F215

Each chromosome contains 1 DNA, DNA associated with histones.

Gene:

• A gene is a length of DNA (sequence of nucleotide bases) that codes for polypeptides.
• Most on linear chromosomes within nucleus.
• Some in motochondria.
• Each occupies a specific place/locus on chromosome. 
• Since they code for enzymes, they are involved in the control of all metabolic pathways and thus in the synthesis of all non-protein molecules found in cells.

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

Examples of polypeptides: Enzymes, collagen, heamoglobin, keratin, tubulin, antibodies, cell surface receptors, antigens, etc.

The genetic code is a set of instructions for the construction of a polypeptide provided by the sequence of nucleotide bases on a gene.

Characteristics:

• Triplet code: A sequence of 3 nucleotide bases code for an amino acid.                                   (4 bases arranged in groups of 3, so the number of different triplet sequences is 4 cubed or 64 = more than enough as only 20 amino acids are used in protein synthesis).
• Degenerate code: All amino acids except methionine have more than one code.
• Stop codes indicate the end of a polypeptide chain and don't code for amino acids.
• Widespread but not universal: Some base sequences code for a particular amino acid in any organism= useful for genetic engineering, however, some amino acids have two codes.

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

• mRNA molecule made by using one strand of DNA as a template. 
• Free DNA nucleotides in nucleoplasm and free RNA nucleotides in nucleolus are activitated by having two extra phosphoryl groups attached.
• A gene to be transcribed unwinds and unzips as 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 on the template strand. This is catalysed by RNA polymerase.
• Two extra phosphoryl groups released, releasing energy for bonding adjacent nucleotides.
• mRNA produced is a copy of of the base sequence on the coding strand as it is complementary to the nucleotide basee sequence on the template strand.
• mRNA is released.

mRNA is a copy of the genetic code (on chromosome in nucleus) which can pass through a pore in the nuclear envelope to the cytoplasm, at ribosomes (where proteins are assembled).

Tanslation is the assembly of polypeptides at ribosomes.

• Polypeptides assembled into the sequence dictated by the sequence of codons (triplets of nucleotide bases) on the mRNA. 
• Genetic code copied from DNA into mRNA is now translated into a sequence of amino acids (polypeptide).

Ribosomes may be free in cytoplasm but many are bound to the rough endoplamic reticulum.

Ribosomes are assembled in the nucleolus of eukaryotic cells from rRNA and protein.

Each ribosome has a grove where mRNA can fit. Ribosome then moves along mRNA which can slide through groove, reading the code and assembling amino acids in the correct order to make a functioning protein.

Why is the sequence of amino acids in a protein important?

• It forms the primary structure of a protein.
• The primary structure determines the terciary structure (3D shape).
• The tertiary structure allows the protein to function properly (eg. enzyme active site or opening of channel protein.

• Made in nucleus and passes into cytoplasm.
• 3 exposed bases at one end where a particular amino acid can bind.
• Anticodon (three unpaired nucleotide bases) at other end.
• Each anticodon can bind temporarily with its complementary codon.

• Molecule of mRNA binds to ribosome.
• Two codons (6 bases) attached to the small subunit of the ribosome and exposed to the large subunit.
• First exposed mRNA codon = AUG.
• Using ATP energy and an enzyme, tRNA with methionine and the anticodon UAC forms hydrogen bonds with the codon (AUG).
• 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 adjacent amino acids. This reaction is catalysed by an enzyme.
• The ribosome now moves along the mRNA, reading the next codon.
• A third tRNA brings another amino acid, and a petide bond forms between it and the dipeptide.
• The first tRNA leaves and is able to collect and bring another of its amino acids.
• The polypeptide chain grows until a stop codon is reached = polypeptide complete because there are no tRNAs for these codons.
• cAMP activates nucleotides so that their 3D shape is a better fit to complementary molecules.

In prokaryotes DNA is not inside nucleus therefore translation begins as soon as mRNA has been made.

• Mutation is a random change in the amount of, or arrangement of, the genetic material in a cell. 
• Chromosome mutation involves changes to parts of or whole chromosomes.
• Mutations may occur due to DNA replication or mutagens (UV light, tar and gamma rays).
• Mutations associated with mitosis = somatic mutations, not passed onto offspring.
• Mutations associated with meiosis = can be inherited.

Point mutation/ substituiton = one base pair substitutes another.

