Lecture 4 Information Flashcards
What are proteins used for in neurons?
involved in the movement of ions across a membrane
involved in the formation of membrane potential
Tertiary structure
the total geometric rearrangement of all atoms in a polypeptide
includes the 1º and 2ºstructure
What stabilizes the tertiary structure?
1) Hydrogen bonds
2) Hydrophobic interactions
3) Disulfide bonds
4) Ionic bonds
5) Van der Waals interactions
When do we see disulfide bonds in the 3º structure?
places that are very hot use Van der Waals interactions to help stabilize
Quaternary structure
Two protein units come together
Protein units can have independent functions
Protomers
quaternary structures with the same peptide subunits
Example of a protomer
hemoglobin has 4 similar groups
Prosthetic groups
a covalently bonded group to the peptide that is not an amino acid
Cofactors
interact with enzymes/proteins through NONCOVALENT means
Example of a prosthetic group
Vitamin K is found in enzyme that modifies thrombin
Fibrous proteins
long, extended rope-like proteins
mainly used to give structure
Globular proteins
compact – blobby proteins
used for “action” (enzymes, regulators, movers)
Huge diversity of globular proteins
Alpha keratin
An example of a fibrous protein
Has a repeating alpha helix structure
Can be strengthened through a disulfide bond
Has hydrophobic regions that point towards each other and stabilize each other
Collagen
An example of a fibrous protein
Found in tendons, cartilage, bone, cornea
Left-handed helix
Chains of collagen are cross-linked by modified lysines
Collagen tripeptide repeat
Gly-X-Y
Glycine is used because it has no R-group. Can be very tightly packed
X is normally proline. This forms a kink which leads to helical structure. Proline can also contribute to a left-handed helix
Y is often times hydroxyproline
What are 2 main uses for glycine?
it allows proteins to be tightly packed or it allows for flexibility/turns
Silk
fibrous protein
Gly and Ala are used because small R-groups can pack tightly with each other in B-sheets
Myoglobin
globular protein
an oxygen storing protein
What is the red section on the inside of myoglobin?
A prosthetic “heme” group
Heme group is found in hemoglobin and myoglobin to bind oxygen because of the presence of the ion atom
Motif
a recognizable folding pattern involving 2 or more 2ºstructures and the connections between them
a+B motif
structures tend to have alpha and beta regions as almost separate subunits of the protein
a/B motif
structures have alpha and beta subunits very close together
hard to separate
Domains
separate units of protein structure
physically part of the same polypeptide
an independently stable and functional part of a protein that can undergo movement as a single entity
Example of types of domains within a protein
Some domains may be used to: bind ligands, enzymatic activity, etc
Three types of post-translational modification of proteins discussed
1) Phosphorylation
2) Glycosylation
3) Add lipids
Phosphorylation of a protein
can accept a phosphate group on amino acids that have a hydroxyl group (T, S, Y)
if you make one of these amino acids have a negatively charged phosphate group, you could lead to repulsion from nearby amino acids
or, you could make the protein more functional
Glycosylation
can attach sugars to a protein
sugar tags allow for better identifcation of a protein
can also increase functionality
Attaching lipids to a protein
creates lipid-anchored proteins
these proteins can embed themselves within the phospholipid membrane
What is the functional state of a protein?
It’s folded state!
Which conformation of a protein will prevail?
the one with the lowest energy
How do polypeptides fold?
they fold in stages
first, independent secondary structures arise
then, these secondary structures collapse into a 3D conformation
Native state of a protein
the fully folded, functional state of a protein
What 4 things will cause a protein to denature?
1) Addition of urea
2) Changes in temperature
3) Addition of organic solvents
4) Changes in pH
What does the addition of urea and mercapoethanol tell us about protein structure? Why?
the primary structure encodes the tertiary structure
disulfide bonds break and the proteins unfold. then, when the urea and mercapoethanol is removed, the protein returns to the same 3D shape
Why does heat denature a protein?
heat breaks the weak Hydrogen Bonds
Why does the addition of organic solvents denature a protein?
organic solvents make the surrounding environment much more hydrophobic
hydrophobic groups of the protein will face outwards now
Why can changes in pH denature a protein?
the R-group ionization states will change
this might cause repulsion or destabilization
What drives protein folding?
the increase in entropy of the aqueous environment by placing hydrophobic groups together in middle of protein
Do proteins have a final 3D structure?
