1.UNIT 3 BIOLOGY EARLY COMMENCEMENT November 2010

2. EARLY COMMENCEMENT HANDBOOK UNIT 3 BIOLOGY 2 3. 3 4. 4 5. Year 12 Biology Textbook 5 6. 6 7. 7 8. 8 9. 9 10. 10 11. 11 12. 12 13. 13 14. 14 15. LOTUS ~ BIOMACROMOLECULES 15 16. The Chemical Nature of Cells Chapter 1 Unit 3 Biology 17. KEY KNOWLEDGE The Chemical Nature of Cells By the end of this chapter, you should: Enhance your knowledge & understanding of the synthesis of biomacromolecules such as polysaccharides, lipids, proteins and nucleic acids. Enhance your knowledge & understanding of the structure & function of nucleic acids. Understand the structural diversity of proteins & how this diversity relates to the variety of functions that proteins carry out in living organisms Develop an understanding of the concept of the proteome of an individual or a cell. 17 18. The Chemical Basis of Life All cells are composed of atoms and molecules which interact in thousands of simultaneous chemical reactions. Organisms are composed of chemicals that react with each other and with the substances in the18 19. Biochemistry The study of the chemicals involved in living organisms is called biochemistry. Investigations in biochemistry allow for the development of pharmaceuticals, vaccines and improvements in medical diagnoses. GENOMICS & PROTEOMICS are two recent fields of science dealing with the study DNA and proteins. 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. 19 20. WATER ~ why is it so important? ALL known life forms require water to survive 75% - 85% of a cells weight is water Almost all substances and chemical reactions of biological significance require water. Cells are constantly bathed by a watery solution Water is essential for the cycling of matter between the living & non-living parts of ecosystems. 20 21. Chemical Properties of Water H2O Water can exist as a solid (ice), a gas (steam) or as a liquid Water molecules are highly polar. The oxygen part of the molecule is negative so it is attracted to the positive end of other water molecules. Water molecules join together by HYDROGEN BONDING Hydrogen bonds involve the bonding between a hydrogen atom on one molecule and the negative atom of another molecule or element21 22. Water: the versatile solvent The polarity of water molecules allows substances to dissolve in it. This ability is due to the water molecules interacting with other charged particles HYDROPHILIC: Polar molecules can form hydrogen bonds with polar molecules of water and so they dissolve (water loving). HYDROPHOBIC: Non-polar substances will not dissolve in water because they cannot form hydrogen bonds with water molecules. 22 23. BIOLOGICAL MACROMOLECULES EVERY living cell is involved in synthesising macromolecules for the following: Building up body parts of the organism Maintain biochemical processes, including: Communication Transforming energy Relaying genetic information The four main classes of macromolecules are: Proteins Nucleic Acids 23 24. Organic Molecules Organic molecules are made up of smaller subunits The subunits are called monomers Polymers are formed when the monomers are bonded together 24 25. Synthesis of Biomacromolecules Some organisms can synthesise their own biomacromolecules whereas others must rely on the substances they have taken in. AUTOTROPH: an organism that is able to synthesise organic molecules from inorganic materials. CHEMOTROPH: an organism that is able to synthesise organic molecules from specific chemicals. HETEROTROPH: an organism that must synthesise their organic molecules from existing organic molecules that are taken in as food. 25 26. Polymerisation Biomacromolecules are synthesised inside the cell. Polymerisation is the process of smaller repeating units (monomers) being linked together to form long chains called polymers. Proteins, carbohydrates & nucleic acids are synthesised in this way and are classed as polymers. Lipids do not form polymers. They are composed of distinct chemical groups of atoms. 