Cellular Control

Transcription: 

1. A gene to be transcribed unwinds and unzips, using DNA Helicase. To do this, the length of DNA that makes up the gene dips into the nucleolus. Hydrogen bonds break between complementary bases. 

2. Activated RNA nuclotides, with hydrogen bonds to their exposed complementary base. U binds with A, G with C, and A with T on the template strand. This is catalyed by RNA polymerase. 

3. The two extra phoshoryl groups are released. This releases energy for bonding adjacent nucleotides. 

4. The mRNA produced is complementary to the nucleotide base sequence on the template strand of the DNA and is therefore a copy of the base sequence on the coding strand of the length of DNA 

5. The mRNA is released from the DNA and passes out of the nucleus, through a pore in the nuclear envelope, to a ribosome 

Ribosomes are assembled in the nucleolus of eukaryote cells, from ribosomal RNA and protein. 

Each is made up of two subuntis and there is a groove into which a length of mRNA can fit 

The ribosome can then move along the mRNA which can slide up trought the ribosomal groove reading the code and assmebling the amino acids in the correct order to make a functioning protein. 

The order of amino acids is crucial because:

• It forms the primary structure of the protein
• The primary structure will determin the tertiary structure 
• The tertiary structure is what allows the protein to function
• If the tertiary structure is altered, the protein can no longer function so effectively, if at all

How the polypeptide is assembled: 

1. A molecule of mRNA binds to a ribosome. Two Codons are attached to the small subunit of the ribosome and exposed to the large subunit. The first exposed subunit is always AUG. Using ATP energy and an enzyme, a tRNA with methinonine and the anticodon UAC forms hydrogen bonds with this codon 

2. A second tRNA, bearing a different amino acid, binds to the second exposed 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 moves along the mRNA strand reading the next codon. The first tRNA leaves and is avaliable to bring another of its amino acids. A thrid tRNA brings another amino acid, and a peptide bond forms between it and the dipeptide 

5.The polypeptide chain grows until a stop codon (UAA, UAC, or UAG). There are no corresponding tRNAs for these molecules so the peptide chain is complete 

Chromosone mutations involves a change to parts of or whole chromosomes. These may occur during DNA replication.

DNA mutations: are changes to genes due to a change in the nucleotide base sequences 

Dna mutations may occur when DNA is replicating before nulcear division, either by mitosis or meiosis. Mutations involved with mitosis are simatic and won't be passed on to offspring and may contribute to the ageing process or may lead to cancer 

There are two main clases of DNA mutations: 

• Point mutations: In which one base pair replaces another. These are also called substitutions 
• Insertion/ deletion mutations: in which one or more nucleotide bases are inserted or deleted froma length of DNA. These cause a Frameshift 

Many genetic diseases are the result of DNA mutations: 

• In 70% of cystic fibrosis, the mutation is a deletion of a triplet of base pairs, deleting an amino acid from the sequence of 1480 amino acids. 
• Sickle cell anaemia results from a point mutation in codon 6 of the gene for beta- polypeptide chains for haemoglobin. This caises the amino acid valine to be inserted, instead of glutamic acid 
• Growth promoting genes are calle protooncogenes. some can be changed into oncogenes by a point mutation. This alters the ability of the protooncogene to be switched off, remaining permenantly switched on. Oncogenes promote unregulatd cellular growth, which can lead to a tumour 
• Huntington disease results from an expanded triple nucleotide repeat- A stutter. 

E.Coli normally respires glucose but it can also respire lactose. At first they cannot metabolise the lactose as they only have small quatities of the enzyme needed, which are:

• beta galactosidase: Catalyses the hydrolysis of lactose to glucose and galactose 
• Lactose permease: Which transports the lactose into the cell

Lactose must trigger the production of the two enzymes, and is therefore known as the inducer 

The Iac operon is a section of DNA within the bacterims DNA, and constist of a number of parts: 

