Chapter 9 Flashcards
translation is???????? (1-5)
- is the synthesis of proteins as directed by mRNA templates
- is the only first step in the formation of a functional protein
- polypeptides chains must fold in a appropriate conformations and often undergo various processing steps, sorting, and transport
- gene expression is regulated at the level of translation in both prokaryotic and eukaryotic cells
- there are also multiple controls on the amounts and activities of intracellular proteins, which ultimately regulate all aspects of cell behavior
- proteins are synthesized from mRNA templates by a process that has been highly conserved throughout evolution.
all mRNAs are read in the _____________. and polypeptide chains are sythesized from the amino to the carboxy terminus
5’ to 3’ direction
- ________ is specified by ____________ in the mRNA
each amino acid is specified by three bases (a codon) in the mRNA
- translation is carried out on_________, with tRNAs serving as adaptors
ribosomes
- protein synthesis involves interactions between 3 types of RNA (_______,_________,________), plus other proteins
mRNA, tRNA, rRNA
______ align amino acids with corresponding _________. They are ____ nucleotide long and have characteristic cloverleaf structures resulting from base pairing between different regions
tRNAs
Codons on the mRNA template
they are 70-80 nucleotides long
structure of RNAS
- all tRNAs fold in compact ________ shapes, to fit onto ribosomes during translation
fold into L shapes
structure of tRNAS
- tRNAs have the sequence _______ at the _____ terminus, and amino acids are covalently attached to the ribosomes of the terminal adosine
- sequence of CCA at the 3’ terminus
sequence CCA
at terminus 3’
structure of tRNAs
- The _________ binds to the appropriate codon by complementary base pairing
anticodon loop
attachment of amino acids to specific tRNAs is mediated by enzymes called __________________
each of these 20 enzymes recognizes a single aminoale amino acid, as well as the correct tRNA to which it should attach
aminoacyl tRNA synthetases
attachment of amino acids to tRNAs
this occurs in two steps
- the amino acid is joined to AMP, forming __________
- the amino acid is transferred to ____________ of the tRNA and AMP is released
- the amino acid is joined to AMP, forming aminoacyl AMP
2. the amino acid is transferred to the 3’ CCA terminus of the tRNA and AMP is released
translation of mRNA
- the amino acid is then aligned on the mRNA template by complementary base paring
- most amino acids are specified by more than one codon
- Cells have about 40 different tRNAs for the 2- different amino acids
- some tRNAs can reconize more than one mRNA codon, as a result of _________ at the _____ codon position
this allows G to pair with U, and inosine (I) to pair with U,C,or A
(guanosine is modified to inosine in the anticodons of some tRNAS)
- as a resulting of NONSTANDARD BASE PARING (WOBBLE) at the 3rd CODON POSITION
______________ are named according to their sedimentation rates in ultracentrifugation. ______ for bacteria and __________ for eukaryotics
Cells have many ribosomes, illustrating the importance of protein synthesis. E. coli has about 20,000; growing mammalian cells can have ten million
ribosomes
70s for bacteria
80s for eukaryotic
all ribosomes have ______ subunits. Each subunit contains ____________ and characteristic proteins
the subunits of eukaryotic ribosomes are larger and have more proteins than prokaryotic ribosomes
TWO subunits
contains rRNA and characteristic proteins
ribosome can be formed in vitro by ___________ from purified ribosomal proteins and rRNAs, which provides important experimental tool
self assembly
rRNAs form characterisitic secondary structures by ____________.
Subsequent folding results in distinct 3D stuctures
complementary base pairing
unambigous evidence for rRNA catalysis came from high-resolution structural analysis of ______ ribosomal subunit, in 2000
50s
ribosomal proteins are absent from the site of the peptidyl transferase reaction showing that _____________________.
It is now thought that ribosomal proteins play a largely structural role, and the large ribosomal subunit functions as a ribozyme
this is evolutionary implications: RNAs are thorugh to have benn the first self-replicating macromolecules
rRNA is responsible for catalyzing peptide bond formation
mRNAs have noncoding ________________ at the end.
most eukaryotic mRNAs are ____________, encoding in a single protien
prokaryotic mRNAs are often _________-, encoding multiple proteins, each of which is translated from an independent start site
untranslated regions (UTRs)
mono-cistronic
poly-cistronic
in both prokaryotes and eukaryotes, translation always _________, usually encoded by ______
always starts with methionine
usually encoded by AUG
the signals that identify initiation codons are different in prokaryotic and eukaryotic cells
- initiation codons in bacterial mRNAs are preceded by ___________, that aligns the mRNA on the ribosomes
They can initiate translation at the 5’ end of an mRNA and at internal initiation sites of polycistronic mRNAS
- eukaryotic mRNAs are recognized by the _____________ at the 5’ terminus.
the ribosomes then scan downstream of this cap until they encounter the initiation codon
- SHINE-DALGARNO SEQUENCE
2. 7-METHYLGUANOSINE CAP
translation occurs in 3 stages: _________,________, and ______.
