Tertiary and Quaternary Protein Structures (Zhao L3) Flashcards
What are some characteristics of the fibrous tert. protein structue?
Insoluble (typically)
Made from a single secondary structure
Structural or Protective function
What are the two protein tertiary structures?
- Fibrous
2. Globular
What are some characteristics of the globular tert. protein structure?
Water soluble OR Lipid soluble (membrane proteins) Generally made up of many secondary structures
Why are loops and turns important in tert. protein structure?
Allow for more diverse 3D structure connecting the secondary (beta sheet, alpha helix) structures
Can play a functional role in the molecule
Which two amino acids are very common in loops and turns?
- Glycine - small = flexibility
2. Proline - ring bond to backbone N makes it disrupt helices and sheets.
How are loops important in antibodies?
The variable region of an antibody have loops with residues that recognize antigens.
What is a “motif” in protein structure?
A common arrangement of secondary structures that occurs similarly in different proteins and has similar functions across different proteins.
What is a “domain” in regards to protein structure?
A stable globular unit in a protein with a more-or-less independent function.
e.g. binding domain vs. activator/repressor domain
Suppose a fibrous protein contains only alpha helices connected by S-S bridges. What is its likely function(s) and location(s)?
It is tough, rigid, hard and likely
found in nails or horns
alpha-Keratin
Suppose a fibrous protein contains mostly cross-linked triple helixes with a flexible (HyPro) linker. What is its likely function(s) and location(s)?
High tensile strength, not stretchy
Tendons, cartilage
Found in Collagen
Suppose a fibrous protein contains mostly non-covalently held beta sheets (van der Waals interactions). What is its likely functin(s) and location(s)?
Soft, flexible, non-stretchy
Egg sac, nest, web.
Silk
Give some examples of globular proteins
myoglobin, ferritin hemoglobin, serotonin transporter antibodies, cytokines actin, myosin chymotrypsin, lysozyme
Ligands bind to binding proteins via ______ forces enabling the interaction to be ________.
non-covalent
transient
Define K_d for a ligand binding to a protein.
The concentration where half the available ligand is bound to the protein.
Describe the lock and key model for ligand binding.
High specificity enabled by size, shape, charge and hydro-phobic/phillic character of the ligand and binding protein.
Describe Induce Fit for ligand binding.
Conformational changes to the ligand and binding protein upon binding to achieve a better fit.
What does Myoglobin do?
Stores Oxygen for later use
Where / How does myoglobin bind oxygen?
“buried” deep in the protein. Heme ring reversibly binds oxygen.
Heme binds CO ___________ than O2.
20,000 times better
How does hemoglobin optimize O2 binding, transport and delivery?
Multiple binding sites interact with each other. Once the first heme group binds, others have higher affinity for O2. (T & R states)
What is the T state of hemoglobin and what tissue is it likely found in?
T = tense. low O2 affinity
found in Tissues to release O2 for use
What is the R state of hemoglobin and what tissue type is it usually found in?
R = relaxed
high O2 affinity
found in the lungs for better O2 binding
What is the Bhor effect in regards to hemoglobin O2 affinity.
Reciprocal relationship of hemoglobin affinity for O2 and CO2 dep. on pH
Low H+, CO2 affinity (High pH) –> high O2 affinity
High H+, CO2 affinity (Low pH) —> low O2 affinity
What are some methods for determining protein structure?
- X-ray crystallography
2. NMR (yay!)
