Cell Division

The rate of cell division is controlled by two things:

Proto-oncogenes :- stimulate cell division
Tumour Supressor Genes :- slow cell division.

Proto-oncogenes code for GROWTH FACTORS. They attatch to a receptor protein on the cell surface membrane, and 'switch on' the genes for DNA replication via relay proteins.
However, the mutated form of a proto-oncogene is a oncogene. Oncognes could either code for a growth factor that is produced in excessive amounts, or just permanently activate the receptor protein, leaving the DNA constantly switched on for replication.

Cells would divide too quickly/too much, meaning a tumour/cancer would occur.

Tumour supressor genes inhibit cell division. It maintains the rate of cell division, and therefore, prevents the growth of tumours. If the tumour supressor gene mutates, it becomes inactive. Most of these mutated cells die, but a small frequency of cells continue to exist and thrive. Being strutually different to other cells in the body, the mutated cells, if built up, on that small chance, can form a tumour.
A tumour that exists without spreading is almost harmless, called Benign. Malignant tumours are cancer. The tumour spreads throughout the body via the blood, existing and affecting multiple locations.

Gene Mutation.

Mutation: Change in quantity or structure or DNA of an organism.

Nonsense mutation:
The mutation creates a stop codon. I.e. The mutation changing one base. Say the recognised stop codon is AUG. And, currently, your codon is ACG. If the C was swapped for a U, this would now be a stop codon, do the polypeptide chain would stop being produced at that point. Final protein would be different, and nto function the same.

Mis-sense Mutation: 
If the codon ends up coding for a different amino acid. Say ACC codes for Alanine, and ACG codes for
Glutamine. If the final C on the initial codon was swapped for a G, the codon would now produce Glutamine, not Alanine.The amino acids determine the tertiary structure - so the shape of the protein is likely to be changed, possibly making it non-fucntional.

Silent Mutation:
The Mutation changes a bases, but the codon still does for the same amino acid as previously. This is due to the genetic code being DEGENERATE. 

These are all SUBSTITUTION

Deletion of Bases:
A single base is deleted from the code. Although initially thought to be a mild effect, this usually causes what is known as a frame shift. Meaning - where the one base has been removed, the entire chain left shifts over by one place to the left. This changes all of the codons after that point, so the nearer to the begining of the chain, the worse off it is.

Genetic mutation is RANDOM. Mutagentic factors can affect this however. So, high energy radiation, and chemicals that alters the DNA structure, or interferes with transcription.

Translation, Assmebling a polypeptide.

Also, little note about splicing: the introns are removed because they would interfere with translation. 

Translation:

1. A ribosome attatches to the start codon on the mRNA. 
2. tRNA, which has an amino acid on one end, and an anticodon on the other. The anti codon in complimentary to the mRNA and joins with it. 
3. Another tRNA joins next to the last, complimentary to the mRNA triplet codon there. 
4. By the means of an enzyme, and ATP, the two amino acids on the top of the tRNA's are joined by a peptide bond. 
5. The ribosome moves on to the next codon in the sequence of the mRNA - another tRNA joining to it, aligning the amino acids in order for these to also be joined via a peptide bond. 
6. This process continues until a stop codon is reached. At this point, there will be a full polypeptide chain formed - the ribosome, mRNA, and final tRNA all detatch. 

Unit 1 Recap: 

Secondary stucture - the polypeptide is coiled or folded 

Tertiary structure - secondary structure is folded 

Quaternary structure - different polypeptide chains linking. 

In Translation, mRNA's function is to act as a template on which the polypeptide is formed.

tRNA acts as a carrier for the amino acid. Without tRNA to carry the amino acid AND attach to the mRNA on opposite sides, the amino acids could not line up.

Transcription, Splicing.

Overview of peptide synthesis:

• DNA provides instruction - in the long sequence of bases on the nucleotides. The order of the bases and which bases are present determined the instruction. 
• Complimentary section of the DNA is formed. This is called pre-mRNA. TRANSCRIPTION
• Pre-mRNA is spliced to form mRNA. 
• mRNA acts as template, where tRNA attaches, lining up amino acids and linking them. TRANSLATION. Forms polypeptides.

Transcription is where a complimentary section of DNA is formed, called pre-mRNA. 

