Assignment Name: Concept Map 5
Due date: Friday, 4/29
Purpose:
The purpose of this assignment is to work on connecting all of the many processes we’ve
learned about. In each of your end of unit concept maps, you’ve illustrated a subset of these
processes in detail. It is expected that you will likely need to decrease the amount of detail
about each of these processes in order to connect all of them together into one concept map.
For this concept map, you should show as much detail as you can about the individual
processes, but focus more on constructing an understanding of how these processes connect.
For example, you should focus more on how transcription is connected to replication,
transcriptional regulation, post-transcriptional processing, RNAi, translation, DNA damage, and
repair than on the smallest details of transcription. The details you’ll want to show will be those
that help you illustrate how transcription is connected to these other processes.
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 5 will also help you to become familiar with the important content knowledge in
this discipline. 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 brings together and summarizes the entirety of the
Central Dogma of Molecular Biology. 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 connections!
As with your previous concept maps, you have a list of terms to work with. This time, we are
back to the long list from the beginning of the semester that comes from all five units of the
course. 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 50 connections even
without using all of the terms on the list.
Although this list is long, it includes the major players, but not all of the details. You are 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.
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
- Makes two or more connections between each of the following:
- Transcription and post-transcriptional processing
- Transcription and gene regulation
- Transcription and translation
- Transcription and DNA damage/repair
- RNAi and translation
- Fine regulation and coarse regulation of transcription
- DNA damage/repair and replication
A-level work (95%): - Contains no major scientific inaccuracies
- Contains no more than 2 minor inaccuracies
- Makes at least 50 connections among terms
- All connections are labeled in a way that is logical
- Makes at least one connection between each of the following:
- Transcription and post-transcriptional processing
- Transcription and gene regulation
- Transcription and translation
- Transcription and DNA damage/repair
- RNAi and translation
- Fine regulation and coarse regulation of transcription
- DNA damage/repair and replication
- 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
- Makes at least four comparisons between prokaryotes and eukaryotes
B-level work (85%): - Contains no major scientific inaccuracies
- Contains no more than 2 minor inaccuracies
- Makes at least 40 connections among terms
- All connections are labeled, some labels may not be completely clear or logical
- Makes at least one connection between each of the following:
- Transcription and post-transcriptional processing
- Transcription and gene regulation
- Transcription and translation
- Transcription and DNA damage/repair
- RNAi and translation
- Fine regulation and coarse regulation of transcription
- DNA damage/repair and replication
- For one or two of the following categories, may include 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 30 connections among terms
- Some connections are not labeled
- May be missing a connection between up to two of the following:
- Transcription and post-transcriptional processing
- Transcription and gene regulation
- Transcription and translation
- Transcription and DNA damage/repair
- RNAi and translation
- Fine regulation and coarse regulation of transcription
- DNA damage/repair and replication
- 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 30 connections among terms
- No connections are labeled
- May be missing a connection between up to four of the following:
- Transcription and post-transcriptional processing
- Transcription and gene regulation
- Transcription and translation
- Transcription and DNA damage/repair
- RNAi and translation
- Fine regulation and coarse regulation of transcription
- DNA damage/repair and replication
- Any of the following categories have no terms or connector:
- Molecules
- Enzymatic functions
- Chemical interactions
- Parts of complexes
Terms:
DNA
RNA
Protein
-10 site
-35 site
3’ exonuclease
3’ OH
5’ capping
5’ exonuclease
5’ phosphate
5’ UTR
Abasic site
Accessibility
Activator
Alkylation
Amino acids
Anticodon
AP Endonuclease
Architectural TFs
AT-rich region
BER
Beta clamp/PCNA
Binary
Branch point A
Bromodomain protein
Chromatin modification
Chromatin remodeling
Chromodomain protein
Cis-acting
Clamp loader
Co-activator
Co-repressor
Coarse regulation
Coding strand
Codon
Cooperative
Deamination
Dicer
Direct repair
DNA Pol III core
DNA Polymerase I
DNA polymerase III
DNA Replication
DNAa
DNAa box
Double strand break
E. coli RNA polymerase
Enhancer
Fine regulation
Gene specific TFs
General transcription factors (TFIID, A, B, F, E, H)
Glycosylase
HATs/HDACs
Helicases
Hemimethylation
Heterochromatin-binding proteins
Histone acetylation/deacetylation
Histone methylation/demethylation
HMTs/HDMs
Homologous recombination
Hydrolytic damage
Initiator
Intrinsic terminator
Intron removal
Lagging strand
Ligases
Mismatch
Mismatch repair
Modular
MutS, MutL, MutH
NER
NHEJ
Nick translation
Okazaki fragment
Oxidative damage
Peptide bond
Phosphodiester bond
Pol delta
Polyadenylation
Polyadenylation signal
Pre-initiation complex
Primase
Primer
Promoter
protein
Replisome
Repressor
Rho-dependent terminator
Ribonucleotide triphosphates
Ribosomes
RISC
RNA (given)
RNA Pol II
RNA Pol II C-terminal domain
RNA polymerase
RNA polymerase core
RNA polymerase holoenzyme
RNA processing
rRNA
Sigma subunit
siRNA, miRNA, shRNA
snRNPs
Solar radiation
Spliceosome
Splicing
SSB
Tau subunit
Telomerase
Template strand
Termination
Trans-acting
Transcription
Transcription factors
Transcriptional activation
Transcriptional initiation site
Transcriptional repression
Translation
Translesion synthesis
tRNA
UvrA, UvrB, UvrC
Variant histone exchange
XPB, XPD