3.1.1 Advantages and disadvantages of reproduction

Asexual reproduction

1. Asexual reproduction produces new individuals from a single parent.
2. No sex cells are made and no two cells fuse together, so no genetic material arrives from a second organism.
3. The new individuals are produced by mitosis, the cell division that copies every chromosome exactly before the cell divides.
4. Each new cell therefore receives a complete copy of the parent's DNA.
5. The offspring are genetically identical to the parent and to one another.
6. Any differences between them come from the conditions they grow in rather than from their genes.

Clones and natural examples

1. Offspring that carry exactly the same genetic material as the parent that produced them are clones.
2. Bacteria divide by binary fission, in which one cell copies its DNA and then splits into two identical daughter cells.
   1. A single bacterium can produce a colony of millions of clones within a day when food and warmth are available.
3. A strawberry plant grows horizontal stems called runners, and a new plant with the same genes forms wherever a runner touches the soil.
4. A potato plant swells the ends of underground stems into tubers, and each tuber can sprout into a new plant identical to the one that made it.
5. A spider plant produces small plants on long arching stems, and each plantlet roots into a separate identical plant.
6. Aphids reproduce asexually through the summer, so a single female can fill a plant with identical young without ever mating.

Asexual reproduction: advantages and disadvantages

1. No mate is needed, so no time or energy is spent searching for one or competing for one.
   1. An organism that is isolated, or that lives in a population spread thinly over a large area, can still reproduce.
2. The reproductive cycle is rapid, so numbers build up very quickly whenever conditions are favourable.
3. Only one parent is needed, so a single organism arriving in a new habitat can populate that habitat on its own.
4. A set of genes that already suits the habitat is passed on unchanged, so the offspring are as well suited to those conditions as the parent is.
5. Less energy goes into making sex cells, into courtship displays and into caring for young, leaving more energy for growth.
6. The central disadvantage is that there is no genetic variation in the population.
7. Because every individual carries the same genes, a new disease affects every one of them in the same way, and the whole population can be wiped out.
   1. A change in conditions, such as a drop in temperature or the loss of one food source, affects every individual equally for the same reason.
8. The population cannot adapt by natural selection, because there is no variation for selection to act on.
9. Offspring grow close to the parent, so they compete with the parent and with each other for the same light, water, mineral ions or food.

Sexual reproduction

1. Sexual reproduction produces offspring from two parents rather than one.
2. Each parent passes on half of the genetic material that the offspring will carry.
3. The two parents carry different alleles, which are different versions of the same gene, so the offspring inherit a combination that neither parent had.
4. The offspring are therefore genetically different from both parents and from each other.
5. Brothers and sisters resemble their parents without matching them, and only identical twins share exactly the same genes.

Gametes and meiosis

1. The sex cells that fuse in sexual reproduction are gametes.
2. In animals the male gamete is the sperm cell and the female gamete is the egg cell.
3. In flowering plants the male gamete is carried inside a pollen grain and the female gamete is the egg cell held in the ovule.
4. Gametes are made by meiosis, the cell division that halves the chromosome number.
5. A human body cell contains $2n=46$ chromosomes, while a human gamete contains $n=23$.
6. Every gamete a parent makes carries a different selection of that parent's alleles, which is the first source of the variation seen in the offspring.

Fertilisation and the zygote

1. Fertilisation is the fusion of the nucleus of a male gamete with the nucleus of a female gamete.
2. The single cell formed by that fusion is a zygote.
3. Each gamete supplied half a set of chromosomes, so the zygote carries the full number again, $2n=46$ in humans.
4. The zygote then divides by mitosis to form an embryo, so every body cell of the new individual carries the same mixture of alleles.
5. Half of those alleles came from one parent and half from the other, which is why the offspring resembles both parents without matching either of them.

Sexual reproduction: advantages and disadvantages

1. Sexual reproduction produces genetic variation, because the offspring receive a mixture of alleles from two parents.
2. When conditions change or a new disease appears, that variation makes it likely that some individuals already carry alleles allowing them to survive.
3. Those survivors live long enough to reproduce and pass the helpful alleles on to their own offspring.
4. The proportion of individuals carrying those alleles rises with each generation, so the species adapts by natural selection.
5. The same variation is what makes selective breeding of crops and farm animals possible.
6. The first cost is that a mate must be found, which takes time and energy and can expose an organism to predators while it searches or displays.
   1. An organism isolated from others of its species cannot reproduce at all.
7. The reproductive cycle is slower, so fewer offspring are produced in the same length of time.
8. Energy is spent building gametes, on courtship, and in many animals on feeding and protecting the young after birth.

