RNA STRUCTURE, TRANSCRIPTION,

TRANSLATION, RNA SYNTHESIS,

PROCESSING, AND MODIFICATION
 COMPONENTS REQUIRED FOR TRANSLATION
• A LARGE NUMBER OF COMPONENTS ARE REQUIRED FOR THE SYNTHESIS OF A PROTEIN.

1. THESE INCLUDE ALL THE AMINO ACIDS THAT ARE FOUND IN THE FINISHED PRODUCT,
2. THE MRNA TO BE TRANSLATED,
3. TRANSFER RNA (TRNA) FOR EACH OF THE AMINO ACIDS,
4. FUNCTIONAL RIBOSOMES,
5. ENERGY SOURCES,
6. ENZYMES, AS WELL AS
7. PROTEIN FACTORS NEEDED FOR INITIATION, ELONGATION, AND TERMINATION STEPS OF POLYPEPTIDE
CHAIN SYNTHESIS.

• AMINO ACIDS
• ALL THE AMINO ACIDS THAT EVENTUALLY APPEAR IN THE FINISHED PROTEIN MUST BE PRESENT AT
THE TIME OF PROTEIN SYNTHESIS.
• IF ONE AMINO ACID IS MISSING (FOR EXAMPLE, IF THE DIET DOES NOT CONTAIN AN ESSENTIAL AMINO
ACID), TRANSLATION STOPS AT THE CODON SPECIFYING THAT AMINO ACID.
• THIS DEMONSTRATES THE IMPORTANCE OF HAVING ALL THE ESSENTIAL AMINO ACIDS IN SUFFICIENT
 MESSENGER RNA

• MRNA COMPRISES ONLY ABOUT 5% OF THE RNA IN THE CELL, YET IS BY FAR THE MOST
HETEROGENEOUS TYPE OF RNA IN SIZE AND BASE SEQUENCE. MRNA CARRIES GENETIC
INFORMATION FROM DNA FOR USE IN PROTEIN SYNTHESIS. IN EUKARYOTES, THIS INVOLVES
TRANSFER OF MRNA OUT OF THE NUCLEUS AND INTO THE CYTOSOL. IF THE MRNA CARRIES
INFORMATION FROM MORE THAN ONE GENE, IT IS SAID TO BE POLYCISTRONIC (CISTRON =
GENE). POLYCISTRONIC MRNA IS CHARACTERISTIC OF PROKARYOTES. IF THE MRNA CARRIES
INFORMATION FROM JUST ONE GENE, IT IS SAID TO BE MONOCISTRONIC AND IS
CHARACTERISTIC OF EUKARYOTES. IN ADDITION TO THE PROTEIN-CODING REGIONS THAT CAN
BE TRANSLATED, MRNA CONTAINS UNTRANSLATED REGIONS AT ITS 5 - AND 3 -ENDS (FIGURE
30.4). SPECIAL STRUCTURAL CHARACTERISTICS OF EUKARYOTIC (BUT NOT PROKARYOTIC)
MRNA INCLUDE A LONG SEQUENCE OF ADENINE NUCLEOTIDES (A POLY-A “TAIL”) ON THE 3 -
END OF THE RNA CHAIN, PLUS A “CAP” ON THE 5 -END CONSISTING OF A MOLECULE OF 7-
METHYLGUANOSINE ATTACHED THROUGH AN UNUSUAL (5 →5 ) TRIPHOSPHATE LINKAGE.
 COMPONENTS REQUIRED FOR TRANSLATION
• TRANSFER RNA
• AT LEAST ONE SPECIFIC TYPE OF TRNA IS REQUIRED FOR EACH AMINO ACID. IN HUMANS, THERE
ARE AT LEAST 50 SPECIES OF TRNA, WHEREAS BACTERIA CONTAIN 30–40 SPECIES.
• BECAUSE THERE ARE ONLY 20 DIFFERENT AMINO ACIDS COMMONLY CARRIED BY TRNA, SOME
AMINO ACIDS HAVE MORE THAN ONE SPECIFIC TRNA MOLECULE. THIS IS PARTICULARLY TRUE OF
THOSE AMINO ACIDS THAT ARE CODED FOR BY SEVERAL CODONS.

