Transcript RiboRobot - mcs.alma.edu

RiboRobot
Mark Meyer, Byong Lee, Dee Parks
Overview
Molecular biology has many mechanistic
features, not unlike robots. Protein translation
consists of reading a sequence of DNA amino
acids and forming a corresponding protein. In
this lab your robot will simulate the ribosome
that moves along the DNA strand. For every
three bases, it selects a certain amino acid and
attaches it to an ongoing protein.
Biology Background
• What DNA looks like (A, C, T, G)
• What RNA looks like (A, C, U, G)
• How RNA is created inside the nucleus and travels
outside where the ribosome (our robot) picks it up
and translates it into a polypeptide
• How polypeptides fold up into complicated shapes
to form a protein (major computational challenge)
Input
• Sequence of colored strips laid side by side
(we know that black, red, white, green are
distinguishable).
• Robot will travel from one strip to the next,
stop and sample the color. We’ll need to
calibrate the travel time to correspond to
strip width.
Task 1 Output
• Play one of 4 tones for every base that is
read.
Task 2 Output
• Display a number between 1 and 20 on the
LCD after every 3rd strip. This corresponds
to an amino acid.
Task 3 Output
• When the robot reaches a special codon
called a stop codon, display all of the amino
acids in sequence from the beginning.
Internals
• Translation mechanism from color to base number
(1, 2, 3, or 4).
• Translation mechanism from every 3 colors to an
amino acid number (1 - 20).
• Stop the robot when the stop codon is found.
• For task 3, store the amino acid into an array.
When done, display array contents in order.
Background Reading
• http://www.wikipedia.org. Search for
“translation (genetics)” and “DNA”.
• Handout on finite state machines.
Pre-Lab Exercises
• Hand in polypeptide sequence given an
RNA sequence and the coding numbers.
• Complete the finite state machine that
translates three bases into an amino acid.
• Turn in hand-written encoding of finite state
machine (nested if-else statements).