Biology - Course Companion - Andrew Allott and David Mindorff - Oxford 2023 (1)-pages-2-pages-compressed.pdf

Molecules A1.2.1 DNA as the genetic material of all living organisms Genetic materia...

Molecules A1.2.1 DNA as the genetic material of all living organisms Genetic material is a store of information. If copied, it c an be passed from cell to cell and also from parent to ospring. Bec ause genetic material is inherited it is sometimes c alled hereditary information. All living organisms use DNA to store hereditary information. The full name for DNA is deoxyribonucleic acid. The other type of nucleic acid is ribonucleic acid or RNA. Nucleic acids were rst discovered in the cell nucleus, hence the name. They are very large molecules, made from subunits c alled nucleotides which link to form a polymer. ▴ Figure 3 The virus shown in the centre Some viruses use RNA as their genetic material, for example, coronaviruses and (black structure) uses DNA as its genetic HIV. This observation does not seem to t the theory that genes are made of DNA material. The virus has burst open and its in all living organisms. However, reproduction is a fundamental property of living DNA has spilled out of the polyhedral head, where it is stored organisms and viruses cannot reproduce themselves. Instead, they rely on a host cell for this process so they are not considered to be true living organisms. Therefore, they do not falsify the claim that all living organisms use DNA as their genetic material. A1.2.2 Components of a nucleotide Nucleotides consist of three parts: a sugar, which has five c arbon atoms so is a pentose sugar a phosphate group, which is the acidic and negatively charged part of nucleic acids a base that contains nitrogen and has either one or two rings of atoms in its structure. phosphate sugar base O O P O CH 2 5 O 1 O C C N 4 3 2 OH OH ▴ Figure 4 Parts of a nucleotide ▴ Figure 5 Simple diagram of a nucleotide Figure 4 shows these parts and how they are linked together to form an RNA nucleotide. The base and the phosphate are both linked by covalent bonds to the pentose sugar. The ve c arbon atoms in the pentose sugar are numbered, with the base linked to C1 and the phosphate to C5. Figure 5 shows a nucleotide in symbolic form, with a circle to represent the phosphate, a pentagon for the pentose sugar and a rectangle for the base. 17  Unity and diversity O A1.2.3 Sugar–phosphate bonding and O O P thesugar–phosphate “backbone” of DNA O and RNA To link nucleotides together into a chain or polymer, covalent bonds are formed CH 2 O between the phosphate of one nucleotide and the pentose sugar of the next HC CH base nucleotide. Whenever nucleic acids are produced by living organisms, the nucleotides are HC CH always added to the growing polypeptide in the same way: the phosphate of the nucleotide being added is linked by a covalent bond to the pentose sugar of OH O the previous nucleotide. Linking together nucleotides in this way creates a series O P O of alternating sugar and phosphate groups, with a chain of c arbon, oxygen and phosphorus atoms covalently bonded together. This chain forms a strong sugar– O phosphate backbone in DNA and RNA molecules that helps to conserve the sequence of bases. CH 2 O HC CH base A1.2.4 Bases in each nucleic acid that form HC CH the basis of a code OH OH There are four dierent bases in DNA and in RNA. Three bases are the same but ▴ Figure 6 The oxygen atom shown in red the fourth one diers. All of the bases contain nitrogen—this is why they are oen forms links between the phosphate of one referred to as nitrogenous bases. nucleotide and the pentose sugar of the next nucleotide E ach nucleotide contains one base so there are four types of nucleotide in DNA and in RNA. Any two nucleotides c an be linked to each other, bec ause the bases in DNA bases in RNA phosphate and sugar used to make the bond are the same. Any base sequence is therefore possible along a DNA or RNA molecule and the number of possible adenine (A) adenine (A) sequences is almost innite. cytosine (C) cytosine (C) The sequence of bases is how information is stored. The information is stored in a guanine (G) guanine (G) coded form—this is the universal genetic code that is shared by all organisms. thymine (T) uracil (U) ▴ Table 1 Data-based questions: Bases in DNA Look at the molecular models in Figure 7 and answer the 3. Identify three similarities between adenine and following questions. guanine. 1. State one dierence between adenine and the 4. Compare the structure of cytosine and thymine. other bases. 