Lecture 3 – Protein Structure & RegulationIntroduction to Proteins

Proteins are polymers of 20 different types of amino acids.

Central C-atom bonded to:o Amino Group –NH2

o Hydrogen Atomo Carboxyl Group –COOH connected to next Amino Group

When the carboxylic group of one molecule reacts with the amino group of another molecule a water molecule is released this is called a condensation reaction.

o Rn group which is connected to 1 of 20 different amino acids. Grouped based on properties of side chains,

Nonpolar Uncharged Polar Negatively Charged (Acidic) Polar Positively Charged (Basic) Polar

Levels of Protein Structure

o Primary Structure Plain string of amino acids.

o Secondary Structure Hydrogen bonding between the Hydrogen on the N-H group and the

Oxygen of a C = O group.

o Tertiary Structure Interactions between the R-Chains of the molecules creates tertiary

structure. Ionic bonds Hydrogen bonds Hydrophobic interactions Disulfide bridges

o Quaternary A protein which contains two or more amino acid chains in 3D space.

Lecture Outcomes

Protein coding genes in the DNA via transcription become mRNA. The mRNA leaves the nucleus and through translation is used to take free amino acids to produce a polypeptide.

Free Ribosomes vs ER Bound Ribosomeso Free ones are located in the cytoplasm of the cell where as some may be

located on the surface of the endoplasmic reticulum.o Free Ribosomes produce proteins used in the cell such as proteins used for

the metabolism of glucose.o Bound Ribosomes produce the proteins transported out of the cell which are

proteins required for a specific function such as digestive enzymes. The Regulation of Protein Abundance

o Transcription: Copying DNA into mRNA (Messenger RNA)o Translation: The process where a Ribosome will translate the mRNA into an

actual protein.o mRNA Decay: The mRNA don’t have an infinite life span and may decay

within minutes or hours. mRNA transcript abundance is affected by rates of transcription and rates of decay.

Measuring protein abundanceo Measuring transcript abundance, a transcript is a specific mRNA which can be

measured in a cell through the lab. Changes in transcript abundance often reflect changes in protein abundance.

What controls transcript abundance? Rate of transcription vs Rate of Decay.

o Protein abundance is the balance between the rate of protein synthesis, rate of translation, and the rate at which proteins break down.

Heat Shock Responseo The cellular response to heat shock, used to study transcript and protein

abundance.o Chlamy cells shifted growth from 24dc to 40dc, they do not enjoy the heat.o Different Gene Expressions

Constitutive Transcript abundance remains the same. Usually for housekeeping genes, the ones which will keep the

cell alive regardless of the heat shock. Induced

Abundance goes up first for transcript abundance which leads to the protein abundance.

Repressed Transcript abundance goes down, and therefore protein

abundance. Possible defects which may or may not account for lower levels of functional

photoreceptors.o Anything which could lower the amount of opsin would affect the number of

photoreceptors.o Protein Decayo Photoreceptors also need retinal (non-protein factor)

o Retinal is not coded by a gene but rather the enzymes convert the precursor which are coded for by different genes. If one enzymes pathway becomes shutdown the retinal will not be made.

Cofactor (Retinal) + Apoprotein, the protein without the cofactor required for it to work. (Opsin) = Functional Protein (Rhodopsin).

Creation of rhodopsin requires post-translational modification. This doesn’t apply to every protein but many enzymes.

o Post-translation modification, making opsin is not all that is required as the opsin must still be binded to retinal.

Proteins must be folded into its correct tertiary confirmation to be functional. Its native conformation is the correct tertiary structure.

Anfesnsen’s Dogmao Protein folding is spontaneous (done within milliseconds) and starts before

the end of translation. Dependent entirely on primary sequence of amino acids. Tertiary structure depends on the primary structure.

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. Anything that interacts with the amino acids could cause the proteins to denature.

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. In cells when there are so many polypeptides being synthesized at the same time it’s an issue because the concentrations of proteins are so high the folding of the proteins gets inhibited. Molecular chaperones will help proteins attain their native confirmations even under conditions of the protein crowding. *REQUIRES ATP*