Cellular Control

A gene is a length of DNA that codes for one or more polypeptides.

The genetic code - the sequence of nucleotide bases on a gene providing a code of instructions for the construction of a protein. It is a triplet code, a degenerate code (all amino acids except methionine have more than one code). Some codes do not correspond to an amino acids, ending the chain. The code is not universal, eg mitochondria has a different code for methionine.

Genes are on chromosomes in the nucleus but proteins are assembled in the cytoplasm, at ribosomes. A copy has to be made which can move out of nuclear pores - Messenger RNA is a copy.

Transcription -  makes the messenger RNA molecule. Free nucleotides in the nucleoplasm are activated -  they have two extra phosphoryl groups attached.

• A gene to be transcribed unwinds and unzips. To do this the length of DNA that makes up the gene dips into the nucleolus. Hydrogen bonds between complementary bases break.
• Activated RNA nucleotides bind, with hydrogen bonds, to their exposed complementary bases break. U binds with A, G with C, and A with T on the template strand. This is catalysed by the enzyme RNA polymerase.
• The two extra phosphoryl groups are released, releasing energy for bonding adjacent nucleotides.
• The mRNA produced is complementary to the nucleotide base sequence on the template strand of the DNA and is a copy of the base sequence on the coding strand.
• The mRNA is released from the DNA and passes out of the nucleus, through a pore in the nuclear envelope, to a ribosome.

Ribosomes -assembles in the nucleolus from ribosomal RNA and protein. Made up of two subunits with a groove into which mRNA fits.

Transfrer RNA Lengths of RNA which fold into hairpin shapes and have three exposed bases at one end where a particular amino acid can bind. At the other end of the molecule are 3 unpaired nucleotide bases, known as the anticodon. Each anticodon can bind with its complementary codon.

1. A molecule of mRNA binds to a ribosome. The first exposed mRNA is AUG. Using ATP and an enzyme, tRNA with methionine and the anticodon UAC forms hydrogen bonds with the codon.

2. A second tRNA, with a different amino acid, binds to the second codon with its complementary anticodon.

3. A peptide bond forms between the two adjacent amino acids. An enzyme, present in the small ribosomal subunit, catalyses the reaction.

4. The ribosome now moves along the mRNA, reading the next codon. A third tRNA brings another amino acid, and a peptide bond forms between it and the dipeptide. The first tRNA leaves and is able to collect and bring another of its amino acids.

5. The polypeptide chain grows until a stop codon is reached. There are no corresponding tRNAs for these codons, so the chain is complete.

Some proteins must be activated by cyclic AMP by changing their 3D shape so it is a better fit to their complementary molecules.

A mutation is a change in the amount of, or arrangement of, the genetic material in the cell. Mutagens cause mutations eg tar, UV light, X-rays and gamma rays. Mutations with mitosis are somatic and are not passed on to offspring. Mutations in meiosis and gamete formation can be inherited. Classes of mutation are POINT MUTATIONS (one base pair replaces another) and INSERTION/DELETION MUTATIONS (this results in FRAME SHIFT)

Neutral effects - If a gene is affected by a change to its base sequence, it becomes another version of the gene - an allele. There may be no change if the mutation is in a non-coding region of DNA or if it is a silent mutation (although the triplet has changed, it still codes for the same amino acid, so the protein is unchanged). If the mutation does change protein structure, but the changed characteristic gives no particular advantage or disadvantage, then the effect is also neutral.

Harmful/Beneficial -  Depending on the environment, a mutation can be beneficial or harmful. Individuals in a population with a certain characteristic may be better adapted to survive in the environment. The well-adapted organisms can out-compete those in the population that do not have the advantageous characteristic. This is natural selection.

1. The regulator gene is expressed and the repressor protein is synthesised. It has two binding sites, one that binds to lactose and one that binds to the operator region.

2. The repressor protein binds to the operator region. In doing so it covers part of the promoter region, where RNA polymerase normally attaches.

3. RNA polymerase cannot bind to the promoter region so the structural genes cannor be transcribed into mRNA. As a result B-galactosidase (hydrolyses lactose into glucose and galactose) and lactose permease (transports lactose into the cell) are not produced.

1. Lactose binds to other site on the repressor protein, causing it to change shape so it cannot bind to the operator region.

2. This leaves the promoter region unblocked. RNA polymerase binds and initiates the transcription of the structural genes into mRNA.

3. Lactose permease and B-galactosidase can then be translated at a ribosome and used to bring lactose into the cell and hydrolyse it.

The glucose and galactose can then be used in respiration.

The development of body plans is genetically mediated by HOMEOBOX GENES.

• Maternal-effect genes - - determine the embryos polarity. Polarity refers to which end is head (anterior) and which end is tail (posterior)
• Segmentation genes - - specify the polarity of each segment.
• Homeotic selector genes - - specify the identity of each segment and direct the development of individual body segments. These are the master genes in the control networks of regulatory genes. There are 2 gene families:

-the complex that regulates development of thorax and abdomen segments.

