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Biopharmaceuticals Final > Module #2 - Biotargets of Drugs > Flashcards

Module #2 - Biotargets of Drugs Flashcards

1
Q

what are the four main types of biological molecules

A

proteins
nucleic acids
polysaccharides
lipids (fats and steroids)

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2
Q

describe simple/overall structure of proteins

A

linear chain of amino acids connected by amide (peptide) bonds

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3
Q

describe structure of nucleic acids

A

linear chain of nucleotides connected by phosphate esters

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4
Q

describe structure of polysaccharides

A

linear chain of sugars, some branched

connected by acetals

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5
Q

describe structure of lipids

A

linear chains of acetate or propionate

connected by reduced aldol

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6
Q

what is responsible for assembling and disassembling proteins

A

ribosomes assemble

proteasome disassemble

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7
Q

why are biological molecules modular?

A

fit together like building blocks

provide body with simple way to make lots of different molecules

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8
Q

why is modular construction important?

A

allows for complex structures to be assembled using simple molecule components

allows for complex structures to be disassembled, and to regenerate parts to re-use

make living systems possible

only one enzyme system required for each biomolecule type and function

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9
Q

how are proteins assembled

A

amino acids are linked together by ribosomes using amide (peptide bonds)

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10
Q

how are proteins disassembled

A

proteasome break apart the chains of amino acids (and the amide bonds between then)

protein is essentially broken down into individual amino acids

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11
Q

what is the most common drug target in the body?

A

proteins

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12
Q

how do drugs produce effects in the body?

A

bind to targets/receptors of biomolecules

results in biological change (ie. shape change)

results in biological response (

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13
Q

importance of 3D effect of biomolecules

A

allows biomolecules to bind and be recognized

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14
Q

why do drugs follow like-dissolves-like rule

A

drug will interact with biological molecules with similar chemical properties

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15
Q

what is the general structure of an animo acid?

A

amine group (NH2)
acid group (COOH)
side chain (r)

all have same stereochemistry/backbones, but different side chains

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16
Q

what are the five major classes of amino acids

A

nonpolar
acidic
basic
polar
special

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17
Q

what is special about cysteine amino acid?

A

has R configuration at alpha carbon

sulfur has higher atomic number than oxygen, which reverses priority

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18
Q

describe the primary structure of proteins (2)

A

involves a sequence of amino acids linked together by peptide (amide) bonds) to form a polypeptide chain

listed in order from N-terminus to C-terminus

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19
Q

describe connections of N and C termini in amino acid linkages (2)

A

N-terminus has an amine group, and C-terminus has a carboxylate group

N-terminus connects to the C-terminus of another amino acid, forming amide bonds

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20
Q

describe secondary structures of proteins (3)

A

areas of regular, local order in the protein backbone chain

tend to hold one of the four main types of structures (due to rotating restrictions)

chemical interactions between side chains can influence the shape of secondary structure

originate from conformations available due to amide bonds, and stereogenic enters which restrict rotations

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21
Q

what are the four types of secondary structures

A

a-helix
b-sheet
loop
turn

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22
Q

what 3 factors lead to the formation of a secondary structure

A

conformational restrictions in amide bonds

conformational restrictions between amide and alpha carbon

interactions between amide bonds

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23
Q

what two possible shapes can an amide form?

A

sigma cis (s-cis) or sigma trans (s-trans) conformations

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24
Q

describe the s-trans conformation of amides

A

2 large groups are far away and don’t interact

preferred/more stable conformation

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25
Q

describe the s-cis conformation of amide

A

2 large groups eclipse and therefore interact

not preferred/less stable

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26
Q

describe side chain interactions that occur in secondary structures of proteins + their result (4)

A

negative charges attract positive charges

H bonding occurs between side chains and backbones of proteins

non-polar side chains interact with other non-polar chains

result = localized structure

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27
Q

what is a localized structure in terms of the secondary structure of proteins

A

the sum of all the effects of side chain interactions adding together to form a secondary structure formation