• The structural genes: Z codes for the enzyme beta glactosidase and Y codes for the enzyme lactose permease. Each constists of a sequence of base pairs that can be transcribed into a length of mRNA 
• The operator region, O: A length of DNA next to the structural genes. It can switch them on and off
• The promoter region, P: A length of DNA to which the enzme RNA polymerase binds to begin the transcription of the structural genes, Z and Y 

When lactose is absent form the growth medium: 

1. The regulatory 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 sothe strucutral genes cannot be transcribed into mRNA 

4. Without mRNA these genes cannot be translated and the enzymes cannot be synthesised 

When lactose is added to the growth medium:

1. Lactose (Inducer) molecules bind to the other site on the repressor protein. This causes the molecules of the rpressor protein to change shape so that its other binding site cannot now bind to the operator region. The repressor disscociates form the operator region

2.This leaves the promoter region unblocked. RNA Polymerase can now bid to it and initiate th transcription of mRNA for genes Z and Y. 

3. The operator- repressor- inducer systmen acts as a molecular switch. It allows transcription and subsequent translation of the structural genes Z and Y into the Iac enzymes 

4. As a result, E.Coli bacteria can use the lactose permease enzyme to take up lactose from the medium, into their cells. The can then convert the lactose into glucose and galactose using the beta galactosidase enzyme. These sugars can then be used for respiration 

Genentic control of Drosophilia development:

The development is genetically mediated by Homeobox genes:

• Some genes (Maternal-effect genes) determins the embryos polarity. Polarity reffers to ehich end is the head (anterior) and which end is the tail (posterior) 
• Other genes, called 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. There are two gene families:
  • The complex that regulates development of thorax and abdomen segments 
  • The complex that regulates the development of head and thorax segments
• Mutations of these genes can change one body part to another. 
• The homeobox genes are arranged in clusters known as Hox Clusters 
• Vertebrates have for clusters, of 9-11 genes located on speerate chromosomes 

Apoptosis is programmed cell death that occurs in mlticellular organisms. Cells should undergo about 50 mitotic divisions (The Hayflick Constant) the undergo a series of biochemical events that lead to an orderly and tidy cell death. This is in contrast to cell necrosis, an untidy and damaging cell death that causes trauma and releases hydrolytic enzymes 

The sequence of events: 

• Enzymes break down cell cytoskeleton
• The cytoplasm becomes dense, with organelles tightly packed 
• The cell surface membrane changes and small bits called blebs form 
• Chromatin condenses and the nucear envelope breaks. DNA breaks into fragments 
• The cell breaks into vesicles that are taken up by phagocytosisThe cellular debris is disposed of and does not damage other cells 
• The whole process occurs very quickly 

The whole process is contorolled by a wide range of signals, which include cytokines. 

Not enough apoptosis can lead to the formation of tumours, where as too much can lead to degeneration and cell loss

prophase I:

• The chromatin condenses and undergoes supercoiling so that the chromosomes shorten and thicken.They can take up stains and been seen by a light microscope
• The chromosmes come together in their homologus pairs to form a bivalent Each member of the pair has the same genes at each loci. Each pair consists of one maternal and one paternal chromosome 
• The non-sister chromatids wrap around eachother and attach at points called chiasmata
• They may swap sections of chromosomes with one another in a process called swapping over
• The nucleolus dissapears and the nuclear envelope disintergrates. A spindle forms, Prophase I may last for days, months or years depending on the species 

Metaphase I:

• Bivalents line up across the equator of the spindle, attached to spindle fibres at the centromeres. The chiasmata are still present 
• The bivalents are arranged randomly , allowing the chromosomes to independently segregate.

Anaphase I:

• The homologus chromosomes in each bivalent are pulled together by the spindle fibres to opposite poles 
• The centromeres do not divide 
• The chiasmata seperate and lengths of the chromatid that have been crossed over remain with the chromatid to which they have become newly attached 

Telophase I

• In most animal cells, two new nuclear envelopes form, one around each set of chromosomes at each pole
• The cell divides by cytokinesis
• In most plant cells the cell goes straight from anaphase I into meiosis I 

Prophase II

• If a nuclear envelope has reformed, it breaks down again 
• The nucleolus dissapears, chromosomes condense and spindles form 

