Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Drug discovery > Flashcard approfondite > Flashcards

Flashcard approfondite

1
Q

Definition of solubility

A

The concentration of compound in a saturated solution when excess solid is present, and
solution and solid are at equilibrium

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Definition of intrinsic solubility

A

the equilibrium solubility (S) of the free acid or base form of an ionisable compound at a
pH where it is fully un-ionised

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Which are the steps of solubility

A
  • Dissociation of the molecule from the crystal: if the interactions between the solid particles are strong, it will be more difficult to have a solubilization.
    ∆G is positive: the process require energy.
    • Formation of a cavity in the solvent: it depends on the strength of the interactions of the molecules of the solvent. When the molecules move from the solid to the solvent, it is necessary that some spaces are formed: some solvent molecules are eliminated.
      ∆G is positive: the process require energy.
    • Insertion of the molecules in the solvent cavity: having a good interaction between our molecules and the solvent is favourable for the solubility.
      ∆G is negative: the process produce energy.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Which kind of solvents exist + examples?

A
  1. Polar solvent = there is a partial charge on the atom (e.g. water, aceton → carbonylic group
    is a polar group);
  2. Apolar solvent = no charge on the atoms (e.g. esan, benzene);
  3. Aprotic solvent = no protons can dissociate (e.g. aceton);
  4. Protic solvent = H bound to polar molecules -> a proton or more can dissociate (e.g. isopropanol, acetic acid, methanol).
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What’s the meaning of the dielectric constant

A

It describes the interaction of charges, if it increase the interactions decrease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

How can we use DMSO?

A

we prepare a mother solution, that allows us to create different solutions with different concentration in order to solubilize the compound

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Which are the limitations of DMSO?

A
  1. We cannot use it to inject a drug into patient because is a little bit toxic;
  2. It modifies the physical chemical properties of our molecules - for example, if DMSO is used
    to study proteins: degradation of proteins increases if solubilized in DMSO and water;
  3. The behavior of compounds in DMSO is different than in vivo.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

How can we measure pH?

A

Indicator papers (semi-quantitative measurements) or pH-meter (quantitative measurement)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

How can we calibrate a pHmeter?

A

We use 3 buffers to calibrate and then we evaluate the parameters of linear regression (E= a x pH + b). Generally it is automatically done by the instrument

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Definition of dissociation constant

A

ratio between the product of the concentrations of the reactive species and the concentration of the undissociated species
Ka = ([H+][A-])/[HA]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Which is the correlation between pKa and pH?

A

when the concentrations of the ionized and non-ionized species are equal pKa=pH

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Which is the role of an ionization plot?

A

They’re used to verify the dominant specie at a given pH

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Definition pKa

A

pH at which a substance is 50% ionized

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Definition of zwitterios

A

Species with an acidic and basic function

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Describe the potentiometric method

A

1- Blank titration:
I. Water + chlorohydric acid until acid pH
II. Add few KOH (base)
III. The instrument measures pH variation
2- You do the same by using a solution of your sample in water (the compound has to be solubilized):
I. Add chlorohydric acid until acid pH
II. Add few KOH (base)
III. The instrument measures pH variation
The pH variation is influenced by the presence of the compound so, the graph is different
3- Potentiometric approach: difference between two plots (making the difference between two points and obtaining a graph). This curve is informative about pKa, but you need to make some adjustments
4- On the Y you have the average number of each atoms bound to the molecule, on the X the pH.
Looking at the graph (and knowing that pKa is the pH in which we have half of the hydrogen bound) you can estimate that the pKa is 9,45

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Describe the spectrometric method

A

you prepare 4 solutions, measure the spectra, select the best wavelength and measure the absorbance, you derive the Henderson-Hasselbalch equation in terms of mole fraction and express the mole fraction as a function of the absorbance which are known values. From this by knowing pH you can measure the pKa of your compounds.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Which databases show the pKa of proteins?

A

ChemSpider: structure + info
iBonD: pKa of small molecules
PKAD: pKa of ionizable lateral chains of proteins
PropKa: pKa of amino acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Definition of buffer

A

Solution that can maintain a nearly constant pH if it is diluted or small amounts of strong acids or cases are added

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Definition of buffer capacity

A

maximum amount of either strong acid or strong base that can be added before a significant change in the pH will occur

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

At which pH you can use a certain substance as buffer?