26 27. Condensation Polymerisation When monomers link together, a water molecule is generated. The hydroxyl group of one monomer reacts with the hydrogen atom of another monomer. This reaction is called Condensation Polymerisation. Monomers Polymers single units/subunits many linked units/ macromolecules polymerisation 27 28. CARBOHYDRATES Carbohydrates are the most common compounds in living things. Organisms use carbohydrates as an energy source and for structural components. Each molecule is composed of the following atoms in the ratio of 1:2:1 1Carbon atom : 2 Hydrogen atoms : 1 Oxygen atom CH2O is the formula Carbohydrates are classified as: Monosaccharides Disaccharides Polysaccharides 28 29. Classification of Carbohydrates 29 30. Monosaccharides Molecules contain a single sugar unit Usually has the formula C6H12O6 Monosaccharides with the same molecular formula have differing structural formula (arrangement of atoms) Soluble in water Usually known as sugars Most important example is GLUCOSE Other examples: Fructose Galactose 30 31. Disaccharides Disaccharides form when two monosaccharides combine. Examples include: Sucrose = glucose + fructose Lactose = glucose + galactose Maltose = glucose + glucose 31 32. Polysaccharides Between ten & several thousand monosaccharides that have joined together The most common sugar component is glucose The differences in properties relate to the ways in which the glucose molecules are linked together. Many polysaccharides are INSOLUBLE in water Examples: Cellulose: structural component of every plant cell wall Starch: main form of storage by most plants 32 33. 2009 VCAA Exam Question An important structural carbohydrate in plants is A. B. C. D. cellulose glucose. chitin. glycogen. 33 34. PROTEINS Almost everything a cell is made up of or does depends on PROTEIN. Proteins contribute to building many different structures and control the thousands of chemical reactions that maintain life processes. 34 35. Building Blocks of Proteins Proteins are made up of AMINO ACIDS. There are 20 different amino acids that contribute to the proteins found in cells. The basic structure of proteins includes up to thousands of amino acids bonded together to form linear polymers that are folded, twisted or coiled. Plants synthesise their own amino acids. Animals rely on their diet to obtain their amino acids. 35 36. Amino Acids All amino acids have the same basic chemical structure: A central carbon atom A hydrogen atom A carboxyl acid group (COOH) An amine group (NH2) An R group this group is different for each type of amino acid Carbon Atom Amine Acid Carboxyl group R Group Hydrogen Atom 36 37. Protein Structure Primary Structure: refers to the sequence of amino acids that form the polypeptide chain. Secondary Structure: coiling (-helices) & folding (-sheets) of the polypeptide chain. Other parts remain unchanged (random loops) Hydrogen bonds form between segments of the folded chain that are close together and help stabilise the 3-D shape 37 38. PRIMARY STRUCTURE SECONDARY STRUCTURE 38 39. Protein Structure (cont) Tertiary Structure: Interactions between R groups Results in hydrogen bonds, ionic bonds or disulfide bridges between cysteine amino acids. Interactions follow the like attracts like rule: hydrophilic + hydrophilic hydrophobic + hydrophobic. The polypeptide chain is folded, coiled or twisted into the proteins functional shape (conformation). Protein molecules with the same sequence of amino acids will fold into the same shape. If an incorrect amino acid is present this will alter the shape of the protein making it non-functional. 39 40. Tertiary Structure (cont) 40 41. Protein Structure (cont) Quaternary Structure: Many large complex protein molecules consist of two or more polypeptide chains. Hydrogen bonds, ionic bonds and/or covalent bonds hold the polypeptide chains together and gives the overall shape to the molecule. 41 42. Protein Structure (cont) 42 43. Functional Diversity of Proteins Motility: movement of cells & organelles Structural: support, strength protection Enzymes: speed up reactions Transport: carry molecules around cell or across membrane Hormones: chemical messengers Cell-Surface Receptors: act as a label to provide identification of the cell Neurotransmitters: chemical messengers between neurons Immunoglobulins: antigens Poisons/toxins: chemicals for defence or capturing food 43 44. 2009 VCAA Exam Question The diagram below shows the structure of a particular protein molecule. 44 45. 