Objectives: Be familiar with the various subcellular compartments in eucaryotic cells.

1. Objectives: Be familiar with the various subcellular compartments in eucaryotic cells.

2. Objectives: Be familiar with the various subcellular compartments in eucaryotic cells. Know types of proteins that would be found in the different subcellular compartments.

3. Objectives: Be familiar with the various subcellular compartments in eucaryotic cells. Know types of proteins that would be found in the different subcellular compartments. Use PubMed to find an article about proteins present in bacteria

4. Objectives: Be familiar with the various subcellular compartments in eucaryotic cells. Know types of proteins that would be found in the different subcellular compartments. Use PubMed to find an article about proteins present in bacteria Recognize amino acids by their single letter codes.

5. Objectives: Be familiar with the various subcellular compartments in eucaryotic cells. Know types of proteins that would be found in the different subcellular compartments. Use PubMed to find an article about proteins present in bacteria Recognize amino acids by their single letter codes. Identify positive, negative or hydrophobic amino acid residues in a protein sequence.

6. Objectives: Be familiar with the various subcellular compartments in eucaryotic cells. Know types of proteins that would be found in the different subcellular compartments. Use PubMed to find an article about proteins present in bacteria Recognize amino acids by their single letter codes. Identify positive, negative or hydrophobic amino acid residues in a protein sequence. Recognize patterns of amino acid residues that serve as signals to target proteins to subcellular locations.

7. Objectives: Be familiar with the various subcellular compartments in eucaryotic cells. Know types of proteins that would be found in the different subcellular compartments. Use PubMed to find an article about proteins present in bacteria Recognize amino acids by their single letter codes. Identify positive, negative or hydrophobic amino acid residues in a protein sequence. Recognize patterns of amino acid residues that serve as signals to target proteins to subcellular locations. Use amino acid sequence information to identify a protein in the NCBI data bases.

8. Objectives: Be familiar with the various subcellular compartments in eucaryotic cells. Know types of proteins that would be found in the different subcellular compartments. Use PubMed to find an article about proteins present in bacteria Recognize amino acids by their single letter codes. Identify positive, negative or hydrophobic amino acid residues in a protein sequence. Recognize patterns of amino acid residues that serve as signals to target proteins to subcellular locations. Use amino acid sequence information to identify a protein in the NCBI data bases. Use computational tools to predict the subcellular location for a protein of given sequence (homework)

9. M-M-S-F-V-S-L-L-L-V-G-I-L-F-W-A-T-E-A-E-Q-L-T-K-C-E-V-F-Q- What does this mean in the language of proteins?

10. M-M-S-F-V-S-L-L-L-V-G-I-L-F-W-A-T-E-A-E-Q-L-T-K-C-E-V-F-Q- What does this mean in the language of proteins? What would be the subcellular location of a protein with this sequence of amino acids?

11. M-M-S-F-V-S-L-L-L-V-G-I-L-F-W-A-T-E-A-E-Q-L-T-K-C-E-V-F-Q- What does this mean in the language of proteins? What would be the subcellular location of a protein with this sequence of amino acids? How would such a protein be delivered to its final location?

12. M-M-S-F-V-S-L-L-L-V-G-I-L-F-W-A-T-E-A-E-Q-L-T-K-C-E-V-F-Q- What does this mean in the language of proteins? What would be the subcellular location of a protein with this sequence of amino acids? How would such a protein be delivered to its final location? First lets review the possible locations in a cell ---> ---->

14. Pathway to secretion of the protein to the outside of the cell. For example, secretion of a digestive enzyme such a lipase from a cell in the pancreas. • Transcription of the mRNA that codes for the protein from DNA in the nucleus.

15. Pathway to secretion of the protein to the outside of the cell. For example, secretion of a digestive enzyme such a lipase from a cell in the pancreas. • Transcription of the mRNA that codes for the protein from DNA in the nucleus. • Export of the mRNA from the nucleus through pores in the nuclear envelope.

16. Pathway to secretion of the protein to the outside of the cell. For example, secretion of a digestive enzyme such a lipase from a cell in the pancreas. • Transcription of the mRNA that codes for the protein from DNA in the nucleus. • Export of the mRNA from the nucleus through pores in the nuclear envelope. • Translation of the mRNA on ribosomes on rough Endoplasmic Reticulum (ER) to make the protein.

