RSS

Monthly Archives: March 2014

More on the Lac Operon

A while ago I wrote two posts about the Lac Operon here. The first pointed to an animation by McGraw Hill Publishers that did a pretty good job illustrating how the operon works. In the second post, I highlighted the notion of polycistronic messages (more than one gene per mRNA molecule) and how this allows for control of a number of related genes at once – a trait not shared by eukaryotic cells. In that second post, I also finished with a graph of how cells grow in the presence of glucose and lactose.

image002

Cell Growth in the presence of glucose + lactose – As glucose is depleted, cells adjust to lactose digestion

One feature of that graph (reproduced here) that is notable is a little bump in the growth rate as glucose runs out and the cell converts to lactose digestion. A second important feature is that the rate of growth slows when the cell is burning lactose as its primary fuel.

 

Together, these features suggest that the cell is regulating lactose digestion very closely. In fact, there are two primary mechanisms of this regulation to appreciate. The first is that the lactose-digesting enzymes are controlled together on an operon that is regulated by lactose itself (or at least we can assume so for simplicity’s sake). In the absence of lactose, no lactase enzymes are made and no lactose is used as fuel. The reason for this is obvious when you look at the slope of cell growth under glucose metabolism (left) and lactose metabolism (right). Clearly, growth is SLOWER when lactose is used as fuel.

Therefore, so long as there is glucose, it is pointless to digest lactose at the same time. So it is best to only turn on the lac operon in the ABSENCE of glucose – regardless of whether lactose is present of not.

If glucose is absent and lactose is absent, turning on lactase enzymes is still useless. However, slow growth is better than no growth. So we should have a mechanism to turn on the operon when there is lactose in the environment.

Here’s a matrix of ideal regulation:

Screen Shot 2014-03-31 at 2.18.05 PM

How can a little, mindless bacteria achieve this exquisite control?

Simple: By using two regulators. One for glucose and one for lactose. Only when both conditions (glucose-, lactose+) are met do we make lactase.

Structure of the Lac Operon

operon1

First, lactose itself serves as an inducer. In the absence of lactose, a regulator protein binds to a DNA site between the polymerase binding site (the promoter) and the structural genes (the enzymes). When the regulator binds, its presence physically prevents the progress of RNA Polymerase.

When lactose is present, it binds the repressor protein in a way that causes its shape to change in a way that can no longer bind the DNA. The repressor then drifts away from its binding site allowing RNA Polymerase a clear shot to the structural genes.

operon2

However, RNA Polymerase is not always parked on the promoter waiting for the repressor to be removed. Its binding requires another protein to help stabilize its interaction with the DNA. This second protein is the CAP protein. The Catabolite Activated Protein. However, CAP alone will not bind either. It requires a signaling molecule called cyclic AMP (cAMP). cAMP is readily broken down when glucose is in the cell, so it only accumulates when glucose is absent. In that case, cAMP accumulates and binds to the CAP protein, which then binds to the CAP site. This site is located adjacent to the promoter, but on the side away from the structural genes. When CAP binds, it assists in recruiting the RNA polymerase to the promoter.

operon3

Therefore, if only one condition is met, it is insufficient to promote gene transcription. Only when the CAP+ cAMP protein is bound will the Polymerase be recruited. And only when lactose is present, will the repressor protein let the Polymerase pass.

operon4

In terms of the matrix we set forth above, we can see that these molecular interactions result in exactly the regulation that is optimal:

post-operon

 

Advertisements
 
Leave a comment

Posted by on March 31, 2014 in Uncategorized

 

Tags: , , , , , , , ,

The AntiSocial Network

Scientific American reports the best use of technology since the TV Remote. Image

The Cloak app, for example, collects location info from Instagram and Foursquare to let you know where your so-called “friends” are—so tat you never have to see them. It scans their most recent check-ins, and plots those locations on a map. It can even alert you when the guy you owe twenty bucks to is nearby.

Cloak developers Brian Moore and Chris Baker say they came up with the idea after too many chance encounters with ex-girlfriends. They plan to expand Cloak to interface with other apps, including Facebook. And they insist their feelings won’t be hurt if they suddenly stop bumping into their Cloak-using friends.

