VCE Biology Unit 3 PDF

How do cells maintain life? In this unit students investigate the workings of the biochemical pathways could lead to improvements in cell from several perspectives. They explore the agricultural practices. relationship between nucleic acids and proteins...

How do cells maintain life? In this unit students investigate the workings of the biochemical pathways could lead to improvements in cell from several perspectives. They explore the agricultural practices. relationship between nucleic acids and proteins Students apply their knowledge of cellular processes as key molecules in cellular processes. Students through investigation of a selected case study, analyse the structure and function of nucleic acids data analysis, and/or a bioethical issue. Examples as information molecules, gene structure and of investigation topics include, but are not limited expression in prokaryotic and eukaryotic cells, and to: discovery and development of the model of the proteins as a diverse group of functional molecules. structure of DNA, proteomic research applications, They examine the biological consequences of transgenic organism use in agriculture, use, manipulating the DNA molecule and applying research, and regulation of gene technologies, biotechnologies. including CRISPR-Cas9, outcomes and unexpected Students explore the structure, regulation, and consequences of the use of enzyme inhibitors such rate of biochemical pathways, with reference to as pesticides and drugs, research into increasing photosynthesis and cellular respiration. They efficiency of photosynthesis or cellular respiration, or explore how the application of biotechnologies to impact of poisons on the cellular respiration pathway. Reproduced from VCAA VCE Biology Study Design 2022-2026 54 UNIT 3 AOS1 What is the role of nucleic acids and proteins in maintaining life? In this area of study students explore the expression of the information encoded in a sequence of DNA to form a protein and outline the nature of the genetic code and the proteome. They apply their knowledge to the structure and function of the DNA molecule to examine how molecular tools and techniques can be used to manipulate the molecule for a particular purpose. Students compare gene technologies used to address human and agricultural issues and consider the ethical implications of their use. Outcome 1 On completion of this unit the student should be able to analyse the relationship between nucleic acids and proteins, and evaluate how tools and techniques can be used and applied in the manipulation of DNA. Reproduced from VCAA VCE Biology Study Design 2022-2026  55 CHAPTER 2 Nucleic acids and proteins 2A Protein structure and function 2D Gene expression 2B Nucleic acids 2E Gene regulation 2C Genes 2F The protein secretory pathway Key knowledge nucleic acids as information molecules that encode instructions for the synthesis of proteins: the structure of DNA, the three main forms of RNA (mRNA, rRNA, and tRNA), and a comparison of their respective nucleotides the genetic code as a universal triplet code that is degenerate and the steps in gene expression, including transcription, RNA processing in eukaryotic cells, and translation by ribosomes the structure of genes: exons, introns, and promoter and operator regions the basic elements of gene regulation: prokaryotic trp operon as a simplified example of a regulatory process amino acids as the monomers of a polypeptide chain and the resultant hierarchical levels of structure that give rise to a functional protein proteins as a diverse group of molecules that collectively make an organism’s proteome, including enzymes as catalysts in biochemical pathways the role of rough endoplasmic reticulum, Golgi apparatus, and associated vesicles in the export of proteins from a cell via the protein secretory pathway Image: UGREEN 3S/Shutterstock.com 56 Chapter 2: Nucleic acids and proteins 2A P ROTEIN STRUCTURE AND FUNCTION Have you been thinking of going to the gym? Want to start working out? Well, if you have, you’ve probably realised that in order to maximise your gains, you need to start loading up on protein powder – after all, that’s what all the professionals do. But how does protein powder actually help gain muscle? Does it have any other functions? Image: Evgeniy Losev/Shutterstock.com Lesson 2A In this lesson you will learn about the functional diversity of proteins, including how their function is determined, and the molecular structure of proteins. Prerequisite knowledge Future applications Year 11 Lesson 2D Ribosomes, which can either be free-floating Gene expression involves the production within a cell’s cytosol or attached to the rough of proteins via the processes of transcription endoplasmic reticulum, are organelles present and translation. in nearly all living cells, serving as the site of protein synthesis. Chapter 3 Enzymes are proteins that serve as biological Year 11 catalysts that increase the rate of chemical Many of the channels and carriers embedded reactions within the body. Their structure and within the plasma membrane are composed folding can be influenced by many factors, such of proteins. as temperature and pH. Study design dot points amino acids as the monomers of a polypeptide chain and the resultant hierarchical levels of structure that give rise to a functional protein proteins as a diverse group of molecules that collectively make an organism’s proteome, including enzymes as catalysts in biochemical pathways Key knowledge units The functional diversity of proteins 3.1.6.1 Amino acid structure 3.1.5.1 Protein structure 3.1.5.2 The functional diversity of proteins 3.1.6.1 O verview Proteins are a diverse group of molecules that perform many different functions in cells, ranging from structural support in skin and hair to catalysing chemical reactions. T heory details Proteins, also known as polypeptides, are one of the four types of biomacromolecules. protein a biomacromolecule They are large complex structures which are crucial to the functioning and development made of amino acid chains folded of all living organisms, serving a variety of different functions. While not an exhaustive list, into a 3D shape some of the functions of proteins are outlined in Figure 1. polypeptide a long chain of amino acids. Proteins can be made of one or many polypeptides  2A THEORY 57 Due to the functional diversity of proteins, they are of particular interest to researchers. proteome all the proteins that are This is especially so because proteins rarely act in isolation, but rather, they often act expressed by a cell or organism at together to form complex structures and processes. Therefore, the proteome, which a given time refers to the entire set of proteins expressed by an organism at a given time, is a topic of significant interest. (a) (b) (c) Function: Function: Function: Enzymes Transport