BIOC385 - Exam 4

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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


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