Search Results for: kinetics

Kinetics #6: Pulse-Chase Experiments

In our sixth post on Understanding Kinetics, we consider pulse-chase experiments which are a common method to study bio-synthetic pathways. In pulse-chase experiments: A “pulse” of labeled metabolite (P) is added to culture media. The down-stream intermediates ((P1, P2, P3, … Continue reading

Kinetics #5: Molecular Complexes (e.g. drug-target)

In our fifth post on Understanding Kinetics, we consider the speed at which molecular complexes form. This is the fundamental mechanism underlying drug action (i.e. drugs inhibition their targets) and cellular signalling (i.e. ligands activate their receptors) and is probably … Continue reading

Kinetics #4: Reversible On-Off States

In our fourth post in the Understanding Kinetics series we consider the speed at which proteins can turn off (A) or on (B). The dynamics of such processes are important to consider when designing experiments (i.e. How long should I … Continue reading

Kinetics #3: Branch Points in Biochemical Pathways

In a follow up to our posts on Intuiting Enzyme Kinetics and Sequential Biochemical Pathways, we next wanted to consider the kinetic curves branch points in biochemical pathways (or equivalently kinetic competitions). Luckily exact mathematical models exist for competitive first-order … Continue reading

Kinetics #2: Sequential Biochemical Pathways

In a follow up to our post our post on intuiting enzyme kinetics, we next wanted to consider the kinetic curves for sequential biochemical pathways. Luckily exact mathematical models exist for sequential first-order processes (see below) and we can use … Continue reading

Kinetics #1: Catalyzed Reaction Timescales

Most chemical and biochemical research concerns reaction that are catalyzed by either an enzyme or a chemical catalyst. Unfortunately, when we learn chemical kinetics, it is usually in the context of idealized: uncatalyzed 0th-order, 1st-order of 2nd-order chemical reactions. Luckily … Continue reading

Timescales, Kinetics, Rates, Half-lives in Biology

Understanding interactions between processes with different rates can made significantly easier when you know the approximate timescales or half-lives for those processes.   Comparing two processes (e.g. alpha helix folding of a peptide chain (micro seconds (10-6s)) and translation of … Continue reading

How do you “Fractionate” a Cell?

Different scientific questions focus on different parts of the cell and it is often necessary to break a cell up into those different pieces (figure above). While various “-omic” methods are well suited to answering global/systems-level questions for the four … Continue reading

ELISA-based High Throughput Screening

  In a follow-up to our post introducing ELISA, we wanted to discuss a common application of this technique: small molecule inhibitor screening. The set up is relatively simple (1) Coat a 96-well plate with your two proteins of interest … Continue reading

Introduction to ELISA

ELISA or Enzyme-Linked Immunosorbent assay is the most commonly used method for measuring proteins concentrations in solution. It is extensively used both in the laboratory (e.g. culture supernatant) and the clinic (e.g. blood tests) due to its simplicity and adaptability … Continue reading

How does pronation affect running?

Pronation describes the roll of the foot from “initial impact” (at the outer heal of the foot) to “toe-off” at the front of the foot.

How Much Time to “Get in Shape”?

For distance running there are three main factors that determine racing performance (or fitness): Oxygen transport (VO2max), Lactate Threshold (LT) and Running Economy (RE). The figures below, illustrate how training/de-training affects each of these factors over time:

The “Impact” of Running

Have you ever wondered why your calves are sore after a 5k but your hamstrings are sore after a marathon? The reason is your calves bear more of your weight as you run shorter/faster and your quadriceps bear more of … Continue reading

The Science of Drafting

Recently, while running a workout on a windy track, I started wondering about the science of air-resistance and drafting.   More specifically, I wondered what difference was between 10 mph tail-wind and the 10mph head-wind I encountered on opposite sides of the track … Continue reading

Estimating Metabolite/Protein Concentrations from RNAseq Data

Under steady-state conditions, it is possible to estimate the concentration of a metabolite from the amount of protein and the amount of protein from the amount of mRNA (see figure above). In general, the conversion factors used for these calculations … Continue reading