BIOC385 - Exam 4
Structure of E. coli DNA polymerase (pol I) where are the catalytic residues found?
- within the Beta sheets of the palm region - the finger and thumb regions form a tunnel through which the DNA passes
eukaryotic gene regulation: binding of enhancer and promoter
1. transcription factors bind to open sites on DNA 2. bound transcription factors recruit other proteins to form complexes 3. recruited transcription factors help assemble a pre-initiation complex at the promoter the intervening DNA can be looped out between the enhancer and the promoter
Where would an amino acid be attached to the tRNA below?
A
In the last step, the RNA polymerase II is phosphorylated on the
C-Terminal domain (CTD)
Which of statement is most correct regarding characteristics of codons in the Genetic Code?
Genetic code is 64 codons with 61 corresponding to the 20 amino acids and 3 that are stop codons
In the wobble position, inosine binds to adenine, cytosine, and uracil, but not guanine. Why not?
Inosine and guanine are chemically incompatible to form hydrogen bonds
Translational initiation in prokaryotes: a specific nucleotide sequence known as the _________ sequence appears upstream of the first AUG to orient mRNA within the ribosome
Shine-Dalgarno sequence
Mismatch repair of replication errors: the MutS-MutL complex then associates with
MutH, which is bound at methylated GATC sequences in the parental DNA strand
A second mismatch repair protein, MutL, forms a complex with
MutS through an ATP dependent association
Which of the following best describes how trans- and cis-acting factors operate?
Trans-acting factors can bind to specific DNA sequences whereas cis-acting sites are DNA sequences.
What will happen to the lac operon when there are elevated levels of glucose in a cell?
Transcription occurs at a very low rate of expression.
Most human cancers are caused by somatic mutations occurring during an individual's lifetime, but some cancers are the
result of inherited mutations
The Nirenberg-Leder experiment was used to assign triplet codons to specific amino acids based on the
retention of radioactive aminoacylated tRNA molecules on a nitrocellulose filter
Retinitis pigmentosa causes degenerative changes in the
retina that lead to total blindness, pigment buildup can be seen as the dark dots on the peripheral edge of the retina
telomerase acts as a
reverse transcriptase and synthesizes telomeric
Post-translational modifications are usually
reversible
Protein transport can occur as a _______ process (for example, between the golgi apparatus and the ER) or as an ________ process ( for example, from secretory granules to the extracellular space)
reversible process irreversible process
Integration of Bacteriophage by recombination: integration of bacteriophage gamma DNA into the E. coli chromosome requires a ___________. DNA sequences in the attP site of the viral DNA align with the DNA sequences in the bacterial _____
site-specific recombination event attB site
The portion of the genome encoding protein coding genes is inversely proportional to the
size of the genome and amount of ncRNA
The 45S precursor transcript is modified by ribonucleoprotein complexes containing
small nucleolar RNA (snoRNA) molecules
Identify one way in which RNA splicing can give rise to multiple RNA transcripts from a gene containing 3 exons and 2 introns
splicing between the 3' end of exon 1 and 5' end of exon 3
Several mutations associated with the development of retinitis pigmentosa (RP) have been found in factors that mediate
splicing of mRNA
In positive control, transcriptional activator proteins
stimulate the transcription of target genes; direct or indirectly
In all organisms, ________ of the mRNA can be regulated, usually at the stage of transcription initiation
synthesis
Protein translocation in the ER often occurs during
synthesis
RNA is dynamically ______ and ________ within the nucleus, where it functions to control numerous biochemical processes
synthesized and degraded
primase function
synthesizes RNA primers on the lagging strand
Pol delta
synthesizes lagging strand
Pol epsilon
synthesizes leading strand
Addition of a CCA trinucleotide to the 3' end is catalyzed by the enzyme
tRNA nucleotidyltransferase
What is the BEST explanation for why there is redundancy in the genetic code?
tRNA wobble position at 5'-position of tRNA anticodon and 3'-position of mRNA codon allows non canonical base pairing to occur
The addition of telomeric DNA sequences to the ends of chromosomal DNA is accomplished by the enzyme
telomerase
The __________ strand of DNA is transcribed into mRNA
template
RNA polymerase synthesizes a complement of the _________ of DNA using ATP, CTP, UTP, and GTP; _______________ contains the enzyme, unwound region of DNA, and an RNA-DNA hybrid helix
template strand transcription bubble
What did Jorgensen and Napoli, and Fire and Mello discover?
that when given sense or antisense RNA to unc-22 it has no effect but when given double stranded RNA (it should have been control result) there was twitching due to the silencing of unc-22 mRNA translation
Prokaryotic and eukaryotic DNA polymerases rarely made mismatched base pairs because
the active site does not fit mismatches well
When a chemically similar but incorrect amino acid (Val) binds loosely to the active site with the same tRNA in step but, then
the aminoacylated tRNA is still generated. However, the chemically similar but incorrect, amino acid is hydrolyzed at the editing site in step 2
Prenylation
the attachment of an isoprenoid group to a cysteine residue via a thioester linkage and occurs at the C terminus of a protein, which is marked by a conserved CaaX motif
Francis Crick proposed the Wobble Hypothesis, which stated that
the base pairing rules may be relaxed at the third position of the codon (the first position of the anticodon)
Double strand breaks in meiotic homologous recombination are initiated by
the binding of two molecules of Spo11, one to each of the DNA strands
A silent mutation occurs when
the change in DNA sequence does not alter the protein sequences
lynch syndrome: Mutations in just one copy of either of these DNA repair enzyme genes lead to HNPCC at a relatively early age, which is not surprising given
the critical role of mismatch repair in maintaining genome integrity
Mismatch repair of replication errors: formation of the heterotrimeric mismatch repair protein complex (MutS - MutL- MutH) activates
the endonuclease activity of MutH, which makes a single strand cut in the unmethylated DNA daughter strand
What did Elizabeth Blackburn and Carol Greider discovered
the enzyme telomerase in 1984 and were awarded a share of the 2009 Nobel l prize in Physiology or Medicine
The function of the lac operon is to provide
the enzymes needed to utilize the disaccharide lactose.
the trombone model of DNA replication- eukaryotic
the eukaryotic and prokaryotic replication forks are largely similar, although two different DNA polymerases are required for leading strand ( Pol epsilon) and lagging strand (pol delta) synthesis
The Ames test is designed to identify mutation rates using a strategy based on
the frequency of new mutations that compensate for an existing mutation
In hammerhead ribosymes, the minimal requirements of the ribozyme are a 15 nucleotide sequence that folds into
three base-paired stems, with the catalytic core formed through interactions between conserved nucleotides
How many tRNA and mRNA binding sites are in the ribosome
three tRNAs 1 mRNA
lysogeny causes the phage DNA
to be replicated with each bacterial replication
When there are high levels of tryptophan in the bacterial cell, the effect it has on the Trp repressor is __________ and the effect on the structure of the Trp operon mRNA is _______
to stimulate operon binding; to promote formation of the regions 3-4 stem loop
In DNA an active prokaryotic replication fork requires
topoisomerase, DNA helicase, primase, single stranded DNA binding proteins, the core polymerase, and a spare Beta clamp (synth of next okazaki fragment)
Specificity comes about by the interaction of proteins, called ____________, which bind to particular sites on DNA, termed ___________
trans-acting factors; cis- acting sites
Which of the following statements best describes how the terms trans-acting and cis-acting apply to gene regulation?
transacting factors are proteins that bind to specific DNA sequences, which are themselves cis-acting sites in DNA
The control point for most gene regulation occurs at the initiation of
transcription
the bacterial lacZ gene to study gene regulatory processes in transgenic mouse embryos is a
way to monitor gene promoter
Values of the portions of RNA are estimates based on bioinformatic analysis of
whole-genome sequencing and transcriptome characterization
When nucleotide base on the right side is correctly positioned within the active site, the base on the left will fit how?
will not fit properly fit into the active site. Significant clashes are shown as red circles
The HIVRT enzyme shares many similarities with a region of E. coli Pol I enzyme
with an analogous region
Noncanonical base pairings can occur between mRNA and tRNA at the _________ position
wobble
Time to complete one round of genome duplication - bacteria
~ 40 minutes
expression of eukaryotic genes is an _____________ in various ways to allow access by transcription machinery
active process that modifies chromatin
transfer RNA function
adaptor function
When do somatic mutations occur?
after zygote formation
DNA polymerase be able to accommodate to which deoxynucleotides
all four
RNA tertiary structure is dynamically _________ by the binding of protein and small molecule ligands
altered
Alkylation of O-6 of guanine and O-4 of thymine, yields stable adducts with
alternative base pairing patterns
DNA mutations can lead to a gain or loss of splice sites, resulting in
alternative splicing and product of aberrant proteins
Ames Test: if bacteria are capable of growing and producing histidine, then it indicates that a
back mutation has occurred, and the agent is indeed mutagenic
RNA is able to participate in functional _________ interactions with RNA or DNA
base pairing
The HIV reverse transcriptase (HIVRT) converts its RNA genome into DNA ________ inserting the viral genome into the host DNA
before
At what point during transcription does the factor dissociate from the RNA polymerase?
before the elongation phase
DNA replication is (directional or bidirectional?
