Cellular Control

• A sequence of nucleotide bases that codes for one or more polypeptides.
• 4 different nucleotides, each with a different base: Adenine, Guanine, Thymine and Cytosine
• Have a pentose sugar- deoxyribose, a phosphate group and the base (all covalently bonded)
• Nucleotides bond by forming phosphodiester bonds between the phosphate group of one and the sugar of the other--forms sugar-phosphate backbone.
• Complementary DNA polynucleotide strands join by forming hydrogen bonds between the bases by complementary base pairing: A-T (2 H bonds) G-C (3 H bonds)
• Two strands wind together in antiparallel directions 
• DNA has histone coat, a protein that keeps it stable and prevents it being damaged.

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

A polypeptide is a polymer consisting of a chain of amino acids joined together by peptide bonds.

A protein is a large polypeptide, usually made of more than 100 amino acids. It can be one long polypeptide, or several chains. 

The genetic code is the sequence of bases on the coding strand of DNA. It is a triplet code, as 3 bases = 1 amino acid. 

• It is a degenerate code, as there are 4 bases, and so there are 64 possible sequences.
• All amino acids (except methionine) have more than 1 triplet of bases. 

Triplet coding= CODON. 
Codon for methionine=ATG=START CODON (this marks the start of a gene for a specific polypeptide) The STOP CODONS are: TAA, TAC, TGA

DNA has coding strand and template strand. Coding=genetic code Template=complemetary bases to coding strand. 

PROCESS THAT USES GENETIC CODE TO PRODUCE POLYPEPTIDE

2 STAGES:-

• TRANSCRIPTION
• TRANSLATION

The creation of a single-stranded mRNA copy of the DNA coding strand.

First stage of protein synthesis:

• messenger RNA (mRNA) is the copy of the genetic code that passes through a pore in the nuclear envelope to the cytoplasm.
• For the mRNA molecule to be made, the template strand is used as a template.
• There are free DNA nucelotides in the nucleoplasm, and free RNA nucleotides in the nucelolus--these are all activated. The RNA mols that are activated are: ATP, GTP, CTP + UTP.

• A gene to be transcribed unwinds and unzips=the DNA that makes up this gene is dipped into the nucleolus+H bonds break between the bases.
• The activated RNA nucleotides in the nucleolus bind w H bonds to the exposed complementary bases.
  U-A G-C A-T (catalysed by DNA polymerase)
• These nucleotides have two extra phosphoryl groups-these are released, releasing energy for bonding adjacent nucleotides.
• mRNA produced is complementary to the nucleotide base sequence on the template strand, and so becomes a copy of the coding strand (exchanging Thymine for Uracil).
• The mRNA is released from the DNA and passes out of the nucleus, through a pore in the nuclear envelope, to a ribosome.

The assembly of polypeptides at the ribosomes.

Amino acids sequence dictated by the codons from the mRNA (triplets of nucleotide bases). The genetic code, copied from DNA into mRNA, is now translated into a sequence of amino acids. The chain becomes a polypeptide, and it happens at ribosomes.

Ribosomes:
-made in the nucleolus, from ribosomal RNA and protein.
-made of two subunits, and there is a groove into which mRNA (which have codons for the sequence of amino acids) can fit.

The sequence is so critical because:
-it forms the primary structure
-Primary structure determines teritary structure-how the protein folds up into 3D shape and is held by H bonds, ioninc bonds and hydrophobic interactions.
-the tertiary structure allows the protein to function- having the correct shape, eg enzyme active site
-if tertiary structure is altered- protein cannot function.

TRANSFER RNA:

Another form of RNA is made in the nucleus and passes into the cytoplasm.
These lengths of RNA fold into hairpin shapes and have 3 exposed bases at one end where a particular amino acid can bind.
At the other end= ANTICODON (three unpaired nucleotide bases). Each ANTICODON can bind temporarily with its complementary codon.

How the polypeptide is assembled:

• molecule of mRNA binds to ribosome. Two codons are attached to the small subunit of the ribosome. The first exposed mRNA codon is ALWAYS AUG. Using ATP energy and an enzyme, a tRNA with methionine + the anticodon UAC forms H bonds with this codon. 
  
