2.1 Nucleic acids the molecules of life

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1 1 2.1 Nucleic acids the molecules of life Nucleic acids information molecules of the cells form new cells stored in chromosomes in nucleus of the cell in the form of a code in DNA / parts of the code are copied into RNA then to another form used to make proteins. Nucleotides building blocks of the nucleic acids DNA/RNA are polymers the monomer is a nucleotide mononucleotide Pentose sugar (ribose/deoxyribose -1 fewer oxygen) / nitrogenous base / phosphoric acid Purine two nitrogen containing rings Pyrimidines one nitrogen containing ring Such rings have the chemical property of being bases because of the nitrogen atoms they contain DNA contains a combination of four different bases with equal numbers of pyrimidines and purines. Purines adenine and guanine Pyrimidines cytosine and thymine In RNA thymine replaced by uracil (U). Inorganic phosphate ions are present in the cytoplasm of every cell. The phosphate group makes the mononucleotides hence the nucleic acids acidic. Phosphodiester bond Hydrogen bond Building the polynucleotides Mononucleotides themselves are linked together by condensation reactions to form polynucleotide strands (nucleic acids) which can be millions of units long. The sugar of one nucleotide bonds to the phosphate group of the next nucleotide so polynucleotides always have a hydroxyl group at one end and a phosphate group at the other. To form DNA nucleotides containing the bases join together, RNA is made up of long chains of nucleotides containing CGAU. RNA molecules form single polynucleotide strands which may be folded into complex shapes or remain as long thread-like molecules. A DNA molecule is made up of two polynucleotide strands twisted around each other. A Purine always pairs with a pyrimidine AT / CG This results in the famous DNA double helix The two strands of the double helix are held together by hydrogen bonds between the complementary base pairs. There are ten of these pairs for each complete twist of the helix. The two strands are known as the 5 and 3 strand, named according to the number of the carbon atom in the Pentose sugar to which the phosphate group is attached in the first nucleotide of the chain. The two strands are antiparallel one runs in one direction and the other in the opposite direction

2 2 Semi-conservative DNA replication 1)Two single strands of the DNA molecule unzip along the line of hydrogen bonds by DNA helicase. 2) Each revealed parent strand acts as a template for a new strand to synthesise. 3)The exposed bases of the parent strand attract free mononucleotides to join each template via complementary base pairing. The enzymes DNA polymerase and DNA ligase join the nucleotides together with hydrogen bonds through condensation reactions to form new DNA strands. 4)The result is two new strands of DNA identical with the original piece. The new molecules automatically coil up into the double helix. Evidence for DNA semi-conservative replication Meselson and Stahl Two isotopes of nitrogen (as DNA contains nitrogen) heavy nitrogen (15N) and light nitrogen (14N) 1) Samples of bacteria grown one in light nitrogen / other with heavy nitrogen as the bacteria reproduced they took up nitrogen to make nucleotides for new DNA so the nitrogen became part of their DNA 2) Sample of DNA was taken from each batch spun in centrifuge heavy DNA sinks lower 3) Heavy nitrogen bacteria placed in light nitrogen broth left for replication sample taken 4) Semi-conservative new bacterial DNA molecules contain strand of each. The DNA settles between where the light/heavy settled originally. 5) The DNA settle in the middle showing that it has mixture of heavy/light the bacterial DNA replicated semi-conservatively in light nitrogen.

3 3 The genetic code The triplet code (three bases) on DNA/RNA is known as a codon (which can either signal start/beginning of sequence or used to code amino acid). mrna is formed as a complementary strand to the DNA mirror of the original base sequence. Once the RNA sequence is known the DNA sequence is simple to deduce the way the bases pair. Genetic code is based on genes- a sequence of bases on a DNA molecule for coding a sequence of amino acids in a polypeptide chain. The DNA is combined within the chromosomes in the nucleus of a cell. The ribosomes where proteins are synthesised are found the cytoplasm and as no nuclear DNA has even been detected there the message can t be carried out directly. The messages are relayed from the nuclear DNA to the active synthetic enzymes on the ribosomes by ribonucleic acids. Protein synthesis RNA is closely related to DNA but it doesn t form complex molecules. The sequence of bases along a strand of RNA is related to the sequence of bases on a small part of DNA in the nucleus different types of RNA take different roles in the process of protein synthesis. Messenger RNA (mrna) carries information from the DNA in the nucleus out into the cytoplasm. It is formed when a smell length of the DNA double helix unzips. The coding or antisense strand of the DNA acts as a template for the formation of the mrna. The mrna then moves out of the nucleus transporting the instruction from the genes to the surface of the ribosomes which are the site of protein synthesis. Transfer RNA (trna) is found in the cytoplasm it picks up particular amino acids from the vast numbers always free there. The trna molecules each carrying an amino acid line up alongside the mrna on the surface of the ribosome building up a long chain of amino acids. Peptide links are formed between the amino acids, joining them together to form a polypeptide chain which in turn can be used to form a larger protein. 1) DNA is transcribed to give a length of mrna 2) trna in the cell attaches to specific amino acids 2a) mrna moves out of the nucleus and becomes engulfed by a ribosome 3) trna molecule carrying amino acid lines up against matching mrna on the ribosome 4) Peptide links are formed between the amino acids brought by the trna 5) When the polypeptide is released into the cytoplasm, the trna units also unbind and return to the cytoplasm to pick up more amino acids. The ribosome may read the mrna again. In protein synthesis the information held in the sequence of bases in a gene is translated into a sequence of amino acids in a polypeptide chain.