No! They are constantly moving about and changing
What is a problem with unfolded proteins?
If unfolded proteins are floating in the cytoplasm, they can interact with other unfolded proteins and form a precipitate
Molecular chaperones
helper proteins that help proteins fold in order to keep proteins from floating around unfolded
HSP
heat shock proteins
type of molecular chaperone
when there is an increase in temperature, more HSPs are found
more proteins unfold at higher temperatures, so need more HSPs
Chaperonins
will bind to unfolded proteins
protein is put inside of complex in order to refold into correct conformation
large percentage of hydrophobic groups within the complex
hydrophobic groups are forced to interact with each other and refold
Do chaperonins require a lot of atp?
yes!
Ubiquitin ligase
marks proteins that are targeted for destruction with a ubitiquin mark
proteasomes will break down proteins with the ubiquitin tag
this allows proteins parts to be recycled
Amyloid diseases
occur due to a misfolding mechanism in proteins
proteins become unfolded and congregate within the cell
Alzheimers and proteins
Alzheimers is an amyloid disease
a large complex of unfolded proteins will congregate outside of the cell and cause surrounding cells to die
this is the “holes” in the brain we see in Alzheimers patients
Prions
misfolded proteins with the ability to transmit their misfolded shape onto normal variants of the same protein
seen in mad cow disease
Mad cow disease
neural protein becomes unfolded and takes on a different shape
unfolded shape exposes phenylalanine and other aromatic amino acids
aromatic amino acids congregate through hydrophobic interactions (amyloid disease)
How does mad cow disease get into human brain?
through lesions digestive tract
prions can get to the brain
Why is mad cow disease hard to treat?
you are trying to breakdown proteins not cells
would have to use something like sodium hydroxide which is very unsafe
Why does mad cow disease have such a high latency period?
unfolded proteins accumulate slowly
there are more normally folded proteins than unfolded proteins
Is myoglobin a motif, domain, or 3D protein?
Myoglobin is all 3
the folded structure is a motif found in all globin proteins and it folds into a single domain which this single domain is also the 3D structure for myoglobin
“Well” energy diagram of protein folding
around the top of the ring is an unfolded protein
secondary structures sample each other at the bottom of the well
when the correct low energy conformation is found, the protein collapses into the well
What happens at the bottom of the energy well for proteins?
even at the bottom there is not one conformation
protein is not static
will move between a couple similarly stable conformations
Parasite Schistosoma mansoni
uses an enzyme to break the collagen sequence in the skin
Gly-Pro-X-Y sequence is cut between X and Y
Parasite Schistosoma mansoni
uses an enzyme to break the collagen sequence in the skin
Gly-Pro-X-Y sequence is cut between X and Y
Structures of proteins in terms of increasing complexity
secondary structure < folding motif < protein domain < tertiary structure < quaternary structures
Structures of proteins in terms of increasing complexity
secondary structure < folding motif < protein domain < tertiary structure < quaternary structures
3 types of motifs
B-a-B, helix-turn-(loop)-helix, B-barrel
Where is the helix-loop-helix motif used?
in the binding of DNA/gene expression
Where is the B-barrel motif used? And give a specific example
a pore in membranes
ex: bacteria will insert a B-barrel into a red blood cell and this will lyse the blood cell
Is myoglobin a single polypetide?
yes!
Where is the helix-loop-helix motif used?
in the binding of DNA/gene expression
Where is the B-barrel motif used? And give a specific example
a pore in membranes
ex: bacteria will insert a B-barrel into a red blood cell and this will lyse the blood cell
What is myoglobin mostly made up of?
alpha helices
Is myoglobin a single polypetide?
yes!
Do heat shock proteins require energy?
yes, it is an endergonic process
What happens if a heat shock protein can’t get a protein to fold?
the protein goes to a chaperonin
Do heat shock proteins require energy?
yes, it is an endergonic process
What happens if a heat shock protein can’t get a protein to fold?
the protein goes to a chaperonin