5. Although the bases have some shared features, each 2. E ach of the bases has a nitrogen atom bonded to a one has a distinctive chemic al structure and shape. hydrogen atom in a similar position (shown lower Remembering the function of DNA, explain why it is le). Deduce how this nitrogen is used when a important for each base to be distinctive. nucleotide is being assembled from its subunits. 18  Molecules Guanine O N NH NH N NH 2 Adenine NH 2 N N NH N Cytosine NH 2 N NH O Thymine O NH NH O ▴ Figure 7 ATL Communic ation skills: Interpreting and evaluating information presented in dierent forms Figure 7 in the data-based questions shows three dierent representations of e ach base. The rst is a structural formula, the second is a ball and stick model and the third is a space lling model. The command term “evaluate” me ans to make an appraisal by weighing up strengths and limitations. Evaluate e ach type of representation. Which was most useful in answering the data-based questions? A1.2.5 RNA as a polymer formed by condensation of nucleotide monomers RNA is a single, unbranched polymer of nucleotides. The nucleotides are subunits of a polymer, so they are monomers. The number of nucleotides in a molecule of RNA is unlimited, but they are always linked in the same way, by a condensation reaction. ▴ Figure 8 RNA polymers c an be represented using circles, pentagons and rectangles 19  Unity and diversity In a condensation reaction, two molecules are combined to form a single molecule and water is eliminated. Hydroxyl groups (OH) on the phosphate of one nucleotide and on the pentose sugar of another nucleotide are used. One of the OH groups is removed entirely. It is combined with the hydrogen from the other OH, producing water. The remaining oxygen forms a new covalent bond, linking the two nucleotides. This is shown in Figure 9. O O O O P O P O O O CH CH 2 2 O O HC CH base HC CH base HC CH HC CH OH OH O OH + H O 2 OH O P O O P O O 5’ end O CH 2 O 3’end CH 2 O HC base CH complementary S base pairs HC base CH P P HC CH S A T S P hydrogen HC CH OH OH C S bonds P P OH OH C G S S ▴ Figure 9 Condensation reaction between two nucleotides P T A S S P P S A1.2.6 DNA as a double helix made of two P G S S antiparallel strands of nucleotides with the P S T A S two strands linked by hydrogen bonding P P G C between complementary base pairs S S P DNA is composed of strands or polymers of nucleotides. The pentose sugar in T S S e ach nucleotide is deoxyribose and the bases are adenine, cytosine, guanine P P sugar–phosphate and thymine. S backbone P P A DNA molecule consists of two strands of nucleotides linked to each other S S by their bases. The links between the bases are hydrogen bonds. Adenine (A) P only forms hydrogen bonds with thymine (T). Guanine (G) only forms hydrogen S S G C 3’end bonds with cytosine (C). This results in complementary base pairing. A and T P complement each other by forming base pairs and similarly G and C complement 5’end each other by forming pairs. ▴ Figure 10 The double helix 20  Molecules The two strands of nucleotides are parallel to each other. However, they run in opposite directions so they are said to be antiparallel. For this reason, one strand ends with the phosphate group of the terminal nucleotide while the other strand ends with a deoxyribose. If the two strands were oriented in the same direction, the bases would not be able to form hydrogen bonds with each other. DNA molecules usually adopt a helic al shape. A helix is a coiled structure that has a constant diameter of 2 nanometres (2 nm). Bec ause of the two strands, DNA is a double helix. Figure 10 shows its features. Drawings of the structure of DNA on paper c annot show all features of the three- dimensional structure of the molecule. Figure 11 shows how the structure of DNA c an be represented simply in a diagram. covalent bond P Key – sugar – phosphate S S P S A T A C – nitrogenous bases P P T G S S C G P P S S T A P P S S G C P CH OH 2 5 H hydrogen bonds are formed O between two bases 4 1 H H ▴ Figure 11 Complementary base pairing between the antiparallel strands of DNA OH 3 2 OH OH A1.2.7 Dierences between DNA and RNA ribose There are three important dierences between the two types of nucleic acid: CH OH 2 1. There are usually two polymers of nucleotides in DNA, whereas there is only 5 H O one in RNA. The polymers are often referred to as strands, so DNA is double- 4 1 stranded and RNA is single-stranded. H H 2. The four bases in DNA are adenine, cytosine, guanine and thymine. The four OH 3 2 bases in RNA are adenine, cytosine, guanine and