DNA and the Genetic CodeGene: a series of base sequencesMultiple genes code for a DNA strand.A DNA strand wrapped up is known as a chromosome.Human Genome ProjectBegan in 1990, unexpectedly finished 4 years earlier in 2001 due to unanticipated technological advancements. Determined the number of all human genes, their locations, and many of their key base sequences. Genomes of other species have also been determined.Genome full set of genes and alleles found in a species Allowed geneticists to identify mutations and investigate the interaction between different genes and the proteins they code for. Made possible by the development of fast computers, international sharing of dataDNADNA is deoxyribonucleic acid is found in all living cells. It is the genetic blueprint of an organism. The DNA molecules of all living things on the Earth have the same general structure, but each species has its own unique DNA that defines the species. There are also slight differences in the DNA between individuals within a species, which is why we are all unique.James Watson and Francis Crick worked together at the University of Cambridge in the United Kingdom during the early 1950s. They discovered the structure of DNA, but did not carry out any experiments.The main advancement which led to Watson and Cricks discovery was carried out by Rosalind Franklin. She carried out X-ray crystallography to obtain pictures of DNA, this hinted that the structure of DNA is a double helix.The four bases of DNA are: adenine (A), guanine (G), thymine (T) and cytosine(C).The structure of DNA is composed of multiple nucleotides, the basic unit of nucleic acids. These are made up of 3 components:A nitrogenous base(A,T,G,C)A 5 carbon sugarA phosphate group

The sugar and phosphate group form the sides of the double helix structure, the sugar-phosphate backbone. The bases are attached to the sugars and form the rungs of the double helix ladder. Any number of nucleotides can join together, in any order, to form the nucleic acid polymer, or polynucleotide chain.Watson and Crick realised that the bases on one of the polynucleotide chains are bonded to bases on the other polynucleotide chain- A always bonding to T and G always bonding to C. These bases were called complementary bases or complementary base pairs.Two polynucleotide chains, or strands, are attracted to each other due to the chemical nature of the complementary bases. This is important for the easy unzipping of the ladder during replication. A large base (adenine or guanine) is always bonded to a small base (thymine or cytosine) because this gives a consistent amount of space between the strands.RNA is a single-stranded polynucleotide with a similar sugarphosphate backbone to that of DNA. However, RNA contains the sugar ribose and the four bases adenine (A), guanine (G), cytosine (C) and uracil (U) instead of thymine (T), it does not contain the phosphate group. RNA plays a key role in protein synthesis.The number of chromosomes per species is always an even number because chromosomes exist in homologous pairs.A gene is a length of DNA that has a specific sequence of base pairs and codes for a particular characteristic.A karyotype is an image of a chromosome extracted from a cell, stained and photographed through a digital microscope. This is used to identify genetic abnormalities.The genes that make up chromosomes hold the code for every characteristic of an organism. A full set of these blueprints is present in almost every cell of a multicellular organism. The few exceptions include red blood cells, which do not have a nucleus, and gametes (sperm and ova), which only have one set of chromosomes rather than pairs.Cell DivisionThere are 2 forms of cell division- mitosis and meiosisMitosis is an organised series of steps of a cell division that ensures each daughter cell is an exact copy of the parent cell. Chromosomes are inner parts of the cell which divide and replicate themselves to create new cells.

