Cell Biology Exam 2

A specific endonuclease recognizes the tail recognition sequence (AAUAAA) and cuts the growing RNA molecule ___ to ____ bases downstream just after a 5′-CA-3′ dinucleotide. Beyond the cutting site is a ______ tract that is also involved in recognition.

1. 10-30 2. GU-rich (he said this question may be on the test/TBL)

1. The first transesterification reaction form the lariat and contains a ____-____ phosphodiester bond. 2. The second transesterification reaction excise the lariat by forming a ____-____ phosphodiester bond.

1. 2' -5' phosphodiester bond 2. 3' -5' phosphodiester bond

eukaryotic genes have ______ steps of transcription while prokaryotic genes have _____ steps. What is the step that is different?

1. 3 2. 4 3. prokaryotes have the preliminary step of promoter recognition by σ factor of the holoenzyme (RNA polymerase)

1. Polymerase advances [core enzyme(α2ββ'ω)] ___ to ___ on template stand. 2. Nascent RNA is transcribed in a ___ to ___ direction beginning at the promoter site.

1. 3' to 5' 2. 5' to 3'

Newly made RNA strands are always transcribed ____ to ____ and they are complimentary to and in opposite polarity to the DNA bases of the ________ strand.

1. 5' to 3' 2. template anti-sense strand

The cap on mRNA consists of guanosine triphosphate within an unusual ________ bond preceding a small 5' UTR. The enzyme for this reaction is ______. This is added shortly after transcription starts.

1. 5'-5' phosphotriester 2. guanyl transferase

After addition of the GTP, the guanine base has a methyl group attached at the ____ position. The enzyme for this reaction is _____. This structure is known as a _____ structure.

1. 7 position 2. methyl transferase 3. "cap0"

prokaryotes: RNA polymerase (α2ββ'ωσ) (holo enzyme) transcribes ___ to ___ bases before falling off. Then ______ completes the RNA elongation.

1. 7 to 9 2. RNA polymerase (α2ββ'ω) (core enzyme)

The tail of RNA polymerase is known as the ________. It consists of a seven-amino acid sequence (Tyr Ser Pro Thr Ser Pro Ser) repeated approximately 50 times. ______ must phosphorylate the serine or threonine residues before RNA Pol II can be released from the promoter. This transcription factor moves along the DNA with RNA Pol II and begins the process of transcription.

1. CTD (carboxy-terminal domain) 2. TFIIH

_____ binds to the AAUAAA sequence and ______ binds to the GU-rich tract in Poly (A) tail addition. These provide a platforms provide for assembly of which 3 other regulatory proteins?

1. Cleavage and polyadenylation specificity factor (CPSF) 2. Cleavage stimulation factor (CST) 3. cleavage factor (CF), poly(A) polymerase and poly(A)-binding protein (PABP).

______ is an allosteric proteins that is required for switching on the genes for using lactose which are less favored than glucose. For this protein to bind to DNA is must first bind ______ to form dimers. The presence of these dimers aids RNA polymerase binding to the promoter.

1. Crp or CAP 2. cAMP

what are the 2 different domains within transcription factors?

1. DNA binding domain 2. activation domain

what are the 2 different types of endogenous agents in DNA mutation? what are the 4 different types of exogenous agents?

1. Endogenous agents include reactive oxygen species and DNA replication errors. 2. Exogenous agents include Sunlight, Radiation, Mutagens, Viruses

the core promoter for RNA polymerase I is rich in _____ sequences. The ____ protein recognizes and binds to both the upstream control element and the core promoter along with ______. Finally, RNA polymerase I binds with the help of general transcription factor ______, and transcription commences.

1. GC sequences 2. UBF1 3. SL1 4. TFIA

When no lactose is available, ________ binds to the operator sequence which overlaps the promoter region of this operon and turns off the operon. When lactose (inducer) is present, it binds and ______ the repressor from the operator site, and the operon is turned on to start transcription.

1. Lac repressor (LacI) 2. removes

1. _______- encodes lactose permease , a transport protein 2. ______ - the transacetylase gene 3. ______ - inducer gene of the lac operon, the I gene is a gene which codes for a repressor protein

1. LacY gene 2. LacA gene 3. Lac I gene

single strand DNA breaks are easily repaired by ______. double strand breaks are _____ (more/less) difficult to repair.

