a: Protein ~
b: different sized noodles
What:
"How is protein gel electrophoresis useful? It's like making spaghetti- when you finish boiling the noodles, you strain the noodles away from the water. The noodles don't do through the holes in the strainer because they're too big. If they were smaller, the noodles could fit through the holes. Proteins are like different sized noodles and the agarose gel is like a strainer, filled with little holes. Proteins that are small moves easily through the holes in the agarose gel, while larger proteins move more slowly, getting stuck in the holes in the gel. Thus, protein gel electrophoresis allows students to spread out the proteins from different bovine tissues, creating a protein fingerprint that serves as a barcode to identify that type of cell or tissue. "
Writer: Not Stated
LCC:
Where:
Date: Feb 21 2014 6:24 PM
They No Like Water
a: protein ~
b: Wicked Witch
What:
"Sometimes proteins are like the Wicked Witch. Add water, wait a nanosecond and you can almost hear that piteous whimper. "I'm mel-l-l-ting!" Well, not really. But there may be an audible groan from biochemists as they observe simulations of a large protein or DNA in water. For a few hundred picoseconds of simulation time it looks fine, then the molecule appears to unravel. It's been a troubling problem, but with a series of computations at the Pittsburgh Supercomputing Center, Tom Darden and Lee Pedersen seem to have it fixed. "
Writer: Tom Darden
LCC:
Where:
Date: Feb 21 2014 6:25 PM
The Slutty G Protein......
a: G protein ~
b: a dancer who takes different forms
What: "One of the questions that scientists ask is how the same protein G is able to generate different responses depending on the signals received. In this paper, researchers show how the beta
subunit of G protein adopts different three-dimensional structures depending on the effector molecule to which it is linked. "The G protein is like a dancer who takes different forms according to its dance partner"
Writer: Ernest Giralt
LCC:
Where:
Date: May 7 2013 6:52 PM
a: ras protein ~
b: operator
What:
"Picture a switchboard operator of old. There she sits, in front of a dizzying array of toggles and lights, ready to push buttons and stretch cords to connect incoming calls to just the right recipient. She might even listen in on the conversations from time to time. The protein Ras is like that operator."
See the link for a good picture and longer discussion.
Writer: Leigh MacMillan
LCC:
Where:
Date: Feb 24 2014 4:18 PM
a: Protein pumps ~
b: channel made of protein
What:
Writer: Not Stated
LCC:
Where: Reference Link Has Evaporated
Date: Sep 14 2014 6:27 PM
Another Molecular Switch....
a: Protein kinase ~
b: switch
What: "Protein kinases are like switches that turn other proteins on or off," said Dr. Wilson. "A number of tumor cells have these switches abnormally turned on or off, and this abnormal activity contributes to the survival of the tumor."
Writer: Dr. Wyndham Wilson
LCC:
Where: Reference Link Has Evaporated
Date: May 9 2013 7:40 PM
a: Protein folding ~
b: a drunk trying to parallel park
What: "Vijay has said that protein folding is like a drunk trying to parallel park a car so here the one who had made most progress was picked as basis for the new Generation. The less successful parkers were added into statistics and their progress was.. well.. canceled. All the new Runs/Clones started from the point where that fastest Run/Clone of the previous Generation had reached. "
Writer: Vijay
LCC:
Where: Reference Link Has Evaporated
Date: Sep 4 2014 8:07 PM
a: protein folding ~
b: playing Pebble Beach blindfolded
What:
"If you just look at the physics of the problem, protein folding is like playing Pebble Beach blindfolded, except much harder. The golf course here is the "conformational phase space" corresponding to a given chain of amino acids, a vast if notional terrain across which are laid out all the possible shapes that a given chain of amino acids could."
Writer: Oliver Morton
LCC:
Where:
Date: Sep 4 2014 8:09 PM
a: Protein folding ~
b: the diffusion of a particle
What:
"In order to make experimental or theoretical progress in understanding the dynamics of folding, we need a simpler description that uses a far smaller number of coordinates. The most optimistic model is one-dimensional: protein folding is like the diffusion of a particle along a one-dimensional path."
Writer: Steve Hagen
LCC:
Where: Reference Link Has Evaporated
Date: Sep 4 2014 8:10 PM
Trial And Error
a: protein folding ~
b: evolution by natural selection
What:
"In reality, protein folding is like evolution by natural selection. As a protein starts to fold, local structures form quickly, leading to a dramatic reduction of the available 'space' to be searched. These local structures then try out a more limited number of structures, with successive steps nailing down more and more of the correct structure. What seemed like a miracle is now quite well-understood, although it's still a challenge to actually predict the specific steps for a given protein."
