Week 3 Flashcards
RNAs carry out their functions as ___ ___ that fold back on themselves and have the potential for much greater __ ___ than DNA.
single strands, structural diversity
RNA has a role in both the ___ and ___ of information as well as in ____.
storage, transmission, catalysis
Catalytic RNAs
ribozymes
RNA proteins complexes
ribonucleoproteins / RNPs
RNAs that encode the amino acid sequence of one or more polypeptides specified by a gene or set of genes
messenger RNAs
RNAs that read the information encoded in the mRNA and transfer the appropriate amino acid to a growing polypeptide chain during protein synthesis
transfer RNAs
RNAs that are constituents of ribosomes
ribosomal RNAs
The sum of all the RNA molecules produces in a cell
transcriptome
Transcription does not require a ___ and generally involves only ___ segments of a DNA molecule. Only one DNA strand serves as a ___ for a particular RNA molecule
primer, limited, template
The 5’ triphosphate group of a newly formed RNA molecule is not cleaved to release ___ but instead remains intact and functions in ___ as a substrate for the _____ ____.
PPi, eukaryotes, RNA-capping machinery
During transcription, e. coli RNA pol generally keeps about ___ bp unwound. The ___ bp RNA-DNA hybrid occurs in this unwound region. Elongation of a transcript by E. Coli RNA pol proceeds at a rate of ___ to ___ nucleotides per second
‘17, 8, 50, 90
Movement of a trancription bubble requires considerable __ __ of the nucleic acid molecules. This is restricted in most DNAs by DNA binding ____ and other structural barriers. Thus, a moving RNA pol generates waves of __ ___ ahead of the transcription bubble and __ ____ behind it. the strain is relieved through ____.
strand rotation, proteins, positive supercoils, negative supercoils, topoisomerases
The strand that serves as atemplate for RNA synthesis
template strand
The DNA strand complementary to the template strand
non template stranding / coding strand
RNA pol in E. coli is a large complex enzyme with ___ core subunits, and a sixth one designated ___. The sixth one can vary in ___ and binds transiently to the core and directs the enzyme to specific __ __ on the DNA / These constitute the DNA polymerase _____.
5, sigma, size, binding sites, holoenzyme
RNA polymerases lack a separate proofreading _____ ____ active site. Thus the ___ __ for transcription is much higher than that for chromosomal DNA replication. Many RNA pol’s can pause when a mispaired base is added during transcription and remove it from the ___ end of a transcript by __ __ of the polymerase reaction
3’–>5’ exonuclease, error rate, 3’ direct reversal
In DNA footprinting, researchers isolate a DNA fragment thought to contain sequences recognized by a ___ ___, and then ____ one end of one strand. Then they use ___ or ___ reagents to introduce random ___ n the DNA fragment. Separation of the labeled products by ______ produces a ladder of radioactive bands. The procedure is repeated on copies of the same DNA in the presence of the ___ ____. The binding protein ___ the DNA, and produces a ___ in the series of radioactive bands. Then the precise location of the protein binding site can be determined by ____ ___ copies of the same DNA fragment on the same gel with the footprint
DNA-binding proteins, radiolabel, chemical, enzymatic, breaks, electrophoresis, binding proteins, protect, gap, directly sequencing
By using different ___ subunits, the prokaryotic cell can coordinate the expression of sets of ____, permitting major changes in __ ___. Availability of the subunits are determined by the regulated rates of ___ and ___, _____ modifications that switch individual subunits between active and inactive forms, as well as ____ proteins.
sigma, genes, cell physiology, synthesis, degradation, posttranslational, anti-sigma
In e coli the __ ___ protein increases the transcription of genes coding for enzymes that metabolize ___ other than glucose when its unavailable.
camp receptor, sugars
proteins that block the synthesis of DNA at specific genes
repressors
A protein in prokaryotes that binds the ribosome and RNA polymerase, coupling translation and transcription
NusG
RNA pol I makes ____ ____, while RNA pol II makes __ and ___. RNA pol III makes ___, _____, and _____.
pre-ribosomal RNA, mRNA, ncRNA, tRNA, ncRNA, 5s rRNA
The largest subunit of RNA pol II, ___ exhibits a high degree of homology to the B’ subunit of ___ RNA polymerase, while another subunit ____ is structurally similar to the B subunit. The ____ and ____ show homology to two bacterial alpha subunits.
