MCB Exam 3 Sapling/Discussion Questions

Identify the functions of an enhancer in transcription: -A cis-regulatory element that regulates gene transcription in specific tissues or cells -A cis-acting regulatory sequence of DNA that reduces levels of transcription -Regulates transcription by providing a cluster of binding sites where transcription factors can bind -Inhibits transcription by blocking the RNA polymerase from the promoter -Begins gene expression by disabling repressors and binding to the repressor elements

-A cis-regulatory element that regulates gene transcription in specific tissues or cells -Regulates transcription by providing a cluster of binding sites where transcription factors can bind

Identify the statements that are features of a promoter: -In prokaryotes, the promoter is recognized by general transcription factors which recruit the RNA polymerase holoenzyme -In prokaryotes, the promoter contains a -35 and -10 region upstream of the transcription start site -In both prokaryotes and eukaryotes, the promoter is located in the 5' direction, upstream from the transcription start site -In eukaryotes, the promoter attracts the small and large ribosomal subunits with the help of initiation factors -In eukaryotes, the promoter recruits the preinitiation complex, which includes the TATA-binding protein (TBP, subunit of TFIID)

-FALSE: in prokaryotes, the promoter is recognized by the sigma factor which helps to form the holoenzyme -TRUE -TRUE -FALSE -TRUE

Which of the following are components of the prokaryotic 30S initiation complex that is required for protein synthesis? -IF-3 -50S ribosomal subunit -mRNA -IF-1 -30S ribosomal subunit -tRNA ^ala

-IF-3 -mRNA -IF-1 -30S ribosomal subunit

Which statement described the central dogma of biology? -RNA is transcribed into DNA. DNA is translated into the amino acid sequence. -DNA is transcribed to an amino acid sequence. RNA is translated into an amino acid sequence. -Transcription is the process of synthesizing RNA from DNA. Translation is the process of synthesizing an amino acid sequence from RNA.

-Transcription is the process of synthesizing RNA from DNA. Translation is the process of synthesizing an amino acid sequence from RNA.

How many molecules of ATP are consumed in the synthesis of aminoacyl-tRNA and why?

2, one when we break AMP off from pyrophosphate and the other when we break the pyrophosphate itself

If the anticodon is 5'-UGA-3', what are the codon possibilities?

3'-ACU-5' OR 3'-GCU-5'

If the anticodon is 5'-AUU-3' , what are the codon possibilities?

3'-UAA-5'

If the anticodon is 5'-IAG-3', what are the codon possibilities?

3'-UUC-5' 3'-AUC-5' 3'-CUC-5'

What are the components of the 70S prokaryotic ribosome?

50 S (bigger subunit): 23S, 5S rRNAs >30 proteins 30S (smaller subunit): 16S rRNA 21 proteins

What are the components of the 80S eukaryotic ribosome?

60 S (bigger subunit): 28 S, 5S, 5.8S rRNAs 40S (smaller subunit): 18S rRNA

The site that binds the a minoacyl-tRNA is the ____

A site

______ may be bound to deacylated (uncharged) tRNA

E site

What can bind to the anticodon in the third position of the codon (first position of the anticodon)? C A U G I

G U A or G U or C U, C, or A (UG, we have to really deal with these difficult ones???)

When examining eukaryotic gene regions on DNA, which promoter listed below would suggest that the gene was constitutively expressed?

GC Box PROMOTER REGION: 1. TATA box located upstream of the initiation site 2. Initiator element (lnr) located between -3 and 5, paired with the TATA box 3. The downstream core promoter element (DPE) located between base pairs 28 and 35 works with with lnr with TATA box absent 4. Other regulatory elements are the CAAT box and GC box. The GC box is common in genes that are constitutively expressed. The CAAT box and GC box can be located on either strand of the DNA

What is the corresponding mRNA sequence for this DNA sequence? CCGTATG

GGCAUAC

How are bases bonded throughout different conformations and loops in the tRNA?

H bonds

The site that binds the peptidyl-tRNA is the

P site

____ binds the tRNA molecule that is attached to the growing peptide chain

P site

Identify whether the statements refer to double-stranded DNA, RNA, both, or neither: -contains the pyrimidine uracil -contains a 2' hydroxyl group -commonly exists in a variety of secondary structures

RNA

not inhibited by alpha-amanatin inhibited by high concentrations inhibited by low concentrations

RNA polymerase I RNA polymerase III RNA polymerase II

synthesizes mRNA synthesizes pre-rRNA synthesizes tRNA and small noncoding RNAs

RNA polymerase II RNA polymerase I RNA polymerase III

What is the first step of the activation of an amino acid so that it can be attached to a tRNA molecule?

activation through adenylation -ATP is required to form the aminoacyl adenlylate or aminoacyl-AMP where the amino acid bonds to the innermost phosphate of AMP and releases pyrophosphate

