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Explain what polycistronic mRNA is
mRNA that often bears coding information transcribed from adjacent genes.
Characterize the structure of RNA polymerase
- Core Enzyme: 5 polypeptides
- Sigma Factor: Recognizes start of gene
- Holoenzyme= Core+Sigma
Describe the step of Initiation in transcription:
- The promoter is bound by RNA poly
- Sigma factor recognizes two regions in the promoter: -10 Pribnow box and -35 site.
- These are consensus sequences.
Describe the process of Elongation in transcription:
- RNA poly unwinds the DNA.
- Transcription bubble produced and moves with the RNA poly as it transcribes mRNA from template strand.
Describe the process of Termination (intrinsic and Rho-dependent) in transcription:
- Core RNA poly dissociates from template DNA
- 2 Types of termination: Intrinsic(AU rich region makes it fall off), and Rho-dependent(rho factor protein) reaches RNA poly and makes it pop off.
Identify the features of transcription in Archaea
- Similar to bacteria: 1RNA poly & polycistronic mRNA
- Similar to eukarya: Promoter w/ TATA box, several transcription factors, some RNA has introns.
Explain the following characteristics of the genetic code: Degenerate
Up to 6 different codons for 1 amino acid
Explain the following characteristics of the genetic code:Codons-sense and nonsense
- Sense-Direct amino acid incorporation into the protein. (They code for actual amino acids.)
- Nonsense-The stop codons, involved in termination of translation.
Explain the following characteristics of the genetic code:Wobble
Loose base pairing on the 5' end of tRNA, used to decrease mutation effects and reduce tRNA production needed.
Describe the structure of tRNA and the charging of a tRNA molecule:
- Structure:Cloverleaf, diamond bases, 2 arms, one acceptor stem and anticodon.
- Charging-Done through Aminoacyl-tRNA synthetase. Attaches AA to 3' hydroxyl. 20 enzymes for each AA,
What function does the Ribosome serve during translation?
Ribosome serves as the binding site of the mRNA, where the proteins are put together (through linking AAs).
Describe the structure of the Ribosome (prokaryotic):
- 70S ribosome= 30S +50S subunits.
- 30S-16S rRNA & 21 proteins
- 50S- 5S and 23S rRNA & 34 proteins
Characterize the binding sites in the ribosome:
- P-Peptidyl Site=Binds initiator tRNA or tRNA attached to growing polypeptide (peptidyl-tRNA)
- A-Aminoacyl site (Acceptor Site)=Binds incoming aminoacyl-tRNA
- E-Exit site=Briefly binds empty tRNA before it leaves ribosome
Describe the following parts of the process of translation:Initiation
Involves: Ribosomal subunits, Initiation Factors (IFs), and Initiator tRNA w/ N-formyl methionine.
- Steps:fMet (N-formyl Methionine) binds to 30S.
- 30S aligns with Shine Delgarno seq and fMet binds with start/initiator codon.
- 50S binds to 30S w/ fMet at P site.
- IF3 prevents 30S binding to 50S prematurely (i.e. without mRNA).
- IF2 binds GTP to fMet and directs it to the P site of 30S.
- IF1 Helps release of IF2 and aids in binding of 50S and 30S.
Describe the following parts of the process of translation:Elongation
- Aminoacyl tRNA binds
- Transpeptidation reaction occurs
- Translocation: Peptidyl tRNA moves from A site to P site, Ribosome moves down 1 codon, Empty tRNA leaves P site.
- EFTu-delivers aminoacyl-tRNA to the site.
- EFT-Converts EFTu-GDP back to EFTu-GTP.
- EFG-Helps with translocation by carrying GTP and GDP (moving the ribosome)
Describe the following parts of the process of translation:Termination
- Ribosome reaches the Nonsense codon (UAA, UAG, UGA) and it occupies the A site
- Release factors aid in recognition of stop (There are 3 RFs in procaryotes)
Describe the process of protein folding:
Eukary- Domains fold independently right after synth. Molecular chaperones=not as important
Prokary-Polypeptide doesn't fold till after entire synth of polypeptide. Moleculare chaperones are important.
explain the role of chaperones:
Chaperones protect cells from thermal damage and aid in transport Xcross membranes. They also help proper folding
Describe the process of protein splicing and characterize inteins and exteins
- Inteins-removed portion
- Exteins- portions that remain
- Splicing-Polypeptide is removed before final shape.
Identify the main features of the following protein secretory pathway:Sec-dependent pathway
- Translocates proteins from cyto across or into plasma membrane.
- Secreted proteins synthed as preproteins having amino-terminal signal peptide
- -Peptide delays protein folding, chaperone proteins keep preproteins unfolded.
Identify the main features of the following protein secretory pathway:ABC type 1 protein secretion pathway
- From cytoplasm across plasma and outer membrane
- Secreted proteins have C-terminal secretion signals
- Gram+ bacteria use modified version of this pathway.
Identify the main features of the following protein secretory pathway:Pathways in gram-negative bacteria
- 5 Secretion pathways
- II and V across outer membrane (Sec Dependent)
- I, III, IV Sec-independent
Pathways in gram - bacteria: Type II and type V protein secretion:
- II-From periplasmic space across outer membrane
- V-Moves proteins across outer membrane, autotransporters: form channel themselves. the Proteins make their own channels.
Pathways in gram - bacteria: Type III and type IV protein secretion:
- III-Secretion of virulence factors in Gram - Bacteria
- From cytoplasm to outside of cell (some type III machinery is syringe shaped)
- IV- Secrete proteins and transfers DNA during Conjucation