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2.1 Week 2 Chemical Nature of Cells Area of Study 1 Molecules of Life This week you will study some of the biologically important organic molecules. Key knowledge Properties of biologically important organic molecules Synthesis of biomacromolecules Key skills Investigate and inquire scientifically Apply biological understandings Communicate biological information and understanding Tasks this week relate to outcome 1 Analyse and evaluate evidence from practical investigation related to biochemical processes. Relevant websites – see online biology course environment. Go to the Links section. Glossary terms for Week 2 can be found here: http://quizlet.com/_c46j 2.2 Chemical Nature of Cells Introduction Read carefully through this week’s work before completing the tasks. Check for any practical exercises that may require you to obtain materials and equipment. This is Week 2 – your second week of work. You do not need a text book to complete it. Make sure that you have ordered the required text book for future weeks of work. The Objectives By the end of this week you should be able to: Describe the basic structures of carbohydrates, proteins, nucleic acids and lipids Make a model of a protein Read through the following text and complete the tasks or questions that follow. Use your own A4 paper or send work as MSWord documents attached to an email. The following text is courtesy of Nelson Biology VCE Units 3 and 4, second edition. Synthesis of Biomacromolecules Autotroph An organism that makes its own food from light energy or chemical energy without eating; most green plants, many protists (one-celled organisms such as slime moulds) and most bacteria are autotrophs. Chemotroph An organism that obtains its energy from the oxidation of chemical compounds. Heterotrophs Organisms that consume other organisms as food; organisms that are not able to make organic molecules from simple inorganic compounds. Some organisms are able to synthesise their own biological macromolecules, whereas others synthesise them from organic compounds that they have ingested. Organisms that can synthesise their own organic compounds from the inorganic materials that they take in from their surroundings are called autotrophs (self-feeders). For example, seaweeds, eucalypts, grass and microscopic algae all produce the basic building unit – simple sugars – through the process of photosynthesis. From the products, autotrophs then synthesise the other kinds of organic compounds that they need. Some autotrophic organisms, such as certain kinds of bacteria, are able to synthesise their organic requirements through chemical processes other than photosynthesis. These organisms are described as chemosynthetic autotrophs or chemotrophs, and are typically found in extreme conditions, such as in the depths of the ocean near hydrothermal vents, in thermal springs or in places deprived of oxygen or light. Heterotrophs, such as humans, have to synthesise their own biomacromolecules from existing organic compounds. Heterotrophs have to take in a range of organic compounds in their food, which they then 2.3 breakdown into simpler substances. These are then synthesised, or built up, into the kinds or organic compounds that are required by the organism. Making a Polymer Large biomacromolecules are synthesised on site inside the cell. Proteins nucleic acids and complex carbohydrates are built up by linking smaller repeating molecules, each called a monomer (mono – one, mer – unit), to form long chains called polymers (poly – many). This process is known as polymerisation. Even though lipids are large biomolecules, they are not polymers; they are composed of distinct chemical groups of atoms. Monomers link together when the hydroxyl (-OH) group of one monomer reacts with a hydrogen atom of another monomer, forming a water molecule. Thus, the reaction is called condensation polymerisation. Polymerisation Single units (monomers) → many linked units (polymer) (small units) (macromolecules) Successive monomers are added in the same way to produce a long polymer chain (see Figure 2.1 above). SEND… Question 1 Which macromolecules are polymers? Question 2 Distinguish between autotrophs and heterotrophs in sourcing nutrients to build their macromolecules. Read through the following text and complete the tasks or questions that follow. Use your own A4 paper or send work as MSWord documents attached to an email. The following text is courtesy of Heinemann Biology Two 4 th Edition. 2.4 Carbohydrates Carbohydrates are the most abundant organic compounds in nature. They Are an important source of chemical energy for living organisms; Are used as energy reserves in plants and animals; Form structural components such as cell walls; Form part of both DNA and RNA; Combine with proteins and lipids to form glycoproteins and glycolipids as in cell membranes. Carbohydrates are found on the surface of every cell in our bodies and are involved in a wide variety of interactions. Cell surface glycoproteins identify a cell as being of a particular type and are important in cell-cell communication and adherence. Carbohydrates are compounds made of carbon, hydrogen and oxygen. In simple carbohydrates (such as glucose) the hydrogen and oxygen are present in the same proportions as in water: there are two hydrogens for each oxygen atom. The general formula is Cn(H2O)n (for example, glucose is C6H12O6). There are three main groups of carbohydrates – monosaccharides, disaccharides and polysaccharides (Figure 2.1). The basic subunits of carbohydrates are the simple sugars, called monosaccharides, meaning ‘single sugars’. For example, glucose is a simple sugar that is formed during photosynthesis. Common 6-carbon sugars include glucose, galactose and fructose. When two sugars are joined together they form a disaccharide (meaning ‘two sugars’) and a molecule of water is removed. Milk sugar (lactose) is made from glucose and galactose whereas can sugar (sucrose) is made from glucose and fructose. When many sugars are joined together they form long chains or polymers called polysaccharides (‘many sugars’). Cellulose, the major component of plant cell walls, is the most abundant organic molecule on Earth. Starch is the polysaccharide used for energy storage in plants. In animals, the polysaccharide glycogen is used or energy storage. These three polysaccharides are each composed of glucose subunits, but they differ in a number of ways (Figure 2.1). Starch is a long chain molecule, glycogen has a branching structure and cellulose has additional bonds cross-linking between the subunits of the chain. 