Chapter 13 Activity Sport Imagery QuestionnaireYouve now had a .docx

Chapter 13 Activity: Sport Imagery Questionnaire
You've now had a chance to experiment with imagery vividness
and control, the two keys to good images. This activity will help
you evaluate your images to determine what aspects of imagery
you need to focus on to develop your imagery skills. This
evaluation is similar to what you might experience before an
imagery training program.
Reprinted, by permission, from American Coaching
Effectiveness Program, 1987, Sport psychology, level two
(Champaign, IL: Human Kinetics), 69-71.
Instructions:
1. Read the four imagery situations.
2. Create an image for each situation. Provide as much detail
from your imagination as possible to make the image seem real.
Think of specific examples of the skill, the people involved, the
place, and the time. There are, of course, no right or wrong
images.
3. Rate your imagery in the tables provided, using a scale where
1 = very poor and 5 = very well.
Top of Form
Imagery Situations
Situation 1: Select a specific skill or situation in your sport.
Imagine yourself performing the activity in the place where you
would normally practice, without anyone else present. Now
close your eyes for about a minute. Try to see yourself at this
place: hear the sounds, feel the body movements, and be aware
of your mood.
Very poor
Very well
Rate how well you...
1

2
3
4
5
Saw yourself performing the activity
Heard the sounds
Felt yourself performing the activity
Were aware of your mood
Controlled your image
Situation 2: You are performing the same activity as in situation

1, but this time the coach and your teammates are present. You
make a mistake that everyone notices. Now close your eyes for
about a minute and imagine making the error and what occurs
immediately afterward.
Very poor
Very well
1
2
3
4
5
Saw yourself
Hear the sounds
Felt yourself performing the movements

Situation 3: Think of a teammate performing a specific activity
unsuccessfully in a contest (e.g., missing a 20-foot shot, being
passed by other runners, falling from the balance beam, missing
a field goal.) Now close your eyes for about a minute to imagine
watching your teammate performing this activity unsuccessfully
in a critical part of the contest as vividly and realistically as
possible.
Very poor
Very well
1
2
3
4
5
Saw your teammate
Heard the sounds

Felt your own physical presence or movement
Felt your own emotions
Situation 4: Imagine yourself performing the same activity that
you imagined your teammate performing in situation 3. Imagine
yourself performing the activity very skillfully. Spectators and
teammates show their appreciation. Now close your eyes for
about a minute and imagine the situation as vividly as possible.
Very poor

Very well
1
2
3
4
5
Saw yourself
Heard the sounds
Felt yourself making the movements
Felt the emotions

Now add up your responses to each question (add up all
responses to all #1 questions, all # 2 questions, etc.) and write
your scores in the spaces provided below. Each rating table
you completed included five ratings. The first rating in each of
the tables is a visual rating, the second is an auditory rating, the
third is a kinesthetic rating, the fourth is a mood rating, and the
fifth is a control rating. The total for each of these ratings is
your dimension score, as follows:
Dimension score
Visual (your total score for rating 1) =
Auditory (your total score for rating 2) =
Kinesthetic (your total score for rating 3) =
Mood (your total score for rating 4) =
Control (your total score for rating 5) =
As you read in the chapter, imagery involves all of the senses.
Which senses were easy or difficult for you to put into your
imagery session? Consider your scores and work on increasing
them. Your goal is create a holistic sensory image. Keep
working!
Bottom of Form

BIOINFORMATICS OF LepA/EF-4 and EF-G
(Adapted from RSCB PDB - www.pdb.org)
This bioinformatics tutorial explores the relationship between
gene sequence, protein structure, and biological function in the
context of the LepA/EF-4 and EF-G proteins. In this tutorial
you will:
· find protein structures using search tools on the RCSB PDB
website;
· use molecular visualization tools to explore LepA/EF-4 and
EF-G structure and function
The PDB archive is the primary repository of experimentally-
determined structures of proteins, nucleic acids, and complex
assemblies. As a member of the wwPDB, the RCSB PDB curates
and annotates structural data from researchers around the world.
The RCSB PDB also provides a variety of tools and resources
for searching, visualizing, downloading, and analyzing
biomolecular structures.
Getting Java to Work With Mac computers at
http://www.rcsb.org/pdb/home/home.do
1. Update Java if it hasn’t already been up dated
a. Download Java at : www.java.com/getjava

2. Go to system preferences
3. Click on the Java Icon
4. Open the Java Control panel
5. Go to the Security Tab
6. Bring the Java security setting to medium
7. Close out of Java
8. Open Safari
9. Click on Safari on the top left corner
10. Click “Reset Safari”
11. Go to http://www.rcsb.org/pdb/home/home.do
What if you get this message?
A. Go to system preferences.
B. Click on the Security and Privacy icon.
C. File that was blocked should appear at the bottom – Click
“Open Anyway.”

