Transcription/Translation 30S initiation complex

A Site Aminoacyl tRNA synthetase

Elongation stage

Initiation Factor 2

Intrinsic terminator

mRNAs

Nonsense codons Operon

What happens when the 30S subunit and initiation factors 1 and 3 bind to the RBS and start codon Acceptor site Charged tRNA with amino acid in a site Protein that attaches correct amino acid to tRNA because tRNA to this with the right amino acid Also attach ATP to amino acid via a pyrophosphate bond at the carboxyl group so that there is AMP. and transfer amino acid from the AMP to the 3 OH of tRNA and activate the COOH group of the amino acid for peptide bond formation by attachment to tRNA during translation Early sigma factor leaves the holoenzyme leaving the core which translocates down the DNA, unwinding another bubble, Core transcribes entire RNA. RNA comes out 53 therefore template was transcribed 3-5 Enters with GTP and the 50s subunit to make the 30S initation complex a 70S initation complex No additional factors are necessary RNA forms stem-loop by having inverted repeats and thus intrastrand base pairing And then a lot of Uracils on the 3 end of the mRNA which goes with a run of adenosines on the DNA U-A base pairsonly 2 h-bonds so they break apart here. contain info specifying amino acid sequence in protein Unstable (lasts for minutes) 3 codons that are not recognized by any tRNA (UAA, UAG, UGA) A group of related genes that are transcribed together to give 1 polycistronic mRNA. Example: a typical bacterial rRNA

P Site Rho-dependent terminator

ribosome

rRNA

Shine Dalgarno Sequence

operon with a lot of genes encoding different things. Peptidyl site Where the polypeptide chain is Protein-depend00>requires protein Rho to bind tightly to the C-rich rut site on the RNA Translocates 53 on RNA Collision of Rho with a paused RNA pol causes termination site of protein synthesis assemble as 2 subunits, each with distinct set of proteins and rRNAs forms the skeleton of ribosome (ribosomal proteins assemble here), catalyze peptide bond formation (23S) stable (lasts for hours) serves a structural role as a scaffold for ribosomal proteins and functional roles in protein synthesis. The sequence on mRNA that the 30s initiation complex identifies to define the start site. Binds to the 3 end of the 16s ribosomal RNA, which becomes a part of the 30S subunit Variety of purine (A,G) sequences, often 510 bases to the 5 side of the start codon. Can have multiple RBS Recognizes a different -35 (upstream) sequence and -10 sequence and used for motility and chemotaxis Recognizes different sequences used for nitrogen regulation. Recognizes a difference -35 (upstream) sequence and -10 sequence used for normal growth Two terminators (intrinsic or Rhodependent sequences) makes the coure pause, RNA_DNA duplex falls apart, RNA pol leaves DNA adaptors between ribosome and

Sigma Factor 28

Sigma Factor 54 Sigma Factor 70

Termination stage

tRNAs

Universal genetic code Wobble base pairing

message, bringing correct amino acid to translation complex Stable (lasts for hours) Flattened structure looks like 4 single-stranded regions with a 3 end +3 loops All tRNAs are transcribed with normal RNA bases, but then many bases are modified and the tRNA folds into a very stable structure Each different tRNA coded by a different gene, despite conserved elements Ranges in length from around 73-93 nucleotides All with the same 3 sequence (CCA) where the amino acid attaches Anticodon loop will base pair with mRNA Most codons are interpreted in same way in different organisms Allows amino acids to have several codons recognized by 1 tRNA Have irregular base pairing at the end because it is more flexible EX. Alanine is encoded by 4 possible codons all of the form GCX.

Transport secretion and mutations Antiporter

1 molecule transfer energizes another one

ATP-dependent transporters

ATP-hydrolyzing protein Base analogs

DnaK/DnaJ Group translocation:

Hsp

Intercalating dyes

Conformational changes in the proteins that result in solute passage are energized by ATP hydrolysis Atp-hydrolyzing protein: 2 ATP for 1 molecule of solute Membrane spannign transporter: for mchannel Periplasmic binding protein: high substrate affinity. 2 ATP for 1 molecule of solute in ATPdependent transporter Incorporate into DNA isntead of normal bases, but base pair incorrectly. Reparied bby mismatch report. Exs. 5-bromouracil: replaces T, but pairs with C 2-aminopurine: replaces A but pairs with C. Prevent protein from folding too quickly chemical modification of the transported substance driven by phosphoenolpyruvate (active transport)no accumulation of solutes because the solute is modified Heat shock protein Attempt for cell to refold denatured proteins. Physically insert themselves and push DNA base pairs apart. Single base pair insertions/deletions

