Advanced Biochemistry Exam 3

Role of General Transcription Factors in Initiation

bind to promoter region of gene to form the pre-initiation complex

Function of beta prime subunit of RNA polymerase holoenzyme in prokaryotes.

binds to and unwinds DNA

Holoenzyme + promoter

closed promoter complex

Lac Operon

consists of 3 structural genes (LacZ, LacY, LacA), promoter, terminator, regulator, and operator

RNA polymerases (do/do not) require a primer.

do not

Most eukaryotic RNA consists of coding regions, called __, and noncoding regions, called __.

exons; introns

RNA Processing: Removing Introns: Lariats

feature of splicing reactions for introns consists of a 2'-5' phosphodiester bond between a bulged adenosine and the 5' end of the intron

The DNA-binding proteins that recognize and accurately initiate transcription at specific eukaryotic promoter sequences are called __.

general transcription factors

__ of Ppi to inorganic phosphate by __ makes the polymerase reaction thermodynamically favorable.

hydrolysis; pyrophosphatases

What is the "Anfinson cage" and how does it assist protein folding?

hydrophobic core in chaperone where protein folding occurs; places hydrophobic amino acids on outside of final folded protein

Genetic Code: Triplet Code

idea that the genetic code is formed from 3 bases coding for each amino acid and the code starts from a specific point

What is the purpose of 5'-G capping and the addition of a 3' poly(A) tail to RNA?

increase stability; label as mRNA

Beta-galactosidase

intracellular enzyme that cleaves the disaccharide lactose into glucose and galactose

What is the purpose of the Shine Dalgarno sequence in translation?

locate rRNA of ribosome on start position for translation

__ direct the synthesis of proteins.

mRNAs

A(n) __ brings distant areas of DNA near promoters to affect transcription.

mediator

Nucleosome-Histone Interactions

move, restructure, or eject the nucleosome to allow for the interaction with transcription factors

Mediators

multiprotein complex that functions as a transcriptional coactivator by interacting with transcription factors and RNA pol II in which it transmits signals from the transcription factor to polymerase

Genetic Code: Not Overlapping

none of the base pairs are used two times; each part of one codon and that one codon specifies one amino acid

RNA pol holoenzyme binds __ to DNA with __ affinity and migrates __ looking for a sigma promoter region.

nonspecifically; low; downstream

Promoters

nucleotide sequences that identify the location of transcription start sites

open promoter complex

polymerase unwinds 12 base pairs in the -9 to +3 region

RNA Processing: Capping of mRNA

protects the 5' end of mRNA from degradation required for creation of stable and mature mRNA that is able to undergo translation

RNA Processing: polyA tail

protects the mRNA molecule from enzymatic degradation in cytoplasm aids in transcription termination, export of mRNA from nucleus, and translation

DNA Binding Protein Motifs: Helix turn helix

protein structural domain consisting of two successive alpha-helices separated by a sharp beta-turn used to recognize DNA on either side of the major groove via N helix and C helix

Protein degradation is compartmentalized either in macromolecular structures known as __, where targeted proteins are degraded, or in degradative organelles such as __, where nonspecific degradation occurs.

proteosomes; lysosomes

Core polymerase can transcribe DNA into RNA, but cannot __.

recognize promoters and initiate transcription

Acetylation

reduces the binding affinity and loosens the bond between chromatin and histones, thereby exposing DNA

Function of alpha subunit of RNA polymerase holoenzyme in prokaryotes.

scaffold and regulation; dimerize

Operon: Operators

sequence near the promoter which regulates the transcription start

DNA Start Sequences: Response Elements

short sequences of DNA within a gene promoter region that are able to bind specific transcription factors and regulate transcription of genes

Binding of __ subunit allows polymerase to recognize __.

sigma; different DNA sequences that act as promoters

RNA Processing: Removing Introns: snRNPs

small nuclear robonucleotide proteins RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome

__ are ribozymes that assist in cutting out introns in RNA processing.

snRNPs

Proteins with __ sequences remain embedded in the ER membrane with their __-termini on the cytosolic face of the ER.

stop transfer; N

The effects of a nonsense mutation are offset by a second mutation called a __.

