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http://members.aol.com/wayneheim/dna-w.jpg P P P P P P P P S A S T S G S C S T S C S G S T T S A S C S G S A S G S C S A S P Key Points : P P P P P P P 1) Double Helix 2) Sugar-phosphate backbone 3) Nucleotide Rungs 4) Hydrogen bonds DNA Nucleotides: Adenine Cytosine Thymine Guanine Complementary Base Pairing: DNA A G T C RNA: Ribonucleic Acid 1) Single stranded (usually) 2) Nucleotide Uracil replaces Thymine 3) Four species (for this course): 3.1) messenger RNA (mRNA) 3.2) ribosomal RNA (rRNA) 3.3) transfer RNA (tRNA) 3.4) “interfering” RNA (iRNA) Complementary Base Pairing: RNA A G U C DNA Packaging: (a) the nucleosome: DNA wraps around histone proteins. (b) solenoids: loop of nucleosomes. Histone protein complex DNA (c): solenoids form a loop. (d): idealized cross (e): portion of a chromosome section of a chromosome: without the protein scaffold. several solenoid loops. http://users.ntua.gr/sofial/DNA.jpg (a) DNA replication: strands separate A A T G C A G G T T T A C G T C C A (b) Synthesis of new, complementary strands. Replication “Stuff” A A T G C A G G T T T A C G T C C A Terms Amino acid = basic building block of polypeptide chains. Phe Tyr Ser Try Polypeptide chain = series of linked amino acids. AKA peptide chain. Arg Ser Ala Phe Phe Tyr Protein = one or more polypeptide chains, folded and taking on a 3 dimensional configuration. Enzyme = a type of protein that speeds up chemical reactions. Genetic Code (mRNA) 1) Triplet 2) Redundant 3) Universal http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPROTSYn.html Five Steps in Protein Synthesis (PETAP): 1) Photocopying 2) Editing 3) Transportation 4) Assembly 5) Packaging Five Steps in Protein Synthesis (PETAP): Common Sense Terms Scientificese 1) Photocopying = Transcription 2) Editing = Post-transcriptional modification 3) Transportation = Transportation 4) Assembly = Translation 5) Packaging = Post-translational modification I. Photocopying (Transcription) Definition: An RNA strand is synthesized from the DNA using complementary base pairing. Process: 1) “Transcription stuff” binds to a promoter region of the DNA. 2) An enzyme “slices” the DNA, making it single stranded. 3) Another enzyme (polymerase) synthesizes a strand of RNA using one of the DNA strands as a template. Transcription “Stuff” C A C A A G T T A T G C G G T A RNA transcript U A C G U C DNA G C A G U A A II. Editing (Post-transcriptional modification) Definition: Nonmessage segments in the newly synthesized RNA strand are edited out. Process: 1) Enzymes excise the introns (nonmessage segments) from the RNA strand. 2) Other enzymes splice together the exons (message segments) giving messenger RNA (mRNA). Punctuation marks exon 1 Punctuation marks RNA transcript: intron 1 exon 2 intron 2 exon 3 exon 2 intron 2 exon 3 Editing: exon 1 intron 1 Punctuation marks exon 1 mRNA messemger RNA exon 2 Punctuation marks exon 3 III. Transportation (Transportation) Definition: mRNA is transported from the nucleus to the cytoplasm and attaches to a ribosome. Process: (same as the definition) IV. Assembly (Translation) Definition: The mRNA codons are “read” and the corresponding amino acid is added to the polypeptide chain. Process: 1) A codon enters the “reading frame” of a ribosome. 2) A transfer RNA (tRNA) molecule with the complementary anticodon binds to the codon of mRNA. 3) The amino acid carried by the tRNA molecule is added to the polypeptide chain. 3) Steps 1 to 3 are repeated until all codons are “read.” Transfer RNA (schematic) anticodon “bar code” A C other RNA amino acid Trp C ribosome mRNA U U U A C G C G G U C U A A A U G C Phe U U U A C G C G G U C U U G C G C C A A A Thr Phe Thr A G A G C C peptide chain A G A Ser Arg tRNA Arg Ser A C C Trp http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPROTSYn.html http://tidepool.st.usm.edu/pix/protsynth.gif Posttranslational Modification: ALWAYS HAPPENS Polypeptide Folding Posttranslational Modification: Sometimes happens • Folded polypeptide chains join (e.g., ALDH-2, hemoglobin) • add a sugar • add a fat Posttranslational Modification: Protein Activation/Deactivation • Phosphorylation (add a phoshate group) • Acetylation (add an acetyl group) • Alkylation (add a ethyl, methyl group) • Ubiquitination (add the protein ubiquitin to an existing protein usually instructs the cellular machinery to degrade/destroy the protein) length in kilobases (kb): 0 10 20 b-like gene cluster on chromosome 11: yb 2 Promoters: TATA CAAT e Gg ATG: Start Translation Here 1 Ag 40 50 yb 1 60 b d TAA: Stop Translation Here Blow up of the b hemoglobin gene: Exon 1 ACATTG: Start transscription here 30 Intron 1 30 Exon 2 31 Intron 2 104 CodonNumber: Blow up of Exon 1 of the b hemoglobin gene: Nucleotides: GTGCACCTGACTCCTGAGGAGAAGTTGGCC..AGG Amino Acids: Val His Leu Thr Pro Glu Glu Lys Ser Ala.. Arg Exon 3 105 Attach a tail of multiple adenines here 146 CATTGC: Stop transscription here length in kilobases (kb): 0 5 10 15 a-like gene cluster on chromosome 16: z2 z1 20 ya 1 25 a2 a1 Open window (A) and fly kite (B). String (C) lifts small door (D) allowing moths (E) to escape and eat red flannel shirt (F). As weight of shirt becomes less, shoe (G) steps on switch (H) which heats electric iron (I) and burns hole in pants (J). Smoke (K) enters hole in tree (L), smoking out opossum (M) which jumps into basket (N), pulling rope (O) and lifting cage (P), allowing woodpecker (Q) to chew wood from pencil (R), exposing lead. Emergency knife (S) is always handy in case opossum or the woodpecker gets sick and can't work. The Self-Operating Napkin: As you raise spoon of soup (A) to your mouth it pulls string (B), thereby jerking ladle (C) which throws cracker (D) past parrot (E). Parrot jumps after cracker and perch (F) tilts, upsetting seeds (G) into pail (H). Extra weight in pail pulls cord (I), which opens and lights automatic cigar lighter (J), setting off sky-rocket (K) which causes sickle (L) to cut string (M) and allow pendulum with attached napkin to swing back and forth thereby wiping off your chin.