bidirectional
DNA replication begins at origin and proceeds
bidirectionally
Sequences near the 3' end of precursor mRNA mediate transcription termination through
binding of cleavage and polyadenylation factors
What is a critical part of the initiation process of using an active prokaryotic replication fork
binding of helicase
signal recognition particle (SRP)
binds to a signal sequence at the N terminus of the nascent polypeptide and directs the ribosome to the SRP receptor in ER. The synthesized protein directly enters the ER lumen
Single stranded DNA binding proteins function
binds to single stranded DNA to prevent reannealing of the DNA double strands
Poly(A) binding protein
binds to the short tract of adenine residues and increases the rate polyadenylation by poly(A) polymerase to generate a poly(A) tail of ~200 adenine residues
The Tus-Ter complex terminates E. Coli DNA synthesis by
blocking the opening of the DNA helix at the fork by helicase
When ___________ are present, a very low level of expression is observed
both sugars (glucose and lactose)
the alpha amino group of the amino acid in the A-site tRNA attacks the carbonyl carbon in the ester bond between the P-site tRNA and its
bound amino acid
The holliday junctions can be moved along the now joined chromosomes by helicase activity a process called ___________. This can inc or dec the size of the heteroduplex region
branch migration
This reaction is similar to Group II intron splicing in which the reaction between the 5' phosphate and adenosine (A) occurs at the ________
branch site
Induced pluripotent stem cells (iPS)
cells are generated by introducing DNA encoding the transcription factors Oct4, Sox2, Klf4, and cMyc which convert differentiated cells into pluripotent cells
How does the level of glucose control the level of cAMP?
cells contain a sugar transport system called the PTS system, in which phosphate groups are transferred sequentially from PEP through a series of proteins and eventually to sugars, including glucose
The lac operon regulatory region contains multiple _________ sites which include the promoter; a primary binding site for lac repressor; and a binding site for a positive activator CRP, that stimulates expression
cis acting sites
transport from the trans-golgi network or from the plasma membrane occurs in
clathrin-coated vesicles
The dicer recognizes double stranded RNA (dsRNA) and
cleaves it into small dsRNA
what are the two structural states of chromatin
condensed and decondensed
bioinformatic analysis of prokaryotic promoter sequences were used to define
consensus sequences for what are referred to as the -35 box (5'- TTGACA-3') and the -10 box (5' -TATAAT- 3')
A nonsense mutation results from
conversion of a normal codon to a stop codon that terminates the protein synthesis
zinc finger motif
coordinates one zinc atom with two cysteine and two histidine residues
The shape of the DNA polymerase active site facilitates formation of the
correct G-C and A-T base pairs
What did Francis Crick discover?
created adapter hypothesis that established link between RNA and protein structure of tRNA was not discovered until the 1970s, but Cricks hypothesis initiated the hunt to isolate, sequence, and determine the secondary and tertiary structure of this molecule
Holliday junctions: if binding occurs such that cuts are made at sites 2 followed by ligation,
crossover occurs
Resolving the Holliday junction produces either a ______ or ______ to the original chromosomes
crossover product or reversion
Adjacent pyrimidines often produce _______ after UV irridiation
cyclobutane pyrimidine dimers
In the ER, prenylation can occur. Prenylation is the attachment of an isoprenoid group to a __________ residue via a(n) _________
cysteine; thioester
Transport from the Golgi apparatus to the endoplasmic reticulum and within the golgi apparatus is mediated by
cytoplasmic coat I (COPI) - coated vesicles
Transport from the ER to the golgi network is mediated by
cytoplasmic coat II (COPII)- coated vesicles
If replication takes place with an abasic site present, a ______ is often inserted opposite the abasic site. This results in a
cytosine C-G to G-C mutation
what is a key step in the transition of the enzyme complex from the initiation to the elongation stage
hypephosphorylation of the CTD
In which direction is mRNA synthesized by RNA polymerase?
in the 5' to 3' direction
tRNA synthetases provide a 2nd genetic code. when the correct tRNA and cognate amino acid (Thr) bind to the active site in step ___, then aminoacylation occurs
in the active site and this aminoacylated tRNA is not hydrolyzed by the editing site in step 2, thus generating the correct aminoacylated tRNA
If replication occurs with the uracil in place, one of the daughter strands will
incorporate an adenine base as a complement to uracil, which will result in conversion of C-G base pair to T-A
Nirenbern and Mattaei discovered that addition of ribosomal RNA (rRNA) ____________ the amount of protein synthesized in vitro by a mixture of lysed bacterial cells
increases
messenger RNA function
information transfer
In negative control, transcriptional repressor proteins
inhibit transcription of target genes; direct or indirectly
The trp repressor __________ transcription when tryptophan levels are HIGH by
inhibits blocking RNA polymerase binding
The most common point of gene regulatory control is the decision to
initiate transcription
Translational initiation in prokaryotes: Three ___________ bind to the 30S ribosome, followed by binding of the mRNA and Met-tRNA to form the 30S initiation complex
initiation factors
polypeptide synthesis is composed of three stages:
initiation, elongation, and termination
DNA sequence elements called __________ counteract the action of enhancers when located between an enhancer and a promoter
insulator sequences
Lysogeny by bacteriophages causes what result to the host DNA?
integration of virus into host DNA
Ribozymes function as catalysts reacting with substrates to mediate either ________ or _________ cleavage of phosphodiester backbone; ribozymes affect reaction rates, not the equilibrium
intramolecular (cis) or intermolecular (trans)
Which of the following components of eukaryotic mRNA are removed by RNA processing?
intronic sequences
Eukaryotic mRNA often contains RNA sequences called ________ which interrupt the protein coding sequences called ______
introns exons
Splicing reactions and addition of the poly(A) tail also
involve processing proteins that bind to the CTD
RNA polymerase II transcriptional termination is coupled to 3' end processing
involving polyadenylation by poly (A) polymerase enzyme
Retinitis Pigmentosa (RP)
is a degenerative disease of the retina characterized by loss of the light- sensing photoreceptor cells
Semiconservative, as it relates to DNA replication, can be defined as when the original duplex DNA template
is separated into single strands before replications.
Holliday junctions: This holliday junction complex is then __________ and a second round of strand cleavage,__________ , and covalent linkage results in recombined sister chromatids
isomerized strand invasion
Allolactose is the inducer of the lac operon; it interacts with _________, causing it to bind weakly to its operator
lac repressor
The lac operon is controlled by the ___________ that blocks RNA polymerase access to the promoter
lac repressor
Significant differences between prokaryotic and eukaryotic translation initiation complexes include the ____________________________ in the mRNA in eukaryotes and the number of initiation factors required
lack of a specific ribosome binding site
In the presence of ______ alone, lac repressor does not bind because allolactose binds the repressor and the complex does not bind the operator
lactose
_______ is imported into the cell by lac permease
lactose
which strand is synthesized discontinuously
lagging strand
A lytic cycle causes production of
large amounts of the virus, followed by cell lysis
Nuclear pore complexes are
large complexes that protrude on both sides of the membrane
All four base pairs present distinctive patterns of potential hydrogen bond donors and acceptors as well as hydrophobic groups in the _________ groove of the DNA
major
a single gene can generate
many mRNAs
The DNase I footprinting method can be used to
map protein binding sites on DNA
When does the highest rate of DNA recombination in eukaryotes occurs during
meiotic cell division
prokaryotic and eukaryotic cells contain abundant protein-synthesizing RNAs being
messenger RNA (mRNA) ribosomal RNA (rRNA) transfer RNA (tRNA)
A common chemical modification found in RNA is
methylation of nucleotide bases in tRNA
What is the function of the MutS-MutL-MutH protein complex?
mismatch DNA repair
Cells have the ability to repair DNA, including _____, ________, and ________
mismatch repair, base excision repair, nucleotide excision repair
How many different RNA base modifications have been identified , with the majority of these occurring in tRNA
more than 100 different
The alternative base pairings created by noncanonical base pairings using wobble position mean that
more than one codon may be recognized by a single tRNA
How does polymerase delta make up for a much lower reaction rate than E coli
multiple eukaryotic replication origins makes up for it
snRNA molecules have many ________ and ________ formed between them
multiple intrastrand and interstrand base pairs
the RNA polymerase II CTD coordinates mRNA transcription and processing and consists of
multiple repeats of the heptapeptide sequence YSPTSPS,
DNA damage can lead to _______, depending on the severity of the damage
mutations
Consider an in vitro experiment in which all components needed for protein synthesis are present. If tRNAs charged with radioactively labeled amino acids are added, over time the radioactivity would be located in which of the following components?
nascent protein
What is the largest portion of eukaryotic RNA in humans made up of?
ncRNA and not transcribed
The Mg2+ ions stabilize the _________ charges on the deoxynucleotide and assist in deprotonation of the _____ by the base
negative 3'-OH
Nirenberg and Matthaei added RNA containing only uridine (polyU RNA) to the system as a ____________ to demonstrate that it was rRNA that uniquely stimulated protein synthesis and surprisingly made _________
negative control; polyphenylalanine
The figure below shows __________ autoregulation and will __________.
