Transfer RNA SS, folded upon themselves into DS section with cloverleaf structure 3’ end of tRNA has CCA terminus added after transcription, for AA binding Each AA has specific tRNA – Aminoacyl tRNA synthetase enzymes attach AAs to tRNAs in two step process tRNAs bring individual AAs to site of protein synthesis Anticodon loop has three base anticodon sequence specific for particular complementary codon on mRNA – tRNA anticodon base pairs with mRNA codon to align AA Redundancy of genetic code allows less stringent base pairing than in other processes Some AAs have more than one codon, more than one tRNA

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4.10 Function of transfer RNA

8.1 Structure of tRNAs

7.43 Processing of transfer RNAs (Part 1)

7.43 Processing of transfer RNAs (Part 2)

8.2 Attachment of amino acids to tRNAs

8.3 Nonstandard codon-anticodon base pairing (Part 1)

8.3 Nonstandard codon-anticodon base pairing (Part 2)

8.3 Nonstandard codon-anticodon base pairing (Part 3)

8.3 Nonstandard codon-anticodon base pairing (Part 4)

8.3 Nonstandard codon-anticodon base pairing (Part 5)

Protein Synthesis Similar in prokaryotes and eukaryotes Occurs on ribosomes Translation starts at specific sequence near 5’ end of mRNA, leaves 5’ UTR Eukaryotic mRNAs code single polypeptide chain (monocistronic), prokaryote mRNAs code for multiple polypeptides (polycistronic) Both prokaryote and eukaryote mRNAs have 3’ UTRs

8.7 Prokaryotic and eukaryotic mRNAs

Ribosomes Sites of protein synthesis in cells Subunits separated by ultracentrifugation, mass measured in Sphedburg units: 70S in prokaryotes, 80S in eukaryotes Made of rRNA subunits and associated proteins Eukaryote 5S, 5.8S, 18S, 28S rRNAs all transcribed from chromosomes – Lower eukaryotes don’t produce all four – Subunits transcribed as a singe unit by RNA Pol I, to precursor that is processed into 40S and 60S subunits that make up 80S ribosome Prokaryotes have 50S and 30S subunits of 70S ribosome Chloroplast and mitochondrial ribosomes resemble bacterial ribosomes Seen as a series of dots on ER, on nuclear envelope, or in cytoplasm Cells have multiple copies of rRNA genes, actively working cells have most ribosomes

7.15 The ribosomal RNA gene

7.16 Initiation of rDNA transcription

7.42 Processing of ribosomal RNAs

8.4 Ribosome structure (Part 1)

8.4 Ribosome structure (Part 2)

8.4 Ribosome structure (Part 3)

8.5 Structure of 16S rRNA

8.6 Structure of the 50S ribosomal subunit

Initiation of Translation AUG is primary start codon for translation – Translation starts with AA methionine in eukaryotes and N- formylmethionine in prokaryotes Signals for initiation codon identification different in prokaryote and eukaryote cells – Shine-Dalgarno sequence in prokaryotes precedes mRNA initiation sequence and base pairs with sequence near 3’ terminus of 16S rRNA – Eukaryote mRNAs bound at 7-methylguanosine cap of 5’ terminus before ribosome locates initiation codon Actual initiation of translation not entirely understood

8.8 Signals for translation initiation

Translation Process Divided into stages of initiation, elongation, and termination First step of initiation is binding of initiation factors to the small ribosomal subunit then initiator Met tRNA and mRNA Large ribosomal subunit added to complex for elongation to proceed Eukaryote initiation needs twelve or more proteins, eIFs, to begin Elongation occurs after initiation, to synthesize polypeptide chain

8.9 Overview of translation

8.10 Initiation of translation in bacteria

8.11 Initiation of translation in eukaryotic cells (Part 1)

8.11 Initiation of translation in eukaryotic cells (Part 2)

8.11 Initiation of translation in eukaryotic cells (Part 3)

Translation Process Three sites in ribosome for tRNA binding: P, A, E Initiator tRNA binds to P site, second binds to A site with help of EF and peptide bond forms Translocation moves ribosome three nucleotides along mRNA, putting empty A site over next codon, shifting peptidyl tRNA from A site to P site, and placing uncharged tRNA in E site for release Elongation continues in this manner until stop codon moves into A site – Release factors recognize stop codons and terminate translation mRNAs translated by series of ribosomes, sometimes simultaneously

8.12 Elongation stage of translation

8.14 Termination of translation

Transcriptional Regulation Positive transcription control best characterized in E. coli by effect of glucose on genes coding for breakdown of other sugars for alternate sources of energy and carbon If glucose available, enzymes for catabolism of other sugars not expressed If glucose levels drop, CAP binds target sequence 60 bp upstream of transcription start site to initiate transcription of other enzymes