Cell Biology I. Overview II. Membranes: How Matter Get in and Out of Cells III. Cellular Respiration IV. Photosynthesis V. DNA, RNA, and Chromosome Structure VI. Protein Synthesis

Why is this important? Well…what do proteins DO?

VI. Protein Synthesis Why is this important? Well…what do proteins DO? Think about it this way: 1)sugars, fats, lipids, nucleic acids and proteins, themselves, are broken down and built up through chemical reactions catalyzed by enzymes. 2)So everything a cell IS, and everything it DOES, is either done by proteins or is done by molecules put together by proteins.

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 U G C U G A C U A C U (m-RNA) (r-RNA) (t-RNA)

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 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 (r-RNA) (t-RNA)

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

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 U G C U G A C U A C U (m-RNA) (r-RNA) (t-RNA) 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. ribosome Amino acid

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 U G C U G A C U A C U (m-RNA) (r-RNA) (t-RNA) 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. ribosome Amino acid glycoprotein

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’ “TAG A CAT” message makes ‘sense’ “ATC T GTA” ‘nonsense’ limited by complementation 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 sense nonsense

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’ 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! 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 sense nonsense intronexon

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. 3’ 5’ Promoters have sequences recognized by the RNA Polymerase. They bind in particular orientation. 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 sense nonsense intronexon Promoter

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. 3’ 5’ 1)Strand separate 2)RNA Polymerase can only synthesize RNA in a 5’  3’ direction, so they only read the anti-parallel, 3’  5’ strand (‘sense’ strand). 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 sense nonsense intronexon Promoter G C A U GUUU G C C A A U AUG A U G A

VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription c. Transcription ends at a sequence called the 'terminator'. Terminator sequences destabilize the RNA Polymerase and the enzyme decouples from the DNA, ending transcription 3’ 5’ 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 sense nonsense intronexon Promoter G C A U GUUU G C C A A U AUG A U G A Terminator

VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription c. Transcription ends at a sequence called the 'terminator'. 3’ 5’ 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 sense nonsense intronexon Promoter G C A U GUUU G C C A A U AUG A U G A Terminator Initial RNA PRODUCT:

VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription c. Transcription ends at a sequence called the 'terminator'. 3’ 5’ 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 sense nonsense PromoterTerminator intronexon G C A U GUUU G C C A A U AUG A U G A Initial RNA PRODUCT:

VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing intronexon Initial RNA PRODUCT: Introns are spliced out, and exons are spliced together. Sometimes these reactions are catalyzed by the intron, itself, or other catalytic RNA molecules called “ribozymes”. G C A U GUUU G C C A A UAUG AU G A

VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing intron exon Final RNA PRODUCT: 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. G C A U GUUU G C C A A U AUG A U G A

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 UU G A

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 UU 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.

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. M-RNA:G C A U G U U U G C C A A UU G A Meth

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 M-RNA:G C A U G U U U G C C A A UU G A MethPhe

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 M-RNA:G C A U G U U U G C C A A UU G A Meth Phe The amino acids are bound and the ribosome moves 3-bases “downstream”

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

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

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 M-RNA:G C A U G U U U G C C A A UU 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. MethPheAlaAsn

VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation 4. Post-Translational Modifications 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. MethPheAlaAsn

VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription - DNA bound to histones can’t be accessed by RNA Polymerase - but the location of histones changes, making genes accessible (or inaccessible) Initially, the orange gene is “off”, and the green gene is “on” Now the orange gene is “on” and the green gene is “off”.

VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 3’ 5’ Transcription factors can inhibit or encourage the binding of the RNA Polymerase. And, through signal transduction, environmental factors can influence the activity of these transcription factors. So cells can respond genetically to changes in their environment. 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 sense nonsense intronexon Promoter RNA POLY

VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 2. Transcript Processing intronexon Initial RNA PRODUCT: Mi-RNA’s and si-RNA’s are small RNA molecules that can bind to m-RNA and disrupt correct spicing, creating non-functional m-RNA’s. G C A U GUUU G C C A A UAUG AU G A U A U A Cut not made

M-RNA:G C A U G U U U U G A A A UU G A Incorrect splicing can result in a ‘premature’ stop codon, terminating translation early, resulting in a non-functional protein. MethPhe VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 2. Transcript Processing 3. Regulating Translation

The patterns of cleavage and modification can vary. MethPheAlaAsn VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 2. Transcript Processing 3. Regulating Translation 4. Regulating Post-Translational Modification

VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 2. Transcript Processing 3. Regulating Translation 4. Regulating Post-Translational Modification Protein ? Affected by other genes Affected by other cells Affected by the environment Gene activity is responsive to cellular and environmental cues