Structural Explanation: Explanation: Explanation: Enzymes are Typically embedded Support cell organic catalysts in membranes, controlling and tissue shape that speed up the entry and exit of The fibrous, chemical reactions RNA polymerase substances from a cell Chloride channels elongated structure embedded within of keratin Examples: Examples: Examples: the plasma Catalase: breaks down hydrogen peroxide Chloride channels Keratin: a tough protein membrane into water and oxygen Glucose channels found in skin, hair, and nails Amylase: a digestive enzyme that breaks Sodium-potassium pumps Elastin: found in elastic connective tissues down starch into maltose such as the skin RNA polymerase: catalyses the formation Collagen: found in connective tissues such of mRNA from DNA as tendons and ligaments (d) Function: Function: Hormones Receptors Explanation: Explanation: Many peptide Receive signal hormones are chemical from the environment messengers used to An insulin receptor communicate and induce Examples: protein (blue) changes in cells Acetylcholine embedded in the receptors plasma membrane Examples: Hormone receptors and bound to Insulin: regulates blood the hormone sugar levels insulin (orange) Amylase: a digestive enzyme that breaks down starch into maltose Adrenaline: increases heart rate and expands airways (e) (f) (g) Function: Function: Defence Motor/contractile Function: Explanation: Storage Involved in the Explanation: contraction and Involved in the immune movement of muscles, Explanation: system by recognising The motor the movement of internal Act as reserves and destroying pathogens The structure protein kinesin cell contents around the for metal ions of an antibody transporting Ferritin storing iron cytoplasm, and the and other molecules a large vesicle movement of cilia throughout organisms along a Examples: and flagella microtubule Antibodies (immunoglobulins) Examples: Examples: Complement proteins Myosin and actin: work together to enable Ferritin: storage of iron muscle contraction Casein: storage of amino acids, Kinesin: moves along microtubules, carbohydrates, and minerals enabling mitosis and vesicular transport Images: (a, b, d) Juan Gaertner, (c, g) StudioMolekuul, (f) SciePro/Shutterstock.com Figure 1 The functional diversity of proteins enzyme an organic molecule, typically a protein, that catalyses (speeds up) specific reactions peptide hormone a protein signalling molecule that regulates The VCAA has not expected students to memorise specific examples of proteins (e.g. keratin, collagen). physiology or behaviour However, students should appreciate the functional diversity of proteins and the fact that they are crucial antibody a protein produced by to the functioning and development of all living organisms. plasma cells during the adaptive immune response that is specific to an antigen and combats pathogens in a variety of ways. Also known as immunoglobulin 58 Chapter 2: Nucleic acids and proteins Amino acid structure 3.1.5.1 O verview Amino acids serve as the building blocks of proteins. Their chemical structure is composed of a central carbon atom, a carboxyl group, an amino group, an R-group, and a hydrogen atom. T heory details In terms of the molecular structure of amino acids, each amino acid consists of a central carboxyl group the functional carbon atom that is bonded to a hydrogen atom, a carboxyl group (COOH), an amino group on amino acid molecules that contains a hydroxyl group group (NH2), and an R-group (Figure 2). Of the 20 different types of amino acids in (OH) and an oxygen double- existence, each has its own specific R-group. Therefore, the R-group uniquely determines bonded to a carbon atom the identity of a particular amino acid. This also explains why proteins are not only made amino group the functional group up of carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) atoms, but they can also be on amino acid molecules that is made up of other elements such as sulphur (S) depending on the R-group present. made up of one nitrogen and two central carbon hydrogens (NH2) amino group H carboxyl group R-group the variable portion of an amino acid molecule. It can be one of twenty variations and H O determines the identity of the N C C amino acid H O H R R-group Figure 2 The basic structure of an amino acid Additionally, each R-group has its own chemical properties, which can affect how hydrophobic having a tendency different amino acids within a protein interact with each other. For example, an amino to repel and be insoluble in water acid with a hydrophobic R-group is more likely to form bonds with other hydrophobic hydrophilic having a tendency R-group amino acids than it would with an amino acid containing a hydrophilic R-group. to be attracted to and dissolve in water (a) alanine (b) tryptophan HN CH3 hydrophobic R-group CH2 HN CH COOH HN CH COOH 2 2 hydrophobic R-group (c) tyrosine hydrophilic R-group CH2 OH monomer a molecule that is the smallest building block HN CH COOH 2 of a polymer polymer a large molecule that Figure 3 The structure of the amino acids (a) alanine, (b) tryptophan, and (c) tyrosine is made up of small, repeated When amino acids are joined together, they form a long chain known as a polypeptide monomer subunits chain, or protein. Because different amino acids have similar basic structures and can act condensation reaction a reaction as repeating subunits, they are known as monomers. When monomers are joined together, where two monomers join to form they form polymers. Therefore, polypeptides or proteins are the polymers of amino a larger molecule, producing water acids. The joining of amino acids together occurs at a cell’s ribosomes via a condensation as a by-product reaction, which results in the formation of peptide bonds between adjacent amino acids. peptide bond the chemical bond linking two amino acids  2A THEORY 59 peptide condensation reaction bond amino acids polypeptide (monomer) (polymer) Figure 4 The formation of polypeptide polymers from amino acid monomers While the VCAA does not expect students to memorise the 20 different amino acids and their R-groups, it is expected that students will be able to draw a generalised diagram of an amino acid, which is depicted in Figure 2. Protein structure 3.1.5.2 O verview There are four levels of protein structure: the sequence of amino acids (primary), their arrangement into alpha-helices, beta-pleated sheets, or random coils (secondary), the functional 3D shape of the protein (tertiary), and the bonding of multiple polypeptide chains together (quaternary). T heory details In order for a protein to function correctly, the polypeptide chain(s) produced must primary structure the first level carefully fold into the correct shape. The four levels of protein structure describe how of protein structure, which refers polypeptide chains fold to form this functional structure, beginning