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Understanding Protein Synthesis: RNA's Role in Genetic Instructions

Learn the process of protein synthesis through RNA, from transcription to translation. Explore RNA's function in linking DNA's genetic instructions to protein production. Discover the significance of nucleotide triplet codons and the stages of transcription. Dive into RNA processing and splicing, understanding terminations, capping, and tailing. Watch informative videos for a comprehensive grasp of protein synthesis.

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Understanding Protein Synthesis: RNA's Role in Genetic Instructions

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  1. PROTEIN SYNTHESIS CHAPTER 17

  2. PROTEIN SYNTHESIS OVERVIEW • RNA LINKS DNA’S GENETIC INSTRUCTIONS FOR MAKING PROTINS TO THE PROCESS OF PROTEIN SYNTHESIS • RNA COPIES (TRANSCRIBES) THE MESSAGE FROM DNA AND THEN TRANSLATES THAT MESSAGE INTO A PROTEIN • THE LINEAR SEQUENCE OF NUCLEOTIDES IN DNA DETERMINES THE LINEAR SEQUENCE OF AMINO ACIDS IN A PROTEIN • 3STEPS: TRANSCRIPTION, RNA PROCESSSING, TRANSLATION

  3. VIDEO: PROTEIN SYNTHESIS OVERVIEW

  4. NUCLEOTIDE TRIPLET CODONS • CODON = A THREE NUCLEOTIDE SEQUENCE IN mRNA THAT SPECIFIES WHICH AMINO ACID WILL BE ADDED TO THE GROWING POLYPEPTIDE CHAIN • READING FRAME = THE CORRECT GROUPING OF ADJACENT NUCLEOTIDE TRIPLETS INTO CODONS THAT ARE IN THE CORRECT SEQUENCE ON THE mRNA

  5. THE TRIPLET CODON

  6. DICTIONARY OF THE GENETIC CODE

  7. TRANSCRIPTION • TRANSCRIPTION = THE SYNTHESIS OF RNA USING DNA AS A TEMPLATE • TRANSCRIPTION OF MESSENGER (mRNA) FROM TEMPLATE DNA IS CATALYZED BY RNA POLYMERASES WHICH: • 1) SEPARATE THE TWO DNA STRAND AND LINK RNA NUCLEOTIDES AS THEY BASE-PAIR ALONG THE DNA TEMPLATE • 2) ADD NUCLEOTIDES ONLY TO THE 3’ END; THUS, mRNA MOLECULES GROW IN THE 5’ TO 3’ DIRECTIONS • ** TRANSCRIPTION OCCURS IN 3STAGES: A) POLYMERASE BINDING AND INITIATION; B) ELONGATION; AND C) TERMINATION

  8. RNA POLYMERASE BINDING AND INIATION • RNA POLYMERASES BIND TO DNA AT REGIONS CALLED PROMOTERS • PROMOTERS = REGION OF DNA THAT INCLUDES THE SITE WERE RNA POLYMERASE BINDS AND WHERE TRANSCRIPTION BEGINS; ABOUT 100 NUCLEOTIDES LONG • TRANSCRIPTION FACTORS = DNA BINDING PROTEINS WHICH BIND TO SPECIFIC DNA NUCLEOTIDE SEQUENCES AT THE PROMOTER AND HELP RNA POLYMERASE RECOGNIZE AND BIND TO THE PROMOTER REGION SO TRANSCRIPTION CAN BEGIN

  9. ELONGATION OF RNA • ONCE TRANSCRIPTION BEGINS, RNA POLYMERASE II MOVES ALONG DNA AND PERFORMS TWO FUNCTIONS: • 1) IT UNTWISTS AND OPENS A SHORT SEGMENT OF DNA EXPOSING ABOUT TEN NUCLEOTIDE BASES; ONE OF THE EXPOSED DN STRAND IS THE TEMPLATE FOR BASE-PAIRING WITH RNA NUCLEOTIDES • 2) IT LINKS INCOMING RNA NUCLEOTIDES TO THE 3’ END OF THE STRAND, THUS RNA GROWS ONE NUCLEOTIDE AT A TIME IN THE 5’ TO 3’ DIRECTION

  10. ELONGATION OF RNA • DURING TRANSCRIPTION, mRNA GROWS ABOUT 30 TO 60 NUCLEOTIDES PER SECOND. AS THE mRNA STRAND ELONGATES: • 1) IT PEELS AWAY FROM ITS DNA TEMPLATE • 2) THE NONTEMPLATE STRAND OF DNA RE-FORMS A DNA-DNA DOUBLE HELIX BY PAIRING WITH TEMPLATE STRAND • 3) SEVERAL RNA POLYMERASE II MOLECULES CAN SIMULANEOUSLY TRANSCRIBE THE SAME GENE; THUS, CELLS CAN PRODUCE PARTICULAR PROTEINS IN LARGE AMTS.