—Larry Greenemeier, Mar 28, 2014

Image

Your Checklist to see if you might benefit from the Cloak App:

  • Do you retreat from others in anticipation of rejection?
  • Are you preoccupied with being rejected or criticized in social situations?
  • Do you fear embarrassment when participating in new activities?
  • Do you have poor self-image or feelings of social ineptitude?
  • Do others think you are self-involved and unfriendly?
  • Do you Create elaborate fantasy lives in your head?

If you agree with two or more of the above, you may be ready to hide away from friends and relations!

Just Click the App Icon and start avoiding today.Image

 
2 Comments

Posted by on March 28, 2014 in Uncategorized

 

Tags: , , , , , ,

Anagram Collection

Below are anagrams which all relate to one another in some way.

Image

not a hint

Unscramble the anagrams and tell me what they all have in common.

  1. Overseas John
  2. Barman Notes
  3. Druid Reefer Keg
  4. Horse Movers
  5. Simmer Key

 

Anyone can answer (send your answers to jtreml.fscc AT gmail  DOT  com) , but these anagrams are also hints for my microbiology class’ quiz on chapter 11. I don’t have any prizes I can offer, but if there is sufficient interest, I may offer future games with prizes in the future either here or at 100filmsin100days.wordpress.com, that’s my other blog on film (mostly bad ones).

 
Leave a comment

Posted by on March 26, 2014 in Uncategorized

 

Tags: , , ,

Ignorance and Misinformation Assist in Measles Resurgence

 

 

Measles cases are on the rise again in the US. Why is it that this ‘eradicated’ (in the USA) virus is still causing harm?

ImageIt’s been about 15 years since Andrew Wakefield first suggested that:

We have identified a chronic enterocolitis in children that may be related to neuropsychiatric dysfunction. In most cases, onset of symptoms was after measles, mumps, and rubella [(MMR)] immunisation. Further investigations are needed to examine this syndrome and its possible relation to this vaccine.(1)

Wakefield clarified this statement in an interview with Brian Deer:

I have to say that there is sufficient anxiety in my own mind of the safety, the long term safety of the polyvalent, that is the MMR vaccination in combination, that I think that it should be suspended in favour of the single vaccines. (2)

Reading the initial publication, there is not a very convincing argument made for the vaccine causing autism. And it would be curious why Wakefield would make such a connection –  except that he was also in the process of forming a company with a patented test for “autistic enterocolitis” that could produce $43 million (US) in revenue for investors according to the prospectus.(3) That might be reason enough. Further, the primary interest that lead to the investigation of whether the MMR vaccine might cause autism came not from a sound scientific hypothesis, but from lawyers willing to pay for study results that could be used in their ongoing prosecution of drug manufacturers. According to the British Medical Journal, Wakefield received $674,000 in compensation as payment for doing this research and also in support of Wakefield’s new diagnostic company, Carmel Healthcare Ltd. (4)

Over the years Wakefield has bobbed and weaved like a boxer shifting his hypotheses on how MMR vaccine causes autism from Measles proteins migrating from the location of the shot, to the gut and then to the brain – to the Mercury preservative, thimerosal – to the number of antigens (immune-stimulating particles) children are faced with as they receive their first vaccines. Nevertheless, his results have not been duplicated (to the extent that they were shown to begin with) and no additional evidence has come forward supporting any of these speculations.

The resulting controversy dealt a heavy blow to immunization efforts in the UK. Meanwhile, in the United states, which officially eradicated Measles in 2000, record numbers of cases are now being reported. So far 20 cases of the disease have been reported in New York (5), while another 32 have been reported in California which “allows parents to opt out of vaccinating their children if they fill out a form stating they don’t believe in vaccinations.”(6)

ImageThanks, Dr. Wakefield. Most of us have forgotten what Measles looks like. Now we can remember.

For more information about Measles, see the WHO fact sheet:

  • Measles is one of the leading causes of death among young children even though a safe and cost-effective vaccine is available.
  •  In 1980, before widespread vaccination, measles caused an estimated 2.6 million deaths each year.

