Lecture 3 Protein Structure & Regulation

Introduction to Proteins

Proteins are polymers of 20 different types of amino acids.

Central C-atom bonded to:

o Amino Group NH2
o Hydrogen Atom
o 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 Ribosomes
o 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 dont 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 abundance
o 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 Response
o 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 Decay
o 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 doesnt 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.
Anfesnsens Dogma
o 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 Denaturation
Frying 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 its 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*