Name ___________________________________________________ Period _______
Beyond the Basics – Protein
Synthesis
Go to the following websites and answer the questions
that follow.
1.
Objective 11 Explain the significance of the reading
frame during translation.
http://www.emunix.emich.edu/~rwinning/genetics/code2.htm
and ( these are two connected pages )
http://www.emunix.emich.edu/~rwinning/genetics/code3.htm
a. What determines the reading frame?
The start codon AUG creates the frame of reference.
b. What could happen if there were no start and stop codons?
There would be no frame of reference for transcription, and transcription
would also happen to parts of mRNA that do not need to be transcribed –
like the A cap.
b. mRNA has sequences of codons on either side of the reading fame, what
are some uses of these sequences, since they do not code for a
polypeptide?
These help the mRNA not be degraded upon passage to the ribosomes,
and are binding sites for promotion and repression factors.
Now we will examine the significance of reading frames during translation.
Let’s go mutate some DNA!!!
http://gcat.davidson.edu/bioinformatics/hemomut.html
c. Go to the above website and follow the directions to see how the
substitution of one nucleotide can change a whole protein. (in this case it
changes normal beta hemoglobin into one of the Sickle Cell variants.
d. Make a single substitution somewhere else and note how different the
amino acid sequence is.
e. Locate the START sequence (ATG, it is six codons in front of the GaG
sequence you mutated in the first step) and remove 2 nucleotides
somewhere after the start sequence.
This is a frame shift mutation. Compare the two mutations that you
caused, which one is more severe?
The frame shift mutation is much more severe, it changes almost every
amino acid that is created.
f. What is the significance of the reading frame during translation?
It ensures that the correct amino acids are attached to create the
polypeptide.
Objective 13 Go to the following web pages and answer the following
questions
http://wwwclass.unl.edu/biochem/gp2/m_biology/animation/m_bio_ga.html#
Watch the animation on transcription
2. Explain how RNA polymerase recognizes where transcription should begin.
a. What is the promoter?
Where promotion factors bind to the DNA to promote the transcription of
a gene or multiple genes in the same operon.
b. What is the terminator?
The sequence of DNA that tells DNA polymerase where to end the
synthesis of mRNA.
c. the transcription or coding unit.
This is the part of DNA that is transcribed. It includes the gene and any
additional binding sites necessary for mRNA use (scission sites for multiplegene operons, mRNA promotion binding sites, etc).
Objective 14 Go to the following website to answer the question below
http://www.emunix.emich.edu/~rwinning/genetics/transcr2.htm
3. Explain the general process of transcription, including the three major steps of
initiation, elongation, and termination.
Stage
What happens here ( explain in your own words)
Initiation
RNA polymerase sigma unit binds to a site 35 bp before
the transcription unit, the polymerase unwinds and the
core protein is left. That core begins to unwind the DNA at
at a TATA box about 10 bp upstream of the transcription
unit. A transcription bubble is formed.
Elongation
Basically the same thing as DNA replication, only there is
only a leading strand, and that strand is made of RNA,
created by RNA polymerase. This strand is created in the
5’ to 3’ direction. RNA quickly unbinds from the DNA once
created.
Termination
When RNA polymerase finds a termination section of the
DNA, it ends RNA synthesis.
Objective 15 Go to
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.html#rna
_processing
4. Explain how RNA is modified after transcription in eukaryotic cells.
What happens in each step? (use the chart below)
Step
Capping
What happens and why is it necessary?
A G-cap is put on the 5’ end. This is necessary
so that bases do not fall off of the complete
mRNA strand so that the translation is done
correctly.
Removal of
Introns are parts of the DNA that do not code
introns and
for genes. They are exised from the pre-mRNA
splicing of
to leave only the exons. Exons are ligated
exons
together to create a continuous chain of
mRNA.
Polyadenation A poly-A tail is put on the 3’ end of the premRNA. This is the final step of posttranscriptional processing.
Why must splicing be done with great precision? What can happen if this
step fails to complete correctly?
There must not be any intron left in the mRNA or the reading frame will be
shifted and the rest of the gene after that failure will not be read correctly.
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.ht
ml#Why_split_genes
Why splice genes? What advantage does it give to the organism?
Creating the final product from different parts allows the organism to
customize the different combinations it can make.
Objective 16 Go to the following website to answer the next
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html
5. Describe the structure and functions of
tRNA.
tRNA is the tool for translating codons into
amino acids. The amino acid always binds into
the 3’ alanine end of the tRNA.
Diagram a typical tRNA molecule in the box
to the side. (You can cut and paste a
picture into the box)
a. How many forms of tRNA are there in a
typical cell?
Up to 32, but only 20 are absolutely
necessary.
b. What is the anticodon? Label it on the diagram.
This is the sequence of three bases that attaches to the mRNA and
recognizes them to translate into amino acids.
c. Where does the amino acid attach on the tRNA to? Indicate on your
diagram
On the 3’ alanine end.
d. What does tRNA do?
It transfers the amino acids to the ribosome in the correct order to create
the polypeptide.
Objective 17 Go to the following website to learn about ribosomes
http://micro.magnet.fsu.edu/cells/ribosomes/ribosomes.html
6. Describe the structure and function of ribosomes.
Describe structure:
Draw a ribosome (you can cut and paste)
What are they made out
of?
About 50/50 made of
rRNA and proteins.
What are the two major
subunits?
There is a large and small
subunit, which are not
connected when it is not
translating mRNA into
protein.
Explain function:
The ribosome allows
mRNA to create protein.
Objective 18 Read the following website to fill in the chart below
http://www.elmhurst.edu/~chm/vchembook/584proteinsyn.html
Watch the animation of translation here:
http://www.johnkyrk.com/DNAtranslation.html
7. Describe the process of translation (including initiation, elongation, and
termination).
Step
What happens (include diagrams)
Initiation
mRNA binds to the aminoacyl site, and the start codon is found
and translated by tRNA.
The mRNA is moved through the ribosome and more tRNA binds
to the aminoacyl binding site, then moves to the peptyl binding
site and deposts the amino acid that it holds. The amino acids
are ligated together to create a polypeptide.
This happens when a tRNA recognizes the stop codon, the amino
acid is hydrolyzed from its tRNA.
Elongation
Termination
Go to the following website and watch the animation
http://wwwclass.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a3.html
a. What amino acid codon initiates translation in eukaryotes?
AUG
b. Describe how a polypeptide must be modified before it becomes fully
functional.
It must be folded to create the correct shape. This can happen spontaneously
from the disufide bridges and hydrogen bond interactions that occur naturally,
or can be mediated by enzymatic and phosphorylating interactions.
Objective 19 Go to the following website to answer the next question
http://webhost.bridgew.edu/fgorga/proteins/proteins.htm
8. Explain what determines the primary structure of a protein.
The primary structure of a protein is determined by the actual amino acids that
make it up and the covalent interactions between them.
Watch the following animation and answer the following questions
http://www.stolaf.edu/people/giannini/flashanimat/proteins/protein%20structur
e.swf
9. What kinds of bonds hold the secondary structures of proteins together?
Hydrogen bonds, creating alpha helixes and beta pleated sheets.
10. How many levels of structure are present in complete functional proteins?
Four, the third is created by disulfide bonds, and the fourth is created by multiple
peptide chains.
Bonus Question
What was the 2009 Nobel Prize in Chemistry awarded for?