Unit Three (chap 13,14, 15, 16, 17 Flashcards
1
Q
Differentiate between the structures of DNA and RNA
A
- RNA contains uracil in place of thymine.
- RNA has a hydroxyl group on the 2’-carbon atom of its sugar, making RNA more reactive (less stable) than DNA
- RNA molecules fold to form secondary structures
- DNA is deoxyribose sugar and RNA is ribose
- RNA is usually single stranded, DNA is usually double strande
- DNA secondary structure is a double helix. RNA secondary structure has many types
The same between RNA and DNA: - composed of nucleotides
- A,G,C
- nucleotides joined together by phosphodiester bonds
2
Q
What is the location and function of rRNA
A
Cell type: prokaryotic and eukaryotic
Location of function in eukaryotic cells: cytoplasm
Function: structural and functional components of the ribosome
3
Q
what is the location and function of mRNA
A
Cell type: prokaryotic and eukaryotic
Location of function in eukaryotic cells: nucleus and cytoplasm
Function: carries genetic code for protiens
4
Q
What is the location and function of tRNA
A
Cell type: prokaryotic and eukaryoitc
Location and Function in Eukaryotic cells: cytoplasm
Function: helps incorporate amino acids into polypeptide chain
5
Q
define transcription
A
Transcription: synthesis of an RNA molecule from a DNA template
RNA synthesis is complementary and antiparallel to template strand
Only certain regions of the DNA are transcribed (mostly gene regions) rather than the entire chromosome
Only 1 of the 2 DNA strands is transcribed for each gene
Nucleotides are added to the 3’ end of the RNA molecule so the direction of synthesis is 5’-3’
* refer to Fig 13.8
6
Q
draw and label a transcription unit
A
7
Q
draw the substrates for transcription
A
8
Q
describe the bacterial transcription apparatus
A
Bacterial cells only possess one type of RNA polymerase, which catalyzes the synthesis of all classes of bacterial RNA.
5 sub units make up the core enzyme: 2 copies of alpha, 1 beta, 1 beta prime, 1 omega
The core enzyme catalyzes the elongation of RNA molecules by the addition of RNA nucleotides.
The sigma factor controls the binding of RNA polymerase to the promoter forming a holoenzyme.
It is said to move downstream during transcription: it binds to the promoter and moves toward the terminator.
9
Q
What is the difference between bacterial RNA polymerase and eukaryotic RNA polymerases
A
Bacteria only have one RNA polymerase that transcribes all RNA (mRNA, tRNA, rRNA), but eukaryotes have many RNA polymerases (names with roman numerals) that transcribe different RNAs.
RNA polymerase II transcribes pre-mRNA
10
Q
what is the function of the promoter
A
the promoter is a DNA sequence that the transcription factor recognizes and binds. It indicates which of the 2 DNA strands is to be read as the template and the direction of transcription. In most cases, the promoter is located next to the transcription start site but is not itself transcribed
11
Q
What is a consensus sequence and why is its presence important within a promoter
A
A consensus sequence is the set of most commonly encountered nucleotides among sequences that possess considerable similarity, or consensus. The presence of a consensus within a set of nucleotides usually implies that the sequence is associated with an important function.
The holoenzyme initially binds weakly to the promoter but then undergoes a change in structure that allows it to bing more tightly and unwind the double stranded DNA
12
Q
What are the steps of bacterial transcription
A
Initiation:
- sigma and core RNA polymerase bind to promoter
- unwinds DNA
- nucleotides incorporated – no primer required
- 2 phosphates cleaved for each new nucleotide added
- sigma released
Elongation:
- RNA polymerase continues adding nucleotides
- unwinding at front of bubble and rewinding behind bubble
- proofreading
Termination- different genes can use different termination mechanisms. This is the only one you need to know:
1. RNA polymerase transcribes a terminator sequence, which consists of a sequence that forms a hairpin structure in the RNA followed by several uracils in the RNA
2. the hairpin structure causes the RNA polymerase to pause
3. at this point, only A-U bonds (weak bonds) are holding DNA and RNA together – DNA and RNA separate
13
Q
What is a transcription factor
A
transcription factors are accessory protiens that bind to DNA sequences and affect levels of transcription. General transcription factors combine with RNA polymerase to form the basal transcription apparatus. Other transcription factors bind to other DNA sequences and bring about higher levels of transcription by stimulating the assembly of the basal transcription apparatus at the start site.
14
Q
what is the difference between general transcription factors and other transcription factors
A
General Transcription Factors:
- necessary for any transcription to occue
- combine with RNA polymerase and other proteins to form the basal transcription apparatus
Other Transcription Factors:
- can increase or decrease transcription levels but not required for transcription.