Comparing sexual and asexual reproduction

1. Asexual reproduction needs one parent, while sexual reproduction needs two.
2. Asexual reproduction involves no gametes and no fertilisation, while sexual reproduction depends on both.
3. Offspring produced asexually are made by mitosis and are genetically identical, while offspring produced sexually begin as a zygote and are genetically different.
4. Asexual reproduction is faster and yields more offspring in a given time, while sexual reproduction is slower and yields fewer.
5. Asexual reproduction gives no variation, so the population cannot adapt, while sexual reproduction gives variation, so natural selection has something to act on.
6. Many organisms use both methods and switch between them as their conditions change.
7. While conditions are favourable they reproduce asexually, so numbers rise quickly and the habitat is exploited.
8. When conditions turn harsh they reproduce sexually, so the varied offspring include some that may survive the new conditions.
9. The malarial parasite reproduces asexually inside the human host, where conditions are constant, and sexually inside the mosquito.
10. A strawberry plant sends out runners through the summer and also produces flowers, whose fertilised ovules become genetically varied seeds.
11. Aphids follow the same pattern, reproducing asexually in summer and sexually in autumn.

3.1.2 Role of meiotic cell division

Chromosomes in body cells

1. A chromosome is a long molecule of DNA in the nucleus that carries the genes controlling a cell's characteristics.
2. The nucleus of a human body cell contains $46$ chromosomes.
3. These chromosomes are arranged in $23$ pairs, and the two chromosomes of a pair carry the same genes in the same order.
4. One chromosome of each pair was inherited from the mother in the egg cell, and the other was inherited from the father in the sperm cell.
5. A cell that contains two copies of every chromosome is described as diploid.
6. The diploid number of a human body cell is written $2n=46$, where $n$ stands for one complete set of chromosomes.
7. Every body cell is diploid, including skin cells, muscle cells and nerve cells.

Haploid gametes

1. Gametes are the sex cells that fuse together in sexual reproduction.
2. In humans the gametes are the sperm cell and the egg cell.
3. In flowering plants the gametes are the nucleus inside a pollen grain and the egg cell inside an ovule.
4. A gamete contains one chromosome from each pair rather than both, so it carries a single set of chromosomes.
5. A cell that carries a single set of chromosomes is described as haploid.
6. A human gamete therefore contains $23$ chromosomes, one from each of the $23$ pairs, written $n=23$.

How meiosis works

1. Meiosis is the type of cell division that produces gametes.
2. In humans, meiosis takes place in the testes, where it makes sperm cells, and in the ovaries, where it makes egg cells.
3. In flowering plants, meiosis takes place in the anthers, which make pollen, and in the ovules, which make egg cells.
4. Meiosis starts with a single diploid parent cell in which every chromosome has been copied.
5. The cell then divides twice, so one parent cell gives rise to four daughter cells.
6. Each daughter cell receives half the number of chromosomes of the parent cell, so each one is haploid.
7. One human cell with $46$ chromosomes therefore produces four cells with $23$ chromosomes each.
8. Each daughter cell is genetically different from the other three and from the parent cell it came from.
9. The role of meiosis is therefore to produce genetically different haploid gametes from one diploid cell.

Fertilisation restores chromosome number

1. Fertilisation is the fusion of the nucleus of a male gamete with the nucleus of a female gamete.
2. Each gamete brings a single set of chromosomes, so the new cell receives $23$ chromosomes from the mother and $23$ from the father.
3. The new cell therefore contains $23+23=46$ chromosomes and is diploid, $2n=46$.
4. The halving in meiosis and the doubling at fertilisation cancel each other out, so the chromosome number of the species stays the same from one generation to the next.
5. If gametes were diploid instead, two gametes of $46$ chromosomes would fuse to give a cell with $92$ chromosomes.
6. That generation would then make gametes of $92$ chromosomes and offspring of $184$, so the number would double at every fertilisation.
7. Halving the chromosome number in meiosis is what prevents this doubling and keeps the chromosome number of the species constant.