from the primary to the sequence of amino acids structure and becoming increasingly more complex to form secondary and tertiary in a polypeptide chain structures. Some proteins can also have a quaternary structure. secondary structure the level of protein structure where the Table 1 The different levels of protein structure amino acid chain forms either alpha-helices, beta-pleated Structure level Diagram sheets, or random coils Primary Arg tertiary structure the functional Met Asp Val Gly Ile Lys Val Asp Leu The primary structure of a protein refers to 3D shape of a polypeptide chain the sequence (or order) of amino acids in a quaternary structure the level polypeptide chain. Ala Leu Gln Ser Leu Ala of protein structure where Phe Lys Leu multiple polypeptide chains bond Secondary together, or other non-protein groups are added to form a fully The secondary structure of a protein is formed functional protein when a polypeptide chain folds and coils by forming hydrogen bonds between amino acids alpha helix an organised coiled of its different sections. When this occurs, secondary structure of proteins structures such as alpha (α α) helices and beta- α-helix β-pleated sheets random coil beta-pleated sheet an organised pleated (β β) sheets are formed. Random coils are folded secondary structure irregular portions of secondary structure that join of proteins alpha-helices and beta-pleated sheets. random coil an irregular Tertiary secondary structure of proteins The tertiary structure refers to the overall that is neither an alpha helix nor functional 3D shape of a protein. For a protein a beta-pleated sheet to be functional, it must at a minimum have a disulphide bond a strong covalent tertiary structure. The tertiary structure of a bond occurring between two protein is formed when the secondary structures sulphur atoms further fold by forming interactions and bonds between amino acids and R-groups of its different sections. Disulphide bonds can also often form between cysteine amino acids due to the presence of sulphur atoms in their R-groups to further stabilise the protein’s 3D structure. cont'd 60 Chapter 2: Nucleic acids and proteins Table 1 Continued Structure level Chain Quaternary The quaternary structure is formed when prosthetic group a non-protein two or more polypeptide chains with tertiary structures join together. Polypeptide chains group bound to a protein. For with tertiary or quaternary structure can have example, a vitamin or ion a prosthetic group attached. However, it is important to remember that not all proteins will have a quaternary structure. A key protein with quaternary structure, Rubisco, will be explored in detail in lesson 5B. HAEMOGLOBIN Haem group Haemoglobin, which is a protein responsible for carrying oxygen in red blood cells, is one example of a protein that has a quaternary structure. It is composed of four polypeptide chains bonded together, and within each of these chains, there is also an iron ion embedded within a haem prosthetic group. Image: Raimundo79/Shutterstock.com Figure 5 The molecular structure of haemoglobin Ultimately, the folding of a protein into its functional tertiary or quaternary structure relies on its primary structure. Depending on the sequence of amino acids, the R-groups will interact with each other differently, forming different bonds that favour folding into specific 3D structures. Therefore, the functional diversity of proteins arises due to the ability to create an unlimited number of complex combinations of amino acids that fold into polypeptides of varying shapes and sizes. Additionally, since protein folding depends on the primary structure of a protein, if there are any changes to the original sequence of amino acids, a protein may no longer be able to fold correctly, preventing it from functioning normally. Theory summary Proteins demonstrate functional diversity through the various roles that they serve in living organisms. Amino acids are the monomers of proteins, and they join together via condensation reactions to form polypeptide chains. The primary level of protein structure refers to the sequence of amino acids, the secondary level of protein structure involves alpha helices, beta-pleated sheets, and random coils, the tertiary level is the functional 3D structure of a protein, and when there are two or more polypeptides in a protein it is said to have a quaternary structure. Protein serves as a core component of muscle. Therefore, by increasing your protein intake, you can increase your muscle mass. But apart from contributing to muscle mass, protein also has a variety of other functions, such as its involvement in signalling and reception, transport, muscle contraction, storage, immunity, and structure.  2A QUESTIONS 61 2A QUESTIONS Theory review questions Question 1 Proteins have a A large range of different functions. B limited number of functions. Question 2 Label the parts of the amino acid. L H M H O N C C H O H R O N Question 3 Which one of the following statements about amino acids is incorrect? A The R-group is specific for each type of amino acid. B The joining of amino acids occurs at the ribosomes. C Amino acids are only composed of carbon, hydrogen, nitrogen, and oxygen atoms. D Amino acids are monomers, which join together to form polymers known as polypeptides. Question 4 Match the level of protein structure to its description. Protein structure Description tertiary I _ sequence of amino acids primary II _ functional 3D structure of the protein secondary III _ composed of two or more polypeptide chains quaternary IV _ formation of alpha helices and beta-pleated sheets SAC skills questions Data analysis Use the following information to answer Questions 5–9. In the human body, proteins rarely act in isolation, but rather, they come together to form large complex processes. For example, the ability of the body to form blood clots to prevent blood loss when blood vessels are damaged involves over 21 different proteins. These proteins are known as coagulation factors and are activated through a complex set of pathways known as the coagulation cascade, which helps form a blood clot. There are two pathways involved in initiating coagulation: the intrinsic and extrinsic pathways. After either of these pathways is activated, they both converge into the common pathway to form a stable blood clot. 62 Chapter 2: Nucleic acids and proteins The coagulation cascade Activation of intrinsic pathway XII XIIa Activation of extrinsic pathway XI XIa IX IXa VIIa VII VIIIa X Xa X Coagulation factors Va Prothrombin (II) Thrombin (IIa) Fibrinogen (I) Fibrin (Ia) XIIIa Formation of blood clot Key Intrinsic pathway Extrinsic pathway Common pathway When doctors conduct coagulation tests, they measure how long each pathway takes to form a clot, allowing them to detect abnormalities in the coagulation cascade. For example, the activated partial