Cell Signaling Essentials: Course Overview

1. CELL SIGNALING AND MOTILITY (BIOL 3373) Course Overview Lecture 1

2. LECTURES • Location:Biology Life Sciences, Room Bio133 • Time: Monday 5:00 pm- 7: 30 pm • Instructor • Antonio Giordano, M.D., Ph.D. • Office hours: Friday 12:00–2:00PM. • Biology Life Sciences, Room 431 • By appointment: • Phone 215-204-9520; • email antonio.giordano@temple.edu

3. PREREQUISITE • BIO 3096, Cell Structure and Function • GRADING • The final grade will be based on the score of four examinations that include both group and individuals assignment. Each exam accounts for 25% of the final grade. There will be no make-up tests during the course. If you have a documented medical excuse and you contact me as soon as possible after the emergency, I will arrange a make-up exam. Complaints regarding the grading will not be considered later than two weeks after the test is returned. • TEXT • Molecular Biology of the Cell 6th edition, Alberts et al. Garland Science. Book is available at the Temple Bookstore

4. COURSE DESCRIPTION: • The communication among cells is essential fortheregulationof thedevelopment ofanorganismandforthecontrolofits physiologyandhomeostasis. • Aberrantcellularsignalingeventsareoftenassociated with human pathologicalconditions, suchascancer, neurologicaldisorders, cardiovasculardiseasesand others. • Thefull characterization of cell signaling systems may provide useful insights into the pathogenesis of several human.

6. WHAT IS A CELL ? • A cell is the minimal self-reproducing living organism. • A cell is a vehicle of the hereditary/ genetic information that defines a species. • A cell contains the necessary machinery to construct an identical daughter cell with a complete copy of the hereditary/genetic information

7. PROKARYOTIC CELL • First cell type on earth ( i.e. Bacteria) • No nucleus • DNA is assembled within a region called nucleoide • Organelles are not bound by membranes

8. EUKARYOTIC CELL • fungi, protists, plant and animal cells • DNA is assembled in chromosomes inside the nucleus • Nucleus is surrounded by a membrane. • Possess many organelles

9. Once a Molecular Black Box

10. Today an Open Box Growth factors Hormones Cytoplasm Nucleus

11. How is the genetic information transmitted from one generation to the next? • The hereditary/genetic information is stored in the form of genes in a double-stranded DNA molecule. • Gene: locus (or region) of DNA that encodes a functional RNA or protein product, and is the molecular unit of heredity • DNA replicates a complete copy of itself (DNA REPLICATION) and transfers it to the two daughter cells, during the cell division (MITOSI): DNA DNA REPLICATION DNA DNA MITOSI daughter cells DNA

12. DOGMA DNA – RNA - PROTEIN • DNA is converted into single-stranded RNA (mRNA), that drives the synthesis of proteins • mRNA is converted into proteins.

13. James Dewey Watson is a biologist , who discovered the molecular structure of the DNA. In 1962 Watson was awarded The Nobel Prize in Medicine together with Francis Crick e Maurice Wilkins

14. DNA DOUBLE HELIX

15. DNA and RNA are polynucleotides: Made by molecules blocks called nucleotides. • DNA is made by two polynucleotide strands: • RNA is made by a single polynucleotide strand: Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide

16. Structure of a nucleotide P Pentose sugar: 5 carbon sugar: • Deoxyribose in DNA • ribosein RNA Phosphate groups (P) are important because they link the sugar on one nucleotide onto the phosphate of the next nucleotide to make a polynucleotide Nitrogenous base In DNA the four bases are: • Thymine • Adenine • Cytosine • Guanine In RNA the four bases are: • Uracil • Adenine • Cytosine • Guanine base Pentose sugar

17. Single polynucleotide strand • A single polynucleotide strand is made up by connecting single nucleotides via the phosphate on one nucleotide and the sugar on the next nucleotide

18. Double polynucleotide strand Two polynucleotide strands run in the opposite direction and are held together by hydrogen bonds between the basis

19. Adenine Adenine Thymine Uracil Guanine Cytosine The bases always pair up in the same way: Adenine forms a bond with Thymine in DNA or Uracil in RNA DNA RNA andCytosine bonds with Guanine • This is because the space between the two polynucleotide strands of DNA exactly allocates one purine and one pyrimidine base.

