Chapter 4 Flashcards
What is Kinesin?
motor protein, transports cellular cargo like organelles
What determines the function of a protein?
it’s shape
What is a primary structure? (1’)
linear sequence of amino acids
What holds together a primary structure?
peptide bonds hold together the linear AA’s
What is a secondary structure? (2’)
They are alpha helixes and beta strands
What holds together a secondary structure?
H-Bonds in the backbone of AA’s
What is a tertiary structure? (3’)
it is a 3D structure of a polypeptide
Other characteristics of the tertiary structure?
- 1 protein and 1 polypeptide
- H-bonds, Hydrophobic bonds, Van Der Waals, and polar/ non-polar bonds hold this together
- all of secondary elements come together
What is a Quaternary Structure? (4’)
It is the same as a tertiary structure but it has 2 or more polypeptides
What is the shape of an alpha helix?
It is helix/ spiral shaped
what is the shape of a beta-strand?
Shaped like an arrow
What type of bond does protein folding depend on?
weak non-covalent bonds
Where are the hydrophobic bonds on the folded protein?
Inside
Where are the non-hydrophobic bonds? (hydrophilic)
Outside
What is a homodimer?
The same peptide twice
What is responsible for denaturing (unfolding) proteins?
- Urea
- Change in PH or Heat
- Noncovalent bonds break first
What happens when the urea is removed?
The protein refolds into it’s original conformation
What is the native state of a protein?
full biological activity
What do chaperones do?
chaperones help proteins fold in the cell
What happens if chaperones are absent?
Proteins won’t have biological activity (which could lead to disease)
What would happen to a protein without chaperones?
They would fold incorrectly
One example of a disease caused by misfolded proteins
Mad Cow Disease (Bovine SPongiform encephalopathy) which is an infectious neurodegenerative disease
What causes Alzheimer’s Disease
plaques in brain amyloid beta protein aggregation
Where do H-bonds occur in an alpha helix?
They make up the back-bone and occur every 4 amino acids
What proteins have the propensity to form an alpha helix?
M.A.L.E.K
What makes up the backbone of the beta-sheet?
H-bonds
What are the two types of beta sheets?
Parallel and Antiparallel
What proteins have the propensity to form beta sheets?
W.I.F.T.Y.V.
What are Amphipathic Motifs?
They are coils comprised of Hydrophobic and Hydrophilic components
Where are Amphipathics Motifs found?
proteins are commonly found within the lipid bilayer
What is a protein domain?
any segment of a polypeptide that can fold independently
Factors for Binding site compatibility
-Size
-Shape
-Specific Interactions
What do Enzymes do?
catalyze reactions
How do Enzymes catalyze reactions?
- Orients two substrate molecules
- Rearrange charges in substrate
- changes shape of substrate
What is a Ligand?
Any substance bound by a protein
What is another way to describe drugs (medicine)?
They are Ligands
What causes Chronic myelogenous leukemia?
reciprocal translocation of chromosomes 9 and 22 (this speeds up cell division and prevents DNA repair)
What is Linade and what does it do?
It is a Phosphorphorylate, it turns on mechanisms
Why are some patients immune to the effects of Gleevec?
Random mutations in the BCR-Abl protein
What is Nilotinib?
It is a second-generation CML drug, created by binding the Gleevec structure to the Abl Kinase domain.
What does the positive track look like?
A makes B, then B makes C.
A -> B -> C
What does Negative feedback look like?
A makes B which makes X, when too much of X is created, the Feedback Inhibitor stops X from being produced.
What is Allosteric Regulation?
The regulatory molecule binds to sites other than the active site (induces conformational change)
What is the role of ADP in Allosteric Regulation?
It is needed so the sugar can bind effectively to the Alosteric site.
What does Protein Kinase do during phosphorylation?
Adds a phosphate group and it turns protein on
What does protein Phosphatase do during Phosphorylation?
It removes the phosphate and turns protein off.
DO eukaryotes have a five prime cap?
yes
do prokaryotes have a five prime cap?
no they have an RBS