suppressor

The RNA adapter molecule that interacts specifically with both nucleic acids and amino acids is __.

tRNA

Chromatin Remodeling

the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression

Genetic Code: Codon

three base pair section of the genetic fode which codes for one specific amino acid

Role of RNA pol II

transcribe mRNA, miRNA, snRNA, and snoRNA genes

Role of RNA pol I

transcribe rRNA genes

Role of RNA pol III

transcribe tRNA and 5S rRNA genes

DNA Binding Protein Motifs: Zn fingers

two different types: C2H2 and Cx C2H2: Cys-x2-Cys and His-x3-His domains separated by at least 7-8 amino acids; can be repeated ~13 times Cx: 4, 5, or 6 Cys residues separated by various numbers of other residues; proteins have a variable number of Cys residues available for Zn chelation

In general, proteins whose folding is chaperone-dependent start the folding process first with __ and then are passed as __ folded intermediates to __. a. Hsp40; un-; Hsp70 b. Hsp90; un-; chaperonin c. Hsp70; partially; chaperonin d. Hsp40; partially; Hsp70 e. Hsp60; partially; Hsp40

C

The actual peptide bond-forming step in translation is referred to as __, and is catalyzed by __. a. peptide bond formation; peptidase b. transpeptidation; transpeptidase c. peptidyl transfer; peptidyl transferase d. translocation; translocase e. none of the above

C

In the proteasomes, the 195 cap acts as a __ complex for the recognition and selection of __ proteins for __ by the 20S proteasome core. a. hydrolysis; unfolded; disposal b. regulatory; unfolded; disposal c. hydrolysis; ubiquitinylated; degradation d. regulatory; ubiquitinylated; degradation e. all are true

D

Nucleotide sequences that identify the location of transcription start sites and regulate the level of transcription are called: a. sigma factors b. Prinbow boxes c. TATA boxes d. promoters e. enhancers

D

Operons are a(n) __ sequence lying adjacent to the DNA being transcribed and are composed of a promoter located next to a(n) __ that interacts and is controlled by a(n) __ protein. a. initiation; operator; repression b. operator; repressor; regulatory c. regulatory; repressor; activator d. regulatory; operator; regulatory e. none are true

D

The Shine-Dalgarno sequence found in prokaryotic systems resides on the __ end of __ and is the __ site. a. 3'; peptidyl-tRNA; formyl transferase b. 5'; DNA; polymerase binding c. 3'; rRNA; initiation factor binding d. 5'; mRNA; ribosome binding e. 3'; aminoacyl-tRNA; formyl methionine binding

D

The __ strand has the same nucleotide sequence and direction as that of the RNA transcript, with the __ end of mRNA encoding the N-terminus of the protein. a. template; 3' b. template; 5' c. nontemplate; 3' d. nontemplate; 5' e. lagging; 5'

D

The folding cycle in the GroES-GroEL complex of E. coli utilizes the following sequence: A - ATP binding to GroEL B - GroES dissociates from the complex C - Partially folded protein hydrophobic residues bind GroEL D - GroES is recruited to GroEL E - GroES promotes ATP hydrolysis and alpha-subunits undergo a conformational change that buries the hydrophobic patches a. A, B, C, D, E b. B, A, C, D, E c. C, D, A, E, B d. C, A, D, E, B e. D, C, E, A, B

D

DNA Start Sequences: Silencers

DNA sequence capable of binding transcription regulation factors (repressors); prevents RNA pol from transcribing DNA into RNA prevent genes from being expressed as proteins

Operon: Promoter

DNA sequence which identifies and binds to the primary transcription site where transcription begins

All RNAs are synthesized from DNA templates by __?

