DNA

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DNA Door Mind Map: DNA

1. Structure

1.1. Nucleotide polymer; double helix; hydrogen bonding; complementary base pairing (A-T; C-G). Differs from RNA in that the sugar in RNA is ribose, thymine is replace with uracil in RNA and that RNA is single stranded.

1.1.1. The two strand of DNA are anti-parallel. DNA is directional: one end, the 5' end, has a protruding phosphate group, while the other end, the 3' end, has a hydroxyl group.

1.1.1.1. In prokaryotes, each cell has a single, large circular chromosome, as well as smaller circular pieces of DNA called plasmids.

1.1.1.2. In eukaryotes, each cell has numerous large pieces of DNA called chromosomes. Organelles such as mitochondria and chloroplasts also contain DNA

1.1.1.2.1. Eukaryotic chromosomes can exist as chromosomes (condensed) or chromatin (dissfused).

2. Function

2.1. Encode genetic information

2.1.1. Gene

2.1.1.1. Structure

2.1.1.1.1. Eukaryotic genes

2.1.1.1.2. Prokaryotic genes

2.1.1.2. Expression

2.1.1.2.1. Central Dogma

3. Analysis

3.1. Restriction enzyme digestion

3.1.1. Restriction enzymes are enzymes (mainly from prokaryotes) that cleave DNA in a sequence-specific manner. Each restriction enzyme recognises a specific DNA sequence, known as its restriction sequence or target sequence. The digested DNA has 'sticky' or 'blunt' ends.

3.1.1.1. Enzymes called DNA ligases join DNA fragments together.

3.2. Electrophoresis

3.2.1. A method of separating DNA in an electric field. DNA is pushed through an agarose matrix by the electric field. DNA is separated according to size - small DNA fragments migrate further on a gel, compared to larger fragments. DNA is visualised by adding a fluorescent dye to the gel and then observing the gel under UV illumination.

3.3. Restriction fragment Length Polymorphism (RFLP)

3.3.1. A method of characterising differences in DNA using restriction enzymes. DNA from different sources are digested and then separated by electrophoresis. The similarity of the DNA profiles (number and sizes of fragments) indicates the degree of similarity or difference between the DNAs.

4. Replication

4.1. Cell cycle. The lifecycle of a cell is composed of four distinct stages, which constitute a cycle. The cell cycle contains several checkpoint, which prevent a cell from progressing to the next stage of the cycle unless the cell is compliant with all conditions. A cell's passage through the cell cycle is regulated by the cyclin-CdK system. CdK is present in a cell's cytoplasm all the time, but cyclins are synthesised at the checkpoint, to drive the cell into the next phase of the cycle. Once the cell enters the next phase, the cyclins are destroyed. Cyclins are synthesised in response to growth factor signalling. If cells are able to bypass the checkpoints in an unregulated manner, then the cell becomes cancerous.

4.1.1. Cancer. A condition caused by the uncontrolled proliferation of cells. This occurs because of the breakdown of controls in the cell cycle.The direct causes of cancer are genetic mutations, although lifestyle and environmental factors alter the risk of developing cancer.

4.1.1.1. Regulation: genetic causes.

4.1.1.1.1. Signal to divide: Growth factors bind to cell surface receptors (usually tyrosine kinase receptors). This activates a signal transduction pathway that causes cells in G1 to enter the S phase. Mutations in certain genes, called proto-oncogenes, convert them into oncogenes. The proteins synthesised by oncogenes maintain the signal trasnduction pathway in an activated state, even though grwoth factors are not bound to the cell surface receptors. One example of an oncogene is Ras.

4.1.1.1.2. Signal to stop dividing. Controls at the checkpoints ensure that the cells do not progress to the next stage of the cycle unless conditions and signals are appropriate. One group of such regulators are the tumour suppressors (e.g. p53). Mutations in the tumour suppressors can cause uncontrolled passage through the cell cycle.

