Non-polar substances will not dissolve in water because they cannot form hydrogen bonds with water molecules. </li></ul>
  11. 11. Dissolving in Water (cont…) <ul><li>The ‘rule’ for substances to form a solution is that “ LIKE DISSOLVES LIKE ”. </li></ul><ul><li>Polar solvent + Polar solute = Solution </li></ul><ul><li>Non-polar solvent + Non-polar solute = Solution </li></ul>
  12. 12. Concentration of Solutions <ul><li>The functioning of cells is affected by the concentration of fluids in and around the cells. </li></ul><ul><li>Movement of water and other substances across the cell membrane depends on the comparative concentration of these substances inside & outside of the cell. </li></ul>The solute is more concentrated on this side The solvent is more concentrated on this side
  13. 13. Acids & Bases <ul><li>ACID : a substance that produces hydrogen ions in solution (low pH). </li></ul><ul><li>BASE : a substance that will take hydrogen ions from an acid (high pH) </li></ul><ul><li>The acidity of a solution is measured by pH. </li></ul><ul><li>Chemical reactions within cells can produce acidic or basic substances. </li></ul><ul><li>Blood pH must be kept within very strict limits around 7.4. </li></ul><ul><li>Cell reactions cannot take place if the pH is too high or too low. </li></ul>
  14. 15. Buffering System <ul><li>In order to maintain a stable pH level, a buffering system is enacted. </li></ul><ul><li>This involves maintaining a steady pH by either releasing more hydrogen ions or using up excess hydrogen ions. </li></ul>ACID BASE
  15. 16. Physical Properties of Water
  16. 17. BIOLOGICAL MACROMOLECULES <ul><li>EVERY living cell is involved in synthesising macromolecules for the following: </li></ul><ul><ul><li>Building up body parts of the organism </li></ul></ul><ul><ul><li>Maintain biochemical processes, including: </li></ul></ul><ul><ul><ul><li>Communication </li></ul></ul></ul><ul><ul><ul><li>Transforming energy </li></ul></ul></ul><ul><ul><ul><li>Relaying genetic information </li></ul></ul></ul><ul><li>The four main classes of macromolecules are: </li></ul><ul><ul><li>Proteins, Nucleic Acids, Carbohydrates & Lipids. </li></ul></ul>
  17. 18. <ul><li>Organic molecules are made up of smaller subunits </li></ul><ul><li>The subunits are called monomers </li></ul><ul><li>Polymers are formed when the monomers are bonded together </li></ul>Organic Molecules
  18. 19. Synthesis of Biomacromolecules <ul><li>Some organisms can synthesise their own biomacromolecules whereas others must rely on the substances they have taken in. </li></ul><ul><li>AUTOTROPH : an organism that is able to synthesise organic molecules from inorganic materials. </li></ul><ul><li>CHEMOTROPH : an organism that is able to synthesise organic molecules from specific chemicals. </li></ul><ul><li>HETEROTROPH : an organism that must synthesise their organic molecules from existing organic molecules that are taken in as food. </li></ul>
  19. 20. Polymerisation <ul><li>Biomacromolecules are synthesised inside the cell. </li></ul><ul><li>Polymerisation is the process of smaller repeating units (monomers) being linked together to form long chains called polymers. </li></ul><ul><li>Proteins, carbohydrates & nucleic acids are synthesised in this way and are classed as polymers. </li></ul><ul><li>Lipids do not form polymers. They are composed of distinct chemical groups of atoms. </li></ul>
  20. 21. Condensation Polymerisation <ul><li>When monomers link together, a water molecule is generated. </li></ul><ul><ul><li>The hydroxyl group of one monomer reacts with the hydrogen atom of another monomer. </li></ul></ul><ul><li>This reaction is called Condensation Polymerisation. </li></ul><ul><li> Monomers Polymers </li></ul><ul><li>single units/subunits many linked units/ </li></ul><ul><li> macromolecules </li></ul>polymerisation