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28
Q

describe the alpha helix secondary structure of proteins (3)

A

corkscrew/spiral shape

forms H bonds between amide groups about 4 amino acids apart

represented by ribbon diagrams that follow plane of amide groups in backbone, and includes arrow pointing from N to C terminus

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29
Q

describe the beta structure of secondary proteins (overall)

A

can take shape of beta strand, beta sheet, or beta barrel

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30
Q

describe the structure of a beta strand (4)

A

a linear strand of amino acids

zig-zag formation (because amides prefer s-trans formation)

backbone organizes itself so everything is on same plane (so coplanar/flat in nature)

side chains stick out on either side

31
Q

describe the structure of a beta sheet (4)

A

formed by several beta strands associating together

can be parallel or antiparallel

held together by hydrogen bonds

flat structures

32
Q

describe the structure of a beta-barrel

A

beta sheets curling around themselves to form a cylinder formation

33
Q

describe structure of a loop (2)

A

area with no defined secondary structure

thin tube structures

34
Q

describe structure of turns (3)

A

areas that change almost 180 degrees with length of 3-4 amino acids

done because of H bonding between nearby amide groups

peptide essentially kinds over onto itself and changes direction

35
Q

describe tertiary structure of a protein (5)

A

overall 3D shape of protein

combination of secondary structures added together

result of interactions between non-adjacent regions

mostly non-bonding interactions

disulphide bonds primarily control structure (between 2 cysteine side chains)

36
Q

what four attractractiv forces are involved in tertiary structures?

A

disulphide bonding
ionic bonding
hydrogen bonding
van der waal interactions

37
Q

what is disulphide bonding

A

most common/strongest covalent bond

involves formation of disulphide bond (typically between 2 cysteine side chains)

38
Q

what is ionic bonding

A

also known as salt bridge

involves complete positive and complete negative charges being attracted to each other

39
Q

what is hydrogen bonding?

A

involves hydrogen being attracted to a pair of electrons on an atom nearby

40
Q

what are van der waal interactions

A

involve greasy side chains interacting with greasy side chains (non-polar non polar interactions)

weak, but not important

41
Q

what are van der waal interactions

A

non-polar non-polar interactions (greasy side chains interacting with greasy side chains)

weakest, but most important interaction

42
Q

why are van der waal interactions important for tertiary structures (4)

A

allow for side chains on inside of protein to be non-polar, creating an inner non-polar environment

side chains on outside are polar, creating polar environment

non bonding interactions (H bonding and dipole) are weaker on the outside because polar + polar = weakened bonds. nonbonding interactions are stronger on inside because polar + non polar = stronger bonds.

strong inner bonds are what hold the protein together

43
Q

what are quaternary structures

A

occurs when two or more tertiary structures of proteins come together to generate larger protein

44
Q

what type of interactions occur in quaternary structures? why so strong? (4)

A

protein protein interactions

strong because:
-lots of surface area
-lots of chemical interactions
-exclusion of water from space between so proteins stick tightly together

45
Q

is most of a protein active or scaffold?

A

most of protein is just scaffold, only a small part is active

46
Q

what are the four types of protein targets for drugs?

A

enzymes
receptors
ion channels
structural proteins

47
Q

what does a drug do if an enzyme is its target in general?

A

stops enzyme from working (inhibitors)

48
Q

what does a drug do if it has receptor for target?

A

activates (agonist) or deactivates (antagonist)

49
Q

what does a drug do if it has ion channel for target

A

opens or closes the channel

50
Q

what does drug do if it has structural protein for target?

A

interferes with assembly/disassembly of protein structures

51
Q

how do enzymes catalyze reactions?

A

creates a custom environment for transition state of reaction

bind to transition states and lower transition state energy/activation energy accelerating the reaction

52
Q

describe general process of enzyme catalyzed reactions? (3)

A

enzyme binds to substrate resulting in some sort of shape change and forming enzyme-substrate complex

reaction occurs forming the enzyme-product complex

product is formed and separates from enzyme

53
Q

what are the two main theories of enzymatic conformational change? which is correct?

