DNA - The Code of Life - Grade 12 Textbook PDF

1: DNA – the code of life Introduction Activity 2: DNA Revision of cellular structure replication The structure of nucleic acids DNA profiling DNA – deoxyribonucleic acid...

1: DNA – the code of life Introduction Activity 2: DNA Revision of cellular structure replication The structure of nucleic acids DNA profiling DNA – deoxyribonucleic acid Activity 3: DNA profiling A brief history of the discovery of Protein synthesis DNA Protein synthesis occurs in two The location of DNA stages The structure of DNA Stage 1: Transcription The role of DNA Stage 2: Translation Activity 1: DNA The effect of mutation on protein structure (DNA sequence) RNA – ribonucleic acid Activity 4: Protein The location of RNA synthesis The structure of RNA Activity 5: Codons and amino acids The role of RNA Comparison between DNA and RNA DNA replication End of topic exercises Errors that occur during DNA replication 6 CHAPTER 1: DNA – THE CODE OF LIFE Introduction  All living organisms contain both DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) – we focus on their location, structure and function.  We explore the discovery of DNA, its role in the human body and how it replicates.  Protein synthesis is vital for life – we examine how proteins are formed by both DNA and RNA. Revision of cellular structure It is important to know the location and functions of certain organelles, illustrated in Figure 1 below. cytoplasm polysomes ribosomes nucleus Figure 1: Structure of a cell Cytoplasm is the base substance in which the organelles of the cell are suspended. It is a watery substance and allows for metabolic reactions to take place. Ribosomes are small, round organelles which are mainly found attached to the endoplasmic reticulum or are free-floating in the cytoplasm. Ribosomes can also be found inside other organelles such as the chloroplast and mitochondria but in smaller numbers. They are the site of protein synthesis and consist of RNA and protein. 7 The nucleus controls all of the cell’s activities. nuclear membrane nucleoplasm nucleolus nuclear pore Figure 2: Parts of the nucleus A nucleus has four main parts:  the double nuclear membrane – it encloses the nucleus and contains small pores to allow for the passage of substances in and out of the nucleus  the nucleoplasm – this is a jelly-like fluid within the nucleus  the nucleolus – a dark body suspended in the nucleoplasm which contains free nucleotide bases and produces ribosomes  the chromatin network – found in the nucleoplasm: contains the DNA which forms the chromosomes containing the genetic code of a person / organism The structure of nucleic acids Key terminology nucleic acid a type of organic compound monomer a building block nucleotide the monomer which forms DNA and RNA There are two types of nucleic acids in the human body – DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Together these form the basis of all life of earth. They consist of monomers (building blocks) called nucleotides. 8 The basic structure of a nucleotide is illustrated in Figure 3 below. Each nucleic acid is composed of a phosphate (P), a sugar molecule (S) and a nitrogenous base (NB). P – phosphate group S – sugar molecule NB – nitrogenous base Figure 3: A nucleotide DNA – deoxyribonucleic acid Key terminology  deoxyribonucleic acid is made up of nucleotides  nitrogenous bases adenine, thymine, guanine and DNA cytosine  carries the genetic code for protein synthesis nuclear DNA DNA found in the nucleus DNA found outside of the nucleus: mitochondrial and extra- nuclear DNA chloroplastic DNA. the shape of DNA consists of two strands joined together double helix and twisted spirally hereditary genetic information passed on from parent to offspring A brief history of the discovery of DNA  1952 – Rosalind Franklin and her assistant Maurice Wilkins researched the structure of DNA using X-ray diffraction images.  Watson and Crick did independent research on DNA. Upon seeing Franklin’s images, they proposed a 3-D double helix model for DNA in 1953.  