2009 VCAA Exam Question (cont)a. The protein contains two distinctive types of polypeptide chains labelled X and Y. What are the names of these two types? Chain X _____________________ Chain Y ______________________ (2 marks) b. Name a polysaccharide found in animals and describe its function. Name: _________________________ Function: ______________________________________ (2 marks) c. What is the function of cholesterol in cell membranes? __________________________________________________ __________________________________________________ ___________________________________________ (1 mark) 45 46. LIPIDS Lipids have three important functions: Energy storage Structural component of cell membranes Specific biological processes (eg: transmission of chemical signals both within and between cells). All lipid molecules contain carbon, hydrogen & oxygen Lipids contain relatively little water Lipid molecules carry more energy per molecule than any other kind of compound found in plants or animals. 46 47. Fats Made up of two kinds of molecules: Fatty acid Glycerol Triglycerides are a common form of fats 47 48. Triglycerides Triglycerides: subunits of fats & oils Three fatty acids attach to the glycerol backbone. SATURATED fats: Found in animals Solid Fatty acids are packed closely in a straight line UNSATURATED fats: Found in plants Liquid Fatty acids form double bonds and are not packed closely together 48 49. Phospholipid HYDROPHOBIC TAIL: Two fatty acids chains Repel water HYDROPHILIC HEAD: Phosphate group attached to the glycerol head Attracted to water Phospholipids are the major component of cell membranes 49 50. Phospholipids & Plasma Membrane Structure 50 51. 2009 VCAA Exam Question B. involved in active transport. C. part of glycoprotein molecules. D. transported by rough endoplasmic reticulum A. used as an energy source. Lipids are 51 52. NUCLEIC ACIDS Nucleic acids are long molecules made up of three distinct chemical parts. Nucleic acids store information in a chemical code for the production of proteins. Nucleic acids are the GENETIC MATERIAL for every living organism. DNA = deoxyribonucleic acid 52 53. DNA vs RNA DNA Linear molecule Double stranded The two strands wind around each other to form a double helix Made up of nucleotides Located in the nucleus Deoxyribose is the sugar component Nitrogenous bases: Adenine Guanine Cytosine Thymine RNA Linear molecule - shorter than DNA Single stranded Made up of nucleotides Formed in the nucleus then moves to the ribosomes in the cytoplasm to function. Ribose is the sugar component ribose has one less oxygen atom than deoxyribose Nitrogenous bases: Adenine Guanine Cytosine Uracil 53 54. Nucleotides Nucleotides are the monomers that bond together to make the nucleic acid polymers. Nucleotides have 3 distinct chemical parts: A 5-carbon sugar (ribose or deoxyribose) A Negatively charged phosphate group An organic nitrogenous base Adenine - A Guanine - G Cytosine - C 54 55. Nucleotides (cont) The sugar molecule of one nucleotide binds with the phosphate group of the next nucleotide. The nitrogenous base is left sticking out and faces the opposite nitrogenous base from the adjoining DNA strand Hydrogen bonds hold the nitrogenous base pairs together forming the rungs of the helix. The bases pair according to the following rule: A pairs with T (T pairs with A) G pairs with C (C pairs with G) This is known as the COMPLIMENTARY BASE PAIRING RULE 55 56. Chemical structure of DNA 56 57. DNA ~ function The sequence of nucleotides in DNA codes for amino acids that will form a particular protein. GENES: the segments of DNA that code for protein formation GENOME: the total set of genes that each cell of an organism carries. GENOMICS: the study of genes and the way they interact with each other. 57 58. DNA ~ function (cont) DNA passes on information from one generation to the next. DNA, usually in the form of chromosomes, is located in the nucleus of cells. 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). DNA is also used as a template for the formation of RNA. Some DNA is located in mitochondria & in chloroplasts. Biotechnology has allowed for the manipulation & modification of DNA. 58 59. MAKING mRNA YouTube Transcription YouTube - mRNA splicing 59 60. Transcription The mRNA used to make proteins is transcribed from a particular region of DNA within the nucleus of a cell. The DNA unwinds and the enzyme RNA polymerase binds to a promoter site at the 5' end. The enzyme moves along the DNA and at each nucleotide a complementary RNA nucleotide is added to the growing mRNA strand. The transcribed mRNA (primary transcript or pre- mRNA) will contain all the nucleotide sequences within a given region of DNA. Some of the transcribed code contains introns, which do not translate into proteins. These have to be spliced out of