VEST 2 Flashcards
The pre-mRNA primary transcript consists of exon 5’ UTR protein coding region 3’ UTR and ______ sequences.
intron
Internal methylation in RNA can influence stability splicing and ________.
translation
Polymerase II transcripts need ________ (snRNA + specific protein complexes) to splice out introns.
snRNPs
snRNP 1 binds to the ________ splice site.
5’
snRNP 2 binds to the ______________.
branchpoint
U2AF binds to the polypyrimidine _________.
tract
Alternative splicing generates multiple mRNAs and ________ from a single primary transcript.
proteins
The polyA tail consists of approximately 200 __ residues and has multiple functions including protecting the mRNA from 3’ degradation and enhancing translation.
A
circRNAs are circular RNAs that regulate ________ in multiple ways.
expression
Histone RNAs are stabilized by a 3’ _______ structure.
stemloop
Stemloop recruits the stemloop binding protein (______).
SLBP
Downstream AAGAAG recruits snRNP ____.
U7
SLBP and U7 recruit the FLASHLsm complex and the histone ______ complex HCC which uses components of the CPSF complex including CPSF73 aka CPSF2 to cleave the 3’ end.
cleavage
SLBP mediates nuclear export by recruiting nuclear export protein ALYREF and TAPNXF1 nuclear export __________.
receptor
lncRNAs like MALAT1 have 3’ triple _________.
helices
These serve to protect the lncRNA from the nuclear ___________ and other RNA decay components.
exosome
MALAT1 is not known to be _____ from the nucleus.
exported
But Addition of the MALAT1 triple helix to a GFP reporter results in efficient nuclear export and _________, so MALAT1 nuclear retention likely requires other sequence in the lncRNA.
translation
Different R radical groups have different chemical structures that confer various chemical __________ to the specific amino acid.
properties
Nonpolar aliphatic R groups: Mainly hydrocarbons uncharged and _______.
hydrophobic
Aromatic R groups: Relatively nonpolar absorb ____ light.
UV
Proteins are _________ consisting of amino acids linked by peptide bonds.
polymers
Amino acid sequence is its structure
primary
This structure folds to create and tertiary structures
secondary
Two or more polypeptide chains associate to form structure
quaternary
A is a set of nucleotides 3 in number that encodes a single amino acid
codon
The genetic code consists of codons
64
AUG is the _________ codon.
initiation
UAA UAG and UGA are _____________ stop codons.
termination
There are 64 possible codons 61 are sense codons and 3 are _____ codons.
stop
Degenerate code: A specific amino acid may be specified by more than one _____.
codon
Synonymous codons: codons that specify the same ___________.
amino acid
Isoaccepting tRNAs different tRNAs can accept the same amino acid but have different __________.
anticodons
Reading frame: three ways in which the sequence can be read; in groups of ________. Each different way of reading encodes a different amino acid sequence.
three
Nonoverlapping: A single nucleotide may not be included in more than one _________.
codon
In Human mitochondria UGA Stop is altered to code for ______.
Trp
In Human mitochondria AUA Ile is altered to code for ______.
Met
In Human mitochondria AGA and AGG Arg are altered to code for _____.
Stop
In human nuclear DNA (in a context-dependent manner) UGA Stop is altered to code for ____.
Sec
The reading frame of a mRNA sequence is determined by the start codon AUG and sets the _________ start site.
translational
The concept of _________ explains why in the 3rd position of the codon 1st position of the anticodon, there is some flexibility in the bonding between the base pairs.
wobble
This flexibility allows some tRNAs to pair with more than one _________ on an mRNA.
codon
Codon _____________ refers to the relative abundance of the corresponding tRNAs.
optimization
Codon optimization is conserved in ___________.
mammals
Codon optimization contributes to _________ of translation.
speed
The genetic code is degenerate: 64 possible codons encode 20 amino acids, 3 codons are ______________ codons.
termination
Some codons are _________.
synonymous
Isoaccepting tRNAs are tRNAs with different __________ that accept the same amino acid.
anticodons
The wobble position 3 in the codon 1 in the anticodon allows one type of tRNA to pair with more than one mRNA ________.
codon
The genetic code is generally nonoverlapping; there are three separate reading frames each set by a _________ codon (usually AUG encoding Met).
start
Any of the three termination codons (UAA UAG ________) signal the end of translation.