negative; reach a steady state
Histone acetylation by HAT enzymes __________ the positive charge
neutralizes
structure of E. coli DNA polymerase (Pol I): editing mode:
newly added nucleotide is flipped out the polymerase active site and into the exonuclease site, where it is excised from the growing DNA strand
A resolvase can bind at either sites 1 or 2. If binding occurs such that cuts are made at sites 1 followed by ligation, then the product shows
no crossover
along with the three primary protein-synthesizing RNA molecules, which are found in all organisms, eukaryotic cells also contain a diverse class of RNA molecules collectively referred to as
non-coding RNA (ncRNA)
The entire evolutionary process is a result of
non-deleterious mutations that occurred very slowly over time
_______________ between tRNA anticodon bases and mRNA codon bases must occur to account for the redundancy in the varying number of tRNA
noncanonical base pairings
The inosine base can form ______________ base pairs with
noncanonical; adenine, cytosine, and uracil
The basic building block of chromatin is
nucelosome
The 40S and 60S ribosomal subunits are assembled in the _________ through complex formation with more than _____ ribosomal proteins to generate the 80S ribosome
nucleolus; 70
Holliday junctions: after strand swapping and covalent linkage of DNA strands through a ___________ by the 5'-hydroxyl on the ___________, a holliday junction is formed
nucleophilic attack phosphotyrosine
the anticodon of the anticodon arm forms base pairs with the corresponding
nucleotide bases in the mRNA
In contrast, eukaryotic RNA synthesis and RNA processing events occur in the
nucleus, whereas protein synthesis takes place in the cytoplasm
TBP is a component of the transcription factor IID (TFIID) complex, which contains
numerous TBP-associated factors (TAF)
bacterial resistance to aminoglycosides is a major health problem and this has led researchers to search for next-generation antibiotics. One class of these new antibiotics are called ___________, which are produced by symbiotic bacteria that live inside _________
odilorhabdins; parasitic nematodes
The ability of the human immune system to generate the large array of antibodies begins with the number
of V, D, and J genes that can be recombined to give rise to the variable regions of antibodies
The Pol III core on the lagging strand template synthesizes an ________ fragment from the __ end of one RNA primer until it reaches the 5' end of the RNA primer farther down the lagging strand template
okazaki 3' 5'
Proteins can also be modified by the addition of ___________ called glycans
oligosaccharide chains
The bacterial beta and beta' subunits of the bacterial RNA polymerase holoenzyme form the catalytic center, with the _______ subunit functioning to stabilize the interaction btw one of the __________ subunits and the Beta' subunit
omega alpha
Nirenberg and Matthaei's method of solving the genetic code can solve how many codons at a time?
one
Definition of conservative replication
one daughter DNA molecule is all new and the other is all old DNA
Once replication is initiated, the replication fork could proceed in
one direction or in both directions from the origin
Single strand DNA breaks and double strand DNA breaks must be
repaired
adult stem cells
replenish dying cells or cells destroted by injury. Most differentiated cells do not continue to divide
the cAMP-CRP activator complex is
required to maximally stimulate expression of the lac operon
The spliceosome _____________.
resembles group II introns in its mechanism and product
Resolution of Holliday junctions is accomplished by ______ enzymes, which are part of the _____________
resolvase part of the recombinase complex
What does the clamp loader do?
responsible for loading Beta Clamp proteins onto DNA binds to one of the Beta monomers and in an ATP- dependent mechanism opens a gap at the interface between the two beta monomer
Time to complete one round of genome duplication - human
8 hours
Rho is an ATP-dependent helicase that binds to the newly synthesized
RNA chain at a C-rich sequence
The two key elements of the oriC include
three 13-bp repeats and four 9-bp repeats with enriched A-T pairs.
Match the bacterial DNA replication component on the left with its primary function on the right. (a) ____Clamp protein (b) _____ Topoisomerase (c) _____ DNA helicase (d) _____ Single-strand binding protein (e) ____ Primase (f) _____ DNA A protein A. Unwind the DNA at OriC B. Unwind the DNA double helix C. Synthesize an RNA primer D. Maximize processivity of DNA pol E. Remove supercoils ahead of fork F. Prevent DNA strand reannealing
(a) __D__Clamp protein (b) ___E__ Topoisomerase (c) ___B__ DNA helicase (d) __F___ Single-strand binding protein (e) __C__ Primase (f) __A___ DNA A protein
Number the steps from start to finish for prokaryotic mRNA translation (a->e). (a)____Translational elongation proceeds in the 3' direction along the mRNA strand (b) ___ Binding of 50S subunit, GTP hydrolysis, release of IFs, 70S ribosome forms (c)____Initiation factors (IFs) bind to the 30S ribosome along with GTP (d)____Stop codon enters A site, binding of RF protein, disassembly of ribosome. (e)___ mRNA Shine-Dalgarno sequence base-pairs with 16S rRNA in 30S subunit
(c)__1__Initiation factors (IFs) bind to the 30S ribosome along with GTP (e)_2__ mRNA Shine-Dalgarno sequence base-pairs with 16S rRNA in 30S subunit (b) __3_ Binding of 50S subunit, GTP hydrolysis, release of IFs, 70S ribosome forms (a)__4__Translational elongation proceeds in the 3' direction along the mRNA strand (d)__5__Stop codon enters A site, binding of RF protein, disassembly of ribosome.
other lncRNA sequences map to opposite strands but are separated by _______ bp or more (_____________) or are located entirely _____________ between exon sequences of a protein-coding gene, or simply in between genes (_________)
- 1,000 bp - bidirectional - within introns - intergenic
How is the Ames test used to quantitate mutagenic potential of chemical compounds? Select the TWO best answers. The Salmonella test strain used in the Ames test contains a mutation in the histidine biosynthetic pathway, which is used to identify compounds that induce back mutations to permit bacterial growth on histidine free plates. Histone deficient plates are used to calculate the background mutation rate, which is the control plate for the filter disk experiment. The more colonies growing on the plate, the better the mutagen. Bruce Ames invented the Ames test to determine which chemical compounds cause human cancer, however bacterial cells are not liver cells and so it is not very useful to prevent gout. The Salmonella tester strain is grown in histidine containing media since it lacks the ability to synthesize its own histidine for protein synthesis; chemical compounds that mimic histidine lead to MORE bacterial growth on the plates. The ratio of bacterial colonies to drug concentration (bc:dc) is used to calculate the mutagenic index of a chemical compound; high bc:dc ratios means the drug functions as a growth factor for the cells. The chemical compound to be tested is added to a filter paper disk and placed on agar plates containing the tester Salmonella strain; potent mutagens result in MORE colonies forming on histidine free plates as compared to control plates. The Ames test uses filter disks containing chemical compounds to quantitate the level at which the compound is lethal to the Salmonella tester strain; the FEWER colonies on the plate, the more toxic is the chemical regardless of mutagenic potential.
- The Salmonella test strain used in the Ames test contains a mutation in the histidine biosynthetic pathway, which is used to identify compounds that induce back mutations to permit bacterial growth on histidine free plates - The chemical compound to be tested is added to a filter paper disk and placed on agar plates containing the tester Salmonella strain; potent mutagens result in MORE colonies forming on histidine free plates as compared to control plates.
What were the three hypotheses of DNA replication?
- conservative replication - dispersive replication - semiconservative replication
Activator proteins can bind to ______________ or to
- enhancer sequences located at a far distance from the gene promoter - cis-acting sequences very near to the gene promoter
What are some chromatin modifications of nucleosomes
- histones can be post-translationally modified -nucleosomes can be moved to new positions - histone variants alter nucleosome properties
Therapeutic treatment steps
- identify disease phenotype - analyze mechanism of disease - screen for drugs that affect disease phenotype - therapeutic drug
the three major RNAs required for protein synthesis and function are:
- mRNA: the carrier of the genetic information - rRNA: the major constituent of ribosomes - tRNA: the adaptor molecule that connects RNA synthesis to protein synthesis
What are the two fragments of DNA pol I proteolytic cleavage
- one contains the 5-> 3' exonuclease activity - the other is referred to as the Klenow fragment shown here bound to DNA
The most common enzyme mediated protein modifications in eukaryotic cells are:
- phosphorylation - methylation - acetylation - ubiquitination - glycosylation - lipid modification
Splicing defects that cause disease can be due to defects in ______________ (cis mutations) or in components of ____________ (trans mutations)
- splicing recognition sequences (cis mutations) - spliceosome complexes (trans mutations)
What are the three molecular processes that are required to convert a skin cell into an induced pluripotent cell after introduction of the four transcriptional factor genes?
- the sox 2/ Oct4/ Nanog complex inhibits expression of cell differentiating genes - the sox 2/ Oct4/ Nanog complex activates expression of stem cell genes - the sox 2/ Oct4/ Nanog complex activates a positive autoregulatory loop
Applications of iPS cells to treat disease
- therapeutic treatment for disease - drug discovery and pharmaceutical intervention
Rate of replication fork movement (micrometers/ minute) human
0.5-2
Number of replication origins: bacteria
1
number of chromosomes bacteria
1 chromosome
Nirenberg and colleagues determined a portion of the genetic code using filter binding assays that included ribosomes, trinucleotides and tRNA molecules charged with radioactively-labeled amino acids. Choose the answer below that correctly answers the following three questions in order: 1) If the trinucleotide sequence is CAG, which amino acid will be bound to the filter paper? 2) If the wobble position of the trinucleotide sequence is changed to a U, which amino acid will be bound to the filter paper? 3) True or False: Two distinct tRNA molecules with different anticodon sequences MUST be used to recognize the codons AGA and AGG.