  11. TERMINATION OF TRANSCRIPTION • TRANSCRIPTION PROCEEDS UNTIL RNA POLYMERASE TRANSCRIBES A DNA SEQUENCE CALLED A TERMINATOR. THIS SIGNALS THE END OF THE TRANSCRIPTION PROCESS

  12. TRANSCRIPTION VIDEO

  13. STAGES OF TRANSCRIPTION

  14. RNA PROCESSING • RNA TRANSCRIPTS IN EUKARYOTES ARE PROCESSED BEFORE LEAVING THE NUCLEUS TO YIELD FUNCTIONAL mRNA. THIS PROCESSING CAN BE DONE IN 2 WAYS: • 1) COVALENT ALTERATION OF BOTH THE 3’ AND 5’ ENDS • 2) REMOVAL OF INTERVENING SEQUENCES

  15. RNA PROCESSING • PRIMARY TRANSCRIPT = GENERAL TERM FOR INITIAL RNA TRANSCRIBED BY DNA • PRE-mRNA = PRIMARY TRANSCRIPT THAT WILL BE PROCESSED TO FUNCTIONAL MRNA

  16. ADDITION OF 5’ CAP • 5’ CAP = MODIFIED GUANINE NUCLEOTIDE THAT IS ADDED TO THE 5’ END OF MRNA SHORTLY AFTER TRANSCRIPTION BEGINS. IT HAS 2 IMPORTANT FUNCTIONS: • 1) PROTECTS THE GROWING mRNA FROM DEGRADATION BY HYDROLYTIC ENZYMES • 2) HELPS SMALL RIBOSOMAL SUBUNITS RECOGNIZE THE ATTACHMENT SITE ON mRNA’S 5’ END. A LEADER SEGMENT OF mRNA MAY ALSO BE PART OF THE RIBOSOME RECOGNITION SIGNAL • LEADER SEQUENCE = NONCODING (UNTRANSLATED) SEQUENCE OF mRNA FROM THE 5’ END TO THE START CODON

  17. ADDITION OF 5’ CAP AND POLY(A) TAIL

  18. ADDITION OF POLY(A) TAIL • THE 3’ END, WHICH IS TRANSCRIBED LAST, IS MODIFIED BY ENZYMATIC ADDITION OF A POLY-A TAIL, BEFORE THE mRNA EXITS THE NUCLEUS • POLY(A) TAIL = SEQUENCE OF ABOUT 30 TO 200 ADENINE NUCLEOTIDES ADDED TO THE 3’ END OF mRNA • MAY INHIBIT DEGRADATION OF mRNA IN THE CYTOPLASM • MAY FACILITATE ATTACHMENT TO SMALL RIBOSOMAL SUBUNIT • MAY REGULATE PROTEIN SYNTEHSIS BY FACILITATING mRNA’S EXPORT FROM NUCLEUS • IS NOT DIRECTLY ATTACHED TO STOP CODON, BUT TO TRAILER SEGMENT

  19. TRAILER SEQUENCE = NONCODING (UNTRANSLATED) SEQUENCE OF mRNA FROM THE STOP CODON TO THE POLY (A) TAIL

  20. RNA PROCESSING VIDEO

  21. RNA SPLICING • GENES THAT CODE FOR PROTEINS IN EUKARYOTES MAY NOT BE CONTINUOUS SEQUENCES • INTRONS = NONCODING SEQUENCES IN DNA THAT INTERVENE BETWEEN CODING SEQUENCES; ARE TRANSCRIBED BUT NOT TRANSLATED • EXONS = CODING SEQUENCES OF A GENE THAT ARE TRANSCRIBED AND EXPRESSED

  22. RNA SPLICING • A PROCESS THAT REMOVES INTRONS AND JOINS EXONS IN PRE-mRNA; PRODUCES MATURE mRNA • snRNPS = SMALL NUCLEAR RIBONUCLEOPROTEINS; ARE INVOLVED IN mRNA SPLICING • SPLICEOSOME = A LARGE MOLECULAR COMPLEX THAT CATALYZES RNA SPLICING REACTIONS; MADE OF snRNPS AND OTHER PROTEINS

  23. SPLICEOSOMES • AS THE SPICEOSOME IS ASSEMBLED, ONE TYPE OF snRNP BASE PAIRS WITH A COMPLEMENTARY SEQUENCE AT THE 5’ END OF THE INTRON • THE SPLICEOSOME PRECISELY CUTS THE RNA TRANSCRIPT AT SPECIFIC SITES AT EITHER END OF THE INTRON, WHICH IS EXCISED • THE INTRON IS RELEASED AND THE ADJACENT EXONS ARE IMMEDIATELY SPLICED TOGETHER BY THE SPLICEOSOME