1962 – Watson and Crick received the Nobel Prize for the discovery of the structure of DNA, and Wilkins received an award for his X-ray photography. Franklin had died of cancer. Rosalind Franklin – background: https://www.youtube.com/watch?v=BIP0lYrdirI 9 The location of DNA DNA is found in two locations in a cell:  Mostly in the nucleus of a cell – this is referred to as nuclear DNA  a small amount is found outside the nucleus – it is referred to as extra- nuclear DNA. There are two types of extra-nuclear DNA: o chloroplastic DNA – found in the chloroplasts of plant cells o mitochondrial DNA – found in the mitochondria (useful for tracing ancestry) The structure of DNA phosphate group nitrogenous base deoxyribose sugar weak hydrogen bonds Figure 4A: DNA double helix Figure 4B: DNA – simplified structure DNA has a double helix structure (Figure 4A), consisting of monomers called nucleotides which link to form long chains, called polymers. The sugar in DNA is deoxyribose sugar and is attached to a nitrogenous base. The phosphate and sugar molecules are attached to one another by strong bonds alternately to form the long chains (Figure 4B). There are four types of nitrogenous bases in DNA: adenine (A) cytosine (C) thymine (T) guanine (G) 10 Nitrogenous bases are complementary, and always join together in a specific order:  adenine always links to thymine (Figure 5A)  guanine always links with cytosine (Figure 5B) A adenine G guanine T thymine C cytosine Figure 5A: adenine with thymine Figure 5B: guanine with cytosine This pairing of bases means that two strands of DNA are joined together, forming a long ladder-like structure. The nitrogenous bases are held together by weak hydrogen bonds. The ladder-like structure becomes coiled and is known as a double helix structure. The DNA strands wind around proteins which are known as histones. The role of DNA DNA carries hereditary information in the form of genes. Genes are short sections of DNA which code for a specific trait, and determine the physical characteristics (e.g. blood grouping, a gene linked to breast cancer) and behaviour of an organism (e.g. whether an organism can be tamed and domesticated). Most of the DNA strands do not code for anything and are known as non-coding DNA. Scientists are still researching the importance of the non-coding DNA. The main functions of DNA include:  Controls the functioning of cells  Regulate the functioning of genes  Passes on hereditary characteristics The structure of DNA: https://www.youtube.com/watch?v=C1CRrtkWwu0 11 Activity 1: DNA The diagram on the next page shows part of a DNA molecule. 1. Label parts 1, 2 and 3 (3) 2. Give the number of nucleotides shown in the diagram (1) 3. Name two places in an animal cell where this nucleic acid may be found. (2) 4. What is the natural shape of this molecule? (1) 5. Draw a nucleotide with the nitrogenous base adenine. (4) (11) RNA – ribonucleic acid Key terminology RNA consists of nucleotides. Nitrogenous bases found in RNA RNA are adenine, uracil, guanine and cytosine mRNA carries the code for protein synthesis from DNA to the messenger RNA ribosome ribosomal RNA rRNA forms ribosomes which are the site of protein synthesis transfer RNA tRNA brings amino acids to the ribosome to form the protein There are three types of RNA (ribonucleic acid), all formed in the nucleus by DNA. They perform different functions in different places in a cell. The types are:  messenger RNA (mRNA)  ribosomal RNA (rRNA)  transfer RNA (tRNA) 12 The location of RNA  Messenger RNA (mRNA) is formed in the nucleus but then enters the cytoplasm where it attaches to ribosomes.  Ribosomal RNA (rRNA) is found in the ribosomes in the cytoplasm of the cell.  Transfer RNA (tRNA) is found freely in the cytoplasm of the cell. The structure of RNA Like DNA, RNA also consists of monomers (nucleotides) which link to form longer chains (polymers). However, RNA is a single-stranded structure which is not coiled. The sugar in RNA is ribose and is attached to a nitrogenous base. The phosphate and sugar molecules are attached to one another alternately to form the chains. The structure of RNA is illustrated in Figure 6 below. phosphate group ribose sugar nitrogenous base Figure 6: RNA – note the chain formed by the phosphate and sugar molecules on the left, and the nitrogenous bases on the right. There are four types of nitrogenous bases in RNA: 13  cytosine (C) adenine (A) uracil (U) – not thymine as in DNA guanine (G) The role of RNA The three types of RNA are very important to the process of protein synthesis, with each type playing a unique role. Comparison between DNA and RNA DNA and RNA are similar in some respects. They both …  contain sugar alternating with phosphate  contain the nitrogenous bases adenine, guanine