Meiosis 1Meiosis 2Meiosis is a type of cell division where gametes are formed in the ovaries or testes of an organism. Meiosis results in a daughter cell receiving half of each parent cell.Meiosis I separates homologous pairs of chromosomesMeiosis II separates chromatids DNA makes copies of itself through a process known as replication. In replicationDNA unzips by breaking the hydrogen bonds between the nitrogenous bases, with the help of enzymes and heat.Spare nucleotides which are floating around in the nucleus are added to the other side of the bases, which ensures that the DNA is replicated fully. Replication is the first stage of both mitosis and meiosis, and every chromosome is replicated. After replication, the doubled chromosomes are still attached at a point called the centromere and the chromosomes often look like an X.Chromosomes are commonly drawn like this because it is the stage at which they are most easily visible under a microscope. Each strand of the doubled chromosome is called a chromatid.Key things to remember about replication: Before replication: single chromosome = 1 molecule of DNA (double-stranded double helix) = 1 copy of every chromosome After replication: doubled chromosome = 2 molecules of DNA = 2 chromatids joined at the centromere = 2 copies of every chromosome Mitosis is the process of replicating exact copies of somatic cells. Meiosis is the process by which diploid cells are converted into haploid gametes and it occurs in the gonads of multicellular, sexually reproducing organisms. The only purpose of a gamete is to fuse or join with another gamete to make a new cell called a zygote. This fusion of gametes is called fertilisation. The zygote will be diploid because it contains two sets of chromosomes, one from each gamete. Therefore, the original number of chromosomes is restored again in the body cells of the new organismMutations Mutations are mistakes made during both replication and cell division. They can involve individual genes or entire chromosomes. A gene mutation is a change to the sequence of bases within a gene and usually happens during replication. Generally mutations are fixed by enzymes, specialised helper proteins that act as proof-readers. The impact of these mutations varies depending on the nature of the change to the genetic code. Sometimes the mutation can cause the base to change, but the new codon still codes for the same amino acid, so this is still fine for the body. Other times the mutation changes the amino acid, and this starts a chain reaction, affecting the protein and eventually the body. Natural, spontaneous mutations occur continuously at a low rate. However, environmental factors called mutagens can increase the frequency of mutations. Mutagens include chemicals, radiation and ultraviolet (UV) light. Somatic mutation- occurs during mitosis of body cells (diploid cells). The effect of this mutation only occurs to the person with the affected cells. Sometimes, somatic mutations lead to illnesses, or even cancer. Germ-line mutations occur during meiosis and the formation of gametes. The effect of this mutation may not be felt by the carrier, but is passed onto their children if the gamete is fertilised. Germ-line mutations are heritable since they can be passed on/inherited by their offspring. There are 3 outcomes for genetic mutations Sequence still codes for the same amino acids (some amino acids have more than one code) so there is no change to the polypeptide. Sequence codes for at least one different amino acid, which alters the structure and function of the polypeptide to varying degrees. Sequence is changed to include an earlier stop codon, shortening the polypeptide and often significantly altering its structure and function. Examples of the effects of types of mutagens Radiation- Ionises biochemical compounds in cells, forming free radicals The free radicals cause damage to DNA and proteins (e.g. breakages in chromosomes) Chemicals- Some chemicals insert into DNA instead of bases (or substitute for bases) Other chemicals insert between bases, causing issues when the DNA replicates UV light- Causes thymine bases that are close together on a DNA polynucleotide chain to bind together, forming thymine dimers. This causes problems during DNA replication Chromosomal mutations classified according to whether they change the structure of chromosomes or alter the number of chromosomes in the cell. often identified by their karyotype. E.g. down syndrome (trisomy 21)- 3 chromosomes in number 21, Jacob's Syndrome (XYY syndrome) where the chromosome number 23 is XYY, with the inclusion of an extra Y chromosome. The genetic code is the sequence of bases in a gene and provides the specific instructions for the synthesis of proteins. Some proteins are the building material for major structures and organelles within the cell, whereas others are functional proteins such as enzymes. Proteins are polymers made up of polypeptides, which are chains of amino acids. Only 20 amino acids that occur naturally in human proteins, but they can be used in millions of different combinations. Each amino acid requires a specific code, which is made up of the DNA bases A, T, C and G. Protein Synthesis- where the relevant section (the gene) of DNA is copied into RNA. The short strands of RNA leave the nucleus and go to a ribosome where they form a template for an amino acid chain. Prokaryote- single celled organism which does not have a membrane-bound nucleus, essentially consisting of free-floating organelles Eukaryote- any organism whose cells contain a nucleus and other organelles enclosed within membranes. Ribosome- the protein builders, they connect amino acids together to form long chainsBase Sequences Codon- base triplet which codes for an amino acid, composed of 3 bases(A,U,G,C) e.g. AUG is the met/start codon.The possibilities for a codon, with there being 4 bases are 4x4x4=64 types of codons, there are more codons that can code for amino acids than there are amino acids, so multiple codons code for the same amino acid. The codons