Finding and Exploring the 3D Structure of LepA/EF-4
We will find a structure of the LepA/EF-4 protein in the RCSB
PDB and use several tools to explore its structure and function.
Task 1: Find structures of LepA/EF-4 at the RCSB PDB
website.
1. Go to the RCSB PDB website at http://www.pdb.org
2. Perform a “PDB ID” search by typing the structure code
“3CB4” in the text box on the search bar at the top of the first
page:
3. Click the Search button.
4. This will take you to the Structure Summary page for the
crystal structure of LepA-EF-4.
5. Scroll down to the “Macromolecules section” to see the
molecular description of LepA/EF-4.
**Question 1a. What is the amino acid length of the protein?
**Question 1b. From which organism was the protein purified
to generate the crystal structure?
6. You’ll notice that there are 6 chains listed (A, B, C, D, E, F)
in the molecular description, which might initially suggest that
this protein has quarternary structure. On the upper left side of
the Structure Summary page, you will see a box containing an

image and links to 3-D molecular viewers such as Simple
Viewer, Kiosk Viewer, Protein Workshop etc. The left arrow
above the image, next to the Biological Assembly tab, switches
between the biological assembly (1-6) vs. the asymmetric unit.
Some viewers only work with asymmetric unit, and others work
with both the asymmetric unit and the biological unit.
The research paper that described the structure indicated that
while 6 copies of the protein (3 sets of dimers) were present in
the crystal, LepA/EF-4 appears to behave differently in solution
under reducing conditions.
**Question 2. Is the biological assembly identical to the
asymmetric unit? If not, is the biological assembly
stoichiometry present as a monomer (1 protein), dimer (2
proteins), trimer (3 proteins), or other?
7. Based on the domain definition of translation elongation
factor EF-G, the LepA/EF-4 protein can be subdivided into 5
domains (I, II, III, V, and CTD).

8. On the left side of the Structure Summary page for
“Biological assembly,” you will see a box containing an image
and links to 3-D molecular viewers such as Simple Viewer,
Kiosk Viewer, Protein Workshop etc. Click on the link that says
Protein Workshop
9. This will download the viewer. In the process of doing this it
will ask you if you want to trust this application. This is part of
the Java security mechanisms; you simply accept/trust each one
and click run when prompted. If nothing happens you may need
to check your internet downloads folder to find the “Protein
Workshop.jnlp file.”
What if you get this message?
A. Go to system preferences.
B. Click on the Security and Privacy icon.
C. File that was blocked should appear at the bottom – Click
“Open Anyway.”
Once the structure is loaded you should see something that

looks like the following:
The viewer is to the left and the control panels are to the right.
If you click and drag the mouse in the viewer you will see the
structure rotate. You can also zoom the structure by clicking the
middle button and dragging (or, shift+click with a one-button
mouse), and translate the structure using the right button (or
ctrl+click with a one-button mouse). Take a minute to get
familiar with these controls.
Protein Workshop automatically displays a ribbon
representation of the protein structure. This representation
represents the polypeptide chain of the protein, but uses flat
arrows to show beta strands and curly ribbons to show alpha
helices. The chain is also colored in rainbow colors from blue to
red from one end of the chain to the other, so you can follow the
chain as it folds into this complex structure.
10. Do the following to figure out which end is the N-terminus

vs. the C-terminus:
A. Select the Visibility tool
B. Select Atoms and Bonds for what you want the tool to affect.
C. (No options in the Visibility Tool)
D. In box 4, open up Chain A by clicking the sideways arrow,
not the folder icon. Scroll down and select the position of the
first amino acid. Selecting and deselecting will cause amino
acid #1 to appear (atom representation) and disappear. You can
rotate the structure to see how this piece fits in the overall
shape of the protein.
E. Follow a similar procedure to select the last amino acid.
**Question 3. Is the N-terminus the blue end or red end of the
protein? Is the C-terminus the blue end of red end of the
protein?
11. Click and rotate the protein to orient it as shown in the
picture below:
B. Select Ribbons for what you want the tool to affect.
D. In box 4, click on 3CB4 to make everything invisible. In
Chain A click the first amino acid 1-MET, hold down “shift”
and select amino acid 188-GLU to highlight all residues 1-188
with Ribbons.
Domain I, which spans residues 1-188, contains the consensus

GTPase fold and constitutes the characteristic G domain found
in all translational GTPases.
**Question 4. Based on your highlighting above, does a
consensus GTPase fold contain secondary structure with alpha
helices? Beta sheets? Both? None?
12. The structure of LepA/EF-4 closely resembles the known
structures of EF-G, as was expected from their high degree of
sequence similarity. To better recognize their similarities and
differences, the structures can be superimposed over one
another.
13. Return to structure summary page and select the “Structure
similarity” tab.
14. This tool searches the PDB database for other proteins that
resemble LepA. In this case, it will identify structure 2YWE.A,
which is a crystal structure of LepA/EF-4 from a different
bacteria than E. coli.
Click on “Show structure comparison results for representative
2YWE.A.” You will see a ranking of multiple structures that
look similar to LepA/EF-4, including Elongation Factor G (EF-
G), which is ranked #2 on the list.
15. Under the Results column, click on “view” next to
Elongation Factor G.