RBP1, RBP2, RBP3, RBP11
The __ ___ ___ is separated from the main body of RNA pol II by an intrinsically disordered __ ____. It consists of many repeats of a consensus heptad amino acid sequence, _____.
carboxyl-terminal domain, linker sequence, YSPTSPS
proteins that are needed to form the active transcription complex, required at every Pol II promoter and highly conserved in all eukaryotes
general transcription factors
transcription protein that recognizes the TATA box
TATA binding protein (TBP)
Transcription protein that stabilizes binding of TFIIB and TBP to the promoter
TFIIAT
Transcription factor that binds to TBP and recruits Pol II-FIIF complex
TFIIB
Transcription factor required for initiation at promoters lacking a TATA box
TFIID
Transcription factor that recruits TFIIH, has ATPase and helicase activities
TFIIE
Transcription factor that binds tightly to pol II and TFIIB and prevents binding of pol II to nonspecific DNA sequences
TFIIF
Transcription factor that unwinds DNA at the promoter (helicase activity), phosphorylates pol II CTD, and recruits nucleotide-excision repair proteins
TFIIH
____ also phosphorylate CTD, primarily on ___ residues of the CTD repeat sequence. During elongation, the phosphorylation state of the CTD changes, affecting which RNA __ ___ are bound to the transcription complexes
pTEFb (CDK9), serine, processing components
Newly synthesize RNA molecule
precursor transcript
Eukaryotic mRNA as it is synthesized, is nestled in a supramolecular ___ ____ complex comprising dozens of proteins. The composition of this complex changes as the transcript is processed, transport to the cytoplasm and delivered to the ___. The associated proteins can dramatically modulate the cellular ___, ___ and fate of an mRNA
messenger ribonucleoprotein, ribosome, destination, function
The 5’ cap helps protect mRNA from ____ and binds to specific ____ complexes of proteins and participates in binding of the mRNA to the ____ to intiate translation
ribonucleases, cap-binding, ribosome
Eukaryotes also contain cellular ___ enzymes, which allows RNAs to be degraded by _____, that hydrolyze the RNA in the ___ direction. Some ____ also have evolved mechanisms for removing the 5’ cap from host mRNAs. The influenza virus borrows cap structures from host cell transcripts in a process called ___ ____.
decapping, exonucleases, 5’->3’, viruses, cap snatching
Group I introns contain ___ RNA and are self splicing using a _______ cofactor. They are found in ____, mitochondrial, and chloroplast genes that encode mRNAs, rRNAs or ____. They can be found in bacteria
catalytic, guanine-derived, nuclear, tRNAs
Group II introns contain catalytic RNA, _____ and __ ___ proteins. They are self-splicing using a ___ within the intron to form a lariat. They are primarily found in ___ and ___ genes of fungi, algae and plants. They also can be found in bacteria
maturase, reverse transcriptase, mitochondrial, chloroplast
Spliceosome introns contain __ ___ and dozens of protein splicing factors. They require a large ___ for processing, using a nucleophile within the intron to form a lariat. They are found in nuclear genes of eukaryotes and are capable of __ ___ to create multiple products from a given transcript
catalytic snRNAs, RNP, alternative splicing
Protein catalyzed introns have ___ ___ and use a splicing __ and ____. They are found in __ and few mRNAs
protein enzymes, endonucleases, ligase, tRNAs
specialized RNP complexes that make up a spliceosome
nuclear ribonucleoproteins (snRNPs)
eukaryotic RNA 100-200 nucleotides that is contained within an snRNP
small nuclear RNAs (snRNAs)
The poly A tail coordinate transcription and translation and protect the mRNA from __ ____. In bacteria, they stimulate ___ of mRNA
enzymatic degradation, destruction
In some cases, the polypeptide coding region of the mRNA is modified by RNA ____. This includes processes that ___ or ___ bases in the coding regions or change the sequence.