  21. 22. CARBOHYDRATES <ul><li>Carbohydrates are the most common compounds in living things. </li></ul><ul><li>Organisms use carbohydrates as an energy source and for structural components. </li></ul><ul><li>Each molecule is composed of the following atoms in the ratio of 1:2:1 </li></ul><ul><ul><li>1Carbon atom : 2Hydrogen atoms : 1 Oxygen atom </li></ul></ul><ul><ul><li>CH 2 O is the formula </li></ul></ul><ul><li>Carbohydrates are classified as: </li></ul><ul><ul><li>Monosaccharides </li></ul></ul><ul><ul><li>Disaccharides </li></ul></ul><ul><ul><li>Polysaccharides </li></ul></ul>
  22. 23. Classification of Carbohydrates
  23. 24. CARBOHYDRATE CLASSES Monosaccharides Disaccharides Polysaccharides Triose Pentose Hexose Maltose Sucrose Lactose Cellulose Starch Glycogen Chitin
  24. 25. Monosaccharides <ul><li>Molecules contain a single sugar unit </li></ul><ul><li>Usually has the formula C 6 H 12 O 6 </li></ul><ul><li>Monosaccharides with the same molecular formula have differing structural formula (arrangement of atoms) </li></ul><ul><li>Soluble in water </li></ul><ul><li>Usually known as ‘sugars’ </li></ul><ul><li>Most important example is GLUCOSE </li></ul><ul><li>Other examples: </li></ul><ul><ul><li>Fructose </li></ul></ul><ul><ul><li>Galactose </li></ul></ul>
  25. 26. Disaccharides <ul><li>Disaccharides form when two monosaccharides combine. </li></ul><ul><li>Examples include: </li></ul><ul><ul><li>Sucrose = glucose + fructose </li></ul></ul><ul><ul><li>Lactose = glucose + galactose </li></ul></ul><ul><ul><li>Maltose = glucose + glucose </li></ul></ul>
  26. 27. Polysaccharides <ul><li>Between ten & several thousand monosaccharides that have joined together </li></ul><ul><li>The most common sugar component is glucose </li></ul><ul><li>The differences in properties relate to the ways in which the glucose molecules are linked together. </li></ul><ul><li>Many polysaccharides are INSOLUBLE in water </li></ul><ul><li>Examples: </li></ul><ul><ul><li>Cellulose: structural component of every plant cell wall </li></ul></ul><ul><ul><li>Starch: main form of storage by most plants </li></ul></ul><ul><ul><li>Glycogen: energy storage in animals </li></ul></ul>
  27. 28. PROTEINS <ul><li>Almost everything a cell is made up of or does depends on PROTEIN. </li></ul><ul><li>Proteins contribute to building many different structures and control the thousands of chemical reactions that maintain life processes. </li></ul>
  28. 29. Building Blocks of Proteins <ul><li>Proteins are made up of AMINO ACIDS. </li></ul><ul><li>There are 20 different amino acids that contribute to the proteins found in cells. </li></ul><ul><li>The basic structure of proteins includes up to thousands of amino acids bonded together to form linear polymers that are folded, twisted or coiled. </li></ul><ul><li>Plants synthesise their own amino acids. </li></ul><ul><li>Animals rely on their diet to obtain their amino acids. </li></ul>
  29. 30. Amino Acids <ul><li>All amino acids have the same basic chemical structure: </li></ul><ul><ul><li>A central carbon atom </li></ul></ul><ul><ul><li>A hydrogen atom </li></ul></ul><ul><ul><li>A carboxyl acid group ( COOH ) </li></ul></ul><ul><ul><li>An amine group ( NH 2 ) </li></ul></ul><ul><ul><li>An “R” group  this group is different for each type of amino acid </li></ul></ul>Carbon Atom Amine Acid Carboxyl group R Group Hydrogen Atom