2.5 Table 2.1 Classes of Carbohydrates Carbohydrate Example Monosaccharides Triose (mono=one, saccharide=sugar) Pentose eg. Ribose Hexose eg. Glucose Disaccharides Maltose (di=two) Sucrose Lactose Polysaccharides Cellulose Starch Glycogen Chitin Description Location and function Single chain of carbon atoms to Glyceraldehyde which hydroxyl groups are attached. Soluble in water. Five carbon atoms in backbone Found in RNA molecules Six carbon atoms in backbone Makes jelly beans sweet; It is an ideal quick energy fix. Two glucose molecules bonded Found in high concentrations in some grains Glucose and fructose bonded Table sugar, sugar cane, sugar beet Glucose and galactose bond In milk together Complex carbohydrates Energy storage and composed of several hundred structural support to several thousand monomers in chains Straight chains that lie next to Form tough, insoluble fibres each other, promoting giving structural support to hydrogen bonding between plant cells them and producing tight bundles called microfibrils. Mixture of two different Energy storage in plants polysaccharides linked in (e.g. starch grains in seeds branched and sometimes eg of wheat, corn) twisted chains Storage compounds in animals Energy storage in muscles and liver of animals Cellulose-like polymer; each Present in the hard monomer glucose molecule has exoskeleton of insects and of an N-containing group crustaceans, such as crabs; attached. cell walls of fungi, such as mushrooms. The above table is courtesy of Nelson Biology VCE, Units 3 and 4, second edition. SEND… Question 4 Describe the chemical composition of a carbohydrate. Question 5 What distinguishes the three classes of carbohydrates from each other? 2.6 Question 6 Glycogen and starch are called storage polysaccharides. In what organisms would you find? a) glycogen b) starch Read through the following text and complete the tasks or questions that follow. Use your own A4 paper or send work as MSWord documents attached to an email. The following text is courtesy of Heinemann Biology Two, 4 th Edition and Nelson Biology VCE Units 3 and 4, 2nd Edition. Proteins – The Work Horses of the Cell Virtually everything a cell is or does depends on the proteins it contains. What does your hair have in common with the feathers of birds, the rattle of a rattlesnake and the spines of an echidna? They are all composed of a strong fibrous protein known as keratin. Keratin is just one of an amazing variety of proteins produced by the activities of cells. The whole set of proteins produced by a cell is called its proteome and the study of proteomes is proteomics – a term first used in 1994 by Marc Wilkins of Macquarie University, Sydney. Functional proteomics refers particularly to what proteins do in different cells and tissues. Proteins are more complex molecules than carbohydrates and make up more than 50% of the dry weight of cells. All proteins contain carbon, hydrogen, oxygen and nitrogen. Many also contain sulphur, and often phosphorus and other elements. There are thousands of different kinds of proteins and their functions vary widely (see Table 2.3). Enzymes catalyse cellular reactions, hormones communicate information throughout the body of an organism, while other proteins form structural components of cells. Some proteins act as carrier molecules, such as haemoglobin which transports oxygen. Proteins may also form channels in membranes, which is important for the transport of certain molecules across membranes. Proteins are composed of chains of smaller subunits called amino acids. Because amino acids in proteins are linked by a certain kind of bond called a peptide bond, proteins are called polypeptides (polypeptide meaning ‘many peptide bonds’). There are 20 different amino acids commonly found in proteins. While carbohydrates and lipids are similar in most plants and animals, each kind of organism has its own unique proteins. Amino acids are small molecules that have the same basic structure – a central carbon atom to which are attached a hydrogen atom, a carboxyl acid group (COOH), an amino group (NH2) and what is called an R 2.7 group. It is the difference in the R group that distinguishes one amino acid from another and gives each amino acid its particular chemical properties. The 20 different R groups mean that there are 20 different amino acids. Some R groups make the protein molecule polar and other kinds of R groups make regions of the protein molecule non-polar. These hydrophobic regions are generally tucked away within the protein molecule, away from the water molecules in the aqueous environment. Eleven amino acids are hydrophilic. They tend to be on the surface of protein molecules because of their affinity (attraction) for the polar water molecules in their environment. Table 2.3 The functional diversity of proteins. (Try to remember the ones in bold). Protein type Motility Structural Enzymes Transport Hormones Cell-surface receptors Neurotransmitters Immunoglobulins Poisons or toxins Function (job) Examples Allow movement of cells and their organelles. Provides support, strength and protection Catalyse biochemical reactions Tubulin forms microtubules to move flagella, cilia, chromosomes and organelles. Actin and myosin work together to move muscles. Collagen (a fibrous protein) supports body tissues. Fibroin makes a spider web stronger, weight for weight, than steel. Keratin forms nails and hair. Catalase removes toxic hydrogen peroxide from cells by breaking it down into water and oxygen. All organisms have DNA polymerase, an enzyme that duplicates genetic information (DNA). Lysozyme is an enzyme found in egg white, tears, and other secretions. It is responsible for breaking down the polysaccharide walls of many kinds of bacteria and thus it provides some protection against infection. Haemoglobin carries oxygen to body cells. Porin forms a hydrophilic pore in the outer membrane of mitochondria for the passage of molecules. Carry molecules from one location to another or across cell membranes Signalling between different cell types; stimulation or inhibition Label cells as targets for hormones, viruses, growth factors, recognition of ‘self’, transmission of nerve impulse Signalling between neurons Insulin travels in the blood and binds to cell receptors to trigger the uptake of glucose. Follicle-stimulating hormone (FSH) stimulates the maturation and release of ova (female gametes). Insulin receptors blind insulin to trigger the uptake of glucose