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Bio 323 - Exam Two > Translation > Flashcards

Translation Flashcards

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1
Q

By convention, codons are always written with the 5ʹ-terminal nucleotide to the _____

A

left.

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2
Q

how many possible nucleotide combinations are there?

A
  • Nucleotides in mRNA are read in consecutive groups of three.
  • RNA is a linear polymer of four different nucleotides.
  • so there are 4 × 4 × 4 = 64 possible combinations
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3
Q

why do organisms contain many different types of tRNA?

A
  • Each type of tRNA molecule can be attached to only one type of amino acid, so each organism has many types of tRNA.
  • Because the genetic code contains multiple codons that specify the same amino acid, there are several tRNA molecules bearing different anticodons which carry the same amino acid.
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4
Q

aminoacyl tRNA synthetase

A

an enzyme that attaches the appropriate amino acid onto its tRNA

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5
Q

whats special about the ends of tRNA?

A
  • There’s two regions of unpaired nucleotides situated at either end of the tRNA.
  • One of these regions forms the anticodon, a set of three consecutive nucleotides that pairs with the complementary codon in an mRNA molecule.
  • The other is a short single-stranded region at the 3ʹ end of the molecule; this is the site where the amino acid that matches the codon is attached to the tRNA.
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6
Q

what is a wobble tRNA

A
  • Some amino acids have more than one tRNA (because the genetic code contains multiple codons that specify the same amino acid)
  • some tRNAs are constructed so that they require accurate base-pairing only at the first two positions of the codon and can tolerate a mismatch (or wobble) at the third position
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7
Q

Why do we see the pattern that alternate codons for the same amino acid tend to differ only at the 3rd position?

A

because of wobble base-pairing

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8
Q

what synthesizes tRNA

A

Eukaryotic tRNAs are synthesized by RNA polymerase III.

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9
Q

How many synthetase enzymes are required for tRNA in eukaryotes?

A

Most cells have a different synthetase enzyme for each amino acid (that is, 20 synthetases in all); one attaches glycine to all tRNAs that recognize codons for glycine, another attaches alanine to all tRNAs that rec-ognize codons for alanine, and so on.

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10
Q

How many synthetase enzyme are required for tRNA in bacteria?

A

Many bacteria have fewer than 20 synthetases, and the same synthetase enzyme is responsible for coupling more than one amino acid to the appropriate tRNAs

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11
Q

Start codons

A

AUG/ATG

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12
Q

stop codons

A

UAA/TAA
UGA/TGA
UAG/TAG

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13
Q

Where does the tRNA anticodon base pair to?

A

the mRNA

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14
Q

which way is mRNA written?

A

5’-____-3’

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15
Q

aminoacyl-­‐synthetases bind to their tRNAs with ____ _____

A

High specificity

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16
Q

Amino acid selectionby aminoacyl-­‐synthetase

A
  • 1st theres the affinity of the amino acid for the binding pocket.
  • in cases of similarity (such as isoleucine and valine which differ only by a methyl group) another step is needed.
  • the synthetase tries to force the adenylated amino acid into a second editing pocket in the enzyme. The precise dimensions of this pocket exclude the correct amino acid, while allowing access by closely related amino acids. In the editing pocket, an amino acid is removed from the AMP by hydrolysis.
17
Q

Ribozymes

A

Ribozymes (ribonucleic acid enzymes) are RNA molecules that are capable of catalyzing specific biochemical reactions, similar to the action of protein enzymes.

18
Q

what is the N-terminis analogous of?

What about the C-terminis?

A

N-term aka 5’

C-term aka 3’

19
Q

Each ribosome has how many binding sites?

A

one binding site for mRNA and three binding sites for tRNA.

20
Q

Once protein synthesis has been initiated, each new amino acid is added to the elongating chain in a cycle of reactions containing four major steps:

A
  • tRNA binding (step 1)
  • peptide bond formation (step 2)
  • large subunit translocation (step 3)
  • small subunit translocation (step 4).
  • As a result of the two translocation steps, the entire ribosome moves three nucleotides along the mRNA and is positioned to start the next cycle. (pg.343)
21
Q

3 tRNA binding sites

A
  • E= exit
  • P = polypeptide
  • A= aminoacylated/acceptor
22
Q

What are tRNA bindingand peptidyltransferase activesitescomposedof?

A

rRNA

23
Q

What parts of translation require energy?

A
  • Activation (ATP).
  • Initiation (GTP).
  • Elongation (GTP)
24
Q

How does activation use energy?

A

The amino acid reacts with ATP in the presence of aminoacyl-tRNA synthetase to form the
aminoacyl-AMP-aminoacyl-tRNA synthetase derivative/complex. (2 ATP’sare required to charge each amino acid).

25
Q

How does initiation use energy?

A

A small ribosomal (30S) subunit binds with a large ribosomal (50S) subunit following the hydrolysis of GTP to form the 70S ribosome.

26
Q

How does elongation use energy?

A

GTP is needed in order to translocate the ribosome down the mRNA

27
Q

GTPase Elongationfactors

A

couple GTP hydrolysis to large movements of the ribosome and tRNAs

28
Q

GTP-binding proteins

A
  • the phosphate is not attached directly to the protein; instead, it is a part of the guanine nucleotide GTP, which binds very tightly to a class of proteins known as GTP-binding proteins.
  • (also called GTPases because of the GTP hydrolysis they catalyze)
29
Q

Active vs Inactive conformations of GTP-binding proteins

A

In general, proteins regulated in this way are in their -active conformations have GTP bound. The loss of a phosphate group occurs when the bound GTP is hydrolyzed to GDP in a reaction catalyzed by the protein itself.
- Its GDP-bound state the protein is inactive. In this way, GTP-binding proteins act as on–off switches whose activity is determined by the presence or absence of an additional phosphate on a bound GDP molecule

30
Q

For GTPases, when id GTP/GDP bound?

A

GTP-binding proteins are controlled by regulatory proteins that determine whether GTP or GDP is bound, just as phosphorylated proteins are turned on and off by protein kinases.

31
Q

ras

A

monomeric GTPase

pg 157 & 158

32
Q

GTPase-activating protein

A
  • Ras is inactivated by a GTPase-activating protein (GAP).
  • GAP binds to the Ras protein and induces Ras to hydrolyze its bound GTP molecule to GDP (which remains tightly bound) and inorganic phosphate which is rapidly released.
33
Q

guanine nucleotide exchange factor

A
  • The Ras protein stays in its inactive, GDP-bound conformation until it encounters a guanine nucleotide exchange factor (GEF)
  • GEF binds to GDP-Ras and causes Ras to release its GDP.
  • Because the empty nucleotide-binding site is immediately filled by a GTP molecule, the GEF activates Ras by indirectly adding back the phosphate removed by GTP hydrolysis.
  • Thus, in a sense, the roles of GAP and GEF are analogous to those of a protein phosphatase and a protein kinase, respectively
34
Q

Is there more GTP or GDP in cells?

A

GTP is present in large excess over GDP in cells

Bio 323 - Exam Two (4 decks)

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