1. Regulating Gene Expression Proteins are not required by all cells at all times Eukaryotes – 4 ways – Transcriptional (as mRNA is being synthesized) – Post- transcriptional (as mRNA is being processed) – Translational (as proteins are made) – Post-translational (after protein has been made)

2. Transcriptional Regulation Activating gene transcription DNA Acetylation DNA wrapped around histones keep gene promoters inactive Activator molecule is used (2 ways) 1. Signals a protein remodelling complex which loosen the histones exposing promoter 2. Signals an enzyme that adds an acetyl group to histones exposing promoter region (acetylation)

3. Transcriptional Regulation Inhibiting gene transcription DNA methylation (Silencing) – Methyl groups are added to the cytosine bases in the promoter of a gene (transcription initiation complex) – Inhibits transcription – silencing – Genes are placed “on hold” until they are needed

4. Post Transcriptional Regulation RBP (RNA binding proteins) Used in: – Pre-mRNA processing – Alternative splicing – Polyadenylation (to 3’ end) Rate of mRNA degradation – Masking proteins used to degrade mRNA – Translation does not occur Hormones – Casein – milk protein in mammary gland – When casein is needed, prolactin is produced extending lifespan of casein mRNA – Translation continues to occur MicroRNA – Produced by DICER protein – Block protein production – Studied for being early cancer detection

5. Translational Regulation Occurs during protein synthesis by a ribosome Polyadenylation – Changes in length of poly(A) tail – Enzymes add or delete adenines – Increases or decreases time required to translate mRNA into protein Deadenylase – Removal of poly (A) tail (polyadenylation) Exonuclease – Degrade mRNA after removal of poly (A) tail

6. Post-Translational Regulation Proteolysis – Removes sections of protein to make it active or inactive Inactivating – Removal of N-methionine Chemical modification – Chemical groups are added or deleted – Puts the protein “on hold” – Phosphorylation Ubiquitination – Proteins tagged with ubiquitin are degraded via proteasome

7. Cancer Lack regulatory mechanisms Mutations in genetic code (mutagens) – Probability increases over lifetime – Radiation, smoking, chemicals Mutations are passed on to daughter cells – Can lead to a mass of undifferentiated cells (tumor) – Benign and malignant Oncogenes – Mutated genes that once served to stimulate cell growth – Cause undifferentiated cell division

8. Genetic Mutations Positive and negative – Natural selection/ evolution – Cancer –death Small-Scale – Single base pair Large-Scale – Multiple base pairs/whole genes

9. Small-Scale Mutations Four groups – Missense, nonsense, silent, frameshift Lactose, sickle cell anemia – SNPs – single nucleotide polymorphisms Caused by point mutations

10. Missense mutation Change of a single base pair or group of base pairs Results in the code for a different amino acid Protein will have different sequence and structure and may be non-functional or function differently

11. Nonsense mutation Change in single base pair or group of base pairs Results in premature stop codon Protein will not be able to function

12. Silent Mutation Change in one or more base pairs Does not affect functioning of a gene Mutated DNA sequence codes for same amino acid Protein is not altered

13. Frameshift mutation One or more nucleotides are inserted/deleted from a DNA sequence Reading frame of codons shifts resulting in multiple missense and/or nonsense effects Any deletion or insertion of base pairs in multiples of 3 does not cause frameshift

14. Large-scale mutations Multiple nucleotides, entire genes, whole regions of chromosomes

15. Large-scale mutations Amplification – gene duplication – Entire genes are copied to multiple regions of chromosomes

16. Large-scale mutations Large-scale deletions – Entire coding regions of DNA are removed Muscular Dystrophy

17. Large-scale mutations Chromosomal translocation – Entire genes or groups of genes are moved from one chromosome to another – Enhance, disrupt expression of gene

18. Large-scale mutations Inversion – Portion of a DNA molecule reverses its direction in the genome – No direct result but reversal could occur in the middle of a coding sequence compromising the gene

19. Causes of genetic mutations Spontaneous mutations – Inaccurate DNA replication Induced mutations – Caused by environmental agent – mutagen – Directly alter DNA – entering cell nucleus – Chemicals, radiation

20. Chemical Mutagens Nitrous Acid – Modify individual nucleotides – Nucleotides resemble other base pairs – Confuses replication machinery – inaccurate copying Ethidium bromide – Used to dye DNA/RNA – insert itself into DNA Aflatoxin produced by aspergillus (fungi) – found in peanut butter, corn – Low levels approved by FDA – Causes mutation of p53 gene (acts as tumor suppressor) – Cancer causing?

21. Radiation - Low energy UV B rays Non-homologous end joining – Bonds form between adjacent nucleotides along DNA strand – Form kinks in backbone – Skin cancer

22. Radiation – high energy Ionizing radiation – x-ray, gamma rays Strip molecules of electrons Break bonds within DNA – Delete portions of chromosomes Development of tumors

23. Large-scale mutations Trinucleotide repeat expansion Increases number of repeats in genetic code CAG CAG CAG CAG CAG CAG CAG CAG Occurs during DNA repair/replication “loop out” structures may form due to repetitive nature of DNA Increase in expansion could cause disease or increase severity of disease – Neuromuscular/ neurodegenerative disorders

24. Transposable Elements (TE) Roughly half the Human Genome is made up TE’s Result in mutation DNA Transposons – Jumping genes “cut and paste” mechanism – Move from one location of the genome to another – Encode protein transposase which is required for insertion and excision – Terminal inverted repeats (9-40) base pairs long – Less than 2% of human genome

25. Transposable Elements (TE) Retrotransposons (RNA transposons) move through action of RNA intermediates Produce RNA transcripts Reverse transcriptase enzymes reverse RNA back to DNA and inserted Give rise to variation in organism Evolution of species 1.LINE – long interspersed transposable elements 6 kilobases long 2.SINE – short interspersed transposable elements (not in humans) Few hundred bases long

26. Genomes and Gene organization Human Body – 22 autosomal chromosomes – 1 pair of each sex chromosome (XX, YY)