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Q: Graph ( Answered,   0 Comments )
Subject: Graph
Category: Science > Biology
Asked by: tedmccall-ga
List Price: $10.00
Posted: 08 Jul 2005 16:03 PDT
Expires: 07 Aug 2005 16:03 PDT
Question ID: 541403
I would just like to know what are graphs used for in relation to
finding proteins. Just comment on what they are trying to say.
Subject: Re: Graph
Answered By: welte-ga on 10 Jul 2005 07:16 PDT
Hi Ted, and thanks for your question.

I believe you are asking about graphs (or charts) in general.  A two
dimensional graph is a way of summarizing how one variable varies with
respect to another.  By convention, the variable plotted on the
vertical (y) axis is the dependent variable and the one along the
horizontal (x) axis is the independent variable.

What this means is that the variable along the horizontal axis is
changed, for example, in an experiment, and we measure what value we
get for the vertical axis variable.  A simple example would be an
independent (x) variable of time spent studying and a vertical axis
(y) of scores on exams.  One would expect that as x increases in this
case, the values of y should also increase.

The graph is a very useful tool for seeing how data vary and trend. 
For example, perhaps after several hours of study, scores on exams
actually drop.  The graph can't tell us why this might happen - maybe
it's due to fatique or some other factor.  Maybe scores plateau at
some value of time spent studying.

With regard to proteins, one might look at conformation vs.
temperature (e.g., at high temperature, proteins lose their
conformation), charge vs. amino acid content, etc.  There is a
tremendous range of graphs that might be made for the study of
proteins, depending on what specifically is being looked at.

Similarly, one can graph a function, usually written as y = f(x),
where f(x) is a function of x.


There are many basic introductions to graphing available online.  Here are several:

A very introductory page can be found here, which explains the
concepts I've outlined above in a somewhat different way.  The first
section on line graphs is likely to be the most relevent for you.

At Education Resources for Adults, you can find a more in depth look
at graphing, including various types of graphs such as line graphs,
bar graphs, pie charts, and scatter plots.  I recommend doing all of
the exercises after each lesson.  The only way to really learn math or
science is to do problems.

The 42Explore site has a good page on graphs.  I recommend doing the
exercises near the bottom of the page after reading the above pages
and completing those exercises.

The Wikipedia has a useful page describing the Cartesian coordinate
system on which line graphs and scatter plots are made.  You can read
about it here:

Monica Yuskaitis has put together a Powerpoint presentation describing
in very straight forward terms how to go from a question to various
types of graphs.  The data in each graph is the same, so you can see
how different graph and chart types can be used to depict the same

Thinking about graphs used to describe proteins specifically, here are
some examples:

As I mentioned above, one can describe a proteins conformational state
using graphs.  One way to do this is to look at the percentage of
alpha helices and beta pleated sheets over time.  Here is an example
for the folding of lysozyme and for cytochrome C:

Somewhat more philosophical is the well-known work of Edward Tuft on
the visual presentation of scientific data and quantitative
information.  He has written several books that go well beyond simple
graphs and make for fascinating reading.  Here's his site and link to
some of his texts:


I hope this information was useful.  Feel free to request clarification.

There are no comments at this time.

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