thromboplastin time (APTT) measures the speed of the intrinsic and common pathways and the prothrombin time (PT) measures the speed of the extrinsic and common pathways. Individuals diagnosed with haemophilia, a blood clotting disorder, have difficulty in forming blood clots, often due to an abnormal version of coagulation factor VIII. Therefore, they often suffer from spontaneous bleeding and bruising. Their coagulation test is characterised by a prolonged activated partial thromboplastin time. Blood test results involving two different individuals Test Individual A (male) Individual B (female) Normal reference values Prothrombin time (seconds) 12.8 11.5 10–13 Activated partial thromboplastin 44.9 30.9 25–36 time (seconds) Red blood cell count (million/ 4.7 2.9 Male: 4.3–5.9 mm3) Female: 3.5–5.5 Haemoglobin level (g/dL) 14.5 12.5 Male: 13.5–17.5 Female: 12.0–16.0 Question 5 To gain an understanding of how coagulation factors interact with each other, researchers would be most interested in studying A individual coagulation factors. B multiple coagulation factors. Question 6 An abnormal coagulation factor VIII could be caused by A malfunctions in other coagulation factors which lead to the production of an abnormal coagulation factor VIII. B an altered primary structure for this protein, which causes different bonds and interactions between nearby R-groups, leading to a different tertiary structure.  2A QUESTIONS 63 Question 7 Haemophilia is characterised by a A decreased extrinsic and common pathway time. B prolonged extrinsic and common pathway time. C decreased intrinsic and common pathway time. D prolonged intrinsic and common pathway time. Question 8 In the table provided, the individual suffering from haemophilia is most likely A individual A. B individual B. C neither individual A nor B. Question 9 Based on the blood test results A individual B suffers from a high haemoglobin level. B individual A suffers from a high haemoglobin level. C individual B suffers from a low red blood cell count. Exam-style questions Within lesson Question 10 (1 MARK) The proteome is A all the proteins in a cell, tissue, or organism. B the complete set of chromosomes found inside a gamete. C the set of genes that code for all the proteins in an organism. D the entire set of proteins expressed by an organism at a given time. Adapted from VCAA 2018 Section A Q2 Question 11 (1 MARK) Consider the structure and functional importance of proteins. Which one of the following statements about proteins is false? A The tertiary structure of a protein can be stabilised by disulphide bridges. B Two proteins with different amino acid sequences will likely have different functions. C A change in the secondary structure of a protein will affect the biological function of the protein. D Proteins with a quaternary structure are always more active than proteins without a quaternary structure. Adapted from VCAA 2017 Section A Q1 Question 12 (1 MARK) For a protein to be functional, it must have a A tertiary structure. B primary structure. C secondary structure. D quaternary structure. 64 Chapter 2: Nucleic acids and proteins Use the following diagram to answer Questions 13 and 14. The following diagram represents the joining of two organic monomers. OH NH2 O H C O R — C — C — OH H—N—C—H H R H2O Question 13 (1 MARK) The diagram represents monomers of an organic molecule being joined together. The monomers are A amino acids. B nucleic acids. C monopeptides. D monosaccharides. Question 14 (1 MARK) The ‘R’ symbol on the monomer represents A one of 25 possible amino acids. B the chemical element rubidium. C a variable group specific to the amino acid. D the continuation of the carbon-hydrogen-nitrogen chain. Adapted from VCAA 2018 Section A Q3 Question 15 (3 MARKS) The diagrams represent four levels of structure with respect to the folding and assembly of a protein. The diagrams are not to scale. W X Y Z Images (left to right): ibreakstock, magnetix, chromatos, Raimundo79/Shutterstock.com a Identify which diagram represents each structural level of a protein. (1 MARK) b Describe how the functional 3D structure of a protein is formed. (1 MARK) c Suggest how the functional diversity of proteins arises. (1 MARK) Adapted from VCAA 2015 Section B Q1 Question 16 (5 MARKS) Oxytocin is a peptide hormone that has an important role in social bonding, childbirth, lactation, and sperm movement. It is produced in an area of the brain known as the hypothalamus and released by a nearby gland called the posterior pituitary gland. a Name the bond that joins the monomers of oxytocin. (1 MARK) b Draw and label the general structure of the oxytocin monomer. (2 MARKS) c Oxytocin is a relatively simple peptide hormone and is composed from a single chain of nine amino acids joined together. Identify and describe the level of protein structure that oxytocin folds into. (2 MARKS) Adapted from VCAA 2017 Section B Q1  2A QUESTIONS 65 Multiple lessons Question 17 (1 MARK) All specialised cells that secrete protein molecules uniquely A have an extensive endoplasmic reticulum. B have a flexible plasma membrane. C have large vacuoles for storage. D contain numerous chloroplasts. Adapted from VCAA 2015 Section A Q5 Question 18 (1 MARK) Consider the diagram of the plasma membrane. S U Identify which of the following molecule(s) are made up of many amino acids. R T A S B R C R&T D S&U Adapted from VCAA 2017 Section B Q1 Image: sciencepics/Shutterstock.com Image: sciencepics/Shutterstock.com Key science skills and ethical understanding Question 19 (10 MARKS) Albumin is a globular protein involved in many different processes within the body, one of which is the transport of substances around the body. It has many hydrophilic R-groups on the outside and many hydrophobic R-groups facing the interior of the protein. It is also highly insoluble in lipids. The given image depicts the structure of albumin. a Explain why albumin is highly insoluble in lipids. (2 MARKS) b Albumin normally constitutes 50% of human plasma protein, making it important for regulating blood pressure. Identify two other functional roles of proteins in living organisms. (2 MARKS) c While low albumin levels are often caused by liver diseases, malnutrition, and burns, high albumin levels are often caused by dehydration. Albumin in the urine can be indicative of kidney disease. A doctor working for Médecins Sans Frontières at a refugee camp was concerned about the blood albumin levels of her patients. She took blood samples from each of her patients to run a test for blood albumin, and documented these results. The normal range of albumin is 3.5 to 5.5 grams per decilitre (g/dL). 