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60 Cards in this Set

  • Front
  • Back
RNA polymerase
responsible for transcription
DNA/RNA helix
short lived, about 9 nucleotides long
differences between DNA polymerase and RNA polymerase
1. RNA polymerase catalyzes the linkage of ribonucleotides, not deoxyribonucleotides
2. RNA polymerases can start an RNA chain without a primer (RNA need not to be as accurate as DNA
3. RNA polymerase makes a mistake about 1 every 10^4 nucleotide
4. repair does occur in RNA polymerase, but more rudimentally
direct the synthesis of proteins
direct the splicing of pre-mRNA to mRNA
constitute the core of ribosomes
form the adaptors that select amino acids and hold them in place on a ribosome for incorporation into protein
small nucleolar RNAs, used to process and chemically modify mRNA
sigma factor on bacterial RNA polymerase
largely responsible for its ability to read the signals in the DNA that tell it where to being transcription, it is responsible for locating the promoter (start of transcription), then unwind DNA (which does not need ATP hydrolysis in transcription)
found on the DNA that tells transcription to stop, release RNA as well, DNA usually has A-T repeats that cause the RNA to make a hairpin loop, wedges open the flap
consensus sequence
transcription start and stop signals are heterogeneous, the consensus sequence is derived by comparing many sequences with the same basic function and tallying up the most common nucleotide found at each position
start point of transcription
what accounts for the difference between promoter sites?
helps in regulating the amount of gene produce, some promoter sites are stronger if they make a gene that needs to be made in abundance
heterogenous levels of terminator sequences vs. promoter sequences
terminator sequences are more heterogenous
choice of template strand
depends entirely on the orientation of the promoter, RNA synthesis only in 5’-3’ direction
different types of RNA polymerase in eukaryotes
RNA polymerase I-5.8S, 18S, and 28S rRNA genes
RNA polymerase II-mRNA, snoRNA and some snRNA
RNA polymerase II-tRNA, 5S rRNA, some snRNA
differences between RNA polymerase II and bacterial RNA polymerase
1. eukaryotic RNA polymerase needs the help of other proteins to initiate transcription (general transcription factors)
2. eukaryotic RNA polymerase must deal with the packing of DNA into nucleosomes and higher order forms of chromatin structure
general transcription factors
help to position RNA polymerase II correctly at the promoter, aid in pulling apart the two strands of DNA and release RNA polymerase II from the promoter into the elongation mode once transcription has begun, carry out functions similar to sigma factor in bacteria, they include, TF II (transcription factor for polymerase II), TF IIA, TF IIB…
TATA box
promoter sequence of eukaryotes, -25
binds to the TATA box through a TBP (TATA box binding protein, bends the DNA), enables the binding of TFIIB, which then allows for all the transcription factors to bind to the promoter including the RNA polymerase II (NOTE: TFIID and TATA do not have to be the beginning of transcription, there are other starting elements and TFs that can be responsible for this)
then uses ATP to pry apart the DNA double helix, also phosphorylates RNA polymerase II so it can release from the other general factors and begin transcription
transcription initiation complex
all of the TFs and RNA polymerase II put together
transcriptional activators
bind to specific sequences in DNA and help to attract RNA polymerase II to the start point of transcription, overcoming the packaging into chromatin, determine the rate and pattern of transcription
allows the activator proteins to communicate properly with the polymerase II and with the general transcription factors
chromatin modifying enzymes
can allow greater accessibility to the DNA present in chromatin, they facilitate the assembly of the transcription initiation machinery into DNA
elongation factors
proteins that decrease the likelihood that RNA polymerase will dissociate before it reaches the end of a gene
DNA supercoiling
presents a problem in transcription, a conformation that DNA will adopt in response to superhelical tension caused by loops or coils in the helix
DNA topoisomerase
in eukaryotes, thought to be able to remove DNA supercoiling
DNA gyrase
in bacteria, thought to be able to remove DNA supercoiling, uses ATP hydrolysis
RNA factory
concept that states that the RNA polymerase also carries multiple pre-mRNA-processing proteins on its tail which are then transferred to the nascent RNA at the appropriate time
5’ Cap
first modification to pre-mRNA, only found on mRNA (not t or r) occurs after about 25 nucleotides of RNA are formed, consists of a modified guanine nucleotide and occurs through three enzymes that work in succession and are bound to the polymerase tail:
1. phosphatase removes one phosphate from the 5’ end of the nascent RNA
2. a guanyl transferase adds a GMP in a reverse linkage (5’-5’)
3. a methyl transferase adds a methyl group to the guanosine
RNA splicing
remove introns and put together exons, undergo transesterification reactions to join exons, remove intron as a lariat, requires many ATP molecules and over 50 enzymes to make sure that the splicing is correct
why have so many introns?