1) Gln 2) His 3) True
Briefly describe the structure and function of the 1) one key E. coli protein that are each needed for high fidelity termination of DNA replication and 2) one key human protein and the one key.
1) Tus protein prevents fork replication past termination, 2) Telomerase prevents lagging strand deletion.
Name two reasons why the regulation mechanisms of trp biosynthetic enzymes in bacterial cells are not found in yeast cells, i.e., how are yeast different?
1) trp is an essential amino acid:no enzymes 2) transcription/translation are uncoupled:no attenuation
Nucleotide polymerization rate (nucleotides/ second) bacteria
1,000
Initiation of DNA synthesis in bacteria steps
1. DnaA protein binds to 9-bp repeats inducing unwinding at 13-bp repeats 2. DnaC loads the DnaB helicase protein at the forks and then dissociates; SSBs bind to the single-stranded regions 3. primase binds to the fork regions by associating with the DnaB and synthesizes RNA primers on the leading strands; fork movement causes DnaA proteins to dissociate 4. Pol III core complexes bind to the forks and begin synthesizing new DNA using the leading and lagging strand templates
number of chromosomes human
23 chromosome pairs
An experiment was performed using E. coli to measure the amount of beta-galactosidase activity in bacterial cultures that were supplemented with glucose and/or lactose. Based on the graph shown in which Experiment #1 is the control and had neither glucose nor lactose present, what do you predict for Experiments #2, #3, and #4 in which one or both sugars were added? Your choices in the table below show which sugars would need to be present in the culture media to explain the observed levels of beta-galactosidase.
1. No sugar 2. glucose 3. lactose 4. glucose/lactose
Match the description of each mode of regulation with the illustration diagrammed at the right and record your answer in the order of 1à4. 1. _ _ Ligand-regulated repression 2. _ _ Ligand-regulated de-repression 3. _ _ Ligand-regulated activation 4. _ _ Ligand-regulated de-activation
1. _ C _ Ligand-regulated repression 2. _ D _ Ligand-regulated de-repression 3. _ B _ Ligand-regulated activation 4. _ A_ Ligand-regulated de-activation
tRNA synthetases provide a 2nd genetic code steps
1. an aminoacyladenylate intermediate is formed between the carboxyl group of the amino acid and the alpha phosphate of ATP 2. cleavage of the phosphodiester bond facilitates the formation of aminoacyl tRNA as the amino acid is transferred to the 2' hydroxyl or 3' hydroxyl of the tRNA acceptor stem
The spliceosome reaction cycle
1. assembly of the active complex and cleavage of 5' end of the intron to form the lariat structure 2. cleavage at 3' end of intron and joining of two exons 3. intron released as a lariat structure, degraded in nucleus
Four mechanisms by which lncRNA molecules could regulate cellular processes: 1. 2. 3. 4.
1. base pairing between nucleotides in the lncRNA and target RNA 2. base pairing between lncRNA and single-stranded regions of DNA 3. formation of functional ribonucleoprotein complexes similar to ribosomes and spliceosomes 4. ligand-induced riboswitches
Post-translational modification of proteins
1. recognizes hydrophobic segment 2. hydrolysis GTP 3. phosphate leaves 4. GDP cleaved off and recycled
Three classes of eukaryotic ncRNA have been characterized
1. short ncRNA (miRNA, siRNA, piRNA) 2. small ncRNA (snRNA, snoRNA) 3. long ncRNA (RNaseP, TERC, IncRNA)
Poly(A) polymerase catalyzes the addition of _______ adenine residues to the 3'-hydroxyl terminus of the precursor mRNA
10
Number of replication origins: human
10,000
Eukaryotic polymerases contain as many as
10-20 protein
The 18 amino acids excluding tryptophan and methionine use how many codons
2 to 6 codons
how much of the yeast genome is ncRNA
2%
Rate of replication fork movement (micrometers/ minute) Bacteria
20
Gobind Khorana method of solving the genetic code can solve how many codons at a time?
3 at time
The DNA polymerase reaction adds a deoxynucleotide to the ___' end of the growing DNA chain
3'
Genome size (base pairs) Human
3.3 x 10^9
the number of tRNAs varies among organisms, most species having _________ different tRNA genes rather than the maximum number of ________
30-35 max number 61
Translational initiation in prokaryotes: in step 3, hydrolysis of GTP facilitates binding of the 50S ribosomal subunit, with the release of IF1 and IF2 to form the functional
70S ribosomal initiation complex
Genome size (base pairs) bacteria
4.6 x 10^6
The U1 snRNA directly base pairs with sequences in the ____ donor site, whereas the U2 snRNA base pairs with
5' residues in the branch site
Introns in primary mRNA transcripts contain short conserved sequences at the ___ and ______ splice sites, as well as in the branch site
5' (GU) 3' (AG)
What are the components of a schematic intron
5' splice site (GU), branch point (A), and 3' splice site (AG)
During RNA synthesis, one strand of DNA is used as a template for synthesis of a complementary strand starting at a transcription bubble. RNA synth proceeds in a
5' to 3' direction down the DNA template
This arrangement of proteins within the E. coli replication fork accommodates
5' to 3' directional DNA synthesis of the leading and lagging strands
Although all DNA polymerases have the ability to synthesize DNA in a ___________direction, some other activities are often associated with certain DNA polymerases that allow them to accomplish more than just
5'->3' polymerization of DNA
In an iteration of the Nirenberg-Leder experiment to assign triplet codons to specific AA, radioactively labeled amino-acyl-tRNA with the anticodon of 3'CUG-5' was retained on the filter at the end of experiment. Which mRNA was used in this iteration of the experiment?
5'-GAC-3'
Nucleotide polymerization rate (nucleotides/ second) human
50
how much of human genome is ncRNA
50%
It has been estimated that as much as __________ % of the human genome is transcribed into noncoding RNA, whereas __________ % of the E. coli genome is noncoding RNA.
50; 10
Most cancerous cells have at least _____ gene mutations which are referred to as
60 gene mutations oncogenes and tumor suppressors
How many codons of the standard genetic code correspond to the twenty amino acids and how many specify termination
61 that correspond with one or more AA 3 codons that specify termination
How many triplet codons does the standard genetic code have?
64
in the oriC sequence, both the 13-bp and 9-bp sequences are very __________ to _______
A-T rich to facilitate unwinding of the double stranded DNA
During elongation a charged tRNA binds first to the _ site and translocates to the _ site after peptide bond formation. After transfer of the polypeptide chain, the tRNA is released from the _ site
A; P; E
When the signal recognition particle (SRP) binds to the endoplasmic reticulum (ER) signal peptide sequence on the amino terminal end of the polypeptide in the early stages of translation, the ribosome pauses on the mRNA and stops translation. What is the purpose of this ribosome pausing?
Allows time for the SRP-Ribosome complex to bind the SRP receptor
The trombone model of DNA replication - prokaryotic
DNA synth at the fork, the Pol III core on the lagging strand template alternates between bound and unbound forms
aminoacyl-tRNA synthetases carry out editing _________
At a site that is distinct from the active site
Francis Crick hypothesized that the Genetic Code must require 3 nucleotides in the mRNA to specify each amino acid based on a simple calculation. What was the logic behind this calculation?
Based on the number of known amino acids and the number of known nucleotide bases
_________ cleaves lactose into glucose and galactose
Beta-galactosidase
Use the nine nucleotide DNA base pairs below to determine the mRNA and protein sequences in Q #2 and Q #3. Section of DNA sequence shown is located somewhere in the middle of the gene not at the start site. 5'....... CCA TAC CGG .......3' 3'....... GGT ATG GCC........5' mRNA 5'..... ___ ____...3' The correct order for codons 1, 2, and 3 written 5' to 3' on the mRNA strand is:
CCA, UAC, CGG
After binding of the virus (HIV) to the _____ receptor and membrane fusion, the RNA genome is inserted into the host celll
CD4 receptor
The XIST gene is transcribed from both X chromosomes in females but only one of the two chromosomes produces enough
CIST lncRNA to cause inactivation
Which base location in the figure below (A, B, C, D) explains the wobble hypothesis?
D (5' end)
mRNA silencing by siRNA and miRNA mediated processes: the precursor miRNA is cleaved in the cytoplasm by _________ to generate the mature miRNA product, which mediates gene silencing by the _____ complex through
DICER; RISC; translational inhibition of ribosome function or mRNA degradation
What are the four key enzymes of prokaryotic replication fork
DNA Pol III Helicase Gyrase Primase
Double strand breaks: cleavage of the strands and dissociation of Spo11 allows for binding by heterotrimeric protein complex that removes
DNA from the 5' ends
Which of the following is a specialized direct DNA repair process?
DNA photolyase system
What are the two principal enzymes for eukaryotic DNA replication are
DNA polymerase delta DNA polymerase Epsilon
Which enzyme synthesizes the RNA primer for DNA replication?