8 Number of people 6 4 2 0.5 1.5 2.5 3.5 4.5 5.5 6.5 7.5 8.5 Blood albumin range (g/dL) i According to these results, how many of her patients have abnormal albumin levels? (1 MARK) ii  During the test, someone used an uncalibrated scale to measure the weight of the albumin in each blood sample. Identify the type of error that has occurred. Justify your response. (2 MARKS) 66 Chapter 2: Nucleic acids and proteins d In Melbourne, another doctor measured blood albumin levels in one patient from several blood samples taken during a single visit. Sample Blood albumin level (g/dL) 1 5.75 2 3.21 3 4.12 4 4.25 i Explain whether these results are precise. (1 MARK) ii  Based on the bioethical concept of non-maleficence, suggest whether the doctor should have taken multiple blood samples from the patient. (2 MARKS)  2B THEORY 67 2B NUCLEIC ACIDS Shopping at IKEA is always an enjoyable experience, providing an immersive adventure within their almost endless and sprawling warehouse. But after you’ve laid your eyes on one of their Swedish furniture masterpieces and bought it, you’re faced with the challenging task of assembling it. But you, knowing that you’re a genius, realise that assembling IKEA furniture is super easy. Who needs the instructions right? How hard could it be? Image: Prachana Thong-on/Shutterstock.com Lesson 2B In this lesson you will learn about the functional and structural differences between the two types of nucleic acids – DNA and RNA. Prerequisite knowledge Future applications Year 11 Lesson 2D DNA is tightly packaged around histone Nucleic acids are fundamental to the proteins to form chromosomes within the production of proteins, serving a role in the nucleus of a cell. transcription of DNA into mRNA, the formation of ribosomes, and the assembly of amino acids Lesson 2A into polypeptides. DNA is responsible for storing the information required to make proteins, determining the Chapter 4 sequence of amino acids, and allowing for the Researchers are capable of manipulating huge functional diversity of proteins. DNA using a variety of different mechanisms, allowing them to edit an organism’s genome and produce genetically modified organisms. Study design dot point nucleic acids as information molecules that encode instructions for the synthesis of proteins: the structure of DNA, the three main forms of RNA (mRNA, rRNA, and tRNA) and a comparison of their respective nucleotides Key knowledge units Introduction to nucleic acids 3.1.1.1 DNA 3.1.1.2 RNA 3.1.1.3 Introduction to nucleic acids 3.1.1.1 O verview Nucleic acids are polymers of nucleotide monomers, which not only store genetic information, but also form molecules that aid in the production of proteins. T heory details Found in every living organism on Earth, nucleic acids are large polymers composed nucleic acid the class of from nucleotide monomers that store genetic information and help produce the proteins macromolecule that includes DNA required for survival. There are two types of nucleic acids – deoxyribonucleic acid (DNA) and RNA. All nucleic acids are and ribonucleic acid (RNA). While there are several distinct differences between DNA polymers made out of nucleotide monomers and RNA nucleotides, at a fundamental level, they both follow the same basic structure (Figure 1). polymer a large molecule that is made up of small, repeated monomer subunits 68 Chapter 2: Nucleic acids and proteins Every nucleotide includes: nucleotide the monomer subunit of nucleic acids. Made up of a a phosphate group nitrogen-containing base, a five- a five-carbon (pentose) sugar carbon sugar molecule (ribose in a nitrogen-containing base. RNA and deoxyribose in DNA), and a phosphate group (a) (b) nitrogenous base monomer a molecule that is the smallest building block phosphate of a polymer phosphate DNA (deoxyribonucleic acid) 5’ nitrogenous a double-stranded nucleic acid 1’ base chain made up of nucleotides. 5’ DNA carries the instructions for five-carbon 4’ 1’ proteins which are required for sugar cell and organism survival 3’ 2’ 3’ RNA (ribonucleic acid) a single- stranded nucleic acid chain made five-carbon sugar up of nucleotides. Includes mRNA, Figure 1 (a) The basic structure of a nucleotide and (b) the chemical structure of a DNA nucleotide rRNA, and tRNA Within the five-carbon sugar, each carbon is assigned a number in a clockwise direction, with the first carbon being labelled 1’ (one prime) and the last carbon being labelled 5’ (five prime). The three carbons of particular interest include: Check out scientific 1’ which attaches to the nitrogenous base investigation 2.1 to put 3’ which attaches to the phosphate of the following nucleotide this into action! 5’ which attaches the five-carbon sugar to the phosphate group of the nucleotide. Therefore, the 3’ and 5’ ends of nucleotides are significant in contributing to the directional nature of nucleic acids (Figure 2). HN2 nitrogenous base five-carbon sugar N 5’-pho phosphate N sphat O N N HN2 e-sug -O O 5’ P O N ar-3’- N sugar O- H H 5’-pho H 3’ H N HN2 -phos O H N sphat -O P O 5’ N phate O N e -suga O H H backb H 3’ H N r- O H N 3’-5’- phosphodiester -O 5’ P O o phosp O ne bond H H O hate- H 3’ H OH H sugar -3’ Figure 2 A polymer of nucleotides joined together When many nucleotides bond together, they form a polynucleotide chain. The bonds phosphodiester bond a strong joining nucleotides are strong covalent bonds known as phosphodiester bonds, which covalent bond linking a five-carbon form via condensation reactions and exist between the sugar group of one nucleotide and sugar to a phosphate group the phosphate group of another. The linkage of sugars and phosphate groups is commonly condensation reaction a reaction referred to as the sugar-phosphate backbone of nucleic acids. where two monomers join to form a larger molecule, producing water as a by-product sugar-phosphate backbone a strong covalently linked chain of five-carbon sugar molecules and phosphate groups in a nucleic acid chain  2B THEORY 69 DNA 3.1.1.2 O verview Deoxyribonucleic acid (DNA) consists of two strands of nucleotides bonded together via complementary base pairing, forming a double-helix which runs in an antiparallel fashion. T heory details Inside the nucleus of human eukaryotic cells, DNA is packaged into 46 chromosomes, chromosome a structure made each of which contains tens of thousands of different genes. Each of these genes carries of protein and nucleic acids that the instructions required to make a protein. Therefore, as DNA determines the structure carries genetic information of a protein, and proteins play a vital role in the structure and function of cells and tissues, gene a section of DNA that DNA is essential for life. carries the code to make a protein Be aware that DNA is found in places besides the nucleus. For example, the mitochondria and chloroplasts have their own DNA. Additionally, as prokaryotes don’t have nuclei, their circular chromosome is located within the nuclear region of the cytoplasm. The complete set of DNA in an organism is referred to as the genome. In order for life to genome the complete set of DNA continue, DNA, and