Biochemistry Quiz 8 Flashcards
What is the Central Dogma?
DNA replication
DNA transcription into RNA
RNA translation into protein
How do you achieve Steady-state protein levels?
transcription- Protein Synthesis (+)
Protein degradation (-)
Transcription and replication both:
A. Use both DNA strands for synthesis
B. Require phosphorylation for activation
C. Use a primer to initiate synthesis
D. Occur mainly in S phase of the cell cycle
B. Require phosphorylation for activation
What is the role of RNA polymerase II?
-transcribes the protein-encoding genes to produce mRNA
What are the components of the initiation complex?
-TATA binding protein (TBP)
-co-activating TBP-associated factors (TAFS)
recruits RNAPII and cofactor proteins TFIIB, TFIIF, TFIIE, TFIIH
What is TFIID?
TATA binding protein (TBP) and TBP-associated factors (TAFs)
What is the DAB complex?
TFIID + TFIIA + TFIIB
-helps to form a kink in the DNA
-helps rest of complex and Polymerase II to bind
What is the last general factor that is added to the complex and aids in transcription intiation?
-TFIIH
has helicase, ATPase and kinase activity
What actions of TFIIH initiate transcription?
- Phosphorylation of RNAPII (kinase activity)
- XPB Helicase unwinds DNA (Helicase activity)
- unwinding is ATP-dependent (ATPase activity); generates transcription bubble
- Allows RNAPII to initiate RNA synthesis
How is DNA specificity achieved with relatively short contact regions of the DNA-binding motifs in the DBDs?
-through protein-protein interactions
-Transcription factors can indirectly interact with other transcription factors/regulatory proteins through changes in DNA structure
-can also directly interact or through adapter proteins (other domains)
-multiple interactions confers added binding free energy and specificity
What is the role of complex promoters?
-extra regulation for either enhancing or repressing transcription
-accelerates and provides specialized regulation
ex. LDL receptor gene
What does Chromatin Remodeling do for the transcription process?
-directs which regions are accessible/ inaccessible to DNA transcription
What is Epigenetics?
-Post-translational modification of histones
What are some covalent modifications on histones?
-Methylation
-Acetylation
(histone acetyl transferases, HATs)
(histone deacetylases, HDACs)
-Phosphorylation
What are some characteristics of genes that are “switched on” and “switched off”?
“Switched on”
-active (open) chromatin
-unmethylated cytosines
-acetylated histones
“Switched off”
-Silent (condensed) chromatin
-methylated cytosines
-deactetylated histones
What are ADNRs?
ATP-dependent nucleosome remodeling factors (ADNR)
What are some differences between activated and repressed nucleosome mobility?
Activated
-histone modification that weaken histone-DNA contacts (acetylation by HATs)
-increased mobility
Repression
-histone modifications that restore contacts (deacetylation by HDACs)
-decreased mobility; repress transcription
What is DNA methylation?
-cytosine methylation at sequences CpG
-correlates with gene inactivation
MBD-containing proteins recruit HDACs, and block TFs from binding
What is the process a protein will go through in synthesis?
- Transcription
- Translation
- Protein folding
- Protein Processing; subcellular targeting; posttranslational modifications
What is the role of molecular chaperones?
-assist in covalent folding or unfolding proteins
-assembly/disassembly of other macromolecular structures (protein oligomerization; protein aggregates)
ex. HSP60, HSP70, HSP90
What is aggregation?
-partially folded or misfolded proteins
-expose hydrophobic residues and unstructured polypeptide backbone
-results in amorphous structures
What does the Proteostasis Network do?
-monitors proteins throughout their life cycle (synthesis, folding, refolding, transport, and degradation)
-protein homeostasis
What is Ubiquitin-proteasome proteolysis?
-for proteins that are targeted for degradation as part of cellular regulation
What is lysosomal digestion?
-membrane-bound organelles containing proteases that can degrade exogenous proteins or aged/damaged organelles
What is Autophagy?
-maintains normal cellular functioning by protein degradation and turnover of damaged organelles (stress)
-vesicle forms around the contents marked for degradation and forms the autophagosome
-autophagosome fuses with the lysosome to become the autolysosome
Describe the Ubiquitin-proteasomal system (UPS)
E1 (activating): ATP hydrolysis to add ubiquitin to a cysteine ATP-dependent
E2 (conjugating): receives ubiquitin on a cysteine residue
E3 (ligase): specific recognition of a protein to be degraded. catalyzes transfer from E2 to substrate
Describe the structure of a 26S proteasome
-20S Proteasome (core complex where actual degradation occurs)
-19S (x2) (where ubiquinated protein is recognized; where protein unfolding occurs)
How do proteins get targeted by the 26S proteasome?
-By degrons (recognition sequence or structure for an E3 ligase)
-ex. N-end rule; PEST sequences; Posttranslational modifications (phosphorylation)
