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BS2091 Biochemistry I: from genes to proteins > Understanding interactions between macromolecules > Flashcards

Understanding interactions between macromolecules Flashcards

1
Q

What do 2 single-stranded DNA molecules make?

A

Duplex DNA

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2
Q

What do DNA and a transcription factor make?

A

DNA-transcription factor complex

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3
Q

What does an enzyme and a substrate make?

A

An enzyme-substrate complex

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4
Q

What does an enzyme and a drug make?

A

An enzyme-drug complex

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5
Q

What does a cell surface signalling receptor and a hormone make?

A

A hormone-receptor complex

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6
Q

What does an antibody and an antigen protein make?

A

An antibody-antigen complex

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7
Q

What is the equation for the dissociation constant?

A

A + B AB

Kd = ([A] [B]) / ([AB])
Units are concentration

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8
Q

What is specificity?

A

The difference in KD for one site versus another

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9
Q

Why is specificity important?

A 
For proteins:
There are many families of similar proteins
For DNA:
Binding sites in a sea of other DNA
For drugs:
On- and off- target activities
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10
Q

In reality there is a continuum of different binding affinities..

A

And a particular protein will be distributed among binding sites according to the different KD’s.

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11
Q

A high degree of specificity does not necessarily mean..

A

High affinity, and vice versa

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12
Q

What methods can you use to measure KD?

A 
Filter binding
Fluorescence anisotropy
Isothermal calorimetry
Equilibrium dialysis
Surface plasmon resonance - BiaCore
Optical interferometry - Octet
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13
Q

Two molecules will interact if there is a loss of..

A

Gibbs free energy on the formation of a complex

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14
Q

What is the equation for Gibbs free energy?

A

(Constant temperature)
deltaG = deltaH - (T deltaS)
where deltaH is enthalpy (heat), and deltaS is entropy (disorder)
Both require intimate contact between two molecules

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15
Q

Describe enthalpy

A

H-bonds, electrostatic interactions, van der Waals interactions

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16
Q

Does freeing bound water increase or decrease entropy?

A

Increases entropy

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17
Q

Does rigidifying macromolecules increase or decrease entropy?

A

Decreases entropy

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18
Q

What types of interactions can you get in terms of rigid and flexible?

A

Rigid:rigid
Rigid:flexible
Flexible:flexible
(Don’t forget the solvent)

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19
Q

How can you measure the change in enthalpy and the change in entropy?

A

Measure KD’s at several different temperatures
Using isothermal calorimetry
delta G = delta H - (T delta S) = RT ln Kd

20
Q

What part of the DNA helix can help to achieve specificity?

A

The major (wide) and minor (narrow) grooves

21
Q

What charges do the blue, red and white parts of the chemical space-fill models represent?

A

Blue - positive potential
Red - negative potential
White - neutral

22
Q

What properties does the 434 repressor binding site have?

A 
Reading head
4-6 base pairs
HTH motif
Helix dipole
Dimer
23
Q

Do hydrogen bonds have a strong or weak dipole? And how does this affect alpha helices?

A

Hydrogen bonds have a weak dipole

Alpha helices ‘add up’ weak dipoles

24
Q

Is a 6 base pair binding site specific enough? And explain why

A

The human genome is ~3 billion base pairs
If sequence is random then a 6 base pair binding site will occur >500000 times
Therefore 6 base pairs is not enough to be specific

25
Q

How many times does a 12 base pair binding site occur in the human genome?

A

Around 200 times

26
Q

What is the KD value for the 434 repressor?

A

10^-9 M

27
Q

What properties does the CAP activator binding site have?

A

HTH motif

Bends DNA

28
Q

What properties does the engrailed homeodomain binding domain have?

A

Eukaryotic HTH
Not a dimer
Arginines in the minor groove

29
Q

What properties does the met repressor binding domain have?

A

Beta-strands in the major groove

30
Q

Give examples of zinc-binding DNA recognition motifs

A

Classical zinc finger (tramtrack), e.g. zif 268 - zinc finger contains tandem repeats to read more sequence
Hormone receptor, e.g. oestrogen receptor DNA binding domain (GATA-I) contains half a NR DBD and a long tail in the minor groove
GAL4
TBP-TATA binding protein contains a protein saddle in the minor groove which is splayed open

31
Q

Are cartoon chemistry figures accurate or misleading?

A

Misleading

32
Q

What does the CAP activator help to do?

A

Bend DNA

33
Q

Name a protein that can cause extraordinary deformation of the DNA

A

TBP-TATA binding protein

34
Q

What are the lifetimes of protein:protein interactions?

A

Obligate (often co-folding)
Transient (often weak but highly specific)
Intermediate

35
Q

What types of interaction can be protein:protein interactions?

A

Rigid:rigid
Rigid:flexible
Flexible:flexible

36
Q

What drives the interaction of protein:protein interactions?

A

Role of enthalpy and entropy

37
Q

What is a rigid:rigid interaction also known as?

A

Lock and key

38
Q

What is a rigid:flexibility interaction also known as?

A

Induced folding

39
Q

What is a flexible:flexible interaction also known as?

A

Co-folding

40
Q

What is the KD value for the barnase:barstar interaction?

A

10^-14 M (= Koff/Kon)

41
Q

Describe the barnase:barstar interaction

A

Buried residues at the interface

Importance of charge steering on on rate

42
Q

Can transient interactions also be co-folding?

A

Yes

43
Q

What do charged surfaces cause?

A

Electrostatic steering

44
Q

Are affinity, specificity and discrimination the same or different?

A

Different

45
Q

What is the additive effect of interactions also called?

A

Multiplies affinity

46
Q

In terms of protein:drug interactions, the affinity of interaction is often driven by entropy, hence often largely..

A

Non-polar character

47
Q

In terms of protein:drug interactions, for specificity, sometimes shape is enough, but often form precisely..

A

Positioned hydrogen bonds

BS2091 Biochemistry I: from genes to proteins (16 decks)

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