by the cell. Rhodopsin in the retina membrane allows us to see dim light. Major histocompatibility complex (MHC) markers allow the immune system to recognise ‘self’ so the body does not destroy its own cells. Endorphins activate nerve receptors to alleviate pain or stress. Enkephalins act as analgesics (pain relievers) and sedatives affecting mood and motivation. Recognition of foreign Antibodies cause foreign material to clump so it can be substances (antigens) ingested by large white cells (macrophages). Chemicals for defence Red means danger. The castor oil plant produces the and to aid in the deadly toxin, ricin. Snake venom contains many proteins capture of food that can paralyse and digest prey. 2.8 The properties of many proteins are determined by their shape, which is determined by their amino acid sequence. There are four levels of proteinstructure – primary, secondary, tertiary and quaternary. Primary structure is the actual sequence of amino acids in a polypeptide. The particular sequence causes arrangements of the polypeptide into secondary structures, such as pleating or coiling, held by hydrogen bonds between the amino acids. The protein then folds into its distinctive threedimensional shape, which is its tertiary structure, usually fibrous or globular. When two or more polypeptides are joined together, such as in the haemoglobin molecule it is called a Quaternary structure. Primary structure DNA determines the sequence of amino acids in the polypeptide. Amino acids bond together in the process of condensation polymerisation and each bond between two adjacent amino acids is called a peptide bond. Secondary structure Once the polypeptide chain is formed, various parts undergo coiling and folding due to hydrogen bonding between the various amino acids that are present. Tight coils are known as ά-helices and the folding forms are known as β-sheets. Other parts of the polypeptide chain remain unchanged and are called random loops. β-sheets and random loops form the basis of the active site in enzymes, being less rigid than ά-helices. Figure 2.2 (a) The order of amino acids in the polypeptide is called the primary structure. (b) Coiling (ά-helices) and folding (β-sheets) Results in the secondary structure of a protein. Coils and sheets are connected by random loops. Tertiary structure Hydrophilic R groups attract other hydrophilic R groups and hydrophobic R groups attract other hydrophobic R groups according to the ‘like attracts like’ rule. These interactions between the R groups of the amino acids cause the polypeptide chains to become folded, coiled or twisted into the protein’s functional shape or conformation. The interactions between the R groups of amino acids result in hydrogen bonds, ionic bonds or disulfide bridges between adjacent cysteine amino acids. Protein molecules with the same sequence of amino acids will fold into the same shape. A change to just one amino acid will alter the shape of the protein molecule and it may not function properly. 2.9 Figure 2.3 The secondary structure shown above, changes shape according to the interactions between the R groups. The specific function of a protein is determined by its tertiary structure. The tertiary structure arises from interactions between R groups of amino acids in the polypeptide chain. The interactions between the R groups will pull the protein chain into a ‘ball’ shape which is the tertiary structure. See Figure 2.4 below. Figure 2.4 A protein in its tertiary structure as a spherical globular shaped molecule. It is the tertiary structure that usually determines the function of the protein – its biological functionality, however the secondary structure may also determine function (see the past exam question at the end of this Week’s work). Some proteins form long, closely packed fibres that are structural components of cells as in silk. Most proteins form spherical or globular-shaped molecules that are soluble in water and perform a variety of functional tasks. Quaternary structure Many large, complex protein molecules consist of two or more polypeptide chains. Haemoglobin, for example, which carries oxygen in the blood, consists of four polypeptide chains (also referred to as amino acid chains). A variety of hydrogen bonds, ionic bond and covalent bonds hold the polypeptide chains together and gives the overall shape to the molecule. Changing the nature of proteins The function of protein molecules may change as a result of a number of factors, apart from misreading the DNA code for proteins. Proteins may lose their functional shape if they are exposed to high temperatures, strong salty solutions or very acidic or alkaline conditions. These 2.10 conditions can denature or change the shape of the protein molecules. If the change is minor, the protein molecule can return to its original shape, but if it is major, then it cannot. Summarising Protein Structure 2.11 How Do Balls of Protein Form Structures? Read through the following text and complete the tasks or questions that follow. Use your own A4 paper or send work as MSWord documents attached to an email. The following text is courtesy of Times Mirror, Mosby college Publishing, Biology 2nd Edition. The Cytoskeleton Proteins Figure 2.5 In this diagrammatic cross section of a cukaryotic cell, the mitochondria, ribosomes, and endoplasmic reticulum are all supported by a fine network of filaments, through which pass microtubules linking various portions of the cell. The cytoplasm of all eukaryotic cells is crisscrossed by a network of protein fibres, which support the shape of the cell and anchor organelles such as the nucleus to fixed locations (Figure 2.5). This network, called the cytoskeleton, cannot be seen with an ordinary microscope because the fibres are single chains of protein, much too fine for microscopes to resolve. The fibres of the cytoskeleton are a dynamic system, constantly being formed and disassembled. Individual fibres form by polymerization, a process in which identical proteins are attracted to one another chemically and spontaneously assemble into long chains. Fibres are disassembled in the same way, but the removal of first one subunit, then another from one end of the chain. Cells from plants and animals contain the following three different types of cytoskeleton fibres, each formed from a different kind of subunit (see Figure 2.6): 1. Actin filaments. Actin filaments (also called microfilaments) are long protein fibres about 7 nanometers in diameter, each fibre composed of two chains of protein loosely twined around one another like two strands of pearls (Figure 2.6, A). Each “pearl” of a filament is a ball- 2.12 shaped molecule of a protein called actin, the size of a small enzyme. Actin molecules left alone will spontaneously form these filaments, even in a test tube; a cell regulates the rate of their formation by means of other proteins that act as switches, turning on polymerization only when appropriate. Tubulin is an example of a fibrous protein. 