editing, add, delete
The pre-MRNA contains ___ ___ for alternative processing pathways, and the pathway favored in a given cell or metabolic situation is determined by __ ____, RNA binding proteins.
molecular signals, processing factors
Complex transcripts can also have more than one site where poly(A) tails can form. If there are two or more sites for __ and ____, use of the one closest to the ___ end will remove more of the primary transcript sequence. This mechanism called ____ ___ ____ generates diversity in the variable domains of _____ ___ ___.
cleavage, polyadenylation, 5’ poly(A) site choice, immunoglobulin heavy chains
non coding RNAs that guide nucleoside modification and some cleavage reactions and ribosomal proteins
small nucelolar RNAs (snoRNAs)
snoRNA-protein complexes including the enzyme that carries out nucleoside modifications
snoRNPs
When two or more different tRNAs are contained in a single primary transcript, they are separated by __ ___. The endonuclease ____ ___ found in all organisms, removes RNA at the __’ end of tRNAs. The 3’ end of tRNAs is processed by one or more nucleases, including the exonuclease ______ ___.
enzymatic cleavage, RNase P, 5, RNase D
special class of non coding RNAs that promote mRNA degradation and suppress translation to fine tune gene expression
microRNAs
the average half-life of the mRNAs of vertebrate cell is about ___ hours, with the pool of each type of mRNA turning over about __ times per cell generation. The half life of bacterial mRNA is only ___ minutes
3, 10, 1.5
in e. coli. mRNAs typically contain ______ ___ remaining from the initiation of transcription that ___ the mRNA from 5’ degradation. As a result, mRNA decay begins with one or several cuts by an _____.
5’ triphosphates, protect, endoribonuclease
A common exoribonuclease responsible for the degradation of many mRNAs in bacteria, chloroplasts, and mitochondria
polynucleotide phosphorylase (PNPase)
PNPase catalyzes the ____ _____ of the mRNA chain using ___ as the nucleophile. This reaction is readily ___ and the enzyme can also add nucleotides to the ___ ends of bacterial mRNAs. Decay of mRNAs containing complex 3’ end structures such as ______ , can involve multiple rounds of ___ and _____ by PNPase until it is finally consumed
reversible, phosphorlysis, reversible, 3’, hairpins, lengthening, shortening
In eukaryotes, ___ the 5’ end and shortening the ____ _____ ___ are critical steps for allowing exonucleases to access the mRNA and degrade it
decapping, 3’ poly(A) tail
large 3’ –> 5’ exoribonucleases that are responsible for the degradation for nearly all types of RNA
exosomes
Specialized exosomes exist in the ___, ___ and ___. The core is a ____ structure through which ___ is threaded. This core serves as an ____ that efficiently channels the RNA to associated enzymes with ______ exonuclease and ___ activity
nucleus, cytoplasm, nucleolus, barrel-like, RNA, adapter, 3’->5’, endonuclease
the steady state complement of proteins that enable the life of a cell at any given moment
proteostasis
Paul Zamecnik and Elizabeth Keller first discovered _____, and after, Francis Crick considered how the genetic information encoded in the ___ language of nucleic acids could be translated into the___ language of proteins. He proposed that one end of a small nucleotide ___ could bind a specific amino acid and the other end could recognize a ____ ___ in the mRNA. This was confirmed when Hoagland and Zamecnik discovered ___
ribosomes, 4-letter, 20-letter, adaptor, nucleotide sequence, tRNA
amino acids, when in the presence of ATP, become attached to a ____ soluble tRNA to form ______. This process is catalyzed by ____. This ____ them for protein synthesis
heat-stable, aminoacyl-tRNAs, aminoacyl-tRNA synthetases, activates
a triplet of nucleotides that codes for a specific amino acid
codon
A specific ___ codon in the sequences establishes a __ ____, in which a new codon begins every ___ nucleotide residues. There is no ___ between codons for successive amino acid residues. Any given single-stranded DNA or mRNA sequence has ___ possible reading frames, and each gives a different sequence of codons, but only one is likely to encode a given protein
first, reading frame, 3, punctuation, 3
An enzyme that requires no template and makes polymers with a base composition that directly reflects the relative concentrations of the nucleoside 5’-di-phosphate precursors in the medium
polynucleotide phosphorylase
The codons ____, ___ and ___ are termination codons while the codon ____ coding for ___ is the initiation codon
UAA, UAG, UGA, AUG, methionine
a reading frame without a termination codon among 50 or more consecutive codons; usually correspond to genes that encode proteins
open reading frame
the genetic code is ____ meaning an amino acid may be specified by more than one codon, and this is not ____. The genetic code is nearly ___
degenerate, uniform, universal
When several different codons specify one amino acid, the difference between them usually lies at the ___ base position.
