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Drug Discovery > Midterm Studies > Flashcards

Midterm Studies Flashcards

1
Q

What are drugs?

A

-Pharmaceutical agents that have a biological effect on the human body or some other
living system
-For the purpose of this project, “drugs” include any agent that can elicit a desired
therapeutic effect

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2
Q

Therapeutic agents can be?

A
  • Chemical compounds
  • Proteins
  • Nucleic Acids
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3
Q

What do drugs target?

A

1) Proteins
2) Carbohydrates
3) Nucleic Acids
4) Lipids and Membranes

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4
Q

Proteins can be?

A
  • Receptors
  • Enzymes
  • Transport proteins
  • Structural proteins
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5
Q

Carbohydrates can be?

A
  • Cell surface carbohydrates

* Antigens and recognition molecules

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6
Q

Nucleic Acids can be?

A
  • DNA

* RNA

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7
Q

Lipids and Membranes can be?

A

• Cell membrane lipids

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8
Q

What are the elements of life?

A 
Carbon 
Hydrogen 
Nitrogen 
Oxygen 
Phosphorus 
Sulfur
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9
Q

What are the organic compounds?

A

Alcohol, aldehydes, ketones, carboxylic acid, thiol, primary/secondary/ tertiary amines

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10
Q

what are the functional groups?

A

hydroxyl, acyl, carbonyl, carboxylate, sulfhydryl, amino, phosphate, and phosphoryl

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11
Q

Fatty acids & lipids are typically comprised of?

A

Esters and ether

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12
Q

Proteins are typically comprised of?

A

Amide

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13
Q

Nucleotides are typically comprised of?

A

Phosphate ester, and phosphoanhydride

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14
Q

Define Macromolecules?

A 
A chain (i.e. polymer) of smaller organic molecules
(i.e. monomers)
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15
Q

What are carbohydrates?

A
  • a.k.a. saccharides
  • Mostly carbon, oxygen, and hydrogen
  • Simple sugar = monosaccharide
  • usually contain either 5 or 6 carbons
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16
Q

What are nucleic acids?

A

-Composed of nucleotides: Adenine (A), Thymine (T), Guanine (G), Cytosine (C), Uracil (U)
-Nucleotides possess: 5-C sugar, a nitrogenous base, at
least one phosphate
-DNA: deoxyribose sugar; RNA: ribose sugar

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17
Q

What is ATP?

A

Adenosine triphosphate, Central energy carrier in all living cells

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18
Q

What are lipids and membranes?

A
  • Lipids are rich in carbon and hydrogen; possess few oxygen atoms
  • Not soluble in water
  • Polar, hydrophilic (“water-loving”) head
  • Non-polar, hydrophobic (“water-fearing”) tail(s)
  • Lipids preferentially form lipid bilayers in aqueous environments: structural basis for all biological membranes
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19
Q

PROPERTIES OF WATER

A

1) Polarity
2) Hydrogen Bonding
3) The Ultimate Solvent
4) Hydrophobicity
5) Nucleophilicity

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20
Q

BIOLOGICAL FUNCTIONS OF PROTEINS

A

 Biochemical catalysis (i.e. enzymes)
 Binding molecules for storage & transport
 Membrane pores and channels
 Cell structural support and shape
 Mechanical work
 Regulation during transcription & translation
 Hormone and signalling molecules
 Receptors
 Specialized functions (e.g. antibodies, toxins)

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21
Q

PI STACKING

A

▪ Interaction between aromatic or heteroaromatic rings
▪ Aromatic rings have regions of high electron density above and below the plane
of the ring.
▪ The atoms in the plane of the ring have low electron density, resulting in a
quadrupole moment

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22
Q

AROMATIC PI STACKING

A

-quadrupole-quadrupole interactions and Van der Waals forces

▪ Arrangements: sandwich (face to face), T-shaped (edge to face) or parallel displaced

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23
Q

RELATIONSHIP BETWEEN PKA AND PI

A

 pKa can be thought of as the point at which the overall charge of a functional group is zero
 Isoelectric point (pI): the pH at which a zwitterionic molecule does not migrate in an electric field because its net charge is zero

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24
Q

POLYPEPTIDES

A

 Linked amino acids in a polypeptide chain are referred to as residues
 Amino acids in a chain are identified by either 3-letter code (e.g. Ala, Glu) or 1-letter code (e.g. A, E)
 Due to polymerization, most charge from carboxy and amino groups is lost; charges come from side chains
 Di-, tri-, oligo- and poly-peptide refers to chains of 2,3, several, or many amino acids

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25
Q

Globular proteins:

A

water-soluble, compact, roughly spherical; have a

hydrophobic interior and hydrophilic outer surface

26
Q

Fibrous proteins:

A

provide mechanical support to cells; typically

assembled into large cables or threads

27
Q

Transmembrane proteins:

A

embedded within membranes through stretches of hydrophobic amino acids; act as receptors or signal transducers

28
Q

Conformation:

A

a spatial rearrangement of atoms that depends on the rotation of functional groups around single bonds (not dependent on bond breakage)

29
Q

Configuration:

A

a spatial rearrangement of atoms that cannot be altered without breaking and re-forming covalent bonds (e.g. stereoisomers)

30
Q

Transport proteins

A

▪ Transport polar molecules across the hydrophobic cell membrane
▪ Polar molecules transported include amino acids and neurotransmitters

31
Q

Enzymes

A
  • Act as catalysts for reactions within the cell
  • Present on the inner surface of the cell membrane or within the cell
  • Bind the substrates for a reaction and release products
32
Q

Receptors

A
  • Present in the cell membrane or within the cell
  • Act as the cell’s ‘post boxes’
  • Receive chemical messages from neurotransmitters and hormones
  • Initiate or inhibit chemical signalling processes within the cell
33
Q

What is X-RAY CRYSTALLOGRAPHY?

