Our stated goal ...
Topic: Energy transduction & use via molecular machines -
pumping/transport, coupled reactions. Cells use a set of closely
related non-equilibrium mechanisms to get things done. We want to
understand the (simple) underlying kinetic mechanisms and discuss a few
examples.
Reading (see References): Read about active transport in your favorite book. Some choices:
- Alberts, Ch. 11
- Baby Alberts, Ch 12
- Berg, Ch 13, Section 14.1
Meeting summary - Tues, May 15 meeting
We attempted to address the
question, “How does driven (coupled) transport work?” Thus, for example, how can a difference in
ion concentrations across a membrane be used to drive the flow of some small
molecule across that membrane?
Our discussion focused around Fig.
13.11 of Berg which shows a putative cycle of states for coupled
transport. The key element in the cycle
is the coupling of binding and conformational change. From a physics point of view, a cycle appears
to be reversible, so it is necessary to understand how a cycle can be
driven. In our discussion, we used
equilibrium as a reference point. In
equilibrium there is equal flow in both directions around a cycle and so no
active pumping can occur. But if a (non-equilbirium)
uni-directional flow can be added at any
point in the cycle, the cycle will be driven in the direction of that flow.
(Here flow refers to flow through the space of states, which typically
also will imply flow of matter.)
Our abstract discussion of cycles
suggested that there is no reason why the same basic description could not be
used to explain both “symporters” and
“antiporters” – that is, where the physical flow of the driven species is in
the same direction or opposite that of the driving species.
We also discussed how a
uni-directional chemical reaction (e.g., hydrolysis of ATP) could be used for
active transport if it can be coupled to a suitable conformational change in a
transporter. A cycle related to that of
Berg Fig. 13.11 can be drawn. In
principle, any “activated” (out-of-equilibrium) molecule/carrier can be used to
drive transport.
Our discussion did not probe the
structural mechanisms by which binding events can be couple to conformational
changes suitable for transport. Hopefully we will cover this next time.