third
The first base of the codon in mRNA read in the ___ direction, pairs with the ___ base of the anticodon.
5’–>3’, third
Anticodons in some tRNAs include the nucleotide _____, which contains the uncommon base ____. This can form hydrogen bonds with three different nucleotides, ___, ___ and ___, although they are weaker than ____ interactions. This is why cells do not have a different tRNA for each amino acid codon
inosinate, hypoxanthine, A, U, C, watson-crick
Crick proposed the wobble hypothesis, which says that the first two bases of an mRNA codon always form ____ ___ base pairs, and confer most of the coding ____. The first base of the anticodon determines the number of codons recognized by the ___. When an amino acid is specified by several different codons, the codons that differ in either of the first _____ bases require different tRNAs. A minimum of ___ tRNAs are required to translate all ___ codons
strong watson-crick, specificity, tRNA, two, 32, 61
When the first base of the anticodon is __ or ___, base pairing is specific and only one codon is recognized by that tRNA. When the first base is ___ or ___, binding is less specific and two different codons may be read. When ___ is the first nucleotide of an anticodon, ___ different codons can be recognized, the maximum for any tRNA
A, C, U, G, I
A and C can only bind to ___ and ___ respectively. U can bind to __ or ___, and G can bind to ___ or ___. I can bind to __, __ and ___.
U, G, A, G, C, U, A, U, C
the wobble of the third base permits __ __ of the tRNA from its codon during protein synthesis due to its ___ pairing
rapid dissociation, loose
____ mutations are mutations in which a single new base pair replaces another. In the wobble position of a codon, single base substitutions produce a change in the encoded amino acid only ____% of the time. Most changes are thus ___ mutations, in which the nucleotide is different but the encoded __ ___ remains the same.
missense, 25, silent, amino acid
When a purine is replaced by a purine or pyrimidine by a pyrimidine; most common missense mutation
transition mutation
All three codon positions evolved so there is ___ to transition mutations. A mutation in the first position will usually produce an amino acid coding change, but often results in an amino acid with similar __ ___. This is true for ____ amino acids.
resistance, chemical properties, hydrophobic
A few genes are structured so that ribosomes change the ___ ____ at a certain point in the translation of their mRNAs. This allows two or more related by distinct ___ to be produced from a single transcript
reading frame, proteins
__ ___ can involve the addition, deletion or alteration of nucleotides in the RNA in a manner that affects the meaning of the transcript when translated. This is most commonly observed in ___ and ___ genomes. Insertions require ______ that act as ___ for the editing process
RNA editing, chloroplast, mitochondria, guide RNAs, templates
RNA editing by alteration of nucleotides commonly involves the enzymatic _____ of ___ or ___ residues, forming ___ or ____ respectively. Inosine is interpreted as a ___ residue during translation
deamination, adenosine, cytidine, inosine, uridine, g
Bacterial ribosomes contain about ____% rRNA and ____% protein. They are composed of two unequal subunits with sedimentation coefficients of ____ and ___ and a combined coefficient of ___.