by extension the traits it codes for, must be heritable and passed down housed within an organism from parents to their children. antiparallel a characteristic of DNA strands describing how Structure of DNA each strand runs in an opposite direction to the other. One strand DNA is composed of two polynucleotide chains which run antiparallel to each runs in a 3’  5’ direction and the other, meaning that while one strand runs in a 3’ to 5’ direction, the other runs in a other runs in a 5’  3’ direction 5’ to 3’ direction. The two chains are subsequently joined together via the rules of complementary base pairing complementary base pairing, which dictates the pairs of nucleotides that can join describes which nucleotides can together to form hydrogen bonds with each other. Each DNA nucleotide is composed form hydrogen bonds with each of a phosphate group, a deoxyribose sugar, and one of four possible nitrogenous other. C pairs with G, A pairs with bases – adenine, thymine, cytosine, or guanine (Figure 3). The base pairing rules are: T (or U in RNA) adenine (A) will always form a pair with thymine (T) guanine (G) will always form a pair with cytosine (C). (a) (c) 3’ A T C G T A G T C T G A T C A G G G T A 5’ 5’ 3’ 5’ T A G C A T C A G A C T A G T C C C A T 3’ G C T A T T (b) A T 5’ 3’ T A C G T A A T sugar-phosphate G C backbones G C G C C G T A A T A = Adenine (A) A G = Guanine (G) A T C = Cytosine (C) A T T = Thymine (T) 5’ 3’ 3’ hydrogen bond 5’ Figure 3 (a) DNA can be represented using the letters corresponding to each nitrogenous base and (b) with complementary base pairing, it forms a double stranded molecule (c) which is wound as a double helix. 70 Chapter 2: Nucleic acids and proteins By understanding complementary base pairing, it is possible to predict the nucleotide double helix the structure of sequence of a strand of DNA given the nucleotide sequence of the complementary strand. double-stranded DNA in the Furthermore, using the same rules, it is also possible to deduce that in a double-stranded nucleus of eukaryotic cells, where DNA molecule, there will always be equal numbers of A and T nucleotides, and equal each DNA strand wraps around a central axis numbers of G and C nucleotides. nuclear DNA DNA that is located Given the sheer length of DNA (the human nuclear genome is approximately three billion in the nucleus of a cell base pairs long or 1.8 m in length), DNA needs to be compressed and stored effectively. To do this, the two strands of DNA twist around each other, forming a double helix, which can help compress and store DNA. In nuclear DNA, this helix structure also coils DNA around proteins known as histones, which then condense further to form tightly packed chromosomes (Figure 4). RNA 3.1.1.3 O verview Ribonucleic acid (RNA) is a single strand of nucleotides that comes in a variety of different forms and is found in many different parts of the cell. histone proteins chromosome T heory details image: Designua/Shutterstock.com While RNA serves many different functions within cells, it is primarily involved in the Figure 4 The packaging of nuclear synthesis of proteins. There are several different types of RNA, including messenger RNA DNA into chromosomes (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA) (Table 1). messenger RNA (mRNA) Table 1 The three types of RNA and their corresponding function and structure RNA molecules that are produced during transcription and carry RNA Function Diagram genetic information from the nucleus to the ribosomes messenger RNA (mRNA) Carries genetic information bases from the nucleus to the transfer RNA (tRNA) ribosomes for protein synthesis RNA that recognises specific codons on the mRNA strand and adds the corresponding amino acid to the polypeptide chain during protein synthesis ribosomal RNA (rRNA) RNA that is a key structural sugar-phosphate backbone component of ribosomes, which assemble proteins transfer RNA (tRNA) Delivers specific amino acids to the ribosome after recognising specific nucleotide sequences on mRNA anticodon Hydrogen bonds create some areas of base pairing, causing folding in the strand ribosomal RNA (rRNA) Serves as the main structural component of ribosomes within cells The roles of mRNA, tRNA, and rRNA will be further explored in lesson 2D, which delves into the formation of proteins through the processes of transcription and translation.  2B THEORY 71 Structure of RNA The structure of RNA is relatively similar to that of DNA. However, instead of a deoxyribose sugar, RNA contains a ribose sugar, and instead of thymine, RNA contains another nitrogenous base known as uracil. RNA is also single-stranded instead of double-stranded. Additionally, while DNA is inherited from generation to generation, RNA is typically synthesised on demand. These differences are summarised in Table 2. Table 2 The differences between DNA and RNA DNA RNA Structure Double-stranded Single-stranded Sugar Deoxyribose sugar Ribose sugar Nucleotides Adenine, thymine, cytosine, guanine Adenine, uracil, cytosine, guanine Lifetime Inherited, long-term storage Temporary, short-lived molecules While RNA is single-stranded, the principle of complementary base pairing still exists and can help RNA fold into many different structures. In RNA, adenine pairs with uracil (A–U) and guanine pairs with cytosine (G–C). The main difference between ribose sugar and deoxyribose sugar is the presence or absence of an oxygen atom at the 2’ position of the five-carbon sugar. This can be easily remembered through the extended names of DNA and RNA, with deoxy- signifying the absence of oxygen (Figure 5). 5’ O 5’ O HOCH OH HOCH OH 2 2 4’ C C 1’ 4’ C C 1’ H H H H H 3’ 2’ H 3’ 2’ H H C C C C OH H OH OH Deoxyribose Ribose Figure 5 The difference between deoxyribose and ribose sugar DNA tends to be double stranded (dsDNA) and RNA tends to be single stranded (ssRNA). However, like most things in biology, there are always exceptions to the rule. Some bacterial viruses (such as those in the Microviridae family) contain single-stranded DNA (ssDNA) and other viruses, including rotaviruses, contain double-stranded RNA (dsRNA). When asked to differentiate between DNA and RNA, if possible, you should rely on the nucleotides present in a strand, as DNA will contain thymine whilst RNA will contain uracil. To double check, you can also look at the five-carbon sugar found within each nucleotide – DNA contains one less oxygen molecule than RNA on the 2’ carbon. Theory summary Nucleic acids are responsible not only for carrying genetic information, but also for synthesising proteins. There are two types of nucleic acids – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), which are each composed of a phosphate group, a five-carbon sugar, and a nitrogenous base. Differences between DNA and RNA include the sugar molecule present, the nitrogenous bases present, and whether they form single or double strands (Table 3). 