Term
| Was sequencing the genome adequate to totally understand molecular biology of the cell? |
|
Definition
| no (it has been critical but not adequate) |
|
|
Term
| simplest case in a genome sequence |
|
Definition
| you have an uninterrupted ORF |
|
|
Term
|
Definition
| the method with which you can discover the proteome |
|
|
Term
| in between sequencing genome & proteome, you need RNA seq to see if that ORF is even being made into an RNA, then _______ |
|
Definition
| mass spec to see if it is made into a protein |
|
|
Term
| does ribosome profiling give you stead-state read-out or real-time answers? |
|
Definition
|
|
Term
| the parts of the genome where there is no ORF...does this mean that there is no gene there? |
|
Definition
|
|
Term
| give some examples of non-coding RNAs (they are increasing in numbers of being discovered...maybe even equal to mRNAs/coding RNAs) |
|
Definition
| ribosomal RNA, tRNA, miRNA, small nuclear RNA, small nucleolar RNA, small cytoplasmic RNA |
|
|
Term
| some non-coding RNAs are very long & contain tiny little _______ |
|
Definition
|
|
Term
| can genes exist with a STOP codon really close to the START codon? |
|
Definition
| yes (ATG --> 15 nt later a STOP --> 1500 nt later another STOP) |
|
|
Term
| in genes with a STOP codon really close to the START codon, what might happen to the first STOP codon? |
|
Definition
| maybe the first STOP codon is sometimes spliced out (within an intron) |
|
|
Term
| how would you know that maybe the initial uORF (short START --> STOP before normal length START --> STOP) is spliced out to make the shorter RNA functional to make a protein? |
|
Definition
| would only know from doing RNA seq to look at the transcripts & ribosome profiling to look at translation |
|
|
Term
| What could be the implication of shifting to the second START in a START --> START --> STOP scenario? |
|
Definition
| depending on how far it is from the first one...if they are in different reading frames could make a completely different protein because it could totally shift the ORF |
|
|
Term
| What would be the point of two START codons in the same reading frame (AKA you would be making the same protein twice depending on where you started & the longer one would just have a longer amino terminus)? |
|
Definition
| what is in the longer one could direct it to a different part of the cell for example |
|
|
Term
| is steady-state concentration of RNA often proportional to steady-state concentration of protein? |
|
Definition
|
|
Term
| ______ helps you compare RNA concentration to how much is being translated into proteins in real time |
|
Definition
|
|
Term
| are ribosomes complicated structures? |
|
Definition
|
|
Term
| _______ is a very dynamic process that requires a complicated machine with many moving parts |
|
Definition
| protein synthesis - translation |
|
|
Term
| mRNA --> _______ --> proteins |
|
Definition
|
|
Term
|
Definition
|
|
Term
| mass spec tells you ______ |
|
Definition
|
|
Term
| ribosome profiling tells you _______ |
|
Definition
|
|
Term
| how protein synthesis has been studied for a very long time (since _______) |
|
Definition
|
|
Term
| 3 things you need for basal protein synthesis |
|
Definition
1. mRNA with a cap on 5' end & (usually) poly-A tail at 3' end
2. ribosomes that catalyze the translation
3. amino acids to polymerize into proteins |
|
|
Term
| how is the amino acid brought in to make the protein? |
|
Definition
| amino acid is attached to tRNA so when the tRNA connects to the mRNA via the 3-base pairing, it brings in the amino acid to make the protein |
|
|
Term
| ______ associates with the mRNA & is a platform for where the tRNA (with amino acid attached) can bind |
|
Definition
|
|
Term
| large or small subunit: has peptidyl transferase center where peptide bond is actually formed |
|
Definition
|
|
Term
| large or small subunit: has decoding center where tRNA & mRNA base pair |
|
Definition
|
|
Term
| how does ribosome/mRNA complex look? |
|
Definition