A

A substance can be used as buffer with pH = to their pKa

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Examples of buffers?

A

Acetic acid 4.5
Phosphoric acid 3, 7.2, 11-12
Carbonic acid 6.8, 9
Ammonia 9

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

How can we prepare a buffer solution

A

We follow the steps provided by a buffer calculator

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Definition of spectroscopy

A

Study of interaction between matter and electromagnetic radiation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Definition of absorption spectrum

A

A graph depicting the absorption of radiation by a chemical compound over a range of wavelenghts

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Definition of absorbance

A

Logarithm of the ratio of incident to transmitted radiant power (A=I0/I)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Definition of transmittance

A

Ratio between the transmitted radiant power and the incident radiant power (T=I/I0)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Definition of chromophore

A

the atom or any isolated covalently bonded
group of atoms responsible for the absorption of light radiation. Chromophores have multiple
bonds, always one at least.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Examples of chromophores

A
  • Aromatic rings
  • Carbonyls
  • Carboxylic group
  • Esters
  • Nitriles
  • Ethylenic groups
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Definition of Auxochromes

A

atoms or groups of atoms which do not absorb radiations by
themselves, but when are present close to a chromophore, enhance or modify the absorbing
properties of the chromophore. All auxochromes have one or more non-bonding pair of electrons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Examples of Auxochromes

A

NH2
NHR
OH
SH

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Which parameters can we use to compare two UV spectra

A
  • When we have a peak which is more intense than the other, we have a hyperchromic effect
  • When we have a peak which is less intense than the other, we have a hypochromic effect
  • To say that we have something more on the right side of the spectrum (red shift), so a higher wavelength and lower energy, we say that we have a batochromic shift
  • To say that we have something more on the left side of the spectrum (blue shift), we have a ipsochromic shift, with lower wavelength but higher energy
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

How can we obtain a UV-Vis spectrum?

A
  • Record it: electrospectrophotometer
  • Retrieve it from databases (spectrabase)
  • Predict it
33
Q

Which cuvette should we use for which wavelenght?

A

200-350 -> quartz
150-800 -> glass

34
Q

How can we prepare the blank for spectrophotometry?

A

It’s a solution of the exact same solvent used to solubilize the sample

35
Q

Which format of microplate exist?

A

from 6 to 1536 well, the most used is 96-well (8x12)

36
Q

Definition of solvent cut off

A

Wavelenght before which the solvent itself absorbs

37
Q

Which experimental factors impact UV spectra?

A

Solvent cut off
buffer absorption
solvent polarity
pH

38
Q

Why is solvent polarity relevant for the UV-spectra?

A

Solvents are characterized by a polarity with a constant ε (dielectric constant), solvent with different ε result in different UV spectra.

39
Q

How does pH influence the UV-Vis spectra?

A

So, the pH is relevant for aromatic chromophores directly linked to ionizable auxochromes:
o If ionization (deprotonation of an acidic group) causes an increase in the number of free
electron pairs → Bathochromic shift due to delocalization and thus decrease in MO
(molecular orbital) bonding and antibonding energy;
o If ionization (protonation of a basic group) causes a decrease in number of free electron
pairs → Ipsochromic shift towards smaller wavelength due to the loss of an electron pair
and thus increase in MO bonding and antibonding energy.

40
Q

Why is UV-Vis spectroscopy useful?

A

thanks to the Beer Lambert law, it allows to quantify how much substance there is in a certain solution
Absorbance = molar absorcion coefficient x concentration x sample depth (A = e x C x L)

41
Q

Definition of calibration curve

A

a method for determining the concentration of a substance in an
unknown sample by comparing the unknown to a set of standard samples of known
concentration.

42
Q

Which deviations can be found in a calibration curve?

A

there could be some deviations from
linearity, in particular when you increase the concentration of your sample. These deviations may
be due to different causes:
* Concentration (dilute)
* Association phenomena → in the majority of cases
* Impurities
* Instrumental issues

43
Q

Definition of R2

A

quality of the fitting procedure:
0 the model does not explain data
1 the model perfectly explay data
0,99 calibration curve

44
Q

Which are the characteristics of fluorescent molecules?