 

 

References:

1. RETRACTED: "Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children" AJ Wakefield, SH Murch, A Anthony, J Linnell, DM Casson, M Malik, M Berelowitz, AP Dhillon, MA Thomson, P Harvey, A Valentine, SE Davies, JA Walker-Smith The Lancet  28 February 1998 (Volume 351 Issue 9103 Pages 637-641 DOI: 10.1016/S0140-6736(97)11096-0)
2. http://briandeer.com/wakefield/royal-video.htm
3. http://www.cnn.com/2011/HEALTH/01/11/autism.vaccines/
4. "Secrets of the MMR scare: How the vaccine crisis was meant to make money" 2011. http://www.bmj.com/content/342/bmj.c5258
5. "Measles Outbreak Now Up To 20 Cases In New York City"20 March 2014. http://www.huffingtonpost.com/2014/03/19/measles-new-york_n_4994100.html?utm_hp_ref=mostpopular
6. "Surge in measles cases continues: California now has 32 in 2014" 14 March 2014. http://www.scpr.org/news/2014/03/14/42809/measles-cases-continue-to-rise-in-california/
 
12 Comments

Posted by on March 21, 2014 in Uncategorized

 

Tags: , , , , , , , , ,

Something for my Micro Students to do Over Spring Break

Image

 

Image

 
Leave a comment

Posted by on March 18, 2014 in Uncategorized

 

Tags: , , , ,

A quick followup on that lac operon post

Last week I posted a quick link about operons for my micro class to check out before taking their quiz on bacterial gene regulation This post is intended to complement that one. To go back to that post, click here. If there’s one thing to remember about operons it is that bacteria, lacking a nuclear membrane, regulate their genes differently than Eukaryotes. Having a nuclear membrane separates transcription and translation into two distinct compartments allowing for more subtle tweaking of Eukaryotic mRNAs before they are exported for translation.

Image

Click on this figure to go to a good description of how polycistronic genes work

One thing this does is it makes it very beneficial to package genes with related function closely on the genome and use a single regulatory region to control them all together. They wind up getting packed so closely together that they are actually expressed as a single messenger RNA – known as a polycistronic (meaning ‘many gene’) message.

Upstream of this polycistronic cassette are regulatory elements. One element common to all regulatory elements is the promoter. The promoter consists of several elements which ‘promote’ the binding of an RNA polymerase to the DNA. Additional regulatory elements exist to ensure that this polymerase only transcribes the genes if they are needed. In doing so, the cell conserves energy and components (e.g. Amino Acids) for only necessary processes.

In the case of the paradigm lac operon, lactose is a fuel source, but not as good as glucose. Therefore, enzymes to digest lactose are only needed when lactose is present, but glucose is not. In order to interrogate both conditions, two additional regulatory elements are present.

First, the operator sequence. This sequence binds a repressor protein that physically blocks the polymerase’s path in the absence of lactose. However, if lactose is present, the sugar binds to the repressor, causing a conformational (shape) change that causes the protein to release its grip on the operator sequence.

Second, a catabolite activator protein (CAP) will only bind to the DNA behind the RNA polymerase if cAMP is present. Let’s not get too distracted, other than to say that cAMP levels are high in the ABSENCE of glucose, and low when that sugar is present. When cAMP binds to the CAP protein it can now bind the DNA and do it’s other job: making a nice binding site for the RNA polymerase. Without CAP, the polymerase binds very inefficiently.

Together, the production of lactase enzymes (those that digest lactose) is exquisitely controlled in a way that conserves the most energy.

ImagePs – take a look at this graph and tell me why (not mechanistically, but rationally) the cell does not make lactase enzymes when both glucose and lactose are present.

 
Leave a comment

Posted by on March 15, 2014 in Uncategorized

 

Tags: , , , , , , , , , ,

Micro Crossword

 

 

 

 

 

 

Image

 

Image

 
Leave a comment

Posted by on March 12, 2014 in Uncategorized

 

Tags: , , , , ,