2. Microtubules. Microtubules are hollow tubes about 25 nanometers in diameter, each a chain of proteins wrapped round and round in a tight spiral (Figure 2.6, B). The basic protein subunit of a microtubule is a molecule a little larger than actin, called tubulin. Like actin filaments, microtubules form spontaneously, but in a cell microtubules form only around specialized structures called organizing centers, which provide a base from which they can grow. 3. Intermediate filaments. The most durable element of the cytoskeleton is a system of tough protein fibres, each a rope of threadlike protein molecules wrapped around one another like the strands of a cable (Figure 2.6, C). These fibres are characteristically 8 to 10 nanometers in diameter, intermediate in size between actin filaments and microtubules; this is why they are called intermediate filaments. Once formed, intermediate filaments are very stable and do not usually break down. The most common basic protein subunit of an intermediate filament is called vimentin, although some cells employ other fibrous proteins instead. Skin cells, for example, form intermediate filaments from a protein called keratin. When skin cells die, the intermediate filaments of their cytoskeleton persist – hair and nails are formed in this way. Figure 2.6 A comparison of the molecules that make up the cytoskeleton. Actin filaments: In the micrograph, actin filaments parallel the cell-surface membrane in bundles known as stress fibres, which may have a contractile function. Microtubules: Each microtubule is composed of a spiral array of tubulin subunits. The microtubules visible in this micrograph radiate from an area near the nucleus (most heavily stained region). Microtubules act to organize metabolism and intracellular transport in the nondividing cell. Intermediate filaments: It is not known how the individual subunits are arranged in an intermediate filament, but the best evidence suggests that three subunits are wound together in a coil, interrupted by uncoiled regions. Intermediate filaments, like microtubules, extend throughout the cytoplasm. In a skin cell, such as the one shown, intermediate filaments form thick, wavy bundles that probably provide structural reinforcement. 2.13 SEND… Question 7 Explain why there are so many different kinds of protein. Question 8 Where in a protein molecule would you find a hydrophilic amino acid? Explain why some amino acids are hydrophilic. Helicase is the name of the protein that unzips DNA so the coded information on it may be read. A zipper is a good model of this. The zipper runner represents helicase. Notice that it has a very specific shape (structure) that makes it work (function) as a zipper runner. Question 9 What level of protein structure determines its function? Below is a collection of some proteins (plant and human) that have been identified and named. Courtesy of PDB Protein Data Bank www.pdb.org The cholesterol and phospholipid molecules have been included to show the phospholipid bilayer which some proteins are embedded in or attached to. 2.14 SEND… Practical Activity 2A – Making A Model of A Protein Now you will do a short practical exercise. You don’t have to present it as a standard prac report – simply complete the tasks. Equipment You will need at least fifteen pipe cleaners, each 30 cm long, available from craft shops and some newsagents. Procedure Interesting fact Spider silks are proteins and are the strongest natural fibre known. The golden orb weaver spider uses a silk ‘dragline’ to escape its web in case of danger. The dragline is a mixture of two types of proteins that are dry and essentially indestructible. They are also elastic and exceptionally strong, features that are directly attributable to the protein structure. Hint: to make the coils you could wind the pipe cleaner around a pencil as shown below. 1. Connect the three pipe cleaners as shown at left, so that you have a long pipe cleaner. This represents the primary structure of your protein (polypeptide). You may like to put texta markings along the pipe cleaners to represent the amino acids that make up the polypeptide. About every 2 cm. 2. Use the diagrams in Figures 2.2, 2.3 and 2.4 and the information given earlier to construct four different models. Each model will show one of the four levels of structure (primary, secondary, tertiary and quaternary) of a protein. 3. Squeeze the tertiary structured (ball) protein in your hand. Can you feel the prickly ends of the wire? Yes! These represent the “sticky” reactive hydrophilic parts of the protein. The hydrophobic (scared of water) parts are “hiding” on the inside of the protein. 4. Send your four models naming the structure they represent, to me. Or send in photos of your made models (including their name). Secondary structure Question 10 What have you learnt from doing this activity? 2.15 Question 11 Explain how your model of a protein is different from the real thing. Question 12 How could you improve your models? Read through the following text and complete the tasks or questions that follow. Use your own A4 paper or send work as MSWord documents attached to an email. Nucleic Acids – Information Molecules Nucleic acids store information in a chemical code that directs the machinery of the cell to produce proteins. Nucleic acids are every organism’s genetic material; they are the means by which the story of life extends through time and across all life forms. Commonly recognised by the letters DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), nucleic acids are large, linear polymers that form when monomers bond together. A molecule of DNA is composed of two long strands of subunits called nucleotides, wound around each other to form the familiar double helix. RNA is usually composed of a single chain of nucleotides and forms a single strand. Analysing DNA: the stuff genes are made of Genes are made up of a chemical called DNA (deoxyribonucleic acid). The DNA of our genes contains all the instructions which control our inherited characteristics. Nucleotides Nucleotides are the monomers that make up these amazing