Metaphase II

• The chromosomes arrange themselves on the equator of the spindle they are attahed to the spindle fibres at the centromeres 
• The chromatids of each chromosome are randomly assorted 

Anaphase II

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

Telophase II

• Nuclear envelopes reform around the two haploid daughter nuclei 
• The two cells now divide to give four daughter cells 

Sexual reproduction increases the genetic variation, as genetic material from cells of two organisms combine. Genetic variation increases the chances of evolution

Meiosis increases genetic variation by:

• Crossing over during prophase I to suffle alleles 
• Genetic reassortment due to the random distribution and subsequent segregation of the maternal and paternal chromosomes in the homologus pairs, during meiosis I
• Genetic reassortment due to the random distribution and segregation of the sister chromatids at meiosis II
• Random mutaion 

Mutation:

• DNA mutations may occur during interphase when DNA replicates. Chromosome mutations may also occur 
• Mutation does increase genetic variation 
• I fmutation occurs in the sperm or egg, then the offspring will have the mutated cell 

Crossing over: 

• Non-sister chromatids wrap around eachother very tightly and attach at points called chiasmata 
• The chromosomes break at these points. The broken ends of the chromatids rejoin to the ends of non sister chromatids in the same bivalent. This leads to similar sections of non sister chromatids being swapped over. These sections contain the same genes but often different alleles 
• It produces new combinations of alleles on the chromatids 
• The chiasmata remain in place during metapahse and the y hold the maternal and paternal homologues together on the spindle 

Reassortment of chromosomes:

• This reassortment is as a result of the random ditribution of maternal and paternal chromosomes on the spindle equator at metaphase I
• Each gamete acquires a different mixture of maternal and paternal chromosomes 

Reassortment of Chromatids:

• This is the result of the random distribution on the spindle equator, of the sister chromatids at metaphase II
• Because of the crossing over, the sister chromatids are no longer genetically identical 
• How they align themsleves at metaphase II determines how they segregate at anaphase II

Fertilisation:

• In humans, only one ovum (actually a secondary oocyte and has not completed the second mitotic division) is released at a time 
• There are about 300 million spermatoza, all of which are genetically different and any one of them can fertilise the secondary oocyte
• Whichever one of them fertilises the ovum, genetic material from two unrealted individulas is combined to make the Zygote 

Genotype: The genetic makeup of an organism. It describes the organism in terms of the alleles is contains, Usually in the context of a particualr characteristic. 

Phenotype: Refers to the characteristics that are expressed in an organism. It is the obervable features.

Dominant: An allele is said to be dominant if it is always expressed in the phenotype, even if a different allele for the same gene is present in the genotype 

Recessive: An allele is said to be recessive if it is only expresed in the phenotype in the presence of another identical allele, or in the absence of a dominant allele

Codominant: Two alleles of the sma gene are described as codominant if they are both expressed in the phenotype of the heterozygote. 

Linkage: Linkage refers to two or more genes that are located on the same chromosome. The linked alleles are normally inherited together as they don't segregate independently at meiosis

Sex-Linked: A characteristic is said to be sex-linked if the gene that codes for it is found on on of the sex chromosomes  

When constructing genetic diagrams there are certain conventions:

• Start by showing the parental phenotypes 
• The gene is represented by a letter, with the upper case being the dominant allele and the lowercase letter representing the recessive allele 

Sickle- cell anaemia 

• All individuals with the disease have the same mutation
• the beta- strands of haemoglobin differ by one amino acid at position 6 
• In normal haemoglobin, glutamic acid is present, but in sickle cell haemoglobin, valine is present instead 
• When this abnormal haemoglobin is deoxygenated it is not soluable and becomes crystaline and aggregates into more linear and less globular shapes. This deforms the red blood cells, making them inflexiable and unable to squeeze through capilaries 
• If enough sickle cells become lodged in capillaries blood flow is impeeded 

Epistasis: The interaction of different gene loci so that one gene loci masks or suppresses the expression of another gene locus. The genes involved may control the expression of one phenotype characteristic in one of two ways: 