• 1. AMINO ACID ATTACHMENT SITE:

• EACH TRNA MOLECULE HAS AN ATTACHMENT SITE FOR A SPECIFIC (COGNATE) AMINO ACID AT
ITS 3'-END. THE CARBOXYL GROUP OF THE AMINO ACID IS IN AN ESTER LINKAGE WITH THE 3'-
HYDROXYL OF THE RIBOSE PORTION OF THE ADENOSINE (A) NUCLEOTIDE IN THE —CCA
SEQUENCE AT THE 3'-END OF THE TRNA.
• WHEN A TRNA HAS A COVALENTLY ATTACHED AMINO ACID, IT IS SAID TO BE CHARGED; WHEN IT
DOES NOT, IT IS SAID TO BE UNCHARGED.
• THE AMINO ACID ATTACHED TO THE TRNA MOLECULE IS SAID TO BE ACTIVATED.
• 2. ANTICODON: EACH TRNA MOLECULE ALSO CONTAINS A THREE-BASE NUCLEOTIDE SEQUENCE
—THE ANTICODON—THAT PAIRS WITH A SPECIFIC CODON ON THE MRNA. THIS CODON SPECIFIES
THE INSERTION INTO THE GROWING PEPTIDE CHAIN OF THE AMINO ACID CARRIED BY THAT
 COMPONENTS REQUIRED FOR
TRANSLATION
• AMINOACYL-TRNA SYNTHETASES

• THIS FAMILY OF ENZYMES IS REQUIRED FOR ATTACHMENT OF AMINO ACIDS TO THEIR

CORRESPONDING TRNAS.
• EACH MEMBER OF THIS FAMILY RECOGNIZES A SPECIFIC AMINO ACID AND ALL THE
TRNAS THAT CORRESPOND TO THAT AMINO ACID (ISOACCEPTING TRNAS).
• AMINOACYL-TRNA SYNTHETASES CATALYZE A TWO-STEP REACTION THAT RESULTS
IN THE COVALENT ATTACHMENT OF THE CARBOXYL GROUP OF AN AMINO ACID TO
THE 3'-END OF ITS CORRESPONDING (COGNATE) TRNA.
• THE OVERALL REACTION REQUIRES ADENOSINE TRIPHOSPHATE (ATP), WHICH IS
CLEAVED TO ADENOSINE MONOPHOSPHATE (AMP) AND INORGANIC PYROPHOSPHATE
(PPI).
• THE EXTREME SPECIFICITY OF THE SYNTHETASE IN RECOGNIZING BOTH THE
AMINO ACID AND ITS COGNATE TRNA CONTRIBUTES TO THE HIGH FIDELITY OF
TRANSLATION OF THE GENETIC MESSAGE.
• IN ADDITION, THE SYNTHETASES HAVE A “PROOFREADING” OR “EDITING” ACTIVITY
THAT CAN REMOVE AMINO ACIDS FROM THE ENZYME OR THE TRNA MOLECULE.
 COMPONENTS REQUIRED FOR
• MESSENGER RNA TRANSLATION
• THE SPECIFIC MRNA REQUIRED AS A TEMPLATE FOR THE SYNTHESIS
OF THE DESIRED POLYPEPTIDE CHAIN MUST BE PRESENT.
• FUNCTIONALLY COMPETENT RIBOSOMES A site
• RIBOSOMES ARE LARGE COMPLEXES OF PROTEIN AND RIBOSOMAL
RNA (RRNA).
• THEY CONSIST OF TWO SUBUNITS—ONE LARGE AND ONE SMALL—
WHOSE RELATIVE SIZES ARE GIVEN IN TERMS OF THEIR
SEDIMENTATION COEFFICIENTS, OR S (SVEDBERG) VALUES.
• PROKARYOTIC AND EUKARYOTIC RIBOSOMES ARE SIMILAR IN
STRUCTURE, AND SERVE THE SAME FUNCTION, NAMELY, AS THE
MACROMOLECULAR COMPLEXES IN WHICH THE SYNTHESIS OF
PROTEINS OCCURS.
1. THE SMALL RIBOSOMAL SUBUNIT BINDS MRNA AND IS
RESPONSIBLE FOR THE ACCURACY OF TRANSLATION BY
ENSURING CORRECT BASE-PAIRING BETWEEN THE CODON IN THE
MRNA AND THE ANTICODON OF THE TRNA.
2. THE LARGE RIBOSOMAL SUBUNIT CATALYZES FORMATION OF THE
PEPTIDE BONDS THAT LINK AMINO ACID RESIDUES IN A PROTEIN.
 COMPONENTS REQUIRED FOR
TRANSLATION
• 1. RIBOSOMAL RNA: EUKARYOTIC RIBOSOMES CONTAIN FOUR RRNAS .THE RRNAS ARE GENERATED FROM A SINGLE PRE-RRNA BY THE ACTION OF
RIBONUCLEASES , AND SOME BASES AND RIBOSES ARE MODIFIED.
• 2. RIBOSOMAL PROTEINS: THESE PROTEINS PLAY A NUMBER OF ROLES IN THE STRUCTURE AND FUNCTION OF THE RIBOSOME AND ITS
INTERACTIONS WITH OTHER COMPONENTS OF THE TRANSLATION SYSTEM.
• 3. A, P, AND E SITES ON THE RIBOSOME: THE RIBOSOME HAS THREE BINDING SITES FOR TRNA MOLECULES—THE A, P, AND E SITES—EACH OF
WHICH EXTENDS OVER BOTH SUBUNITS.
• TOGETHER, THEY COVER THREE NEIGHBORING CODONS.
DURING TRANSLATION,
1. THE A SITE BINDS AN INCOMING AMINOACYL-TRNA AS DIRECTED BY THE CODON CURRENTLY OCCUPYING THIS SITE. THIS CODON SPECIFIES THE
NEXT AMINO ACID TO BE ADDED TO THE GROWING PEPTIDE CHAIN.
2. THE P-SITE CODON IS OCCUPIED BY PEPTIDYL-TRNA. THIS TRNA CARRIES THE CHAIN OF AMINO ACIDS THAT HAS ALREADY BEEN SYNTHESIZED.
3. THE E SITE IS OCCUPIED BY THE EMPTY TRNA AS IT IS ABOUT TO EXIT THE RIBOSOME.

