1. Chapter 17
From Gene to Protein

2. Main Questions:
The information content in DNA is the specific sequence of nucleotides along the DNA strands.
How does this information determine the organism’s appearance?
How is the information in the DNA sequence translated by a cell into a specific trait?

3. Translation
Translation is when the cell interprets the genetic message and builds the polypeptide. tRNA acts as the interpreter.
tRNA transfers aa’s from the cytoplasm to the ribosome where they are added to the growing polypeptide.
All tRNA molecules are different.

5. tRNA Structure and Function
tRNA , like mRNA, is made in the nucleus and is used over and over again.
tRNA has an aa at one end and an anticodon at the other end. The anticodon acts to base pair with the complementary code on the mRNA molecule.

6. tRNA Structure and Function
As tRNA reads the mRNA transcript, it brings an aa to the ribosome and adds it to growing polypeptide.
The 2D shape is similar to a cloverleaf.

7. tRNA
tRNA is about 80 nucleotides long and full of complementary stretches of bases that H-bond to one another giving it a 3D shape like an “L.”

8. tRNA
From this, the anticodon loop comes out of one end and at the other end protrudes the 3’ end that carries the aa.

9. 2 Recognition Steps in Translation
1. There must be a correct match between tRNA and an aa.
2. The accurate translation of the mRNA molecule.

10. 1. The Correct Match
1. Each aa gets joined to a tRNA by aminoacyl-tRNA synthase--there are 20 of these, one for each amino acid.
This enzyme catalyzes the attachment of aa to tRNA.
The activated aa is now ready to deliver the aa to the growing polypeptide.

11. 2. Accurate Translation
The tRNA must correctly match up the tRNA anticodon with an mRNA codon.
There is not a 1:1 ratio of the tRNA molecules with mRNA codons.
Some tRNA’s can bind to more than one codon.
This versatility is called “wobble.”

12. 2. Accurate Translation
Wobble enables tRNA to bind differently in one of its base pairs.
This is why codons for some aa’s differ in their 3rd base.
For example: the uracil at the 5’ end of a tRNA anticodon can pair with an A or a G in the third position of the 3’ end of the mRNA codon.

13. Translation
Movie

14. Ribosomes These are the sites of protein synthesis.
They consist of a large and a small subunit and are comprised of RNA and protein.
The RNA is ribosomal RNA (rRNA).
Bacterial (70s, 50S + 30s)
Eukaryotic (80s, 60S + 40s)

15. Ribosomes
rRNA genes are found on chromosomal DNA and are transcribed and processed in the nucleolus.
They are assembled and transferred to the cytoplasm as individual subunits.
The large and small subunits form one large subunit when they are attached to the mRNA.

16. Ribosomes The structure of ribosomes fit their function.
They have an mRNA binding site, a P-site, an A-site and an E-site.
P-site (peptidyl-tRNA) holds the tRNA carrying the growing peptide chain.
A-site (aminnoacyl-tRNA) holds the tRNA carrying the next aa to be added to the chain.
E-site is the exit site where the tRNAs leave the ribosome.
Each of these are binding sites for the mRNA.

17. rRNA
rRNA is the most abundant form of RNA in the cell because there are thousands of ribosomes within a cell and about 2/3’s the mass of a ribosome is rRNA.

18. The 3 Stages of Protein Building
1. Initiation
2. Elongation
3. Termination
All three stages require factors to help them “go” and GTP to power them.

19. 1. Initiation
Initiation brings together mRNA, tRNA and the 2 ribosomal subunits.
Initiation factors are required for these things to come together.
GTP is the energy source that brings the initiation complex together.

20. 2. Elongation
The elongation stage is where aa’s are added one by one to the growing polypeptide chain.
Elongation factors are involved in the addition of the aa’s.
GTP energy is also spent in this stage.

21. 3. Termination
Termination occurs when a stop codon on the mRNA reaches the “A-site” within the ribosome.
Release factor then binds to the stop codon in the “A-site” causing the addition of water to the peptide instead of an aa.
This signals the end of translation.

22. Polypeptide Synthesis
As the polypeptide is being synthesized, it usually folds and takes on its 3D structure.
Post-translational modifications are often required to make the protein function.
Adding fats, sugars, phosphate groups, etc..
Removal of certain proteins to make the protein functional.
Separately synthesized polypeptides may need to come together to form a functional protein.

23. Eukaryotic Ribosomes Recall the 2 types: Free and bound.
They function exactly the same and can switch from free to bound.
This switch can occur when the protein that is being translated contains a signal peptide instructing the ribosome to attach to the ER.
Once attached to the ER, synthesis will continue to completion and can then be exported from the cell.

25. Signal Peptide Recognition
The signal peptide is recognized as it emerges from the ribosome by a protein-RNA complex called signal-recognition particle.
The particle functions by bringing the ribosome to a receptor protein built into the ER where synthesis continues and the growing peptide finds its way into the lumen.

26. Signal Peptide Recognition
Once in the lumen of the ER, the newly synthesized polypeptide is modified.
The signal peptide is cut out by an enzyme.
The protein then undergoes further processing and is shipped where it needs to go.

27. 3 Useful Properties of RNA
1. It can H-bond to other nucleic acids.
2. It can form a specific 3D shape by H-bonding on itself.
3. It has functional groups that allow it to act as a catalyst.

28. Differences in Prokaryotic and Eukaryotic Gene Expression
Prokaryotic and eukaryotic RNA polymerases are different, but perform the same function.
Transcription is terminated differently.
Prokaryotic and eukaryotic ribosomes are different.
Transcription and translation are streamlined in prokaryotes, it is compartmentalized in eukaryotes.
Eukaryotic cells have a complex system of targeting proteins for their final destination.

29. Mutations Mutations are changes in genetic material.
They can cover large portions of DNA or they can be a point mutation.
There are 2 broad categories of point mutations:
Base-pair substitutions
Insertions or deletions
Mutations can be caused by a number of things:
Errors in replication, recombination, or repair
Mutagens--X, , UV radiation, chemicals
Spontaneous

31. Base-Pair Substitutions
One base pair gets substituted for another.
Sometimes these are silent because of the redundancy of the genetic code.
Other times they are silent because the mutation codes for an aa/protein that is not essential to the protein’s function.
Also, there are times when the two aa’s behave the same even though they are different.

33. Missense Mutations Vs. Nonsense Mutations
Missense mutations code for an aa, usually the wrong aa.
In a nonsense mutation, the wrong aa is encoded and it usually results in a stop codon and the production of a non-functional protein.

34. Insertions and Deletions
These are often referred to as “frame-shift” mutations because they alter the reading frame of the mRNA.
They almost always result in a nonfunctional protein.