A

UV active
condensed aromatic rings fused together
structural rigidity

45
Q

definition of quantum yeld

A

the ratio of the number of
photons emitted over the number of photons absorbed.

46
Q

How could a molecule acquire fluorescence?

A

using small fluorescent molecules (fluorescein, dansile) as tags or inserting a fluorescent peptide in the dna (gfp)

47
Q

What do we have to take into consideration when tagging a molecule?

A

we are modifying its chemical structure and thus properties and functions
tags are often ionized
tagging changes according to the dimension of the molecule
tags may have biological activity

48
Q

Definition of quenching

A

a modification in the environment that means a decrease in fluorescence.

49
Q

Which is the dimension of a peptide?

A

less than 50aa

50
Q

How can we synthetize peptides?

A
  • Solution phase synthesis (SPS): a standard synthesis in which
    you have 2 aminoacids in solution and you create a bond between
    them.
  • Solid phase peptide synthesis (SPPS): they are automatized.
    There is a resin support in which you immobilize an amino acid and
    then you add another amino acid that will bond the first one and so
    on. Finally, you wash away any excess amino acids and there is the
    cleavage.
51
Q

Why is the 3D structure of a protein important?

A

From the 3D structure depends the physiological action of proteins and it’s essential to
modulate the biochemical mechanism

52
Q

Why do we use X-ray crystallography?

A

To observe the structure of a protein we can’t use ordinary microscope: we need a wavelength of light that is no larger than the distance between atoms (no more than 1,5A ̇).

53
Q

What is an electron density map?

A

An incident x-ray beam can produce positive or negative interferences depending on the chemical structure of the sample, from these interferences, we will obtain some points with different intensity. Then, by measuring the radiations, data regarding the position of the atoms are obtained,

54
Q

Which parameters define X-ray crystallography?

A

R can be used as a measure of error between the observed intensities and the predicted intensities that are calculated from the model:
- R=0 -> perfect fit
- R=0,2 -> good value
- R=0,6 -> bad value

Another parameter is the resolution: it’s the distance related to the smaller observable feature. The smaller the resolution, better the structure is.

55
Q

How does TEM works?

A

The electron beam is transmitted through a thin sample, it is then detected by a camera and the results are interpretated by a computer

56
Q

How do you prepare a TEM sample?

A

1- the sample must be a pure mix of protein and water
2- the sample is frozen in liquid ethane rapidly: the protein are held in their shape in a very thin layer of ice

57
Q

Pro and cons of Cryo-EM

A

Pro: easy sample preparation, structure in native state, small sample size

Cons: relatively low resolution, sample must have a high molecular weight, dependent on EM which is costly

58
Q

Definition of force field

A

the tool that help you to obtain the conformer with the lowest energy

59
Q

What is a FASTA file?

A

Is a file in the FAST format: a text-based format for representing nucleotide sequences or amino acid sequences with single-letter codes

60
Q

Definition of RMSD

A

root mean square deviation: measure of the average distance between the atoms of superimposed proteins

61
Q

Describe an alpha helix

A

The polypeptide chain starts to twist to form a rod-like structure with a backbone and the R group on the outside.
The rotation can be in clockwise direction (right hand helix) or in counterclockwise direction (left hand helix). The latter is much less stable because its energy level is higher.
There are single bonds, which instead allow rotation, and hydrogen bonds, between the NH of one amino acid and the CO of another four units ahead.

62
Q

Describe a beta turn

A

stabilized by H bonds, the bond is between the CO of one amino acid and the NH group of the N+3 amino acid.
These turns are usually found on the surface of the polypeptide.
They’re the one that interact with the polar solvents found ouside the protein as well as the macromolecules that interact with the protein in general.

63
Q

Which is the difference between parallel and anti parallel beta sheets?

A

Parallel (2): an amino acid on one strand connect with two amino acids on the opposing strand via hydrogen bond.
Anti parallel (1): the NH and the CO group of an amino acid on one strand interact with the CO and NH groups of the opposing amino acid on the other strand.

64
Q

Which factors play a role in the formation of the tertiary structure?