a specific initatior _________ and the mRNA binds to the ______________________
initiation, elongation, termination
a specific initator METHIONYL tRNA and the mRNA bind to the SALL RIBOSOMAL SUBUNIT
the LARGE RIBOSOMAL unit then joins, forming a functional ribosome
many nonribosomal protiens are also required for various stages of translation? (true/false)
true
in _________________, initiation starts with a 30S ribosomal subunit bound to __________________- IF1 and IF3
then the mRNA, initator N-formylmethionyl (fMet) tRNA, and IF2 (bound to GTP) joint the complex
IF1 and IF3 are released, a 50S subunit binds to the complex and IF2 is released
in bacteria
initation factors
______________- initiation is more ocmplex, and requires at least 12 proteins, designated elFs (eukaryotic initation factors)
the initiator ______________ is bound to ____________ and the _____ is brought to the complex by __________-
in eukaryotes
the initiator METHIONYL tRNA is BOUND TO eLF2, and the mRNA IS BROUGHT TO THE COMPLEX by eLF4E
“Initation of translation in cells”
- ribosome scan down the mRNA to identify ____________
- ATP hydrolysis
- when AUG is identified, ______ triggers the hydrolysis of GTP bound to _____
- release of 2IF2 and other initation facotrs
- initation factors are then released, and the 60S subunit joins the complex
identify AUG initiation codon
when AUG is identified, eLF5 tiggers hydrolysis of GTP bound to elF2
“elongation stage of translation”
- the mechanism of elongation in prokaryotic and eukaryotic cells is similar
- the ribosomes has three binding sites: _____,_________,________-“
the initiator _____________ is bound at ________-
the __________ binds to the _______
- three binding sites: P (peptidyl) , A (aminoacyl), and E (exit)sites
the initiator METHIONYL tRNA is bound at the P SITE
the NEXT AMINOACYL tRNA bind to the A SITE
“elongation stage of translation”
hydrolysis of GTP bound to eEF1a and release of the ________
then the peptide bond is formed, catalyzed by the large ribosomal subunit and the now initator tRNA is at the P site
release of the elongation factor
“translation of mRNA”
The steps of ___________
- ribosome then moves three nucleotides laong the mRNA, positioning the ext codon in an empty A site
- This step translocates the peptidyl tRNA from A to P, and the uncharged tRNA from P to E
translocation
“translation of mRNA”
translocation requires another _____________ (EF-G in prokaryotes and ________ in eukaryotes) and is coupled to _________
translation requires another ELONGATION FACTOR (EF-G in prokaryotes, eEF2 in eukaryotes) and is coupled to GTP HYDROLYSIS`
“regeneration of eEF1 a GTP”
as elongation continues, the __________ (or EF-Tu) released from the ribosome bound to GDP must be reconverted to its GTP form
this requires another elongation factor, _____ (EF-T in prokaryotes). regulation of eEF1 alpha by GTP binding and hydrolysis is a common method of protein regulation
eEF1a
eEF1b
“termination of translation”
elongation continues until a _________ ( UAA,UAG, UGA) is translocated into the ____________.
_________ recognize the signals and terminate protein synthesis
in prokaryotic cells RF1 recognizes UAA or UAG, RF2 recognizes UAA or UGA.
in eukaryotic cells eRF1 recognizes all 3 stop codons
elongation continues until a STOP CODON is located into the A SITE
RELEASE FACTORS recognize the sigals and terminate protein synthesis
mRNAs can be translated simultaneously by several ribsomes. once a ribosome has moved away from the initiation site, another can bind to the mRNA and begin sythesis.
a group of ribsomes bound to an mRNA molecule is called a polyribosome, or a __________
polysome`
regulation of translation plays a key role in gene expression, include:
- ___________________
- ___________________
Global translation activity is modulated in response to _____, _____________, ______________.
Example: regulation of ferritin translation (a protein that stores iron) by repressor proteins: when iron is absent, ______________________________ binds to the iron response elements (IRE) in the 5’ UTR, blocking translation
- translation repressor proteins
- noncoding microRNAs
global translational activity is modulated in response to STRESS, NUTRIENT AVAILABILITY, and GROWTH FACTOR STIMULATION.
when iron is absent, IRON REGULATORY PROTEIN (IRP)
Some translational repressors bind to specific sequences in the 3’ UTR
some bind to initiation factor eLF4E, interfering with itis interaction with eLF4G and inhibiting initiation of translation
General
______________________-mediated by short double-stranded RNAs, is used as an experimental tool to block gene expression at the level of translation
RNA interference (RNAi)
in cells, it is an important mechanism of translational regulation. RNA interference is mediated by: two types of small RNAS mediated RNA interference
small interfering RNAs (siRNAs)- produced from __________ by nuclease Dicer
MicroRNAs (miRNAs)-transcribed by _________________, then cleaved by nucleases Drosha and Dicer
doulbe stranded RNAS
RNA polymerase II
one strand of miRNA or siRNA is incorporated into an RNA induced silencing complex (RISC)
siRNAs generally pair with their targets and induce cleavage of the mRNA
most miRNAs from ___________ that repress translation
mismatches
as many as 1000 miRNAs are encoded in mammals; each can target up to 100 different mRNAs
up to one-half of protein-coding genes may require regulatation by __________.