Where is the aminoacyl-AMP located during the entire process?

active site of the synthetase

Expression of an _____ alters gene transcription in E. coli by activating transcription of specialized heat stress response genes.

alternative sigma factor Bacteria can express multiple different sigma factors. E. Coli has 7 of them that recognize different promoter sequences in E. Coli in DNA

What is the total sum of the reaction?

amino acid + H2O + ATP + tRNA yields aminoacyl-tRNA + AMP + 2 Pi

What catalyzes the aminoacylation of tRNA where an amino acid is activated and attached to the tRNA that places it properly in a growing peptide chain?

aminoacyl-tRNA synthesis

Which structural feature of the trp leader sequence, trpL, explains why tanscription of the full trp operon is prevented even when the repressor not bound to the oepron?

an A-rich region of the template strand acts as a factor-independent transcription terminator When there is an abundance of trp, it binds to the leader sequence and forms an attenuator that strops transcription When there isn't enough trp, it forms an alternative structure that allows for transcription

Where does the amino acid bind to the tRNA?

at the top at the acceptar CCA arm

What prevent the spread of heterochromatin?

barrier sequences

What is another name for the nontemplate strand?

coding strand

Sort the terms based on whether they are associated with tRNA, mRNA, or rRNA: -anticodon -smallest RNA molecule -transports amino acids

tRNA

Determine whether initiation, elongation, or termination: -the ribosome has mRNA, an empty A site, and a deacylated tRNA in the P site

termination

What is the second step in the attachment of the amino acid to tRNA?

the aminoacyl group is transfered to a specific tRNA that is recognized by the synthetase (substitution, where aminoacyl-AMP + tRNA yields aminoacyl-tRNA + AMP)

What is the antisense strand?

the template strand, or the strand that the RNA polymerase binds to

Where is the anticodon loop located?

towards the middle of the tRNA

Sort each phrase or relating to replication, transcription, or translation: -single DNA strand is used to produce mRNA

transcription

Sort each phrase or relating to replication, transcription, or translation: -amino acids added to peptide chain -requires tRNA -ribosome

translation

In eukaryotes, transcription factors and enhancer sequences are used to regulate transcription. Classify as true or false: enhancer sequences can be located thousands of base pairs downstream from the transcription start site

true

In eukaryotes, transcription factors and enhancer sequences are used to regulate transcription. Classify as true or false: transcription factors are composed of amino acids

true

Which would you expect to have more types of sigma factors-- a free-living prokaryote in a fluctuating environment or a prokaryote in a stable environment with adequate nutrients?

-the organism in the fluctuating environment, because it is exposed to more extremes

Identify whether the statements refer to double-stranded DNA, RNA, both, or neither: -contains the purine guanine -sugars are connected with a 3'-5' phosphodiester link

both DNA and RNA

Sort the terms based on whether they are associated with tRNA, mRNA, or rRNA: -combines with protein to form ribosomes

rRNA

Prokaryotic promoters, eukaryotic promoters, or both? -contains highly conserved DNA sequences

both prokaryotic and eukaryotic promoters

Identify whether the statements refer to double-stranded DNA, RNA, both, or neither: -contains the sugar 2'-deoxyribose -%G=%C -secondary structure is primarily a double helix

double-stranded DNA

According to the central dogma, DNA serves as the template for the production of RNA during transcription. Which of the two DNA strands serves as the template for transcription?

either strand of DNA may be used as a template by RNA polymerase, but a single DNA strand oriented in the 3' to 5' direction is used as a template each time transcription occurs (so it can transcribe in the 5' to 3' direction)

How is the amino acid attached to the tRNA?

ester bond

What drives the reaction forward after the first step?

hydrolysis of PPi

Assume that there was a mutation in the lac repressor in which prevented the binding of an inducer to the lac repressor. Which would you expect?

lacZ, lacY, and lacA would never be substantially expressed, even in the presence of high lactose The lac repressor is constitutively expressed and will always bind to the operator unless it is specifically induced not to. The lac repressor protein in the absence of lactose binds to the operator and blocks transcription Ligand binding can INDUCE the structural change in GRP and we call these inducers.