Writer: Ashutosh Jogalekar
LCC:
Where:
Date: Sep 4 2014 8:12 PM
a: protein folding ~
b: a child growing up
What:
"One could say that a protein folding is like a child growing up. If he grows up nice, clean and proper (folds), Great!. If he's a foul mouthed hoodlum (sp?) mis-fold. Hmmmm "
Writer: BuiesCreek847
LCC:
Where:
Date: Sep 4 2014 8:02 PM
a: protein folding ~
b: a ball rolling down a funnel
What:
" The process of protein folding is like rolling a ball from the top of the
funnel to the bottom. The funnel-shaped free energy landscape predict that
the protein folding is a parallel event rather than a sequential event."
Eventually it finds its lowest energy state at the bottom of the funnel, but the process is not a direct path.
Writer: Taisong Zou
LCC:
Where:
Date: Sep 4 2014 8:15 PM
a: protein channel ~
b: a gate
What:
"So, a protein channel is like a gate that is put into the membrane to allow glucose to pass through the gate and get across the membrane"
Writer: Rebekah
LCC:
Where:
Date: Feb 8 2015 8:19 PM
a: protein crystal ~
b: a string of beads
What:
"You can make move the string of
beads to make different patterns. A
protein crystal is like a string of
beads that is held in a certain
pattern so that it has its own shape."
Writer: Not Stated
LCC:
Where:
Date: Jul 22 2015 9:52 AM
a: Protein synthesis ~
b: factory or ipod
What:
From the link:
"In this activity you are asked to show your understanding of the different parts of the protein synthesis process by identifying them with a comparable step from another similar process. The Construction Analogy has the steps in order of their action in the cell. The IPOD and Candy Factory analogies have their steps mixed up and you will need to think a little harder to figure them out."
Writer: Not Stated
LCC:
Where:
Date: Jul 26 2014 3:24 PM
a: Protein synthesis ~
b: stringing beads
What: "Two other concepts were also revolving around in my head. One was an idea proposed two years earlier by scientists in California and in Paris to explain how cells manage to make proteins as accurately as they do. Protein synthesis is like stringing beads, but the trick is to select the right bead each time from the twenty different kinds that are available, and to do this at speed using rather basic molecular machinery. The new idea, called "kinetic proofreading," showed that cells could in principle be as accurate as they liked, but only at a cost. The cost was the use of extra chemical energy that would be needed to fuel the high-accuracy selection process. This was important because the model of error catastrophe showed that cellular meltdown could be avoided if proteins were made very accurately."
Writer: Tom Kirkwood
LCC:
Where:
Date: Oct 25 2013 6:49 PM
a: Protein synthesis ~
b: building a paper clip chain
What: "Protein synthesis is like building a paper clip chain in the dark: you clip on the next amino acid, then pass it to the other hand as a handle for the growing chain. If you didn't successfully snap a new clip onto the growing chain, then when you pass it to the other hand, you won't have anything to hold onto, and the chain will fall to the ground"
Writer: Orpheus
LCC:
Where: Reference Link Has Evaporated
Date: Oct 25 2013 6:51 PM
a: Protein synthesis ~
b: making candy in a candy factory
What: The link is a .doc file with a worksheet.
Writer: Not Stated
LCC:
Where:
Date: Oct 25 2013 6:57 PM
a: protein synthesis ~
b: factory or ipod
What: From the link: "In this activity you are asked to show your understanding of the different parts of the protein synthesis process by identifying them with a comparable step from another similar process. The Construction Analogy has the steps in order of their action in the cell. The IPOD and Candy Factory analogies have their steps mixed up and you will need to think a little harder to figure them out."
Writer: Not Stated
LCC:
Where:
Date: Jul 26 2014 3:24 PM
a: protein structure ~
b: opening up a clock
What:
"Looking at the protein's structure is like opening up a clock and understanding how all the parts fit together and work in unison," said co-author Joseph Noel. "With x-ray instruments from our lab at the Salk Institute, we looked at Orf2 from 30 feet away. With SSRL, we can look at it with a magnifying glass if we need to. That's an essential part of the whole process."
Writer: Joseph Noel
LCC:
Where:
Date: Sep 4 2014 11:45 AM
a: protein structure ~
b: a ball on a sloping floor
What:
"..Seattle biochemist David Baker explains it, a protein's structure is like a ball on a sloping floor: It will find its lowest energy state just as the ball will naturally roll to the surface's lowest point. Figuring out the "correct" shape of a given protein, then means finding the shape with the lowest energy level."
Writer: David Baker
LCC: QD
Where:
Date: Sep 4 2014 11:49 AM
a: Lipoprotein lipase ~
b: squirrels of the forest
What:
"Lipoprotein lipase is like the squirrels of the forest, gathering nuts and burying them in secret places as insurance against droughts or a long winter."