• They may work against eachother (antagonistically) resulting in masking 
• They may work together in a complementary fasion 

Recessive epistasis: The epistatic gene has to have two recessive alleles (eg. aa) for it to mask the expression of a second gene. Ratio of 9:3:4

Dominant epistasis: Occurs when a dominant allele at one of the gene locus masks the expression od the alleles at a second gene locus. Ratio of 12:3:1 OR 13:3

Complementary fashion: One gene codes for an intermediate and a second gene locus will code for an enzyme that will convert this intermedicate into a final product. Ratio of 9:7

X² = The sum of (obsevered values (o) – expected numbers(E))²

                                            Expected Numbers (E) 

Null Hypothesis: There is no statistically significant difference between the observed (Dihybrid cross) numbers and the expected (Mendelian) numbers and any difference is due to chance 

The number that is calculated is then compared against a table, with the degrees of feedom (Class number- 1) and the probability that it is due to chance.

We normally work at the 5% probability that it is due to chance as a critical value, and if it is below this value then we accept the null hypothesis. However, if it is above, we must reject the null hypothesis and develop an alternative theory (Genes could be linked) 

Discontinuous Variation: 

• This describes the qualitative differences between the phenotypes- There are no intermediate quantaties 
• Different alleles at a single gene locus have large effects on the phenotypes 
• Diferent gene loci have quite different effects on the phenotype 
• Examples include codominance, dominance and recessive patterens of inheritance 

Continuous Variation: 

• This describes quantitative deifferences between phenotypes Traits exhibiting continuous variation are controlled by two or more genes 
• Each gene provides an additative component to the phenotype 
• A large number of genes can have an effect on the phenotype. These are known as polygenes and the characteristic they control is describes as polygeneic 

The biological species concept: is a group of similar organisms that can interbreed and produce fertile offspring. However, this concept is probematic when biologists want to classify living organisms that don't reproduce sexually, or species that have died

The phylogenetic species concept: A group of organisms that have similar morphilogy, physiology, embryology, and behaviour, and occupy the same ecological niche. 

All living organisms contain DNA RNA and Proteins. Closely related organisms have similar molecular structures for these substances. With improved methods of DNA sequencing, biologists have used systematic molecular analysis to compare particular base sequences on chromosomes of particular organisms 

A monophyletic group is one that includes an ancstral organism and all its descendent species 

Cladistics is the hieriachal classification of species based on their evolutionary ancestory It:

• Focuses on evolution rather than similarities between species 
• It places grat importance on using objective and quantitative molecular analysis 
• Uses RNA and DNA sequencing 
• Makes no distinction between extinct and extant species 

Natural selection is the mechanism for evolution. The organisms best adapted to survive are more likely to pass on their alleles to their offspring 

 In Artificial selection:

• Humans select the organism with the most favourable characteristics
• Humans allow those with useful characteristics to breed
• Thus, humans have a significant effect upon the evolution of these populations or species

The Modern Dairy cow:

• Each cows milk is meausered and recorded
• The progeny of bulls is tested
• Only a few good quality bulls need to be keept as the semen from one bull can be collected and artificially inseminate many cows
• Some elite cows are given hormones so they produce many eggs
• The eggs are fertilised in vitro and the embryos are implanted into surrogate mothers
• These embryos could also be cloned and divided into many more identical embryos  

How Artificial selection has produced bread wheat:

• Most wild species of bread wheat are diploid with 14 chromosomes; n=7 
• Grasses are able to undergo polyploidy- Their nuclei can contain more than one diploid set of chromosomes 
• Mordern bread wheat is hexaploid, 6n, having 42 chromosomes in the nucleus of each cell. Because the nucleus is larger the cells are also larger
• Genetic analysis of modern wheat has shown that it is a hybrid, containing three distinct species
• The genome, A^U A^U Which has come from a wild wheat species
• The genome BB comes from another wild emmer wheat (A tetraploid, 4n)
• The genome DD 

Characteristics that are still being focused on for improvement are:

• High protein content 
• Staw Stiffness, and Resistance to lodging
• Resistance to fungal infections, and increased Yield 
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