Cell Biology I. Overview II. Membranes: How Matter Get in and Out of Cells

1. Cell Biology I. Overview II. Membranes: How Matter Get in and Out of Cells III. Cellular Respiration IV. Photosynthesis V. Protein Synthesis

2. VI. Protein Synthesis A. Overview A T G C T G A C T A C T G T A C G A CT G A T G A C Genes are read by enzymes and RNA molecules are produced… this isTRANSCRIPTION (t-RNA) (r-RNA) U G C U G A C U A C U (m-RNA)

3. VI. Protein Synthesis A. Overview A T G C T G A C T A C T G T A C G A CT G A T G A C Genes are read by enzymes and RNA molecules are produced… this is TRANSCRIPTION (t-RNA) (r-RNA) U G C U G A C U A C U (m-RNA) Eukaryotic RNA and some prokaryotic RNA have regions cut out… this is RNA SPLICING

4. VI. Protein Synthesis A. Overview A T G C T G A C T A C T G T A C G A CT G A T G A C R-RNA is complexed with proteins to form ribosomes. Specific t-RNA’s bind to specific amino acids. (t-RNA) (r-RNA) U G C U G A C U A C U Amino acid (m-RNA) ribosome

5. VI. Protein Synthesis A. Overview A T G C T G A C T A C T G T A C G A CT G A T G A C The ribosome reads the m-RNA. Based on the sequence of nitrogenous bases in the m-RNA, a specific sequence of amino acids (carried to the ribosome by t-RNA’s) is linked together to form a protein. This is TRANSLATION. (t-RNA) (r-RNA) U G C U G A C U A C U Amino acid (m-RNA) ribosome

6. VI. Protein Synthesis A. Overview A T G C T G A C T A C T G T A C G A CT G A T G A C The protein product may be modified (have a sugar, lipid, nucleic acid, or another protein added) and/or spliced to become a functional protein. This is POST-TRANSLATIONAL MODIFICATION. (t-RNA) (r-RNA) U G C U G A C U A C U Amino acid (m-RNA) ribosome glycoprotein

7. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription a. The message is on one strand of the double helix - the sense strand: 3’ 5’ sense A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A nonsense 5’ 3’ “TAG A CAT” message makes ‘sense’ “ATC T GTA” ‘nonsense’ limited by complementation

8. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription a. The message is on one strand of the double helix - the sense strand: 3’ 5’ sense A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A nonsense 5’ 3’ exon intron exon In all eukaryotic genes and in some prokaryotic sequences, there are introns and exons. There may be multiple introns of varying length in a gene. Genes may be several thousand base-pairs long. This is a simplified example!

9. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription b. The cell 'reads' the correct strand based on the location of the promoter, the anti-parallel nature of the double helix, and the chemical limitations of the 'reading' enzyme, RNA Polymerase. Promoter 3’ 5’ sense A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A nonsense 5’ 3’ exon intron exon Promoters have sequences recognized by the RNA Polymerase. They bind in particular orientation.

10. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription b. The cell 'reads' the correct strand based on the location of the promoter, the anti-parallel nature of the double helix, and the chemical limitations of the 'reading' enzyme, RNA Polymerase. Promoter 3’ 5’ sense A C T A T A C G T A C A A A C G G T T A T A C T A C T T T G C A U GUUU G C C A A U AUG A U G A T G A T A T G C A T G T T T G C C A A T A T G A T G A A A nonsense 5’ 3’ exon intron exon • Strand separate • RNA Polymerase can only synthesize RNA in a 5’3’ direction, so they only read the anti-parallel, 3’5’ strand (‘sense’ strand).

11. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription c. Transcription ends at a sequence called the 'terminator'. Promoter Terminator 3’ 5’ sense A C T A T A C G T A C A A A C G G T T A T A C T A C T T T G C A U GUUU G C C A A U AUG A U G A T G A T A T G C A T G T T T G C C A A T A T G A T G A A A nonsense 5’ 3’ exon intron exon Terminator sequences destabilize the RNA Polymerase and the enzyme decouples from the DNA, ending transcription

12. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription c. Transcription ends at a sequence called the 'terminator'. Promoter Terminator 3’ 5’ sense A C T A T A C G T A C A A A C G G T T A T A C T A C T T T G C A U GUUU G C C A A U AUG A U G A T G A T A T G C A T G T T T G C C A A T A T G A T G A A A nonsense 5’ 3’ exon intron exon Initial RNA PRODUCT:

13. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription c. Transcription ends at a sequence called the 'terminator'. Promoter Terminator 3’ 5’ sense A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A nonsense 5’ 3’ exon intron exon Initial RNA PRODUCT: G C A U GUUU G C C A A U AUG A U G A

14. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing G C A U GUUU G C C A A U AUG A U G A exon intron exon Introns are spliced out, and exons are spliced together by an RNA/protein complex called a ‘spliceosome’. Sometimes these reactions are catalyzed by the intron, itself, or other catalytic RNA molecules called “ribozymes”. Initial RNA PRODUCT:

15. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing AUG A G C A U GUUU G C C A A U U G A This final RNA may be complexed with proteins to form a ribosome (if it is r-RNA), or it may bind amino acids (if it is t-RNA), or it may be read by a ribosome, if it is m-RNA and a recipe for a protein. intron exon exon Final RNA PRODUCT:

16. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation a. m-RNA attaches to the ribosome at the 5' end. M-RNA: G C A U G U U U G C C A A U U G A

17. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation a. m-RNA attaches to the ribosome at the 5' end. M-RNA: G C A U G U U U G C C A A U U G A It then reads down the m-RNA, one base at a time, until an ‘AUG’ sequence (start codon) is positioned in the first reactive site.

19. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation a. m-RNA attaches to the ribosome at the 5' end. b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence, binds to the m-RNA/ribosome complex. Meth M-RNA: G C A U G U U U G C C A A U U G A

21. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation a. m-RNA attaches to the ribosome at the 5' end. b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence, binds to the m-RNA/ribosome complex. c. A second t-RNA-AA binds to the second site Meth Phe M-RNA: G C A U G U U U G C C A A U U G A

22. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation a. m-RNA attaches to the ribosome at the 5' end. b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence, binds to the m-RNA/ribosome complex. c. A second t-RNA-AA binds to the second site d. Translocation reactions occur Phe Meth M-RNA: G C A U G U U U G C C A A U U G A The amino acids are bound and the ribosome moves 3-bases “downstream”

23. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation e. polymerization proceeds Ala Asn Meth Phe M-RNA: G C A U G U U U G C C A A U U G A The amino acids are bound and the ribosome moves 3-bases “downstream”

24. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation e. polymerization proceeds Asn Meth Phe Ala M-RNA: G C A U G U U U G C C A A U U G A The amino acids are bound and the ribosome moves 3-bases “downstream”

26. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation e. polymerization proceeds f. termination of translation Meth Phe Ala Asn M-RNA: G C A U G U U U G C C A A U U G A Some 3-base codon have no corresponding t-RNA. These are stop codons, because translocation does not add an amino acid; rather, it ends the chain.

27. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation 4. Post-Translational Modifications Meth Phe Ala Asn Most initial proteins need to be modified to be functional. Most need to have the methionine cleaved off; others have sugar, lipids, nucleic acids, or other proteins are added.