Zygote growth by mitosis

1. The diploid cell formed at fertilisation is called a zygote.
2. The zygote divides repeatedly by mitosis to form a ball of cells that develops into an embryo.
3. Every chromosome is copied before each of these divisions, so each new cell receives a full set of $46$ chromosomes.
4. All of the body cells built in this way are diploid and genetically identical to the zygote they came from.
5. The chromosome number of an organism can therefore be tracked through the whole cycle: diploid body cell, haploid gamete, diploid zygote, diploid body cell.

Comparing mitosis and meiosis

1. Both divisions begin after the chromosomes have been copied, but they differ in the number of divisions, daughter cells, chromosome sets, genetic similarity and biological role.
2. Number of divisions: mitosis divides the parent cell once, while meiosis divides it twice.
3. Number of daughter cells: mitosis produces two daughter cells, while meiosis produces four.
4. Chromosome number: the daughter cells of mitosis are diploid with $46$ chromosomes, while the daughter cells of meiosis are haploid with $23$.
5. Genetic make-up: the daughter cells of mitosis are genetically identical to the parent cell and to each other, while the daughter cells of meiosis are genetically different.
6. Use in the organism: mitosis is used for growth, for the repair of damaged tissue and for asexual reproduction.
7. Meiosis is used only to make gametes for sexual reproduction, and it takes place only in the reproductive organs.

How meiosis creates variation

1. The four gametes made by one meiosis are all genetically different from one another.
2. Each gamete receives one chromosome from each pair, and which chromosome of a pair it receives varies from gamete to gamete.
3. Every gamete therefore ends up with a different combination of the chromosomes the parent inherited from its own mother and father.
4. Because a human cell has $23$ pairs to choose from, the number of different combinations a single person can produce is very large.
5. Fertilisation is also random, because any sperm cell can fertilise any egg cell.
6. Any one of a huge number of genetically different sperm cells can fuse with any one of a huge number of genetically different egg cells, so the number of possible zygotes is enormous.
7. This is why offspring produced by sexual reproduction differ from each other and from both of their parents, while offspring produced by mitosis alone do not.

3.2.1 DNA structure as a polymer

Where DNA is found

1. DNA is the molecule that carries the genetic instructions an organism needs to build and run itself.
2. In an animal or plant cell, DNA is found inside the nucleus.
3. Within the nucleus the DNA is coiled up tightly and packaged into structures called chromosomes.
4. Each chromosome contains one very long DNA molecule, and that coiling is what allows a molecule of such length to fit inside a nucleus.
5. A DNA molecule is far too large to be a single simple unit, so its structure is best understood as one small unit repeated over and over.

DNA as a polymer

1. A polymer is a long molecule built from many small repeating units joined together in a chain.
2. The repeating unit that DNA is built from is called a nucleotide, so DNA is a polymer of nucleotides.
3. A single nucleotide is made of three parts joined together.
4. One part is a sugar, which sits at the centre of the nucleotide.
5. A phosphate group is joined to that sugar.
6. A base is also attached to the same sugar.
7. There are four different bases in DNA: adenine ($A$), thymine ($T$), cytosine ($C$) and guanine ($G$).
8. Every nucleotide in DNA contains the same sugar and the same phosphate group.
9. The only difference between one nucleotide and another is therefore which of the four bases is attached to its sugar.

The sugar-phosphate backbone

1. Nucleotides join end to end to build a long strand of DNA.
2. The phosphate group of one nucleotide joins to the sugar of the next nucleotide.
3. Repeating that join thousands of times produces a chain in which sugars and phosphates alternate along the whole length of the strand.
4. This alternating chain of sugars and phosphates is the sugar-phosphate backbone of the strand.
5. The bases are not part of the backbone, because each base stays attached to its own sugar and points inwards, away from the backbone.
6. A complete DNA molecule is made of two such strands lying alongside each other, with the bases of one strand facing the bases of the other.