15
Q
what is a basal transcription apparatus
A
a group of proteins that assembles near the transcription start site and is sufficient to initiate minimal levels of transcription
16
Q
what is the difference between a core promoter and a regulatory promoter within eukaryotes
A
the core promoter is located immediately upstream of the gene and is the site to which the basal transcription apparatus binds (required for transcription). It usually includes one or more consensus sequences. Must know the TATA box is at -25
The regulatory promoter is located immediately upstream of the core promoter. It affects the rate of transcription, but it is not required for transcription.
17
Q
what are the steps of eukaryotic transcription (for RNA polymerase II)
A
Initiation:
- TFIID contains a TATA- binding protein (TBP) which binds to the TATA box within the core promoter
- General TFs + RNA polymerase + mediator bind to core promoter via TFIID
- TBP of TFIID positions active site of RNA polymerase over start site
- other transcription factors:
- may bind to regulatory promoter
- may bind to enhancers
- affect transcription rate by interacting with the basal transcription apparatus via the mediator
Elongation:
- similar to bacterial elongation
Termination:
- there are proteins that assist to remove the RNA polymerase and the RNA transcript from the DNA
18
Q
what is the difference between an exon and an intron
A
exons are RNA coding regions, and the noncoding regions are called introns. All the introns and exons are initially transcribed into RNA but during or after transcription the introns are removed and the exons are joined to yield mature RNA.
19
Q
what organisms are introns common within and what organisms are introns rare within
A
common in eukaryotic genes but rare in bacterial genes
introns have been observed in archaea, bacteriophages, and some bacteria
present in mitochondrial and chloroplast genes as well as in the nuclear genes of eukaryotes.
20
Q
Draw and label the structure of a mature mRNA
A
21
Q
what are the 3 main steps in pre-mRNA processing
A
- Addition of the 5-cap
- Addition of the poly(A) tail
- RNA splicing
22
Q
what type of cells does pre-mRNA processing occur and where inside the cell
A
it occurs in eukaryotic cells within the nucleus
23
Q
How is the 5’ cap added (in pre-mRNA processing) and what is its function
A
It is a guanine nucleotide added backwards (5’ to 5’ bond) to the 5’ end of the mRNA.
then methyl groups are added to the mRNA
Function:
1. assist with binding of ribosome to mRNA for translation
2. stabilizes mRNA
24
Q
How is the poly(A) tail added and what is its function
A
- cleavage 11-30 nucleotides downstream of AAUAA consensus near 3’ end
- Polyadenylation: many adenines are added
Function: - increases stability of mRNA
- required for ribosome binding to 5’ cap
25
what is splicing
RNA splicing is the removal of introns. This takes place in the nucleus before the RNA moves to the cytoplasm. Splicing requires the presence of of 3 seuqneces in the intron ( 5' splice site, 3' splice site, and branch point)
26
Define splicesome as well as its makeup
splicesome is a large complex where splicing occurs
consists of several snRNPs ( 'snurps' )
snRNP= 1 snRNA + proteins
each snRNP plays a different role in the splicing process
27
What are the three consensus sequences required for splicing
5' splice
3' splice
branch point
28
describe the process of splicing (shown in fig 14.9)
1. the mRNA is cut at the 5' splice site
2. the 5' end of the intron attaches to the branch point
3. A cut is made at the 3' splice site
4. The intron is released as a lariat
5. the two exons are spliced together
6. the bond holding the lariat is broken, and the linear intron is degraded
7. The spliced mRNA is exported to the cytoplasm and translated.
29
What is alternative splicing
alternative splicing is when the same pre-mRNA can be spliced in more than one way to yield different mRNAs that are translated into different amino acid sequences thus different proteins. Alternative splicing uses different combinations of exons
30
What is multiple 3' cleavage sites
Two or more potential sites for cleavage and polyadenylation are present in pre-mRNA. mRNA products of different lengths are produced after splicing
*the calcitonin gene is a good example but it doesn't need to be memorized
31
What is the function of tRNA
tRNA serves as a link between the genetic code in mRNA and the amino acids that make up a protein. Each tRNA attachs to a particular amino acid and carries it to the ribosome, where the tRNA adds its amino acid to the growing polypeptide chain at the position specified by the genetic instructions in the mRNA.
