Biochemistry Quiz 8

Question 1

What is the Central Dogma?

Answer 1

DNA replication
DNA transcription into RNA
RNA translation into protein

Question 2

How do you achieve Steady-state protein levels?

Answer 2

transcription- Protein Synthesis (+)
Protein degradation (-)

Question 3

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

Answer 3

B. Require phosphorylation for activation

Question 4

What is the role of RNA polymerase II?

Answer 4

-transcribes the protein-encoding genes to produce mRNA

Question 5

What are the components of the initiation complex?

Answer 5

-TATA binding protein (TBP)
-co-activating TBP-associated factors (TAFS)
recruits RNAPII and cofactor proteins TFIIB, TFIIF, TFIIE, TFIIH

Question 6

What is TFIID?

Answer 6

TATA binding protein (TBP) and TBP-associated factors (TAFs)

Question 7

What is the DAB complex?

Answer 7

TFIID + TFIIA + TFIIB
-helps to form a kink in the DNA
-helps rest of complex and Polymerase II to bind

Question 8

What is the last general factor that is added to the complex and aids in transcription intiation?

Answer 8

-TFIIH
has helicase, ATPase and kinase activity

Question 9

What actions of TFIIH initiate transcription?

Answer 9

1. Phosphorylation of RNAPII (kinase activity)
2. XPB Helicase unwinds DNA (Helicase activity)
3. unwinding is ATP-dependent (ATPase activity); generates transcription bubble
4. Allows RNAPII to initiate RNA synthesis

Question 10

How is DNA specificity achieved with relatively short contact regions of the DNA-binding motifs in the DBDs?

Answer 10

-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

Question 11

What is the role of complex promoters?

Answer 11

-extra regulation for either enhancing or repressing transcription
-accelerates and provides specialized regulation
ex. LDL receptor gene

Question 12

What does Chromatin Remodeling do for the transcription process?

Answer 12

-directs which regions are accessible/ inaccessible to DNA transcription

Question 13

What is Epigenetics?

Answer 13

-Post-translational modification of histones

Question 14

What are some covalent modifications on histones?

Answer 14

-Methylation
-Acetylation
(histone acetyl transferases, HATs)
(histone deacetylases, HDACs)
-Phosphorylation

Question 15

What are some characteristics of genes that are “switched on” and “switched off”?

Answer 15

“Switched on”
-active (open) chromatin
-unmethylated cytosines
-acetylated histones
“Switched off”
-Silent (condensed) chromatin
-methylated cytosines
-deactetylated histones

Question 16

What are ADNRs?

Answer 16

ATP-dependent nucleosome remodeling factors (ADNR)

Question 17

What are some differences between activated and repressed nucleosome mobility?

Answer 17

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

Question 18

What is DNA methylation?

Answer 18

-cytosine methylation at sequences CpG
-correlates with gene inactivation
MBD-containing proteins recruit HDACs, and block TFs from binding

Question 19

What is the process a protein will go through in synthesis?

Answer 19

1. Transcription
2. Translation
3. Protein folding
4. Protein Processing; subcellular targeting; posttranslational modifications

Question 20

What is the role of molecular chaperones?

Answer 20

-assist in covalent folding or unfolding proteins
-assembly/disassembly of other macromolecular structures (protein oligomerization; protein aggregates)
ex. HSP60, HSP70, HSP90

Question 21

What is aggregation?

Answer 21

-partially folded or misfolded proteins
-expose hydrophobic residues and unstructured polypeptide backbone
-results in amorphous structures

Question 22

What does the Proteostasis Network do?

Answer 22

-monitors proteins throughout their life cycle (synthesis, folding, refolding, transport, and degradation)
-protein homeostasis

Question 23

What is Ubiquitin-proteasome proteolysis?

Answer 23

-for proteins that are targeted for degradation as part of cellular regulation

Question 24

What is lysosomal digestion?

Answer 24

-membrane-bound organelles containing proteases that can degrade exogenous proteins or aged/damaged organelles

Question 25

What is Autophagy?

Answer 25

-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

Question 26

Describe the Ubiquitin-proteasomal system (UPS)

Answer 26

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

Question 27

Describe the structure of a 26S proteasome

Answer 27

-20S Proteasome (core complex where actual degradation occurs)
-19S (x2) (where ubiquinated protein is recognized; where protein unfolding occurs)

Question 28

How do proteins get targeted by the 26S proteasome?

Answer 28

-By degrons (recognition sequence or structure for an E3 ligase)
-ex. N-end rule; PEST sequences; Posttranslational modifications (phosphorylation)