| large subunit on top, mRNA + tRNA in middle, small subunit on bottom |
|
|
Term
|
Definition
| bind to the tunnel exit & help the protein start to fold into tertiary structure |
|
|
Term
| ______ is the tunnel through which every protein made must travel to enter the world & fold |
|
Definition
| nascent polypeptide exit tunnel |
|
|
Term
| proteins just outside of the tunnel help with ______ |
|
Definition
|
|
Term
| is the nascent polypeptide exit tunnel in the large or small subunit |
|
Definition
|
|
Term
| what is the implication that the center of the ribosome where peptide bonds are formed have nothing but RNA in it? |
|
Definition
| this means that everything is catalyzed by an RNA molecule! |
|
|
Term
| amino terminal _______ is made from start codon & is cleaved off by the nurse molecules |
|
Definition
|
|
Term
| sequence of amino acids = ______ |
|
Definition
|
|
Term
| you need to decode the genetic code in order to ______ |
|
Definition
| catalyze peptide bond formation |
|
|
Term
| 40 S is also called the _______ |
|
Definition
|
|
Term
| where is the decoding center located? |
|
Definition
|
|
Term
| ______ is made up of 1 long RNA & 32 proteins |
|
Definition
|
|
Term
| how does the small ribosomal subunit act like an enzyme? |
|
Definition
| brings the two RNAs together to cause binding/peptide formation |
|
|
Term
| _______ is made up of 3 RNAs & 47 proteins |
|
Definition
|
|
Term
| where is the peptidyl transferase center? |
|
Definition
|
|
Term
| _______ has an anticodon that binds to codon in mRNA |
|
Definition
|
|
Term
| about ______ amino acids are put together every second! |
|
Definition
|
|
Term
| how long has ribosomal machinery been around? |
|
Definition
| since the beginning of life |
|
|
Term
|
Definition
| not permanent members of the ribosome but work with the ribosome to help with the translation process |
|
|
Term
| 3 kinds of translation factors |
|
Definition
1. initiation factors
2. elongation factors
3. termination factors |
|
|
Term
| some factors associate with small subunit --> help it _______ |
|
Definition
|
|
Term
| some factors associate with the 5' end of the mRNA --> ? |
|
Definition
| work with small subunit factors to help small subunit find the end of the mRNA |
|
|
Term
|
Definition
| small subunit binds to the 5' end of mRNA |
|
|
Term
|
Definition
| once small subunit is bound, it moves down the mRNA until it finds the first AUG |
|
|
Term
|
Definition
| once the small subunit has found the AUG to where it will start translation |
|
|
Term
|
Definition
| large subunit joints small subunit at the AUG |
|
|
Term
|
Definition
|
|
Term
|
Definition
| stopping at the STOP codon |
|
|
Term
| what is the implication that ribosomes can translate multiple RNAs in its lifetime? |
|
Definition
| once done with one, can move onto the next mRNA |
|
|
Term
| what does it mean that ribosomes are "recycled"? |
|
Definition
| ribosomes can translate multiple RNAs in its lifetime |
|
|
Term
|
Definition
| small dynamic changes cause the chain reaction that leads to peptide formation |
|
|
Term
| genetic approach to figure out ribosomal system |
|
Definition
| discovering things via breaking things & seeing what happens (mutants) |
|
|
Term
| biochemistry approach to figure out ribosomal system |
|
Definition
| purifying parts & reconstituting them to make a small subset of the total reaction to see which parts are involved when |
|
|
Term
| structural biology approach to figure out ribosomal system |
|
Definition
| x-ray crystallography determined the crystal structure of the ribosome |
|
|
Term
| high throughout tools approach to figure out ribosomal system |
|
Definition
| mostly ribosome profiling, mass spec, & RNA seq to see what RNAs are present, what proteins are present, & which of those RNAs are being translated by ribosomes at present |
|
|
Term
| _______ has the most factors |
|
Definition
|
|
Term
| what is implied by initiation having the most factors? |
|
Definition
| getting everything going properly is the most important thing to get totally right |