32
What is the basic structure of tRNA
All tRNAs are similar in their secondary structure, which is critical to their function. Most tRNAs are short molecules with 74-95 nucleotides some are complementary to each other forming hydrogen bonds. Each tRNA has a cloverleaf structure with four major arms. Starting at the top and going right its the acccpetor arm, the TC arm, the anticodon arm, and the DHU arm. Three of the arms (TC, anticodon and DHU) consist of a hairpin formed by the pairing of complementary nucleotides.
33
Can tRNA processing occur in both prokaryotes and eukaryotes?
tRNA processing can occur in both eukaryotes and prokaryotes but occurs differently than mRNA processing.
34
what is the purpose of RNA interference (RNAi)
defense mechanism against viruses
regulation of gene expression
*RNAi is only found in eukaryotes
35
How does RNAi work
Double-stranded RNA gets chopped up by the enzyme dicer
The resulting RNA pieces are called microRNAs (miRNAs) or small interfering RNAs (siRNAs)
miRNAs/siRNAs form a complex with proteins- this complex is called RISC
RISC pairs with the target mRNA (because the miRNA/siRNA is complementary to the target mRNA)
The target mRNA can no longer be translated
Thus the mRNA has been 'interefered' with so that the gene that the mRNA came from will no longer be expressed (no protein produced)
36
Explain the purpose of CRISPR RNA (crRNA)
it is like the immune system of prokaryotes
they defend prokaryotic cells against invasion of foreign DNA (DNA from bacteriophages and plasmids)
37
describe the action of CRISPR RNAs
- Foreign DNA (ie phage DNA) gets incorporated into the bacterial DNA -- specifically it is inserted into a CRISPR array region of the bacterial genome
- The CRISPR array gets expressed (transcribed into crRNA)
- the crRNA and CAS protein form a complex
- now when the foreign DNA enters the cell again, the crRNA-CAS complex will bind to it (because the crRNA is complementary to it) and CAS cuts the foreign DNA rendering it non functional
38
The following diagram represents DNA that is part of the RNA-coding sequence of a transcription unit. The bottom strand is the template strand. Give the sequence found on the RNA molecule transcribed from this DNA and label the 5′ and 3′ ends of the RNA.
3′ ATAGGCGATGCCA 5′
5′ TATCCGCTACGGT 3′ ← Template strand
5' ACCGUAGCGGAUA 3'
39
Which of the following is true about transcription (select all that apply)?
- DNA is made in a complementary and antiparallel manner
- only 1 of the 2 DNA strands is transcribed
- RNA is made antiparallel to the temple strand
- RNA is made in a 5' to 3' direction
- DNA is the template for making RNA
only 1 of the 2 DNA strands is transcribed
RNA is made antiparallel to the temple strand
RNA is made in a 5' to 3' direction
DNA is the template for making RNA
40
The following types of RNA must be processed in both prokaryotes and eukaryotes: (Select all that apply)
tRNA
mRNA
rRNA
tRNA and rRNA
41
Eukaryotes have 2 types of transcription factors. Put the terms in the correct category:
TFIID
can bind to regulatory promoter
required for minimum levels of transcription
can increase or decrease levels of transcription
part of the basal transcription apparatus
can bind to enhancer
not required for transcription
bind to core promoter
General Transcription factors:
TFIID
required for minimum levels of transcription
part of the basal transcription apparatus
bind to core promoter
Other Transcription Factors:
not required for transcription
can bind to enhancer
can increase or decrease the levels of transcription
can bind to regulatory promoter
42
Which of the following is the consensus sequence for the following set of nucleotide sequences?
T G G A G T T
A G C T G T T
T G C A A T A
A C G A G A A
T C C T G A T
T G C A A T T
T G C A G T T
43
Which of the following is true about RNA interference?
- it is a process that allows for tRNA to be appropriately spliced
- it occurs in both prokaryotes and eukaryotes
- it requires an enzyme called dicer
- it generates tRNAs and siRNAs
it requires an enzyme called dicer
44
Which of the following elements would NOT be found in an mRNA molecule?
- 3' untranslated region
- 5' untranslated region
- protein-coding region
- start and stop codons
- promoter
promoter
45
Which of the following is/are a part of pre-mRNA processing? (Select all that apply)
- joining of exons to introns
- addition of a polyA tail
- removal of introns
- addition of a 5' cap
- addition of a polyA tail
- removal of introns
- addition of a 5' cap
46
Place the terms in the correct category: (RNA interference or CRISPR RNAs)
-CAS proteins
-miRNAs
-found in eukaryotes
-found in prokaryotes
- siRNAs
RNA Interference:
-miRNAs
-found in eukaryotes
-siRNAs
CRISPR RNAs:
-found in prokaryotes
- CAS proteins
47
Differentiate between bacterial and eukaryotic transcription by placing the terms in the correct category:
-sigma factor
- TFIID
-Transcription factors
-TATA Box
- One RNA polymerase transcribes all types of RNA
- Multiple RNA polymerases
- TBP
Bacterial transcription:
- sigma factor
- One RNA polymerase transcribes all types of RNA
Eukaryotic transcription:
-TFIID
-Transcription factors
-TATA Box
- Multiple RNA polymerases
TBP
48
What is occurring in the following figure?
multiple 3' cleavage sites
49
What is occurring in the following figure?
alternative splicing
50
Which of the following describes the terminator sequence in bacterial genes?