1. Firstly, DNA HELICASE breaks the hydrogen bonds on a section of a strand of DNA, exposing the nuclotide bases. 
2. RNA POLYERMASE moves along one of the strands (template strand), casuing it's nucleotides to join with free nucleotides in the nucleus.
3. The strand of DNA reforms behind this. This forms a strand of pre-mRNA, and the DNA left reformed.
4. The RNA Polyermase stops attatching bases when it reaches a particluar sequence of bases, arranged as a 'stop code' 

Splicing is the transformation of pre-mRNA into mRNA. This is done by removing the introns. Introns are regions of non coding, non functional DNA. Exons are regions of coding DNA (for proteins, enzymes, polypeptides.) After splicing, translation happens. 

SO 

:- Transcription -> Splicing -> Translation. ^____^ 

DNA Helicase breaks the hydrogen bonds, RNA polymerase adds free nucleotide, DNA Helicase closes it up 12 bp behind. Strand of pre-mRNA is formed. pre-MRNA is spliced (introns removed). mRNA left over.

The Genetic Code, Polypeptide Synthesis, Gene Mutation. ^-^

The genetic code is the sequence of nitrogenous bases on the mRNA - which codes for amino acids. The main features of the genetic code are: 

• 1 Amino acid is coded for by three bases on the mRNA (codon)
• Few amino acids only have a single codon
• The code is degenerate. This means that MOST amino acids can be coded for by multiple codons. 
• Three codons act as a stop codon 
• The code is non-overlapping. This means that it is read straight off, each base only read once. 
• It is universal - the same codon codes for the same amino acid across organisms. 

RNA
RNA is a single strand of nucleotides. It has the bases A,C,G, and U. ALL RNA has Uracil instead of Thymine. 

There are two types, mRNA, and tRNA. mRNA is LINEAR. It is single stranded. It forms from DNA copying part of one of it's two strands. This then passes out of the nucleous through the nuclear pores. The mRNA associates with ribosomes, allowing it to act as the templates on which proteins are made. 
tRNA is in a clover leaf shape arrangement. It is made up of about 80 nucleotides. It lines up the animo acids with the mRNA in peptide synthesis. The unpaired bases on the tRNA are complimentary to an amino acid. The anticodon is complimentary to the codon on the mRNA, thus, lining the two up in the right position. 


Differences: 

1. DNA is a double stranded chain, mRNA + tRNA are single. 
2. DNA is large, mRNA is a lot smaller, and tRNA is the smallest, at only 80 bp. 
3. DNA is a double helix structure, mRNA is single helix, tRNA is clover shaped. 
4. DNA's nucleotide sugar is Deoxyribose. mRNA + tRNA have ribose. 
5. DNA has bases C,T,A + G. mRNA + tRNA have U,C,G, and A. 
6. DNA is mostly found in the nucleus. mRNA + tRNA are made in the nucleous, but found throughout the cell. 
7. The amount of DNA in the cells of a species is the same, this mRNA+tRNA it vareis due to factors such as metabolic activity. 
8. DNA is very chemically stable. mRNA is least chemically stalbe, tRNA is slightly more. 

ALL the synthetic routes reactions. xD Chem4

REACTIONS:

• ALKANE → HALOALKANE, mechanism: free radical substitution, condition: UV light
• HALOALKANE → AMINE (primary, secondary, tertiary, quaternary ammonium salt), mechanism: nucleophillic substitution, reagent: ammonia, condition: heat
• HALOALKANE → NITRILE, mechanism: nucleophillic substitution, reagent: Cyanide OR Potassium/Hydrogen Cyanide, conditions: ethanol, reflux
• NITRILE → PRIMARY AMINE, reaction: reduction, reagent: LiAlH4, conditions: in DRY ether
• HALOALKANE → ALCOHOL, reagent: NaOH, condition: Reflux
• HALOALKANE → ALKENE, mechanism: elimination
• ALKENE → HALOALKANE, mechanism: electrophyllic addtion, reagent: HBr, condition: twenty degrees
• ALCOHOL → ALDEHYDE/KETONE, reaction: oxidation, reagent: acidified potassium dichromate, condition: distil
• ALDEHYDE → CARBOXYLIC ACID, reaction: oxidation, reagent: acidified potassium dichromate, condition: heat + reflux
• ALDEHYDE/CARB ACID/KETONE → ALCOHOL, reaction: reduction, reagent: NaBH4, condition: in water with methanol
• CARBOXYLIC ACID → ESTER, reagent: alcohol, conditions: strong acid catalyst, reflux
• ESTER → CARBOXYLIC ACID, reagent: water, conditions: strong acid catalyst, room temperature.
• ALDEHYDE/KETONE → reagent: HCN, conditions: twenty degrees
• ACYL CHLORIDE → ESTER, mechanism: addition elimination, reagent: alcohol, conditions: twenty degrees
• ACYL CHLORIDE → PRIMARY AMIDE, reagent: Ammonia, ADDITION ELIMINATION. Twenty degrees
• ACYL CHLORIDE → AMINE, reagent: amine, conditions: twenty degrees.
• ACYL CHLORIDE → CARBOXYLIC ACID, reagent: water, conditions: twenty degrees.