4 4 Mutation -Changes in the codons The genetic code carried on the DNA is translated into living cellular material during protein synthesis. The nucleic acids are central to the process, as both the carriers and the translators of the genetic code. If a single codon is changed or misread during the process, the amino acid for which it codes may be different and so the whole polypeptide chain and the final protein may be altered. A change like this is known as a mutation. Mutations are changes in the arrangement of bases in an individual gene or in the structure of the chromosome, which change the arrangement of the genes on the chromosome. These changes can happen when gametes are formed although they also occur during the division of somatic cells. The chance of a mutation taking place during DNA replication is rare. The body has its own DNA repair system (DNA ligase) specific enzymes cut out / repair parts of the strands that become broken however some remain and are copied from the DNA when the new proteins are made. Point mutation - caused by the miscopying of just one or a small number of nucleotides. A point mutation can have no effect if there are several different arrangements of nucleotides for the same amino acid. Chromosomal mutations involve changes with the positions of genes within the chromosomes. Whole-chromosome mutations entire chromosome is either lost during meiosis or duplicated in new cell by errors in the process e.g. Down s syndrome Types of mutation point mutation / gene deletion / duplication / inversion / translocation The effect of mutations on the organism Mutations are a source of variation within an organism sometimes this can occur and produce a superior protein. This may help the organism gain a reproductive advantage so that it leaves more offspring than other individuals of that species. Most mutations are neutral meaning that they neither improve nor worsen the chances of survival. Some mutations cause great damage disrupting the biochemistry of the entire organism. Mutations can happen to any cell at any time, though they occur most commonly when the DNA is copied for cell division. Mutations in the cells of the body can cause serious problems such as cancer. The most damaging mutations are the ones that occur in the gametes because they will be passed on to future offspring. These are the mutations that give rise to genetic diseases. Exposure to mutagens e.g. X-rays /ionising radiation / certain chemicals increase the rate at which mutations occur exposure to these should be kept minimal.

5 5 Revision - Enzymes Biological catalysts A catalyst is a substance that speeds up a chemical reaction without being used up in the reaction itself. In this sense, they only change the rate of reaction and not the products. They have high molecular activity/ turnover number small quantity of enzyme can affect many molecules. 1 They catalyse metabolic reactions in our bodies (catabolic breakdown / anabolic build up) 2 Enzyme action can be intracellular or extracellular 3 They are globular proteins 4 They have a level of specifity due to their 3D shape the active site has a particular shape for certain substrate molecules to bind to. Activation energy - Activation energy amount of energy required for chemicals before reaction can start (heat) - Enzymes lower activation energy reactions happen at lower temperatures Enzyme-substrate complex lowers activation energy - - If two substrate molecules need to be joined, being attached to the enzyme holds them close together reducing any repulsion between the molecules so they can join more easily. - If the enzyme is catalysing a breakdown reaction, fitting into the active site puts strain on bonds in the substrate so the substrate molecule breaks up more easily. Lock and key substrate fits into the enzymes active site specific shapes for each Induced fit enzyme and substrate have to fit together in the first place enzyme-substrate complex changes shape slightly to complete the fit locking the substrate more tightly to the enzyme. The substrate also has to make the active site change shape in a particular way. Enzymes are specific because of their 3D structure 1 They only catalyse one reaction 2 Only one substrate can fit into the active site 3 The active sites shape is determined by the enzymes Globular 3D structure (from primary structure) 4 Different enzyme 3D structure shaped active site - 5 3D structure of protein is altered active site changes substrate wont fit enzyme stops Immobilized enzymes - packed into columns and used over long periods - higher temperatures can be used thermal stability - high operating temperatures increase rate of reaction - product doesn t have to be separated from enzyme saves money - reusability

6 6 Enzyme experiments- Measuring the initial rate of an enzyme-controlled reaction / repeat it / exponential / correlation Measure how fast the product of the reaction appears Catalase > hydrogen peroxide - state what variables are controlled - measure how much oxygen is given off in a gas cylinder - different concentrations of enzyme (state them 10%, 20% etc.) - measure the amount of oxygen given off after certain time period e.g. 1 min - divide the volume of oxygen produced by the time initial rate of reaction - more given off in first minute faster initial rate of reaction. Rate of reaction Affected by enzyme concentration - More enzyme molecules more likely a substrate molecule will collide with one and form an enzyme-substrate complex. - If the amount of substrate is limited there comes a point when there are more than enough enzyme molecules to deal with all the available substrate, so adding more enzymes has no further effect. Affected by substrate concentration The enzyme can become saturated all of the active sites are occupied by substrate molecules and a further increase in substrate concentration will not increase the reaction further. This point is called v-max which is the maximum rate of reaction. Temperature Higher temperature more kinetic energy > more heat energy more collisions rate of reaction increases. Optimum temperature enzymes catalytic activity is greatest (37.5) in humans. Above this level the enzyme structure begins to break down (denature) (third/fourth structures unravel) High levels - molecular bonds break down in protein permanently altering active site rendering it functionless. Exceptions thermophillic / temperature coefficient rate of reaction at (x+10) / rate of reaction at x ph level A lower ph more acidic higher number of hydrogen to form bonds with enzyme protein structure High ph alkaline less bonds form (both affect structure that holds 3D protein structure. - alteration of intermolecular bonds in extremes can denature the active site making it functionless - enzymes have an optimum ph range works most effectively Inhibition active site-directed: occupy active site to prevent substrate molecule from binding. non-active site-directed: inhibitors that attach to other parts distorting its shape