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Biochemistry and molecular science > Module 3 > Flashcards

Module 3 Flashcards

Protein function

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Biology 101 flashcards
1
Q

What does immunoglubilin consist of and how are they bonded to each other

A

4 sub units, 2 heavy chains and 2 light chains, interchain disulfide bonds

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2
Q

Why does antibodies evolved to be multivalent

A

Due to avidity

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3
Q

Why has hemoglobin evolved to be mltimeric

A

Because it exhibits allosteric

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4
Q

What is allosteric

A

regulation of an enzyme by binding an effector molecule at a site other than enzyme’s active site

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5
Q

what is multivalent

A

Having several sites at which attechment to an antibody or antigen can occur

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6
Q

What is multimeric

A

Having multiple polypeptide chains

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7
Q

What is the saturation of myoglobin and hemoglobin in comparison

A

myoglobin has higher affinity with O2 at lower pressure that exhibits a hyperbolic curve while hemoglobine have a lower affinity with O2 at a lower pressure which exhibits a sigmoidal curve

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8
Q

What are the two functions of Mb

A

storage of oxygen in muscles, it can release oxygen when rapidly contracting muscle

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9
Q

Where does the oxygen bind to in Mb

A

Binds to Fe2+ of the heme prosthetic group

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10
Q

What is oxygen in Mb

A

Ligand

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11
Q

What is equilibrium dissociation constant, Kd?

A

Free protein(P)*free ligand(L) divide by protein ligand complex(PL)

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12
Q

What is the equation for fraction of protein binding sites occupied, deter

A

deter = [PL]/([P]+[PL]

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13
Q

What is the mid point of the dissociation graph called

A

Kd

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14
Q

What is the mid point of protein-ligand interaction graph called

A

P50

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15
Q

Can myoglobin transport O2?

A

No, because the affinity with O2 is too high, does not release even when pressure drops in tissues(4kPa) be cause the P50 is too small. But it binds well in lungs (13kPa)

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16
Q

What is the tense state of hemoglobin’s purpose

A

more interactions, more stable, lower affinity for O2

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17
Q

What is the relaxed state of hemoglobin’s purpose

A

Fewer interactions, more flexible, higher affinity for O2

Triggers from T to R state when O2 is binding

18
Q

What happens during the conformational change from T state to R state?

A

Breaking salt bridges between the residues at alpha 1-beta 2 interface

19
Q

What are cooperative proteins

A

They have multiple ligand-binding sites
n=number of binding sites

Ka = [PLn]/[P][L]^n Deter = [L]^n/([L]^n + Kd)

log (deter/1-deter) = n log [L] - log Kd

20
Q

What does the hill plot slope give

A

measure of the degree of interaction (ie, the degree of cooperativity) between binding sites. It is called Hill coefficent (nh). It show taht nh is realted to the average occupancy of the binding site

21
Q

In the hill plot of cooperativity, What does nh>1, nh=1, n<1 (rare)

A

If nh>1 (eg Hb/O2), positive cooperativity, binding at one site increases binding at other sites on other subunits.

If nh= 1, binding is not cooperative, the sites are independent.

If nh<1, negative cooperativity, binding at one site decreases binding at another site on another subunit

22
Q

What is the limit of nh

A

theoretical is equal to the number of binding site =n

experimentally, nh places a lower limit on the number of interacting sites : nh is always < n

23
Q

What is the difference between the 2 model of cooperativity?

A

Concerted is all or none, absence of L are thought to inactive T or active R form, dia=stabilised by L binding, successive binding of L to the inactive state makes the transition to the active state more likely.

Sequential, each subunit can be either T or R form, L produces change in conformation of subunit, a change in conformation in one subunit induces a similar change in an adjacent subunit.

Not mutually exclusive

24
Q

What are the end products of metabolism in tissues

A

H+ and CO2

25
Q

Are H+ and CO2 transported the same way as O2?

A

No, they do not compete with O2 for binding to the heme group

26
Q

How are H+ produced in tissues?

A

From metabolism directly and from the conversion of CO2 and HCO3-

27
Q

How does acidity affect O2 binding to hemoglobin?

A

As pH increase, Kd decrease, affinity increase

Lower pH (higher concentration of H+, O2 affinity decreases because H+ stabilises Hb in the T state. pH in tissue decrease due to metabolism that produces acids(lactic acid). This help to off load O2 from Hb to tissues. (catalyzed by carbonic anhydrase near the lungs)
HHb+ + O2  HbO2 + H+
28
Q

What is the bohr effect?

A

pH difference between lungs and metabolic tissues increase efficiency of the O2 transport. where does

29
Q

where does H+ bind to in Hb

A

N-termini of the alpha- subunit
His146 of the beta-subunit
other amino acids residues

30
Q

What doe His 146(His HC3 and Asp FG1 (Asp94) do in Hb

A

stabilises the T state of Hb, causing a shift of the binding curve to the right

31
Q

How does CO2 exported

A

In the form of a carbomate on the amino terminal residues of each of the polypeptide subunits

32
Q

What does the carbamate do to the Hb

A

Forms additional salt bridges, stabilising the T state

33
Q

What does 2-3-bisphosphoglycerate (BPG) have an effec on O2 to Hb?

A

Interacts with Hb at a separate site to the O2-binding site, present in red blood cells, increase with lower pressure.
Negative allosteric regulator of Hb function.
small negatively charged molecule binds to the positively charged central cavity of Hb, stabilizes the states

34
Q

What is the mechanism of 2,3-BPG

A

Binds to Hb and decreases the affinity of Hb of O2. BPG binding is larger in Tstate

35
Q

What is the overall effect of BPG

A

As pressure reduce,BPG increase ( eg, pO2 pressure lower in tissues) , affinity for O2 decreases and more O2 is delivered to tissues.

36
Q

What stabilise T state

A

H+, BPG and CO2 to lower affinity of Hb for O2

37
Q

What does the allosteric effects of H+, BPG, and CO2?

A

Give rise to the cooperativity of binding due to changes in the conformation that are transmitted through the subunit of Hb

38
Q

What is the effect of CO in Hb

A

Binds strongly to Hb, HbCO accumulate

Increase the affinity of remaining Hb subunit for O2, this makes it difficult to release O2 in the tissues

39
Q

what does the deter in the protein ligand interaction graph mean

A

represent the fractional saturation of all the binding site at P

40
Q

What is the y-axis and x axis on protein ligand interaction

A

y = deter, x = pO2

Biochemistry and molecular science (12 decks)

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