A

Intermolecular interactions: Van der Walls interactions

Intramolecular interactions: Disulphide bridges, covalent bonds, H bonds, Ionic interaction

Hydrophobic effect,

65
Q

Definition of homology

A

the relationship between biological structures or sequences that are derived from a common ancestor

66
Q

Which are the steps of homology modelling? (list)

A
  1. Template recognition
  2. Alignment correction
  3. Backbone generation
  4. Loop modeling
  5. Side-chain modeling
  6. Model optimization
  7. Model validation
67
Q

Homology modelling: template recognition

A

using the software BLAST you have to check if there’s at least a 30% similarity between target and template. The software can calculate different target at the same time.
You also need to check if the template’s environment (all the factor that determine protein structure except for its sequence) is the same.
Basic Local Alignment Search Tool’s (BLAST) functioning:
I. Break the molecule into small pieces of a specific length (words)
II. Compare these words with any sequence in a database (PDB)
III. Extend the alignment in both directions until its score decreases in value

68
Q

Homology modelling: loop modelling

A

you can use two approaches:
o Knowledge based: you can check the database for the same list of amino acids and model the loop based on other experimental structures
o Energy based: an energy function is used to judge the quality of a loop

69
Q

Homology modelling: side chain modelling

A

you have to consider different aspects:
o Knowledge based: to choose the best rotamer for a given substitution, you can look into the database for the most common ones
o Energy considerations: you choose the best rotamer according to the position with the lowest energy
It’s possible that there are two positions with the same quality, in this case you need to consider the two different conformations due to the different orientation of the lateral chain.

70
Q

Homology modelling: model optimization

A

it’s made in two steps:
I. Energy minimization of the whole protein using a force field
II. Molecular dynamics simulation: it allows to check which is the motion of the protein in a limited period and if it’s stable or not. You can see the effect of a solvent (ex: water) on the structure

71
Q

Homology modelling: model validation

A

there are different strategies:
o Predict the structure with two different tools based on different algorithms and check if the results are similar
o You can use QMEAN Z-score which tells if the model has some characteristics in common with other protein in the database

72
Q

What is alpha fold?

A

It’s a protein structure database (AI system) that provides open access to 3D protein structures predictions.
So instead of homology model, it’s based on artificial intelligence

73
Q

Which are the output of alpha fold

A
  • The 3D structure of the protein
  • The regions of high confidence
  • The regions of low confidence
74
Q

Definition of virtual screening

A

It’s an ensemble of computational techniques used to search in libraries of small molecules for those structures which are most likely to bind a given drug target, typically a protein receptor or enzyme (you can use it to find an agonist or an antagonist of your protein of interest).

75
Q

Structure-based approach for virtual screening

A

The algorithm takes one or two molecules at a time and generate a number of poses, then it verify the capacity of every conformation determining the best pose for each ligand.
At the end it rank all the ligands according to specific criteria (scoring function):
o Knowledge based: look how the crystallized ligand is bound to the pocket in PDB, and use this information to see which conformation of our compound is closer to the one reported in the PDB
o Energy based: a force field is used to calculate the energy of interaction between our conformer and the protein or the ligand and the receptor
o Empirical functions: the software optimizes, on the basis of available dataset, a function able to reproduce the experimental free energy of binding

76
Q

Which are the limits of docking?

A
  • The entropic effect is not taken into consideration
  • It treat the molecules as rigid bodies when in reality they can be flexible
77
Q

What is molecular dynamics

A

Is a strategy that allows to follow the movements of a protein in time. It consists in solving the classical motion equations for atoms and molecules to describe their trajectory. These equations are solved by algorithms and in this way it is possible to describe how a protein is moving, which is strongly related to its physiological action.

78
Q

Why is timescale a problem of molecular dynamics?

A

the larger the protein,
the higher the number of the equations to be solved, the longer the time.
Structural changes in proteins can take nanoseconds, microseconds, milliseconds, or longer. A considerable time of molecular dynamics simulation is about nanoseconds. Up to now,
simulations of 1 microsecond are rare. Even if these are all approximations, many information
can be retrieved.

79
Q

How can we obtain the 3D structure of a protein?
What is swiss model?

A

Homology modelling, swiss model, alphafold

Drug discovery (4 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions