Year 12 Biology: Nucleic Acids - WJEC 2022 PDF

**Year 12 Biology** **Unit 1.5 Nucleic acids and their functions** Objectives Name: **By the end of this unit, you should be familiar with:** **Can do this** **Need to improve** ---------------------------------------------------------------------- ----------------- ----------...

**Year 12 Biology** **Unit 1.5 Nucleic acids and their functions** Objectives Name: **By the end of this unit, you should be familiar with:** **Can do this** **Need to improve** ---------------------------------------------------------------------- ----------------- --------------------- The structure and roles of nucleotides. The importance of chemical energy and the structure and role of ATP. The structure of DNA and RNA and be able to compare them. The functions of DNA. The way in which DNA replicates. The characteristics of the genetic code. The difference between exons and introns. The processes of transcription and translation in protein synthesis. How to extract DNA from living material. **Work through the WJEC Blended Learning activities:** [[Nucleic acids and their functions - Blended Learning (d3kp6tphcrvm0s.cloudfront.net)]](https://d3kp6tphcrvm0s.cloudfront.net/el20-21_20-11) **Nucleic acids and their functions** Nucleic acids are common to all living organisms and are essential for many functions including inheritance and metabolism. DNA, RNA and ATP are all nucleic acids. Nucleic acids are polymers made up of monomer sub-units called nucleotides. A molecule containing many nucleotides is a polynucleotide and can be millions of molecules long. **Nucleotide structure** Nucleotides are made up of three components combined by condensation reactions. These are: - A **phosphate groups** (H~3~PO~4~). This has the same structure in all nucleotides. May be more than one. - A **pentose sugar**. The pentose is ribose in RNA and in deoxyribose in DNA. - An **organic/nitrogenous base** **Task:** Draw and label a diagram of a nucleotide. The nitrogenous organic base belongs to one of two different groups. The **pyrimidine** bases are T -- th**y**mine, C- c**y**tosine and U - **u**racil. These are single ringed structures. The **purine** bases are A- adenine and G - guanine. These are double ringed structures.  **The Importance of chemical energy in biological processes** In biological systems, it is chemical energy that makes changes because chemical bonds must make or break for reactions to happen. Heterotrophic organisms, such as animals, get their chemical energy from food. Autotrophic organisms, green plants, get energy from light energy which they convert to chemical energy during photosynthesis. **ATP -- adenosine triphosphate** Organisms store their energy as lipids or carbohydrates, but it is the molecule ATP that makes energy available when it is needed. ATP molecules are a reservoir of potential chemical energy and act as a common intermediate in metabolism, linking energy-requiring and energy-yielding reactions. **The structure of ATP adenosine triphosphate** ATP is a nucleotide. It is made up of three parts: - An organic nitrogenous base - Adenine - A five carbon (pentose sugar) - Ribose - Three phosphate groups linked together -- P **Task:** On the diagram of ATP below, ring and label the organic base adenine, the pentose sugar ribose and three phosphate groups.  **ATP as a universal energy currency** We make and break down about 50 kg ATP every day, but the body only contains about 5g ATP, so it is [not an energy store]. It is sometimes called the **'universal energy currency'** of the cell because it *provides the energy for all reactions in all cells in all organisms*. ATP is synthesised when energy is made available in the cytoplasm, mitochondria, and chloroplasts, and it is broken down when energy is needed, such as in muscle contraction or nerve impulse transmission. **ATP and energy** When energy is needed, the enzyme ATPase hydrolyses the bond between the middle and terminal phosphate groups by adding a molecule of water. Adenosine diphosphate (ADP) and an inorganic phosphate ion are formed with the release of chemical energy. Every mole of ATP hydrolysed releases 30.6kJ. As energy is released, this is an **exergonic** reaction. It is linked to energy-requiring reactions in cells. The reaction is reversible, so ADP and an inorganic phosphate ion can combine in a condensation reaction to make ATP and water. This requires an energy input of 30.6kJ per mole of ATP. **The enzyme, ATP synthetase** catalyses this reaction. As energy is required, this is an **endergonic** reaction. The addition of phosphate (P~i~) to ADP is called **phosphorylation.** ATP transfers free energy from energy-rich compounds, like glucose, to cellular reactions where it is needed. But energy transfers are inefficient, and some energy is always *lost as heat*. The uncontrolled release of energy from glucose would produce a temperature increase that would destroy cells. Instead living organisms release energy gradually, in a series of small steps called respiration. When a phosphate group is transferred from ATP to another molecule it makes it more reactive and *so lowers the activation energy* of a reaction involving that molecule. **Task:** What is activation energy? (YouTube- ATP The Cellular Currency Metabolism Part 3) (How cells obtain energy) **Task:** Complete the table below outlining the uses of ATP. **ATP provides energy for** **Description** ----------------------------- ------------------------------------------------------------------------------------------------------------------------------------------- To build large complex molecules from smaller simpler ones e.g., polypeptides from amino acids and DNA from nucleotides To change the shape of carrier proteins in cell membranes to allow molecules and ions to be transported against a concentration gradient. Movement Muscle contraction Sodium-potassium pumps actively transport sodium and potassium ions across the axon cell membrane The packaging and transport of secretory products into vesicles in cells. **Task:** Explain the advantages of ATP. - A single reaction - One enzyme - Small amounts of energy released - Soluble and easily transported - Common source of energy for many different chemical reaction **DNA -- Deoxyribonucleic acid** DNA contains the information about an organism, in the form of a genetic code. DNA is contained in the nucleus of the cells of the organism and determines its inherited characteristics. **The Structure of DNA** DNA is made up of **two** polynucleotide strands wound around each other in a double helix. Each **DNA nucleotide** is made up of: 1. a **phosphate** group (H~3~PO~4~) 2. a pentose sugar which is always **deoxyribose** C~5~ H~10~ 0~4~ 3. one of the four **organic/nitrogenous bases**  The nucleotides in one strand are arranged in the opposite direction from those in the complementary strand. The two polynucleotide strands are arranged **antiparallel** to each other i.e., parallel but facing in opposite directions. A DNA molecule is very long and thin and is tightly coiled within a chromosome. The double helix is 2nm in diameter. The DNA molecule in the human chromosome number 1 is estimated to be 85mm long. DNA is like a twisted ladder with the uprights of the ladder being made up of alternating sugars and phosphate groups and the rungs made up of the bases. **Task:** Erwin Chargaff was an Austrian Chemist, what is Chargaff's rule? **Task:** Explain how DNA is well suited to carrying out its functions. - - - - **Task:** Write an account of how the molecular structure of DNA was discovered and which scientists contributed to this discovery. You should word process your account and include some relevant images. **RNA -- Ribonucleic acid** RNA is a **single stranded** polynucleotide. Each RNA nucleotide consists of: 1. a **phosphate** group (H~3~PO~4~) 2. a pentose sugar which is always **ribose** C~5~ H~10~ 0~5~ 3. one of the four **organic/nitrogenous bases** There are 3 types of RNA which all have a role in [protein synthesis]. - Messenger RNA mRNA - Ribosomal RNA rRNA - Transfer RNA tRNA **Messenger RNA (mRNA)** mRNA is a long, single stranded molecule wound into a helix. It is made in the nucleus during the process of [transcription]. It carries the genetic code for one gene from the DNA in the nucleus to the ribosomes in the cytoplasm. Each gene codes for a particular polypeptide. Different mRNA molecules have different lengths. **Ribosomal RNA (rRNA)** rRNA is found in the cytoplasm and is a component of ribosomes. The other component is protein. Ribosomes are synthesised in the nucleolus and leave the nucleus via nuclear pores. rRNA is a large, complex molecule made up of both double and single helices. Ribosomes are the site of protein synthesis by a process called [translation]. **Transfer RNA (tRNA)** tRNA is a small single stranded molecule which folds so that in places there are base sequences forming complementary pairs. It forms a clover-leaf shape. One end of the chain, the 3' end, has the base sequence CCA at which point the specific amino acid that it carries attaches itself. At the opposite end is a sequence of three bases called the [anticodon]. tRNA molecules transport specific amino acids to the ribosome so that proteins can be synthesised. **Task:** List the similarities between the structure of DNA and RNA. Then tabulate the differences. **Task:** Watch this Crash Course video to remind you of the nucleic acids: **The functions of DNA** DNA has **2** main functions: **1. Replication in dividing cells** DNA is made up of two complementary strands, the base sequence of one determines the base sequence of the other. If the two strands of a double helix are separated, each parent strand acts as a **template** for the synthesis of a new **complementary strand**, so that two identical double helices can be formed. **2. Protein synthesis** The sequence of bases represents the genetic code whereby the sequence of bases on the DNA determines the sequence of amino acids in proteins. **DNA Replication** Chromosomes must make copies of themselves so that when cells divide, each daughter cell receives an exact copy of the genetic information. This copying of DNA is called replication. Replication occurs in the nucleus before a cell divides by either mitosis or meiosis during a stage called **interphase**. When Watson and Crick built their model of the structure of DNA in 1953, they suggested a mechanism for DNA replication. They realised that complementary base pairs implied that if the two strands were separated, they would each make another complementary strand. Two new identical molecules would form, each with one **original** **strand** and one **newly synthesised** **strand**. This is **semi--conservative** replication. Experimental evidence was later collected by Meselson and Stahl in 1958. The steps involved in DNA replication are as follows: 1. **DNA helicase** unwinds and unzips the double helix by breaking the hydrogen bonds between the complementary base pairs of the two strands of the DNA molecule. This eposes the unpaired bases of DNA on the template strand. 2. The enzyme **DNA polymerase** reads the sequence of DNA bases on the template strand and catalyses the addition of free DNA nucleotides to the exposed bases (C + G, A + T). Finally, it catalyses the condensation reaction between the 5' phosphate group of a free nucleotide to the 3' OH on the growing DNA chain to form the sugar-phosphate backbone. Each chain acts as a **template**. 3. Two **DNA molecules** result, each made up of **one newly synthesised strand and one strand conserved from the original molecule**. Stages in semi conservative replication: **Task:** Look carefully at the diagrams below that illustrate the two other suggested mechanisms for the replication of DNA. **The Meselson -- Stahl experiment** Meselson and Stahl's evidence for the semi conservative replication of DNA involved culturing the bacterium *Escherichia coli* for several generations on a medium containing amino acids made with the heavy isotope ^15^N. The bacteria incorporated the ^15^N into the organic base of their nucleotides. After several generations, all the DNA contained ^15^N. They then washed the bacteria and transferred them to a medium containing the normal lighter isotope ^14^N. After each generation, extracts of the DNA were centrifuged, and their results are shown below. **Task:** Read pg. 96 in your textbook and then look carefully at the diagram below.  **Generation** **Explanation of results** ---------------- --------------------------------------------------------------------------------------------------------------------------------------------- **0** All DNA heavy due to presence of ^15^N only. **1** Heavy DNA acts as a template to synthesise new strands containing ^14^N, forming 2 molecules of hybrid or intermediate DNA. **2** Both heavy and light strands act as templates forming both hybrid and light molecules of DNA in a 1:1 ratio. **3** As more light strands act as templates and only light isotope is available for replication, more light molecules are formed in a 3:1 ratio. **Task:** How would the tubes differ if replication was conservative or dispersive? Which generation disproves the other 2 theories? **Task**: Complete the summary review sheet on nucleic acids, DNA and RNA **The Genetic Code** The second function of DNA is to act as a store of genetic information that can be used to make proteins. This genetic information is coded in the sequence of bases in the DNA in thousands of sections along its length, called genes. The length of DNA making up a gene carries the information to make a particular polypeptide. This information is called the **genetic code**. The [sequence] of bases in the DNA determines the sequence that amino acids join together, the [primary structure] of a protein. DNA determines which proteins are made and because enzymes are proteins, it determines which reactions take place in an organism. By determining which enzymes are produced, the DNA determines the characteristics of an organism. The **genetic code is a triplet code**: - Biochemical experiments showed that a polynucleotide strand always had three times the number of bases than the amino acid chain it coded for. - If three bases were removed from a polynucleotide chain, the polypeptide made would have one fewer amino acid. - If the polynucleotide chain had three extra bases, the polypeptide made would have one more amino acid. These experiments suggested that the code is a **triplet** code and 3 base pairs code for an amino acid. The 3 base pairs coding for an amino acid are called a **codon**. There are **4** bases in DNA (ATCG) and **20** commonly occurring amino acids. If 1 base pair coded for 1 amino acid, you could make 4^1^ or 4 codes for amino acids. If 2 base pairs coded for 1 amino acid, you could make 4^2^ or 16 codes for amino acids. Amino acids can be abbreviated as follows: This is a [codon chart] and shows which triplets of **RNA** code for which amino acids. **Task:** What amino acids are coded for by the following RNA codons: AUG = CAC = UGA = The characteristics of the genetic code are: - It's **linear** -- the bases are read in a line - It's **triplet** -- three base pairs or a codon code for one amino acid - It's **degenerate** -- most amino acids have more than one code - It's **unambiguous** -- each codon specifies one amino acid only - It's **punctuated** - some codons are start or stop codons - It's **universal** -- exactly the same for all living organisms - It's **non-overlapping** -- each triplet is read separately The 'one gene one polypeptide hypothesis' states that the length of DNA in one gene codes for a single polypeptide chain. **Task**: Why is the 'one gene, one enzyme' hypothesis incorrect? And why 'one gene one protein' hypothesis incorrect? **Exons and Introns** DNA contains the information for making polypeptides. An RNA version of the code is first made from the DNA. In prokaryotes, this is **messenger RNA (mRNA),** and it directs the synthesis of the polypeptide (continuous genes). But in Eukaryotic cells, the RNA has to be processed before it can be used to synthesise the polypeptide. The RNA molecule first formed is much longer than the final mRNA and it contains sequences of bases that have to be removed (discontinuous genes). This RNA is sometimes called **pre-messenger RNA (pre-mRNA)** and the sequences to be removed are called **introns.** They are not translated into proteins. The introns are cut out of the pre-mRNA using **endonucleases** and the sequences left are the **exons**, which are joined or spliced together using **ligases**.  **Task:** What are introns? What are exons? **Protein Synthesis** Protein synthesis is a 2-stage process: **1. Transcription** This is the first stage of protein synthesis. DNA **stays** in the nucleus and acts as a **template** for the formation of mRNA. The mRNA is copied from a specific region of DNA called the cistron. The cistron is equivalent to a gene and codes for a specific polypeptide. Messenger RNA carries the instructions needed for protein synthesis from the nucleus out through the nuclear pores into the cytoplasm. Transcription involves the following steps: 1. The enzyme **DNA helicase** acts on a specific region of the DNA, the **cistron**. The enzyme breaks the hydrogen bonds between the bases and causes the 2 **strands** of the DNA molecule to separate and expose the nucleotide bases. 2. The enzyme **RNA polymerase** binds to **1** of the **strands** of DNA called the **template strand** at the beginning of the sequence to be copied or **transcribed**. 3. Free RNA nucleotides (with bases C G A and **Uracil instead of T**) align opposite the **template strand** based on the complementary relationship between the bases in DNA and the free RNA nucleotides. 4. RNA polymerase moves along the DNA forming bonds that add nucleotides one by one. 5. A **mRNA** molecule is synthesised alongside the unwound portion of DNA. Behind the RNA polymerase the DNA strands rewind to form the double helix. 