DNA-dependent RNA polymerases

All are correct about enhancer sequences in eukaryotic cells EXCEPT: a. they can occur either upstream or downstream of the gene b. they can be in either orientation (bi-directional) c. enhancer function is dependent on recognition by a specific transcription factor d. specific transcription factor binding at an enhancer stimulates transcription by interacting with RNA pol II e. all are correct

E

All are true for the "wobble position" EXCEPT: a. it is the third base of the codon b. a certain amount of play might occur in base pairing at this position c. the first-base anticodon U could recognize either an A or G in the wobble position d. the first-base anticodon G could recognize either a U or C in the wobble position e. all are true

E

One of the termination mechanisms in bacteria utilizes the __ factor that is an ATP-dependent helicase. a. alpha b. beta c. gamma d. delta e. rho

E

The appropriate order for the basic steps of protein synthesis are: A - the elongation reaction transfers the peptide chain from the peptidyl-tRNA in the P site to the aminoacyl-tRNA in the A site B - the P site is occupied by peptidyl-tRNA carrying the growing polypeptide chain C - binding of mRNA by the small subunit followed by association of a particular initiator aminoacyl-tRNA that recognizes the first codon D - the large ribosomal subunit joins the initiation complex, preparing it for the elongation stage E - the new, longer peptidyl-tRNA moves from the A site into the P site as the ribosome moves one codon further along the mRNA a. A, C, E, B, D b. B, E, C, D, A c. C, D, A, B, E d. D, C, E, B, A e. C, D, B, A, E

E

The subunit in E. coli RNA pol which is required for recognition of the promoter sequence is: a. rho b. alpha c. beta d. beta prime e. sigma

E

T/F: Addition of SUMO targets a protein for destruction by a slightly different pathway than attachment of ubiquitin.

F

T/F: All chaperones bind and release from their target proteins via cycles of ATP binding and hydrolysis.

F

T/F: All proteins follow the same pathway through the various chaperones during their folding.

F

T/F: Eukaryotic translation always begins with fmet-tRNAi^fmet.

F

T/F: The Hsp70 proteins bind to hydrophilic regions of the protein, thus preventing aggregation.

F

T/F: The lac operon is negatively controlled via the lac repressor, a protein that only binds to DNA in the absence of lactose.

F

Lac Operon Structural Genes

LacZ - encodes beta-galactosidase LacY LacA

List 2 major structural motifs of DNA binding proteins.

Zn finger; leu zipper, helix turn helix

Operon: Structural Genes

a gene that codes for any RNA or protein product other than a regulatory factor

DNA Start Sequences: Enhancers

a short region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur

Core polymerase structure

alpha x 2, beta, beta-prime

Subunits of RNA polymerase holoenzyme.

alpha x 2, beta, beta-prime, sigma

RNA Processing: Removing Introns: Spliceosomes

assembled from snRNAs and SR protein removes introns from a transcribed pre-mRNA, a type of primary transcript

DNA Start Sequences: Promoters: Consensus Sequences

TATA box INR box BRE CCAAT-box GC-box

Prokaryotic Promoters

TATA box at -10 region; -35 region TTGACA

Roles of CDT Regions

(C-terminal domain) exists only in RNA pol II and stretches from the core to the exit channel involved in initiation of transcription, capping of RNA transcript, and attachment to the spliceosomes

Four stages of transcription

1. Binding of RNA pol holoenzyme to template DNA at promoter sites; 2. initiation of polymerization; 3. chain elongation; 4. chain termination

DNA Binding Protein Motifs: Leu Zippers

28-residue sequence with Leu every 7th position and a "basic region" aka dimerization motif because it is dimerized either as homo- or hetero-dimers homodimers - recognize dyad-symmetric DNA heterodimers - recognize non-symmetric DNA

RNA polymerase moves along the template strand in the __ direction, and the RNA chain grows in the __ direction.

3' --> 5'; 5' --> 3'

Amino-acyl tRNA synthetases catalyze the reaction of a: a. specific amino acid attachment to the 3'-OH at the 3'-CCA of a specific tRNA b. specific amino acid attachment to the 5'-OH at the 5-CCA of a specific tRNA c. specific tRNA with ATP to form a so-called "charged tRNA" that interacts with a specific site on mRNA d. all of the above e. none of the above

A

The ribosome and the __ form a common conduit for transfer of the nascent protein through the __ membrane. a. translocon; endoplasmic reticulum b. signal sequence; plasma c. EF-G; endoplasmic reticulum d. chaperonin; plasma e. all are true