Insertion/deletion mutations = one or more nucleotide pairs are inserted or deleted from a lenght of DNA- cause frameshift.

• Cystic fibrosis caused by deletion of a triplet of base pairs.
• Sickle cell anemia results from point mutation.
• Huntington desease results from an expanded triplet repeat.
• Cancer results from point mutation.

Mutations with neutral effects

Alleles produced by mutation:

Allele is an alternative version of a gene. It is still at the same locus on the chromosome and still codes for the same polypeptide but the alteration of the DNA base sequence may alter the protein's structure.

It may not produce any change in the organism if:

• The mutation is in a non-coding region of the DNA.
• It is a silent mutation.

E.g Some people can smell honeysuckle and some cannot, some can tongue roll and some cannot but this is no particular advantage or disadvantage.

• Early Africans had dark skin (melanin) to protect themselves from UV light, white skin would have burned and suffered from skin cancer.
• Mutations happend to help them survive in their environment = natural selection = evolution.

Some people can't taste PCT which is poisonous and tastes bitter, these people can end up eating too much and dying. 

• E.coli can be placed in a medium with lactose.
• At first they cannot metabolise lactose as they have limited  amounts of B-galactosidase (which catalyses the hydrolysis of lactose to glucose and galactose) and lactose permease (which transports lactose into cell).
• A few minutes later, lactose acts as an inducer which triggers an increase in the production of these two enzymes.

The lac operon is a section od DNA within the bacterium's DNA. It consists of:

• Structural genes: Z codes for B-galactosidase, Y codes for lactose permease. Each consists of a sequence of base pairs that can be transcribed into a lenght of mRNA.
• Operator region: O is a length of DNA next to structural genes. It can switch them on and off.
• Promoter region: P is a lenght of DNA to which the enzyme RNA polymerase binds to begin the transcription of the structural genes Z and Y.

When lactose is absent from the growth medium:

• Regulator gene expressed (transcribed and translated) and the repressor protein is synthesised. It has two binding sites, one that binds to lactose and one that binds to the operator region.
• The repressor protein binds to the operator region. In doing so it covers part of the promoter region, where RNA polymerase normally attaches.
• RNA polymerase cannot bind to the promoter region so the structural genes cannot be transcribed into mRNA.
• Without mRNA these genes cannot be translated and the enzymes B-galactoside and lactose permease cannot be synthesised.

Homeobox genes contol the development of the body plan of an organism including polarity and positioning of organs.

• Apoptosis is programmed cell death.= benefitial and tidy cell death. 
• Necrosis is untidy and damaging cell death that occurs after trauma.

Sequence of events in apoptosis:

• Enzymes break down the cytoskeleton.
• Cytoplasm becomes dense with organelles tightly packed.
• Cell surface membrane changes and blebs are formed.
• Chromatin condenses and nuclear envelope breaks. DNA breaks into fragments.
• The cell breaks into vesicles that are taken up by phagocytosis (endocytosis of large solid molecules into a cell). The cellular debris is disposed of and does not damage any other cells or tissues.
• The whole process occurs very quickly.
• Proteins released into cytosol which bind to apoptosis inhibitor proteins and allow the process to take place.
• Apoptosis can be controlled by cell signals such as cytokines, hormones, growth factors and nitric oxide.
• Nitric oxide induces apoptosis by making the inner mitochondrial membrane more permeable to hydrogen ions and dissipating the proton gradient.

• Apoptosis is tightly regulated during cell development, different tissues use different signals to induce it.
• It weeds out harmful T lymphocytes during the development of the immune system.
• Not enough apoptosis leads to the formation of tumours.
• Too much leads to cell loss and degeneration.

When lactose is added to the growth medium

• Lactose molecules bind to the other repressor protein. This causes the molecules of repressor protein to change so that its other binding site cannot now bind to the operator region.
• This leaves the promotor region unblocked. RNA polymerase can now bind to it and initiate the transcription of mRNA for genes Z and Y.
• The operator-repressor-inducer system acts as a molecular switch. It allows transcription and subsequent translation of the structural genes Z and Y into the lac enzymes B-galactosidase and lactose permease.
• As a result, E.coli bacteria can use lactose permease to take up lactose from the medium into their cells. They can convert lactose to glucose and galactose using B-glactosidase. These sugars can then be used for respiration thus gaining energy from lactose.

A repressor protein can bind to the operator region, and RNA polymerase binds to the promoter region to transcribe the structural genes.