Test 2 Notes Study Guide Flashcards
What are the three major components required for transcription?
- DNA template
- The ribonucleotide-triphosphates required to build the new RNA molecule.
- The transcription apparatus: proteins necessary from catalyzing the synthesis of RNA, and RNA polymerase
How do RNAs relate to the template strand?
RNAs are complementary and antiparallel to the template strand
What is the name of the 5’->3’ strand?
sense/coding strand
What is the name of the 3’-5’ strand?
antisense/noncoding strand
What is the difference between the template stand and the non template strand?
The template strand is complementary and antiparallel to RNA.
What does a transcription unit (gene) include?
A promotor, an RNA coding region, and a terminator.
What is the promotor?
A DNA sequence that RNA pol recognizes and binds
What is the transcription start site?
where the 1st nucleotide is laid
What is the function of RNA polymerase?
- synthesizes RNA in a 5’-3’ direction
- unwinds and rewinds DNA
Why are the consensus sequences AT rich?
because AT only has 2 hydrogen bonds so it is easier to break.
Where are the consensus sequences on the bacterial promotors?
-35 and -10 (pribnow box)
What does a consensus sequence consist of?
the most commonly encountered bases at each position in a group of related sequences.
What does the transcription apparatus consist of?
Core polymerase and holoenzyme
What is the core polymerase?
made-up of five subunits and actually transcribes/ builds RNA
What is a holoenzyme?
made up of the core polymerase and sigma factor
What does the sigma factor do?
recognizes -10 and -35 consensus sequences and binds to promotor sequence and recruits pol
What are the steps of transcription initiation?
- sigma factor binds promotor; -10 and -35 consensus sequence
- sigma attracts core pol
- Holoenzyme is at promotor
- Holoenzyme melts promotor + opens transcription bubble
- RNA pol adds 1+ nucleotide complementary to ssDNA
- sigma factor leaves
What happens during transcription elongation?
RNA pol extends seq 5’->3’ until termination sequence in DNA ; RNA pol unwinds and rewinds DNA
What are the two types of transcriptions termination?
1) Rho-dependent termination
2)Rho-independent termination
What happens during Rho dependent termination?
- Rho finds rut site on RNA
- goes up till it reaches polymerase and stops it
*works like helices but doesn’t have to unwind so it goes faster
What happens during Rho-independent termination?
1) inverted repeats in RNA bind to each other and cause hair pin loop
2) weak AU base pairs is enough to destabilize pol and pol lets go
What does the concept of collinearity suggest?
that a continuous sequence of nucleotides in DNA encodes a continuous sequence of amino acids in a protein
What are the ends of mRNA called?
5’ UTR and 3’UTR
What part of prokaryotic mRNA tells the ribosome to bind there?
Shine dalgarno sequence
What tells the ribosome to start and stop translation?
stop and start codons
What recruits the ribosome in prokaryotes?
shine-dalgarno sequence
What recruits the ribosome in eukaryotes?
5’ cap
What interrupts the coding sequences of many eukaryotic genes?
noncoding introns
When are intron removed?
RNA processing
What makes up the 5’ cap?
a single nucleotide with a 7-methylguanine attached to the pre-mRNA by a unique 5’-5’ bond
What are the functions of the 5’ cap?
- protection
- required to get out of the nuclear. pre/export
- recruit ribosome
What does the AAAAAA tail do?
bind ribosome
What are the steps of splicing?
- spliceosome binds consensus sequences at intron/exon boundaries
- mRNA is cut at 5’ end of intron
- 5’ end of intron attaches branch point A (lariat)
- 3’ end of intron cut
- exons joined, lariat (intron) free to be degraded
What does a spliceosome consist of?
five RNA molecules and 300 proteins
What is the branch point?
the adenine “A”, ~ 18-40 nucleotides upstream of 3’ splicing site
What are the steps of pre-mRNA processing?
1) the addition of the 5’ cap
2) the addition of the poly(A) tail
3) splicing removes the introns
What is alternative splicing.
alternative splicing enables exons to be spliced together in different combinations to yield mRNAs that encode different proteins
- multiple 3’ cleavage sites allow pre-mRNA to be cleaved and polyadenylated at different sites
What is the function of 3’cleavage and addition of poly(A) tail
- increases stability of mRNA
- aids in export of mRNA form nuclease
- ## facilitates binding of ribosome to mRNA
What is the function of RNA splicing?
- removes noncoding intron from pre-mRNA
- facilitates export of mRNA to cytoplasm
- allows for multiple proteins to be produced through alternative splicing
What is the structure of tRNA?
- made of rare modified RNA nucleotide bases (ribothymin, pseudourine)
- common secondary structure: clover leaf structure
- contains anticodon
What is the function of tRNA?
delivers amino acids to ribosome
What is RNA interference?
limits the invasion of foreign genes and censors the expression of their own genes
What do microRNAs do and where are they made?
Function: inhibits translation of mRNA
Made: body
What is the function of small interfering RNAs and where are they made?