nucleic acid molecules. A nucleotide has three distinct chemical components: 1. a five carbon sugar (ribose in RNA and deoxyribose in DNA) 2. a negatively charged phosphate group 3. an organic nitrogen-containing compound called a base (Figure 2.7). There are four kinds of nitrogenous (nitrogen-containing) bases in DNA: Adenine (A) Thymine (T) Guanine (G) Cytosine (C) Figure 4.1 The four nucleotides found in DNA (with cytosine labelled fully) 2.16 In each nucleotide strand, the sugar molecule of one molecule binds to the phosphate groups of the next nucleotide, leaving the nitrogenous base sticking out from each sugar and opposite the nitrogenous base of the second strand. Hydrogen bonds between the opposing pairs of nitrogenous bases hold the double helix together, much like the rungs of a twisted ladder or a spiral staircase. The bonding of the nitrogen bases does not happen by chance: A bonds with T and C bonds with G, giving rise to the base-pairing rule. When nucleotides link to form a strand, a bond forms between the sugar on one nucleotide with the phosphate group on the next nucleotide. The phosphate end is called the head and is known as the 5/ end. The sugar end is known as the tail and is the 3/ end (see cytosine labels above). Experiments on the DNA of various organisms show that the amounts of the nucleotide Adenine (A) equal those of Thymine (T). The amount of Guanine (G) equals those of Cytosine (C). The levels of A and T were different from those of G and C. The difference between DNA and RNA The difference between DNA and RNA is that DNA has deoxyribose sugar and RNA has ribose sugar. The nitrogenous base thymine in DNA is replaced by the base uracil (U) in RNA. RNA is usually single stranded and DNA is usually a double stranded chain forming a double helix. Nucleotides link together in what is called a 51 to 31 direction to form long polymers. See Figure 2.7 & 2.8 (two different visual representations of DNA and RNA). Translated this means that the phosphate group attached to the 51 carbon of one ribose monomer bonds to the hydroxyl group attached to the 31 carbon of another ribose monomer, forming a particular bond called a phosphodiester bond. In the process of polymerisation, the hydrogen from the sugar and the hydroxyl from the phosphate ‘condense’ out as a water molecule. 2.17 Figure 2.7 Above image courtesy of Nature of Biology Book 2 by Jacaranda DNA consists of two complimentary polynucleotide strands held together by hydrogen bonds. If we know the nucleotide sequence on one strand, we also know the nucleotide sequence on the other strand because we know which nucleotide bonds with which. One strand is a template (strand) for the other strand called the complementary strand. DNA is the master code that determines the very nature of cells and therefore of life forms. Owing to its unique ability to replicate, DNA is a semi-conservative molecule that passes on this information form one generation of cells to the next and from one generation of organisms to the next. Thus, it is an incredibly significant biomacromolecule. The DNA of a cell is largely contained within the nucleus of cells so the coded ‘message’ has to be carried out of the nucleus into the cytoplasm of the cell where the proteins are actually synthesised in organelles (‘little organs’) called ribosomes. RNA molecules carry out this function. The Function of DNA The particular sequence of nucleotides in the DNA molecule forms a code which, until 1966, had not been cracked. The code carried by the DNA is organised in triplets (three nucleotides) that determine the order in which the amino acids are sequenced and, in turn, this sequence determines which protein is formed. It sounds simple but when we consider that each cell of our body carries well over a metre in length of DNA, twisted and coiled into 46 chromosomes that have more than three billion base pairs (bp), it is not surprising that there is such diversity of proteins. However, not all the length of the DNA molecule codes for proteins. The parts that code are the genes and the total set of genes that each cell of an organism has is called its genome. The study of these sets of genes and the way they interact with each other is called genomics 2.18 Figure 2.8 (a) DNA is made up of deoxyribose sugars and RNA of ribose sugars. (b) Nucleotides link together to form a singlestranded DNA molecule. (c) The DNA helix is a double-stranded molecule. The two strands are held together by hydrogen bonding between complementary nitrogenous bases. Image below courtesy of Biology VCE Units 3 & 4 by Nelson Thomson. 1 2 4 A=adenine, T=thymine, C=cytosine, G=guanine, P=phosphate group, S=sugar, B=base. The Quizlet for week 2 might help with the following Questions http://quizlet.com/_c46j 2.19 SEND… Question 13 a) Describe, by means of a simple annotated (labels and notes) diagram, the structure of a nucleotide. b) What distinguishes one nucleotide from another? Question 14 Where is DNA located in a cell? Describe its function and explain its significance. Read through the following text and complete the tasks or questions that follow. Use your own A4 paper or send work as MSWord documents attached to an email. DNA forms a double helix Figure 2.9 5/ Each DNA molecule consists of two nucleotide strands, twisted in a double helix structure (like a spiral staircase) in a regular manner. The strands are ‘antiparallel’ – they run in opposite directions. The ‘rungs’ of the DNA ladder, or the bonds between the two strands, are formed by weak hydrogen bonds between the base pairs - cytosine always pairs with guanine while thymine always pairs with adenine and vice versa. These are called complimentary base pairs. Bonding of these bases results in specific sequences of nucleotides on a chromosome, which accounts for differences in genes. A single gene may contain thousands of these base pairs. 3/ Model of a small part of a DNA molecule. 