DNA primase
primary miRNA transcripts are processed by _________ to produce precursor miRNA, which is exported to cytoplasm
Drosha
What function do HAT and HDAC enzymes perform in the chromatin-modifying process? A. HAT acetylates and represses the gene. HDAC deacetylates and activates the gene. B. HAT acetylates the gene and HDAC deacetylates the gene. Both repress the gene. C. HAT enzymes methylate DNA, HDAC enzymes do not. D. HAT acetylates the gene and HDAC deacetylates the gene. Both activate the gene. E. HAT acetylates and activates the gene. HDAC deacetylates and represses the gene.
E. HAT acetylates and activates the gene. HDAC deacetylates and represses the gene.
What is the difference between models for semiconservative and dispersive DNA replication? A. Semiconservative replication yields two DNA molecules: one that is all template DNA and one that is all new DNA; dispersive replication yields two DNA molecules that are mixed DNA. B. Semiconservative replication yields two DNA molecules; where one is all new DNA strands and the other is mixed DNA strands; dispersive replication yields two DNA molecules that are both new DNA. C. Semiconservative replication yields two DNA molecules where each contains one template and one new DNA strand; dispersive replication yields two DNA molecules with one mixed strand and one new strand. D. Semiconservative replication yields two DNA molecules that are both made of a mixed DNA; dispersive replication yields two new DNA molecules and two old DNA molecules, so four total DNA molecules. E. Semiconservative replication yields two DNA molecules where each contains one template strand and one new DNA strand; dispersive replication yields two DNA molecules that a both mixed DNA.
E. Semiconservative replication yields two DNA molecules where each contains one template strand and one new DNA strand; dispersive replication yields two DNA molecules that a both mixed DNA
The work of Francois Jacob and Jacques Monod led to our understanding of gene regulation using the
E. coli lac operon as a model system
Shown here is a G nucleotide base in the 5' position of tRNA can base pair with
EITHER a C nucleotide base or a U nucleotide base in the 3' position on mRNA
Localization of synthesized depends on if it is
ER membrane-associated or not
targeting of a ribosomal complex to the rough ER depends on the presence of a specific amino acid sequence at the N-terminus of the nascent polypeptide known as the
ER signal peptide sequence
Semiconservative replication
Each daughter DNA molecule contains one new strand and one old strand
Francis Crick proposed what hypothesis?
Wobble Hypothesis
A protein release factor
G protein that promotes disassembly of the ribosomal complex
A conserved ____ base pair in each of the Ter sequences plays a functional role in determining whether the Tus-Ter complex is
G-C permissive or nonpermissive for replication forkmovement
The four most common noncanonical base pairings between the 5' position of the tRNA anticodon and the 3' position of the mRNA codon are
G-U I-C I-U I-A
the pre-RC is formed early in the ___ phase, but is not activated until _ phase, when it becomes a Replisome progression complex (RPC)
G1, S
In an iteration of the Nirenberg-Leder experiment to assign triplet codons to specific amino acids, radioactively labeled aminoacyl-tRNA with the anticodon of CUG was used. The radioactivity was retained on the filter at the end of the experiment. Which mRNA was used in this iteration of the experiment?
GAC
An experimental prep is able to separate the following membrane fractions: nuclear membrane, Golgi apparatus membrane, transport vesicle membrane, and mitochondrial membrane. The membrane fractions can then be analyzed via Western blotting for the presence of specific proteins. Which fraction would indicate the presence of t-SNAREs?
Golgi apparatus membrane
What function do HAT and HDAC perform in the chromatin-modifying process?
HAT activates the gene and HDAC represses the gene
If 15N DNA (heavy) replicated using conservative replication in 14N (light) media, the outcome would be different from semi-conservative replication, and in this case, the two daughter DNA double strands would be _______________ after one generation
Heavy only for one daughter DNA and light only for the other daughter DNA
Lynch syndrome is marked by which of the following characteristics?
Higher cancer rates due to autosomal dominant mutations in genes encoding mismatch repair enzymes hMLH1 and hMSH2
double strand breaks: ligation of the ends forms a region where multiple DNA strands come together called a
Holliday junction
Assume that you have identified all the cis-acting sites in a prokaryotic genome for a particular trans-acting transcription factor. What is the function of this transcription factor when binding to these sites?
It is not possible to predict the function from the sites since could activate or repress at different sites.
Why does the initiator fMet-tRNAfMet bind to the P site rather than the A site of the ribosome?
It needs to bind to the P site so AA2-tRNAAA2 can bind to the A site and a peptide bond can be formed.
Which of the following sequences is most likely a nuclear localization signal?
Lys-Lys-Arg-Gly-Arg
Who deciphered the genetic code and what did they use?
Marshall Nirenberg with his postdoc Heinrich Mattaei using defined in vitro protein synthesis reactions
three primary protein-synthesizing RNA molecules
Messenger RNA, Transfer RNA, Ribosomal RNA
What is the type of molecular defect that has been linked to the disease retinitis pigmentosa?
Mutation in a splicing protein causing defects in the spliceosome machinery
Although many glycosylation events occur after translation, _______________ also occur during translation as the nascent polypeptide is emerging into the lumen of the ER
N-linked glycosylations
covalent linkage of oligosaccharides to proteins occur as
N-linked or O-linked attachments
is DNA is packaged into nucleosomes - bacteria
No
Translational initiation in prokaryotes: the prokaryotic initiation complex contains fMet-tRNAi Met bound in the _ site, with the _ site and _ site empty until elongation begins
P site, with the E site and A site empty until elongation begins
What is the primary DNA polymerase in E. coli?
Pol III
Beta clamp function
Prevents DNA polymerase III from dissociating from the DNA
What is the amino acid sequence (start at N-term) encoded by these three mRNA codons?
Pro-Tyr-Arg
What accounts for the accuracy of DNA synthesis at the replication fork?
Proofreading function of DNA polymerase that removes incorrect nucleotides in 3' to 5' direction
Some ribozymes are composed only of ______, whereas others contain both ______ and __________
RNA RNA and protein subunits
How are RNA tertiary structures different from protein tertiary structures?
RNA adopts multiple structures, whereas protein structures are restricted
Gobind Khorana synthesized DNA to make _____________. The repeating triplet nucleotide RNA sequence AUCAUCAUC contains three potential codons, AUC, UCA, and CAU. In vitro translation of this RNA resulting in polypeptides of repeating
RNA of specific seq Ile, Ser, or His residues
Eukaryotic promoters contain conserved DNA sequences that function to specifically recruit
RNA polymerase I, II, and III protein complexes
What are also control for gene regulatory
RNA processing, RNA degradation, protein synthesis, protein modifications, and protein degradation are also control
Prokaryotic protein synthesis occurs at the same time as
RNA synthesis
mRNA silencing: The interaction between siRNA and the target mRNA is mediated by a family of
RNA-induced silencing complexes (RISC), composed of ribonucleoproteins
Eukaryotic tRNA begins with cleavage of the primary transcript from the surrounding region or cleavage of a 5' sequence of variable length by
RNaseP, similare to prokaryotic tRNA processing
Processing of Eukaryotic rRNA: The modified precursor rRNA is then cleaved by ____________ to successively process the transcript, eventually yielding the mature ____________________ rRNA products
RNaseP-like ribozymes 28S, 18S, and 5.8S
With the exception of mRNA, processed RNA is transported with the assistance of the
Ras-related nuclear protein (Ran)
What is the function of the resolvase enzyme in DNA recombination?
Repair of Holliday junctions
bacterial transcriptional termination occurs as either a ______ or __________ process at sequences in the 3' untranslated region
Rho-dependent Rho-independent
Different types of membranes contain variations of these _________________ so that only the correct association between matching v-SNAREs and t-SNAREs results in vesicle fusion to the target membrane
SNARE proteins
A suspected mutagen is analyzed in the Ames test by incubating it with his- __________ and ________, which is then added to a medium containing a minimal amount of histidine
Salmonella typhimurium and rat liver extract
Okazaki fragments
Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.
DNA polymerase function
Synthesizes nascent DNA on leading and lagging strands
Record T (true) or F (false) for statements below regarding protein synthesis. Record as aàe. T F a. Prokaryotic and eukaryotic ribosomes both contain RNA that functions as a catalytic enzyme. T F b. Accurate protein synthesis requires tRNA synthetases to link GTP to 3' end of tRNA molecules. T F c. Ribosomal E, P, and A sites align tRNA anti-codons with the corresponding mRNA codons. T F d. Cells contain only ~30 tRNA molecules, of which 3 correspond to termination tRNA molecules. T F e. The wobble position in tRNA is 5' nucleotide in the anti-codon and 3' nucleotide in mRNA codon.
T F T F T
The RNA polymerase II complex is recruited to gene promoter regions by the
TATA binding protein TBP, which is functionally analogous to the bacterial s factor protein
one example of a functional lncRNA is the sequence ______, which regulates __________ in females on only one or two X chromosomes
XIST x inactivation
The transcription factors TFIIA and TFIIB bind to the transcriptional initiation complex, followed by
TFIIF in association with RNA polymerase II and the TFIIE and TFIIH
Choose the one correct statement regarding tRNA synthetases below.