-the complex that regulates development of head and thorax segments.

Homeobox genes work in similar ways in most organisms, including vertebrates, Drosophilia, plants and fungi.

The homeobox genes are arranged in clusters known as HOX CLUSTERS.

Apoptosis - programmed cell death in multicellular organisms, orderly and tidy. (Cell necrosis is untidy and damaging after trauma.)

The sequence of events:

• Enzymes break down the cell cytoskeleton.
• Cytoplasm becomes dense, with organelles tightly packed.
• Cell surface membrane changes and BLEBS form
• Chromatin condenses and the nuclear envelope breaks. DNA fragments.
• The cell breaks into vesicles that are taken up by phagocytosis. The cellular debris is disposed of so it does not damage any other cells/tissues.
• Quick process.

Controlled by cell signalling - cytokines, hormones, growth factors and nitric oxide (makes the inner mitochondrial membrane more permeable to H+. Proteins are released into the cytosol. These bind to apoptosis inhibitor proteins and allow the process to take place.

The rate of cells dying should = rate produced by mitosis. If not, not enough apoptosis leads to tumours, too much leads to cell loss and degeneration.

Prophase 1 - Chromatin condenses and supercoils. The chromosomes come together in homologous pairs to form a bivalent. Each pair has one maternal and paternal chromosome. The non-sister chromatids wrap around eachother and attach at CHAISMATA. They swap sections of chromatids in CROSSING OVER. The nucleolus disappears and the nuclear envelope disintegrates. A spindle forms made of protein microtubules.

Metaphase 1 - Bivalents line up at the equator of the spindle, attached to spindle fibres at the centromeres. Bivalents are arranged randomly (random assortment) with each member facing opposite poles. This allows the chromosomes to independently segregate when they are pulled apart in anaphase 1.

Anaphase 1 - The homologous chromosomes are pulled apart to opposite poles. The centromeres do not divide. The chiasmata separate and swapped chromatid lengths remain with their newly attached chromatids.

Telophase 1 - In animals, two new nuclear envelopes form, one around each set of chromosomes at each pole - and the cell divides by cytokinesis. Plants - cell skips this phase.

Prophase 2 - If a nuclear envelope has reformed, it is broken down again. The nucleolus disappears, chromosomes condense and spindles form.

Metaphase 2 - The chromosomes arrange themselves on the equator of the spindle, attached to spindle fibres at the centromeres. The chromatids of each chromosome are randomly assorted.

Anaphase 2 - The centromeres divide and the chromatids are pulled to opposite poles by the spindle fibres. The chromatids randomly segregate.

Teleophase 2 - Nuclear envelopes reform around the haploid daughter nuclei. In animales the two cells divide to give two daughter cells. In plants, a tetrad of four haploid cells is formed.

 In interphase, before meiosis 1, the DNA replicates.

Allele - a version of a gene (a difference in DNA base sequence).

Locus - the position of a gene on a chromosome.

How meiosis and fertilisation can lead to genetic variation:

• Crossing over in prophase 1 - produces new combinations of alleles on the chromatids.
• Reassortment of chromosomes - a consequence of the random distribution of maternal and paternal chromosomes on the spindle equator at metaphase 1, and segregation in anaphase 1. Each gamete acquires a different mixture of maternal and paternal chromosomes.
• Reassortment of chromatids - the result of the random distribution on the spindle equator, of the sister chromatids, at metaphase 2.  How they align at metaphase 2 determines how they segregate at anaphase 2.
• Fertilisation
• Mutation of DNA - can occur in interphase as it replicates. Chromosome mutations may also occur, leading to genetic variation. If it occurs in gametes the mutated gene will be present in every cell of the offspring.

Genotype - Alleles present within cells of an individual, for a particular characteristic.

Phenotype - Observable characteristics of an organism.

Dominant - Characteristic in which the allele responsible is expressed in the phenotype even those in heterozygous genotypes.

Recessive - Characteristic in which the allele responsible is only expressed in the phenotype if there is no dominant allele present.

Codominant - A characteristic when both alleles contribute to the phenotype.

Linkage - Genes for different characteristics that are present at different loci on the same chromosome are linked. At crossover, the alleles from one chromatid become linked to alleles on another chromatid, reducing the number of phenotypes resulting from a cross.

Females - **

Males - XY

Occurs when one gene masks the expression of another gene.

Antagonistic

Recessive Epistasis - the homozygous presence of a recessive allele prevents the expression of another allele at a second locus. In the F2 generation there will be a ratio of 9:3:4 between the phenotypes.

Dominant Epistasis - a dominant allele at one locus masks the expression of the alleles at a second gene locus. There will be a phenotypic ratio of 12:3:1.

Complementary

ccRR x CCrr = CcRr (purple flowers)

Interbreeding gives 9:7 ratio of purple to white flowers. This gives that both C and R need to be present for purple flowers.

A homozygous recessive condition at either locus masks the expression of a dominant allele at the other locus.

Tests the null hypothesis - that there is no significant difference between the observed and expected numbers, and any difference is due to chance.