A
  • The standard method for protein structure determination
  • Involves purifying high concentrations of protein to generate a protein crystal
  • X-ray beams are shot through the crystal to get a diffraction pattern, which is
    then interpreted to obtain a structure
34
Q

Challenges of X-RAY CRYSTALLOGRAPHY?

A
  • Getting crystals is difficult
  • Membranes do not form crystals
  • Protein must be stable at high concentration
  • Proteins that have flexible do not crystallize easily
35
Q

What is CRYO-ELECTRON MICROSCOPY

A
  • Involves the purification of high concentrations of protein, which are flashfrozen to preserve the structure (vitreous ice)
  • Proteins are analyzed using a highly powerful electron microscope
  • Useful for larger proteins and protein complexes, but only provides information about the surface shape of the protein
36
Q

What is Nuclear magnetic resonance spectrometry

A
  • Involves the study of proteins in solution; doesn’t need such high
    concentrations
  • Protein is placed in a magnetic field; absorption of electromagnetic radiation of nuclei along with amino acid structure provides information about structure
37
Q

ATOMIC FORCE MICROSCOPY

A

Based on the detection of movements of a flexible cantilever containing an atomically sharp probe across a
surface
Uses:
- Determining the molecular weight of a protein
- Protein complexes (including oligomeric state determination)

38
Q

Advantages of Atomic Force Microscopy

A
  • it is non-destructive
  • straightforward sample preparation
  • can operate in air or liquid on a wide range of physical properties of the sample
  • Can study membrane proteins, including receptor: ligand interactions
39
Q

define Genome

A

total genetic content (i.e. inheritable
material) of an organism, organized in one or
multiple chromosomes; can consist of DNA or
RNA

40
Q

define Gene

A

a genetic unit which encodes information
necessary for the production of a protein or
RNA

41
Q

define Catalyst

A

a substance that speeds up attainment of equilibrium by decreasing the energy required for reaction to proceed

42
Q

define Substrate

A

the specific reactant for an enzyme

43
Q

define Effector

A

a molecule or protein which elicits an effect on an enzyme (e.g. inhibitor)

44
Q

define Metalloenzymes

A

enzymes whose cofactor is a metal

45
Q

define Prosthetic groups

A

coenzymes that are bound covalently

46
Q

six categories of ENZYME CLASSIFICATION

A

1) Oxidoreductases
2) Transferases
3) Hydrolases
4) Lyases
5) Isomerases
6) Ligases

47
Q

Derive the Lineweaver-Burk equation from the Michaelis-Menten equation

A

1) Reciprocal:
2) Redistribute:
3) Lineweaver-Burk:

48
Q

TYPES OF REVERSIBLE INHIBITION

A

1) Classical competitive inhibition
2) Non-classical competitive inhibition
3) Uncompetitive inhibition
4) Noncompetitive inhibition

49
Q

IRREVERSIBLE ENZYME INHIBITION

A
  • Inhibitor forms a stable covalent bond with enzyme, permanently altering it
  • Serves to titrate functional enzyme out of the population
  • Typically occurs by alkylation or acylation of active site residue side chain
  • Can be used to investigate important residues in enzyme active sites
50
Q

How can ENZYME REGULATION occur

A
  • Total enzyme amount via gene expression and degradation – slow
  • Substrate concentration and feedback inhibition - fast
  • Allosteric modulation – fast
  • Cooperativity - fast
51
Q

ALLOSTERIC MODULATION

A
  • Allosteric enzymes are those whose activity is altered by change in structure
  • Controlled by an allosteric modulator (a.k.a. effector, inhibitor, or activator)
  • Modulators are usually small molecules
  • Typically reversible and due to non-covalent binding of the allosteric modulator
  • Modulators will bind the enzyme at a regulatory (a.k.a. allosteric) site away from the catalytic site
52
Q

ALLOSTERIC ENZYMES – GENERAL PROPERTIES

A
  1. Activities of enzymes are changed by metabolic inhibitors and activators, which do not resemble substrate/product.
  2. Allosteric effectors bind non-covalently to their cognate enzyme and are not chemically modified.
  3. Regulated enzymes are usually multi-subunit proteins.
  4. Enzymes usually has at least one substrate which Vo vs. [S] curve is sigmoidal rather than hyperbolic.
53
Q

define Pathogen

A

a biological agent that causes disease or illness to its host

54
Q

define Infectious Diseases

A

disorders caused by organisms, such as bacteria, viruses, fungi, or parasites.

55
Q

define Principle of chemotherapy

A

A chemical can directly interfere with the

proliferation of microorganisms at concentrations tolerated by the host

56
Q

define Selective toxicity

A

chemical shows greater toxicity to microbial cells than

host cells

57
Q

Define Bacteriostatic

A

inhibit cell growth; rely on immune system to kill pathogens

58
Q

Define Bactericidal

A

mechanism of action actively kills bacterial cells

59
Q

Define Broad-spectrum

A

can target a broad range of bacteria (both Gram positive and Gram negative)

60
Q

Define Narrow-spectrum

A

will target specific types or species of bacteria (e.g. only tuberculosis)

Drug Discovery (1 decks)

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