4.1.2. Stages

4.1.2.1. M

4.1.2.1.1. Mitosis: DNA that was replicated in S phase is separated in mitosis. Mitosis occurs in somatic cells. Two daughter cells are produced from a parental cell and the daughter cells have identical genetic makeup to that of the parental cell.

4.1.2.1.2. Meiosis. Occurs in testes and ovaries durinng the formation of gametes. Results in the formation of 4 daughter cells from one parental cell. the genetic complement of the daughter cells is different to that of the parental cells. Genetic diversity occurs becuase of (i) crossing over of non-sister chromatids of homologous chromosomes - prophase I, (ii) random assortment of homologous chromosomes during metaphase I and (iii) random fertilisation of gametes during fertilisation. Sexual reproduction brings new combination of alleles together, which may bring about new properties in populations. It is thought that the evolution of immunological defense against rapidly evolving pathogen is one of the main advantages conferred by sexual reproduction.

4.1.2.2. G2

4.1.2.2.1. Cell recovers from S-phase. Cell contains twice the amount of DNA as it did in the G1 phase. At the G2/M checkpoint, the cell prepares for mitosis by synthesising proteins for that stage (spindle sibres, etc).

4.1.2.3. S

4.1.2.3.1. DNA replication: DNA is unwound by enzymes (DNA gyrase or DNA topoisomerase). DNA helicases open up the double helix at special sites called 'origins of replication' (which are kept apart by single stranded binding proteins (SSSB)). Primase synthesises a short RNA fragment (primer). DNA polymerase extends the primer towards the 3' end (this is the replication of the leading strand). For the other stand, primase synthesises a short primer slightly away from the origin of replication, which DNA polymerase extend towards the origin of replication. This strand is the lagging strand. The lagging strand is replicated as several short strand (called Okazaki fragments). Then, another form of DNA ploymerase replaces all RNA primers with DNA. the enzyme DNA ligase joins the backbones of the newly synthesised strands. Replicated DNAs remain attached together and each replicated molecule is referred to as a sister chromatid. This type of replication is known as semi-conservative replication.

4.1.2.4. G1

4.1.2.4.1. Growth phase of the cell. At the G1/S checkpoint, the cell prepares for the S-phase by synthesisng the porteins required for DNA replication.

5. Genomics

5.1. Only 1.5% of human genome encodes for proteins. The remaining components are considered to be 'junk' DNA

5.1.1. The sizes of genomes is unrelated to complexity.

6. Discovery

6.1. Miescher discovered nucleic acids in nuclei.

6.2. Geneticists confirm that chromosomes are involved in sex-determination and heredity. Chromosome are the 'heritable factors' described by Mendel. But chromosomes are composed of DNA and proteins. Proteins are more diverse, leading to the suspicion that proteins were the molecules of heredity.

6.3. Fred Griffiths discovers the transformation principle, which is able to transform non-pathogenic Streptococcus bacteria (R form) into pathogenic ones (S form). The transformation can be transmitted to subsequent generations, indicating that it is heritable. Avery and co-workers prove that the transforming principle is DNA, not RNA or proteins.

6.3.1. Thus DNA carries the genetic information that specifies biological traits (e.g. pathogenic, non-pathogenic, etc).

6.4. Using radioactive phosphorus (found in DNA, but not proteins) and radioactive sulphur (found in proteins, but not DNA), Hershey and Chase confirm, using bacteriophages, that DNA is the molecule of heredity. Only when the 'parent virus'' DNA was labelled did the progeny viruses also contain radioactive DNA.

6.4.1. This confirms that only DNA can be passed from parents (i.e. parental viruses in this example) to offspring (virions in this example). Thus it is the molecule of heredity.

6.5. Waston, Crick, Franklin, Wilkins discover the structure of DNA using X-ray crystallography.

7. Evolutionary genomics

7.1. Large scale changes in genomes are often the result of errors during meiosis. This results in cells having extra DNA, which is the raw material on which evolution works.