1. Ligase 2. more

_____ experiment is used to visualize introns. What is the formula for determining the number of introns/exons in this experiment?

1. R-Loop analysis 2. Number of R-loop (n)= number of introns (n) = (n+1) number of exons in the gene

________ opens up the DNA to form the transcription bubble and thus initiate transcription at +1 nucleotide of the DNA and form first 3'-5' phosphodiester to the RNA chain.

1. RNA polymerase (α2ββ'ωσ) (holo enzyme)

1. RNA polymerase ____ synthesizes rRNA. 2. RNA polymerase ____ synthesizes 5S rRNA and tRNA. It also makes small nuclear RNAs (snRNAs). 3. RNA polymerase ____ synthesizes mRNA (protein coding).

1. RNA polymerase I 2. RNA polymerase III 3. RNA polymerase II

During ρ-dependent termination, ______ accompanies the RNA polymerase as it synthesizes the growing mRNA. Once the recognition site for this protein is made, it binds to form a conformational change and untwists the mRNA strand from the DNA.

1. Rho

the GC box is recognized by the _____ transcription factor. The octamer element is recognized by both the ____ and ____ proteins, which are located in different body tissues.

1. SP1 2. Oct-1 and Oct-2

label the transcription factor corresponding to its function: 1. ____ - bind upstream of TATA box, required for binding of RNA Pol II to the promoter 2. ____- accompanies RNA Pol II as it binds to promoter 3. ____ and ____ - required for promoter clearance and elongation 4. ____ - binds to TATA box and is a part of TFIID

1. TFIIA 2. TFIIF 3. TFIIE and TFIIJ 4. TBP

The binding of ______ to the TATA box via TBP is the first step of transcription initiation. ____ and ____ bind next. Finally, RNA polymerase II arrives, accompanied by ______, which probably helps RNA polymerase bind.

1. TFIID 2. TFIIA and TFIIB 3. TFIIF

label the transcription factor corresponding to its function: 1. ____ - phosphorylates the tail of RNA Pol II, retained by polymerase during elongation 2. ____- binds downstream of TATA box, required for binding of RNA Pol II to promoter 3. _____- includes TBP, recognizes Pol II specific promoter

1. TFIIH 2. TFIIB 3. TFIID (=TBP + TAFs)

Transcription of class III genes requires the binding of either of two proteins known as ______ and ______ to a region over 50 bp downstream from the start site. Once these have bound, they enable _____ to bind to the region around the start of transcription.

1. TFIIIA and TFIIIC 2. TFIIIB

______ snRNA recognizes the sequence flanking the branch point A and ______ snRNA recognizes the 5′ splice site. Branch point A has only free 2' OH for _______ reaction

1. U2 2. U1 3. transesterification

match the following snurp with its function: 1. _____ and _____ bind to U2. 2. _____ binds the 5′ splice site 3. ______ displaces U1 from the spliceosome and U4 departs as well. 4. _____ binds the 3′ splice site. 5. _____ binds to the downstream exon. 6. _____ binds the branch site.

1. U4 and U6 2. U1 3. U6 4. U2AF 5. U5 6. U2

Lac-operon produces _______ to break down lactose into Galactose and Glucose. Lac-operon is regulated by lactose and glucose.

1. beta-galactosidase

Mature eukaryotic mRNA has _____ structure at the 5' end and _____ structure at the 3' end due to RNA Processing. Eukaryotic pre-mRNA undergoes ______ to remove introns after capping and poly (A) tailing of pre-mRNA is complete.

1. cap 2. Poly (A) 3. splicing

After cap0, further methyl groups may be added to the ribose sugars. This gives rise to the _____ and _____ structures. The cap2 structure is especially typical of mammalian mRNA and appears to _____ (increase/decrease) the efficiency of translation.

1. cap1 and cap2 2. increase

Once this polyadenylation complex is assembled, the RNA is cut by the ______ and a poly(A) tail is added by the _______. The tail consists of 100-200 adenine residues

1. cleavage factor (CF) 2. poly(A) polymerase

______ are the coding sequences of genes and _____ are the non coding sequences.

1. exons 2. introns

true/false: The promoter region is far from the start site and usually binds several transcription factors. 2. Binding of the transcription factors to enhancer sequences influences polymerase activity and gene expression.