|
|
Term
| job of the large & small subunit within the process of translating the coding region of the mRNA & catalyzing protein synthesis |
|
Definition
small: translate/decode the code
large: synthesize the chain of polypeptides given that translation of the information |
|
|
Term
| can translation be regulated? |
|
Definition
|
|
Term
| how could you find nodes for regulation? |
|
Definition
| find places where there are "challenges" & if you want to upregulate you overcome those challenges & if you want to downregulate you can make those challenges harder |
|
|
Term
| 6 molecules involved in translation |
|
Definition
1. mRNA
2. aatRNA (amino-acyl transfer RNA)
3. ribosomes
4. initiation factors
5. elongation factors
6. release factors |
|
|
Term
| scaffold initiation factors |
|
Definition
| structural proteins, not enzymatic; provides a place for other proteins to bind |
|
|
Term
| enzyme initiation factors |
|
Definition
| bind ATP --> hydrolyze it to use the energy to move themselves & whatever else they're next to |
|
|
Term
|
Definition
| stall things or start things |
|
|
Term
| why does translation require timers? |
|
Definition
| to not let things happen prematurely or to tell the process to start doing something when it is the correct time |
|
|
Term
| why is accuracy of translation important? |
|
Definition
| if you make a mistake in protein synthesis you could die/get sick |
|
|
Term
| why is flexibility of translation important? |
|
Definition
| if you need to make different proteins in different circumstances |
|
|
Term
| why is efficiency of translation important? |
|
Definition
| so that it can get done fast |
|
|
Term
| what happens to ribosomes when they are done with one mRNA? |
|
Definition
| they move on to translate another one |
|
|
Term
| why is where translation starts really important? |
|
Definition
| if you start outside of +1, you get a frameshift; if you start in frame but at the wrong place, you could get extra amino acids or lack some |
|
|
Term
| why is where translation ends really important? |
|
Definition
| adding extra amino acids at the end could be detrimental |
|
|
Term
| why does the AUG codon sit in the middle of the mRNA (as opposed to the very first codon just being the start)? |
|
Definition
| the geometry of the ribosome is such that the decoding center wouldn't fit very close to the beginning & transcription usually has heterogeneous 5' ends so it would be really hard to get it to get that starting AUG at the very start every time |
|
|
Term
| the methionine gets cut off of the protein by the _______ |
|
Definition
|
|
Term
| what is meant by the first "best" AUG is the START codon? |
|
Definition
| if there were choices, it was one that has purines at +4 & -3 |
|
|
Term
| if translation initiated at a fixed distance from the mRNA cap, where would all of the starts be? |
|
Definition
| +20 from the 5' end (that is how far away the P site is in the ribosome if the two ends matched up) |
|
|
Term
| is the 5' cap necessary under most conditions for translation of mRNA? |
|
Definition
|
|
Term
| describe look of small subunit |
|
Definition
| has a head, body, platform sticking out to one side from the body, beak sticking out on same side from the head, & neck |
|
|
Term
| small subunit body has three sites: ? |
|
Definition
|
|
Term
| initiation = _______ tRNA in the P site |
|
Definition
|
|
Term
| second tRNA comes into the ______ site in elongation |
|
Definition
|
|
Term
| peptidyl transferase reaction |
|
Definition
| attaches amino acid in P site to amino acid in A site |
|
|
Term
|
Definition
1. methionine tRNA in the P site
2. next tRNA comes into the acceptor site
3. attaches amino acid in P site to amino acid in A site
4. empty tRNA moves to E site, growing peptide chain moves to P site, next aatRNA comes into A site
5. chain attaches to amino acid at A site, now there is an empty tRNA at E & P site
6. E site empty gets kicked out, P site empty moves into E, growing chain moves into P, new aatRNA moves into A |