• 4. CELLULAR LOCATION OF RIBOSOMES: IN EUKARYOTIC CELLS, THE RIBOSOMES ARE EITHER “FREE” IN THE CYTOSOL OR ARE IN CLOSE
ASSOCIATION WITH THE ENDOPLASMIC RETICULUM (WHICH IS THEN KNOWN AS THE “ROUGH” ENDOPLASMIC RETICULUM, OR RER).
• THE RER-ASSOCIATED RIBOSOMES ARE RESPONSIBLE FOR SYNTHESIZING PROTEINS THAT ARE TO BE EXPORTED FROM THE CELL, AS WELL AS
THOSE THAT ARE DESTINED TO BECOME INCORPORATED INTO PLASMA, ENDOPLASMIC RETICULUM, OR GOLGI MEMBRANES, OR IMPORTED INTO
LYSOSOMES.
• CYTOSOLIC RIBOSOMES SYNTHESIZE PROTEINS REQUIRED IN THE CYTOSOL ITSELF, OR DESTINED FOR THE NUCLEUS, MITOCHONDRIA, AND
PEROXISOMES. NOTE: MITOCHONDRIA CONTAIN THEIR OWN SET OF RIBOSOMES AND THEIR OWN UNIQUE, CIRCULAR DNA.
• MOST MITOCHONDRIAL PROTEINS, HOWEVER, ARE ENCODED BY NUCLEAR DNA, SYNTHESIZED IN THE CYTOSOL, AND POSTTRANSLATIONALLY
TARGETED TO MITOCHONDRIA.
 COMPONENTS REQUIRED FOR
TRANSLATION
• PROTEIN FACTORS
• INITIATION, ELONGATION, AND TERMINATION (OR RELEASE) FACTORS ARE REQUIRED
FOR PEPTIDE SYNTHESIS.
• SOME OF THESE PROTEIN FACTORS PERFORM A CATALYTIC FUNCTION, WHEREAS
OTHERS APPEAR TO STABILIZE THE SYNTHETIC MACHINERY.
• A NUMBER OF THE FACTORS ARE G PROTEINS, AND THUS ARE ACTIVE WHEN BOUND
TO GTP AND INACTIVE WHEN BOUND TO GDP. G. ATP AND GTP ARE REQUIRED AS
SOURCES OF ENERGY.
• CLEAVAGE OF FOUR HIGH-ENERGY BONDS IS REQUIRED FOR THE ADDITION OF ONE
AMINO ACID TO THE GROWING POLYPEPTIDE CHAIN:
1. TWO FROM ATP IN THE AMINOACYL-TRNA SYNTHETASE REACTION—ONE IN THE
REMOVAL OF PPI, AND ONE IN THE SUBSEQUENT HYDROLYSIS OF THE PPI TO
INORGANIC PHOSPHATE BY PYROPHOSPHATASE —
2. AND TWO FROM GTP—ONE FOR BINDING THE AMINOACYL-TRNA TO THE A SITE AND
 STEPS IN PROTEIN SYNTHESIS
• THE PROCESS OF PROTEIN SYNTHESIS TRANSLATES THE THREE-LETTER ALPHABET OF NUCLEOTIDE
SEQUENCES ON MRNA INTO THE 20-LETTER ALPHABET OF AMINO ACIDS THAT CONSTITUTE PROTEINS.
• THE MRNA IS TRANSLATED FROM ITS 5'-END TO ITS 3'-END, PRODUCING A PROTEIN SYNTHESIZED FROM ITS
AMINO-TERMINAL END TO ITS CARBOXYL-TERMINAL END.
• PROKARYOTIC MRNAS OFTEN HAVE SEVERAL CODING REGIONS, THAT IS, THEY ARE POLYCISTRONIC.
• EACH CODING REGION HAS ITS OWN INITIATION AND TERMINATION CODON AND PRODUCES A SEPARATE
SPECIES OF POLYPEPTIDE.
• IN CONTRAST, EACH EUKARYOTIC MRNA HAS ONLY ONE CODING REGION, THAT IS, IT IS
MONOCISTRONIC.
• THE PROCESS OF TRANSLATION IS DIVIDED INTO THREE SEPARATE STEPS:

1. INITIATION,
2. ELONGATION,
3. TERMINATION.
• EUKARYOTIC PROTEIN SYNTHESIS RESEMBLES THAT OF PROKARYOTES IN MOST ASPECTS. INDIVIDUAL
DIFFERENCES ARE NOTED IN THE TEXT.
• ONE IMPORTANT DIFFERENCE IS THAT TRANSLATION AND TRANSCRIPTION ARE COUPLED IN
PROKARYOTES, WITH TRANSLATION STARTING BEFORE TRANSCRIPTION IS COMPLETED. COUPLING IS A
 ENZYMES

• CORE ENZYME: FIVE OF THE ENZYME’S PEPTIDE SUBUNITS, 2Α, 1Β, 1Β , AND 1Ω,
ARE REQUIRED FOR ENZYME ASSEMBLY (Α, Ω) TEMPLATE BINDING (Β ), AND THE
5 →3 RNA POLYMERASE ACTIVITY (Β), AND ARE REFERRED TO AS THE CORE
ENZYME
• . HOWEVER, THIS ENZYME LACKS SPECIFICITY (THAT IS, IT CANNOT RECOGNIZE
THE PROMOTER REGION ON THE DNA TEMPLATE).
• 2. HOLOENZYME: THE S SUBUNIT (“SIGMA FACTOR”) ENABLES RNA POL TO
RECOGNIZE PROMOTER REGIONS ON THE DNA. THE S SUBUNIT PLUS THE CORE
ENZYME MAKE UP THE HOLOENZYME. [NOTE: DIFFERENT S FACTORS RECOGNIZE
DIFFERENT GROUPS OF GENES.]
 ACTION OF ANTIBIOTICS:

Some antibiotics prevent bacterial cell growth by inhibiting RNA

synthesis. For example, rifampin (rifampicin) inhibits transcription by
binding to the β subunit of prokaryotic RNA pol, and preventing chain
extension beyond three nucleotides Rifampin is important in the
treatment of tuberculosis. Dactinomycin (known to biochemists as
actinomycin D) was the first antibiotic to find therapeutic application
in tumor chemotherapy. It binds to the DNA template and interferes
with the movement of RNA pol along the DNA.
 POSTTRANSCRIPTIONAL MODIFICATION OF
RNA
• A PRIMARY TRANSCRIPT IS THE INITIAL, LINEAR, RNA COPY OF A TRANSCRIPTION
UNIT (THE SEGMENT OF DNA BETWEEN SPECIFIC INITIATION AND TERMINATION
SEQUENCES). THE PRIMARY TRANSCRIPTS OF BOTH PROKARYOTIC AND
EUKARYOTIC TRNA AND RRNA ARE POSTTRANSCRIPTIONALLY MODIFIED BY
CLEAVAGE OF THE ORIGINAL TRANSCRIPTS BY RIBONUCLEASES. TRNAS ARE
THEN FURTHER MODIFIED TO HELP GIVE EACH SPECIES ITS UNIQUE IDENTITY. IN
CONTRAST, PROKARYOTIC MRNA IS GENERALLY IDENTICAL TO ITS PRIMARY
TRANSCRIPT, WHEREAS EUKARYOTIC MRNA IS EXTENSIVELY MODIFIED BOTH
CO- AND POSTTRANSCRIPTIONALLY.
 RIBOSOMAL RNA

• RRNAS OF BOTH PROKARYOTIC AND EUKARYOTIC CELLS

ARE GENERATED FROM LONG PRECURSOR MOLECULES
CALLED PRE-RRNAS. THE 23S, 16S, AND 5S RRNA OF
PROKARYOTES ARE PRODUCED FROM A SINGLE PRE-RRNA
MOLECULE, AS ARE THE 28S, 18S, AND 5.8S RRNA OF
EUKARYOTES (NOTE: EUKARYOTIC 5S RRNA IS
SYNTHESIZED BY RNA POL III AND MODIFIED SEPARATELY.]
THE PRE-RRNAS ARE CLEAVED BY RIBONUCLEASES TO
YIELD INTERMEDIATE-SIZED PIECES OF RRNA, WHICH ARE
FURTHER PROCESSED (TRIMMED BY EXONUCLEASES AND
MODIFIED AT SOME BASES AND RIBOSES) TO PRODUCE THE
REQUIRED RNA SPECIES. [
 RIBOSOMAL RNA

• NOTE: IN EUKARYOTES, RRNA GENES ARE FOUND IN LONG, TANDEM ARRAYS.

RRNA SYNTHESIS AND PROCESSING OCCUR IN THE NUCLEOLUS, WITH BASE AND
SUGAR MODIFICATIONS FACILITATED BY SNORNA. SOME OF THE PROTEINS
DESTINED TO BECOME COMPONENTS OF THE RIBOSOME ASSOCIATE WITH PRE-
RRNA PRIOR TO AND DURING ITS MODIFICATION
 ROLE OF SMALL NUCLEAR RNAS:

• IN ASSOCIATION WITH MULTIPLE

PROTEINS, URACIL-RICH SNRNAS FORM
SMALL NUCLEAR RIBONUCLEOPROTEIN
PARTICLES (SNRNPS, OR “SNURPS,”
DESIGNATED AS U1, U2, U4, U5, AND U6)
THAT MEDIATE SPLICING. THEY
FACILITATE THE REMOVAL OF INTRONS
BY FORMING BASE PAIRS WITH THE
CONSENSUS SEQUENCES AT EACH END
OF THE INTRON
 ROLE OF SMALL NUCLEAR RNAS:

• [NOTE: IN SYSTEMIC LUPUS ERYTHEMATOSUS, AN AUTOIMMUNE DISEASE,

PATIENTS PRODUCE ANTIBODIES AGAINST THEIR OWN NUCLEAR PROTEINS SUCH
AS SNRNPS.]