A

lock and key - enzyme is perfect shape to fit into substrate

induced fit - enzyme/substrate binding changes shape

both correct, but induced fit more realistic

54
Q

what are Michaelis Menten kinetics?

A

used to describe efficiency of enzyme

shows kinetics behind enzyme catalyzed reactions

55
Q

what does a Michaelis Menten plot do?

A

tracks how an enzyme produces product over time

56
Q

what are the 4 main types of enzyme inhibition?

A

competitive inhibition
non-competitive inhibition
un-competitive inhibition
irreversible inhibition

57
Q

describe competitive inhibition (30

A

drug competes with substrate molecule for the active site

binds to active site and changes its shape

prevents substrate from binding, therefore product cannot be produced

58
Q

describe kinetics of competitive inhibition (3)

A

alters Km and Kcat, but Vmax stays same

Y-intercept stays same

Slope changes

59
Q

what type of inhibitor is disulfiram? what does it do?

A

drug for alcoholics

inhibits/blocks acetaldehyde dehydrogenase (chemical that stops body from getting sick due to hangover)

essentially produces wicked hangover to prevent alcoholics from drinking

60
Q

describe non-competitive inhibition (3)

A

inhibitor binds to enzyme in spot other than the active site

causes a conformational change to occur which prevents the substrate from being able to properly bind to active site

prevents formation of the enzyme substrate complex

61
Q

describe kinetics of non-competitive inhibition

A

changes both slope and y-intercept

alters Kcat and Vmax, but does not change Km

62
Q

describe uncompetitive inhibition (3)

A

very rare

inhibitor binds to enzyme-substrate complex instead of enzyme itself (so attaches after substrate has already binded to enzyme)

destroys the catalytic ability of it ES complex (catalysis cannot occur)

63
Q

describe kinetics of uncompetitive inhibition

A

alters Kcat Km and Vmax

64
Q

describe irreversible inhibitors

A

covalent (suicide) inhibitors

bond covalently to enzyme (usually in active site) and alter conformation/disable functional groups

65
Q

what is a receptor

A

a molecule that moves information from one side of membrane to other

specialized proteins in cell membrane

66
Q

how do receptors transfer information across membrane (4)

A

messenger approches receptor

shape of receptor changes upon interaction

receptor on other side of membrane becomes activates/changes shape allowing info to be carried

once information has been transmitted, receptor spits out messenger and process starts again

67
Q

what two ways does information transfer in receptors take place?

A

binding of messenger changing conformation of receptor allowing another molecule to bind or be released

binding of messenger changing conformation of receptor creating an enzyme active site on receptor

68
Q

how do ion channels work

A

acts like a valve

when messenger binds, valve opens allowing ions to flow from one side of membrane to other

69
Q

what are the 5 main classes of drugs

A

agonists
antagonists
allosteric antagonists
partial agonists
inverse agonists

70
Q

what are agonists (3)

A

activates the receptor in a normal way (essentially acts as messenger)

usually binds in same place as messenger, and induces shape change very similar to normal messenger

biological response increases with increased concentration

71
Q

what is an allosteric modulator? what drug class does it correspond with? (4)

A

type of agonist

binds to receptor, but not in same place as normal messenger

alters shape/sensitivity of receptor towards normal messenger which alters the way the two interact going forward

work with ion channels

72
Q

what are antagonists (4)

A

binding induces abnormal shape change that results in no signal transmission

changes shape of receptor into shape that is not accessible by regular messenger molecule so that is cannot bind and info cannot be transmitted

may bind at same site as messenger or different

essentially prevent transmission of information

73
Q

what are allosteric antagonists (3)

A

binds to active site or somewhere near

does not bind at same place as messenger

disrupts shape of receptor so that messenger cannot bind and therefore information cannot be transmitted

74
Q

what are partial agonists

A

similar to agonists but not as strong

binds to receptor and produces non-ideal conformational change.

Biopharmaceuticals Final (2 decks)

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