|
|
Term
| for translation to be correct, the ribosome must somehow be selective at the ______ site |
|
Definition
|
|
Term
| how does the tRNA move through the ribosomes? |
|
Definition
| tRNA enter from right --> enter A --> then P --> then E --> then leave |
|
|
Term
| met-tRNA base pairs with ______ |
|
Definition
|
|
Term
| tRNA is brought to the complex by an _______ |
|
Definition
|
|
Term
| whole process of translation ratchets mRNA between subunits ______ codons at a time |
|
Definition
|
|
Term
| there are 3 sites where three tRNAs fit on _____ |
|
Definition
|
|
Term
| 5 things needed for initiation of translation |
|
Definition
1. 40S EPA sites (ribosomes)
2. mRNA 5' cap------3' AAA (tail)
3. there is a consensus sequence (Kozak), AUG, & purine (best start site)
4. amino-acyl tRNAs (aatRNA) --> this may be rate limiting step because it takes a while to make
5. initiation factors --> work with elements 1 - 4 |
|
|
Term
| 3 things that make up the 48S attachment |
|
Definition
1. 43S complex
2. CBP
3. mRNA |
|
|
Term
| once they attach, ribosome scans until it can find ______ |
|
Definition
|
|
Term
| 5 steps of translation initiation |
|
Definition
1. attach --> 43S complex + CBP + mRNA --> bind to each other = 48S (attachment)
2. scan
3. then stops & recognizes AUG
4. recruit 60S
5. start |
|
|
Term
| which initiation factor promotes "open complex" so RNA can move through & when ribosome finds AUG, closes |
|
Definition
|
|
Term
| eIF1 is active in the _____ site |
|
Definition
|
|
Term
| CTD tail of eIF1A promotes ______ |
|
Definition
|
|
Term
| how does eIF1A work with eIF1? |
|
Definition
| tail gets in the way of A site |
|
|
Term
| how do eIF1 & eIF1A regulate open state? |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| sitting on back & reach around to front |
|
|
Term
| _______ grabs Met-tRNA & delivers it to ribosome (initiation factor) |
|
Definition
|
|
Term
| ______ comes into ribosome & binds with tRNA (initiation factor) |
|
Definition
|
|
Term
|
Definition
| recognizes & binds cap (recognition protein) |
|
|
Term
|
Definition
| binds to CBP & RNA helicase (scaffold protein) |
|
|
Term
|
Definition
|
|
Term
| polyA binding protein binds to ______ |
|
Definition
|
|
Term
| once attached, the ______ scans when ready |
|
Definition
|
|
Term
| what needs to happen to the RNA to get attachment? |
|
Definition
|
|
Term
| 2 initiation factors needed to keep ribosome open |
|
Definition
|
|
Term
| 3 ways to regulate proteins that block scanning? |
|
Definition
1. uORF
2. proteins that block
3. add secondary structure (cis) to mRNA |
|
|
Term
| 3 things that happen once hits Kozak sequence |
|
Definition
1. ribosome recognizes AUG
2. eIF1 moves
3. Met-tRNA binds |
|
|
Term
| 3 things that happens once recognition of AUG occurs |
|
Definition
1. 1 moves out of the way
2. 1A locks down recognizing body to the Kozak
3. Met-tRNA is in place |
|
|
Term
| ______ hydrolyzes GTP --> GDP & Pi once hit Kozak sequence |
|
Definition
|
|
Term
| what is open ribosome complex |
|
Definition
|
|
Term
| what is closed ribosome complex |
|
Definition
| it can attach, but it is no longer sliding |
|
|
Term
|
Definition
| P site to block tRNA (keeps it "open") |
|
|
Term
|
Definition
| A site but has C terminus to also stretch to block tRNA at P site |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| is complex closed or open when it reaches AUG? |
|
Definition
|
|
Term
| when complex reaches AUG, ______ hydrolyzes GTP |
|
Definition
|
|
Term
| 4 eIFs that leave when complex reaches AUG |
|
Definition
|
|
Term
| when complex reaches AUG, ______ comes in to bring in the large subunit to join the small subunit |
|
Definition
|
|
Term
| when large & small subunit join: ______ hydrolyzes GTP |
|
Definition
|
|
Term
| 2 eIFs that leave when large & small subunit join |
|
Definition
|
|
Term
| next step in translation process that occurs when large & small subunit join |
|
Definition
|
|
Term