  30. 31. Amino Acids & ‘R’ Groups <ul><li>The R group can either give the protein molecule a polar region or a non-polar region. </li></ul><ul><li>Non-polar regions are hydrophobic and will usually be tucked inside the protein molecule so as not to be exposed to the watery environment. </li></ul><ul><li>Polar regions are hydrophilic and tend to be on the surface of protein molecules. </li></ul>
  31. 32. Structural Formulae of the 20 Amino Acids used to make proteins in living organisms
  32. 33. Protein Structure <ul><li>Primary Structure : </li></ul><ul><ul><li>refers to the sequence of amino acids that form the polypeptide chain. </li></ul></ul><ul><li>Secondary Structure : </li></ul><ul><ul><li>coiling ( α -helices) & folding ( β -sheets) of the polypeptide chain. </li></ul></ul><ul><ul><li>Other parts remain unchanged (random loops) </li></ul></ul><ul><ul><li>Hydrogen bonds form between segments of the folded chain that are close together and help stabilise the 3-D shape </li></ul></ul>
  34. 35. Protein Structure (cont…) <ul><li>Tertiary Structure : </li></ul><ul><ul><li>Interactions between R groups </li></ul></ul><ul><ul><li>Results in hydrogen bonds, ionic bonds or disulfide bridges between cysteine amino acids. </li></ul></ul><ul><ul><li>Interactions follow the ‘like attracts like’ rule: hydrophilic + hydrophilic; hydrophobic + hydrophobic . </li></ul></ul><ul><ul><li>The polypeptide chain is folded, coiled or twisted into the protein’s functional shape ( conformation ). </li></ul></ul><ul><ul><li>Protein molecules with the same sequence of amino acids will fold into the same shape. </li></ul></ul><ul><ul><li>If an incorrect amino acid is present this will alter the shape of the protein making it non-functional. </li></ul></ul>
  35. 36. Tertiary Structure (cont…)
  36. 37. Protein Structure (cont…) <ul><li>Quaternary Structure : </li></ul><ul><ul><li>Many large complex protein molecules consist of two or more polypeptide chains. </li></ul></ul><ul><ul><li>Hydrogen bonds, ionic bonds and/or covalent bonds hold the polypeptide chains together and gives the overall shape to the molecule. </li></ul></ul>
  37. 38. Protein Structure (cont…)
  38. 39. Functional Diversity of Proteins <ul><li>Motility : movement of cells & organelles </li></ul><ul><li>Structural : support, strength protection </li></ul><ul><li>Enzymes : speed up reactions </li></ul><ul><li>Transport : carry molecules around cell or across membrane </li></ul><ul><li>Hormones : chemical messengers </li></ul><ul><li>Cell-Surface Receptors : act as a ‘label’ to provide identification of the cell </li></ul><ul><li>Neurotransmitters : chemical messengers between neurons </li></ul><ul><li>Immunoglobulins : antigens </li></ul><ul><li>Poisons/toxins : chemicals for defence or capturing food </li></ul>
  39. 40. Conjugated Proteins <ul><li>Proteins whereby the chains of amino acids ‘conjugate’ with other groups </li></ul><ul><li>Occurs most commonly in the nucleus </li></ul><ul><ul><li>Nucleoproteins – contain both protein & nucleic acid </li></ul></ul><ul><li>Haemoglobin is another example of a conjugated protein </li></ul><ul><ul><li>The tertiary structure associates with a heme group </li></ul></ul>
  40. 41. Activating Proteins <ul><li>When proteins, such as insulin, are produced they are inactive </li></ul><ul><li>The protein molecule needs to be activated in some way, usually by an ‘activating enzyme’ </li></ul>
