Lecture 3: Protein Structure & RegulationProtein Abundance: Points on ControlProtein coding genes are found in DNA and via transcription the DNA gets turned into mRNA. This mRNA will leave the nucleus and through translation the information in the mRNA is used to take free amino acids along with the ribosome to produce a polypeptide (Protein). How much of a specific mRNA do I have in a cell? (Transcript Abundance). Changes in transcript abundance often reflect changes in protein abundance.

mRNA molecules being produced or rate of transcription vs mRNA decay, These are two competing processes. *EVERYTHING BREAKS DOWN IN BIOLOGY*

Protein abundance can be directly measured also. Rate of synthesis, translation, and the rate at which they break down.

Heat Shock Response, Chlamy cells shifted growth from 24dc to 40dc.Take 10mL of cells out and check transcript and protein abundance, then put it in a 40dc room and take out another 10mL to once again check a transcript and protein abundance.

Constitutive (Actin, housekeeping protein or gene) staying the same expression. Induced (HSP, relatively low amounts and the heat shock increases transcription

abundance and protein abundance.) Repressed (When the transcription abundance and protein abundance will decrease in

response to the heat shock. The repression is caused by? What causes transcription abundance or the repression?)

Photoreceptor Abundance Rgill mutation in mouse affects vision (Makes them Blind) Retinal is not coded by a gene! These are molecules that are products of biosynthetic

pathways. Retinal is not a gene but the enzymes that make it are coded by genes.o Retinal is a cofactor + apoprotein Functional Protein.o Post-Translational Modification

Protein Folding

For a protein to be functional it must acquire the correct tertiary structure.

Urea ^If the Urea is replaced with a buffer then the protein will refold. Itself. Native Confirmation: The state which makes the protein functional. Protein folding does NOT require anything to fold but the folded shape is spontaneous and done in milliseconds.

What drives protein folding?

Native confirmation is considered the lowest energy state. Predicting native confirmation is really tricky because if you have a protein that’s 100 aa long there are 5 x 10^47 difference confirmation yet it only takes milliseconds for it to occur.

The protein doesn’t test anything. There is an algorithm. It starts with hydrogen bonding and the strong secondary structure starts which is a hydrophobic effect, there is an urge that drives protein folding in amino acids.

Folding@Home is a way to pool CPUs to predict folding a CPU.

Protein DenaturationFrying an egg is looking at a protein denaturation. The native confirmation has been lost since it requires hydrogen bonding, ionic bond, covalent bond which could be lost by things like heat and pH and other chemicals like salt.

Sometimes denaturation is reversible and sometimes not reversible. Denatured proteins results in misfolding. Incorrect molecular interaction and loss of activity. Protein concentrations too high will inhibit normal protein folding. Molecular chaperones will help proteins attain their native confirmations even under conditions of the protein crowding. *REQUIRES ATP*