1. false -close to the start site 2. true

true/false: 1. there are 2 defined spacer elements in the coding strand containing 17-19 and 5-9 base sequences, respectively, that are not essential to transcription. 2. The strength of a promoter depends partly how closely it matches the ideal consensus -10 and -35 sequence

1. false -they are essential 2. true

true/false: 1. Cap promotes mRNA degradation by nuclease and destabilizes mRNA. 2. Cap is required for efficient translation of mRNA

1. false 2. true

which enzymes catalyze the following reactions in capping? 1. _____- adds GMP by 5'-5' linkage 2. _____- adds methyl group to guanosine 3. _____-adds methyl groups to 2' hydroxyl oxygen of bases 1 and 2

1. guanyl transferase 2. methyl transferase 3. methyl transferase

The end of a gene is marked by a terminator sequence that forms a _____ structure in the RNA. When RNA polymerase sees this structure in the RNA followed by a _______ stretch, it terminates RNA synthesis. This is known as _______ termination.

1. hairpin 2. poly (U) stretch 3. ρ-independent termination

match the 4 DNA-binding domains with their descriptions: 1. ______-Motif is an amphipathic α−helix with hydrophobic amino acids concentrated to one side (Leu every 7th position). Found in many eukaryotic transcription factors and a few prokaryotic proteins 2. ______- Steroid hormone receptors. Most common DNA binding motif in human genome. 3.______- Some bacterial repressors. In eukaryotes, homeodomain proteins which have master control functions in development. 4. ______-Two α-helical regions linked by a loop of variable length. Common structural motif in proteins implicated in the development of multi-cellular eukaryotic organisms

1. leucine zipper 2. zinc fingers 3. helix-turn-helix 4. helix-loop-helix

1. Only when glucose runs out, the other sugars are consumed. The genes for using these other sugars (such as lac operon for lactose) is turned ______. 2. When glucose is available, the genes for using other sugars (such as lac operon for lactose) is switched _____ because lac repressor is bound to the operator site.

1. on 2. off

The promoter lacP is regulated by binding of the repressor at the ______, and of Crp protein at the Crp site. Crp are _______ receptor proteins and are also called CAP. The single lac mRNA is translated to produce which 3 proteins?

1. operator, lacO 2. cyclic AMP 3. LacZ (β-galactosidase), LacY, and LacA proteins.

Direct breaks in the phosphate backbone after ionizing radiation are caused by the impact of _____ on DNA. Indirect breaks are caused by the creation of _______, which attack the DNA.

1. photons 2. reactive oxygen species

1. in ____ regulation, the presence of an activated regulatory protein helps in the binding of RNA polymerase. 2. in _____ regulation, activation of a repressor-blocking promoter releases it from the gene and allows RNA polymerase to bind.

1. positive 2. negative

A newly synthesized RNA molecule is called a _________. These further undergo _______ to become mature RNA. The RNA is trapped inside the nucleus until it is completely processed.

1. primary transcript 2. RNA processing

Alkylating agents mutate DNA by attacking the ______. Many carcinogens mutate DNA by the addition of _______ to bases.

1. purine ring 2. bulky side groups

Prokaryotes: Polymerase recognition occurs by the _______ and/or holoenzyme (α2ββ'ωσ) binding to the _____ and _____ boxes of the prokaryotic promoter

1. sigma factor 2. -10 sequence (TATAAT) and -35 sequence (TTGACA)

Introns are removed from pre-mRNA by splicing carried out by _______. This consists of several ribonucleoproteins ("snurps") numbered ____ through ____.

1. spliceosome 2. U1 through U6 (U3 missing)

_______ is the synthesis of an RNA copy (rRNA, tRNA,mRNA) of information that is encoded on DNA. Genes are expressed by making ______.

1. transcription 2. RNA

A variety of proteins that interact with cis-acting elements, known as ______, are also needed for the correct functioning of eukaryotic RNA polymerases. These may be divided into 2 categories known as _____ and _____.

1. transcription factors 2. General transcription factors (TFI for RNA polI, TFII for RNA pol II, TFIII for RNA pol III) OR Specific transcription factors (Activators and repressors proteins in eukaryotes)

The assorted __________ bind to and recognize specific sequences on the DNA. These DNA sequences are of two major classes, those comprising the promoter itself, _______, and a variety of enhancer sequences.

