1st sem transcription and translation

Question 1

eukaryotic RNApol 1

Answer 1

5.8S 18S and 28S ribosomal RNAs, and some small RNAs

Question 2

eukaryotic RNApol 2

Answer 2

transcribes genomic mRNA

Question 3

eukaryotic RNApol3

Answer 3

tRNAs, 5S rRNA, and small RNAs

Question 4

what RNA polymerase trasnlates mitochondrial mRNAs

Answer 4

a unique mitochondrial RNA pol (not 1, 2, or 3)

Question 5

function of EF-Tu

Answer 5

prokaryotic elongation factor, mediates entry of an aminoacyl-tRNA into the A site of a ribosome when bound to GTP. GTP hydrolysis provides a proofreading step.

Question 6

function of EF-Ts

Answer 6

prokaryotic elongation factor, A GTP-exchange factor for EF-Tu

Question 7

function of EF-G

Answer 7

Mediates movement of tRNAs from the A and P sites to the P and E sites, by GTP hydrolysis.

Question 8

How is tranlsation terminated in prokaryotes?

Answer 8

By Release Factors (RFs). RF1 or RF2 plus RF3
RF1 binds UAA and UAG codons. RF2 binds UAA and UGA codons. RF3 binds the release of the factors and dissolution of the ribosome, mRNA, peptide complex.

Question 9

Retention signal for ER proteins

Answer 9

KDEL retrieval sequence for ER luminal proteins. Lys-Asp-Glu-Leu. Bound by some ER lumen receptor to retain them.

KKXX retrieval sequence for resident ER membrane proteins.

Question 10

COP I mediates transport from where to where

Answer 10

from golgi back to ER, retrograde transport

Question 11

COP II mediates transport from where to where

Answer 11

from ER out to golgi, anterograde

Question 12

Clatrin mediates transport from where to where

Answer 12

from membrane to intracellular vesicles, and from golgi to lysosomes.

Question 13

Peptide targeted to mitochondria

Answer 13

Signal sequence is alpha helix of positive charged a.a.s on one side and hydrophobics on the other.
Must be unfolded to be read, and is maintained in cytosol by chaperone proteins.
Transport is mediated by TOM, TIM, and SAM protein transporters in the mitochondrial membranes.
Membrane anchoring sequences are stretches of hydorphobic regions.

Question 14

Dynamin function

Answer 14

a GTPase which surrounds and pinches off the inward-budding membrane for ENDOCYTOSIS of vesicles.

Question 15

v-SNARES is

Answer 15

synaptobrevin

Question 16

t-SNAREs are

Answer 16

Syntaxin and Snap25

Question 17

a trans-SNARE complex is-

Answer 17

A bound t-SNARE and v-SNARE complex.

Question 18

Endocytosis is mediated by

Answer 18

Clathrin and dynamin-GTP

Question 19

Exocytosis is mediated by

Answer 19

t-SNARES, v-SNARES, Ca++

NSF-ATPase is used AFTER fusion in order to unwind the bound trans-SNARE complex.

Question 20

Rab proteins

Answer 20

Monomeric GTPase proteins used to identify membranes within the cell, and for intracellular vesicular transport.

Every type of vesicle expresses a different, unique Rab GTPase protein.

Inactive in its GDP bound state.

When GTP bound, it recruits Rab-Effector proteins, which recruit/are motor proteins that bind to Rab-GTP and facilitate movement of the vesicle to its target membrane..

At target membrane, the Rab-GTP binds another Rab-effector protein, a tethering protein in its target membrane which positions the v-SNAREs and t-SNARES in position to interact.

Question 21

Ran proteins

Answer 21

Used for nuclear transport.
Stimulates the dropping of cargo from nuclear import receptors and their nuclear export.
Stimulates the binding of nuclear export receptors with their cargo and their export.

Question 22

ER protein modifications

Answer 22

1) Addition of the Precursor Oligosaccharide: 14 sugar block of N-acetylglucosamine, mannose, and glucose, in that order with 2 glucose being the most exterior and 9 Mannose units in the middle.

Bound to the side chain of an Aparagine.

Glucose are removed as the protein is processed, but are continually added BACK (using UDP-glucose) by a resident glucosylase that binds unfolded proteins.

Calnexin and calreticulin are ER membrane integral proteins that bind proteins with a single glucose moeity, preventing unfolded proteins from leaving ER.

The underlying mannoses are also gradually cleaved in the time betweeen glucose cleavage and re-addition, and are used as a time indicator of how long a protein has remained in the ER in an unfolded state, if it can’t fold properly before too many of the mannose are removed, it is targeted for degradation.

and N-glycanase in the cytosol removes this tag once the protein has been released to the cytosol

Question 23

Misfolded protein response

Answer 23

Misfolded proteins in the ER bind 3 transmembrane ER receptors: IRE1, PERK, and ATF6.

on ligand binding:
IRE1 autophosphorylates, then is an active EndoRiboNuclease which cleaves a cytosolic mRNA to an actively spliced form, inducing expression of a transcription factor, stimulating HS-protein expression.

PERK autophosphorylates, and then is a kinase that inactivates Initiation Factors for protein translation.

ATF6 translocates to the Golgi where its cytosolic portion is cleaved, which then acts as a transcription factor stimulating HS-proteins and other proteins of the misfolded protein response.

Question 24

Lac Operon

Answer 24

Components:

2 Operator sequences - 1) cAMP-CAP binding site 2) repressor binding site.
Promoter - where sigma subunit of RNA-pol binds.
LacZ gene - codes for beta-galactosidase
LacY gene- codes for permease
LacA gene- codes for transacetylase
Terminator sequence

Mechanism:
Lac repressor protein (Rep) normally binds to the operator region.

If lactose is present, lactose binds to Lac-Repressor protein and inactivates it, allowing for the possibility of genes to be transcribed.

Transcription is very low if glucose concentration is high.

If glucose concentration drops, {cAMP} increases (after [AMP] increases.

cAMP-CAP complex forms and binds the cAMP-CAP operator site (promoter) inducing meaningful gene transcription, by increasing RNApol affinity about 50X.

Question 25

What is an operon

Answer 25

A group of prokaryotic genes that are regulated and transcribed together as one polycistronic mRNA.

Question 26

What is the other name for the Anaphase Promoting Complex?

What type of reaction does it catalyze and what are its main targets?

Answer 26

Cyclosome, APC/C.

A ubiquitin ligase that targets the Securin proteins and the S- and M- cyclin proteins.

Securins attach the sister chromatids together, so its degradation allows them to be pulled apart (anaphase)

S- and M- cyclins need to be destroyed so that anaphase can complete and the cell can proceed back to G1/G0