| 2 necessary factors for an AUG to be the right AUG |
|
Definition
1. A or a G at -3
2. A or a G at +4 |
|
|
Term
| when you reach the AUG, ______ moves out of the way so tRNA can move in |
|
Definition
|
|
Term
| 5 stimulates 2 to hydrolyze GTP --> energy needed to ______ |
|
Definition
| move in tRNAs & lock down ribosome |
|
|
Term
| how does eIF3 position itself? |
|
Definition
| kind of wraps around the ribosome from the back to the front |
|
|
Term
| 5 proteins found at mRNA for necessary translation complex |
|
Definition
1. cap
2. cap binding protein ("CBP")
3. scaffold ("G") (holding helicase, cap-binding protein, & poly-A binding protein in place)
4. helicase
5. poly-A binding protein ("PABP") |
|
|
Term
| is regulation global or at one specific gene/mRNA at a time? |
|
Definition
|
|
Term
| is regulation of translation negative or positive? |
|
Definition
|
|
Term
| 3 ways to disrupt G-PABP interaction |
|
Definition
1. post-transcriptionally modify either directly or indirectly
2. put in a protein that gets in the way of the interaction
3. cut off cap --> no CBP --> nothing for G to bind onto --> no availability for G/PABP interaction |
|
|
Term
| what does IRES stand for? |
|
Definition
| internal ribosome entry site |
|
|
Term
| how would a cell get around cut off cap --> nothing for ribosome to recognize to bind to? |
|
Definition
|
|
Term
| Hox proteins have a cap & an IRES...why does it do the IRES translation instead of the normal cap? |
|
Definition
| there is a translational inhibitory element (TIE) that represses use of the cap |
|
|
Term
| Hox proteins require a specific protein on the ribosome (______) |
|
Definition
|
|
Term
| what is weird about histone mRNA? |
|
Definition
| have no poly-A at 3' end --> no PABP --> cannot form G-PABP complex |
|
|
Term
| histone solution to lacking a poly-A tail |
|
Definition
| there is a sequence at the 3' end that forms its own complex with G! |
|
|
Term
| secondary role for SLBP in histones |
|
Definition
| also protects end from exonuclease because there is no PABP for protection |
|
|
Term
| how could you keep ribosome in the closed state? |
|
Definition
| complex could be modified by some sort of PTM --> block scanning |
|
|
Term
| how would a big tertiary structure block scanning? |
|
Definition
| ribosome could not overcome it |
|
|
Term
| how could a protein binding to the RNA block scanning? |
|
Definition
| get in the way of the ribosome |
|
|
Term
| can regulation turn up OR down translation pathway? |
|
Definition
|
|
Term
|
Definition
| CBP complex assembling on cap, TC assembling, 43S assembling with eIFs1, 1A, etc., polyA binding protein --> all coming together for attachment of 40S subunit to 5' end of the mRNA |
|
|
Term
| second step of initiation |
|
Definition
|
|
Term
|
Definition
|
|
Term
| fourth step of initiation |
|
Definition
|
|
Term
| how could you alter the presence/amount of any eIF? |
|
Definition
| alter expression of the gene encoding for any of the eIF |
|
|
Term
| how could you alter the functionality of any of the eIFs? |
|
Definition
| regulating the activity of a helicase |
|
|
Term
| 2 kinds of interactions that could regulate initiation |
|
Definition
1. protein-protein
2. protein-RNA |
|
|
Term
| what does it mean that regulation can be global |
|
Definition
| turn up or down translation of all or most mRNAs in a cell/sample/tissue etc. |
|
|
Term
| what does it mean that regulation can be local/specific? |
|
Definition
| turn up or down translation of one or a few mRNAs but not all of them |
|
|
Term
| 4 ways regulation of translation initiation can be achieved |
|
Definition
1. expression of a gene encoding one of the eIFs
2. PTMs of any of the eIFs
3. alter protein-protein interactions
4. alter protein-RNA interactions |
|
|
Term
| example of an external signal that could cause translational regulation |
|
Definition
| maybe the environment is changing & cells need to grow faster or slower |
|
|
Term
| example of hard-wired regulation of translation |
|