for the amino acids are typically listed using RNA rather than DNA. All proteins start with the amino acid methionine, which is coded for by the start codon AUG. They end with the codon TAG or the stop codon. The base sequence, or base order in DNA is extremely important. Even 1 change in the bases can affect the amino acid produced which affects the protein produced. They could affect the normal functioning of the organism. This error could occur during replication, although the aim of replication is to create exact replicates, mistakes can be made during this process. Genetic inheritance Gregor Mendel was an Austrian monk, he carried out the majority of his work before the structure of DNA was known. His success in understanding genetic inheritance was due to Studying a large sample size, studying a large number of pea plants (30 000)and a large number of characteristics (7 characteristics) Carrying out a large number of crosses- repetition of his experiment to ensure accuracy Using pure breeding lines- eliminating the possibility of the plants not breeding properly His experiment essentially involved 2 true breeding parental generations. One was a round seed, the other a wrinkly seed. These seeds had their pollen grains transferred by hand. The resultant offspring were all rounded seeds. This was odd, since the parental generation were a mix of half round and half wrinkly seeds, it appeared that the wrinkly seeds had vanished. The seeds of the parental generations (known as F1) were allowed to interbreed. Since the seeds were both round, then the resultant offspring should be round, bearing in mind that the parents were both round and the parental generation were true-breeding. The resultant F2 generation contained roughly round and wrinkly seeds. The wrinkly seeds had somehow formed from 2 round seeded parents. Mendel proposed that There must be factors inside the cell which control the characteristics-these were later called genes 2 copies of the factor that are present in each cell, and control each characteristic, with one factor from the male parent and one factor from the female parent Each factor is separated before fertilisation (meiosis and gamete formation) and combines again at fertilisation, but the 2 factors do not blend. The factors which control different characteristics are passed on to the next generation independently of each other These proposals expanded into 2 fundamental laws of genetics The law of segregation- during meiosis the 2 copies of every gene, that controls each characteristic, separate and each copy going to the gamete. The chromosomes recombine at fertilisation. The law of independent assortment- when the homologous pairs of chromosomes segregate, they do so independently of other chromosomes. When the chromosomes line up in their homologous pairs, the side each chromosome takes is completely random. Allele- different forms of the same gene. E.g. the gene is seed shape, and the allele is wrinkly or rounded Genotype- the specific combination of alleles Phenotypes- the physical characteristics of the genotype, noting the concept of dominant alleles and incomplete dominance. E.g. TT and Tt both code for a tall pea plant, but have different genotypes. Homozygous- true breeding individuals, they contain the same genotypes. E.g. TT and tt Heterozygous- having different genotypes. E.g. Tt One of the alleles in the genotype may be dominant, so its characteristic is expressed instead of the recessive allele. E.g. Tt, the T dominates over the t so the Tt genotype is expressed as TT The recessive phenotype is only expressed if the genotype contains no dominant alleles, e.g. tt Autosomal chromosomes- chromosomes which do not have any effect on gender differentiation Sex chromosomes- chromosomes which effect gender (chromosomes number 23). The possibilities for sex chromosomes are XY and XX. Monohybrid cross- genetic cross between 2 individuals which are heterozygous, possible producing homozygous offspring- the results being tt, TT and Tt. Test cross- where an individual with the dominant phenotype but unknown genotypes is crossed with a recessive individual. This takes advantage of the recessive individual supplying the recessive allele to the offspring, the offsprings phenotypes determining its genotype, hence determining the genotype of the dominant phenotype parent. Sex-linked inheritance The genotype of females is XX, the genotype of males is XY The X chromosome is much larger than the Y chromosome The X chromosome carries genes which are responsible for sexual characteristics as well as well as other non-sexual characteristics. Traits/phenotypes which are carried on a sex chromosome are sex-lined. More genes are traits are linked to the X chromosome since it is much larger than the Y chromosome. Males are more likely to show x-linked traits compared to females. This is due to males only having 1 X-chromosome, whereas females have 2 X-chromosomes. Females have the ability to mask the X-linked trait, since they could have an allele on the other X-chromosome which dominates the affected X-chromosome. On the other hand, males only have 1 X-chromosome, which means that they cannot mask the affected allele, also the Y chromosome is much smaller, so it cannot mask the x-linked trait. Examples of X-linked traits include red-green colour blindness and haemophilia. Red-green colour blindness Gene on the X chromosome controls the colour receptors in the retina of the eye. If the gene is defective, then the person cannot distinguish red from green. Around 8% of males and less than 1% of females have red-green colour blindness Haemophilia X-linked recessive disease which prevents blood from clotting. This means that even a small cut could result in extended bleeding and excessive blood loss or bruising. Today, this disease can be treated more easily, with clotting factors being able to be produced from blood donations or made in the laboratory. Carrier- someone who has an allele for the genetic disorder but does not show the disorder in their phenotypePedigrees

