D1.

2 Protein Synthesis Guiding Questions

Sub-Topic Clarification Questions
D1.2.1— 1. What is the central dogma of molecular biology?
Transcription as the 2. Where in the cell does transcription take place?
Students should understand the roles of RNA
synthesis of RNA 3. What polymer is synthesized during transcription?
polymerase in this process.
using a DNA 4. How does RNA polymerase recognize the start of a gene during transcription?
template
D1.2.2—Role of 5. What parts make up the transcription initiation complex?
hydrogen bonding 6. Where on the DNA strand does the transcription initiation form?
Include the pairing of adenine (A) on the DNA
and 7. What is the role of hydrogen bonding in transcription?
template strand with uracil (U) on the RNA
complementary 8. What is the base-pair rule for a DNA strand matching an RNA strand?
strand.
base pairing in
transcription
Single DNA strands can be used as a template 9. Why is the stability of DNA templates crucial in somatic cells that do not divide?
for transcribing a base sequence, without the 10. How are single DNA strands used as templates for transcribing base sequences without changing the DNA
D1.2.3—Stability of
DNA base sequence changing. In somatic cells base sequence?
DNA templates
that do not divide, such sequences must be
conserved throughout the life of a cell.
11. Click on the “Central Dogma” menu tab at the top of the screen. The table below outlines the steps in
eukaryotic gene expression. Click on each tab or scroll through the page and briefly summarize each step
below.
Gene Expression Molecules Involved What molecules and Summary What happens during this
Steps proteins are involved in this step? step?
Transcription
RNA Splicing
D1.2.4— Limit to understanding that not all genes in a cell mRNA Transport
Transcription as a are expressed at any given time and that Translation
process required for transcription, being the first stage of gene Protein Processing
the expression of expression, is a key stage at which expression of 12. Complete the table below to outline the functions of the different types of gene expression regulation by
genes a gene can be switched on and off. proteins that occur in eukaryotes.
DNA Binding Function
Sequence protein
Enhancers Activator
Silencers
A region of DNA located close to a specific gene. Once bound to the
sequence RNA polymerase transcribes the gene.
13. State an example of how the environment of an organism impacts gene expression.
D1.2.5—Translation 14. What is the primary goal of translation in cellular processes?
as the synthesis of The base sequence of mRNA is translated into 15. How is the amino acid sequence determined during translation?
polypeptides from the amino acid sequence of a polypeptide.
mRNA
D1.2.6—Roles of 16. During translation the ribosome moves across the mRNA until it encounters the stop codon. Outline the events
Students should know that mRNA binds to the
mRNA, ribosomes that follow.
small subunit of the ribosome and that two tRNAs
and tRNA in 17. Create a diagram outlining the structure of a ribosome, including protein and RNA composition, large and
can bind simultaneously to the large subunit.
translation small subunits, three tRNA binding sites and mRNA binding sites.
 18. Use the diagram to explain the roles of mRNA, tRNA, and ribosomes in translation:

19. For tRNA to do its job, each tRNA molecule must be attached to the correct amino acid that corresponds to
the anticodon in that type of tRNA. To know which amino acid should be attached to each tRNA molecule,
D1.2.7— use the base-pairing rules to complete this table.
Complementary
Amino acid Threonine Histidine Proline Leucin Glutamic acid Valine
base pairing Include the terms “codon” and “anticodon”.
(Thr) (His) (Pro) e (Leu) (Glu) (Val)
between tRNA and
Anticodon in tRNA molecule
mRNA UGA
that carries this amino acid
mRNA codon ACU CAU CCU CUG GAG GUG
20. Considering that we are all made up of the same 4 nucleotides in our DNA, the same 4 nucleotides in our
RNA, and the same 20 amino acids in our proteins, why are we so different from each other? For example,
Students should understand the reasons for a why do some people have sickle cell anemia and others don't?
D1.2.8—Features of
triplet code. Students should use and understand 21. A student says that “ALL DNA codes for proteins.” Do you agree with her? Why or why not?
the genetic code
the terms “degeneracy” and “universality”. a. Claim-
b. Evidence-
c. Reasoning-
22. Using the table below, compare the nucleotide sequence in the “Beginning of Normal Hemoglobin Gene” vs.
the “Beginning of Sickle Cell Hemoglobin Gene”. What is the only difference?

D1.2.9—Using the
Beginning of Normal
Hemoglobin Gene CACGTAGACTGAGGACTC
genetic code Students should be able to deduce the Transcription produces: codon1 codon 2 codon 3 codon 4 codon 5 codon 6
expressed as a sequence of amino acids coded by an mRNA
table of mRNA strand.
Beginning of Normal
codons Hemoglobin mRNA
amino amino acid amino acid amino acid amino amino
Translation produces:
acid 1 2 3 4 acid 5 acid 6
Beginning of Normal
Hemoglobin Protein
 Beginning of Sickle Cell
Hemoglobin Gene CACGTAGACTGAGGACAC
Transcription produces: codon 1 codon 2 codon 3 codon 4 codon 5 codon 6

Beginning of Sickle Cell

Hemoglobin mRNA
amino amino acid amino acid amino acid amino amino
Translation produces:
acid 1 2 3 4 acid 5 acid 6
Beginning of Sickle Cell
Hemoglobin Protein

23. Complete the table to summarize the process of translation.

Stage Key steps Diagrams and Notes

Initiation 1. mRNA binds to the small subunit of the

ribosome.

2.

3.