17. Pathway to secretion of the protein to the outside of the cell. For example, secretion of a digestive enzyme such a lipase from a cell in the pancreas. • Transcription of the mRNA that codes for the protein from DNA in the nucleus. • Export of the mRNA from the nucleus through pores in the nuclear envelope. • Translation of the mRNA on ribosomes on rough Endoplasmic Reticulum (ER) to make the protein. •The protein is threaded into the lumen of the ER because of signal sequence of amino acids (blue) near amino terminus of the protein.

18. Pathway to secretion of the protein to the outside of the cell. For example, secretion of a digestive enzyme such a lipase from a cell in the pancreas. • Transcription of the mRNA that codes for the protein from DNA in the nucleus. • Export of the mRNA from the nucleus through pores in the nuclear envelope. • Translation of the mRNA on ribosomes on rough Endoplasmic Reticulum (ER) to make the protein. •The protein is threaded into the lumen of the ER because of signal sequence of amino acids (blue) near amino terminus of the protein. •The protein is passed on to the Golgi.

19. Pathway to secretion of the protein to the outside of the cell. For example, secretion of a digestive enzyme such a lipase from a cell in the pancreas. • Transcription of the mRNA that codes for the protein from DNA in the nucleus. • Export of the mRNA from the nucleus through pores in the nuclear envelope. • Translation of the mRNA on ribosomes on rough Endoplasmic Reticulum (ER) to make the protein. •The protein is threaded into the lumen of the ER because of signal sequence of amino acids (blue) near amino terminus of the protein. •The protein is passed on to the Golgi. •The protein is enclosed in a membrane vesicle which leaves the Golgi and takes it to the Plasma Membrane (PM)

20. Pathway to secretion of the protein to the outside of the cell. For example, secretion of a digestive enzyme such a lipase from a cell in the pancreas. • Transcription of the mRNA that codes for the protein from DNA in the nucleus. • Export of the mRNA from the nucleus through pores in the nuclear envelope. • Translation of the mRNA on ribosomes on rough Endoplasmic Reticulum (ER) to make the protein. •The protein is threaded into the lumen of the ER because of signal sequence of amino acids (blue) near amino terminus of the protein. •The protein is passed on to the Golgi. •The protein is enclosed in a membrane vesicle which leaves the Golgi and takes it to the Plasma Membrane (PM) •The membrane of the vesicle fuses with the PM releasing the protein to the outside of the cell (eg., lipase secreted from pancreatic cells)

21. Figure 7.16 Review: relationships among organelles of the endomembrane system 

26. Proteins that follow this ER/Golgi pathway can also go to - Plasma Membrane, eg. Integrins Integrins are proteins that recognize other cells, cause cells to stick together.

27. Human diseases result from defects in integrin genes. A defect in integrin beta3 causes prolonged bleeding, because blood plateletes can’t stick together. Glanzman's Thrombasthenia. With defects in either alpha6 or beta4 integrin skin cells cannot stick together well. Patients are born with blistering epidermis and also have blisters within the mouth and digestive tract...depending on the severity of the disease. Some die within days and others live.Junctional epidermolysis bullosa

28. Proteins that follow this ER/Golgi pathway can also go to - Plasma Membrane, eg. Integrins Integrins are proteins that recognize other cells, cause cells to stick together. Lysosomes, Hydrolases. Hydrolases are digestive enzymes that use water to break apart molecules such as proteins, DNA, lipids, polysaccharides.

29. Proteins that follow this ER/Golgi pathway can also go to - Plasma Membrane, eg. Integrins Integrins are proteins that recognize other cells, cause cells to stick together. Lysosomes, Hydrolases. Hydrolases are digestive enzymes that use water to break apart molecules such as proteins, DNA, lipids, polysaccharides. Defects in lysosomal genes result in “storage diseases” If a hydrolase is defective the molecules it digests accumulate in lysosomes.

30. Other proteins are translated from their respective mRNA’s in the cytosol and then delivered to different subcellular locations: Mitochondria Peroxisomes Chloroplasts (in plant cells) - Nucleus Or some remain in the cytosol - What types of proteins go to these different locations and what information directs them to those locations?

31. Mitochondria - e.g., Dehydrogenases Peroxisomes - e.g., Oxidases Chloroplasts (in plant cells) - proteins of photosynthesis Nucleus - e.g., proteins that replicate DNA or regulate genes Cytosol - e.g., enzymes that metabolize glucose

32. Do all cells have all these different proteins and subcellular compartments? Eucaryotes Animals, flies, worms, yeast cells have these compartments and many proteins that are homologous.

33. Do all cells have all these different proteins and subcellular compartments? Eucaryotes Animals, flies, worms, yeast cells have these compartments and many proteins that are homologous. Plant cells have all the compartments plus chloroplasts and a central vacuole.