65, 35, 30, 50, 70
The ribosomal subunits are huge ___ molecules. In the 50S subunit, the ____ and ____ rRNAs form the structural core. The proteins are secondary elements to the complex, decorating the ___. There is no protein within ____A of the active site for peptide bond formation. This makes the enzyme a _____.
RNA, 5S 23S, surface, 18, ribozyme
Eukaryotic ribosomes are ___ and more complex than bacterial ribosomes. They have a combined sedimentation coefficient of ____, and two subunits of ____ and ____.
larger, 80, 60S, 40S
The ribosomes of ___ and ___ are somewhat smaller and simpler than bacterial ribosomes
mitochondria, chloroplasts
In both bacteria and eukaryotes, ribosomes are assembled through ____ incorporation of r-proteins as the rRNAs are synthesized. Much of the processing of pre-RNAs occurs within large ____ ___. The composition of these changes as new r-proteins are added and rRNAs acquire their ___ ___. In eukaryotes, the early stages of assembly occur in the ____. with the final maturation of the ribosome completed after export to the ___.
hierarchical, ribonucleoprotein complexes, final form, nucleolus, cytosol
Transfer RNAs are relatively ___ and consist of a ___ ___ of RNA folded into a precise 3D structure. eight or more of the nucleotide residues have ___ __ and sugars, many of which are ____ derivatives of the principle bases. Most tRNAs have a _____ residue at the 5’ end, and all have a ____ sequence at the 3’ end. All also have a ____ pattern that forms a ___ structure with four arms.
small, single strand, modified bases, methylated, guanylate, CCA, hydrogen-bonding, cloverleaf
The ______ ____ arm carries the specific amino acid ___ by its carboxyl group to the ___ or ___ hydroxyl group of the adenine residue at the 3’ end of the tRNA.
amino acid, esterified, 2’, 3
The resulting ester linkage between the amino acid and the tRNA has a highly negative ___ ___ ___ of _______KJ/mol. Two highly energy phosphate bonds are expended for each amino acid molecule ____, rendering the overall reaction for amino acid activation essentially ____.
standard free energy, -29, activated, irreversible
The aminoacylation of tRNA activates an ___ _ for peptide bond formation and ensure appropriate ___ of it in a growing polypeptide
amino acid, placement
For Ile tRNA synthetase, the R group of valine is slightly ____ than that of isoleucine, so it fits the ______ site of the Ile-tRNA. Thus Val-AMP is hydrolyzed to ___ and AMP in the ____ active site, and tRNA bound to the _____ does not become aminoacylated to the wrong amino acid
smaller, hydrolytic, valine, proofreading, synthetase
Most aminoacyl-tRNA synthetases can hydrolyze the ___ linkage between amino acids and _____ in the aminoacyl-tRNAs. This is greatly accelerated for ______ ____ tRNAs. The few aminoacyl-tRNA synthetases that activate amino acids with no close ___ ____ demonstrate little or no ____ activity
ester, tRNAs, incorrectly charged, structural relatives, proofreading
An individual aminocyl-tRNA synthetase must be specific not only for a single __ ____ but for certain ____ as well. This is referred to as a second __ ___>
amino acid, tRNA, genetic code
Nucleotide positions necessary for discrimination by the aminoacyl-tRNA-synthetases seem to be concentrated in the ___ ____ arm and the ___ arm.
amino acid, anticodon
___ of more specific nucleotides may be involved in recognition of a tRNA by its specific aminoacyl-tRNA-synthetase,. The primary determinant of tRNA recognition by the _____ synthetases is a single ____ base pair in the amino acid arm of the tRNA(ala).