Complementary base pairing

1. The two strands of a DNA molecule are held together by their bases, which pair up across the middle of the molecule.
2. The pairing is fixed rather than random, because $A$ always pairs with $T$, and $C$ always pairs with $G$.
3. Each of these joined pairs is called a base pair.
4. Because the base on one strand fixes which base must sit opposite it, the two strands are described as complementary.
5. This means that the sequence of bases along one strand determines the sequence of bases along the other strand.
6. It also means that a DNA molecule contains equal amounts of adenine and thymine, since every $A$ is matched by a $T$ opposite it.
7. For the same reason, a DNA molecule contains equal amounts of cytosine and guanine.
8. The four bases account for every base in the molecule, so their four percentages add up to $100\%$.

Hydrogen bonds between bases

1. Each base pair is held together by weak hydrogen bonds between the two bases.
2. A single hydrogen bond is easily broken, and that weakness is the useful part of the structure rather than a fault in it.
3. When a cell copies its DNA or reads a section of it, the hydrogen bonds along that section are broken so that the two strands can be pulled apart and the bases exposed.
4. Strong bonds would lock the strands together permanently, and the order of the bases could never be reached.
5. A DNA molecule contains millions of base pairs, and every pair adds its own hydrogen bonds to the total.
6. So many weak bonds acting together hold the two strands firmly, even though any single one of them gives way easily.

The double helix

1. The two strands of a DNA molecule do not lie flat alongside each other.
2. They are twisted around each other along their whole length, so the molecule takes the shape of a spiral.
3. Two strands coiled around each other in this way form a double helix, and that is the overall shape of a DNA molecule.
4. The two sugar-phosphate backbones run along the outside of the helix, and the base pairs sit on the inside, joined by their hydrogen bonds.

Base sequence

1. The order of the bases along a strand is the information that a cell reads.
2. A section of DNA that codes for one protein is a gene, and the complete set of DNA in an organism is its genome.
3. A single DNA molecule carries many genes, one after another along its length.

3.2.2 Genome and gene definitions

The genome

1. The genome of an organism is the entire DNA that the organism contains.
2. That total includes every chromosome, every gene carried on those chromosomes, and the DNA that lies between and around the genes.
3. The human genome is about three billion base pairs long, which is written as $3\times 10^9$ base pairs.
4. Spread through that length are roughly $20000$ genes.
5. A complete copy of the genome sits in the nucleus of almost every body cell, so a liver cell and a skin cell hold the same instructions as each other.
6. A large part of the genome does not code for a protein at all, so the genome is far more than a list of genes.
   1. This non-coding DNA still has effects on how the genes are used, and a later article deals with what it does.

Organising genetic material

1. In a body cell the DNA is held inside the nucleus.
2. Inside the nucleus the DNA is packaged into chromosomes, and a human body cell contains $46$ chromosomes arranged as $23$ pairs.
3. Each chromosome is one very long DNA molecule, coiled up tightly so that its full length fits into the nucleus.
4. A gene is one section of that molecule, picked out by where it begins and ends along the strand rather than by being a separate molecule of its own.
5. Within that section the bases lie in a particular order, and this base sequence is what carries the coded instruction.
   1. The levels therefore run in this order: nucleus, then chromosome, then the DNA molecule the chromosome is made of, then a gene as one section of that molecule, then the sequence of bases inside the gene.
6. One chromosome carries many genes, set out one after another along its length.
7. Every gene sits at a fixed position on one particular chromosome.
8. Because that position is fixed, the same gene is found in the same place on the same chromosome in every member of a species.

Genes code for proteins

1. A gene is a section of a DNA molecule that codes for a specific protein.
2. Proteins are built from amino acids, small molecules joined end to end into a long chain.
3. The phrase codes for has an exact meaning here: the order of the bases along the gene determines the order of the amino acids in the protein made from it.
4. The order in which the amino acids are joined decides how the finished chain folds, and therefore which protein it becomes.
5. A different gene has a different base sequence, so it sets a different order of amino acids and produces a different protein.
6. The protein itself is assembled outside the nucleus, and later articles set out the steps by which the coded instruction is read and used.

