Flashcards in EXAM1- AA_pH_Hb_Mb Deck (40)
What is a coiled-coil? Example?
two a-helix combine; hydrophobic residues packed on inside of coiled coil.
How many amino acids make one turn of alpha helix? Primary structure. What happens to R groups in alpha helix?
3.6 amino acids per turn. Turn to outside
What stabilizes secondary structure interactions between peptide bonds?
Hydrogen bonds n peptide and a residue N+4 residues away
Describe the peptide bond
Planar, rigid, stabilized by hydrogen bonds between C=O and N-H groups in the peptide bond itself rather than the side chains.
How are beta sheets stabilized? What happens to R groups?
Strands lie next to each other and stabilized by inter-strands Hydrogen bonds between C=O and N-H groups in adjacent chains or strands.
R- Groups are pointed Above and Below the pleated sheet
Loops vs Turns?. What is most common turn?
Loop is a connecting region sequence.
Loops of 4-5 residues are called TURNS
Usually present in antiparallel beta strands
Types of tertiary structure
Fibrous or Globular. Can be all ahelix, all beta sheets, or combo.
Covalent, non-covalent (ionic, Hbond), and Hydrophobic forces stabilize Tertiary structure
Chymotrypsin and elastase are 40% primary sequence identity but have very similar tertiary structure. How is this possible?
Because of Conserved sequences where the residues are not identical but are very similar and can substitute for each other
When to use Xray crystallography? NMR? Cryo-Electron microscopy?
Xray- any size but proteins crystallize
What causes Sickle cell anemia?
single mutation at 6th Hb beta chain from Glu (hydrophilic) to Val (hydrophobic) - Hides Valine inside the membrane and causes sickle shaped cell no function/destroyed
Sickeling: HbS polymerizes into fibers that change shape of RBC and block blood capillaries when oxygen levels are low
Rosy color meat
High Hb- Store oxygen- high binding to 02.
75% ahelix, (8 alpha, named a-h), No quaternary structure
Tertiary structure results in GLOBIN FOLD DOMAIN
GLOBIN FOLD domain
crevice between helicies E/F for heme binding. Heme lays in the globin fold lined with mostly nonpolar AA's
HbA tetramer two ab Dimers.
Dimers Stabilized mainly by non-polar and some polar interactions.
Tetramer stabilized by ionic & Hydrogen bonds between two ab dimers.
What chains similar in Hb and Mb
alpha and beta chains similar to Hb.
Mb binds one heme via single globin fold while Hb binds 4 hemes via its 4 globin folds
group essential for proteins function (Heme group)
Protoporphyrin IX ring
Fe2+ with 6 coordination sites (4N and 2Water).
Hb containing ferric iron Fe3+. Not active in binding O2.
Why is the heme group necessary instead of just Fe2+?
O2 binding to Fe2+ would be irreversible w/ insoluble iron oxides and hydroxides. w/ Fe-Heme, binding O2 is looser and reversible.
What does the 5th and 6th coordination site bind to?
5th - proximal histidine of a helix of protein (f-helix)
6th- O2 molecule stabilized by Distal histidine residue (E-helix) of surrounding protein
What protein structure results in globin fold domain? what crevices?
tertiary structure hold globin fold domain of E/F helices.
Ehelix- heme- fhelix
Hyperbolic curve reps. sigmoidal?
hyperbola is Mb (o2 released at very low pressures)
sigmoid is Hb (o2 released at tissue level pressures)
Where/when is Hb in T(deoxyhb) or R (oxyhb) state?
T state in tissues as oxygen dropped off, when in lungs as T state, high oxygen gets T state to bind and cooperativity binds more oxygen till its in R state in the lungs then transports to the tissues and returns to T state
What creates a "relaxed" state?
binding of o2 changes tertiary and quaternary structure.
O2 binding, rotates on ab dimer 15 degrees. Beta subunits get closer. several ionic and Hbonds are disrupted in the rotation making a relaxed conformation.
What changes in tertiary structure when Hb binds O2?
Fe2+ moves into the plane of the porpyrin ring & pulls the proximal his along with it. The F Helix moves position relative to the heme group due to STERIC REPULSION
When Hb is in the R form what happens to the solvent filled central channel?
gets smaller. (R form is when oxygen is bound) and has less space
Can Mb be allosterically regulated? why?whynot?
NO! ONLY PROTEINS WITH QUATERNARY STRUCTURE CAN BE REGULATED ALLOSTERICALLY
What kind of binding curves to allosteric proteins have?
O2 is an example of what kind of effector? CO is what kind of effector molecule?
O2 is a HOMOTROPIC (true ligand)
CO is a HETEROTROPIC (different from true ligand)
What 6 effectors for Hb? Which ones Positive/Negative What shift?
1. 2,3bpg (negative) right shift
2. CO2 (negative) right shift
3. Temp (negative) right shift
4. H+ (bohr effect) right shift
5. CO (positive) left shift
6. O2 (positive) left shift
How does 2-3BPG work?
Negative charges form ionic bonds with positive inner channel of Hb and restrict the channel from getting smaller thus stabilizing the T state. Negative effector. Right shift. (this lets oxygen get delivered to tissues at higher pressures).
Cross links the two beta units of Hb and acts like a car jack, holding them apart in the T state..
What happens when to oxygen when Hb T-->R or R-->T
T-->R : oxygen in lungs "picking up O2" to go to tissues
R-->T: Hb "delivering O2" to tissues
If you interrupted glycolysis how would this affect Hb?
2,3BPG is a byproduct of glycolysis, so it could potentially have an effect on 2,3BPG concentrations in the cells?
how does Hb react w/o 2-3BPG? What does curve look like?
Hb reacts like Mb, hyperbolic curve- relaxed state favored
What makes fetal HbF have higher affinity for O2 than HbA of maternal?
HbF has no beta subunits so 2-3BPG can't bind. Without this negative allosteric effector, Hb binds o2 w/higher affinity
Where does Exhaled Co2 come from?
20% binds to positive charged N terminus of Hb- creating a negative carbamate ion which ionically bonds and stabilizes the T state. (carried from tissues to lungs)
75% is exhaled as bicarbonate (HCO3-)
What are 3 points of NEGATIVE EFFECTORS?
1. Stabilizes T state,
2. Shifts binding curve RIGHT,
3. Decrease o2 affinity (increases O2 release).
Where does H+ bind on Hb?
Beta subunit (fetal Hb doesn't have Bsubunit)
Role of Carbonic anhydrase?
converts H2CO3 into H20 and CO2 to get exhaled.
Protons from Hb released and react with HCO3- to form H2CO3
Why does Heme bind to CO much more than Hb or Mb?
Distal Histidine Sterically hinders CO from binding in Hb/Mb.
The binding affinity is still 210X higher for CO than O2 in Hb/Mb. (25,000X greater if heme alone).