EXAM1- AA_pH_Hb_Mb

Question 1

What is a coiled-coil? Example?

Answer 1

two a-helix combine; hydrophobic residues packed on inside of coiled coil.
Example: a-KERATIN

Question 2

How many amino acids make one turn of alpha helix? Primary structure. What happens to R groups in alpha helix?

Answer 2

3.6 amino acids per turn. Turn to outside

Question 3

What stabilizes secondary structure interactions between peptide bonds?

Answer 3

Hydrogen bonds n peptide and a residue N+4 residues away

Question 4

Describe the peptide bond

Answer 4

Planar, rigid, stabilized by hydrogen bonds between C=O and N-H groups in the peptide bond itself rather than the side chains.

Question 5

How are beta sheets stabilized? What happens to R groups?

Answer 5

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

Question 6

Loops vs Turns?. What is most common turn?

Answer 6

Loop is a connecting region sequence.

Loops of 4-5 residues are called TURNS
Usually present in antiparallel beta strands

Question 7

Types of tertiary structure

Answer 7

Fibrous or Globular. Can be all ahelix, all beta sheets, or combo.

Covalent, non-covalent (ionic, Hbond), and Hydrophobic forces stabilize Tertiary structure

Question 8

Chymotrypsin and elastase are 40% primary sequence identity but have very similar tertiary structure. How is this possible?

Answer 8

Because of Conserved sequences where the residues are not identical but are very similar and can substitute for each other

Question 9

When to use Xray crystallography? NMR? Cryo-Electron microscopy?

Answer 9

Xray- any size but proteins crystallize

NMR- small

Question 10

What causes Sickle cell anemia?

Answer 10

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

Question 11

Sickeling

Answer 11

Sickeling: HbS polymerizes into fibers that change shape of RBC and block blood capillaries when oxygen levels are low

Question 12

Rosy color meat

Answer 12

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

Question 13

GLOBIN FOLD domain

Answer 13

crevice between helicies E/F for heme binding. Heme lays in the globin fold lined with mostly nonpolar AA’s

Question 14

Hb Composition

Answer 14

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.

Question 15

What chains similar in Hb and Mb

Answer 15

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

Question 16

Prosthetic group

Answer 16

group essential for proteins function (Heme group)
Protoporphyrin IX ring
Fe2+ with 6 coordination sites (4N and 2Water).

Question 17

MetHb

Answer 17

Hb containing ferric iron Fe3+. Not active in binding O2.

Question 18

Why is the heme group necessary instead of just Fe2+?

Answer 18

O2 binding to Fe2+ would be irreversible w/ insoluble iron oxides and hydroxides. w/ Fe-Heme, binding O2 is looser and reversible.

Question 19

What does the 5th and 6th coordination site bind to?

Answer 19

5th - proximal histidine of a helix of protein (f-helix)

6th- O2 molecule stabilized by Distal histidine residue (E-helix) of surrounding protein

Question 20

What protein structure results in globin fold domain? what crevices?

Answer 20

tertiary structure hold globin fold domain of E/F helices.

Ehelix- heme- fhelix

Question 21

Hyperbolic curve reps. sigmoidal?

Answer 21

hyperbola is Mb (o2 released at very low pressures)

sigmoid is Hb (o2 released at tissue level pressures)

Question 22

Where/when is Hb in T(deoxyhb) or R (oxyhb) state?

Answer 22

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

Question 23

What creates a “relaxed” state?

Answer 23

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.

Question 24

What changes in tertiary structure when Hb binds O2?

Answer 24

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

Question 25

When Hb is in the R form what happens to the solvent filled central channel?

Answer 25

gets smaller. (R form is when oxygen is bound) and has less space

Question 26

Can Mb be allosterically regulated? why?whynot?

Answer 26

NO! ONLY PROTEINS WITH QUATERNARY STRUCTURE CAN BE REGULATED ALLOSTERICALLY

Question 27

What kind of binding curves to allosteric proteins have?

Answer 27

sigmoidal

Question 28

O2 is an example of what kind of effector? CO is what kind of effector molecule?

Answer 28

O2 is a HOMOTROPIC (true ligand)

CO is a HETEROTROPIC (different from true ligand)

Question 29

What 6 effectors for Hb? Which ones Positive/Negative What shift?

Answer 29

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

Question 30

How does 2-3BPG work?

Answer 30

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..

Question 31

What happens when to oxygen when Hb T–>R or R–>T

Answer 31

T–>R : oxygen in lungs “picking up O2” to go to tissues

R–>T: Hb “delivering O2” to tissues

Question 32

If you interrupted glycolysis how would this affect Hb?

Answer 32

2,3BPG is a byproduct of glycolysis, so it could potentially have an effect on 2,3BPG concentrations in the cells?

Question 33

how does Hb react w/o 2-3BPG? What does curve look like?

Answer 33

Hb reacts like Mb, hyperbolic curve- relaxed state favored

Question 34

What makes fetal HbF have higher affinity for O2 than HbA of maternal?

Answer 34

HbF has no beta subunits so 2-3BPG can’t bind. Without this negative allosteric effector, Hb binds o2 w/higher affinity

Question 35

Where does Exhaled Co2 come from?

Answer 35

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-)

Question 36

What are 3 points of NEGATIVE EFFECTORS?

Answer 36

1. Stabilizes T state,
2. Shifts binding curve RIGHT,
3. Decrease o2 affinity (increases O2 release).

Question 37

Where does H+ bind on Hb?

Answer 37

Beta subunit (fetal Hb doesn’t have Bsubunit)

Question 38

Role of Carbonic anhydrase?

Answer 38

converts H2CO3 into H20 and CO2 to get exhaled.

Protons from Hb released and react with HCO3- to form H2CO3

Question 39

Why does Heme bind to CO much more than Hb or Mb?

Answer 39

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).

Question 40

Where does CO bind? what happens?

Answer 40

CO binds same site as O2
Reduces O2 transport by Hb
Increases affinity of O2 for Hb (OXYGEN wont release)
LOCKS R STATE (oxyhb).
if CO binds, Hb now acts more like a O2 storage than a carrier.