The editing site hydrolyzes an amino acid-AMP or a tRNA-amino acid if the amino acid is not correct.
The _____ gene on the human X chromosome is transcribed into an lnc RNA that
XIST gene regulates the process of X inactivation
is DNA is packaged into nucleosomes - human
Yes
Which of statement is most correct regarding the "trombone model" of DNA synthesis?
The lagging strand template is released by Pol III when it reaches the 5' end of the RNA primer
negatice regulation can take place, but most regulation is due to the action of
activators
What happens during protein synthesis if a tRNA is charged with the wrong amino acid?
The protein will contain the wrong amino acid in the corresponding codon position.
A ribozyme is an RNA enzyme that functions as a catalyst to mediate substrate reactions. Which of the following is true regarding ribozyme-mediated cleavage?
The ribozyme reaction involves a phosphodiester cleavage through acid-base and metal ion catalysis
How can DNA strands be synthesized using bidirectional replication?
They are synthesized through Okazaki fragments.
How do bacterial sigma factor proteins promote RNA synthesis?
They recruit RNA polymerase to specific sequences at the 5' end of genes
CRP-cAMP complex makes direct contacts with the the alpha-CTD of RNA polymerase;
Thr158 and His159 in CRP contact Gly286, Val287, and Glu288 in RNA polymerase
What is the main purpose of the Ames test?
To determine if chemicals mutate DNA by quantifying their effect on reverting a His- phenotype
the trp operon is regulated by negative control by the __________, which binds tryptophan and turns off transcription of the operon, as well as ___________, which inhibits after the initiation of transcription
Trp repressor attenuation
DNA helicase function
Unwinds the DNA double helix ahead of the replicating complex
recombination of immunoglobulin genes has the capacity to generate billions of different antibodies through the process of
V(D) J recombination
A missense mutation results from
a change in the amino acid sequence
If a mismatched nucleotide arises during DNA replication, it must be repaired before the second cell division after it occurs or else it will become
a fixed mutation
The elongation process continues until one of the three stop codons enters the A site of the ribosome, which leads to the entry of
a protein release factor
A Holliday junction can best be defined as a region of
a quadruplex DNA structure
Double-Strand Break Repair by BRCA proteins: a large collection of proteins is required, including
a recombinase known as Rad51 and the breast cancer susceptibility proteins BRCA1 and BRCA2
prokaryotic replication is initiated at
a single sequence oriC, consists of three repeats of a high conserved 13-bp sequence and four repeats of a conserved 9-bp sequence
Translational initiation in prokaryotes: Shine-Dalgarno sequence
a specific nucleotide sequence that appears upstream of the first AUG to orient mRNA within the ribosome
Pol alpha
a third DNA polymerase is associated with primase. Moreover, unlike prokaryotic DNA, eukaryotic DNA is packaged into nucleosomes
In the Group I intron, the 3'-OH of a guanosine cofactor (G) participates in
a transesterification reaction with the phosphate at the 5' end of the intron
Which statement below is most correct regarding the function of a) mRNA and b) rRNA?
a) mRNA is the carrier of genetic information, b) rRNA is the major RNA constituent of ribosomes.
what type of RNA do eukaryotic cells also contain?
abundant noncoding RNA (ncRNA)
tRNA consists of four structural components known as the
acceptor stem, the TWC arm, the anticodon arm, and the D arm
Ribosyme-mediated phosphodiester cleavage can be accomplished through
acid-base catalysis and two-metal ion catalysis
Oct4, Sox3, and Nanog transcription factors __________the expression of pluripotency genes and ________ the expression of differentiation genes
activate inhibit
Which component of the Nirenberg-Leder experiment, that assigned triplet codons to specific amino acids, was radioactively labeled?
aminoacyl-tRNA
tRNAs are charged with amino acids by ______
aminoacyl-tRNA synthetases
The acceptor stem is the site of
aminoacylation
Since uracil is not supposed to be present in DNA, it is generally removed fairly quickly by glycosylases, leaving
an abasic site
streptomycin is
an antibiotic that alters the structure of the 30S subunit, causing errors in translation targets protein synthesis
Chloramphenicol is
an antibiotic that binds to the 50S subunit and prevents peptide bond formation targets protein synth
Tetracyclines is
an antibiotic that prevents tRNA binding to the A site in the ribosome targets protein synthesis
Crick's adaptor hypothesis implied the need for
an enzyme to catalyze the attachment of an amino acid to the tRNA
Erythromycin is
antibiotic that binds to the 50S subunit and prevents translocation targets protein synthesis
trans acting factors are usually highly specific, they can operate on
any DNA sequence present in the genome
Eukaryotic rRNA genes are ______________ in the genome and are transcribed in the nucleolus by a transcriptional initiation complex containing the enzyme
arrayed in tandem; RNA polymerase I
DnaB helicase: ATP provides the energy for translocation along the DNA, with the ATP binding pocket found
at the interfaces between the monomers
Many posttranslational modifications involve
attachment of a functional macromolecule to the fully synthesized protein
Palmitoylation and Myristoylation are
attachment of a saturated 16- carbon or 14- carbon fatty acid, respectively, to the target protein
_____________________ retinitis pigmentosa is linked to mutations in genes that encode components of the spliceosome complex, which are required for assembly of the U5-U4-U6 trimer
autosomal dominant
Lynch syndrome is caused by ___________ in the genes encoding the human mismatch repair enzymes ______ and ______
autosomal dominant mutations hMLH1 and hMSH2
Peptidyl transferase reaction is catalyzed by __________________and extends the polypeptide on the AA-tRNAAA in the ribosome A site
catalyzed
CRP DNA binding activity is stimulated by
cAMP
post translational modification
can alter the structure or function of the target protein
Homologous recombination
can only be used during late S phase or G2 phase, because it requires the presence of an intact sister chromatid as a template for DNA polymerase
Mutations can lead to a _______ cell growth; many mutations accumulate to become ________
cancerous cancerous
Somatic mutations to genes that are regulators of cell division often lead to
cancerous growths, since such mutations allow the cell to out-compete those cells around it
histone deactylases (HDACs)
deactylation of histones
How is inosine produced?
deamination of adenosine and is a common mod in tRNA at the anticodon wobble position
Inosine is formed through a
deamination of adenosine.
One of the most common types of DNA damage is the spontaneous
deamination of cytosine to uracil
Individuals with mutations of BRCA have increased incidence of cancer because of their
decreased ability to repair double-strand DNA breaks
iPS cells can be defined as __________ cells.
dedifferentiated
trans mutations
defects in components of spliceosome complexes
cis mutations
defects in splicing recognition sequences
The N-7 of guanine is commonly alkylated, with the product subject to spontaneous
deglycosylation
If a protein is covalently modified by ubiquitin, it will be
degraded
The enzyme responsible for generating siRNA from double strand RNA is
dicer
The enzyme responsible for making siRNA is
dicer
Many antibiotics specifically inhibit bacterial translation because of
differences in the structures of prokaryotic and eukaryotic ribosomes
Vesicles bud from their associated membranes and travel through the cytosol before fusing with a
different organelle or the outer cell membrane
Translational initiation in prokaryotes: In order for the initial AUG codon to be brought into the correct orientation below the P site, the ribosome must be able to
differentiate between the 5' and 3' end of the mRNA
Synthesis of the lagging strand is performed in a _________ fashion, producing
discontinuous small fragments that must be joined at a later time, okazaki fragments
Insulator sequences may divide chromosomes into __________, perhaps by long-range looping, so that an enhancer can work only on a promoter that lies in the same domain
discrete domains
Many resolvases are dimeric such that they have two active sites for cleavage of two DNA strands without
dissociation from the holliday junction
The overall structures of class I and class II aminoacyl-tRNA synthetases are
distinct
Special culture conditions can be used to differentiate iPS cells into
distinct cell types
how do mismatches fit into the active site pocket and thus are ________ excluded
do not fit well largely
histone acetyltransferases (HATs)
does histone acetylation
RNA is a ________ biochemical polymer
dynamic
Elongation cycle in prokaryotes and eukaryotes is similar. The six step elongation cycle requires the _________________, one to promote binding of the AA tRNA AA to A site and one to facilitate translocation of the ribosome in the 3' direction
hydrolysis of 2 GTP
A common feature of protein synthesis in both eukaryotes and prokaryotes is ___________
hydrolysis of GTP to facilitate binding of the AA-tRNA AA
A common feature of translation in both eukaryotes and prokaryotes is
hydrolysis of GTP to promote binding of the AA-tRNAAA.
Number the steps from start of RNA synthesis to start of protein synthesis in eukaryotes (aàg). (a)____ U1/U2 form a complex at the 5' end of introns (b) ____Poly(A) polymerase adds ~200 adenine residues (c)____Guanine-N7-methyltransferase adds the m7G cap (d)____ CStF protein binds to AAUAAA sequence at 3' end (e)____ RNA Pol II CTD is hyperphosphorylated by TFIIH (f)_____U6/U5/U2 complex cleaves the 3' end of introns (g)____mRNA is exported through the nuclear pore complex
e)__1__ RNA Pol II CTD is hyperphosphorylated by TFIIH (c)__2__Guanine-N7-methyltransferase adds the m7G cap (a)__3__ U1/U2 form a complex at the 5' end of introns (f)__4___U6/U5/U2 complex cleaves the 3' end of introns (d)__5__ CStF protein binds to AAUAAA sequence at 3' end (b) _6___Poly(A) polymerase adds ~200 adenine residues (g)__7__mRNA is exported through the nuclear pore complex
dispersive replication definition
each daughter DNA molecule contains a mixture of old and new DNA
Definition of semiconservative
each daughter molecule composed of one newly synth strand and one template strand
Because most of the heteroatoms of the bases are nucleophilic, they react rapidly with many
electrophilic alkylating agents
structure of E. coli DNA polymerase (Pol I) In the polymerizing mode, nucleotides are added to the
end of the growing chain in the polymerase active site
Removal of intergenic spacer RNA from prokaryotic tRNA and rRNA primary transcripts involves
endoribonucleolytic cleavage by the ribozyme ribonuclease P (RNaseP) release functional RNA molecules
telomeres function
ends of each chromosome, which must be replicated to protect chromosomes from shortening
What did Rich Jorgensen and Carolyn Napoli at UA study?
enzymes involved in generating the violet color in petunia flowers
Ribozymes
enzymes that contain a catalytically active RNA component
Telomerase carries an RNA template that encodes the telomere sequences at the end of the chromosomes. This template is used to
extend the ends of the DNA, thus ensuring that the telomeres are not shortened during replication
Lipid modifications include
farnesylation and prenylation
What is the wobble position?
first 5' position of the tRNA anticodon and the third 3') position of the mRNA codon
Coatomer proteins
first recruited to the donor membrane surface, which initiates vesicle formation
how do correct base pairs fit into the DNA polymerase active site
fit well
Producing an iPS cell is remarkable because the pathway
for conversion is general, not specific.
the 5'm7G cap protects mRNA from the 5' to 3' exonucleases and is a binding site
for factors in splicing, nuclear export, and efficient translation
How does the DnaB helicase work in E. coli
forming a barrel like structure through which the nucleic acid passes, whether DNA or RNA
The amino acid alanine (Ala) is specified by a total of ______ codons and ______ tRNAS
four codons two tRNA Ala1 tRNA Ala2
The leader sequence of the trp operon encodes
four related DNA segments that can pair up in two different ways to form stem-loop structures when transcribed into the corresponding mRNA transcript
Reprogramming of differentiated cells to iPS cells is done by introduction of the
four transcription factor genes Oct4, Sox2, Klf4, and m-Myc
Replication bubbles in eukaryotic DNA eventually _______________ to complete the the replication process, which requires resolution of opposing replication forks
fuse to
Gln33 and Gln44 in the _ repressor protein make specific contacts with DNA in the region of an A-T base pair in the DNA
gamma
RNA interference (RNAi) refers to
gene silencing, a process that is mediated by long or short double stranded RNA molecules that can form base pairs with a target RNA and direct its degradation or inhibit translation
In both the import cycle and export cycle, the ____________ of Ran is activated by GTPase activating proteins (GAPs) in the cytoplasm to
generate Ran-GDP and release the importin or exportin proteins
In recombination, movement can be from one place in the genome to another or from one organism to another. Recombination gives rise to
genetic diversity
The fraction of genomic DNA corresponding to transcribed protein-coding genes is inversely related to
genome size and to the amount of DNA transcribed into ncRNA
In the presence of ______, CRP does not bind because cAMP levels are low
glucose
Glycoproteins are produced by
glycosylation
stem cells
grow and give rise to more cells like themselves. In addition they can differentiate into specialized cell types
Ran-GDP is then recycled back into the nucleus, where ________________ proteins stimulates replacement of GDP with GTP to regenerate activated Ran-GTP
guanine nucleotide exchange factor (GEF)
The decay of mRNA decreases the abundance of functional proteins by the
half-life of their mRNAs
Why do helicase and gyrase need to work together to keep the replication fork moving forward?
helicase unwinds DNA and gyrase relieves the torsional strain created by the unwinding
The E. coli replication fork consists of Pol III as well as
helicase, primase, gyrase, and single stranded DNA binding proteins
One of the most common DNA-binding motifs found in transcription factor proteins called the
helix-turn-helix motif
lysine acetylation is carried out by ____________, which is associated with actively transcribed genes
histone acetyltransferases (HATs)
Deacetylation by _______________ is associated with transcriptional repression
histone deactylases (HDACs)
Which protein would initially have been translated on free ribosomes?
histone subunit H2A
Homologous recombination requires a double-strand break to allow the formation of a
holliday junction
One of the most common binding interactions between proteins and DNA are __________ bonds
hydrogen
The amino acid Gln33 functions as a hydrogen-bond donor to a phosphate group in DNA, whereas Gln44 functions as both a
hydrogen bond acceptor andf a hydrogen bond donor
The DNA sequence of prokaryotic gene promotors were found to be
largely conserved.
The mechanism of spliceosome-mediated trans RNA splicing is similar to the self-splicing mechanism found in Group II introns, involving the formation of a
lariat structure to remove the intronic sequences
Which strand is synthesized continuously?
leading strand
ligand regulated deactivation
ligand binds to activator causing it to dissociate and transcription OFF
Ligand-regulated activation
ligand binds to activator protein which turns transcription on
ligand regulated repression
ligand binds to repressor and transcription OFF
ligand-regulated de-repression
ligand binds to repressor protein and transcription ON
What is a difference between group I and group II introns?
linear versus lariat intron products
The most common cis mutations in splicing that cause human disease are the _________________ generating proteins that lack a required exon
loss of an exon-coding sequence
Transcriptional elongation is favored by the trp operon when tryptophan levels are
low
DNA polymerase delta has an extremely high processivity but it has a much _______ reaction rate than E. coli
lower
After bacteriophage gamma infection, the viral DNA can enter a
lytic cycle or undergo lysogeny
Eukaryotic mRNA is processed in the nucleus to remove intron sequences (splicing), protect the 5' end of a ___________ and facilitate mRNA translation by adding a ____________ at the 3' end
m7Guanine cap poly(A) tail
Alternative splicing
mRNA can increase genomic complexity but can also cause disease
The C-terminal domain (CTD) in eukaryotic RNA polymerase II is required for coordinating precursor
mRNA processing, and its functions are regulated by phosphorylation on the heptapeptide sequence YSPTSPS
If 15N DNA replicated using conservative replication in 14N media, the outcome would be that new DNA has
one high density and one low density strand.
What does each replication fork produce?
one leading strand and one lagging strand
Lynch Syndrome
one of the most common types of inherited cancers which is also called hereditary non-polyposis colorectal cancer (HNPCC)
Recombination moves genetic material from
one place to another
Elongation cycle in prokaryotes and eukaryotes is similar. The six step elongation cycle requires the hydrolysis of 2 GTP, which do what?
one to promote binding of the AA tRNA AA to A site and one to facilitate translocation of the ribosome in the 3' direction
Cis-acting sites affect
only the DNA element to which they are physically linked
Conversion of the RNA polymerase- DNA closed complex (inactive) to the ___________ (active) at the gene promoter requires DNA unwinding
open complex
What is the specific site on the E. coli genome where DNA replication can initiate?
oriC
The DNA molecule is labeled at one end with radioactive phosphate. _________ with endonuclease DNase I is essential to get a representative data set
partial digestion
Upon binding of SRP to the ER signal peptide sequence, the ribosome
pauses on the mRNA to halt translation
Formation of this peptide bond moves the polypeptide chain from the ________ (_ site) to the ___________ (_ site). Elongation factors facilitate the release of the uncharged tRNA from the _________ (_ Site) and frees the _ site for a new charged tRNA
peptidyl site (P site) aminoacyl site (A site) Exit site (E site) frees the A site
ribosomal RNA function
peptidyl transfer reaction
Binding of the Tus protein to the Ter sequence is directional such that one side of the Tus protein is
permissive for replication fork movement, whereas the opposite side of the Tus protein is not
Processing of precursor mRNA occurs during transcription and is coordinated by the ______________ of RNA pol II, which serves as a binding domain for ______________ such as the 5' capping enzyme, guanine-N7 methyltransferase
phosphorylated CTD; mRNA processing complexes
post translational modification: common modifications include
phosphorylation, methylation, acetylation, glycosylation, and ubiquitination
The lesions formed by UV damage are often referred to as
photoproducts
DNAse I foot priming method determines
physical location of DNA binding proteins to DNA
The processing proteins CFI and CFII bind to the complex, as well as the enzyme ____________, which synthesizes the poly(A) tail
poly(A) polymerase
Nucleosome is made up of a
protein core containing two molecules each of four histones called the histone octamer, and a 147 bp segment of DNA
The precursor mRNA sequence that promotes polyadenylation is 5'-AAUAAA-3', which is bound by a protein called the cleavage and
polyadenylation specificity factor (CPSF)
Most regulation in eukaryotes is
positive
The Oct4/Sox2 heterodimeric complex, along with the transcription factor nanog function in a _____________ to reinforce transcription of each of the three corresponding genes
positive autoregulatory loop
For some proteins transport into the endoplasmic reticulum begins before translation is complete; for others, this is a
posttranslational process
transcriptional activator proteins interact with general transcription factors to recruit them to the
pre-initiation complex
initiation of DNA synthesis in eukaryotes: The complex of ORC and MCM2-7 bound at an origin sequence is referred to as the
pre-replicative complex (pre-RC)
Puromycin acts as an acceptor for the growing polypeptide chain and causes
premature termination of translation
RNA is typically more susceptible to backbone hydrolysis than DNA because of the
presence of a 2' OH group.