they are important in embryonic development, and may play a role in cancer and other diseases
miRNA
translation can also be regulated by modification of initiation factors. This results in a global effects on overall translational activity rather than translation of specific _____________
mRNAs
__________________________ by regulatory ________________ blocks the exchange of bound GDP for GTP, inhibiting initiation of translation
phosphorylation of eLF2 and elF2B
protein kinases
feedback inhibition is an example of ___________________, in which a regulatory molecule binds to an enzyme site that is distinct from the catalytic site
allosteric regulation
“phosphorylation and other modifications”
phosphorylation is ________; can activate or inhibit proteins in response to environmental signals
catalyzes by ______________, which transfer phosphate groups from ATP to the hydroxyl groups of side chains of serine, threonine, or tyrosine
phosphorylation is reversible
catalyzed by PROTEIN KINASE
phosphorylation is reversed by ______________ , which catalyze hydrolysis of phosphorylated amino acids
protein kinases are often components of signal transduction pathways.
Sequential action of a series of protein kinases can transmit a signal from the cell surface to target proteins in the cell, resulting in changes in cell behavior in response to environmental stimuli
protein phosphatases
Example: in muscle cells epinphrine signals breakdown of glycogen to glucose-1-phosphate, providing energy for increased muscular acitivity
this is catalyzed by _____________ phosphorylase, which is regulated by protein kinase
the signalling pathway is initiated by allosteric regulation-epinephrine binds to cell surface receptor, and cAMP binds to cAMP-dependent kinsase
the sinal is then transmitted to its target by the sequental action of protien kinase
catalyzed by glycogen phosphorylase
other covalent modifications include:
acetylation of lysine
methylation of lysine and arginine
nitrosylation (addiiton of NO groups) to cysteine
glycosylation of serine and threonine
some proteins are regulated by covalent attachment of _________.
addition of _____________ and other ubiquitin like proteins, such as __________, affect a variety of function
attachment of polypeptides
addition of ubiquitin
such as SUMO
addition of ubiquitin (ubiquitylation) is a multistep process
the specificity of ________________________ selectivity targets proteins for degration
E3 enzymes
“protein- protein interactions”
many proteins consist of multiple subunits; interactions between them can regulate protein activity
Example: cAMP-dependent protein kinase has two _____________ and two __________ subunits in the inactive forms
cAMP binds to the regulatory subunits, which induces conformational change and dissociation of the complex
the free catalytic subunits are then enzymatically active protein kinases
cAMP acts as an allosteric regulator by altering protein-protein interactions
cAMP-dependent protein kinase has two REGULATORY and two CATALYTIC subunits in active form
protein levels in the cells are determined by rates of __________ and ________
half-lives of proteins vary greatly; differential rates of degradation are important in cell regulation
many regulatory proteins have short half lives; this allows levels to change quickly in response to external stimuli
faulty or damage protein are recognized and rapidly degraded
protein levels in cells are determined by RATES OF SYNTHESIS and RATES OF DEGRADATION
the major pathway of protein degradation in eukaryotes is the __________________.
________ is highly conserved in all eukaryotes
ubiquitin-proteasome pathway
ubiquitin
ubiquitin is attached to the amino group of the side chain of a lysine residue, then more are added to form a chain.
polyubiquinated proteins are recognized and degraded by a large protease complex the _________________–
the proteasome
what are the four stages of mitosis?
phrophase
metaphase
anaphase
telophase
many proteins that control fundamental cellular processes are targets for regulated ___________ and ____________
example: cyclins that regulate progression through the divsion cycle of eukaryotic cells
ubiquitylation and proteolysis
entry of cells into mitosis is controlled in part by ___________, a regulatory subunit of Cdk1 protein kinase
the active cyclin B-Cdk1 complex induces entry into ____________
degradation of cyclin B by the proteasome then leads to inactivation of the Cdk1 kinase, allowing the cell to exit mitosis and return into interphase
cyclin B
mitosis
protein degradation can also take place in _________________- membrane-enclosed organelles that contain digestive enzymes, including proteases
lysosomes digest extracellular proteins taken up by endocytosis, and take part in turnover of organelles and proteins
containment of digestive enzymes in lysosomes prevents uncontrolled degradation of cell contents
proteins move into lysosome by _________; vesicles (autophagosomes) enclose small areas of cytoplasm or organelles and then fuse with lysosomes
lysosomes
autogphagy
autophagy is activated in nutrient starvation, allowing cells to degrade ____________ and ________ and reutilize the components
autophagy also plays a role in many developmental processes, such as insect metamorphosis, which involve extensive tissue remodeling
nonessential proteins
organells