- consensus sequences in the core promoter
- TATA box
- inverted repeats followed by a string of adenines
- 5' splice site
inverted repeats followed by a string of adenines
51
RNA interference directly prevents __________ from occurring.
translation
52
A TATA box associated with the human gene ABC is inactivated via mutation. Predict the effect on ABC.
- The ABC gene will not be properly replicated during the next cell cycle
- Sigma will no longer be able to leave the core promoter thereby blocking ABC mRNA elongation
- ABC transcription will proceed but at slower pace without TATA-dependent enhancer interaction
- The mutation will have no effect because human cells do not reply upon a TATA box.
- The TBP portion of TFIID will no longer recognize the promoter for transcription of ABC mRNA
The TBP portion of TFIID will no longer recognize the promoter for transcription of ABC mRNA
53
What does the structure of an amino acid look like and how many amino acids are there
- an amino acid has a central carbon and starting at the top going clockwise, a hydrogen, a carboxyl group, an R group, and an amino group. The R group is the only thing that changes on an amino acid
- there are 20 amino acids
54
What does the linkage of two amino acids joined by a peptide bond look like
the amino end of one bonds to the carboxyl group of another to form peptide bonds
55
what are primary, secondary, tertiary, and quaternary protein structures
primary: the proteins sequence of amino acids
secondary: interactions between amino acids cause the primary structure to fold into a secondary structure
tertiary: the secondary structure folds further into a tertiary structure
quaternary structure: 2 or more polypeptide chains may associate to create a quaternary structure.
56
what is a codon
a set of nucleotides that encodes a single amino acid. They are the basic unit of genetic code.
57
what is meant by the degeneracy of genetic code
genetic code is redundant: amino acids may be specified by more than one codon. Because there are 64 codons but only 20 amino acids; 1 amino acid may be specified by more than one codon
58
What is the genetic code chart used for and how do you read it
the chart gives mRNA codons and the codons are written 5' to 3'
59
What is meant by wobble in the code
there are 61 different sense codons, but there are less than 61 different tRNAs. Wobble is a non standard base pairing at the third position of the codon (3') and it allows 1 anti codon to pair with more than one codon
60
what are the start and stop codons and what do they encode
Start (initiation codon): AUG
- in prokaryotes AUG codes for n-formyl methionine
- in eukaryotes AUG codes for methionine
Stop Codons: there are 3 stop codons.
- no tRNA corresponds to stop codons, thus no amino acid is encoded by them
- also called nonsense codons or termination codons
61
What are general characteristics of the genetic code
1. Genetic code consists of a sequence of nucleotides in DNA or RNA (A,G,C,U/T)
2. Each amino acid is encoded by a sequence of 3 nucleotides (codon)
3. Genetic code is degenerate: 64 codons, 20 amino acids
4. Wobble allows anticodon on one type of tRNA to pair with more than one type of codon on mRNA
5. non-overlapping; each nucleotide in an mRNA sequence belongs to a single reading frame
6. Reading frame is set by an initiation codon (AUG)
7. codons are read as successive groups of 3 nucleotides
8. no amino acids are encoded by termination codons. Termination codons signal the end of translation
9. the genetic code is almost universal
62
what is translation
translation is how amino acids are assembled into proteins.
Only mRNAs are translated into proteins.
63
where does translation take place within the cell?
Translation takes place on the ribosomes. Ribosomes can be thought of as moving protein-synthesis machines.
64
what does tRNA charging do
tRNA charging is the process that allows the tRNA to be loaded (charged) with the appropriate amino acid.