7.1.1. Gene duplication provide extra copies of genes, which can acquire new mutations and diversify. The mutated forms of 'original' genes are referred to as alleles. Sometimes alleles confer new functions (e.g. a slightly different trait). New genes are also created by shuffling domain-encoding exons.

7.1.1.1. Groups of sequences within a genome are referred to as markers and can be used to identify individuals. This allows us to trance the movement of DNA during evolution. Mitochondrial DNA enables us to trance our matrilineal ancestry, which Y-chromosome markers allows us to trance our partilineal ancestry (only in males). Such studies strongly support that modern humans arose in Africa and emigrated to other parts of the world. Prior to that, the lineage leading to the Neanderthals had left Africa for Europe and Asia. Although modern humans and the Neanderthals remained largely separate, molecular evidence suggests tjhat a small degree of intermingling did occur between these hominids. Molecular data has also provided information on the migration of large groups of peoples around the world in our history.

8. Science

8.1. Science is an exploration of the natural world. It produces a body of knowledge that describes and explains the universe at large.

8.1.1. Two key aspects of scientific investigations are the development of hypotheses and theories. BOTH describe aspects of science - they are equally valide, but differ in scope.

8.1.1.1. Scientific hypotheses are testable and falsifiable. Controlled experiments are used to the validity of hypotheses

8.1.1.1.1. Scientific approaches often use either inductive or deductive reasoning.

9. Evolution

9.1. The underlying principles of evolution were developed by many scientists over a long period of time, but were 'formalised' by Darwin and Wallace. Darwin called his ideas 'descent with modification'.

9.1.1. The basic ideas of evolution are (1) biological variation of traits exist in populations and are inherited; (2) changes in the environment or competition may favour individuals with specific traits over others; (3) individual possessing favourable traits are better adapted to survive and produce more offspring than others, thus producing a change in the structure of populations.

9.1.1.1. There is overwhelming evidence for evolution as a biological process: fossils, biogeography, molecular evidence, etc.

10. Mutations

10.1. Mutations. Mutations are changes to the genetic script that an individual inherits. Mutation may occur between generations through meiosis. Errors during DNA replication is another source of mutations. They may be caused by chemicals in the environment (carcinogens) or by ionising radiations.

10.1.1. Types of mutations

10.1.1.1. Chromosomal mutations. Insertions, deletions, inversion, deletions, translocations

10.1.1.2. Point mutations. Silent, Missense, Nonsense, Frameshift (substitutions,insertions and deletions)

10.1.2. Effects of mutations

10.1.2.1. Gain-of-function mutations: confers new biological functions

10.1.2.2. Loss-of-function mutations: Loss of biological function.

10.1.3. Repair

10.1.3.1. Cells contain numerous mechanisms to repair damaged DNA, including excision repair

11. Reproduction & Development

11.1. Fertilisation: union of two dissimilar nuclei. Binding of sperm onto eggs induces acrosome reaction, which leads to the fusion of sperm and egg cell membranes. It also stimulates the cortical reaction in eggs, which prevents other sperms from fertilising the egg. This is the first stage of development in multicellular organisms. The product of fertilisation is a zygote.

11.1.1. Cleavage: rapid mitotic division of zygote to produce an embryo with a large numer of cells. Cells in the interior die by apoptosis, resulting in a fluid filled interior. this is the blastula stage.

11.1.1.1. Cellular migration. Also known as gastrulation. Results in the formation of tissue layers (endoderm, mesoderm and ectoderm).

11.1.1.1.1. Laying down of the body axes (anterio-posterior/dorso-ventral). Body plan/patterning/positioning. Cellular migration into the interior of the embryo is guided by cytoplasmic protein gradients, called morphogen gradients. A cell knows where it is located within the embryo by determining the concentration of different morphogens it is exposed to. Depending on its locations within the embryo, cells will turn on the expression of homeobox genes (Hox genes) that are specific to the embryonic regions they are located in.