If the sex is unknown, then the person is represented with a triangle Offspring are listed in order of birth, the eldest being on the left.Genome- the full set of genes and alleles found in a speciesGene TechnologyRestriction enzymes- proteins which can cut DNA at specific base sequences. They restrict the growth of other organisms by destroying their DNA. Their natural role is to protect bacteria from foreign DNA which they cut up and destroy.DNA ligases- they attach or link pieces of DNA together. However, they are less specific compared to restriction enzymes.Sanger sequencing- artificially replicating DNA with bases that have radioactive or fluorescent tags attached onto a computer. The DNA with the tag is analysed by a computer, and reads the tags, records them and analyses them. Allows for the fast identification of basesGenetic engineering- the manipulation of a genome of an organism, usually through altering the base sequence of specific genes or by transferring genes from one organism to another. First the genetic sequence is determinedThen it is cut out with the use of restriction enzymesThen it is inserted into the new organism with DNA ligases. Note: the new organism does not have to be the same species as the donor organism.Organisms with the new, inserted genes are known as transgenic organisms.

To copy a genetic sequence, the sequence is transplanted into bacteria, the bacteria multiple rapidly, and the sequences are cut out again with the same restriction enzymes. This is how the cloning of base sequences works.Gene therapy- the process of cutting out faulty genes and inserting in normal genes. It has been successful in the treatment of cystic fibrosis.Recombinant DNA- DNA with the new gene, often found in the surrogate bacteria.

Applications of gene technologies:Environmental applicationsDNA profiling is used to solve criminal cases.DNA profiling used to identify the father of a childDevelopment of bacteria containing genes to break down oil deposits and mining wastes. These help to ease the effects of an oil spill and waste products from mining.Agricultural applicationsCrops have been engineered to be resistant against pesticides and/or diseases, so that when pesticides are sprayed, the crops are undamagedIncreasing the nutrient value of cheap crops (e.g. rice and wheat) can reduce starvations and malnutrition in poor areas.Genetic screening and testingTesting for a variety of conditions regardless of a previous family history of genetic disease.Helps with the diagnosis of genetic diseases and hence interventionAmniotic fluid testing- the fluid in the amniotic sac is withdrawn using a needle, and this is tested to indicate if there are any potential problems with the babyStem cells- undifferentiated cells which can differentiate into many different types of specialised cell types. E.g. muscle, nerve and blood cells.There are 2 types of stem cellsEmbryonic stem cells- can become most cells typesAdult stem cells- can only become certain types of cellsAdult stem cells are used more commonly and there are no ethical concerns raised about the use of themEmbryonic ethical concernsEmbryos can be produced by fertilising ova in labs.The use of embryonic cells is considered unethical by some due to the collection of stem cells means that the embryo is destroyed.Some parents may want to choose to have certain embryos compared to others. E.g. some may want a male or female child, or one with a certain physical characteristic.When an embryo is considered a personCloningA clone is an exact copy of something elseIt is possible to clone an entire organism by nuclear transfer. Dolly the sheep was the first cloned mammalGenetically modified organismsGM crops pose a threat to bio-diversity, they replace a number of natural varieties of plants with one variety (the GM plant). GM plants with a resistance to a certain pest can cause a resistance in the pest, one which cannot be controlled with current GM, so this is a major issue. Chromosomes are made of strands of DNA, DNA has genes encoded onto themGamete- sex cell