65
What is the story of translation initiation in prokaryotes
- IF-3 binds to the small subunit, preventing it from binding to the large subunit. This allows the small subunit to attach to mRNA. (the rRNA in small sub unit is complementary to shine dalgarno sequence)
- tRNA charged with n-formylmethionine forms a complex with IF-2 and GTP and the anticodon binds to the start codon. IF-1 joins this complex
- All initiation factors dissociate from the complex and GTP is hydrolyzed to GDP
- the large subunit joins to create the initiation complex
66
Explain the story of translation elongation
- After inititian the fMet-tRNA is in the P site of the ribosome
- EF-Tu + GTP + charged tRNA enters the A site
- GTP hydrolyzed to GDP and EF-Tu/GDP leaves
- Peptide bond forms between amino acids in P and A sites (pepitdyl transferase is the enzyme that does this)
- tRNA in P site releases its amino acid so now the peptide chain is entirely on chain is entirely in the tRNA at the A site
- ribosome shifts down by one codon (translocation) with the help of EF-G and GTP
- tRNA that was in the P site is now in the E site and then immediately leaves
- A site is now available to receive the next charged tRNA and the cycle continues
67
Tell the story of translation termination
- when stop codon is in the A site, a release factor comes to the A site
- Another release factor joins the ribosome and all components are released
68
what is the difference of translation initiation in prokaryotes and eukaryotes
- in eukaryotes, small ribosomal subunit binds to 5' cap and poly(A) tail assists with this binding
- small subunit then moves along mRNA searching for the start codon (scanning)
- Once start codon is found, the rest of initiation is similar to prokaryotes, but there are more initiation factors involved
69
What is simultaneous transcription and translation? does this happen in eukaryotic or prokaryotic cells?
in prokaryotic cells transcription and translation are simultaneous; multiple ribosomes may be attached to the 5' end of the mRNA while transcription is still taking place at the 3' end.
(mRNA molecules are translated simultaneously in both prokaryotes and eukaryotes but that is different)
70
What are polyribosomes? do these occur in prokaryotic or eukaryotic cells?
an mRNA with several ribosomes attached is a pilyribosome this occurs in both prokaryotes and eukaryotes
71
what are posttranslational modifications and why are they important
many proteins need modified after translation to become functional. proteins in both eukaryotic and prokaryotic cells undergo posttranslational modifications (alterations following translation).
72
What is gene regulation
gene regulation is the mechanisms and systems that control the expression of genes
73
What is environmental induction of gene expression
when the environment changes, new genes are expressed, and proteins appropriate for the new environment are synthesized.
74
What are the levels of gene regulation? which ones apply to eukaryotes and which ones apply to prokaryotes
- alteration of DNA or chromatin structure: eukaryotes
- transcription: prokaryotes and eukaryotes. Moste economically favorable place to do gene regulation
- mRNA processing: only eukaryotes
- regulation of mRNA stability
- translation
- posttranslational modification
75
what is an operon? Do prokaryotes or eukaryotes have operators?
an operon is a group of bacterial genes transcribes together, along with their promoter, and additional sequences that control their transcription. The operon regulates the expression of the structural genes by controlling transcription, which in bacteria is the most important level of gene regulation. Prokaryotes have operators
76
Draw the structure of an operon and label: structural genes, promoter, operator, and operon
77
What is a regulator gene and a regulator protein? how is this related to an operon?
A regulator gene helps control the expression of the structural genes of the operon by increasing or decreasing transcription. The regulator gene has its own promoter and is transcribed into a short mRNA, which is translated into a small protein. This regulator protein can bind to the operator of the operon and affect whether transcription can take place.
78
what is the difference between positive and negative control in respect to operons
Negative: regulator protein is a repressor; repressor binds to DNA and turns transcription off
Positive: regulator protein is an activator; activator binds to DNA and stimulates transcription
79
What is the difference between inducible and repressible operons
Inducible: transcription is off unless something turns it on (induces transcription)
Repressible: Transcription is on unless something turns it off (represses transcription)
80
What is a negative inducible operon
- Regulator protein is a repressor
- because it is an inducible operon, it is "able to be induced," meaning transcription is off and something would have to turn it on
- since transcription is off, the repressor must be made in an active state, so that it can repress the operon
81
how does a negative inducible operon function in the presence and absence of an inducer
No inducer present: the regulator protein binds to the operator and prevents transcription of structural genes
Inducer present: inducer binds to to the regulator, making the regulator unable to bind to the operon so transcription and translation of the structural genes takes place
82
What is a negative repressible operon
- regulator protein is a repressor
- because it is a repressible operon, it is "able to be repressed," meaning transcription is on, and something would have to turn it off
- since transcription is on, the repressor must be made in an inactive state, so that it is not repressing- it would have to be activated to repress the operon
83
how does a negative repressible operon function in the presence and absence of product?