3/ 5/ Courtesy: Nature of Biology-book 2-Judith Kinnear and Marjory Martin 2.20 Figure 2.9 above gives you an idea of the structure of the DNA molecule. Only a small part of the whole DNA molecule is shown here. It is quite a large molecule. This complementary structure gives DNA the following properties: It can be a template for its own replication (make sure you understand what template means before going on) It contains genetic instructions (e.g. the code for protein production) It can undergo change or mutation. DNA as a template Due to the pairing of bases from one strand to the other it is possible to tell what the bases in one strand are from the base sequence (order of bases) in the other strand. Remember that A pairs with T and C pairs with G. If part of one DNA strand is: GGTACCATA Then the other DNA strand must be: C C A T G G T A T. Relating DNA to genes and chromosomes A chromosome is made of a single, double-stranded DNA molecule. The length varies depending on the size of the chromosome and within its length are all the genes on that chromosome. Gene structure Genes are made of DNA and are a part of a DNA molecule. One of the two strands contains the information in a particular gene. This is called the template strand. The complementary strand is often called the nontemplate strand. Example of a small part of DNA represented by its bases: The base sequence of the template strand of DNA is represented as follows: 3/ A A T C C G T G A T T C 5/ Its non-template or complementary strand could be written below from 5/ to 3/ 3/ A A T C C G T G A T T C 5/ 5/ T T A G G C A C T A A G 3/ While this does not show the actual shape of the molecule it reveals the base pairing rule and base sequence or genetic code. It is a simpler and more informative way of presenting a piece of DNA. 2.21 5/ & 3/ What the …? 5/ is said as “five prime” and 3/ is said as “three prime”. Nucleotides link together in what is called a 5′ to 3′ direction to form long polymers. Translated this means that the phosphate group attached to the 5′ carbon of one ribose sugar bonds to the hydroxyl group attached to the 3′ carbon of another ribose monomer, forming a particular bond called a phosphodiester bond. See page 33 of your text book for more detail. Gene sequencing As nucleotides only differ from one another by their different bases A, T, C, G, if you know the base sequence you know the nucleotide sequence. Gene sequencing is the process of identifying the order of nucleotides along a gene. The sequences of nucleotides are different for different species of organisms. This seems very logical when you consider that the DNA of an organism contains the instructions for making that organism. Nature of the genetic code The DNA of genes carries all the genetic information of an organism. It is in the form of a code made up of different combinations of just four nucleotides: A, T, G and C. The genetic code contains information for joining amino acids into proteins. Proteins in turn control the biochemistry, structure and physiology of an organism. In other words the genes have all the instructions to make a particular organism. Organisation of the genetic code The code is a triplet code as three bases make one genetic instruction. See below for some examples. A mnemonic for remembering that a triplet (three) code is made up of three nucleotides (letters) such as TTA, CCG, GGG, etc. is to remember that the word DNA is made up of three letters. Example Consider a piece of DNA (template strand) with the following base sequence (broken up into four triplets): TACAAACAAACT It then gets transcribed (copied) into mRNA. Notice that U replaces T in mRNA: TACAAACAAACT TRANSCRIPTION (copying) Base sequence in mRNA AUGUUUGUUUGA TRANSLATION Amino acid sequence in polypeptide chain. met phe val Stop translation 2.22 This DNA has four triplets, four coded instructions. Below is a list of what the above codes (codons) mean to the cell: The DNA triplet code (codon) on the template strand TAC What it is transcribed to on mRNA AUG AAA CAA ACT UUU GUU UGA What it means to the cell. What it instructs the cell to do. start building a protein, commencing with the amino acid methionine abbreviated as met …then … add the amino acid phenylalanine abbreviated as phe… add the amino acid valine abbreviated as val… now stop. See Figure 4.3 below for the genetic code used in the example above: Figure 4.3 The genetic code. The mRNA codons correspond to the 20 amino acids made by translation on the ribosomes found in the cytosol. Ribosomes “make proteins” by reading the mRNA codons. Three codons act as stop codons and under certain conditions the codon AUG initiates protein synthesis. Image courtesy of Biology VCE Units 3 & 4, 2nd edition by Nelson Thomson. SEND… Question 14 Describe using an example what is meant by the ‘base-pairing’ rule. 2.23 Question 15 Have a go at the following animation http://learn.genetics.utah.edu/content/begin/dna/transcribe/ (a) Write down the RNA strand you created (b) Name the amino acids you created. Question 16 Draw a table comparing DNA to RNA. So … why should we care about proteins? Below is an article taken off the internet. It presents a real life example of how we use knowledge about bacteria and the proteins they produce. It is also an example of biomimcry – looking to nature for solutions to our questions and problems. I don’t expect you to understand the whole article as it is written for industrial scientists. I do want you to understand that what you are learning has very real applications to your life now and in the future. You do not have to answer any questions related to this. It is for your interest only. The following edited article is from: http://www.istc.ru/istc/sc.nsf/html/projects.htm?open&id=3060 Full Title Producers of the protein - Bacteriorhodopsin (BR) Leading Institute Institute of Genetics and Selection of Industrial Microorganisms Collaborators University of Amsterdam Sogang University / Department of Chemical and Biomolecular Engineering Project Summary Project Objective: Construction of Halobacterium salinarum strains as a promising source for the industrial production of bacteriorhodopsin. Halophilic bacteria Halobacterium possess a unique biosystem, converting solar energy into electrochemical energy. Bacteriorhodopsin (BR) is a key element of this natural system. BR is a retinal-containing protein of the purple membranes of halobacteria. $US 43 – 61 billion for a protein!! Hey lets start making it!! NOW! Experts in advanced applied biotech research, in particular, nanotechnology, emphasize a dramatic growth in the amount of funding allocated to such studies [Research Review, 2002, 15(2)]. In the estimate published by the Journal Nanotechnology the cost of such research activities, performed in the U.S. since 2000, has exceeded $US 2 billion. And the increment rate of venture capital investments in nanobiotechnology in the last two or three years has achieved 313%. This 2.24 area of science is also considered as the most promising for long-term capital investments [Nanotechnology, The Nanotech Report, 2003]. German experts, referring to the US Int. Trade Commission, state that the international