ChemistryAcids in the stomach- NaCl, HCl, KClAcidic Oceans- Respiration Aerobic Respiration:glucose + oxygen carbon dioxide + water + energy (stored in an ATP molecule)C6H12O6 + 6O2 6CO2 + 6H2O + ATP Anaerobic Respiration for animalsglucose lactic acid + energyC6H12O6 2C3H6O3 + energy Anaerobic Respiration for plantsglucose ethanol + carbon dioxide + energyC6H12O6 2C2H5OH + 2CO2 + energy Iron and SteelReaction 1Carbon + Oxygen Carbon DioxideC(s) + O2(g) CO2(g) Exothermic- produces heatThis reaction is used to produce heat to break down the iron ore. Reaction 2calcium carbonate calcium oxide + carbon dioxideCaCO3(s) CaO(s) + CO2(g)This is a decomposition reaction. The calcium oxide produced in this process helps to remove some of the other materials contained in the iron ore by reacting with them.The carbon dioxide reacts with some of the coke to produce carbon monoxide (CO).Reaction 3carbon + carbon dioxide carbon monoxide C(s) + CO2(g) 2CO(g)The carbon monoxide then reacts with the iron ore and takes the oxygen.Reaction 4carbon monoxide + iron oxide carbon dioxide + iron 3CO(g) + Fe2O3(s) 3CO2(g) + 2Fe(s) Purifies the Iron(II) oxide into pure iron. AcidBase

Corrosive, can cause severe burnsCaustic, feels slippery

Taste sourTastes bitter

sulfuric acid(H2SO4)- used extensively in industry and to make other acids. It is used in car batteries and to clean oxide layers off metals before they are plated with other metals. react with fats and oils to produce soaps.

Nitric acid(HNO3)- manufacture fertilisers, plastics, dyes and explosives. Some bases, such as ammonia solution, are used in cleaning agents.

Hydrochloric acid(HCl)- clean metals, bricks and tiles.Sodium hydroxide (NaOH) is used in the manufacture of soap and paper. It is also used in drain cleaner and oven cleaner.

Phosphoric acid(H3PO4)- ingredient in cola drink, used in industry to produce fertilisers, small amounts are used in drinks to give a distinctive tangy taste. Also preserves the drink since it kills microorganismsCalcium hydroxide(Ca(OH)2) is used to make plaster and mortar.

Indicator substance that changes colour in the presence of an acid or base e.g. Flavin, litmus paper, universal indicator.Types of ReactionsNeutralisation: Acid + base salt + waterAcid + metal salt + hydrogen gasAcid + carbonate salt + water + carbon dioxideCombustionfuel + oxygen combustion products + heathydrocarbon + excess oxygen carbon dioxide + waterhydrocarbon + limited oxygen carbon monoxide + wateriron + water + oxygen iron (III) oxide [rusting/corrosion]CorrosionMetal + Oxygen -> metal oxide (basic oxides)Corrosion: e.g. rust. 4Fe(s) + 6H2O(l) + 3O2(g) 4Fe(OH)3(s)Aluminium oxide forms a skin over the top of the metal. Extra oxygen/moisture cannot get through to the aluminium underneath. Decomposition: AB + energy -> A + Be.g. water ---electricity---> Hydrogen + oxygenDisplacement and Precipitation

Motion Types of GraphsPosition-Time graphGradient= velocityVelocity-Time graphGradient= accelerationArea under graph= displacementAcceleration-Time graphArea under curve= velocity

Scalar Quantity- Containing only the magnitude Vector quantity- contains both magnitude and direction Distance- how far an object has travelled Displacement- the relationship between the final position and the initial position(contains a magnitude and a direction) Speed- how fast an object is moving Velocity- the rate of change of displacement over time OR speed in a particular direction Acceleration- the rate of change of velocity over time Average Speed- the total distance over the total time Instantaneous speed- the speed of an object at that moment in time