EXAM 3 Flashcards
the synthesis of proteins as directed by mRNA templates
Translation of mRNA
Translation of mRNA is _____ in the formation of a functional protein.
the first step
____________ must fold into appropriate conformations and often undergo various processing steps, sorting, and transport.
Polypeptide chains
Gene expression is regulated at the level of _________ in both prokaryotic and eukaryotic cells.
translation
these ultimately regulate all aspects of cell behavior
intracellular proteins
polypeptide chains are synthesized from the __________ to the ___________
amino; carboxy terminus
Each amino acid has:
3 bases - a codon in the mRNA
tRNAs align amino acids with corresponding _________________________
codons on the mRNA template
They are 70–80 nucleotides long and have characteristic cloverleaf structures.
tRNAs
All tRNAs fold into:
compact L shapes.
Which sequence is at the 3’ terminus
CCA
This binds to the appropriate codon by complementary base pairing.
anticodon
Attachment of amino acids to specific tRNAs by these enzymes
aminoacyl tRNA synthetases.
Each of ___ enzymes recognizes a single amino acid, and correct tRNA.
20
Attachment of amino acids to tRNAs occurs in two steps:
- Amino acid join AMP – form aminoacyl AMP.
- Amino acid is transferred to the 3′ CCA terminus of the tRNA and AMP is released.
The amino acid is aligned on the mRNA template by:
complementary base pairing.
most amino acids are specified by: (how many codons)
more than one
____ different tRNAs for the 20 different amino acids.
40
Some tRNAs can recognize more than one mRNA codon, as a result of:
nonstandard base pairing (wobble) at the 3rd codon position.
Nonstandard base pairing allows G to pair with __, and inosine (I) to pair with ________.
U; U, C or A
Ribosomes are named according to their:
sedimentation rates in ultra-centrifugation
bacterial ribosome name
70S
eukaryotic ribosome name
80S
Amount of ribosomes in growing mammalian cells
ten million
Ribosomes have _____ subunits
Two
Ribosomal subunits contain:
rRNA and proteins
rRNA is responsible for:
catalyzing peptide bond formation
The large ribosomal subunit functions as a
ribozyme.
mRNAs have noncoding __________ at the ends.
untranslated regions (UTRs)
Most eukaryote mRNAs are _________, encoding a single protein.
mono-cistronic
Prokaryotic mRNAs are often _________, encoding multiple proteins, each of which is translated from an independent start site.
poly-cistronic
In both prokaryotes and eukaryotes, translation always starts with:
Methionine (encoded by AUG)
Initiation codons in bacterial mRNAs are preceded by a ______________, that aligns the mRNA on the ribosome.
Shine-Dalgarno sequence
Eukaryotic mRNAs are recognized by __________________ at the 5′ terminus.
the 7-methylguanosine cap
3 stages of translation:
- Initiation
- Elongation
- Termination
First step of translation initiation
a specific initiator methionyl tRNA and the mRNA bind to the small ribosomal subunit.
Second step of translation initiation
The large ribosomal unit then joins, forming a functional ribosome.
A group of ribosomes bound to an mRNA molecule
polysome
In eukaryotes initiation is complex, and requires at least ____ proteins, designated eIFs (eukaryotic initiation factors).
12
The initiator methionyl tRNA is bound to ____ and the mRNA is brought to the complex by ______.
eIF2
eIF4E
Ribosome scan down the mRNA to identify:
AUG initiation codon
When AUG is identified, ____ triggers the hydrolysis of GTP bound to _____.
eIF5
eIF2
Initiation factors are released, and the ____ subunit joins the complex.
60S
In elongation, these are the 3 binding sites on the ribosome:
Peptidyl (P)
Aminoacyl (A)
Exit (E)
The initiator methionyl tRNA is bound at the ____ site.
P
The next aminoacyl tRNA binds to the ____ site
A
Which elongation factor brings the aminoacyl tRNA to the ribosome?
eEF1α
Translocation (3 steps)
- Ribosome moves three nucleotides along the mRNA, positioning the next codon in an empty A site.
