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Flashcards in RNA to Protein Deck (107):
1

The study of the mechanisms of transcription and translation

Molecular biology

2

Protein synthesis is very important in part because it is the last opportunity for

Regulating gene expression

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The genetic code is degenerate, with the exception that

The UGA stop codon encodes selenocysteine in humans

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Mutation that changes the codon to a termination codon

Nonsense mutation

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Mutation that changes the codon to another sequence coding the same amino acid

Silent muttion

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Mutation that changes the codon to a sequence that encodes an entirely different amino acid

Missense mutation

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What are the six features of a typical mammalian mRNA?

1.) 5' Cap
2.) 5' UTR
3.) Start codon (AUG)
4.) Stop codon (UAA)
5.) 3' UTR
6.) Poly A tail

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The region between the start and stop codon

Coding region

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Specialized nucleotide (7-methyl-GMP) that is required for binding of initiation factors

5' cap

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The start codon AUG codes for

Methionine

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What are the three stop codons

UGA, UAG, and UAA

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The sequence between the stop codon and the poly(A) tail, and the site of key regulatory sequences

3' UTR

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Protects mRNA from degredation and increases translational efficiency

-Un-templted

Poly(A) tail

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Deletion of a base can be disastrous because it will change the

Reading frame

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The 3' CCA end of tRNA is not trancribed, but is added after processing and it

Attaches to amino acids

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Recognize tRNAs and add the appropriate amino acid to them

aminoacyl tRNA synthetases

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Aminoacylation requires

ATP

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Recognize the anticodon as well as other structural features in the tRNA

aminoacyl tRNA synthetases

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The eukaryotic ribosome (80S) is made up of

1.) A large subunit (60S)
2.) A small subunit (40S)

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The ribosome is mostly RNA. Peptide bond formation occurs without the contribution of any protein, meaning the ribosome is a

ribozyme

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Fill the gap between the large and small subunits of the ribosome

tRNAs

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What are the three tRNA binding sites in a ribosome?

1.) A (aminoacyl) site: initial tRNA binding site for next codon
2.) P (peptidyl) site: where peptide bond is formed
3.) E (exit) site: tRNA is released

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Initiation and elongation occur simutaneously, yielding multiple ribosomes on a single mRNA molecule. This very large mRNA/ribosome complex is called a

Polysome

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Encompasses the assembly of the ribosome and mRNA and the positioning of the ribosome on the start codon

Initiation

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The first step of initiation is the formation of the

Pre-initiation complex (made up of elongation factors like GTP dependant elF2)

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The second step of initiation is the pre-initiation complex

Sans the mrNA for the AUG codon

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Part of the initiation complex that binds to the 5' cap

elF4E

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Part of the initiation complex the binds and delivers initiator Met-tRNA

-requires GTP

elF2

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PArt of initiation complex that serves as a scaffold protein that binds elF4E required for assembly of the pre-initiation complex

elF4G

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The initiator tRNA is special in that it is not used during

Elongation or to incorporate Met

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The initiator tRNA moves along the RNA searching for the first start codon. During this process, it utilizes

Helicase activity and ATP hydrolysis

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The third step of initiation is that after the start codon has been located, the

Large subunit joins the complex

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Causes elF2 release, signalling the large ribosomal subunit to bind

GTP hydrolysis

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A common theme in many steps of translation. It often provides a signal for the next step (i.e. the binding of the 60S subunit)

GTP-dependent release of factors

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The movement of the ribosome down the mRNA, coordinated with aminoacyl tRNA delivery

Elongation

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During initiation, the very first tRNA is bound in the P site. All subsequent tRNAs first bind to the

A site

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What is step one of elongation

Delivery of aa-tRNA to the A site and E site release

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The incoming tRNA is bound to the GTP-dependent factor

eEF1A

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What is step two of elongation?

GTP hydrolysis and eEF1A release, followed by proofreading

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What is step three of elongation?

eEF2 (w/ GTP) binding to catalyze translocation

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What is step four of elongation?

GTP hydrolysis and eEF2 release (completion of cycle)

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Binds to all canonical tRNA's (i.e. all tRNAs except the initiator tRNA and the selenocysteine tRNA

eEF1A

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A G-protein that is required for ribosome translocation

eEF2

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Occurs in the ribosomal A-site, where codon/anticodon pairs are "checked" by ribosome conformation

Proofreading

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Is there a terminator tRNA?

No

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A tRNA mimetic that catalyzes the release of the completed peptide, signalling termination

eRF1 (enzyme release factor 1)

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Unlike in eukaryotes, bacterial transcription and translation are

Coupled

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Bacterial mRNAs are different from eukaryotic mRNAs in that they are

Polycystronic (a single code encodes multiple proteins)

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In bacteria, initiation is dictated by a sequence upstream of the start codon, which directly base pairs to the ribosomal RNA. This is called the

Shine-Dalgarno sequence

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Bacterial ribosomes are smaller and sufficiently divergent from mammalian ribosomes, to allow

Selective inhibition by the ribosome inhibitor class of antibiotics

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Typically do have residual toxicity due to their effects on mitochondrial ribosomes, which are more similar to bacterial ribosomes

Ribosome inhibitors

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What are the sedimentation coefficients for the large and small ribosomal subunits of the prokaryotic ribosome?

30S and 50S for a 70S ribosome

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What are the prokaryotic counterparts for the following eukaryotic enzymes?