help in gene recombination, allows for the ready combination of the exons of different genes
importance of RNA splicing
can splice eukaryotic genes in different ways to give a variety of different mRNAs and different proteins
sequences that initiate splicing
GU at the start of the intron and AG at the end of the intron
snRNAs and splicing
5 types (U1, 2, 4, 5, 6), each is complexed with at least seven protein subunits to form snRNP
snRNP (small nuclear ribonucleoproteins)
forme the core of the spliceosome (responsible for pre-mRNA splicing in the cell
nuclear pore complex
recognizes and transports only completed mRNAs to the cytosol for translation, to be properly exported the mRNA must be bound by the appropriate set of proteins (these act as appropriate signals for protein export from the nucleus)
hnRNPs (heterogenous nuclear ribonuclear proteins)
most abundant proteins on pre-mRNA, found on introns and mark them for retention and destruction
constitutes about 80% of the RNA in an actively dividing cell, made through RNA polymerase I, genes for rRNA are abundant (there are multiple copies of it)
RNA polymerase I
does not have a C terminal tail, explains why rRNA is neither capped nor polyadenylated (helps distinguish between noncoding RNAs and mRNAs)
types of RNA
4 types (18S, 5.8S, 28S, and 5S), the first three of these are made by chemically modifying and cleaving a single large precursor rRNA
small nucleolar RNAs (snoRNAs)
perform their functions in a subcompartment of the nucleus called the nucleolus, processed from excised intron sequences
nucleolus and ribosome production
the nucleolus is a ribosome-producing factory, processes rRNA and assembles them into ribosomes, also site of tRNA production
start codon
stop codon
UAA, UAG, UGA, not recognized by tRNA and does not specify an amino acid, signals to the ribosome to stop translation, release factors bind and force the peptidyl transferase in the ribosome to catalyze the addition of a water moleucle
amino acid binding site on tRNA
found on the 3’ end of the tRNA
in tRNAs, formed from the deamination of guanine, can bind to the pyrimidines U and C at the third position
tRNA processing
occurs before they exit the nucleus, have some introns, removed through a cut and paste mechanism that is catalyzed by proteins, 1 in 10 nucleotides also undergo some type of chemical modification
aminoacyl-tRNA synthetases
responsible for matching the proper amino acid to its tRNA, adenylates the amino acid which is then transferred to the hydroxyl at the 3/ end of the tRNA, there is a different synthetase for each amino acid
tRNA editing
occurs by RNA synthetases, ensures accuracy, has a polymerizing site and an editing site
how does the synthetase get the right amino acid?
1. the correct amino acid has the highest affinity for the active-site pocket of tis synthetase and is favored, also amino acids to large are excluded from the active site
2. occurs after the amino acid has been covalently linked to AMP, forces the amino acid into a second pocket, the right one does not fit, but closely related do, if they do fit, they are then hydrolyzed and removed
how does the synthetase attach to the right tRNA?
extensive structural and chemical complementarity between the synthetase and the tRNA allows various features of the tRNA to be sensed, it matches the anticodon, nucleotide sequence of the acceptor stem, and other nucleotides found on the tRNA
where are amino acids added to the growing polypeptide chain?
the C-terminal end, remains active by being bound to a tRNA molecule, has energy for the next addition not its own addition
site of protein synthesis, composed of rRNAs (2/3) and ribosomal proteins (1/3), small subunit responsible for providing a framework on which the tRNAs can be accurately matched to the codons of the mRNA while the large subunit is responsible for the formation of the peptide bonds that link the amino acids together into a polypeptide chain, these subunits are separate when they are not actively synthesizing protein, adds about 2 amino acids/second
binding sites in the ribosome
A-aminoacyl tRNA, P-peptidyl tRNA, and E-exit, also a binding site for mRNA (in the small subunit)
peptidyl transferase
contained in the large subunit, catalyzes the carboxyl end of the polypeptide chain to join to the free amino group of the amino acid linked to the tRNA at the A-site
EF-Tu and EF-G
enter and leave the ribosome during each cycle, each hydrolyzes GTP to GDP and undergoes conformation changes, this speeds up protein synthesis
1. EF-Tu-thought to increase the accuracy of translation by monitoring the initial interaction between a charged tRNA and a codon, charged tRNAs enter the ribosome with a bound GTP form EF-Tu, GTP is only hydrolyzed once it is confirmed that the right codon-anticodon reaction is completed, then the EF-Tu is released, also makes sure that the right amino acid is attached to the right tRNA
2. EF-G-speeds up the movement from the A to P site and the P to E site
RNA molecules that possess catalytic activity, ex: RNA splicing reactions, RNA, not protein, probably served as the first catalysts for living cells
eukaryotic initiation factors (eIFs)
additional proteins needed during initiation of translation