Ecology Definitions A2 ^-^

Sorry I haven't posted in a while. To be honest, there hasn't really been a large amount of notes to take at the time, however, I will try to consolidate them myself over the coming weeks.

Anywho...

Habitat: The place in which an organism lives.

Population: A group of organisms of the same species within a particular habitat.

Community: The total number of different populations within a particular habitat.

Niche: The position of an organism within an ecosystem dependant upon the amount of resources it uses. The more resoures looked into, the more carefully definied the niche of the organism will be.

Ecosystem: The BIOTIC communtity, living in an ABIOTIC environment.

1.3 Factors affecting K

The effect of a change in temperature on K: Reactions depend on kinetic energy, and temperature is a measure of the amount of kinetic energy. Therefore, with an increased tempereature, more particles have kinetic energy, and therefore, more will sucessfully collide in order to exceed the activation energy.

The effect of a change in presure on K: No effect.

The effect of a change in species concentration on K: Concentration is within the equation. As the concentration increases, so does K.

1.2 The rate expression and order of reaction

The rate expression tells us by how much a reactant participates in the reaction, and the contribution they have. In a simple reaction, one species may have more of an effect then another. Also, species that are not involved in the chemical reaction could also affect the rate of reaction, e.g. catalysts.

This is expressed via reaction ORDERS. An order is a reaction expresses to which power the concentration of that species affects the rate. How the rate dpeends on that chemical and it’s concentration.

Order Zero: A change in concentration of the species does NOT affect the rate.

Order First: A change is concentration of the species has exactly the same effect on the rate. (If the concentration doubles, the rate doubles.)

Order Second: A change in concentration of the species has a squared effect on the rate. If the concentration doubles, the rate would quadruple. Or, if it tripled, the rate would multiply by nine, and so on.

A rate equation is set out as: Rate = k[A][B].

The letters in square brackets represent the concentrations of particular species. The orders apply to these. So, if A was order two, and B was order one, the rate equation would look like this:

Rate=k[A]2[B]

(There need not be a ‘1’ to show first order, as like ‘x’ meaning ‘1x’ in algebra, the single, un-numbered bracket shows order one.)

When a sepecies is order zero, it is not shown in the rate equation. So, if A was order 1, B was order 0, and C was order 2, it would look like this:

Rate=k[A][C]2

K is the equilibrium constant. K is different for every different reaction, dependant upon what is reacting, and the conditions.

To work out K’s units, you use cancelling. In Rate=k[A][B],

moldm-3s-1 = k x moldm-3 x moldm-3

moldm-3s-1= Units of rate.

moldm-3 = Units of species concetration.

Cancelling… moldm-3s-1 = k x moldm-3 x moldm-3

Therefore, K= mol-1dm3s-1, as the s-1 has multiplied with the moldm-3.

The overall order of a reaction, is all of the orders added together. So, if Rate=k[A][B]2, the overall order would be 1+2=3.

1.1 The rate of chemical reactions

Rate of reaction: The change in concentration of any of the reactants or products with unit time.

Rate of reaction is measured in the units moldm-3s-1

The gradient about a tangent on a reaction rate graphs shows the reaction rate at that specific time. This is also to the units moldm-3s-1. The larger the gradient, the bigger the rate of reaction at the particular instance. For example, in a reaction rate graph of a reactant, the graph would start of with a steep gradient at zero. This is because at the beginning of a reaction, there is a high concentration of reactant, increaing the rate of reation, as there are more particles to make sucessful collisions and exceed the activation energy.