No product present: the regulator protein (inactive repressor) is unable to bind to the operator, so transcription of the structural genes takes place, levels of product build up and it transitions to product present function
Product present: product binds to the regulatory protein, making it active and able to bind to the operator, and this prevents transcription
84
Exaplain how the lac operon works in detail
- Permease actively transports lactose into the cell where B-gal breaks it down into galactose and glucose. B-gal also converts lactose into allolactose and converts allolactose into galactose and glucose
IN THE ABSENCE OF LACTOSE
- the regulator protein (a repressor) binds to the operator and inhibits transcription
IN THE PRESENCE OF LACTOSE
- when lactose is present some is converted into allolactose, which then binds to the regulator protein, making the protein inactive
- the regulator can not bind to the operator and the structural genes are transcribed and translated
85
what are the lac operon mutations
B-gal mutants (LacZ-): no B-gal produced
Permease mutants (LacY-): no permease produced
Regulator gene mutation (LacI-): no regulator (repressor) produced
- LacIs (superrepressor): cannot be inactivated- always represses
Promoter mutation (LacP-): RNA polymerase cant bind
Operator mutation: (LacOc): repressor can't bind to the operator
86
How can the lac operon also be under positive control using catabolite repression
- in addition to being a negative inducible operon, the lac operon also has positive control exerted on it
- this positive control is termed catabolite repression
- regulator protein is an activator (positive control)
- bacteria prefer to use glucose over other sugars
- when glucose is present, genes that metabolize other sugars (such as lactose) are repressed
-CAP is a catabolic activator protein
87
What happens to the lac operon when glucose levels are low
- when glucose is low levels of cAMP are high, cAMP readily binds CAP, and the CAP-cAMP complex binds DNA increasing the efficiency of polymerase binding.
- When lactose is present, the result is high rates of transcription and translation of the structural genes and the production of glucose from lactose
88
What happens to the lac operon when glucose levels are high
- when glucose levels are high, levels of cAMP are low and cAMP is less likely to bind to CAP
- RNA polymerase can't bind to DNA as efficiently so transcription is at a low rate
89
what are the two requirements for maximum transcription of the lac operon
lactose present and low glucose levels
90
How is the trp operon in E. coli an example of a negative irrepressible operon
- trp controls the synthesis of tryptophan
- repressor is made in an inactive form because this is a irrepressible operon
- when tryptophan is high, tryptophan binds to the repressor and makes it active. The trp repressor then binds to the operator and shuts transcription off
91
How is the trp operon also controlled by attenuation
- transcription is initiated but terminates prematurely before structural genes are transcribed.
- it is dependent on simultaneous transcription and translation
When intracellular levels of tryptophan are high: the ribosome does not stall at the trp codons so when region 3 is transcribed the ribosome is covering region 2 which results in a 3+4 secondary structure of the 5' UTR and termination of transcription of the trp operon.
When intacellular levels of tryptophan are low: the ribsomes stalls at the trps codons and the ribosome is covering region 1 when region 3 is transcribed, which results in a 2+3 hairpin secondary structure of the 5' UTR, so transcription of the trp operon continues.
92
How can antisense RNA be used to regulate bacterial gene expression
antisense RNA control gene expression by binding to sequences on mRNA inhibiting translation
this is translational control
93
How can riboswitches be used to regulate bacterial gene expression
regulatory molecules can bind to riboswitches and affect gene expression by influencing the formation of secondary structures in mRNA. When the regulatory protein in present the riboswitch blocks the ribosome binding site with its shape. When the regulatory protein is absent riboswitches change there shape to ensure the ribosome binding site is open.
94
A nontemplate strand on bacterial DNA has the following base sequence. What amino acid sequence will be encoded by this sequence?
5′–AAATTTCCCGGG–3′
Lys-Phe-Pro-Gly
95
A tRNA has the following anticodon: 3' GCU 5' Give all possible codons with which this tRNA can pair. Select all that apply.
3' CGG 5'
3' UGG 5'
3' AGC 5'
3' UGA 5'
3' AGU 5'
3' GGC 5'
3' CGA 5'
3' AGC 5'
3' GGC 5'
96
Arrange the following events of translation in the order in which they occur in initiation of prokaryotic protein synthesis:
- tRNA carrying n-formyl methionine + IF-2 + GTP all come in together and anticodon binds to start codon
- GTP is hydrolyzed to GDP and all IF’s leave the complex
- IF-3 binds to small ribosomal subunit
- large ribosomal subunit joins the complex
- IF-3/small subunit bind to mRNA
- GTP is hydrolyzed to GDP and all IF’s leave the complex
- IF-3 binds to small ribosomal subunit
- IF-3/small subunit bind to mRNA
- tRNA carrying n-formyl methionine + IF-2 + GTP all come in together and anticodon binds to start codon
- IF-1 binds to small ribosomal subunit
-GTP is hydrolyzed to GDP and all IF’s leave the complex
-large ribosomal subunit joins the complex
97
Which of the following is true regarding the elongation phase of prokaryotic translation?