Frameshift mutations Lesions often fixed by mismatch repair systems Exs. Acridines or ethidium bromide. Lead to formation of free radicals, leading to both ss and ds breaks in DNA Ds breaks=most damaging and only reparable by recombination and/or errorprone repair ssDNA=opposing strand can repair by being a template. Three things UvrA, UmuCD, lexA Repressor of expressor of SOS regulation that is inactivated by the activation of the RecA protein Forms the channel for transport in ATPdependent transporter Reduced/no activity Interact with newly synthesized or with misfolded polypeptides to help acquire normal, final structures Can also help polypeptide attain structure, but are NOT PART of the final protein structure. Chaperones often hydrolyze ATP during proper protein folding. Chaperones can also prevent folding or aggregation before localization of proteins beyond cytoplasm. Absorbed by the bases on nucleic acids, the bases can be affected. Examples include pyrimidine dimers, which can cause misreading by DNA pol. Effect: production of pyrimidine dimers and where 2 adjacent pyrimidine dimers on same DNA become covalently bonded. Single base substitution change A carrier with high substrate affinity in ATP-dependent transporter. Repear damage in DNA by UV light cleaves pyrimidine dimers generated by UV radiation, all organisms except mammals have this. Light energizes a photolyase (enzyme that absorbs E from light) which removes

Ionizing radiation

Lex A responses LexA protein

Membrane spanning transporter Missense mutation Molecular chaperones

Non-ionizing radiation (ultraviolet light)

Nonsense mutation Periplasmic binding protein Photo-reactivation systems

Reactive chemicals

RecA protein:

Sec apparatus

lesion. Deaminate various bases, causing faulty bping during replication. Repair with specific DNA glycosylases Exs. Nitrous acid or hydroxylamine Senses DNA damage and activated to become protease that cleaves receptor protein Step 1: SecA + SS-precursor, SecB chaperone associates. Step 2: Complex to membrane due to SecA-SecEYG; secA cleaves ATP and threads precursor into SecEYG pore like a sewing machine. Step 3: repeat ATP-driven SecA cycle feeding 20-30 aa segments through Sec; PMF driven SecEYG cycle. SS-cleavage by Lep occurs early. SUMMARY: Essential: SecA, SecEY, Lep Helpful: SecB, SecG, SecDF Spontaneous formation. H-bonding between oxygen and nitrogen atoms. Include alpha helices and B strands. Used in both proks and euks to direct precursor proteins for secretion. SS are cleaved from precursor during localization processmature potion is then in cellular destination. One of the first molecules to be synthesized so translation can occur early on Wide variety of amino acid sequences can be used N-terminal domain: 15-25 aa First: Region of 3-8 residues with 1-3 amino acid Next: hydrophobic core (7-15 hydrophobic amino acids) Last: sometimes a more polar region where cleavage by specific peptidase occurs. Change in genotype no change in phenotype

secondary protein structure

Signal Sequences (SS)

Silent mutation

Simple transport SOS response to DNA damage

Symporter Tat secretion

driven by the energy in the proton motive force. System of three things RecA activated by DNA damageLexA inactivatedSOS response no longer repressed Simultaneous movement inwards using 1 protein Alternative appartus used in export of folded bacterial prtoeins: TatABC Tat substrates with distinct N-terminus targeting signal (Twin Arg Tag): 25-40 amino acids with a motif in the basic region. Tat signal-containing folded protein binds TatBC TatA Membrane transporter that is dependent on PMF that relies on TAT secretion from TATBC Involved in TAT secretion that recognizes arginine residues on proteins Can occur spontaneously but is frequently aided by molecular chaperones (chaperonins)protein-folding factors. : periplasmic binding proteins are involved and energy comes from ATP. Are there because passive diffusion is not very effective Generally are specific for particular solute Usually consume energy in some form during the transport process Usually transport the solute without any chemical modification of that solute. Error prone DNA repair. One molecule movement Error free DNA repair

TatA

TatBC tertiary/quaternary protein folding

The ABC System Transport proteins

Umu CD Uniporter UvrA

Regulation