UGA
The genetic code is almost ________.
universal
The translation of an mRNA molecule takes place on a __________.
ribosome
The specificity between an amino acid and its tRNA is determined by each individual aminoacyl-tRNA __________.
synthetases
There are exactly ___ different aminoacyl-tRNA synthetases in a cell.
20
An amino acid attaches to the 3’ end of a ______ in translation.
tRNA
tRNA charging: the attachment of a tRNA to its appropriate _________.
amino acid
The Shine–Dalgarno consensus sequence in bacterial cells is recognized by the _______ unit of ribosome.
small
The Kozak sequence in eukaryotic cells facilitates the identification of the ______ codon.
start
The initiation or start codon in bacterial cells is usually _________, which codes for formyl-methionine amino acid.
AUG
When AUG encodes an internal methionine, the amino acid is not formylated and utilizes a different tRNA molecule.
formylated
The initiation codon in eukaryotic cells is usually AUG and encodes an _________ methionine both at the initiation and internal positions.
unformylated
However, like in bacterial systems, the tRNA which codes for this initiator methionine is ________ than the internal methionine tRNAs.
different
During initiation in bacterial cells, the nucleotides in the Shine-Dalgarno sequence base pair with their complementary nucleotides in the 16s small ribosomal RNA, allowing the small ribosomal subunit to attach to the mRNA in position for the initiation of ____________.
translation
The Kozak sequence is a _______ sequence in eukaryotic cells that surrounds the start codon.
consensus
Translation initiation requires initiation factors and _______.
GTP
Note that mRNA secondary structures are unwound by _________ activity located in the small ribosomal subunit.
helicase
In eukaryotes, translation initiation is facilitated by interactions between the proteins binding the polyA tail and the _______ proteins.
cap-binding
Initiation factor eIF4G and eIF4E interact with both the polyA binding proteins and ________ proteins.
capbinding
A-site aminoacyl – tRNA site – holds the tRNA carrying the next amino acids to be added to a polypeptide ______.
chain
P-site peptidyl – tRNA site – holds the tRNA attached to the growing ________ chain.
polypeptide
E-site – the exit site from which tRNA molecules leave the _________.
ribosome
Each amino acid added to the growing end of the polypeptide chain is selected by complementary base-pairing between the _________ on its attached tRNA molecule and the next codon on the mRNA chain.
anticodon
____________ formation between the 2 amino acids occurs in the large ribosomal subunit; the catalytic activity for this reaction is a property of a large rRNA component.
peptide bond
Numerous studies link m6A to _________ translation via 3 distinct mechanisms.
increased
The m6A reader DF1 binds the eukaryotic translation initiation factor eIF3, the multiprotein complex that recruits the ________ ribosome subunit to mRNAs which enhances their translation.
small
Since DF1-binding sites are mostly around stop codons in the 3’ UTRs, this model implies DF1 recruits ______ to these regions.
eIF3
Presumably when the 3’ UTR region loops to interact with the 5’ _______ complex, translation is enhanced.
cap
5’ UTR m6A residues bind to ______.
eIF3
The ______ bypasses the normal requirement for eIF4E normally recruited by the 5’ cap complex.
m6A
Because only a few 5’ UTRs have m6A residues, this mechanism is limited to a small number of ___________.
mRNAs
Direct translation activation is done by ________, the m6A methylating complex.
METTL3
The _______ protein complex is thought to bind eIF3 to create the loop between the 3’ and 5’ UTRs, which might facilitate ribosomal assembly and function.
METTL3
The termination codons are UAA, UAG, and _____.
UGA
Translation ends when a ________ codon is encountered.
stop
Translation consists of tRNA charging, initiation, elongation, and _________. In this process, amino acids are linked together in the order specified by mRNA to create a polypeptide chain. A number of initiation elongation and release factors take part in the process and energy is supplied by ATP and GTP.
termination
RQC – __________ Quality Control Complex exists to monitor harmful peptides and mRNA lacking a stop codon.
Ribosome
Ribosomal _________ occurs due to the ribosome translating through a stop codon, lack of a stop codon, or defective tRNAs.
stalling
Inhibition of translation _______ through ribosomal defects occurs.
elongation
The RQC complex facilitates _________ of the peptide which targets it for lysosomal or proteasomal degradation.
ubiquitination
Selenocysteine is encoded by ____ stop codons.