- EF-G assists in ribosome translocation
- peptide bonds are formed between amino acids
- a release factor binds to the A site
- a charged tRNA comes into the P site
- GTP is required
- EF-G assists in ribosome translocation
-peptide bonds are formed between amino acids
-GTP is required
98
Categorize the following to describe differences between prokaryotic and eukaryotic translation:
- small ribosomal subunit binds to the Shine-Dalgarno sequence
- ribosome scans the mRNA until it reaches the start codon
- there are many more initiation factors involved
- IF-1, IF-2, and IF-3 work during initiation of translation
- small ribosomal subunit binds to the 5' cap
Prokaryotic translation:
- IF-1, IF-2, and IF-3 work during initiation of translation
- small ribosomal subunit binds to the Shine-Dalgarno sequence
Eukaryotic translation:
- ribosome scans the mRNA until it reaches the start codon
- there are many more initiation factors involved
- small ribosomal subunit binds to the 5' cap
99
If a ribosome has an amino acid chain attached to the tRNA in the P site, and an empty A site, the ribosome is waiting for:
EF-Tu to bring a charged tRNA to the A site
100
Which of the following is true regarding wobble?
- nonstandard base pairing can occur at the 3' end of the anticodon and the 5' end of the codon
- one anticodon is able to pair with more than one codon
-one codon is able to pair with more than one anticodon
one anticodon is able to pair with more than one codon
101
When glucose levels are low and lactose levels are high, the level of cAMP is _____, and the CAP protein _____ to DNA to assist RNA polymerase in transcription. Additionally, ________ binds to the regulator protein so that it is _____
When glucose levels are low and lactose levels are high, the level of cAMP is high, and the CAP protein binds to DNA to assist RNA polymerase in transcription. Additionally, allolactose binds to the regulator protein so that it is inactivated
102
A strain of E. coli has the following genotypes at the lac operon. For each genotype, indicate whether the enzyme will be synthesized (+) or not synthesized (-) when lactose is present or absent.
I+P+O+Z-Y+
IsP+OcZ+Y-
I+P-O+Z+Y-
I+P-O+Z+Y+ / I-P+O+Z+Y-
I+P+O+Z-Y- / I+P+OcZ+Y+
I+P- Oc Z+Y+ / I- P+O+Z+Y-
I+P+O+Z-Y+
- absence of lactose: B-gal: - Permease: -
- presence of lactose: B-gal: - Permease: +
IsP+OcZ+Y-
- absence of lactose: B-gal: + Permease: -
- presence of lactose: B-gal: + Permease: -
I+P-O+Z+Y-
- absence of lactose: B-gal: - Permease: -
- presence of lactose: B-gal: - Permease: -
I+P-O+Z+Y+ / I-P+O+Z+Y-
- absence of lactose: B-gal: - Permease: -
- presence of lactose: B-gal: + Permease: -
I+P+O+Z-Y- / I+P+OcZ+Y+
- absence of lactose: B-gal: + Permease: +
- presence of lactose: B-gal: + Permease: +
I+P- Oc Z+Y+ / I- P+O+Z+Y-
- absence of lactose: B-gal: - Permease: -
- presence of lactose: B-gal: + Permease: -
103
What serves as the corepressor in the trp operon?
tryptophan
104
Consider a hypothetical operon that is controlled by an activator. When the activator is made, it is made in an inactive form. Which of the following describes this operon?
negative inducible
negative repressible
positive repressible
positive inducible
positive inducible
105
When trp is scarce in the cell, the trp operon initiates transcription because
Trp does not bind to the repressor protein, preventing the repressor protein from binding to the operator
106
Attenuation of the trp operon involves:
secondary structure formation in RNA molecules.
high tryptophan levels.
a 5' UTR.
all of the above
all of the above
107
The formation of 1+2 and 3+4 secondary structures of 5′ UTR region mRNA from the trp operon is triggered when:
the tryptophan level inside the bacterial cell is high.