market of BR comprises about $US 43-61 billion [www.archiv.ub.uni-marburg.de]. Germany is known for the most active studies of bacteriorhodopsin application areas, in particular, in the protection of securities against counterfeiting. In the last years some evidence has been obtained that halobacteria could be put on the list of industrial microorganisms as bacteriorhodopsin producers. Based on our data, the world practice has no industrial technology of continuous cultivation of halobacteria for bacteriorhodopsin production, while the available laboratory techniques for the production of this protein are capable to generate this product only in a gram scale. Strong arguments have been generated to demonstrate that the introduction of purple membrane preparations of halobacteria (containing bacteriorhodopsin in high concentration and in the condition, applicable for bioelectronic devices) to the world market will facilitate completion of the relevant studies and development of commercially available instruments. Thus, a successful project implementation would advance bacteriorhodopsin production that will undoubtedly attract consumers in the world market. Future applications: The potential areas of BR application are impressively diverse. They include a double-side holographic memory, ultra-fast random access memory (RAM), spatial light modulation, non-linear optic filters, recognition systems, high-contrast displays, optic switches, and picosecond detectors. Bacteriorhodopsin is also used in the production of materials, protecting securities against counterfeit and as antioxidants in medicine, pharmacy, and cosmetology. Currently, halobacterium strains, capable to produce BR, are primarily used in the laboratory conditions mainly for research purposes. It is known from the literature that individual attempts were made to launch semiindustrial production of BR. However, no strains have been developed which meet all the requirements for the industrial strains-producers. In our opinion, the industrial strains of halophilic bacteria should be characterized by the enhanced efficiency of nutrition, high growth rate, and the maximal level of accumulation of the key target product – bacteriorhodopsin. The following tasks should be solved to meet the stated objective: 1. To review factors, restricting growth and accumulation of the biomass of H. salinarum in the course of their massive cultivation. 2. To select H. salinarum strains, characterized by the highest production rates. As source strains, promising for practical applications, it will be possible to use wild H. salinarum strains and several strains with mutations of the structural gene of bacteriorhodopsin (bop). 3. To clone structural bacteriorhodopsin gene of H. salinarum in Bacillus cells, ensuring the highest level of production and secretion of the target protein. 2.25 Key Summary Points Courtesy of Heinemann Biology Two, 4th Edition Macromolecules (polymers) are large organic molecules formed by joining together many smaller molecules. The four main types of organic molecules are carbohydrates, lipids, proteins and nucleic acids. Carbohydrates are the most abundant organic compounds in nature. Their general formula is Cn(H2O)n. They are grouped into monosaccharides, disaccharides and polysaccharides and have many different properties. Proteins are more complex molecules than carbohydrates or lipids, and make up more than 50% of the dry weight of cells. All proteins contain carbon, hydrogen, oxygen and nitrogen; many also contain sulphur, phosphorus and other elements. Proteins are chains of amino acids known as polypeptides. The properties of proteins are determined by their shape, which is determined by their amino acid sequence. The nucleic acids DNA and RNA are the genetic materials of organisms and they determine inherited features. Lipids are non-polar hydrophobic molecules and can form an effective barrier between two watery environments. They have a much smaller proportion of oxygen than carbohydrates, and often contain other elements, such as phosphorus and nitrogen. Lipids include fats and oils (important as energy-storing molecules), phospholipids (the important component of cell membranes) and steroids (hormones and vitamins). Key Terms Carbohydrate, protein, nucleic acid, lipid, phospholipid, macromolecules, autotroph, heterotroph, chemotroph, polymer, monosaccharide, disaccharide, polysaccharide, glucose, glycogen, amino acids, polypeptide, hydrophilic, hydrophobic, DNA, RNA, nucleotide genes, genome Challenging Activity: Mnemonic Activity Choose one or more of the terms encountered during this week from the Key terms above and create a memory aid to help you remember the definition of that term. You may use drawings, poetry, song, sound, whatever works for you! Share your ‘mnemonic’ (memory aid) with the other students of your class via the chat room. Look at the examples I’ve given throughout this weeks notes for help and guidance. Feel free to discuss your ideas with me. 2.26 Here’s an example for this week: Hydrophobic: Think of water when you see the word “hydro” as in hydroelectricity – electricity generated by water from dams. With the “phobic’ part, think of ‘phobia’ as in ‘fear of’. So, hydrophobic is ‘fear of water’. This helps you to work out ‘hydrophilic’ which is the opposite that is, ‘love of water’. So when something is hydrophobic it repels water, moves away from it, is “scared” of it. So the hydrophobic parts of a protein will hide themselves inside the ‘protein ball’ because proteins are made in the watery environment of the cell, whereas the hydrophilic parts will be found around the outside of the protein ball in contact with the surrounding water. Log on to the www.decvonline.vic.edu.au check out the back of your DECV book for your login details if you have forgotten. Click on the link to the Unit 3 Biology course. Click on the button “Discussion Room” Place your Mnemonic as a comment to the Discussion post titled Mnemonics Week 2. Make sure you check out the other Mnemonics left by your classmates and leave them a comment. Challenging Activity: Personal Reflection Log on to the VCE Biology Course. Place your Personal Reflection in the Biology Blog as outlined on 0.7 in the introduction of this book. Checklist This week you should have submitted the following work to me. Please tick the items you have sent, and keep this as your record. Responses to Questions 1-16 Practical Activity 2A Making A Model of A Protein At least one mnemonic of a biological term placed online Your Personal