  41. 42. Changes in Proteins <ul><li>Proteins are non-functional if the DNA code is translated incorrectly. </li></ul><ul><li>Other factors that can cause protein molecules to change are: </li></ul><ul><ul><li>High temperatures </li></ul></ul><ul><ul><li>Strong salty solutions </li></ul></ul><ul><ul><li>Very acidic or very alkaline conditions </li></ul></ul><ul><li>Protein molecules will DENATURE under such conditions. </li></ul><ul><li>The shape of the protein molecule will alter. </li></ul><ul><li>If the change is minor it could be reversed and the protein resumes its function. </li></ul><ul><li>If the change is major the protein will no longer be functional. </li></ul>
  42. 43. Proteome <ul><li>PROTEOME : the whole set of proteins produced by a cell. </li></ul><ul><li>PROTEOMICS : the study of proteomes. </li></ul><ul><li>FUNCTIONAL PROTEOMICS : what proteins do in different cells and tissues. </li></ul>
  43. 44. LIPIDS <ul><li>Lipids have three important functions: </li></ul><ul><ul><li>Energy storage </li></ul></ul><ul><ul><li>Structural component of cell membranes </li></ul></ul><ul><ul><li>Specific biological processes (eg: transmission of chemical signals both within and between cells). </li></ul></ul><ul><li>All lipid molecules contain carbon, hydrogen & oxygen </li></ul><ul><li>Lipids contain relatively little water </li></ul><ul><li>Lipid molecules carry more energy per molecule than any other kind of compound found in plants or animals. </li></ul>
  44. 45. Fats <ul><li>Made up of two kinds of molecules: </li></ul><ul><ul><li>Fatty acid </li></ul></ul><ul><ul><li>Glycerol </li></ul></ul><ul><li>Triglycerides are a common form of fats </li></ul>
  45. 46. Triglycerides <ul><li>Triglycerides: subunits of fats & oils </li></ul><ul><li>Three fatty acids attach to the glycerol backbone. </li></ul><ul><li>SATURATED fats: </li></ul><ul><ul><li>Found in animals </li></ul></ul><ul><ul><li>Solid </li></ul></ul><ul><ul><li>Fatty acids are packed closely in a straight line </li></ul></ul><ul><li>UNSATURATED fats: </li></ul><ul><ul><li>Found in plants </li></ul></ul><ul><ul><li>Liquid </li></ul></ul><ul><ul><li>Fatty acids form double bonds and are not packed closely together </li></ul></ul>
  46. 47. Phospholipid <ul><li>Two fatty acids attached to a glycerol </li></ul><ul><li>Also have a phosphate group attached to the glycerol </li></ul><ul><li>Phospholipids are the major component of cell membranes </li></ul>
  47. 48. Classification of Lipids <ul><li>Lipids are classified according to their solubility </li></ul><ul><li>The solubility of lipids is dependent on the shape of their molecules and the intramolecular bonding. </li></ul><ul><li>Lipid molecules have large non-polar hydrophobic regions meaning they are insoluble in water. </li></ul><ul><li>Non-polar lipid molecules CAN dissolve in other non-polar substances. </li></ul><ul><li>Some other types of lipid molecules have both a hydrophilic region and a hydrophobic region. </li></ul>
  48. 49. TYPES OF LIPIDS Fats & Oils Terpenes Waxes & Cutins Oils in plants; Fat deposits under the skin Essential oils giving plants their colour & odour Waterproof coating on leaves, fruits, insects Phospholipids Glycolipids Steroids Form part of cell membranes Provide energy; marker on cell membrane Hormones, vitamin D, cholesterol
  49. 50. NUCLEIC ACIDS <ul><li>Nucleic acids are long molecules made up of three distinct chemical parts. </li></ul><ul><li>Nucleic acids store information in a chemical code for the production of proteins. </li></ul><ul><li>Nucleic acids are the GENETIC MATERIAL for every living organism. </li></ul><ul><li>DNA = deoxyribonucleic acid </li></ul><ul><li>RNA = ribonucleic acid </li></ul>