From:
"The Right Bite"
Writer: Stephanie Dalvit-McPhillips
LCC:
Where:
Date: Sep 18 2014 11:15 AM
a: protein translation ~
b: misnomer
What:
In a cell mRNA is translated into proteins. Proteins are synthesized from mRNA. It's important to use the correct words in this context.
Writer: Your Mammal mother
LCC:
Where: Reference Link Has Evaporated
Date: Oct 24 2015 11:03 AM
Wtf
a: Protein confirmation ~
b: that of an ideal chain
What: "In the first case the protein conformation is like that of an ideal chain. whereas it is similar to an excluded volume chain in the second one. The corresponding values of the contour length, the statistical length, and the apparent radius of the chain cross-section are given."
Writer: Calmettes, P.
LCC:
Where:
Date: May 3 2013 12:15 PM
Often A One Way Street......
a: Protein denaturation ~
b: a turkey cooking
What: "Protein denaturation is like a turkey cooking-globular proteins turning into stringy bits from heat forcing them to unfold. Amyloid formation is more like the plastic timer thingies that come in the turkey, they get to a certain point and go POP, then turn into something longer that can't be re-set."
Writer: Big Blue
LCC:
Where:
Date: May 6 2013 10:19 AM
Hmmmm......?
a: Protein denaturation ~
b: destroying a lock but not opening the door
What: "To use an analogy Digestion of proteins is like putting a key into a lock & opening it. Protein denaturation is like blowing the lock apart but the door remaining closed....Protein digestion breaks the structure of the various amino acids links into its components, whilst denaturation basically renders them ''gloop'' to the body which it cannot do anything with.
"
Writer: Not Stated
LCC:
Where:
Date: May 6 2013 10:22 AM
More Physical Than Chemical
a: Protein denaturation ~
b: melting wax, a very soft wax
What: This change is more physical than chemical. Proteins in their native natural active state are not really solid, but kinda globular gelatinous in nature. When they are heated, in the 35 to 45 degree range, they ,in essence, melt. Melting is a phase transformation not a chemical reaction. The melting changes the 3-d structure of the protein usually rendering it inactive. This would be the result with an enzyme such as a protease.
Writer: Lucretia
LCC: QD
Where: Reference Link Has Evaporated
Date: May 6 2013 10:29 AM
a: protein purification ~
b: a frozen tear drop
What:
"protein purification is like a frozen tear drop, you can never know its
implication until you experience
it."
Writer: Edwin Kamau
LCC:
Where:
Date: Dec 2 2014 11:56 AM
a: Protein phosphorylation ~
b: switch on an enzyme
What: "Phosphorylation happens when a phosphate group is added to a protein. Phosphorylation is like a switch that activates proteins, altering their function and changing cell signalling pathways. These signalling pathways are like cellular control panels. Deregulated cell signalling, when the control panel malfunctions, is a common hallmark of disease."
Writer: Alicia Lundby
LCC:
Where:
Date: May 14 2013 2:19 PM
10 Reasons
a: Protein crystallization ~
b: Dating
What: 1) In the beginning, you have no idea what you are doing.
2) Some people use score cards.
3) You may have to try a lot of conditions before finding one that works. The rest are in the link.
Writer: sassysubstrates
LCC:
Where:
Date: Jul 26 2013 4:29 PM
Go Home An D Go To Bed.....
a: Protein crystallization ~
b: watching paint dry
What: But one thing I have noticed is, watching a crystallization is like watching paint dry. I usually try to do my crystallizations overnight, so I don't fuss over them (and usually disturb them, or put them in the fridge too soon, etc).
Writer: smuv
LCC:
Where:
Date: Jul 26 2013 4:32 PM
A Nano-sculpture.....
a: Building a 3-d protein model ~
b: looking at a piece of sculpture in a gallery
What: "Building a 3-D model is like looking at a piece of sculpture in a gallery. Only by walking around the piece and viewing its various sides and angles can the brain build a mental image of the art and fully comprehend its dimension, perspective, and scale. The same is true using a computer. Only by piecing together many different views of a molecule from a microscope can a computer build a model of the molecular assembly."
Writer: Jason Socrates Bardi
LCC:
Where:
Date: Oct 8 2014 4:34 PM
The Letters Matches
a: Inferring protein function from homology ~
b: solving an American crossword puzzle
What: "View it in these terms: Inferring protein function from knowledge of the function of a close homologue is like solving the clue of an American crossword puzzle. Finding the word that satisfies the definition may be difficult but the task is in principle straightforward. Working out
the function of a protein from its sequence and structure is like solving the clue of a British
crossword puzzle. It is by no means obvious which features of the definition are providing the
real clues, as opposed to misleading ones. Also, for both types of puzzle and for the suggestion
of a protein function, even if your answer appears to fit it may be wrong."
Writer: Arthur M. Lesk
LCC:
Where:
Date: May 9 2013 5:45 PM