AZT is such a good HIV drug because it
prevents new DNA from being replicated.
deadenylation
primary pathway to degrade eukaryotic mRNA begins with the removal of the poly(A) tail
What is aminoacylation?
process by which an enzyme known as an aminoacyl-tRNA synthetase attaches a specific amino acid to the 3' acceptor stem of the cognate tRNA
the mRNA can be _______, especially in eukaryotes and is usually unstable, so that processing and __________ are possible sites of regulation
processed degradation
Eukaryotic RNA splicing occurs when an intron is removed in a transesterification reaction, which is coupled to rejoining of the 5' and 3' ends to generate a
processed transcript
Retinitis pigmentosa is a heterogenous disease affectimg 1 in 4000 individuals and is characterized by
progressive retinal degeneration
Translational initiation in prokaryotes: 50S ribosomal subunit then binds to 30S initiation complex to form the functional
prokaryotic 70S ribosome
What is the largest portion of prokaryotic RNA in E. coli made up of?
protein coding
Binding of a __________ to a termination codon in mRNA halts translation and leads to dissociation of the ribosomal complex
protein release factor
Some antibiotics target
protein synthesis
The antibiotics streptomycin, tetracycline, and chloramphenicol all interfere with
protein synthesis.
Protein synthesized on free ribosomes are targeted to various locations by
protein-encoded targeting sequences
What is the Meselson-Stahl experiment?
provided evidence that DNA replication is semiconservative When allowed to divide in a 14N containing medium, a hybrid DNA is produced that contains one strand heavy DNA and one strand of light DNA
The most common noncanonical base pairing is with the ______________, which is formed by the deamination of adenosine by the enzyme tRNA-specific adenosine deaminase
purine nucleotide inosine
in Nirenberg-Leder experiment. With the nitrocellulose filter, if the anticodon and codon were not complementary then the
radioactive aminoacyl-tRNA passed through the filter
Common damaging agents include
reactive oxygen species, UV light, alkylating agents, and errors of replication
Holliday junctions are resolved by the enzyme _________ to separate the joined chromosomes
recombinase
One function of eukaryotic transcriptional activator proteins is to ________
recruit chromatin modifying proteins such as HAT and HDAC enzymes
leucine zipper motif and helix-loop-helix motif
refer to protein-protein interface found in transcription factors containing these motifs
DNA gyrase function
relieves torsional stress in front of the fork ( a type II topoisomerase)
Base excision repair removes which kind of bases?
those damaged by ROS
transcription is initiated by binding of
s factor protein to RNA polymerase
Transposon
segment of DNA that can move from one region in the genome to another, either within the same chromosome or between two chromosomes
DNA replication is
semiconservative
Circle the underlined words describing the process of DNA synthesis and record the number. DNA replication is conservative (1) / semiconservative (2), which requires that helicase (3) / gyrase (4) unwinds the DNA double helix. Next, DNA Pol III (5) / DNA Pol II (6) binds and forms the replisome and moves along the template strand in a 5'--3'direction (7) / 3'--5'direction (8). If a mistake is made on the newly synthesized strand of DNA, DNA Pol III corrects the error in a 5'--3'direction (9) / 3'--5'direction (10). After DNA replication is complete, the double stranded DNA is a left (11) / right (12) -handed DNA helix.
semiconservative (2) helicase (3) DNA Pol III (5) 5'--3'direction (7) 3'--5'direction (10) right (12)
lncRNA sequences can be found in the same orientation and on the same DNA strand (__________) or can be derived from the opposite DNA strand (_________)
sense antisense
TATA binding protein (TBP) is a single polypeptide chain that generates a
sharp bend in the DNA as a result of the two Phe residues on each side that insert into the minor groove and force a kink in the DNA
Which type of RNA facilitates RNA interference by resulting in degraded mRNA?
siRNA
In bacteria the alpha2BetaBeta'omega holoenzyme is associated with a family of auxillary proteins called _________ factors, which are transcription factors that bind to specific DNA sequences known as the ________ and ________ near the promoter
sigma factors -35 and-10 boxes
In bioinformatic analysis, not all positions are equally conserved because different
sigma factors recognize distinct coding regions
The ER signal sequence emerges from the ribosome and is bound by the
signal recognition particle (SRP)
Single nucleotide mutations can be silent or can cause
single amino acid substitutions or production of a truncated protein
chromosomal crossover
sister chromatids generated during prophase of the first meiotic division are able to exchange DNA through homologous recombination
The invariant G from the 5' end of the intron is linked to the branch point A through a 2',5' phosphodiester bond to form
the lariat
In which direction is mRNA synthesized by prokaryotic and eukaryotic RNA polymerases?
the mRNA is synthesized with 5' to 3' phosphodiester linkages
A process of mismatch repair in E. coli is initiated when a homodimer of
the mismatch repair MutS recognizes and binds to adjacent to a base pair mismatch
In condensed chromatin
the nucleosomes are tightly packed structures involving interactions between the N-terminal tails of histone proteins
Formation of the pre-initiation complex in the 5' region of the mRNA transcript involves binding of
the small and large ribosomal subunits and tRNA
Long noncoding Rnc (lncRNA) is generated from
the transcription of genomic DNA
Long noncoding RNA (lncRNA) is generated from
the transcription of genomic DNA.
Bioorthogonal labeling
the use of chemically modified metabolites to label proteins in vivo during protein synthesis and carbohydrate modification
It was discovered that different tRNAs with the SAME AMINO ACID and recognize different mRNA codons because of
the wobble position
Activator proteins have two major functions:
they counteract the repressive effects of chromatin and they help recruit components of the transcription machinery to promoters
In 1998, andrew fire and Craig Mello found similar results to Jorgensen and Napoli. HOW
they injected RNA into worms, which led to the discovery of RNAi and the 2006 Nobel Prize
____________ termination is either a Rho-dependent termination or Rho-independent termination process
transcriptional
Two ______ steps result in the release of an excised lariat intron and the correctly spliced exonic sequences
transesterification
Eukaryotic RNA splicing occurs when an intron is removed in a
transesterification reaction
What step in the process of translation of a nascent protein into the lumen of the ER requires hydrolysis of GTP?
transfer of the signal peptide sequence into the translocon
Antibiotics can be used as biochemical tools to investigate
translation
DNA transposons require a ________ for both removal of the transposon from its current site and insertion into a new site in the genome
transposase protein
Yeast precursor tRNA is processed in the nucleus by removal of 5' ribonucleotides, addition of the _______________ to the 3; end, and chemical modification of some bases
trinucleotide sequence CCA
Stem-loop structures: located on the 5' side of region 1 is a series of ______________, which is critical to understanding how tryptophan levels in the cell control transcription of the trp operon
triplet codons specifying tryptophan
Which two amino acids are encoded by a single codon each?
tryptophan and methionine
The trp operon of E. coli contains a gene regulatory region and coding sequences for enzymes needed for
tryptophan biosynthesis
transcriptional termination by RNA polymerase is favored when __________________ because the abundance of charged Trp-tRNATrp means the ribosome ________ synthesizes the leader polypeptide and the termination structure generated by the region _________ stem loop is allowed to form
tryptophan levels are high; quickly; 3-4
transcriptional elongation is favored when ________________ because the ribosome stalls at the pair of Trp codons owing to low levels of Trp-tRNATrp in the cell. The ribosome stalling allows _________________, which favors transcriptional elongation (stem 3-4 does not form_
tryptophan levels are low region 2 to pair with region 3
Each core domain is associated with a Beta clamp, which is a structure consisting of
two Beta subunits that forms a ring completely encircling the double stranded DNA
Proteolytic cleavage of the 103- kDA polypeptide of Pol I produces how many fragments
two fragments
Termination of DNA synthesis in Bacteria: Bidirectional replication of the circular E. coli genome produces
two molecules that are catenated as interlocking rings, in the same way two links in a chain are catenated
aminoacyl-tRNA synthetases catalyze a
two-stage reaction in which the amino acid is first adenylated using ATP, and then linked to the tRNA at the 3' end (CCA)
Each tRNA must contain __________ that allow it to be recognized by the aminoacyl-tRNA synthetase enzyme that will covalently join the _______
unique features, tRNA with its cognate amino acid
the canonical transcription, splicing and polyadenylation pattern for a hypothetical gene with three exons is shown. Translation on each mRNA results in a
unique protein
How was bidirectional replication proven?
using radioactive nucleotides, shown that newly synthesized DNA appeared at both junctions confirming that replication is bidirectional from a single origin
Transport between the ER and other cellular organelles occurs through the formation of
vesicles
The HIV infection cycle requires conversion of the
viral genome to DNA (cDNA) that is then integrated into the host cell genome by a recombination event
A human tissue sample is grown in culture, and then ________ carrying the transcription factor genes are introduced into the cells
viruses