uracil, so uracil is present OH H instead of thymine in RNA. deoxyribose 3. The pentose sugar within DNA is deoxyribose, whereas the sugar in RNA is ribose. Figure 12 shows that deoxyribose has one fewer oxygen atom than ▴ Figure 12 Ribose has an OH group and ribose. The full names of DNA and RNA are based on the type of sugar in an H atom attached to c arbon 2, whereas them—deoxyribonucleic acid and ribonucleic acid. deoxyribose has two H atoms 21  Unity and diversity parental DNA A1.2.8 Role of complementary base pairing in allowing genetic information to be C C G C G replic ated and expressed A T In DNA, adenine c an only pair with thymine and cytosine c an only pair with guanine. This is complementary base pairing. It allows an exact copy of a DNA G C T A molecule to be made in a process c alled replic ation. In DNA replic ation, the T A two strands of the double helix separate. E ach of the original strands serves as a C G guide, or template, for the creation of a new strand. The new strands are formed replic ation fork A T by adding nucleotides one by one and linking them together. G C A T E ach nucleotide that is added must be c arrying the base that is complementary to G C C the next base on the template strand. This means the newly synthesized strand on T A T A T A T A each of the two template strands should have exactly the same base sequence as C C G the other template strand. Replic ation changes one original DNA molecule into C two identic al DNA molecules, each with one strand from the original molecule G C G A and one new strand. This is c alled semi-conservative replic ation. T A A T A T A T A T Genetic information consists of sections of DNA called genes. Each gene contains information needed for a particular purpose. When the information in a gene has G C C A T an eect on the cell, this is called gene expression. The rst stage in expressing a A T T A gene is the copying of its base sequence, but the copy is made of RNA rather than T A G G DNA. Only one of the two DNA strands is used as a template for this. The rules of complementary base pairing are followed but adenine on the template strand parental new new parental pairs with uracil on the new strand of RNA, rather than thymine. This process of strand strand strand strand making an RNA copy of the base sequence of DNA is called transcription. ▴ Figure 13 Semi-conservative replic ationof DNA RNA that is produced by transcription may have a regulatory or structural role in the cell, or it may be used in protein synthesis. To synthesize a protein, the base sequence of the RNA molecule is translated into the amino acid sequence of a protein. Again, complementary base pairing is involved. Both transcription and translation are more fully described in Topic D1.2 A1.2.9 Diversity of possible DNA base sequences and the limitless c apacity of DNA for storing information Genetic information is stored in the base sequence of one of the two strands of a DNA molecule. Any sequence of bases is possible. There are four possibilities for each base in the sequence—A, C, G or T. 2 There are 4 or 16 possibilities for a sequence of two bases—AA, AC, AG and so on. 3 There are 4 or 64 possibilities for a sequence of three bases—AAA, AAC, AAG and so on. n With n bases, there are 4 possible sequences. As n increases, the number of possibilities becomes immense. With a sequence of just 10 bases, there are over a million possibilities. DNA molecules c an be any length, adding to the potential diversity of base sequences. The range of possible sequences is eectively limitless, which is an ideal feature for an information storage system. 22  Molecules The diameter of a DNA molecule is just 2 nanometres, so immense lengths of DNA c an be stored in a very small volume. Compared with data-storage systems devised by humans, DNA is very economic al, both in terms of the space it takes up and the amount of material used to make it. ◂ Figure 14 A sperm is a DNA delivery system. These human sperm cells each contain 3.3 picograms of DNA, with a total length of about 2 metres and over 3 billion base pairs in total. The microscope image has a grid of lines 50 micrometres apart. How long is each sperm and how wide is the head where the DNA is stored? Data-based questions: DNA lengths 1. In Homo sapiens, the smallest chromosome (and Its genetic material is single-stranded DNA. Suggest therefore the shortest DNA molecule) is the Y one advantage and one disadvantage of this DNA chromosome which has 57,227,415 base pairs. being single-stranded. Assuming that the human genome has 3.08 billion 4. Bacteria c an store genetic information in small circular base pairs in total, what percentage of this does DNA molecules c alled plasmids. A plasmid with the Y chromosome contain? 