These results will show a direct comparison of LepA/EF-4 with
EF-G, with similar regions overlapped in orange/cyan, and
dissimilar regions indicated by gray coloring.
16. To get a better idea of which regions are identical/similar,
scroll down further until you reach the alignment blocks. Here,
the analysis is showing amino acid numbers (in 1 letter
abbreviation) of LepA/EF-4 (top row) and EF-G (bottom row).
Note the color coding key, which indicates which regions are
identical, similar, and/or structurally equivalent.
**Question 5a. Based on the alignment blocks, the regions of
~1-188 are highly similar/identical between LepA/EF-4 and EF-
G. What is the function for this region in these proteins?
**Question 5b. What stretch of amino acids within the 1-188
alignment is most similar/identical between the 2 proteins?
Hint: Look for both structural equivalence and identical
residues.
17. The GTPase fold domain I is one of the most conserved
regions of LepA/EF-4 and EF-G. Despite the presence of the
nucleotide-binding pocket, the researchers were unable to
cocrystallize GDP or GTP with the LepA/EF-4 protein crystals.
However, a previous structure of EF-G contains GDP bound in
the nucleotide binding pocket.

18. Go to the RCSB PDB website at http://www.pdb.org
19. Perform a “PDB ID” search by typing the structure code
“1FNM” in the text box on the search bar at the top of the first
page. Click the Search button.
20. This will take you to the Structure Summary page for the
crystal structure of a mutant EF-G protein co-crystallized with
bound GDP.
21. On the left side of the Structure Summary page for
“Biological assembly,” you will see a box containing an image
and links to 3-D molecular viewers such as Simple Viewer,
Kiosk Viewer, Protein Workshop etc. Click on the link that says
Protein Workshop
22. This will download the viewer. In the process of doing this
it will ask you if you want to trust this application. This is part
of the Java security mechanisms; you simply accept/trust each
one and click run when prompted. If nothing happens you may
need to check your internet downloads folder to find the
“Protein Workshop.jnlp file.”
The EF-G structure will look something like below, with Chain
A containing the amino acids, position 900 containing GDP, and
position 950 containing a magnesium (Mg2+) ion cofactor.

23. Do the following to analyze how GDP and Mg2+ interact
with EF-G:
B. Select Atoms and Bonds for what you want the tool to affect.
D. In box 4, open up Chain A by clicking the sideways arrow,
not the folder icon. Scroll down and select the following 3
amino acids:
A 26 THR, A 22 ASP, A 141 LYS
Selecting and deselecting will cause amino acids to appear
(atom representation) and disappear. You can rotate the
structure to see how this piece fits in the overall shape of the
protein.
**Question 6a. The authors of the EG-F structure suggest that
Thr26, Asp22, and Lys141 and Mg2+ are all involved in helping
to coordinate the GDP in the nucleotide binding pocket. Does
this coordination make sense based on their location relative to
GDP? Why or why not?
**Question 6b. How can amino acids Asp22 and Lys141 be in
such close spatial proximity even though there 119 other amino
acids located in between them?
**Question 6c. Ifyour GFP donor DNA inserted into the GTP
binding pocket of LepA/EF-4, do you believeGFP-LepA/EF-4
fusion protein would be functional? Why or why not?

**Question 6d. Based on the overall EF-4 structure, where do
you think the most likely location(s) would be for functional
GFP insertions? Write our your hypothesis and justify based on
EF-4 structure and function.
While crystal structures have been solved for EF-G and
LepA/EF-4, the precise mechanism of these proteins is still
unclear. To better understand their potential role in translation,
the authors of the LepA structure paper modeled EF-G and
LepA onto the structure of the 70S ribosome (tRNAs shown
bound to E/P site in (A – lower left) or E, P, and A sites in (B –
lower right). The high degree of sequence identity and
structural similarity of domains I and II of LepA and EF-G
supports the idea that they occupy similar binding sites on the
ribosome. However, homology modeling also suggests some
differences in their binding.
**Question 7. Based on the model below, do EF-G and LepA
appear to bind the ribosome differently? How might this
ribosome binding lead to differences in their function in
promoting ribosomal forward translocation or backwards
translocation?
Hint: Pay particular attention to the “A” site and reference
Figure 3 of your lab manual.

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