Function: triggers degradation of other RNA molecules
Made: scientists
What do ds RNAs prevent?
translation
What is the one gene, one enzyme hypothesis?
genes function by encoding enzymes and each gene encodes a separate enzyme
What is a protein?
a long polymer of amino acids joined by peptide bonds
Describe primary organization.
sequence/chain of amino acids, n’-c’ (Shoe string)
Describe secondary organization.
back bone atoms bond
- alpha helix: shoelace around finger
- beta sheet: ribbon candy
both are held by hydrogen bonds
Describe tertiary organization?
folding of secondary into 3D globular shapes
*side chains make bonds (r-groups)
Describe quaternary organization?
two or more products interact to be functional
What is a codon?
a triplet RNA code
- 64 possible codons
What is a sense codon?
codons that encode amino acids
What is the initiation codon?
AUG
What are the termination codons?
UAA, UAG, UGA
What is the degenerate code? (wobble)
amino acid may be specified by more than one codon
What are synonymous codons?
codons that specify the same AA
What are isoaccepting tRNAs?
different tRNAs that accept the same amino acid but have different anticodons
What is wobble?
When the tRNA and mRNA pair in a antiparallel fashion, odd base pairing occurs in wobble be there is more than 1 option for an amino acid
What is the reading frame?
three ways in which the sequence can be read in groups of three. Each different way of reading encodes a different amino acid sequence
What is non overlapping?
a single nucleotide may not be included in more than one codon.
What is the universality of the code?
the code is near universal with some exceptions
What determines the specificity between an AA and its tRNA
Each individual aminoacyl-synthetase in a cell.
How do amino acids attach to the 3’ end of tRNAs?
The carboxyl group of the amino acid attaches to the hydroxyl group of the 2’ or 3’ carbon atom of the final nucleotide at the 3’ and of the tRNA in which the case is always adenine
Why is the cap and poly(A)tail are important for Eukaryotic translation initiation?
proteins that attach to the 3’ poly(A)tail interact with cap binding proteins to attract and bind ribosome
In elongation, the creation of peptide bonds between AA is catalyzed by?
rRNA
What is polyribosomes in proks and euks?
multiple ribosomes per mRNA strand
What do the release factor bound to the termination codon cause the release of?
- the polypeptide from the last tRNA
- the tRNA from the ribosome
- the mRNA from the ribosome
What are the steps of prokaryotic translation initiation?
- IF-3 bound to small subunit (so large subunit can’t attach)
- small subunit + IF 3 bind at shine dalgarno sequence on mRNA
- F-met +RNA+IF2+GTP +IF1(stabilizes base pairing) base pari the anti codon of the tRNA to start codon (AUG)
- GTP hydrolyzes; GDP and IFs disassociate
- Large subunit binds -> F-met tRNA is in the p-site
What are the steps of prokaryotic translation elongation?
- Fmet tRNA in p site
- EF-Tu w/ GTP bind next tRNA and bring it to A-site
- GTP hydrolyzed to GDP and EF-Tu disassociates (Efts recycles EFtu +GTP)
- Peptide bond between Met-AA2 catalyzed by ribosome (rRNA)(2OH-)
- Ribosome translocates 1 codon w/ EF-G +GTP; Fmet tRNA in E site
- uncharged tRNA exits
What are the steps on prokaryotic translation termination.
- ribosome reaches stop codon and there is no tRNA to pair with stop codon in the a-site
- RF1 attaches to the a-site and RF3 forms a complex with GTP and binds to the ribosome
- The polypeptide is released from the tRNA in the p site
- GTP associated with RF3 is hydrolyzed to GDP
- The tRNA, mRNA and release factors are released from the ribosome.
What are structural genes?
genes that encode proteins
What do regulatory genes encode?
encoding products that interact with other sequences and affect the transcription and translation of these sequences
What are regulatory elements?
DNA sequences that aren’t transcribed but play a role in regulating other nucleotide sequences
What is cleavage of proteins?
chopping in half/ piece cut off
What is glycolysation?
adding a sugar to a protein (makes it slippery so cells can slide past each other)
What is phosphorylation?
adds phosphate group change protein charge
What is lipidization?
adds lipid to protein (binds it to lipid membrane)
What is ubiquitination?
ubiquitin protein is added to protein which tags it for destruction and it gets sent to proteosome
What are the 6 levels that gene expression can be controlled?
- chromatin packaging
- transcription
- mRNA processing
- mRNA stability
- translation
- post-translational modification
What is an example of chromatin packaging modification?
heterochromatin vs. euchromatin
example of transcription regulation
RNA pol, promotor, enhancer
, GTF, TF, silencer
example of mRNA processing regulation
spliceosome alt splicing, no cap
tail (alt poly(a) site)
example of mRNA stability regulation
short half life cycle, siRNA
example of translational regulation
miRNA, ribosome can’t bind, ribosome function, aa availibility
Why is transcription a particularly important level of gene regulation in both bacteria and eukaryotes
bacteria-respond to environment
eukaryotes- specialized cell project
What is TBP?
TATA binding protein: protein that recognizes Eukaryote promoter (works like sigma)
What does each promoter respond to in euks?
a unique combination of transcription factors
What is an enhancer?
DNA sequence stimulating transcription a distance away from promoter
How does the binding of transcription factors to enhancers affect transcription at genes that are thousands of base pairs away?
can loop up the chromosome so transcription factors touch polymerase
What type of RNA makes up a spliceosome?
snRNA
What all is required for eukaryotic transcription?
TBP, Transcription Factors, Mediator, Coactivator, enhancer sequence, RNA polymerase.
What makes up the basal transcription factor?
RNA Pol, TATA binding protein, general transcription factors, TATA sequence
