Chapter 20 Gene Expression

Gene mutations could arise spontaneously during DNA replication but mutagenic agents like high energy ionising radiation and chemicals. 

Deletion of Bases - loss of a nucleotide in the DNA sequence. This causes a frame shift. The reading frame shifts to the left. As a result, coded information is now altered because the gene is now read differently form the original. Diff. codon = diff. amino acids = diff. polypeptide chain = production of a non-functional protein. 

Substituion of bases: bases are replaced -  3 possible consequences

• Formation of one of the 3 stop codons - nonsense substitution - production of the polypeptide would stop permaturely. 
• Formation of a diff. amino acid -  missense substituiton - diff. shape of protein produced so diff. polypeptide chain which alters the tertiary structure so a non-functioning protein is formed. 
• Formation of a diff. codon but one that codes for the same amino acid - silent substitution

Addition - causes frame shift to the right

Duplication - one or more bases are repeated - frame shift to the right.

Inversion - a group of bases are separated from the DNA sequence and rejoin at the same position but in the reverse order so base sequence at this potion is reversed.

Translocation - group of bases become separated onone chromosome and joins into the DNA sequence of another chromosome. 

Stem cells could duplicate themelves in order to maintain the stem cell pool. It could also differentiate into different cells by switching on and off genes to replace dead or damaged cells throughout life time. 

Totipotency refers to the ability of a stem cell to specialise into any type of cell. 

Totipotent stem cells - found in the early embryo. They can differentiate into any type of cell but they lose their totipotency once they've become specialised. 

Pluripotent stem cells -  found in the blastocyst in the 'inner cell mass'. They could specialise into almost any type of cell except placenta cells. Embryonic stem cells could be taken from the inner cell mass and be cultured in a lab. 

Multipotent stem cells - tissue stem cells- commonly found in the bone marrow and skin. They could only differntiate into a limited number of cells. For example, bone marrow stem cells could only differentiate into blood cell types.

Unipotent - could only differentiate into one cell type. They are made in adult tissue. 

Induced pluripotent cells (iPS) - they are produced form unipotent cells which are genetically altered in the lab by turning on genes that are otherwise off. This results to these cells acquiring the behvaiour of an embryonic stem cell. 

Transcription factors are regulatory proteins which could inhibit (repressor)  or activate (activator) binding of RNA polymerase onto the promotor region of the DNA. 

Role of Oestrogen: switches on a gene

• lipid - soluble so it could pass the phospholipid bilayer
• It binds to the receptor molecule of the transcriptional factor, causing the DNA binding site of the transcriptional factor to change. 
• The transcriptional factor could now enter the nucleus through a nuclear pore and binds to DNA to start transcription.

Small interfering RNA (siRNA) - prevents the breaking down of mRNA before it could translate to a protein.

• Double stranded molecules are cut by dicer enzymes to produce siRNA which forms a complex with a protein
• siRNA - protein complex binds to mRNA
• mRNA is cut by siRNA - protein complex
• mRNA is broken down so it prevents further protein synthesis since translation can't occur. 

Epigenetics is the process by which environmental factors causes inheritable changes in gene function without changing the base sequence of DNA. 

A nucleosome contains a portion of double stranded DNA wrapped around histones. DNA has a negative charge while histones have a positve charge so they attract.  Any chemical modifications to this structure signals whether or not a particular region ofthe genome is open or close for transcription. 

• DNA  and Histone methylation - cytosine is methylated by adding a methyl group at carbon 5 to form methylcytosine. Methylation of proteins usually occurs on the arginine or lysine amino acid part of the chain. Methylation cause the nucleosomes to be tightly packed to form heterchromatin. This makes it inaccessible for transcription. Tehrefore, genes are not expressed. 
• Protein Acetylation - an acetyl group is added to histones which causes the nucleosomes to pack loosely by reduicing the positive charge of the histones. This forms eurochromatin which makes it  accessible to transcription. Therefore, genes are expressed.

NOTE: Epigenome are chemical tags which determine the shape of the DNA - histone complex.

Tumour - a group of abnormal cells growing uncontrollably. 

Proto-oncogens - stimulates a cell to divide which activate genes that caue DNA to replicate. This could mutate to an ONCOGENE. As a result, the gene could become permanently activated:

• receptor protein on the cell membrane is permanently activated so cell division is switched on always. 
• Oncogene may code for a growth factor that is then produced in excessive amounts. 

Tumour Supressor genes - slows down cell division, repairs DNA mistakes and responsible for programmed cell death (apoptosis)

E.g. TP53 codes for protein P53 which is responsible for apoptosis of a cell with damaged DNA. If it is not functioning properly, cells with damaged DNA would continue to divide. 

Abnormal Methylation of Tumour Suppresor genes: 

• Hypermethylation in the promotor region of the gene so it becomes inactivated. 
• Transcription is prevented 
• Protein to slow down rate of cell division is not synthesised. 
• No control of mitosis. 

Bioinformatics - the science of collecting and analysing complex biological data. 

DNA sequencing  - uses whole genome shotgun (WGS) sequencing. Researcers cut the DNA into small easily sequenced sections and then use computer algorithm to align the entire genome. Researchers have already found over 1.4 million single nucletiode polymorphisms which are associated with disease and disorders. 

Proteome - all the proteins that the genome could code for in a given type of cell or organism at a given time under specific conditions.