Reflection for week 2 placed online The signed Student Declaration from page 0.15 (if you didn’t do so in Week 1) Don’t forget to drink plenty of water! Most of us do not drink enough water. Generally, adults need to drink at least 2.5 litres of water per day! Simple dehydration is a common cause of tiredness and fatigue. We need water to transport nutrients, chew and digest food, create blood, move muscles, breathe and think! Using thirst as the reason for drinking water is not a good indicator for when you need to drink. Water should be drunk at regular intervals whether you desire it or not. 2.27 Exam Practice Exercise Past Exam Questions Each week you will get at least one question that relates to the weeks work, that comes from a past VCE exam paper. The purpose of this task is to familiarize yourself with the type of questions you will encounter during the exam and the timing you should devote to each. Timing You should allow 1 minute and 10 seconds per mark assigned to the question. Here are your practice exam questions: Question 1 taken from the 2006 VCE Biology Unit 3 exam paper. Question 3 taken from the 2003 VCE Biology Unit 3 exam paper. Question 8 taken from the 2003 VCE Biology Unit 4 exam paper. Question 1 Scientists are now turning to the study of the proteome (all of the proteins) of an organism rather than the study of single proteins. a. Briefly outline one reason why the emphasis is now on the study of all the proteins of an organism rather than on one protein at a time. 1 mark Protein molecules come in many shapes and forms that can be classified into primary, secondary, tertiary and quaternary. The secondary, tertiary and quaternary shapes arise as a result of different kinds of folding of a primary structure. One kind of secondary structure is a pleated sheet where the primary molecule extends along the folded sheet. The primary structures in the layers are held together by hydrogen bonding. 2.28 b. Explain why such a structure may be important in the function of a particular protein. 1 mark Proteins can also be classified on the basis of their general function. Three of these functions are shown in the table below. c. Complete the table by giving an example of a protein for each of the functions listed. Function of protein Example Structural Transport Regulatory 3 marks Total 5 marks The following are multiple choice questions each worth one mark. You should allow yourself 1 minute and 10 seconds to complete each question. Choose the correct response for each question. Question 3 Many biological compounds are large molecules made of many smaller units joined together. Each of the units has the same basic structure. Such molecules are called polymers. Biological polymers include A. cellulose composed of glucose. B. glycogen composed of glycerol. C. starch composed of amino acids. D. proteins composed of fatty acids. Question 8 In DNA, the number of A. phosphate groups equals the number of nitrogen bases. B. adenine nucleotides equals the number of cytosine nucleotides. C. phosphate groups equals twice the number of sugar molecules. D. guanine nucleotides equals the number of uracil nucleotides. Feedback If anything needs to be improved, corrected, cleared up or presented better from the material presented in this week please let us know. Your honesty is appreciated. Write your comments on the back of the cover sheet. END OF WEEK 2 2.29 Answers to Past Exam Questions Question 1a. The emphasis is on the study of all proteins because of the interaction between proteins, and the reliance that some have on others. Although this question was well answered by many students, others failed to identify either of the points above. Question 1 b. Structures may be important because: • of the ability of the protein to stretch or contract (elongate or shorten) in particular situations • pleating may strengthen the molecule and that may be important for its function • particular structures may provide an active or binding site for an enzyme or other molecule. Few students appeared to understand that secondary-structure proteins may have a particular function in that state, with many writing only about them being part of a tertiary-structure protein. Answers that gave general comments, such as ‘the protein could be an enzyme’, without explaining the relevance of structure received no credit. Question 1c. Function of protein Structural Transport Regulatory Example collagen, keratin, silk, cytoskeleton, cilia, fibrin, fingernails haemoglobin, protein carrier, serum albumin hormone (or specific example), enzyme (or specific example), major histocompatibility complex (MHC) This question was generally well answered. Incorrect answers generally referred to compounds such as carbohydrates and other non-protein compounds. Question 3: A - cellulose composed of glucose (glycogen and starch are composed of glucose and proteins are composed of amino acids.) Question 8: A – Phosphate groups equal the number of nitrogen bases. 2.30 315 Clarendon Street, Thornbury 3071 Telephone (03) 8480 0000 FAX (03) 9416 8371 (Despatch) Toll free (1800) 133 511 Fix your student barcode label over this space. SCHOOL NO. 64802 [64802] STUDENT NUMBER ___________________ SCHOOL NAME _______________________ STUDENT NAME ______________________ SUBJECT Biology Unit 3 YEAR/LEVEL TEACHER 12 WEEK 2 ________________________ [ZX] PLEASE ATTACH WORK TO BE SENT. NOTE: Please write your number on each page of your work which is attached to this page. SEND Please check that you have attached: Responses to Questions 1-16 Practical Activity 2A – Making A Model of A Protein At least one mnemonic of a biological term placed online Your Personal Reflection for week 2 placed online The signed Student Declaration from page 0.11 (if you didn’t do so in Week 1) If you have not included any of these items, please explain why not. _____________________________________________________________________________ _____________________________________________________________________________ Use the space on the back of this sheet if you have any questions you would like to ask, or problems with your work that you would like to share with your teacher. 2.31 YOUR QUESTIONS AND COMMENTS Please provide the following information: Were you able to complete the tasks in the time frame allocated? ____________________ Roughly how long did it take for you to complete this week of work? _____________ Use this space for any queries or comments you have, (or maybe errors you’ve found). 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