1. transcription factors 2. Proximal promoters

when a pyrimidine is substituted for a pyrimidine during mutation it is known as a ______. When a purine is substituted for a pyrimidine (and vice versa) it is known as a ______.

1. transition 2. transversion

true/false: 1. The stretch of DNA in front of a gene (i,e., at the 5'end) is referred to as upstream region 2. The first base of the mRNA for a protein-coding gene is the first base of the protein coding sequence (A of AUG codon)

1. true 2. false

true/false: 1. All eukaryotic RNAs (rRNA, tRNA, and mRNA) are processed to produce functional mature RNA 2. there is similar processing of RNAs in prokaryotes 3. only mature RNAs participate in protein synthesis in eukaryotes

1. true 2. false 3. true

true/false: 1. The TFII proteins are general transcription factors because they are always required. 2. The upstream elements are the recognition sites for many of the specific transcription factors. 3. Binding of the specific transcription factors hinders the assembly of the transcription apparatus and therefore decreases the frequency of initiation.

1. true 2. true (specific transcription factors most commonly bind to TFIID) 3. false -helps assembly of the transcription apparatus and therefore increases the frequency of initiation.

The enzyme ______ splits lactose into galactose plus glucose. It can also interconvert lactose with its isomer, _______, which is the true inducer of the lac operon.

1. β-galactosidase 2. allo-lactose (not lactose itself)

1. Polymerase recognizes stop sequence on template strand during ___________ (ρ-independent/ρ-dependent) termination. 2. Polymerase stalls then falls off DNA complex during __________ (ρ-independent/ρ-dependent) termination.

1. ρ-independent 2. ρ-dependent

A single transcribed unit of DNA yields an initial RNA molecule of 45S in nucleus, a special zone of the nucleus. The 45S RNA is processed to yield the final _____ and _____ subunits of rRNA.

18S and 28S

what kind of bonds are formed during RNA synthesis?

3' -5' phosphodiester bonds

which of the following is not a common upstream element? a. TATA box b. GC box c. CA AT box d. Octamer element e. AP1 element

A

Transcripts destined to become mRNA have a tail recognition sequence—________—close to the 3′ end. The RNA polymerase that is making the RNA molecule continues past this point.

AAUAAA

Poly (A) addition site is located between ______ and ______ sequences.

AAUAAA and GU rich

mRNA can be controlled by all of the following except? a. RNA polymerase II b. general transcription factors c. temperature d. regulatory proteins

C

which of the following is not a transcription factor required for the release of RNA polymerase II from the promoter and elongation of RNA? a. TFIIF b. TFIIJ c. TBP d. TFIIH

C

The _____ strand has the same sequence of the RNA & same 5'-3' direction (only T is replaced by U).

Coding strand (sense or non-template strand)

which of the following is not one of the 4 types of DNA-binding domains? a. zinc finger b. helix-turn-helix c. leucine zipper d. B pleated sheet e. helix-loop-helix

D

which of the following is not one of the 4 primary differences in the regulation of transcription between prokaryotes and eukaryotes? a. eukaryotes have many more gene regulatory proteins b. RNA polymerase II cannot start itself in eukaryotes and requires many different transcription factors for initiation and upstream regulation c. eukaryotic DNA is packaged into chromatin d. eukaryotes are polycistronic while prokaryotes are monocistronic

D -eukaryotes are monocistronic while prokaryotes are polycistronic

_______ is the ultimate source of all genetic variation.

DNA mutation. -Most DNA mutation (variation) within genes is silent due to redundancy of the genetic code

_____ and ____ bind to RNA Pol II and pause transcription of the gene after the transcript has been initiated. When these 2 proteins are phosphorylated along with CTD, transcription continues.

DSIF and NELF

which of the following is not a step in intron splicing? a. free 5′ end of the intron loops around and is joined to the adenine at the branch site b. intron is released as a branched lariat structure that is later degraded c. intron and exon are cut apart at the 5′ splice site d. intron displaced from the 3′ splice site e. all of the above are steps

E

The most frequent class of intron in eukaryotic nuclear genes is the ______ group of intron variants.

GT-AG (or GU-AG in RNA code)

In the laboratory, the lac operon is induced by _______ because it is not degraded by β-galactosidase, the product of the LacZ gene that this induces.