34. Do all cells have all these different proteins and subcellular compartments? Eucaryotes Animals, flies, worms, yeast cells have these compartments and many proteins that are homologous. Plant cells have all the compartments plus chloroplasts and a central vacuole. Procaryotes Bacterial cells do not have the compartments and have fewer genes, fewer proteins.

35. Do all cells have all these different proteins and subcellular compartments? Eucaryotes Animals, flies, worms, yeast cells have these compartments and many proteins that are homologous. Plant cells have all the compartments plus chloroplasts and a central vacuole. Procaryotes Bacterial cells do not have the compartments and have fewer genes, fewer proteins. Each cell of an organism has DNA that encodes all the possible genes for that organism. Are all the possible proteins present in every cell of the organism?

36. Questions about the genome in an organism: How much DNA, how many nucleotides? How many genes are there? What types of proteins appear to be coded by these genes?

37. Questions about the proteome: What proteins are present? Where are they? When are they present - under what conditions?

38. Questions about the proteome: What proteins are present? Where are they? When are they present - under what conditions? What other proteins and molecules does each protein interact with? It depends on the type of cell, bacteria, yeast, worm, fly, plant, human

39. Animal cell - is a EUCARYOTE

40. Animal cell - is a EUCARYOTE - has a nucleus and other membrane enclosed subcellular compartments, mitochondria, peroxisomes, etc.

41. Plant cell - is also a EUCARYOTE - has a nucleus, mitochondria, peroxisomes, plus chloroplasts, central vacuole.

42. Vibrio cholerae - causes cholera ATP drive motor protein complex E. Coli - normal inhabitant of human gut Bacterial cells - are PROCARYOTES

43. Vibrio cholerae - causes cholera ATP drive motor protein complex E. Coli - normal inhabitant of human gut Bacterial cells - are PROCARYOTES - NO nucleus, NO membrane enclosed subcellular compartments, NO mitochondria, NO peroxisomes, etc.

44. E. coli genome • 4,639,221 nucleotide pairs • Protein-coding genes yellow or orange bars • genes coding only RNA green arrows What are all the different types of RNAs?

45. Organism Genome size Estimated number Type of . (Megabases, 10^6) of genes Organism . H. influenzae 1.8 Mb 1700 Procaryote, (bacterium) no nucleus

46. Organism Genome size Estimated number Type of . (Megabases, 10^6) of genes Organism . H. influenzae 1.8 Mb 1700 Procaryote, (bacterium) no nucleus S. cerevisae 12 Mb 6000 Eucaryote, (Yeast) Unicellular

47. Organism Genome size Estimated number Type of . (Megabases, 10^6) of genes Organism . H. influenzae 1.8 Mb 1700 Procaryote, (bacterium) no nucleus S. cerevisae 12 Mb 6000 Eucaryote, (Yeast) Unicellular C. elegans 97 Mb 19,000 Eucaryote, (nematode worm) Multicellular

48. Organism Genome size Estimated number Type of . (Megabases, 10^6) of genes Organism . H. influenzae 1.8 Mb 1700 Procaryote, (bacterium) no nucleus S. cerevisae 12 Mb 6000 Eucaryote, (Yeast) Unicellular C. elegans 97 Mb 19,000 Eucaryote, (nematode worm) Multicellular Arabidopsis 100 Mb 25,000 Eucaryote (plant) Multicellular

49. Organism Genome size Estimated number Type of . (Megabases, 10^6) of genes Organism . H. influenzae 1.8 Mb 1700 Procaryote, (bacterium) no nucleus S. cerevisae 12 Mb 6000 Eucaryote, (Yeast) Unicellular C. elegans 97 Mb 19,000 Eucaryote, (nematode worm) Multicellular Arabidopsis 100 Mb 25,000 Eucaryote (plant) Multicellular Drosophila 180 Mb 13,000 Eucaryote (fruit fly) Multicellular

50. Organism Genome size Estimated number Type of . (Megabases, 10^6) of genes Organism . H. influenzae 1.8 Mb 1700 Procaryote, (bacterium) no nucleus S. cerevisae 12 Mb 6000 Eucaryote, (Yeast) Unicellular C. elegans 97 Mb 19,000 Eucaryote, (nematode worm) Multicellular Arabidopsis 100 Mb 25,000 Eucaryote (plant) Multicellular Drosophila 180 Mb 13,000 Eucaryote (fruit fly) Multicellular Homo sapiens 3200 Mb 40,000 Eucaryote (human) Multicellular