72 Chapter 2: Nucleic acids and proteins Table 3 Similarities and differences between DNA and RNA DNA RNA Similarities nucleotides follow the same basic structure (phosphate group, five-carbon sugar, nitrogen-containing bases) contain the nucleotides adenine, guanine, and cytosine contain a sugar phosphate backbone follow the complementary base pairing rule: C pairs with G, A pairs with T (or U) Differences nucleotides contain a deoxyribose sugar nucleotides contain a ribose sugar contains the base thymine (T) contains the base uracil (U) double-stranded single-stranded inherited/long-term storage temporary molecules There’s a reason for IKEA printing instructions – and wasting paper is certainly not one of them. Instructions are included so that you can accurately and efficiently assemble your IKEA furniture. Just like our cells, nucleic acids, and in particular DNA and RNA, form the instructions for the production of proteins, and without them life would not be able to exist. Image: Nattapat.J/Shutterstock.com 2B QUESTIONS Theory review questions Question 1 Fill in the blanks with the following terms. Terms may be used multiple times or not at all. uracil polymers ribose monomers thymine deoxyribose guanine single-stranded cytosine double-stranded Nucleic acids are _of nucleotide _. While DNA is composed of a _ sugar, RNA is composed of a _ sugar. Additionally, DNA contains the nitrogenous base _, whereas RNA contains the nitrogenous base _. DNA is also a _ molecule, allowing it to form a double helix, whereas RNA is a _ molecule. Question 2 Label the parts of the nucleotide. X 3’ Y Z  2B QUESTIONS 73 Question 3 Which one of the following sequences correctly represents DNA? 3’ A A A T C G T C A T 5’ A 3’ T T T A G C A G T A 5’ 3’ G G T A A A T T T T G U A 5’ B 5’ C C A T T T A A A A C A T 3’ 3’ A A T G C T A T G C A T C G A T C C 5’ C 5’ T T A C G A T A C G T A G C T A G G 3’ 5’ A A T G C G C T G C U T C A T G T T A A G 3’ D 5’ T T A C G C G A C G A A G T A C A A T T C 5’ Question 4 Match each type of RNA to its appropriate description. RNA Description mRNA I _ serves as the main structural component of ribosomes within cells rRNA II _ carries genetic information from the nucleus to the ribosomes for protein synthesis tRNA III _ delivers specific amino acids to the ribosomes after recognising specific nucleotide sequences SAC skills questions Case study analysis Use the following information to answer Questions 5–8. In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Physiology or Medicine for the discovery of the structure of DNA as well as its shape as a double helix. However, the absence of Rosalind Franklin, another researcher who heavily contributed to the discovery, is certainly notable. Unfortunately, her pivotal role in contributing to the discovery has been largely forgotten, shrouding the work in controversy. In fact, the discovery of the structure of DNA would not have been possible if it were not for the work of Rosalind Franklin. Her work and expertise in the field of X-ray crystallography, which is a technique used to photograph the molecular structure of compounds, provided the crucial X-ray photographs that were used to interpret and determine the structure of DNA. While Franklin was not able to fully interpret the photographs herself, Watson and Crick obtained the photographs through unconventional methods without asking for her permission, effectively stealing her work. Then, through their interpretation of her work, they were finally able to determine the structure of DNA. Unfortunately, Franklin passed away in 1958 from ovarian cancer and due to the stringent rules of the Nobel Prize, recipients must be alive to receive the award. Due to an unfortunate series of events and her premature death, she was not given the credit that she fully deserved for her contribution to the discovery of the structure of DNA. Question 5 Rosalind Franklin could not be awarded the Nobel Prize because A to be awarded the Nobel Prize, the recipient must be alive. B her contribution to the discovery of the structure of DNA was unrecognised. Question 6 Reference to the double helix shape of DNA refers to it being a A double-stranded molecule. B single-stranded molecule. 74 Chapter 2: Nucleic acids and proteins Question 7 Without complementary base pairing, DNA would not be able to form a A chain of nucleotides. B double helix. Question 8 The use of Franklin’s X-ray crystallography photographs by Watson and Crick without her permission primarily violates the bioethical concept of A non-maleficence. B beneficence. C integrity. D respect. Exam-style questions Within lesson Question 9 (1 MARK) A particular DNA double helix is 100 nucleotide pairs long and contains 40 cytosine bases. The number of adenine bases in this DNA double helix would be A 10. B 20. C 40. D 60. Adapted from VCAA 2012 Exam 1 Section A Q5 Use the following information to answer Questions 10 and 11. The following diagram represents a chain of nucleic acids. W X 5’ Y 3’ Z 3’ 5’ Question 10 (1 MARK) A nucleic acid is made up of nucleotides which are linked by a sugar-phosphate backbone. According to the diagram, structure(s) A Y and Z must make up the sugar-phosphate backbone. B Y and X must make up the sugar-phosphate backbone. C Y is a ribose sugar molecule. D X is a phosphate group. Adapted from VCAA 2015 Section A Q3  2B QUESTIONS 75 Question 11 (1 MARK) If the nucleotide structure W is the base thymine, then A sub-unit X must be the base uracil. B sub-unit X must be the base adenine. C sub-unit Y must be the base cytosine. D sub-unit X must be the nucleotide adenine. Question 12 (1 MARK) Which one of the following rows correctly describes a difference between DNA and RNA? DNA contains RNA contains A the same number of guanine and thymine nitrogen bases a different number of guanine and thymine nitrogen bases B ribose sugar deoxyribose sugar C the nitrogen base thymine the nitrogen base uracil D no hydrogen bonding between strands hydrogen bonding between complementary strands Adapted from VCAA 2017 Sample Exam Section A Q2 Question 13 (1 MARK) A gene involved in the function of the male reproductive system has been sequenced. A small section of this gene is shown in the diagram. The sequence of nucleotides on the complementary sequence of DNA would be C G T G A G G C C A A GCACUCCGGU. B CGTGAGGCCA. C GCACTCCGGT. D TCCAGAATTG. Question 14 (1 MARK) A particular mRNA strand is 50 nucleotide bases long and contains 10 adenine bases. The number of thymine bases in this mRNA strand would be A 0. B 10. C 40. D 50. Adapted from VCAA 2012 Exam 1 Section A Q5 Question 15 (1 MARK) A fragment of DNA on chromosome 7 from a person, Doug, is sequenced. The nucleotide sequence is shown. G A T G G A T C G A G G T C Doug For the sequence of nucleotides shown, the total number of cytosine bases on the complementary