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

V. Protein Synthesis A. DNA/RNA Structure DNA is the genetic material in all forms of life (eubacteria, archaea, protists, plants, fungi, and animals). - genetic information (recipe for proteins) RNA performs a wide array of functions: - genetic information (copy of recipe) - enzymatic function - regulatory function

V. Protein Synthesis A. DNA/RNA Structure 1. Monomers are “nucleotides” - 3 parts: - sugar

V. Protein Synthesis A. DNA/RNA Structure 1. Monomers are “nucleotides” - 3 parts: - sugar, “nitrogenous base”

1. Monomers are “nucleotides” - 3 parts: - sugar, “nitrogenous base” V. Protein Synthesis A. DNA/RNA Structure 1. Monomers are “nucleotides” - 3 parts: - sugar, “nitrogenous base” Nitrogenous base binds to the 1’ carbon

1. Monomers are “nucleotides” - 3 parts: V. Protein Synthesis A. DNA/RNA Structure 1. Monomers are “nucleotides” - 3 parts: - sugar, “nitrogenous base”, phosphate Nitrogenous base binds to the 1’ carbon

1. Monomers are “nucleotides” DNA/RNA Structure 1. Monomers are “nucleotides” 2. Polymerization by dehydration synthesis OH OH O-P-O O H2O OH Energy released by cleaving the diphosphate group can be used to power the dehydration synthesis reaction

DNA/RNA Structure 1. Monomers are “nucleotides” 2. Polymerization by dehydration synthesis 3. DNA strands are antiparallel and complementary

1. Monomers are “nucleotides” DNA/RNA Structure 1. Monomers are “nucleotides” 2. Polymerization by dehydration synthesis 3. DNA strands are antiparallel and complementary 4. RNA is made as a single strand, but can loop back upon itself to make double-stranded regions. A C G U A C A U G C A U G A

Ribosomal RNA (r-RNA) is bound to proteins in a RIBOSOME Messenger RNA (m-RNA) is a copy of a DNA protein recipe that is ‘read’ by a ribosome, and particular AA’s are linked together there. 5’ 3’ | | | | | | | | | | | | A C G C C A U C U A C C … Transfer RNA (t-RNA) attaches to free amino acids and transports them to the ribosome for polymerization into proteins

FUNCTIONS OF NUCLEIC ACIDS: PROTEIN SYNTHESIS CATALYZE REATIONS (RNA ONLY: “RIBOZYMES”) REGULATION OF GENE ACTIVITY AND EXPRESSION - TURNING GENES ON AND OFF - REGULATING THE PROTEIN PRODUCT MADE FROM A GENE

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)

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

R-RNA is complexed with proteins to form ribosomes. 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

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

POST-TRANSLATIONAL MODIFICATION. (t-RNA) (r-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 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

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

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!

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.

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).

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

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:

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’ intron exon 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 intron exon Initial RNA PRODUCT: G C A U GUUU G C C A A U AUG A U G A 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”.

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

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

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.

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

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 Phe Meth M-RNA: G C A U G U U U G C C A A U 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. 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 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”

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”

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”

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.

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.

mitosis Gene Regulation A. Overview All cells in an organism contain the same genetic information; the key to tissue specialization is gene regulation – reading some genes in some cells and other genes in other cells. zygote mitosis

C. Regulation of Protein Synthesis 1. Regulation of Transcription a. CHROMOSOME ARCHITECTURE - 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”.

C. Regulation of Protein Synthesis 1. Regulation of Transcription a. CHROMOSOME ARCHITECTURE b. Proteins that REPRESSOR or INDUCE transcription (more tomorrow) 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 RNA POLY Proteins can inhibit or encourage the binding of the RNA Polymerase. And, through signal transduction, environmental factors can influence the activity of these proteins. So cells can respond genetically to changes in their environment.

VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 2. Transcript Processing intron exon Initial RNA PRODUCT: G C A U GUUU G C C A A U A UG A C C C… Proteins can bind to m-RNA and change splicing patterns. This can turn protein synthesis off completely …. (here, a UGA is retained and stops synthesis prematurely…..)

VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 2. Transcript Processing Or, a different combination of exons are spliced together…resulting in DIFFERENT PROTEINS produced from the SAME GENE. A calcium regulator in the thyroid Initial m-RNA A hormone made in the brain

VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 2. Transcript Processing Ds-RNA intron exon Initial RNA PRODUCT: G C A U GUUU G C C A A U A UG A U G A… C G G U Or, micro-RNA’s (mi-RNA’s) can bind to the m-RNA. These are recognized by other enzymes and are cleaved incorrectly, Or simply block the ribosome from translating the sequence.

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 Meth Phe Ala Asn The patterns of cleavage and modification can vary.

PROCESS REGULATION GENE In DNA Transcription: DNA is read RNA is made Chromosome architecture or protein binding enhances or represses RNA polymerase activity 2) RNA Splicing: Introns cut out exons spliced together Proteins binding to sites may enhance or inhibit spliceosome and change splicing pattern 3) Translation: Amino acids joined based on codon sequence in m-RNA mi-RNA binding may stimulate incorrect splicing and m-RNA destruction, or block ribosome: no protein produced either way 4) Post-translational Processing: Protein spliced; molecules added Other enzymes present determine how the protein is modified PROTEIN