A

__ recognize the sorting signals as they emerge from the ribosome and, together with __, deliver the nascent protein chain to specific membrane complexes called __ that mediate integration into and across the membrane. a. signal recognition particles; signal receptors; translocons b. signal receptors; translocons; signal recognition particles c. translocons; signal recognition particles; signal receptors d. signal receptors; signal recognition particles; translocons e. translocons; signal receptors; signal recognition particles

A

Enzymes that acetylate the epsilon-amino group of lysine in the histidine tails are called__ and are involved in __. a. histone deacetylases; restoring chromatin to a repressed state b. histone acetyltransferases (HATs); initial events in transcriptional activation c. histone activases; formation of the de-repression complex d. Schiff base formation; promoting the formation of closed complexes e. none of the above

B

In E. coli, __ bound to large ribosomal subunits facilitates transfer to __ to bind __ residues, thus avoiding non-productive folding. a. chaperonin; trigger factor; H-binding b. trigger factor; DnaK; hydrophobic c. DnK; Hsp70; ionic d. Hsp70; chaperonin; hydrophilic e. all are true

B

Most eukaryotic RNA consists of coding regions, called __, and noncoding regions, called __. a. introns; exons b. exons; introns c. spliceons; codons d. codons; spliceons e. introns; codons

B

The genetic code has all of the following characteristics EXCEPT: a. it is degenerate b. it is read 3'-->5' c. it is read from a fixed starting point without punctuation d. it is not overlapping e. a group of three bases codes for one amino acid

B

The initial event in the conversion of an hnRNA to the mature RNA which leaves the nucleus is: a. formation of ribonucleoprotein particles (RNPs) b. capping the 5' end of the transcript with a guanylyl group by guanylyl transferase c. addition of a poly(A) tail to the 3' end of the transcript by pol(A) polymerase d. splicing together of the exons e. transesterification reactions in lariat formation

B

The proper sequence for transport of mitochondrial matrix proteins would be: a. TOM; TIM22 b. TOM; TIM23 c. SAM; TOM; TIM22 d. TOM; SAM; TIM22 e. SAM; TOM; TIM23

B

The strand of dsDNA that is read by RNA pol is termed the __ strand with RNA pol moving __along it. The polymerase forms a __, growing in the __ direction. a. template; 5'-->3'; transcript; 3'-->5' b. template; 3'-->5'; transcript; 5'-->3' c. transcript; 3'-->5'; template; 5'-->3' d. nontemplate; 5'-->3'; template; 3'-->5' e. nontemplate; 3'-->5'; template; 5'-->3'

B

nonsense suppression is the production of isoacceptor tRNAs called __ tRNAs that read __ codons and insert an amino acid. a. nonsense; nonsense b. suppressor; nonsense c. suppressor; suppressive d. nonsense; suppressive e. codon; anticodon

B

A highly conserved protein that is involved in protein degradation is: a. ricin b. met-aminopeptidase c. ubiquitin d. degradase e. peptidyl transferase

C

All are characteristics of eukaryotic mRNA EXCEPT: a. pol(A) tail b. no Shine-Dalgarno sequence c. codon-binding directs for an initiator tRNA carrying Met d. 5'-7-methyl-GTP cap e. all are characteristics

C

Elongation factor Tu (EF-Tu): a. binds GTP promoting translocation of ribosomes along mRNA b. displaces GDP rom the elongation complex c. binds aminoacyl-tRNA in the presence of GTP d. binds initiator tRNA and GTP e. binds to 30S subunit and drives mRNA binding

C

__ can act as a chaperone at low temps, but as a protease at high temps.

HtrA

RNA polymerases link __ in the order specified by base pairing with a DNA template.

NTPs

Function of beta subunit of RNA polymearse holoenzyme in prokaryotes.

Part of polymerase active site

Transcription is initiated in prokaryotes by __.

RNA polymerase holoenzyme

T/F: Intact 70S ribosomes are inactive in initiation of protein synthesis because only free 30S subunits can interact with initiation factors.

T

T/F: The genetic code degeneracy is most likely to occur on the 3' end of the codon.

T

T/F: cAMP enhances CAP's affinity for DNA.

T