Functions of proteins

1. Genes matter because proteins do the work of the body, and different genes code for different proteins.
2. Amylase is an enzyme that digests starch, breaking it down into sugars small enough to be absorbed.
3. Haemoglobin is the protein inside red blood cells that binds oxygen in the lungs and carries it to the tissues.
4. Keratin is a structural protein that makes hair and nails tough and hard-wearing.
5. Antibodies are proteins made by white blood cells, and they bind to pathogens as part of the immune response.
6. Each of these four proteins is coded for by its own gene, with its own base sequence, in a fixed position on a chromosome.
7. Because the genome carries the code for every protein an organism can make, it controls how that organism is built and how its body works.

Chromosomes, genes and genomes

1. A chromosome is a whole DNA molecule, coiled up, carrying many genes along its length.
2. A gene is one section of that molecule, and it codes for one specific protein.
3. The genome is all of an organism's DNA taken together, which means every chromosome and every gene along with the DNA between them.
4. The three terms name three different scales of the same material rather than three different substances.
5. Different versions of the same gene are called alleles, and they are covered in the inheritance articles.

3.2.3 Extracting DNA from fruit

Why fruit is used

1. DNA can be extracted from any tissue whose cells contain nuclei, and soft fruit is the usual starting material because it is easy to work with at the bench.
2. Fruit tissue is soft, so it is broken up by mashing alone, without the grinding or heating that tougher tissue would need.
3. The cells of the fruit are packed closely together and each one holds a nucleus, so even a few grams of tissue contains a very large number of nuclei and therefore a large amount of DNA.
4. Strawberries and kiwi fruit work particularly well, because their cells contain several sets of chromosomes rather than the two sets found in a human body cell.
   1. Each extra set is a further copy of the same DNA, so a given mass of strawberry tissue yields more DNA than the same mass of most other tissue.
5. Fruit is also cheap, safe to handle and needs no preservation, so the whole extraction can be done in a single lesson with everyday materials.

Barriers around DNA

1. In a fruit cell the DNA is held inside the nucleus, which is enclosed by its own membrane.
2. The nucleus sits in the cytoplasm, and the cytoplasm is enclosed by the cell surface membrane.
3. Outside the cell surface membrane there is a rigid cell wall made of cellulose, which gives the plant cell its strength.
4. Four layers therefore lie between the DNA and the outside of the cell: the cell wall, the cell surface membrane, the cytoplasm and the membrane around the nucleus.
5. Every step of the extraction method exists either to remove one of these layers or to separate the released DNA from everything else that comes out of the cell with it.
6. The cell wall is broken by physical force, the two membranes are broken down chemically, and the DNA is then separated from the liquid it has dissolved in.

Releasing DNA from cells

1. Mashing or grinding the fruit breaks the cell walls by physical force, so the cell contents are released into the mixture.
   1. No reagent in the method breaks down cellulose, so the cell walls can only be broken mechanically and this step cannot be left out.
2. Washing-up liquid is added because it is a detergent, and detergents break down lipids.
3. The cell surface membrane and the membrane around the nucleus are both made largely of lipids, so the detergent breaks these membranes apart and the DNA passes out of the nucleus and out of the cell into the mixture.
4. Salt is added because a DNA molecule carries a negative charge along its whole length, since every nucleotide in it contains a phosphate group.
5. Two negatively charged DNA molecules repel each other, so on their own they stay spread out and dissolved in the liquid.
6. The positively charged sodium ions from the salt are attracted to the negative charges on the DNA and screen them, so the DNA molecules stop repelling one another.
   1. The DNA molecules can then clump together, which makes them come out of solution far more readily once the ethanol is added.

Separating the DNA

1. After mashing, the mixture contains the released DNA together with broken cell walls, lumps of tissue that were not broken up and the rest of the cell contents.
2. Filtering the mixture holds back the insoluble cell walls and lumps of tissue on the filter paper, so only a liquid containing the dissolved DNA passes through into the tube.
3. Ice-cold ethanol is then layered on top of this filtrate.
4. DNA is insoluble in cold ethanol, so as the DNA meets the ethanol it comes out of solution and appears as solid white threads.
5. Ethanol is less dense than the fruit extract, so pouring it slowly down the side of a tilted tube keeps it as a separate layer, and the threads form at the boundary where the two liquids meet.
6. The colder the ethanol, the less DNA stays dissolved, so more DNA comes out of solution and a larger, clearer mass of threads is seen.