and cytosine  play a role in protein synthesis DNA and RNA also have significant differences, tabulated in Table 1 below. Table 1: The main differences between DNA and RNA. DNA RNA contains deoxyribose sugar contains ribose sugar double helix and coiled single stranded contains the nitrogenous base thymine contains the nitrogenous base uracil found in the nucleus, ribosomes and found in the nucleus only cytoplasm of cells A comparison DNA and RNA. It is very important to know the differences. https://www.youtube.com/watch?v=0Elo-zX1k8M DNA replication DNA replication is the process through which DNA makes an identical copy of itself. This occurs during interphase of the cell cycle in the nucleus. In Figures 7A to 7E, a small portion of DNA is shown undergoing replication. 14 1. The DNA double helix unwinds 2. The weak hydrogen bonds between the (Figure 7A) nitrogenous bases are broken. The DNA strands separate (they unzip)(Figure 7B) Figure 7A Figure 7B 3. Each original DNA strand 4. Free nucleotides build a DNA strand onto serves as a template on which its each of the original DNA strands, attaching complement is built (Figure 7C) their complementary nitrogenous bases (A to T and C to G) (Figure 7D) Figure 7D Figure 7C 15  5. This results in two identical DNA molecules. Each molecule consists of one original strand and one new strand (Figure 7E). Figure 7E Figure 7A – 7E: The process of DNA replication DNA replication is important for cell division, particularly mitosis. It allows each chromosome to be copied so that each new identical daughter cell produced contains the same number and type of chromosomes. Errors that occur during DNA replication  Errors that occur during DNA replication may sometimes lead to mutations (a change in the nitrogenous base sequence)  If the incorrect nitrogen base attaches to the original strand and a nitrogen base is added or deleted … o the sequence or order of the bases changes on the new DNA molecule … o resulting in a change in the gene structure DNA replication: Understand the process. https://www.youtube.com/watch?v=Qqe4thU-os8 Activity 2: DNA replication Study the diagram below and answer the questions that follow. 16  4 A 1 G 2 3 1. Name the process illustrated in the diagram above. (1) 2. State the significance of the process mentioned in question 1. (1) 3. Identify the parts labelled as 1, 2, 3 and 4. (4) 4. Describe how this process takes place. (6) 5. Give one location of extra-nuclear DNA. (1) (13) DNA profiling A DNA profile is a pattern produced on X-ray film. This pattern consists of lines which are of different lengths and thicknesses and in different positions, as shown in Figure 8. All individuals, except identical twins, have a unique DNA profile. Figure 8: DNA profiles for three different individuals. 17 DNA profiles are used to:  identify crime suspects in forensic investigations  prove paternity (father) and maternity (mother) (biological parents)  determine the probability or causes of genetic defects  establish the compatibility of tissue types for organ transplants  identify relatives DNA profiling is generally accepted as being extremely reliable. The interpretation and comparison of profiles should however be approached with caution, for the following reasons:  Humans interpret the results which means mistakes could be made  The method of profiling may be different in different laboratories producing inconsistencies  Only a small piece of DNA is used in profiling, so the profile might not be 100% unique to a particular individual  DNA profiling is expensive and therefore not readily accessible to those who cannot afford it, particularly in criminal cases  DNA profiles may reveal information about a person which could be used against them in a prejudicial way. For example: being HIV positive or having genetic abnormalities may lead to insurance companies not covering a person or prejudice in the court room Activity 3: DNA profiling DNA profiles from a crime scene. Victim CSS Suspect 1 Suspect 2 Suspect 3 Suspect 4 18 In a fight involving a number of people, one person was seriously injured. Police took blood samples from the victim, the crime scene (CSS – crime scene sample) and four suspects. The DNA was then extracted from each sample. The results of these tests are shown in the diagram above. 