108
what are a few differences in prokaryotic and eukaryotic gene control
- most gene regulation in bacterial cells takes place at the level of transcription. Gene regulation in eukaryotic cells takes place on many levels
- chromatin plays a role in eukaryotic but not prokaryotic gene control
- initiation of transcription is simple in eukaryotic cells but complex in prokaryotic cells
- anti sense RNAs can act as regulators in prokaryotic cells
- regulation by siRNAs and miRNAs is abundant in eukaryotic cells but absent in prokaryotic cells
- Eukaryotes do not have operons. Eukaryotes have their own promoters and are transcribed separately
- Eukaryotes do not have riboswitches, but prokaryotes do and can use it to control gene expression
- Presence of the nuclear membrane in eukaryotic cells separates transcription and translation in time and space so eukaryotic gene transcription has greater diversity
109
What is the relationship between how tightly DNA is packed and whether transcription occurs or not
transcription can not take place when DNA is wrapped tightly around histone proteins because there is no room for the transcription machinery to fit and get by. Before transcription, chromatin structure changes so that DNA becomes more accessible to transcription machinery
110
What are DNase I hypersensitive sites? Does transcription occur at these sites?
as genes become transcriptionally active, regions around the gene become highly sensitive to DNase I. The relaxation of the chromatin structure allows regulatory proteins to access binding sites on the DNA.
111
what is chromatin remodeling
chromatin remodeling complexes alter the chromatin structure without altering the chemical structure of the histones directly.
They bind directly to sites on DNA and repostion the nucleosomes, allowing other transcription factors and RNA pol to bind to promoters and initiate transcription
112
what are two ways that histones can be modified and what are the effects of these modifications and what enzymes are involved
1. Methylation of histones:
- the addition of methyl groups to the tails of histone proteins. This results in activation or repression depending on which histone is modified.
- Enzymes called histone methyltransferases add methyl groups to specific amino acids of histones.
- enzymes called histone demethylases, remove methyl groups from histones.
2. Acetylation of histones:
- the addition of acetyl groups to histones. This usually stimulates transcription
- in general, acetyl groups destabilize chromatin structure allowing transcription to take place.
- acetyl groups are added to the histones through acetyltransferase enzymes.
- deacetylases strip acetyl groups from histones and restore chromatin structure, which represses transcription
113
How is DNA methylation associated with gene regulation? what gets methylated and how does this result in gene regulation?
DNA methylation is most common on cytosine bases adjacent to guanine nucleotides.
-heavily methylated DNA is associated with the repression of transcription
- when genes are not being transcribed CpG islands are often methylated, but the methyl groups are removed before the initiation of transcription. CpG methylation is also associated with long term gene repression
-
114
What are CpG islands
DNA regions with many CpG sequences and they are commonly found near transcription start sites.
115
define:
- transcription factors
- other transcription factors
- basal transcription apparatus
- core promoter
- regulatory promoter
Transcription factors: transcription in eukaryotes is regulated by transcription factors that bind to specific DNA sequences
General transcription factors: bind to the core promoter and are part of the basal transcription apparatus. These are required for transcription
Basal transcription apparatus: the complex of RNA polymerase, transcription factors, and other proteins that assemble to carry out transcription. This binds to the core promoter
Core promoter: located immediately upstream of a gene and is capable of minimal levels of transcription
Regulatory promoter: others transcription factors bind here and it is located upstream of the core promoter.
116
What is the difference between enhancers and silencers. What transcription factors bind to them? where are they located in respect to a gene
Enhancers are regulatory elements that affect the transcription of distant genes. In man eukaryotes, enhances are highly abundant. Enhancers usually regulate genes in a cell type specific manner- they turn on different sets of genes in different cell types and help establish the traits that characterise cells of different tissues.
Silencers have an inhibitory effect on the transcription of distant genes
117
what is the purpose of an insulator, and how does it work?
insulators are DNA sequences that block the effect of enhancers in a position-dependent manner. If an insulator lies between an enhancer and a promoter, it blocks the action of the enhancer, but if it lies outside that region it has no effect.
Insulators are important because most enhancers are capable of stimulating any promoter in their vacinity
118
How is the stability of mRNA a means of regulating eukaryotic gene expression
the amount of protein synthesized is dependent on the amount of corresponding mRNA that is available for translation. The amount of mRNA available depends on the rate of mRNA degradation and mRNA synthesis. The variation in the stability of mRNA produce large differences in the amount of protein synthesized
119
Why is RNAi an important tool for eukaryotic gene regulation
as many as 30% of human genes are regulated by RNAi.
miRNAs and siRNAs
siRNAs and miRNAs regulate gene expression through 4 distinct mechanisms: 1) cleavage of mRNA 2) inhibition of translation 3) transcriptional silencing 4) degradation of mRNA