20. DNA DOUBLE HELIX The two polynucleotide strands in DNA molecule are coiled into a spiral called DOUBLE HELIX bases sugar-phosphate chain

21. DNA Replication Before a cell divides, the DNA strands unwind and separate DNA bases on each strand act as a template to synthesize a complementary strand The process is semiconservative because each new double-stranded DNA contains one old strand (template) and one newly-synthesized complementary strand

22. DNA replication is executed by the DNA Polymerase, the enzyme that catalyzes the covalent bond between the phosphate of one nucleotide and the deoxyriboseof the next nucleotide DNA polymerase can only build the new strand in the 5’ to 3’direction. It uses the strand in 3’ to 5’direction as DNA template.

23. 1 PROTEIN SYNTHESIS DNA provides the instructions for how to build proteins: the sequence of nucleotides (AGC) in DNA dictate the order of amino acids that make up a protein Protein synthesis occurs in two primary steps 2

24. There are 3 main types of RNA: • mRNA(messenger RNA): copy of a gene used as a template for protein synthesis • rRNA (ribosomal RNA):participates in the structure of ribosomes together with proteins • tRNA (transfer RNA):functions as amino acid (AA) carrier during the protein synthesis.

25. Eukaryotes: transcription occurs in the nucleus and translation occurs in the cytoplasm Prokaryotes: Transcription and translation occur simultaneously in the cytoplasm

26. RNA TRANSCRIPTION • RNA polymerase enzyme binds to a region on DNA (promoter), which signals the start of a gene. • Transcription factors assemble at the promoter forming a transcription initiation complex • Gene expression can be regulated (turned on/off or up/down) by controlling the amount of each transcription factor 1) INITIATION

27. RNA TRANSCRIPTION 2) ELONGATION RNA polymerase unwinds the DNA and breaks the H-bonds between the bases of the two strands, separating them from one another. Base pairing occurs between incoming RNA nucleotides and the DNA nucleotides of the gene (template)

28. RNA TRANSCRIPTION 3) TERMINATION • A region on DNA known as the terminator signals the stop of a gene • RNA polymerase disengages the mRNA and the DNA

29. RNA ALTERNATIVE SPLICING (eucaryotic only) Exons are “coding” regions Introns are “ non coding” regions • In eucaryotic cells entire gene ( both exons and introns) are transcribed to mRNA. • before protein synthesis introns are removed from the mRNA strand • exons are spliced together forming a mature mRNA that exit the nucleus and assemble with ribosomes in the cytoplasm

30. Transcription tRNA synthesis 1 mRNA • mRNA copy of a gene is synthesized • Cytoplasm of prokaryotes • Nucleus of eukaryotes Translation TRANSLATION 2 mRNA mRNA is used by ribosomes to build proteins Ribosomes attach to the mRNA and use its sequence of nucleotides to determine the order of amino acids in the protein

31. TRANSLATION • Three mRNA nucleotides (codon) specify an amino acid • tRNA have an anticodon region that specifically binds to its codon • Each tRNA carries a specific amino acid. • By using the mRNA as template, tRNAs assemble specific amino acids in a new peptide chain.

32. PROTEIN STRUCTURE • Proteins are made of 20 amino acids linked by peptide bonds • Polypeptide backbone is the repeating sequence of the N-C-C-N-C-C… in the peptide bond • The side chain or R group is not part of the backbone or the peptide bond

33. Amino Acids Hydrophilic Hydrophobic

34. PROTEIN STRUCTURE • Proteins shape is determined by the sequence of the amino acids • The peptide bond allows for rotation around it and therefore the protein can fold and orient the R groups in favorable positions • Weak non-covalent interactions hold the protein in its functional shape • The final shape is called the conformation and has the lowest free energy possible