IPTG (iso-propyl-thiogalactoside)

_____ stays associated with the mRNA and binds to the poly(A) tail. It also binds to the other end and appears to protect the cap from being cut off.

PABP

Antibiotic _____ or ______ is an inhibitor of bacterial RNA polymerase but not mammalian RNA polymerases and can be used to treat tuberculosis.

Rifamycin or Rifampin

RNA polymerase enzyme copies RNA from DNA. ______ synthesize all 3 classes of RNAs (rRNA,tRNA,mRNA) in prokaryote

Single RNA polymerase

the _______ assembles RNA polymerase II and general transcription factors to form pre-initiation complex. RNA polymerase II transcribes most eukaryotic genes that encode proteins.

TATA box

Eukaryotic cells can sometimes choose to use different splice sites within the same gene during a process called _________. This allows a single original DNA sequence to be used to make several different proteins that have distinct but overlapping functions.

alternative splicing

Eukaryotic promoters are ______, which means that they contain a core promoter + upstream control elements.

bipartite

In the absence of glucose, _____ binds to crp or CAP which then binds to Crp (CAP) site upstream of the promoter

cAMP

_____ to _____ is the most common DNA mutation in the human genome. This occurs via deamination reaction.

cytosine to thymine

______ sequences are most often located far from the genes they control and promote the initiation of transcription as a result of binding specific transcription factors. They must make contact with the transcription apparatus.

enhancer sequences -repressors can also repress transcription at a distance

true/false: Transcriptional Regulation in Eukaryotes Is Less Complex Than in Prokaryotes

false -more complex

In front of each gene is a region of regulatory DNA sequence that is not transcribed which contains the _______. These sequences can control gene transcription.

gene promoter sequences

the _______ complex allows contact of the activators and/or repressors with the RNA polymerase and transmits information. It combines the signals from multiple activators and/or repressors and sends the final result to the RNA polymerase II enzyme.

mediator complex

_______ - Any sequence of DNA or RNA that could, in theory, encode a protein without interrupted by stop codon prematurely.

open reading frame

The site where the repressor binds is called the ______ sequence

operator

Prokaryotic genes are _______. This means that several genes are transcribed as single RNA from the same operator and promoter.

polycistronic

5' splice sites, 3' splice site, and branch site on the pre-mRNA are recognized by ______ of snurps

snRNAs

The ________ promoter has emerged as a target of cancer-specific mutations due to shortening of DNA sequences.

telomerase reverse transcriptase (TERT)

_______ can be caused by point mutations in sequence elements that lead to dysfunctional globin mRNA or protein.

thalassemia

true/false The lacI gene that encodes the LacI repressor has its own promoter and is transcribed in the direction opposite to the lacZYA operon

true

true/false: Production of an abnormally spliced transcript of Ron (MST1R) proto-oncogene has been found to be associated with increased levels of the SF2/ASF in breast cancer cells. The abnomal isoform leads to cell motility which can cause cancer.

true

true/false: The two strands of the DNA to be transcribed are separated locally.

true

true/false: the genes and mRNA that encode histones are regarded as "special" and do not get a poly(A) tail but are processed differently

true

true/false: it is believed that over 60% of human disease causing mutations affect splicing rather than directly affecting coding sequences.

true (ex. DNMT gene mutations from abnormal splicing may cause cancer)

true/false: RNA polymerase II can bind and initiate transcription at a minimal promoter consisting of just initiator and TATA boxes.

true -However, this is extremely inefficient unless upstream elements are also present

true/false unlike prokaryotes, eukaryotes can control transcription when bound to DNA far away from the promoter.

true -These DNA sequences are called gene control region (or cis-acting elements) including the promoter and are within 200 bps of the +1 site.

Adjacent Thymine nucleotides can be cross-linked by ________, forming thymine dimers

ultraviolet light

there are regions at each end of the mRNA that do not code for translation known as _______.

untranslated regions (5' and 3' UTRs)

_______ is a toxin and inhibitor of RNA polymerase II produced by certain mushrooms. Eating those mushrooms causes severe gastrointestinal discomfort and liver damage.

Αlpha-amanitin

_____ recognizes promoter and initiates transcription. This allows for RNA chain elongation.

σ factor