- This step translocates the peptidyl tRNA from A to P, and the uncharged tRNA from P to E.
- A new aminoacyl tRNA binds to the A site and induces release of the uncharged tRNA from the E site.
Translocation requires another elongation factor _______ and is coupled to GTP hydrolysis.
eEF2
As elongation continues, the eEF1α (or EF-Tu) released from the ribosome bound to GDP must be:
reconverted to its GTP form.
Regulation of eEF1α by GTP binding and hydrolysis is a common method of:
protein regulation.
Elongation continues until a _______ is translocated into the A site.
stop codon
examples of stop codon sequences
UAA
UAG
UGA
___________ recognize the signals and terminate protein synthesis.
Release factors
Some translational repressors bind to:
specific sequences in the 3′ UTR.
Some translational repressors bind to initiation factor _____, interfering with its interaction with eIF4G and inhibiting initiation of translation.
eIF4E
mediated by short double-stranded RNAs, this is used as an experimental tool to block gene expression at the level of translation.
RNAi (RNA interference)
RNA interference is mediated by: (2 things)
siRNAs produced from double stranded RNAs
miRNAs transcribed by RNA polymerase II
Most miRNAs form:
mismatches that repress translation.
siRNAs generally pair perfectly with their targets and induce:
cleavage of the mRNA.
These are important in embryonic development, and may play a role to cancer and other diseases.
miRNAs
Translation can also be regulated by:
modification of initiation factors
Phosphorylation of eIF2 and eIF2B by _______ blocks the exchange of bound GDP for GTP, inhibiting initiation of translation.
regulatory protein kinases
In the absence of growth factors, the nonphosphorylated 4E-BPs bind to _____ and inhibit translation.
eIF4E
Polypeptide chains must undergo folding and other modifications to become:
functional proteins.
3-D protein conformation results from interactions between:
the side chains of the amino acids.
act as catalysts that assist the self-assembly process without becoming part of the folded protein.
Chaperones
Chaperones bind to and stabilize:
unfolded or partially folded polypeptides intermediates.
Chaperones bind to polypeptide chains that are:
still being translated on ribosomes.
The chain must be protected from ___________ until synthesis of an entire domain is complete.
aberrant folding or aggregation with other proteins
Chaperones also stabilize ___________ during their transport into organelles.
unfolded polypeptide chains
Many chaperones were initially identified as ____________, expressed in cells subjected to high temperatures.
heat-shock proteins (Hsp)
Hsp70 proteins stabilize polypeptide chains during translation by binding to:
short hydrophobic segments.
The polypeptide is then transferred to a _______, where folding takes place
chaperonin
Chaperonins consist of:
subunits arranged in 2 stacked rings to form a double-chambered structure.
Chaperonin structure isolates the protein from:
the cytosol and other unfolded proteins.
catalyzes disulfide bond formation and is abundant in the ER, where an oxidizing environment allows (S—S) linkages.
Protein disulfide isomerase (PDI)
catalyzes isomerization of peptide bonds that involve proline residues.
Peptidyl prolyl isomerase
Isomerization between the cis and trans configurations of prolyl-peptide bonds could otherwise be a ________ in protein folding.
rate-limiting step
Process where cleavage of the polypeptide chain removes portions such as the initiator methionine from the amino terminus.
Proteolysis
Proteolytic processing includes formation of ________ by cleavage of larger precursors.
active enzymes or hormones
Example of proteolytic processing
Insulin is synthesized as a precursor polypeptide that goes through 2 cleavages to produce the mature insulin.
Most enzymes are controlled by changes in conformation, often as a result of:
binding small molecules.
Small molecule regulation is common in controlling metabolic pathways by:
feedback inhibition.