1.) eIF2
2.) eEF1A
3.) eEF2

1.) IF2
2.) EFTu
3.) EFG

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Post transcriptional, but pre-translational, regulation

mRNA editing

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The apolipoprotein B is made in the liver and intestine. However, the intestine requires a shorter version. Thus

apoB mRNA is edited to induce a premature stop codon for the intestinal apoB

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Short RNA molecules that base pair with mRNAs and regulate translation

micro RNAs (miRNAs)

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miRNAs usually bind to the 3' UTR and

inhibit translation

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A protein complex thought to physically impede translation initiation

RISC

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Many miRNAs are correlated with

Diseases

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Iron homeostasis is regulated by an

-binds the iron regulatory element (IRE) and prevents translation

Iron sensing protein (IRP)

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The IRP can not bind the IRE if it is bound to

+Fe2+

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Some mRNAs encoding proteins that regulate iron homeostasis contain an "iron response element (IRE)" that binds to an iron-sensing protein (IRP) that regulates

Translation or mRNA stability depending on cellular ion concentrations

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Nutritional status regulates

Translation

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Phosphorylation of an initiation factor (eIF2) causes translation inhibition in response to

1.) Low amino acid concentration
2.) Cellular stress (e.g. oxidative stress)
3.) Immune response
4.) Unfolded proteins

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To assist in re-binding GTP after hydrolysis, the G-protein eIF2 requires a

Guanine Nucleotide Exchange Factor (GEF) (which for eIF2 is eIF2B)

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GEFs are required because the

Affinity for GDP is much higher than that for GTP

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Under normal conditions, GDP is echanged for GTP by the action of eIF2B. However, poor nutrition (i.e. reduced amino acid concentrations) causes eIF2 phosphorylation, which

Causes eIF2 to bind eIF2B as an inactive complex.

68

What happens to protein synthesis when phosphorylated eIF2 binds eIF2B?

There will be an excess of inactive eIF2 (the GDP bound form), and protein synthesis slows dramatically

69

Hypoxia regulates

translation

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The mTOR (mammalian Target Of Rapamycin) signaling pathway represses translation in response tohypoxia by regulating the function of

eIF4E

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Is like a cellular rheostat - it upregulates
translation during growth and downregulates
during stress. It is constitutively in an
active state in order to keep growth in check.

The mTOR pathway

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Normoxia (growth conditions) induces

mTOR signaling

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Proteins that bind to eIF4E and inhibit translation

4EBPs

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When 4EBPs are phosphorylated, they are

Released from eIF4E (ending inhibition)

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The mTOR pathway is a key regulator of

4EBP phosphorylation

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Activation of mTOR (during growth) causes

4EBP phosphorylation and increased translation

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Inhibits mTOR, and thus allows 4EBP dephosphorylation and binding to eIF4E, causing decreased translation

Hypoxia

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What is often called the 21st amino acid?

deficiency causes hyperthyroidism

Selenocysteine (Sec)

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Selenocysteine incorporation requires alternative usage of the

UAG stop codon

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The deiodinases are required for TH synthesis, thus among other things, selenium is essential for

Proper thyroid function

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Selenocysteine incorporation requires a unique set of

Translation factors

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A specialized elongation factor, similar to eEF1A,
that binds to the Sec-tRNA

eEFSec

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A specialized tRNA that recognizes UGA codons and carries the selenocysteine amino acid

Sec-tRNA^Sec

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An RNA element in the 3' UTR required for Sec incorporation

SECIS element

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Binds to the SECIS element and assists in getting eEFSec ternary complex to the ribosome at UGA Sec codons

SECIS binding protein 2 (SBP2)

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Encoded by a UGA stop codon that has been "re-coded" to allow Sec-tRNA binding

Selenocystein

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Required for the "re-coding" of the stop codon

SBP2

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Caused by SBP2 mutations in humans because reduced Sec incorporation leads to reduced production of the deiodinases

Some rare forms of hypothyroidism

89

Creating more than one protein from a single mRNA

-Utilized by viruses like HIV

Ribosomal frameshifting

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A single mRNA can encode more than one protein product if the ribosomes are signaled to

Frameshift

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Frameshift signals include the

RNA pseudoknot, and an RNA sequence called the "slippery site"

92

The efficiency of frameshifting determines the amount of each protein that is

Made

93

Targets translation by modifying the elongation factor responsible for translocation (eEF2)

Diptheria toxin

94

Transcriptional regulation sometimes takes too long, for a faster response, we want

Translational regulation

95

Typically, a frame shift mutation will result in

Premature termination (Stop codon formation)

96

Typically, a ribozyme is an enzyme that can cleave

RNA

97

Place where you maintain the registry of the mRNA and maintain the reading frame. The actual function of the is still debated

E-Site

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Most proteins in the translation process are

-Act as switches to sequence the events of translation

G-proteins (GTP dependent)

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The pre-initiation complex comes across a lot of secondary structural motifs. In order to break these structures up, it relies on a

Helicase (Only step in protein synthesis that requires ATP)

100

Occurs in step 2 of elongation. If there are no errors, then we will get GTP hydrolysis and eEF1A release

Proofreading

101

Uses GTP hydrolysis to catalyzes the translocation mechanism that moves the new peptide from the A site to the P site

eEF2

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eEF2 binds into the A site, which forces the A site tRNAs to move into the P site. GTP hydrolysis allows the release of eEF2 from the A site and the ribosome shifts by

One codon

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Feedback on the initiation complex and physically block translation

RISC complex

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Can not bind the IRE and thus, translation is normal and we produce ferratin

Iron-bound iron regulatory protein

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Bind and inhibit eIF4E, the protein which binds to the cap to allow translation to occur

4E Binding Proteins (4EBP)

106

In children, deficiencies in selenium present as

Hypothyroidism

107

caused by SBP2 mutations in humans because reduced Sec incorporation leads to reduced production of the deiodinases

Some rare forms of hypothyroidism

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