  50. 51. DNA & RNA <ul><li>DNA </li></ul><ul><li>Linear molecule </li></ul><ul><li>Double stranded </li></ul><ul><li>The two strands wind around each other to form a double helix </li></ul><ul><li>Made up of nucleotides </li></ul><ul><li>Located in the nucleus </li></ul><ul><li>Deoxyribose is the sugar component </li></ul><ul><li>Nitrogenous bases: </li></ul><ul><ul><li>Adenine </li></ul></ul><ul><ul><li>Guanine </li></ul></ul><ul><ul><li>Cytosine </li></ul></ul><ul><ul><li>Thymine </li></ul></ul><ul><li>RNA </li></ul><ul><li>Linear molecule - shorter than DNA </li></ul><ul><li>Single stranded </li></ul><ul><li>Made up of nucleotides </li></ul><ul><li>Formed in the nucleus then moves to the ribosomes in the cytoplasm to function. </li></ul><ul><li>Ribose is the sugar component – ribose has one less oxygen atom than deoxyribose </li></ul><ul><li>Nitrogenous bases: </li></ul><ul><ul><li>Adenine </li></ul></ul><ul><ul><li>Guanine </li></ul></ul><ul><ul><li>Cytosine </li></ul></ul><ul><ul><li>Uracil </li></ul></ul>
  51. 52. Nucleotides <ul><li>Nucleotides are the monomers that bond together to make the nucleic acid polymers. </li></ul><ul><li>Nucleotides have 3 distinct chemical parts: </li></ul><ul><ul><li>A 5-carbon sugar (ribose or deoxyribose) </li></ul></ul><ul><ul><li>A Negatively charged phosphate group </li></ul></ul><ul><ul><li>An organic nitrogenous base </li></ul></ul><ul><ul><ul><li>Adenine - A </li></ul></ul></ul><ul><ul><ul><li>Guanine - G </li></ul></ul></ul><ul><ul><ul><li>Cytosine - C </li></ul></ul></ul><ul><ul><ul><li>Thymine - T </li></ul></ul></ul>
  52. 53. Nucleotides (cont…) <ul><li>The sugar molecule of one nucleotide binds with the phosphate group of the next nucleotide. </li></ul><ul><li>The nitrogenous base is left sticking out and faces the opposite nitrogenous base from the adjoining DNA strand </li></ul><ul><li>Hydrogen bonds hold the nitrogenous base pairs together forming the ‘rungs’ of the helix. </li></ul><ul><li>The bases pair according to the following rule: </li></ul><ul><ul><li>A pairs with T </li></ul></ul><ul><ul><li>G pairs with C </li></ul></ul>
  53. 54. Chemical structure of DNA
  54. 55. DNA ~ function <ul><li>The sequence of nucleotides in DNA codes for amino acids that will form a particular protein. </li></ul><ul><li>GENES: the segments of DNA that code for protein formation </li></ul><ul><li>GENOME: the total set of genes that each cell of an organism carries. </li></ul><ul><li>GENOMICS: the study of genes and the way they interact with each other. </li></ul>
  55. 56. DNA ~ function (cont…) <ul><li>DNA passes on information from one generation to the next. </li></ul><ul><li>DNA, usually in the form of chromosomes, is located in the nucleus of cells. </li></ul><ul><li>One of the strands of DNA acts as a template so that the complimentary strand of DNA can be formed (following the base pairing rule). </li></ul><ul><li>DNA is also used as a template for the formation of RNA. </li></ul><ul><li>Some DNA is located in mitochondria & in chloroplasts. </li></ul><ul><li>Biotechnology has allowed for the manipulation & modification of DNA. </li></ul>
  56. 57. RNA ~ function <ul><li>The major function of RNA is to produce proteins. </li></ul><ul><li>GENE EXPRESSION: the information from the DNA strand is taken by the RNA and the appropriate proteins produced. </li></ul><ul><li>mRNA: messenger RNA – the code from DNA is transferred to mRNA in a process called transcription. The mRNA strand moves out of the nucleus into the cytoplasm and attaches to the ribosomes. </li></ul><ul><li>rRNA: ribosomal RNA – ribosomes are composed of rRNA and other proteins. </li></ul><ul><li>tRNA: transfer RNA – each tRNA molecule has an amino acid attached at one end and an anti-codon on the other end. The anti-codon pairs up with the corresponding codon on the mRNA. This ensures the correct sequence of amino acids for the polypeptide chain. </li></ul>
  57. 59. tRNA molecule