Mmbio 240 Final Winter 2012

Front 1

Describe the nature of the genetic code

Back 1

-Triplet
-Nonpunctuated
-Nonoverlapping
-Degenerate (more than one codon codes for each aa)
-Universal (almost completely) except in the mitochondria

Front 2

Codon:

Back 2

The three letter “words” of the genetic code

Front 3

Open Reading Frame:

Back 3

The part that codes for a protein between the start and stop codons

Front 4

Stop codons

Back 4

UAA
UAG
UGA

Front 5

Describe the parts of a tRNA and their function:

Back 5

There are four arms...
- The amino acid arm binds amino acids
- The anticodon (loop) arm reads mRNA base pairs with the codon
- The 2 other arms are for shape and stability

Front 6

How does tRNA work as an adapter molecule?

Back 6

- It has the amino acid on one arm and has an anticodon that can base pair with the mRNA
- Can help with the process of converting mRNA to proteins because it has an arm for amino acids and an arm for mRNA
- the tRNA reads the codons on the mRNA and inserts the proper amino acid to the growing polypeptide chain
- It can read both languages (adapter b/n nucleic acid and protein)

Front 7

How can "wobble" and modified bases affect the reading of the genetic code?

Back 7

-Wobble: Sometimes the 3rd base can be less important because due to the curvature of the tRNA vs. the straight mRNA things won’t align quite correctly and bases that “shouldn’t” base pair with each other will. This means that some tRNA can read multiple codons (expands the ability to read). (note that although it’s the 3rd base in the codon it’s the 1st in the anticodon due to being antiparallel)
- Modified Bases: Can either extend or restrict wobble pairs (Eg: Inosine can base pair with three different bases)

Front 8

Describe how tRNA synthases choose the proper amino acid to attach:

Back 8

- Has double sieve mechanism where the first set of holes keeps things too big to be correct out and the second set of holes (editing site) lets things too small to be correct fall out.
-Each synthetase (what ensures that the correct amino acid gets to the tRNA) does only one amino acid

Front 9

Identify the parts of the ribosome:

Back 9

- large and small subunits
- mostly rRNA with proteins for structure
- A, P, E site (in that order from left to right, 3' to 5')
- The rRNA is where the active site is
- tRNA recognizes the codons
- Proteins provide support

Front 10

Describe initiation of translations, including the function of initiation factors 2, 3, and 4

Back 10

- The small subunit of the ribosome binds the initiator tRNA and the mRNA
- Large subunit binds last, forming the initiation complex
- IF1 and IF3 keep ribosomal subunits separate
- IF2 brings in initiator tRNA
- eIF4F - binds to the cap & tail.
-Note initiation factors leave before elongation happens

Front 11

Describe initiator tRNA:

Back 11

- A special tRNA that is only used for initiation.
- It can directly enter the P site.
- In bacteria it’s formylated (N-formyl Methionine) and in eukaryotes it’s just a normal Methionine.
- Can be recognized by IF2

Front 12

What is the role of termination factors in termination?

Back 12

- look like tRNA and which enter the A site, break off the peptide, and break apart the small and large units of the ribosome for recycling
- Stop Codons are not recognized by tRNAs, thats why RFs are needed.

Front 13

Describe how prokaryotes and eukaryotes deal with non-stop RNA's:

Back 13

-Prokaryotes: tmRNA
Floats in with tRNA and mRNA looking site, puts tRNA region into A site and mRNA region into the “foot” of the ribosome, makes a little peptide (which marks the peptide for destruction), hits the release factors, and is released

- Eukaryotes: polyA tail and exosome
Translates string of A’s (into Lysine) and gets stuck and recruits exosome which eats the RNA and breaks the ribosome off (protein is destroyed then too)

Front 14

Describe the importance of the shine-dalgarno sequence:

Back 14

It's a sequence found right before AUG that binds the mRNA to the ribosome by binding to the 16s. It is only found in Prokaryotes! (communication between mRNA and rRNA)

Front 15

Describe the importance of a kozak sequence:

Back 15

It's a sequence signifying good context - way for ribosome to tell where it’s supposed to start translating i n. Surrounds the start codon (AUG). Only found in Eukaryotes

Front 16

Compare and contrast initiation between prokaryotes and eukaryotes:

Back 16

- Prokayotes:
Shine-Dalgarno sequence
formylated initiator met
IF3 and IF1 keep subunits separated, IF2 brings in initiator tRNA puts it into the P site

- Eukaryotes
Kozak (good context)
normal methionine on initiator tRNA
also has eIF4 (an extra initiation factor) which binds to the cap and tail
use IRES to do polycistronic DNA

Front 17

What is the importance of the cap and the tail?

Back 17

The cap and tail both help the mRNA get out of the nucleus, the tail gives the mRNA stability because once it gets in the cytosol RNAses start eating the mRNA - which is how the mRNA gets degraded - thus the tail gives the RNAses something to chew on while the mRNA is being used, also the cap and tail are bound by eIF4 thus telling ribosome where to start

Front 18

How do the cap and tail support translation in eukaryotes?

Back 18

- eIF4 binds them (instead of Shine-Delgarno sequence) and then binds the mRNA to the initiation complex (the tRNA and the two ribosome parts)
- non-stop RNA will keep being transcribed until the tail.

Front 19

Describe the peptidyltransferase reaction:

Back 19

- process of making the peptides
- One tRNA in P site which has growing peptide chain on its head
- New tRNA brought into A site, they get bonked together and the peptide chain on tRNA in the P site gets transferred to the one in the A site. Bond is between P and A sites.
- Everything shifts down and repeats
- rRNA of the large subunit does this
- EF-Tu brings in charged tRNA and controls the rate of the reaction. If it is the right tRNA then GTP hydrolyzes to GDP and EF-Tu leaves.