1. Which suspect probably injured the victim? (1) 2. Give a reason for your answer to the previous question. (1) 3. List one application of DNA profiling other than for solving crime. (1) 4. Give two reasons why DNA profiling may sometimes be challenged. (2) (5) Protein synthesis Key terminology amino acids monomers of proteins base triplet three nitrogenous bases one after the other on DNA 1st stage of protein synthesis – mRNA formed from DNA transcription carrying code for the protein to be made 2nd stage of protein synthesis – amino acids combine to form translation a protein three nitrogenous bases one after the other on mRNA – codon these are complementary to the triplet on DNA three nitrogenous bases one after the other on tRNA – these anti-codon are complementary to the codon on mRNA The process in which proteins are made is called protein synthesis. Proteins are made by linking various amino acids that are present in the cytoplasm of cells. There are 20 different amino acids, and they combine in a large variety of combinations. The number of amino acids and the sequence of the amino acids determine the type of protein that is formed. Figure 9 illustrates a protein with different amino acids represented by the different shapes and colour. The bond between the amino acids is known as a peptide bond. peptide bond Figure 9: Amino acids linked by peptide bonds The genes found in DNA contain the code which determines which type of protein that will be formed. 19   The smallest protein contains 50 amino acids linked together  Proteins generally contain 300 or more amino acids. Three consecutive nitrogenous bases on the DNA strand are called the base triplet. The base triplets determine which amino acid will be placed into the protein as well as the sequence in which the amino acids will be joined. Protein synthesis occurs in two stages Stage 1: Transcription Stage 2: Translation Stage 1: Transcription The first stage of protein synthesis, called transcription, occurs in the nucleus (see Figure 10 below). Stage 1 DNA nucleus cytoplasm mRNA transcription mRNA transport to cytoplasm for next phase of protein synthesis – translation Figure 10: Transcription 20  1. A section of the DNA double helix unwinds. As a result,  the weak hydrogen bonds between the nitrogenous bases of DNA break  the DNA unzips (in this particular section of the DNA) 2. One strand acts as a template 3. This DNA template is used to form a complementary strand of messenger RNA (mRNA)  This is done using free RNA nucleotides in the nucleoplasm  The mRNA now contains the code for the protein which will be formed  Three adjacent nitrogenous bases on the mRNA are known as codons. These code for a particular amino acid. 4. mRNA moves out of the nucleus through a nuclear pore into the cytoplasm, where it attaches onto a ribosome Stage 2: Translation The second stage of protein synthesis, called translation (Figure 11) , occurs in the cytoplasm. Stage 2 amino acid protein forming tRNA with amino acid cytoplasm mRNA Figure 11: Translation 21  5. Transfer RNA (tRNA) in the cytoplasm has three adjacent nitrogenous bases known as the anti-codon  mRNA’s codon will be complementary to a tRNA’s anti-codon  Each tRNA will carry a specific amino acid  According to the codons on the mRNA, the tRNA will bring the required amino acid to the ribosome 6. The amino acids are linked by a peptide bond to form the required protein. Figure 12 below shows the full process of protein synthesis DNA nucleus mRNA transcription mRNA cytoplasm transport to cytoplasm for the next phase of protein tRNA synthesis – translation mRNA cell membrane Figure 12: Protein synthesis 22 Note: it is important to know the difference between base triplets (DNA), codons (mRNA) and anti-codons (tRNA). The effect of mutation on protein structure (DNA sequence)  A mutation is a change in the nitrogenous base sequence of a DNA molecule (or a gene)  since mRNA is copied from the DNA molecule during transcription.  This will result in a change in the codons.  As a result, different tRNA molecules carrying different amino acids will be required.  The sequence of amino acids changes, resulting in the formation of a different protein.  If the same amino acid is coded for, there will be no change in the protein structure. Protein synthesis: https://www.youtube.com/watch?v=oefAI2x2CQM&t=43s Activity 4: Protein synthesis The diagram below represents a process that occurs during protein synthesis. B A C D E 1. Identify the process above. (1) 23