  24. RNA SPLICING

  25. ROLES OF snRNPs AND SPICEOSOMES IN mRNA SPLICING

  26. RIBOZYMES • OTHER KINDS OF RNA PRIMARY TRANSCRIPTS, SUCH AS THOSE GIVING RISE TO tRNA AND rRNA, ARE SPLICED BY MECHANISMS THAT DO NOT INVOLVE SPLICEOSOMES; HOWEVER, AS WITH mRNA SPLICING, RNA IS OFTEN INVOLVED IN CATALYZING THE REACTIONS • RIBOZYMES = RNA MOLECULES THAT CAN CATALYZE REACTIONS BY BREAKING AND FORMING COVALENT BONDS

  27. PROTEIN SYNTHESIS • IN A NUTSHELL, PROTEIN SYNTHESIS IS TAKING THE AMINO ACIDS FROM FOOD WE EAT AND LINKING THEM BACK INTO POLYPEPTIDES, PROTEINS THAT THE BODY USES FOR VARIOUS FUNCTIONS THROUGHOUT THE BODY

  28. VIDEO: PROTEIN SYNTHESIS OVERVIEW

  29. TRANSLATION

  30. TRANSFER RNA (tRNA) • ALL TYPES OF RNA, INCLUDING tRNA, ARE TRANSCRIBED FROM TEMPLATE DNA • tRNA MUST TRAVEL FROM THE NUCLEUS TO THE CYTOPLASM FOR TRANSLATION • tRNA MOLECULES CAN BE REUSED

  31. tRNA STRUCTURE • tRNA IS A SINGLE-STRANDED RNA ONLY ABOUT 80 NUCLEOTIDES LONG • THE STRAND IS FOLDED, FORMING SEVERAL DOUBLE-STRANDED REGIONS WHERE SHORT BASE SEQUENCES OF HYDROGEN BOND WITH COMPLEMENTARY BASES • A SINGLE-PLACE VIEW SHOWS A CLOVER LEAF SHAPE • A LOOP PROTRUDES A ONE END OF THE L AND HAS A SPECIALIZED SEQUENCE OF 3 BASES CALLED THE ANTICODON • AT THE OTHER END OF THE L PROTRUDES THE 3’ END OF THE MOLECULE, THE ATTACHMENT SITE FOR AN AMINO ACID

  32. STRUCTURE OF tRNA

  33. WOBBLE EFFECT • THERE ARE ONLY ABOUT 45 TYPES OF tRNA, BUT THIS ENOUGH TO TRANSLATE THE 64 CODONS DUE TO THE WOBBLE EFFECT • WOBBLE EFFECT = THE ABILITYOF ONE tRNA TO RECOGNIZE 2 OR 3 DIFFERENT mRNA CODONS; THE THIRD BASE (5’ END) OF THE tRNA ANTICODON HAS SOME PLAY OR WOBBLE, SO THAT IT CAN HYDROGEN BOND WITH MORE THAN ONE KIND OF BASE IN THE 3RD POSITION (3’END) OF THE CODON • A SINGLE tRNA WITH THE ANTICODON CCG WILL RECOGNIZE THREE mRNA CODONS: GGU, GGC, GGA, ALL OF WHICH CODE FOR GLYCINE

  34. AMINOACYL-tRNA SYNTHETASES • A TYPE OF ENZYME THAT CATALYZES THE ATTACHMENT OF AN AMINO ACID TO ITS tRNA • EACH OF THE 20 A.A. HAS A SPECIFIC AMINOACYL-tRNA SYNTHETASE • IN AN ENDERGONIC REACTION DRIVEN BY THE HYDROLYSIS OF ATP, A SYNTHETASE ATTACHES AN A.A. TO ITS tRNA IN 2 STEPS: • 1)ACTIVATION OF THE A.A. WITH AMP • 2) ATTACHMENT OF THE A.A. TO THE tRNA

  35. AN AMINOACYL-tRNA AT WORK THE ACTIVE SITE BIND THE A.A AND ATP; THE ATP LOSES 2 PHOSPHATES AND ATTACHES TO THE A.A. AS AMP THE tRNA COVALENTLY BONDS TO THE A.A, DISPLACING AMP

  36. RIBOSOMES • RIBOSOMES COORDINATE THE PAIRING OF tRNA ANTIOCODNS TO mRNA CODONS • RIBOSOMES HAVE 2 SUBUNITS (SMALL AND LARGE) WHICH ARE SEPARATED WHEN NOT INVOLVED IN PROT. SYNTHESIS • THEY ARE COMPOSED OF ABOUT 60% RNA (rRNA) AND 40% PROTEIN