Identifying the DNA

1. The extracted DNA is seen as white stringy threads at the boundary between the ethanol layer and the fruit extract, often with small bubbles trapped in them.
2. The threads are firm enough to be wound onto a glass rod and lifted out of the tube.
3. A single DNA molecule is far too thin to be seen, and cannot be resolved even with a light microscope.
4. What is visible is very many DNA molecules, released from the nuclei of thousands of cells and clumped together, so the threads are a mass of DNA rather than one molecule.
5. The threads contain the whole genome of the fruit cells, because every chromosome is released and precipitated together.
6. Nothing about the appearance of the threads reveals which genes the DNA carries, so the extraction shows only that DNA is present and can be handled.

3.2.4 Base order determines protein shape

Amino acid order and protein shape

1. The order of bases in a gene sets the order of amino acids in the protein.
2. The chain of amino acids folds up into a particular three-dimensional shape.
3. This shape decides what the protein can do, so its shape determines its function.
4. For example, an enzyme's active site has a shape that fits its substrate, and a structural protein such as collagen has a shape suited to its role.

How base changes affect proteins

1. A change in the order of bases can change one or more amino acids in the protein.
2. A different amino acid can make the protein fold into a different shape.
3. A changed shape can weaken or stop the protein's function.
4. For example, a change to an enzyme's active site can mean the substrate no longer fits.
5. If the protein is changed, the characteristic it controls can also change.

3.2.5 Stages of protein synthesis

Genes as protein codes

1. The order of bases in a gene is a coded instruction for making a protein.
2. Each group of three bases, called a triplet or codon, codes for one amino acid.
3. The order of the triplets sets the order in which amino acids are joined.
4. This set of rules linking bases to amino acids is the genetic code.

Transcription

1. Protein synthesis begins in the nucleus. RNA polymerase binds to a non-coding region immediately in front of the gene, positioning the enzyme at the correct starting point.
2. The enzyme RNA polymerase separates the two DNA strands over the gene and builds a complementary copy.
3. This copy is a molecule of mRNA (messenger RNA).
4. The mRNA is a short, single strand that can leave the nucleus.
5. It carries the coded instructions out into the cytoplasm.

Translation

1. In the cytoplasm the mRNA attaches to a ribosome.
2. The ribosome reads the mRNA code three bases at a time.
3. Transfer RNA (tRNA) molecules carry specific amino acids to the ribosome. Each tRNA matches a particular mRNA codon, placing the amino acids in the order set by the base sequence.
4. The ribosome links the amino acids with peptide bonds to form a polypeptide, which then folds into a protein with a specific three-dimensional shape.
5. Whether a protein is made, and how much, can also be affected by the non-coding DNA around a gene.

How DNA controls cells

1. Each gene in the DNA carries the code for one protein.
2. Proteins do most of the work in a cell, including enzymes, structural proteins and hormones.
3. By deciding which proteins are made, the DNA controls what the cell does.
4. So a cell's activities are set by the genes that are used to make proteins.

3.2.6 Non-coding DNA variants affecting phenotype

Coding and non-coding DNA

1. Coding DNA is DNA that is used to make a protein.
2. Non-coding DNA is DNA that does not code for a protein.
3. Some non-coding DNA sits near genes and helps to control them.
4. So a stretch of non-coding DNA can still be important, even though it is not made into a protein.

How non-coding variants affect genes

1. Gene expression means whether a gene is used and how much protein is made from it.
2. Some non-coding DNA controls the expression of nearby genes.
3. A variant in this non-coding DNA can turn a gene on or off, or change how much protein is made.
4. This can change the phenotype, the organism's features.
5. It does this without changing the amino acid sequence of the protein itself.

3.2.7 Coding DNA variants affecting phenotype

Alleles and base sequences

1. A variant is a difference in the base sequence of a gene.
2. Different alleles of a gene are simply different variants of that gene.
3. Variants arise through mutations, which are changes to the DNA.
4. This is a source of the genetic variation found within a species.

How coding variants affect phenotype

1. A variant in the coding DNA can change the protein made, and so change the characteristic.
2. A variant in the non-coding DNA can change how much protein is made, and so change the characteristic.
3. Most variants have no effect on the phenotype.
4. Some variants have a small effect on the phenotype.
5. Very few variants, on their own, determine the phenotype.
6. Together, all these variants produce the range of phenotypes seen in a population.