10, ala-tRNA, G-U
In bacteria, the amino acid incorporated in response to the 5’ AUG initiation codon is ________, which arrives at the ribosome as _______. This is the same in ___ and ____ ribosomes. In eukaryotic cells, all polypeptides synthesized in cytosolic ribosomes begin with a ___ residue, but the cell uses a specialized ___ __ that is distinct from the tRNAmet used at the 5’ AUG codons at ____ ____ in the mRNA
N-formylmethionine, fmet-tRNAfmet, chloroplast, mitochondrial, met, initiating tRNA, interior positions
A consensus sequence in bacteria that is an initiation signal of four to nine purine residues, 8-13 bp to the 5’ side of the initiation codon
shine-dalgarno sequence
The particular _____ where fmet-tRNAfmet is to be bound is distinguished from other methionine codons by its proximity to the ____ sequence in the mRNA
5’AUG, shine-dalgarno
All incoming aminoacyl-tRNAs bind first to the ___ site and subsequently to the __ and ___ site. The latter is where the ____ tRNAs leave during elongation. Both the ___ and ___ subunits contribute to the characteristics of the A and ___ sites, whereas the E site is largely confined to the ___ subunit
A, P, E, uncharged, 50S, 30S, P, 50S
The 70S initiation complex is ensured by at least 3 points of ___ and attachment: the codon-anticodon interaction involving the initiation ____ fixed in the __ site, the interaction between the -___ sequence and the _____ rRNA, and the binding interactions between the P site and the _____.
recognition, AUG, P, shine-dalgarno, 16S, fMet-tRNAfmet
the formation of each aminoacyl-tRNA uses two high energy ___ groups. An additional ___ is consumed each time an incorrectly activated amino acid is hydrolyzed by the _____ activity of an aminoacyl-tRNA synthetase as part of its ____ activity. A GTP is cleaved during the first ____ step and another during the ___ step. The net free energy change during peptide bond synthesis is thus ____ kJ/mol.
phosphate, ATP, deacylation, proofreading, elongation, translocation, -101
a complex of an mRNA molecule and two or more ribosomes, also called a polyribosome
polysome
the connecting mRNA in a polysome is being translated __ by many ___ ___ ribosomes, allowing the highly efficient use of it
simultaneously, closely spaced
A complex made of the mRNA, ribosomes, and RNA pol, that begins translation long before transcription is complete in the bacteria
expressome
During of after its synthesis, the polypeptide progressively assumes its ___ ____. ___, ___ and specific enzymes aid in folding in part by restricting formation of ____ ___ and limiting the __ __ that a polypeptide may explore as it folds. ____ is hydrolyzed as part of this process. Some newly made proteins do not attain their final active conformation until they have been altered by one or more ___ ___
native conformation, chaperones, caperonins, unproductive aggregatives, conformational space, ATP, posttranslational modifications
In as many as ___% of eukaryotic proteins, the ___ group of the amino-terminal residue is ______ after translation. ____ residues are also sometimes modified
50, amino, N-acetylated, carboxyl-terminal
the ___ groups of certain Ser, Thr, and ___ residues of some proteins are enzymatically ___ by ATP, which add ___ ___ to them
hydroxyl, Tyr, phosphorylated, negative charges
the ___ to ___ residues at the amino-terminal end of some proteins direct the protein to its ultimate destination and are _____ by specific ____.
15, 30, removed, peptidases
The carbohydrate side chains of ___ are attached ___ during or after the synthesis of the polypeptide. They are attached enzymatically to ___, ___ or ___ residues
glycoproteins, covalently, Asn, Ser, Thr
Some eukaryotic proteins are modified by the addition of groups derived from ______. A -__ bond is formed between the group and a ___ residue of the protein
isoprene, thioester, Cys
many proteins require ____ ____ ___ groups for their activity. Example is the __ group of hemoglobin
covalently bound prosthetic, heme
Many proteins are initially synthesized as ___, ____ _____ polypeptides that are ____ trimmed to form their smaller, active forms
large, inactive precursor, proteolytically
After folding into their native conformations, some proteins form ___ or ____ ___ bridges between Cys residues. In eukaryotes these are common in proteins to be ___ from cells. The cross links formed in this way help to protect the native conformation from ___ in the extracellular environment, which is generally ____.
intrachain, interchain disulfide, exported, denaturation, oxidizing