If X2 is bigger that the critical value then the null hypothesis must be rejected as there is a significant difference between the expected and observed results and the difference cannot be due to chance.

Discontinuous - describes quantitative differences between phenotypes, which fall into clearly distinguishable catagories, there are no intermediate catagories.

• If more than one gene involved - they interact in an epistatic way.
• Different alleles at a single gene locus have large effects on the phenotype
• examples include codominance, dominance and recessive patterns of inheritance
• The characteristic they control is described as MONOGENIC.

Continuous - describes quantitative differences between phenotypes, there is a wide range of variation in the population and there are no distinct catagories.

• Traits controlled by two or more genes
• Different alleles at each gene locus have a small effect on the phenotype
• A large number of genes have a combined effect on the phenotype. These are known as polygenes and the characteristic they control is POLYGENIC. The genes are unlinked as they are on different chromosomes.

Environmental factors may limit the expression of genes, so phenotypic variation is controlled by the environment and the phenotype. Expression of polygenetic traits is influenced more by the environment than monogenetic traits.

Variation in a population is important for natural selection to occur.

The Hardy - Weinberg Principle. Assumptions:

• The population is very large (eliminating sampling error)
• The mating within the the population is random
• There is no selective advantage for any phenotype
• There is no mutation, migration or genetic drift

Environmental factors act as stabilising and evolutionary forces in natural selection. Many populations reach their carrying capacity (the maximum population size the environment can sustain) and remain stable. Factors that limit population growth include space, availability of food, light, minerals or water, predation and infection by pathogens. These offer environmental resistance. If this is great enough, the population will shrink, reducing competition so the population will grow again. As it increases, there will be intraspecific (within the population) competition for resources, so the population decreases again.

Selection pressures, such as predation, act to alter the population size. Stabilising selection occurs when a new phenotype arises and is unlikely to confer an advantage, so is not selected. If the environment changes, the selection pressure changes and directional selection may occur, which leads to an evolutionary change (a force of natural selection).

A large population of organisms may be split into sub-groups by isolating mechanisms:

• geographic (ecological) barriers, such as a river (leading to allopatric speciation)
• seasonal (temporal) barriers, such as climate change
• reproductive mechanisms (not able to mate) - (leading to sympatric speciation)

Genetic Drift - the change in allele frequency in a population, as some alleles will pass on to the next generation and some will disappear. This causes some phenotypic traits to be rarer or more common.

When the population is small, genetic drift may lead to the chance of elimination of one allele from the population. This reduces genetic variation and may reduce the ability of a population to survive in a new environment. It could contribute to the extinction of a population or species or could lead to the production of a new species. 

When the population is large, there will be not much genetic drift.

How do small populations occur in nature?

A natural distaster, eg a volcanic eruption, may cause a shrinkage in the population size.

The biological species concept - a group of similar organisms that can interbreed and produce fertile offspring and is reproductively isolated from other such organisms. This is problematic though when considering organisms that do not reproduce sexually, and when genders and castes look different in certain species.

The phylogenetic species concept - Closely related organisms have similar molecular structures for DNA, RNA and proteins. DNA analysis takes place to mark out the differences. Any group of organisms with similar base sequences to others is called a CLADE. Hence the use of analysis is a CLADISTIC approach to classification. It assumes classification corresponds to their phylogenetic decent. A clade is a taxonomic group comprising of a single ancestric organism and its descendents, and is so monophyletic. This type of classification makes no distinction between extinct and extant species. It does not use the groups kingdom, phylum or class as it regards the evolutionary tree as complex.

The Linnaean system of classification - reflects the phylogenies (evolutionary relationships) between different species of organisms. But it shows both monophyletic and paraphyletic (includes the most recent ancestor but not all descendants) groups as taxa.

Cladistic approach confirms the Linnaean system but sometimes leads to reclassification.

Natural Selection - those organisms best adapted to their environments are more likely to survive to reproductive age and to pass on the favourable characteristics to their offspring. The environment is providing the selection pressure.

Artificial Selection - Humans select the organisms with useful characteristics and allow those with useful characteristics to breed and prevent the ones without the characteristics from breeding. Thus, humans have a significant effect upon the evolution of these populations or species.

1) The Dairy Cow - Cows milk measured and recorded. Progeny of bulls is tested to find which bulls have produced daughters with a high milk yield. Elite cows given hormones to produce many eggs, which are fertilised in vitro and the embryos placed in surrogate mothers. The embryos could also be cloned and divided into many more identical embryos. More offspring are produced than would be naturally.

2) Bread Wheat - Modern wheat is a hexaploid, having 42 chromosomes and making the cell and the nucleus larger. The modern wheat is a hybrid containing 3 genomes, AuAuBBDD. AuAu comes from the wild wheat species, BB is from wild emmer wheat and DD is from the wild oat grass. Breeders carry out selection programmes to produced improved varieties. Characteristics are - resistance to fungal infections, high protein content, stem stiffness, resistance to lodging and increased yield.