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Drug Discovery > Midterm Studies > Flashcards

Midterm Studies Flashcards

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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
Globular proteins:
water-soluble, compact, roughly spherical; have a | hydrophobic interior and hydrophilic outer surface
26
Fibrous proteins:
provide mechanical support to cells; typically | assembled into large cables or threads
27
Transmembrane proteins:
embedded within membranes through stretches of hydrophobic amino acids; act as receptors or signal transducers
28
Conformation:
a spatial rearrangement of atoms that depends on the rotation of functional groups around single bonds (not dependent on bond breakage)
29
Configuration:
a spatial rearrangement of atoms that cannot be altered without breaking and re-forming covalent bonds (e.g. stereoisomers)
30
Transport proteins
▪ Transport polar molecules across the hydrophobic cell membrane ▪ Polar molecules transported include amino acids and neurotransmitters
31
Enzymes
- 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
Receptors
- 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
What is X-RAY CRYSTALLOGRAPHY?
- 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
Challenges of X-RAY CRYSTALLOGRAPHY?
- 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
What is CRYO-ELECTRON MICROSCOPY
- 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
What is Nuclear magnetic resonance spectrometry
- 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
ATOMIC FORCE MICROSCOPY
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
Advantages of Atomic Force Microscopy
- 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
define Genome
total genetic content (i.e. inheritable material) of an organism, organized in one or multiple chromosomes; can consist of DNA or RNA
40
define Gene
a genetic unit which encodes information necessary for the production of a protein or RNA
41
define Catalyst
a substance that speeds up attainment of equilibrium by decreasing the energy required for reaction to proceed
42
define Substrate
the specific reactant for an enzyme
43
define Effector
a molecule or protein which elicits an effect on an enzyme (e.g. inhibitor)
44
define Metalloenzymes
enzymes whose cofactor is a metal
45
define Prosthetic groups
coenzymes that are bound covalently
46
six categories of ENZYME CLASSIFICATION
1) Oxidoreductases 2) Transferases 3) Hydrolases 4) Lyases 5) Isomerases 6) Ligases
47
Derive the Lineweaver-Burk equation from the Michaelis-Menten equation
1) Reciprocal: 2) Redistribute: 3) Lineweaver-Burk:
48
TYPES OF REVERSIBLE INHIBITION
1) Classical competitive inhibition 2) Non-classical competitive inhibition 3) Uncompetitive inhibition 4) Noncompetitive inhibition
49
IRREVERSIBLE ENZYME INHIBITION
- 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
How can ENZYME REGULATION occur
- Total enzyme amount via gene expression and degradation – slow - Substrate concentration and feedback inhibition - fast - Allosteric modulation – fast - Cooperativity - fast
51
ALLOSTERIC MODULATION
- 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
ALLOSTERIC ENZYMES – GENERAL PROPERTIES
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
define Pathogen
a biological agent that causes disease or illness to its host
54
define Infectious Diseases
disorders caused by organisms, such as bacteria, viruses, fungi, or parasites.
55
define Principle of chemotherapy
A chemical can directly interfere with the | proliferation of microorganisms at concentrations tolerated by the host
56
define Selective toxicity
chemical shows greater toxicity to microbial cells than | host cells
57
Define Bacteriostatic
inhibit cell growth; rely on immune system to kill pathogens
58
Define Bactericidal
mechanism of action actively kills bacterial cells
59
Define Broad-spectrum
can target a broad range of bacteria (both Gram positive and Gram negative)
60
Define Narrow-spectrum
will target specific types or species of bacteria (e.g. only tuberculosis)

Drug Discovery (1 decks)

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