A key reaction in gene activation of eukaryotic genes is the acetylation of ____ amino acids in histones.

lysine Histone acetylation can activate transcription through 3 mechanisms: 1. reducing affinity of histones for DNA 2. recruiting other components of transcriptional machinery 3. initiating remodeling of the chromatin structure

Sort the terms based on whether they are associated with tRNA, mRNA, or rRNA: -carries genetic information from the nucleus to the cytoplasm -serves as a template for protein synthesis

mRNA

Identify whether the statements refer to double-stranded DNA, RNA, both, or neither: -bases are attached to sugars in an alpha N-glycosidic linkage -in base composition, %A=%C always -sugars are connected with a 2'-5' phosphodiester link

neither

Which of the following would form a structure that is a cue for transcription termination of some genes? Sequence shown are mRNA. There is more than one right answer -a stem-loop hairpin structure followed by a sequence of uracil residues (in the RNA) -5'-GCAUCUUACUGAUGCUUUU-3' -a palindromic region followed by a sequence of adenine residues (in the RNA) -a sequence of uracil-adenine RNA-DNA base pairs

-a stem-loop hairpin structure followed by a sequence of uracil residues (in the RNA) -5'-GCAUCUUACUGAUGCUUUU-3'

The RNA polymerase holoenzyme alpha2betabetaprimesigma carries out transcription in prokaryotes. Which of the following are functions of the RNA polymerase subunit sigma? -recognize the promoter DNA sequence -form part of the core RNA polymerase enzyme -increase rate of translation -terminate transcription -decrease the affinity of RNA polymerase for most DNA

-recognize the promoter DNA sequence -decrease the affinity of RNA polymerase for most DNA

Which scenario would you expect to find when there are low levels of iron in the blood? A) Endonucleases will cleave transferrin receptior mRNA, casusing the mRNA to be rapidly degraded. B) Iron response proteins (IRPs) will be bound to IRE elements on the 3' UTR of transferrin receptor mRNA, preventing translation of transferrin. C) Ferritin, the iron storage protein, will be translated efficiently. D) Iron response proteins (IRPs) will contain iron in their binding sites. E) Iron response proteins (IRPs) will be bound to IRE elements on the 5' UTR of ferritin mRNA, preventing translation of ferritin.

Iron response proteins will be bound to the IRE elements of the 5' UTR of ferritin mRNA, preventing translation of ferritin and allowing translation of transferrin Ferritin-- iron storage (active when there are high levels) Transferrin-- iron transfer (active when there are low levels) IRON STARVATION: IRP binds to IRE elements of ferritin mRNA to block their translation because transferrin is needed (when you need one to be made, the IRP will bind to the IRE of the other one to inhibit translation)

Euakryotic gene expression can be regulated in many ways. Which step along the pathway from DNA to active protein does miRNA play an important role in the regulation of gene expresion?

between the DNA process that converts to prmary RNA transcripts (miRNA play an important role in transcription control, they associate with Argonaute to form RISC (RNA-induced silencing complex) that regulates translation by: 1. base pairing with mRNA through Watson-Crick base pairs to regulate mRNA 2. if base-pairing not precise, translation of mRNA is inhibited Either way.. miRNA forms a complex that will halt transcription in its tracks 60% of all human genes regulated by miRNA

Determine whether initiation, elongation, or termination: -peptidyl transferase catalyzes peptide bond formation -kinetic proofreading occurs -in E. Coli, EF-Tu delivers an aminoacyl-tRNA to the ribosome

elongation

Prokaryotic promoters, eukaryotic promoters, or both? -requires multiple proteins called general transcription factors -may include a TATA box (not the Pribnow box) upstream of the transcription start site -may include sequences downstream from the transcription start site

eukaryotic promoter

In eukaryotes, transcription factors and enhancer sequences are used to regulate transcription. Classify as true or false: enhancer sequences can alter transcription levels in the absence of a bound protein

false

In eukaryotes, transcription factors and enhancer sequences are used to regulate transcription. Classify as true or false: transcription factors always increase transcription levels

false

In eukaryotes, transcription factors and enhancer sequences are used to regulate transcription. Classify as true or false: transcription factors bind to the entire enhancer sequence

false

Determine whether initiation, elongation, or termination: -the first AUG codon is recognized -IF2 dissociates -initiator tRNA enters the P site

initiation

What are the protein-binding sequences that direct enhancers to interact with the intended promoter and that block communication between enhancers and other promoters in euakryotes?

insulator sequences

How would transcription be affected if the sigma subunit were part of the core?

it would be slower (helps with processivity)

Prokaryotic promoters, eukaryotic promoters, or both? -recognized by the sigma factor of RNA polymerase -includes two conserved sequences at -35 and -10

prokaryotic promoter

The primary action of steroid hormones binding to nuclear hormone receptors is to

recruit coactivators to modify local chromatin

Sort each phrase or relating to replication, transcription, or translation: -both DNA strands are duplicated -semi-conservative -DNA polymerase

replication

An mRNA whose translation is controlled by binding of a metabolic end product like FAD or guanine is called a____

riboswitch Some bacterial mRNA can sense environmental signals as well as encode proteins. RIboswitches are special mRNA structures that bind small molecules that cause a structural change in the riboswitch that terminates the synthesis of mRNA (ie. GUanine riboswitch-- with high levels, termination is activated and mRNA is not produced)