1,440 base pairs has been found in the bacterium 2. The bacterium Carsonella ruddii has just 173,904 Acetobacter pasteurianus. The main chromosome of base pairs in its genome, with an estimate of 224 this bacterium has 3.155 Mb (Mb = megabase pairs). genes. Of these, 194 code for proteins. A surprisingly What is the ratio between the length of the plasmid low 7.3% of the bases are guanine. C alculate the and the length of the main chromosome? percentage of bases that are adenine, cytosine and 5. C an you nd examples of DNA molecules from thymine. animals, bacteria, viruses or plasmids that are shorter 3. C anine circovirus has a genome of 2,063 bases with than the examples given here? C an you nd an two protein-coding genes. This type of virus has a example of DNA with less than 7.3% guanine? protein coat that is only 17 nanometres in diameter. A1.2.10 Conservation of the genetic code across all life forms as evidence of universal common ancestry The sequence of bases in DNA or RNA contains information in a coded form. The information is decoded during protein synthesis. Groups of three bases are c alled codons and have meanings in the code. There are 64 dierent 23  Unity and diversity codons, bec ause each base in a codon c an be any of four, so there are 4 × 4 × 4 combinations. E ach of the 64 codons has a meaning: most codons specify one particular amino acid one codon signals that protein synthesis should start three codons signal that protein synthesis should stop. Details of the genetic code are described in Topic D1.2 It is an extraordinary fact that—with a few minor exceptions—all living organisms and all viruses use the same genetic code. It represents a sort of genetic language. Humans use many dierent spoken languages, each of which is an eective form of communication. Many dierent versions of a genetic code could be devised and they would probably function perfectly well, but all life forms use essentially the same version. For this reason, it is called the universal genetic code. The minor exceptions to the universal genetic code found in some organisms are changes to the meaning of one of the 64 codons. In most c ases, one of the three stop codons has changed to code for a specic amino acid instead. Life has been diversifying by evolution over billions of years so it is not surprising that there have been a few very small changes to the genetic code in some organisms. It is noteworthy that the code has changed so little and that all forms of life still speak essentially the same genetic language. ATL Thinking skills: Evaluating the role of emotions and attitudes in science The words below were spoken by M arshall Nirenberg, one with nature is very real and in fact is very true: we who was awarded the Nobel Prize in Physiology or all use the same genetic language. Medicine in 1968 for his work on the genetic code. 1. Why did the universality of the genetic code have The nding that the code is universal had a terric such a profound eect on M arshall Nirenberg and philosophic al eect on me. I knew everything about others at the time? evolution at the time, but these ndings were so 2. What are the implic ations of the recognition of the immediate and so profound, bec ause I understood unity of life, to scientists and to other people? that most or all forms of life on this planet use the 3. Are there other examples of scientic discoveries same genetic instructions and so we are all related. c ausing a profound change in attitudes? We’re related to all living things and when I c ame in the garden and saw the plants, the squirrels and some 4. To what extent do emotional responses such as of the birds, it really had a profound eect on me, the one described here support or run counter to which lasts to this day. I think that the feeling of being stereotypic al representations of scientists? ATL Thinking skills: Evaluating the role of languages in science A language is a code which ascribes agreed meanings to 3. Esperanto is (see Figure 15) an international language symbols. created by Ludwik Zamenhof in 1887. He hoped that a universal second language would promote world 1. What are the benets of sharing a common language? peace and understanding. What are the diculties in 2. For scientists, why is the standardization of creating a new language? Why does Esperanto not terminology viewed as essential? persist widely today? 24