  37. RIBOSOMAL SUBUNITS • THE SMALL AND LARGE SUBUNITS ARE: • CONSTRUCTED IN THE NUCLEOLUS • DISPATCHED THROUGH NUCLEAR PORES TO THE CYTOPLASM • ONCE IN CYTOPLASM, ARE ASSEMBLED INTO FUNCTIONAL RIBOSOMES ONLY WHEN ATTACHED TO AN mRNA

  38. RIBOSOMAL BINDING SITES • 1) mRNA BINDING SITE-CREATES COMPLEX • 2) P SITE - HOLDS THE tRNA CARRYING THE GROWING POLYPEPTIDE CHAIN • 3) A SITE - HOLD THE tRNA CARRYING THE NEXT A.A. TO BE ADDED • 4) E SITE - DISCHARGED tRNAs LEAVE THE RIBOSOME • ** AS THE RIBOSOME HOLDS THE tRNA AND mRNA MOLECULES TOGETHER, ENZYMES TRANSFER THE NEW A.A. FROM ITS tRNA TO THE CARBOXYL END OF THE GROWING POLYPEPTIDE

  39. ANATOMY OF A RIBOSOME

  40. BUILDING A POLYPEPTIDE • THE BUILDING OF A PROTEIN, OR TRANSLATION, OCCURS IN 3 STAGES: • 1)INITIATION • 2) ELONGATION • 3) TERMINATION ALL 3 STAGES REQUIRE ENZYMES AND OTHER PROTEIN FACTORS INITIATION AND ELONGATION REQUIRE ENERGY PROVIDED BY GTP

  41. INITIATION • INITATION BRINGS TOGETHER mRNA, A tRNA ATTACHED TO THE FIRST A.A.(METHIONINE), AND THE 2 RIBOSOMAL SUBUNITS • A) A SMALL RBIOSOMAL SUBUNIT BINDS TO A MOLECULE OF mRNA. AN INITIATOR tRNA, WITH ANTICODON UAC, BASE-PAIRS WITH START CODON AUG. THIS tRNA CARRIES METHIONINE • B) LARGE RIBOSOMAL SUBUNIT ARRIVES. THE INITIATOR tRNA IS IN THE P SITE. THE A SITE IS AVAILABLE FOR NEXT A.A. • GTP PROVIDES THE ENERGY FOR INITIATION

  42. INITIATION OF TRANSLATION

  43. ELONGATION • SEVERAL PROTEINS CALLED ELONGATION FACTORS TAKE PART IN THIS 3-STEP CYCLE, ADDING A.A’S • 1)CODON RECOGNITION: AN INCOMING AMINOACYL tRNA BINDS TO THE CODON IN THE A SITE • AN ELONGATION FACTOR DIRECTS tRNA INTO A SITE • HYDROLYSIS OF GTP PROVIDES ENERGY

  44. 2) PEPTIDE BOND FORMATION: THE RIBOSOME CATALYZES THE FORMATION OF A PEPTIDE BOND BETWEEN THE NEW A.A. AND THE CARBOXYL END OF GROWING PROTEIN • 3) TRANSLOCATION- THE tRNA IN THE A SITE, WHICH IS NOT ATTACHED TO THE GROWING PEPTIDE, IS MOVED TO P SITE. THE tRNA THAT WAS IN THE P SITE IS TRANSLOCATED TO THE E SITE AND EXITS • THE mRNA IS MOVED THRU RIBOSOME IN THE 5’ TO 3’ DIRECTION • GTP HYDROLYSIS PROVIDES ENERGY

  45. ELONGATION

  46. TERMINATION • 1) WHEN RIBOSOME REACHES A TERMINATION CODON ON mRNA, THE A SITE ACCEPTS A PROTEIN CALLED A RELEASE FACTOR • 2) THE RELEASE FACTOR HYDROLYZES THE BOND BETWEEN THE tRNA IN THE P SITE AND THE LAST A.A. OF THE PEPTIDE CHAIN. IT IS FREED FROM THE RIBOSOME • 3) THE TWO RIBOSOMAL SUBUNITS AND THE OTHER COMPONENTS DISSOCIATE

  47. TERMINATION

  48. TRANSLATION VIDEO

  49. SUMMARY OF PROTEIN SYNTHESIS

  50. POLYRIBOSOMES • A SINGLE RIBOSOME CAN MAKE AN AVERAGE SIZED PROTEIN IN LESS THAN A MINUTE, BUT CLUSTERS OF RIBOSOMES, CALLED POLYRIBOSOMES, CAN SIMULTANEOULSY TRANSLATE AN mRNA MOLECULE • ONCE A RIBOSOME PASSES THE INITIATION CODON, A SECOND RIBOSOME CAN ATTACH TO THE LEADER SEQUENCE OF mRNA • SEVERAL RIBOSOMES MAY TRANSLATE AN mRNA AT ONCE, MAKING MANY COPIES OF A POLYPEPTIDE

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