UGA
Approximately 25 _______ exist in the human genome.
selenoproteins
Selenoproteins are involved in cell signaling and redox _________.
homeostasis
Examples of __________ include: Glutathione peroxidases (GPX18), Thioredoxins reductases (THX 13), Iodothyronine deiodinases (DIO13), and Selenoprotein P (SELENOP) and related.
selenoproteins
Serine is converted to selenocysteine on the charged ______.
tRNA
SECIS recruits the SECIS binding protein (SBPB2), which scaffolds the elongation factor Sec (________).
EFSec
EFSec facilitates Sec-charged tRNA binding to the _____ codon.
UGA
Messenger RNA surveillance: Detect and deal with errors in _____.
mRNA
Nonsense-mediated mRNA decay: eliminating mRNA containing premature _________ codons; recruited by exon _______ complexes.
termination
Ribosomal _______, also known as translational frameshifting or translational recoding, is a process that occurs during translation that results in the production of multiple unique proteins from a single mRNA.
frameshifting
Ribosomal frameshifting can be programmed by the nucleotide sequence of the mRNA and is sometimes affected by the secondary mRNA _________.
structure
In viruses, ribosomal frameshifting allows encoding of multiple types of _______ from the same mRNA.
proteins
Ribosomal frameshifting is controlled by a _________ sequence and a RNA secondary structure.
slippery
Slippery sequences can potentially make the reading ribosome slip and skip a number of nucleotides (usually only 1) and read a completely different _______ thereafter.
frame
The RNA secondary structure (which can be a stemloop) pauses the ribosome on the slippery site during translation, forcing it to relocate and continue replication from the _____ position. It is believed that this occurs because the structure physically blocks movement of the ribosome by becoming stuck in the ribosome mRNA tunnel.
-1
Both gag and pol proteins are required for reverse _________, which is essential to HIV1 replication.
transcriptase
Polyribosomes are multiple ________ attached to the same mRNA strand.
ribosomes
Polyribosomes make multiple copies of the same _______ from a single mRNA strand.
protein
Polyribosomes allow a cell to quickly make many copies of the _________.
protein
Protein synthesis consists of 4 steps:
1) binding of amino acids to the appropriate tRNAs
2) _________
3) elongation
4) termination
initiation
The binding of an amino acid to the appropriate tRNA requires the presence of a specific aminoacyl-tRNA _________ and ATP. The amino acid is attached by its carboxyl end to the 3’ end of the tRNA.
synthetase
In bacterial translation, initiation the _____ ribosomal subunit attaches to the mRNA over the initiation codon by mRNA and rRNA interactions at the Shine-Delgarno region. The initiator tRNA and its associated formyl-methionine amino acid along with the large ribosomal subunit join the complex.
small
In eukaryotic translation initiation, the small ribosomal subunit binds to the ___ end of the mRNA after recruitment by proteins on the 5’cap complex and polyA tail. The small subunit then scans downstream until it encounters the first AUG start codon at the Kozak consensus sequence; at this point, the initiator methionine tRNA and the large ribosomal complex are added to form the complete ribosome.
5’
In elongation, a charged tRNA enters the ____ site of the ribosome, a peptide bond is formed between the amino acids in the A and P sites, and the ribosome moves (translocates) along the mRNA to the next codon. GTP is a required energy source for these processes.
A
Translation is terminated when the ribosome encounters a ________ codon. Release factors and GTP are required to bring about termination.
termination
Each mRNA molecule may be simultaneously translated by several ribosomes in what is called a __________ or polysome.
polyribosome
Cells possess mRNA ________ mechanisms that eliminate mRNAs with errors that may create problems in translation.
surveillance
Some proteins undergo __________ modifications to support or modify their functions.
posttranslational
DNA – Triplet code mRNA – _____ tRNA – Anticodon
Codon
The genetic code determines how nucleotide sequences specify the amino acid sequence of a protein DNA → RNA → _______. Each codon, consisting of 3 mRNA nucleotides, encodes a specific amino acid. The codons are written and read in a 5’→ 3’ direction as they appear in the mRNA.
Protein
Amino acids are assembled into polypeptides proteins in the _______ through the mechanism known as “translation”. tRNAs bring specific amino acids to be added to the polypeptide chain. The specific amino acid is determined by the codon sequence.
ribosome
Translation consists of initiation, elongation, and ________ processes
termination
In some cases the UGA stop codon encodes _________ (Sec)
selenocysteine
The Sec tRNA is recruited by a stem-loop structure in the 3’ UTR, the stem loop binding protein (SLBP), and the selenocysteine elongation factor ______.
EFSec