• A second tRNA, bearing a different amino acid binds to the second exposed codon with its complementary anticodon. 
• A peptide bond forms between the two amino acids- an enzyme in the ribosome catalyses this reaction.
• The ribosome now moves along the mRNA, reading the next codon...a third tRNA brings another amino acid and a peptide bond joins the already standing dipeptide bond.
• The first tRNA leaves and brings another amino acid anticodon
• The polypeptides chain grows and grows until a stop codon is reached-there are no complementary tRNA's for UAA, UAC or UAG. 

Mutation= a change in the amount of, or arrangmenent of the genetic material in the cell

Chromosome mutations= changes to parts or whole chromosomes

DNA mutations= changes to genes due to changes in nucleotide base sequences

Mutations with mitosis are somatic and so won't be passed on to offspring, but may lead to cancer. Mutations with meisos can be passed on to offspring. 

Two main classes of DNA mutations:
-Point mutations= one base pair replaces another
-Insertion/deletion mutations= one or more nucleotide pairs inserted or deleted from a length of DNA=frameshift. 

Mutations cause changes to the sequence of nucleotides in DNA molecules. 

Mutations w/ neutral effects:

• If there has been an alteration to a the nucleotide bases, it simply becomes another version of the same gene, eg an allele.
• It may produce no change if:
  -the change occurs on a non-coding region of DNA
  -a silent mutation; even though there as been a change in the codon, it still codes for the same amino acid. 

Also if change gives no particular advantage or disadvantage then the effects are neutral- eg, some people can smell honeysuckle and some can't- but this has nothing to do with adaptiveness.

Mutations with harmful or beneficial effects: SKIN COLOUR

• Early humans in Africa had dark skin
• This protects them from the effects of the ultraviolet light, yet they were still able to absorb Vit. D from the intense sunlight on their skin (an important and sole source bc little Vit. D in food)
• Humans with paler skin due to a skin mutation would've burned and died from skin cancer
• As humans migrated to more temperate regions, the sunlight wasn't enough for people with darker skin to absorb Vit. D, and so paler people better adapting to producing their own Vit. D would survive in these places and those with darker skin would develop rickets, a narrow pelvis which could kill both mother and child in childbirth. 

Depending on the environment, mutations can be either an advantage or disadvantage. The well-adapted organisms can usually out-compete those without the characteristic, leading to natural selection, a survival of the fittest. 

When lactose is absent:-

-The regulatory gene is transcribed and translated and the repressor protein is synthesised. It has two binding sites, one that binds to lactose, and the other to the operator gene.
-The repressor protein binds to the operator region-in doing so it covers the promoter region, meaning RNA polymerase cannot catalyse the structural genes being transcribed into mRNA.
-Without mRNA, these genes cannot be translated and the enzymes needed to break down lactose eg lactase permease cannot be formed. 

When lactose is added to growth medium:-
-Lactose (inducer) molecules bind to the other side of the repressor protein, changing its 3D shape so that is no longer complementary to bind to the operator region. 
-It breaks away from operator region.
-RNA polymerase can now bind to promoter gene, and the transcription of structural genes can occur
-operator-repressor-inducer system is molecular switch. It allows transcription and translation of structural genes into the lac enzymes. 
-As a result-E.coli can use lactose permease enzyme to take up lactose-glucose-galactose-aerobic resp. 

Homebox genes: control the development of the body plan of an organism, including the head and tail ends (polarity) and positioning of the organs.

"Programmed cell death"
The sequence of events:-

• Enzymes break down the cytoskeleton
• The cytoplasm becomes becomes denser, and the organelles tightly packed
• The CSM changes, and blebs form
• Chromatin condenses, nuclear envelope breaks down and DNA breaks into fragments
• Cell breaks into vesicle and is taken up by phagocytosis
• V quick process

Controlling the process:
Nitric oxide-induces apoptosis by making the mitochondria more permeable to hydrogen and dissipating the proton gradient.
Proteins- released into the cytosol and bind to apoptosis inhibitor proteins to allow it to take place.

• Used to stop harmful enzymes being formed 
• Weeds out ineffective or harmful T-lymphocyte cells 
• During limb development-causes fingers and toes to separate from eachother
• By adulthood, the rate of cells dying should balance the rate of cells produced by mitosis

If not balanced:-

-not enough apoptosies leads to the formation of tumours
-too much leads to cell degeneration and loss.