transport proteins

transport proteins!

A mnemonic for remembering the types of transport proteins:
Can I Carry The Ruddy Red Apple?

  • Can: Channel Proteins
    • open passageways for certain hydrophilic substances (polar/charged molecules)
    • example: aquaporins are a passage for water
  • I: Ion Channels
    • passage for ions
    • example: gated channels (nerve/muscle cells) open to specific chemical/electrical signals
  • Carry: Carrier Proteins
    • bind to specific molecules that are transferred across when protein changes shape
    • example: glucose enters cells by carrier proteins
  • The: Transport Proteins
    • use energy (ATP) to actively transport materials across membrane
    • example: sodium potassium pumps use ATP to maintain Na+/K+ concentrations outside/inside cell
  • Ruddy: Recognition Proteins
    • gives cells unique identification, recognize self and foreign cells
    • actually glycoproteins, proteins with short polysaccharide chains
    • example: different blood types have cells with different recognition proteins
  • Red: Receptor Proteins
    • binding sites for hormones/other triggering molecules
    • specific cell response activated
  • Apple: Adhesion Proteins
    • attach cells to neighboring cells 
    • provide anchors for internal filaments/tubules

List of proteins from (Cliffsnotes AP Biology Workbook 4th Edition)
Mnemonic credits to Caitlin ^-^

Molecule of the Day: Methylphenidate

Methylphenidate (C14H19NO2), also known as Ritalin, is a white powder that is slightly soluble in water. It is commonly used to treat ADD, ADHD, and narcolepsy.

Methylphenidate inhibits dopamine and norepinephrine transporter proteins, thus preventing dopamine and norepinephrine in the synaptic cleft from being reuptaken into the presynaptic knob. The resultant higher concentration of these substances in the synapse causes the receptors on the postsynaptic knob to be stimulated at a greater frequency, thus achieving greater synaptic transmission. This produces a psychostimulant effect, allowing it to be used in the treatment of ADHD.

In small amounts, methylphenidate has also been shown to enhance memory and control, caused by the activation of dopamine and adrenergic receptors. However, in large doses, it can have the opposite effect.

It has few side effects, which include loss of appetite, nausea, and insomnia. However, like many strong dopamine reuptake inhibitors, it can result in dependence, and is often seen as a gateway drug. 

Methylphenidate is industrially synthesised through a multi-step pathway from 2-bromopyridine and benzyl cyanide.

Requested by @zenbra

Consciousness is Self Awareness

Self awareness is not thinking. That is cognition. A dandelion doesn’t think as we do as it has no brain nor nervous system. Yet it “knows” that it is this and not that. A stone or a star doesn’t. It is a conceit of human beings to think that the consciousness of other beings is somehow inferior because it is not like ours. A dandelion will fight for its survival as anybody who has ever maintained a lawn can attest. It will compete for water, soil, sun and growing space. Yet even at a smaller level, within the cells of the dandelion are machines made of just a few molecules. These machines bend proteins. They move within the cell with directed purpose carrying out the actions which need to be done for survival. Life is all about purpose. 

Here is a transport protein in action. It has no brain. No nervous system. No onboard intelligence of any kind yet it reacts with the world. It will transport this molecule where it is needed within the cell and then go back for more. It is clearly self aware. Again, not with thought. But by its purposeful action.

How I memorise numbers

As a student in biochemistry I often end up having to memorise proteins that have names like Cdc65/Rab51/Sec61/eIF4E…

I’ve found a good technique to memorize them: I visualise the numbers as different colours!

1 is black, 2 is light blue, 3 is orange, 4 is light purple, 5 is red, 6 is yellow, 7 is dark green, 8 is and 9 is brown.

It’s probably better if you try to find which colour you personally associate each number with.

It really helps when you have to learn lots of different steps and all the proteins have weird names with numbers in them and none of them are in the right order. If you just remember “So first comes blue, then comes red” then you can work out for yourself that the first factor is *protein*2 then the second one is *protein*5.

For example, I can always remember Sec61 (an important translocator for transporting nascent proteins across the ER membrane) because I just have an image in my head of it as something yellow and black!

Visualising numbers as colours is something that people who experience synesthesia naturally do. I just “taught” myself how to do it aswell!

I hope this comes in handy for all you studyblrs :)

~ studyingbiochem

Na+ / K+ pump
  • moving sodium and potassium ions across the cell membrane is an active transport process 
  • involving the hydrolysis of ATP to provide the necessary energy. 
  • enzyme = Na+/K+-ATPase
  • process is responsible for maintaining the large excess of Na+ outside the cell and the large excess of K+ inside
  • sodium-potassium pump is an important contributer to action potential produced by nerve cells. 
  • (P-type ion pump –> ATP interactions phosphorylates the transport protein and causes a change in its conformation)

For each ATP that is broken down, it moves 3 sodium ions out and 2 potassium ions in. As the cell is depleted of sodium, this creates an electrical gradient and a concentration gradient, both of which are put to use for many tasks.

Mechanism

(from wikipedia lol)

  • The pump, after binding ATP, binds 3 intracellular Na+
    ions.
  • ATP is hydrolyzed, leading to phosphorylation of the pump + release of ADP.
  • change in the pump exposes the Na+ ions to the outside. The phosphorylated form of the pump has a low affinity for Na+ ions, so they are released.
  • The pump binds 2 extracellular K+ ions. This causes the dephosphorylation of the pump, reverting it to its previous conformational state, transporting the K+ ions into the cell.
  • The unphosphorylated form of the pump has a higher affinity for Na+
    ions than K+ ions, so the two bound K+ ions are released. ATP binds, and the process starts again.