strand would be A 0. B 2. C 6. D 8. Adapted from VCAA 2012 Exam 2 Section A Q15 76 Chapter 2: Nucleic acids and proteins Multiple lessons Question 16 (1 MARK) Genes A are made up of the five nucleotide bases: adenine, thymine, cytosine, guanine, and uracil. B contain the genetic information required to make proteins. C can only be found in the nuclear DNA of a eukaryotic cell. D are made up of amino acid monomers. Use the following information to answer Questions 17 and 18. The diagrams represent two of the four major groups of biomacromolecules. Group A Group B Question 17 (1 MARK) Each monomer of a macromolecule from Group A is made up of a A carboxyl group, an R group, and an amino group. B carboxylic acid, an R group, and an amino acid group. C ribose sugar, a phosphate group, and a nitrogen-containing base. D deoxyribose sugar, a phosphate group, and a nitrogen-containing base. Adapted from VCAA 2016 Section A Q3 Question 18 (1 MARK) A feature that can be seen in the diagram of the macromolecule in Group B is A its deoxyribose subunits. B the double-helical structure of DNA. C the complementary base pairing of C–G and A–U. D the antiparallel arrangement of two complementary strands of amino acids. Adapted from VCAA 2015 Section A Q4 Question 19 (1 MARK) Nitrogen is an essential component of many of the molecules needed for growth and reproduction. Some bacteria live in the root systems of certain plant species, taking the nitrogen from our atmosphere and producing nitrogen-containing compounds (such as ammonia). These compounds can then be taken up by the plants and used to produce molecules that are essential for life. Soils lacking in these bacteria and nitrogen-containing fertilisers may become nitrogen deficient. Plants growing in these soils may be unable to produce sufficient levels of A carbohydrates. B nucleic acids. C fatty acids. D cellulose. Adapted from VCAA 2012 Exam 1 Section A Q6  2B QUESTIONS 77 Question 20 (4 MARKS) Researchers studying macromolecules found two tightly packed polymers in the nucleus of an animal cell. A short section of these macromolecules is shown in the diagram. Image: StudioMolekuul/Shutterstock.com a Name the two types of macromolecules shown in the diagram. (2 MARKS) b Identify the monomers of the two types of macromolecules identified in part a. (2 MARKS) Adapted from VCAA 2014 Section B Q9 Key science skills and ethical understanding Question 21 (10 MARKS) Two scientists were busy analysing two biological polymer samples. a All polymers are made up of repeating sequences of monomers. Scientists can determine the sequence of monomers in a sample by sequencing the sample. i What information is obtained from protein sequencing? (1 MARK) ii What information is obtained from gene sequencing? (1 MARK) Adapted from VCAA 2017 Northern Hemisphere Exam 1 Section B Q7 b Sample 1 only contained single-stranded sequences of DNA while sample 2 contained double-stranded sequences of DNA. After sequencing one of the samples, they plotted the number of individual nucleotides on a graph. 140 number of nucleotides 120 100 80 60 40 20 0 Sample 1 Sample 2 adenine guanine X Y nucleotide 78 Chapter 2: Nucleic acids and proteins i Identify the nucleotides represented by the bars labelled X and Y on the graph. (1 MARK) ii  Scientist A argued that the graph shows data from Sample 1, while Scientist B argued that it is more likely that the graph shows data from Sample 2. Which scientist is correct? Explain your reasoning. (2 MARKS) iii What is the length of the DNA strand in the sequenced sample? (1 MARK) iv Draw a labelled diagram of a single monomer of the macromolecule found in Sample 2. (2 MARKS) Adapted from VCAA 2014 Section B Q9 c When obtaining DNA samples from other individuals, consent must be given prior to the extraction of DNA. Identify the bioethical concept which researchers must follow in order to satisfy this requirement. Justify your response. (2 MARKS)  2C THEORY 79 2C GENES 01000101 01100100 01110010 01101111 01101100 01101111 00100000 00100011 00110001. Zeros and ones form the foundation of all your electronic devices through what is known as the binary code. The binary code consists of different sequences and combinations of zeroes and ones that can be translated into specific functions. Can you decipher the code written above? But more importantly, is there a similar phenomenon occurring in our own cells? How do our cells store genetic information? Is there another code that can be used? Image: SVshot/Shutterstock.com Lesson 2C In this lesson you will learn how the genetic code enables nucleic acids to encode the information required for protein synthesis as well as the general structure of genes. Prerequisite knowledge Future applications Lesson 2A Lesson 2D The genetic code provides a series of rules Gene expression involves the production of followed by living organisms via the production functional proteins through the processes of of proteins. transcription, RNA processing, and translation. Lesson 2B Lesson 9A Genes are sections of DNA that carry the Genes can often be altered through the instructions required to make a protein. occurrence of mutations, which involves Important properties of DNA include its permanent changes to the DNA sequence double-stranded helical structure, as well of genes, potentially leading to abnormally as its directional nature. functioning proteins. Study design dot points the genetic code as a universal triplet code that is degenerate and the steps in gene expression, including transcription, RNA processing in eukaryotic cells, and translation by ribosomes the structure of genes: exons, introns, and promoter and operator regions Key knowledge units DNA to protein 3.1.2.1 Gene structure 3.1.3.2 DNA to protein 3.1.2.1 O verview Protein synthesis relies on the existence of the genetic code, which is a series of rules that determine how genetic information is transcribed and translated into functional proteins. T heory details Cells produce proteins by reading and interpreting the genetic information stored gene a section of DNA that within genes through a series of processes known as transcription, RNA processing carries the code to make a protein (post-transcriptional modifications), and translation. During transcription and RNA transcription the process processing, the DNA sequence of the gene is copied into RNA nucleotides in the form of whereby a sequence of DNA is mRNA. The mRNA is then decoded during translation to specify the sequence of amino used as a template to produce a acids required for the polypeptide chain. These processes are only possible due to the complementary sequence of mRNA existence of the genetic code (Figure 1). translation the process where an mRNA sequence is read to produce a corresponding amino acid sequence to build a polypeptide 80 Chapter 2: Nucleic acids and proteins messenger RNA (mRNA)