Definition
| build into your genome is a plan to alter translation at specific times at the lifetime of your cell on purpose |
|
|
Term
| does regulation only occur in one way? |
|
Definition
| no (there are multiple mechanisms & multiple steps at which it might occur) |
|
|
Term
| what does it mean that regulation can be global or local? |
|
Definition
global = most or all
local = more specific; one or a few mRNA |
|
|
Term
| 4 ways regulation can occur in response to signals |
|
Definition
1. external signals
2. cell specific
3. pathway specific
4. hard wired (such as in development) |
|
|
Term
| how does viral infection work? |
|
Definition
| shut off most host protein synthesis in favor of viral protein synthesis |
|
|
Term
| viral protease cleaves G...cleavage of a protein is an example of a ______ |
|
Definition
| post-translational modification |
|
|
Term
| viral infection can induce miRNA to block expression of eIF4E...this would result in no ______ |
|
Definition
|
|
Term
| viral infection can decrease phosphorylation of E...this makes E ______ |
|
Definition
|
|
Term
| viral infection can increase amount of 4E-binding protein....4E-binding protein binds 4E so ______ |
|
Definition
| it sequesters it away from being able to bind to the cap |
|
|
Term
| why can viruses still do protein synthesis under infection conditions? |
|
Definition
|
|
Term
| when does most regulation occur? |
|
Definition
| when the 3' end forms the complex with the 5' end to recruit the 40S subunit |
|
|
Term
| can a host mRNA have an IRES? |
|
Definition
|
|
Term
| why would a host mRNA have an IRES? |
|
Definition
| enables them to be specifically translated under stress conditions |
|
|
Term
| what did fruit fly embryos demonstrate about protein translation during development? |
|
Definition
| certain genes would be active in one part of the embryo & not another |
|
|
Term
| there is a 6 - 8 nucleotide long sequence found at the _______ that binds proteins that somehow mess up the attachment complex |
|
Definition
|
|
Term
| fruit fly example of protein at 3' UTR that messes up attachment complex |
|
Definition
| hunchback mRNA --> pumilio binds 3' UTR --> nanos binds pumilio --> another protein binds nanos --> that protein prevents E from binding to the cap |
|
|
Term
| TOR (target of rapamycin) |
|
Definition
| master regulator of growth |
|
|
Term
|
Definition
|
|
Term
| TOR = inactive when ______ |
|
Definition
|
|
Term
| genes found in vertebrates that regulate body plan |
|
Definition
|
|
Term
| Hox mRNA translation is _______ |
|
Definition
| temporally & spatially regulated |
|
|
Term
| Hox mRNA have an IRES, but they do have a cap...why is this? |
|
Definition
| they also have a TIE (sequence in the 5' UTR) that prevents use of the cap & thus the mRNA can only be translated through the IRES |
|
|
Term
| What is weird about histone mRNA? |
|
Definition
| have no poly-A (therefore no poly-A binding protein either) |
|
|
Term
| why do histones have a weird method to initiate translation? |
|
Definition
| need to be made at a very specific time (during replication!) |
|
|
Term
| in the ______, there are short sequences that can base pair with a miRNA |
|
Definition
|
|
Term
| ______ are specifically present in some cells at some times to base pair with the 3' UTR of some mRNA |
|
Definition
|
|
Term
|
Definition
| turnover of the mRNA to which it binds |
|
|
Term
| cis element involved in regulation via miRNA |
|
Definition
| sequence in the 3' UTR that binds the miRNA which binds the protein which binds another protein which induces turnover, etc. |
|
|
Term
| how would scanning be regulated by a protein binding between the ribosome & the AUG? |
|
Definition
| impede ribosome scanning down the mRNA |
|
|
Term
| how would scanning be regulated by an RNA secondary structure forming between the ribosome & the AUG? |
|
Definition
| impede ribosome scanning down the mRNA |
|
|
Term
| many diseases are caused by mutations in the pathway that regulate _____ |
|
Definition
|
|