the mRNA before it can move to the ribosome. When introns are spliced out by enzymes in the 60 61. Animations on Transcription http://207.207.4.198/pub/flash/26/trans menu_s.swf http://www- class.unl.edu/biochem/gp2/m_biology/ animation/gene/gene_a2.html http://www.johnkyrk.com/DNAtranscrip tion.html http://medlab.lzu.edu.cn/image/flash/8. swf http://www.fed.cuhk.edu.hk/~johnson/t eaching/genetics/animations/transcript61 62. Pre-mRNA to mature mRNA Non-coding regions (introns) are spliced out Methylated cap is added on the 5 end Poly-A tail is added on the 3 end 62 63. RNA ~ function The major function of RNA is to produce proteins. GENE EXPRESSION: the information from the DNA strand is taken by the RNA and the appropriate proteins produced. 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. rRNA: ribosomal RNA ribosomes are composed of rRNA and other proteins. 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 63 64. 2009 VCAA Exam Question mRNA is A. a double-stranded molecule. B. found only in eukaryotic cells. C. found exclusively in the nucleus. D. formed during transcription of DNA 64 65. PROTEIN SYNTHESIS YouTube - Translation 65 66. Translation mRNA moves into the cytoplasm and is used as a template to direct the assembly of amino acids at the ribosome. The code on the mRNA is read as a triplet of nucleotides, a codon. Given that there are 20 amino acids commonly found in cells, four nucleotides alone cannot code for this many different molecules. The nucleotides cannot be read in pairs because this will produce only 16 different combinations. The nucleotides must be read as groups of three, which will be more than enough combinations to make the 20 amino acids. Some amino acids have more than one codon sequence. 66 67. Translation (cont) To begin the translation of proteins, the ribosomes attach to the codon sequence AUG on the mRNA. As the ribosome passes each codon on the mRNA, transfer RNA (tRNA) with a complementary anticodon binds to the exposed codon on the mRNA. At the top of the tRNA molecule is a specific amino acid that attaches to the growing polypeptide chain. Of the 64 codons, three of them (UAA, UAG, UGA) are stop codons and will stop the synthesis. 67 68. tRNA molecule 68 69. 69 70. 70 71. The codon sequences that code for all 20 amino acids 71 72. TRANSLATION: protein synthesis at the ribosome 1. New amino acid being added ~ PHE corresponds to the mRNA codon UUU 2. The amino acids join to form the growing polypeptide chain 3. The tRNA has detached from the amino acid and will leave the ribosome to find another free-floating amino acid in the cytoplasm. 4. Three of the bases on the mRNA form a base-triplet, called a CODON. 72 73. 73 74. 74 75. 75 76. Animations on Translation http://www- class.unl.edu/biochem/gp2/m_biology/a nimation/gene/gene_a3.html http://www.biostudio.com/demo_freema n_protein_synthesis.htm http://highered.mcgraw- hill.com/sites/0072437316/student_view 0/chapter15/animations.html# 76 77. 2009 VCAA Exam Question a. A section of one of the strands of a DNA molecule has the sequence of bases shown. DNA: C T T A C A T T A C T C In the spaces below, enter the sequence of bases in the corresponding mRNA which is complementary to this DNA. (1 mark) mRNA 77 78. 2009 VCAA Exam Question (cont) b. The percentage of base T in a molecule of DNA is 30%. What is the percentage of G bases in the same DNA molecule? ______________________________ (1 mark) Another type of nucleic acid is tRNA. c. i. Where is tRNA found in a cell? ___________________________ ii. Describe the role of tRNA. ____________________________ ____________________________ (1 mark) 78 79. 2009 VCAA Exam Question (cont)d. The table shows the names of six amino acids together with some of their DNA codes. Use the information in the table and write the order of amino acid coded for by the DNA sequence given in part a. __________________________________ (1 mark) AMINO ACIDS DNA TRIPLET(S) cysteine ACA, ACG glutamic acid CTT, CTC aspartic acid CTA, CTG asparagine TTA, TTG leucine GAA, GAG, GAT, GAC methionine TAC 79 80. 2009 VCAA Exam Question (cont) Nucleic acids are made up of nucleotides. Each nucleotide consists of three components, sugar (S), phosphate (P) and nitrogen base (B), linked together in a particular way. e. In the empty box, draw a diagram to show the way the three components are joined to make a nucleotide. (1 mark) Use the following symbols in your diagram 80