6. At the end of the sequence the RNA polymerase detaches when it reaches a **stop codon,** and the newly formed pre-mRNA detaches from the DNA. 7. Post transcriptional modification then occurs, and the intron regions are removed by endonuclease enzymes and the exon regions are re-joined by ligase enzymes to form functional mRNA. 8. The mRNA leaves the nucleus via a nuclear pore and attaches to a ribosome in the cytoplasm for the next stage of protein synthesis -- translation. **2. Translation** This is the second stage of protein synthesis. It occurs in the cytoplasm on a ribosome. Messenger RNA (mRNA) and transfer RNA (tRNA) are involved. The codons on the mRNA are translated into a sequence of amino acids to form a polypeptide. Each ribosome is made of two subunits. The larger subunit has two sites for the attachment of tRNA molecules, so two tRNA molecules are associated with a ribosome at any one time. The smaller subunit binds to the mRNA. **Task:** Draw, label and annotate a ribosome in the space below. Find out what a polysome is. **Task:** Draw, label and annotate a tRNA molecule in the space below. What is **activation** of the tRNA? The ribosome acts as a framework moving along the mRNA and holding the codon-anticodon complex together, until the two amino acids attached to adjacent tRNA molecules bind. The ribosome moves along the mRNA, adding one amino acid at a time, until a polypeptide is formed. The order of bases in the DNA determines the order of amino acids in the polypeptide. Translation involves the following steps: 1. **Initiation**: a ribosome becomes attached to the 'start' codon at one end of the mRNA molecule. 2. The first tRNA with an anticodon complementary to the first codon of the mRNA attaches to the ribosome at one attachment site. The three bases of the codon on the mRNA bond to the three complementary bases of the anticodon on the tRNA, with hydrogen bonds. A **codon-anticodon complex** is formed. 3. A second tRNA with an anticodon complementary to the second codon on the mRNA attaches to the other attachment site. The codon and anticodon bond with hydrogen bonds 4. **Elongation**: The 2 amino acids are close and form a peptide bond catalysed by a ribosomal enzyme. This is a condensation reaction. 5. The first tRNA leaves the ribosome, leaving its attachment site vacant. It returns to the cytoplasm to bind to another copy of its specific amino acid. 6. The ribosome moves one codon along the mRNA and the vacant site is occupied by a new appropriate tRNA. 7. **Termination**: The sequence repeats until a 'stop' codon is reached. The polypeptide is released and can be modified by the cell into a protein. 8. The ribosome-mRNA- polypeptide complex separates.  Usually, several ribosomes bind to a single mRNA strand each reading the coded information at the same time. This is called a polysome. Each ribosome produces a polypeptide, so several are made at once. **Task:** Complete the table below using your codon dictionary **mRNA codon** **DNA base sequence** **tRNA anticodon** **Amino acid** ---------------- ----------------------- -------------------- ---------------- **GGA** **UAC** **CCA** **CUG** **UUU** **AAG** **UGC** **Task:** Write an essay: 'Describe how the base sequence of a gene is converted into the primary structure of a protein.' (10 marks) **Genes and polypeptides** Genes are defined as a sequence of DNA bases that codes for one polypeptide. This is known as the **one gene-one polypeptide hypothesis**. **Post-transitional modification** The base sequence of a gene determines the primary structure of a polypeptide. Polypeptides made on the ribosomes are transported to the Golgi body where the polypeptide is folded into secondary, tertiary, or quaternary structures. It may be chemically modified as well. This modification is known as **post-transitional modification.** Proteins include enzymes, antibodies, transport proteins and structural proteins Polypeptides can be chemically modified by combining with: - Carbohydrates to make glycoproteins - Lipids to make glycolipids - Phosphate to make phospho-proteins Some polypeptides can be combined e.g., haemoglobin. There are 4 polypeptides, each has α- helix regions (secondary structure) and is folded (tertiary structure). The four polypeptides are combined (quaternary structure). In addition, the protein is modified by combination with four non-protein haem groups to make the functional molecule. **Task:** Explain how a mutation in the DNA molecule could result in a non-functional protein being synthesised. Use your knowledge of protein structure and function from the molecules topic. **Examiner's Foibles** - Remember to use **molecule** and **strand** correctly when describing DNA. The molecule of DNA is made up of two complementary strands. **Task:** Draw a summary mind map of this topic in the space below.