Unit 4 – Post-transcriptional Regulation and Translation

(Unit 4 – Post-transcriptional Regulation and Translation)

Purpose:
The purpose of this assignment is to help you solidify your understanding of the processes other
than transcription that go into gene regulation — how does the cell sense changes and transmit
this information to the nucleus to increase or decrease transcription? What happens to
transcripts after we make them? How can we experimentally alter the amount of a transcript
present or its likelihood of being translated to make protein? And how does translation actually
happen?
As in our previous concept maps, our goal is to work toward constructing an understanding of
how the concepts and processes we are learning about are related. You’ve already concept
mapped parts of this through your Seesaw assignments in this Unit, so you have a good starting
point; now you can work on connecting them as well as beginning to think about how you will
later connect this concept map to your previous ones. You do not need to connect them now or
include details about replication or transcriptional regulation on this concept map — but it might
help you to begin thinking about where those connections will be now so that you can make this
map in a way that will connect with your replication map later, when it’s time to make the final
concept map.
Skills:
The concept map assignments in this course are intended to help you practice the following
skills that are necessary for scientists within all fields of biology:
● Explaining molecular processes that occur within living cells,
● Comparing and contrasting similar molecules, chemical interactions, or cellular
processes,
● Connecting multiple complex processes to begin to create an understanding of the
complex workings of living cells.
Knowledge:
Concept Map 4 will also help you to become familiar with the important content knowledge in
this discipline. Specifically, this concept map addresses Learning Outcomes 69-87. (It is unlikely
that the concept map that you create will address every single one of these learning outcomes,
but what you choose to depict is drawn from these.)
Task:
Your task is to create a concept map that explains the connections among the molecules,
processes, chemical interactions, and enzymatic functions we discussed in Unit 4. As with all of
your concept maps, the basis should be the Central Dogma in its most basic form (DNA → RNA
→ Protein). For this concept map, your focus is on the RNA → protein “arrow”…as well as some
other arrows attaching to “RNA” that might not be in the original Central Dogma diagram we
started with. The other “arrows” should be shown, but you are not expected to have any detail
there. This time, we are working on the translation arrow, as well as some other details that may
happen before we get to that arrow. We’ll put all of this back together at the end of the semester!
As with your previous concept maps, you have a list of terms to work with. This time, the terms
are only those from Unit 4. You do not necessarily have to use every single term, and you can
also use terms that are not on this list. You can use the terms as the nodes (i.e., the thing in a
box that is connected to another thing), or you can use them as the connectors (i.e., a word
above an arrow or connecting line explaining what the connection between two nodes is). You
can also convert a noun into a verb or a verb into a noun. You can also use a term as both a
node and a connector if that makes sense in your concept map. In addition to the terms on the
list, you will likely use simple wording like “is”, “is part of”, “is an example of”, or “interacts with”
as some of your connectors. There is not one right way to do this: this is about representing how
your mind makes sense of this information. The goals are to: 1. Make as many connections as
possible, 2. Be as scientifically accurate as possible, 3. Explain how things are related (is one
term an enzyme that acts on another term? Are several terms all smaller parts of a whole?).
You are welcome to create the concept map in any format that works for you. This could be on
paper (scan or take a phone photo and upload), on a whiteboard, with a bunch of Post-it notes,
in Powerpoint, or using a website specifically designed for concept mapping like LucidChart or
Mural. If you struggled with the construction of your first concept map, I suggest trying
something like LucidChart or Mural to start, as they make it very easy to move nodes around
when it starts to get complicated and your connectors start to get all tangled up.
Criteria for Success:
The key criteria for success are the goals listed above: 1. Make as many connections as
possible, 2. Be as scientifically accurate as possible, 3. Explain how things are related (is one
term an enzyme that acts on another term? Are several terms all smaller parts of a whole?).
After you complete your concept map, you will briefly reflect on the process and assign yourself
a grade based on the criteria below. You will notice that the criteria for A- through C-level work
are based directly on the three goals listed above. You will also notice that the minimum number
of connections you are aiming for is greater than the number of terms on the list. This is to
encourage you to make multiple connections among the terms: the relationships among the
terms are not one-to-one, but many-to-many. You should be able to make 30 connections even
without using all of the terms on the list.
You will again notice that the list is not as long as some of the earlier lists — it includes the major
players, but not all of the details. You are more likely to need to use additional terms not on this
list. This is intentional — this list of terms will help you get started, and you can add in the details
that you feel are more important. You may also want to include some of the terms you used in
your previous concept maps to show how upstream signaling processes influence transcription
— but do not feel like you need to entirely recapitulate your transcription and transcriptional
regulation concept maps.
A+-level work (100%):
Meets all criteria for A-level work, AND

• Includes terms beyond the suggested list of terms
• Includes examples and/or definitions
• Includes examples of how RNAi can be used experimentally (in addition to its evolved
  biological functions)
  A-level work (95%):
• Contains no major scientific inaccuracies
• Contains no more than 2 minor inaccuracies
• Makes at least 30 connections among terms
• All connections are labeled in a way that is logical
• Includes at least two nodes or connectors that fall into each of the following categories
  (some of these categories will likely have many more than two, but two is a minimum for
  each):
• Molecules
• Enzymatic functions
• Chemical interactions
• Parts of complexes
  B-level work (85%):
• Contains no major scientific inaccuracies
• Contains no more than 2 minor inaccuracies
• Makes at least 30 connections among terms
• All connections are labeled, some labels may not be completely clear or logical
• For one or two of the following categories, includes only one node or connector:
• Molecules
• Enzymatic functions
• Chemical interactions
• Parts of complexes
  C-level work (75%):
• Contains no more than 2 major scientific inaccuracies
• Contains no more than 4 minor inaccuracies
• Makes at least 15 connections among terms
• Some connections are not labeled
• For three or more of the following categories have less than two nodes or connector:
• Molecules
• Enzymatic functions
• Chemical interactions
• Parts of complexes
  Less than C-level work (65%):
  Any of the following are true:
• Contains more than 2 major scientific inaccuracies
• Contains more than 4 minor inaccuracies
• Makes fewer than 15 connections among terms
• No connections are labeled
• Any of the following categories have no terms or connector:
• Molecules
• Enzymatic functions
• Chemical interactions
• Parts of complexes
  Terms:
  DNA
  mRNA
  Protein
  5’ capping
  5’ UTR
  Activator
  Amino acids
  Anticodon
  Co-activator
  Co-repressor
  Codon
  Dicer
  Intron removal
  Peptide bond
  Polyadenylation
  Polyadenylation signal
  Repressor
  Ribosomes
  RISC
  RNA Pol II C-terminal domain
  RNA polymerase
  RNA processing
  rRNA
  siRNA, miRNA, shRNA
  snRNPs
  Spliceosome
  Splicing
  Termination
  Transcription
  Translation
  tRNA