GDP- bound form of protein is:
Inactive
GTP- bound form of protein is:
Active
The regulation of translation factors such as ______ by GTP binding is a common mechanism of by which the activities of intracellular proteins are controlled.
eEF1α
_________ is reversible; can activate or inhibit proteins in response to environmental signals.
Phosphorylation
Phosphorylation is catalyzed by _________, which transfer phosphate groups from ATP to the hydroxyl groups of side chains of serine, threonine, or tyrosine.
protein kinases
Phosphorylation is reversed by __________, which catalyze hydrolysis of phosphorylated amino acids.
protein phosphatases
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.
Interactions between ________ can regulate protein activity.
protein subunits
cAMP-dependent protein kinase components
2 regulatory subunits
2 catalytic subunits
cAMP acts as an ________ by altering protein-protein interactions.
allosteric regulator
Protein levels in cells are determined by:
rates of synthesis and rates of degradation.
Many regulatory proteins have _______; this allows levels to change quickly in response to external stimuli.
short half lives
The major pathway of protein degradation in eukaryotes
ubiquitin-proteasome pathway.
attached to the amino group of the side chain of a lysine residue, then more are added to form a chain.
Ubiquitin
The specificity of ________ selectively targets proteins for degradation.
E3 enzymes
These are recognized and degraded by a large protease complex, the proteasome.
Polyubiquinated proteins
4 stages of Mitosis
- Prophase
- Metaphase
- Anaphase
- Telophase
Many proteins that control fundamental cellular processes are targets for:
regulated ubiquitylation and proteolysis.
Example of regulated ubiquitylation and proteolysis
Cyclins regulate progression through the division cycle of eukaryotic cells.
separates the nuclear contents from the cytoplasm
Nuclear envelope
The nuclear envelope controls traffic of _______ through nuclear pore complexes, and plays a critical role in regulating gene expression.
proteins and RNAs
The nuclear envelope consists of: (3 things)
2 nuclear membranes
Nuclear lamina
Nuclear pore complexes
The outer membrane of the nuclear envelope is continuous with:
endoplasmic reticulum (ER).
The inner membrane of the nuclear envelope has proteins that bind to the:
Nuclear lamina
Nuclear membranes are:
phospholipid bilayers
__________ are the only channels for small polar molecules, ions, and macromolecules.
Nuclear pore complexes
a fibrous mesh that provides structural support
Nuclear lamina
intermediate filament proteins that associate to form higher order structures.
lamins
Two lamins interact to form a:
dimer
the α-helical regions wind around each other to form a:
coil
_____________ associate with each other to form the lamina.
Lamin dimers
Lamins bind to:
Inner membrane proteins
Chromatin
________ are composed of about 30 different pore proteins (nucleoporins).
Nuclear pore complexes
RNAs synthesized in the nucleus must be exported to the ________ for protein synthesis.
cytoplasm
Proteins needed for nuclear functions must be imported from:
synthesis sites in the cytoplasm.
Molecules pass through pore complexes by two mechanisms:
- Small molecules and protein (<40kd) pass freely in either direction
- Proteins and RNAs are selectively transported; recognized by specific signals.
______ are connected to rings at the nuclear and cytoplasmic surfaces.
8 spokes
The spoke-ring assembly surrounds a:
central channel.
Proteins that must enter the nucleus have amino acid sequences called:
nuclear localization signals.
nuclear localization signals are recognized by:
nuclear transport receptors
The amino acid sequence responsible for nuclear localization was determined using:
T antigen mutants.
The T antigen nuclear localization signal is a single stretch of amino acids in rich basic amino acid residues – (2 types)
lysine and arginine.
The nuclear localization signal of ________ is bipartite, consisting of a Lys-Arg sequence, followed by a Lys-Lys-Lys-Lys sequence located ten amino acids farther downstream.
nucleoplasmin
Nuclear localization signals (NLS) are recognized by receptors called _______, which carry proteins through the nuclear pore complex.
importins
Importins work in conjunction with the GTP-binding protein _____, which controls directionality of movement.
Ran
