Translation

Question 1

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

Answer 1

left.

Question 2

how many possible nucleotide combinations are there?

Answer 2

• 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

Question 3

why do organisms contain many different types of tRNA?

Answer 3

• 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.

Question 4

aminoacyl tRNA synthetase

Answer 4

an enzyme that attaches the appropriate amino acid onto its tRNA

Question 5

whats special about the ends of tRNA?

Answer 5

• 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.

Question 6

what is a wobble tRNA

Answer 6

• 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

Question 7

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

Answer 7

because of wobble base-pairing

Question 8

what synthesizes tRNA

Answer 8

Eukaryotic tRNAs are synthesized by RNA polymerase III.

Question 9

How many synthetase enzymes are required for tRNA in eukaryotes?

Answer 9

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.

Question 10

How many synthetase enzyme are required for tRNA in bacteria?

Answer 10

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

Question 11

Start codons

Answer 11

AUG/ATG

Question 12

stop codons

Answer 12

UAA/TAA
UGA/TGA
UAG/TAG

Question 13

Where does the tRNA anticodon base pair to?

Answer 13

the mRNA

Question 14

which way is mRNA written?

Answer 14

5’-____-3’

Question 15

aminoacyl-­‐synthetases bind to their tRNAs with ____ _____

Answer 15

High specificity

Question 16

Amino acid selectionby aminoacyl-­‐synthetase

Answer 16

• 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.

Question 17

Ribozymes

Answer 17

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

Question 18

what is the N-terminis analogous of?

What about the C-terminis?

Answer 18

N-term aka 5’

C-term aka 3’

Question 19

Each ribosome has how many binding sites?

Answer 19

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

Question 20

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:

Answer 20

• 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)

Question 21

3 tRNA binding sites

Answer 21

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

Question 22

What are tRNA bindingand peptidyltransferase activesitescomposedof?

Answer 22

rRNA

Question 23

What parts of translation require energy?

Answer 23

• Activation (ATP).
• Initiation (GTP).
• Elongation (GTP)

Question 24

How does activation use energy?

Answer 24

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).

Question 25

How does initiation use energy?

Answer 25

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

Question 26

How does elongation use energy?

Answer 26

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

Question 27

GTPase Elongation factors  

Answer 27

couple GTP hydrolysis to large movements of the ribosome and tRNAs

Question 28

GTP-binding proteins

Answer 28

- 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)

Question 29

Active vs Inactive conformations of GTP-binding proteins

Answer 29

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

Question 30

For GTPases, when id GTP/GDP bound?

Answer 30

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.

Question 31

ras

Answer 31

monomeric GTPase | pg 157 & 158

Question 32

GTPase-activating protein

Answer 32

- 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.

Question 33

guanine nucleotide exchange factor

Answer 33

- 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

Question 34

Is there more GTP or GDP in cells?

Answer 34

GTP is present in large excess over GDP in cells