D1.2.10—Stepwise 4. The large subunit of the ribosome binds

• The mRNA contains a series of codons (3
movement of the to the tRNA and small subunit
bases) each of which codes for an amino
ribosome along
acid.
mRNA and linkage Focus on elongation of the polypeptide, rather
Elongation 5. A second tRNA (with amino acid
of amino acids by than on initiation and termination.
attached) complementary to the
peptide bonding to
second codon on the mRNA then
the growing
binds to the A site of the ribosome
polypeptide chain
6. • charged tRNA contains energy in the
7. bond with the amino acid attached
8. Another tRNA binds, complementary which will be used to form the peptide
to the next codon on the mRNA, binds bond.
to the A site. • There are three binding sites on the large
9. Steps 6, 7, and 8 are repeated until a subunit of the ribosome, but only two can
stop codon is reached. contain tRNA molecules at a time.
Termination 10. When a stop codon is reached
translation is stopped

24. Central Dogma. Select the “Genetic Medicine” tab located on the top right of the screen. Click on the tab
corresponding to the genetic medicine(s) that your instructor assigns to you, or scroll through the interactive
and click on the pink “+” sign labeled with that genetic medicine. Read the “Genetic Medicine” tab material,
D1.2.11—Mutations watch the video, and read the information in the “Learn more” link. Then, complete the appropriate row(s)
Include an example of a point mutation
that change protein below.
affecting protein structure.
structure Detailed Description Describe how this
Short Summary Write a one-sentence
genetic medicine would be used to
Genetic Medicine summary of how this genetic medicine
treat a genetic disease. (For example,
works.
mention how it would fix the disease-
 causing mutation and/or result in a
functioning protein.)
CRISPR-Cas9
Gene Therapy
Gene Switches
Exon Skipping
RNA Interference
Small Molecule Drug
25. Sickle-Cell Anemia is caused by a ___________ mutation in the protein ____________________ that causes the __th
amino acid to be changed from glutamic acid to _______________.
D1.2.12— 26. Define 5' to 3' transcription and explain its significance in cellular processes.
Directionality of Students should understand what is meant by 5' 27. Define 5' to 3' translation and explain its significance in protein synthesis.
transcription and to 3' transcription and 5' to 3' translation
translation AHL
28. Fill-in the following blanks:

D1.2.13—Initiation of Consider transcription factors that bind to the

transcription at the promoter as an example. However, students are
promoter AHL not required to name the transcription factors.

D1.2.14—Non- 29. Coding regions are used as a guide for the production of polypeptides, but non-coding regions are not. Non-
coding sequences Limit examples to regulators of gene expression, coding regions do however have important functions, for example promoters. Outline how promoter regions
in DNA do not code introns, telomeres and genes for rRNAs and of DNA molecules aid the production of polypeptides.
for polypeptides tRNAs in eukaryotes. 30. Explain the role of regulators of gene expression as non-coding sequences.
AHL 31. Explain the role of genes for rRNAs and tRNAs as non-coding sequences in eukaryotic DNA.
D1.2.15—Post- Include removal of introns and splicing together 32. Use the following diagram to answer the questions below:
transcriptional of exons to form mature mRNA and also the
modification in addition of 5' caps and 3' polyA tails to stabilize
eukaryotic cells AHL mRNA transcripts.
 a. What has been removed from the pre-mRNA to make it into mRNA?
b. What has been added to the mRNA that was not present in the pre-mRNA, and where on the mRNA
strand are the additional items located?
c. Identify the structure through which the mRNA leaves the nucleus.
d. The nucleotides on the mRNA will be “read” in the next step to producing a polypeptide. What
sequence of bases indicates the starting point for the polypeptide “blueprint”?
D1.2.16—Alternative Students are only expected to understand that 33. Use the diagram to answer the following questions:
splicing of exons to splicing together different combinations of exons
produce variants of allows one gene to code for different
a protein from a polypeptides. Specific examples are not
single gene AHL required.
 a. Does the pre-mRNA contain introns and exons?
b. What happens to the introns during RNA splicing? The exons?
c. What happens to the open reading frame of the gene during RNA splicing?
d. What is the splicesome and what does it do?
e. If you, as a cell, needed to produce several different forms of a protein to carry out specialized
functions, how might you use RNA splicing to accomplish this?
Include attachment of the small ribosome 34. What happens after the small ribosome subunit reaches the start codon during translation initiation?
subunit to the 5' terminal of mRNA, movement to 35. What are the three binding sites for tRNA on the ribosome during elongation, and what are their roles?
the start codon, the initiator tRNA and another
D1.2.17—Initiation of 36. Draw a ribosome during translation with the three binding sites.
tRNA, and attachment of the large subunit.
translation AHL
Students should understand the roles of the three
binding sites for tRNA on the ribosome (A, P and
E) during elongation
D1.2.18— 37. Once translated the polypeptide will naturally fold into a structure. The structure is the result of the polar
Students should appreciate that many
Modification of polypeptides must be modified before they can nature of water in the cytoplasm, hydrogen bonds and interactions between the R-groups. The R-groups of an
polypeptides into function. The examples chosen should include amino acid are classified as having one of a number of different properties. List the properties can they
their functional the two-stage modification of pre-proinsulin to possess.
state AHL insulin. 38. Outline the two-stage modification of pre-proinsulin to insulin.
D1.2.19—Recycling Limit to the understanding that sustaining a 39. Why is the recycling of amino acids essential for sustaining a functional proteome?
of amino acids by functional proteome requires constant protein 40. Describe the process of protein breakdown by proteasomes.
proteasomes AHL breakdown and synthesis. 41. How does the recycling of amino acids by proteasomes contribute to protein synthesis?