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Pharmacogenomics > Basics > Flashcards

Basics Flashcards

1
Q

Biotechnology defintion

A

the use of tissue culture, living cells, or cellular enzymes to produce a defined product

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2
Q

Approximtely how many biotechnologies are approved by the FDA each year?

A

12

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3
Q

how many biotechnologies are in development whether it be by clinical trials or other means

A

approximetley 1000 being developed for over 100 diseases

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4
Q

what kind of diseases are biotechnologies being developed for?

A

cancer, rare diseases, neurological, HIV/AIDS, heart and stroke disease, mental helath disorders, alzehimer’s disease, skin disease, asthma and allery

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5
Q

cDNA define

A

only coding DNA - DNA transcribed from specific mRNA via enxyne reverese trasncription

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5
Q

What therpauetic categories have the highest biotechnology development rate?

A

pediatric, neurological, etc

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6
Q

Stages of the cell cycel

A

G1
S
G2
M

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7
Q

What is circular DNA

A

Forms a closed loop and has no ends

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8
Q

What is a cloning gene

A

a common practice in molecular biology labs that is used by researchers to create copies of a particular gene for downstream applications

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9
Q

what is an endonuclease

A

an enzyme that breaks down a nucleotide chain into two or more shorter chains by cleaving internal covalent bonds

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10
Q

What is DNA restriction?

A

restrcition enzymes bind to certain DNA sequences

they then cut the sugar-phosphate backbone of DNA strands leaving stticky ends

the sticky ends can be reattached via enzyme liagse, whihc is used to catalzye the chemical reaction that rejoins DNA

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11
Q

What is DNA transformation

A

using restriction and liagse to combine various gene segemnst

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12
Q

How are low temperatures and heat shock used in DNA transformatiom

A

the lipid membrane has a negative charge and so does the DNA making them un able to interact

by reduce the temperature we are able to stabilize the cell membrane and add Ca2+ to stabilize the membrane.

Then using a heat shock a temperature imbalnce is formed on either side of the membrane and this sets up a current. Since we have a ionic shield in place the DNA can be swept through the adhesion zone

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13
Q

What is Gentic enigneering

A

we can add or remove segments of DNA plasmids via DNA restriction and DNA ligase

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14
Q

What is gel electrophoresis

A

it separates DNA fragments based on size and charge

it does so by having a current run through gel containing the molecules of interest

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15
Q

what is a model organism?

A

a non-human species that is studied to understand biological processes

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16
Q

How does PCR work

A

Raise temeprature - denature
Annel
extend primers

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17
Q

Descrieb how monclonal antibodies are produced

A

a mouse is immunized with the desired antigen

the mouse will then porduce antibodies to combat this antigen

via test bleeds we can determine whether the mouse has the desires antoboides and if it does then the spleen is removed and dissocated in culture mediums

in this culture, we also have myeloma cells and the B cells can fuse with these cells and produce hybridomas

When exposed to PEG all unfused b-cells die and we have hybridoma and myeloma cells left

Then using HAT medium we can eliminated all myelominoma cells

the surviving cells then are put in indiviual wells these are knonw as clonla cultures

after culturally for a week weeks we can screen the lqiuid for the desires antigen to see wehther they bond with the desires antigen

clones that produced the right antibody are then frozen or used for mass culture

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18
Q

What are monoclonal antibodies used for?

A

diagnostic and anti cancer drugs

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19
Q

what is molecular biology used for?

A

tracers, genetic engineering, and DNA technology

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20
Q

What are the building blacks for DNA, Peptides/proteins, and oligosaccharides?

A
  • nucelotides - nucleosides
  • AA
  • carbohydrate sugars
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21
Q

What are the different nucleotides?

A

AGCT and U in RNA

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22
Q

What are the fours groups of amino acids ?

A

acidic, basic, uncharges polar side chains, nonpolar side cahins

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23
Q

What do we know about optical isomers?

A

all L-form (mammalian cells) except Gly

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24
Q

what are the acidic aa

A

glu, asp

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25
Q

what are the basic aa

A

lys, arg, his

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26
Q

what are the uncharged polar sidechains aa

A

asn, gln, ser, thr, tyr

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27
Q

what are the nonpolar side chains aa

A

Ala, Val, Leu, Ile, Pro, Phe, Met, Trp, Gly, Cys

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28
Q

What do stability and degradation in pharamcy mean?

A

to define how much of the active drug is available for use

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29
Q

What kind of drugs can retain 100% oof the chemcial composition of the biologically active protein yet be biologically inactive

A

protein drugs

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30
Q

How are traditional drugs degraded?

A

chemical degradation - oxidation, hydrolysis, racemization, etc

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31
Q

How are protein drugs degraded?

A

chemical degradtaion
physical degradtion

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32
Q

when talking about chemical insatbility whta bonds are we focusing on?

A

covalent bond modification of proteins via bond formation or cleavage

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33
Q

What is deamination and what drugs are suscpetible to it?

A

the removal of NH2 and replcing it with OH

can only happen to aa with amide such as: Asn and Gln

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34
Q

whats another word for hydrolysis?

A

Proteolysis

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35
Q

What hydrolysis reaction is of special note?

A

Pro and Asp this creates a hot spot

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36
Q

What does oxidatio affect? proteins in solution or lypholized form?

A

both

37
Q

How can we redue oxidization?

A

by packaging lympholized pretin under a nitorgen atmosphere

38
Q

What are common targets of oxidation?

A

Sulfur containing aa such as cysteine and methionine

39
Q

what does the oxidation of cysteine to sulfonic acid look like?

A

RSH - RSOH - RSO2H- RSO3H
thiol from cysteine - sulfenic acid - sulfinic acid - fulfonic acid

40
Q

what can happen to unpaired cysteins?

A

they can be oxdized to form cystein di sulfide

RSH + R’SH -> RS-SR’

41
Q

what does the oxidation of methionine look like?

A

Refer to the diagram on slide 36

42
Q

What does Disulfide exchange look like?

A

RSH + R’S-SR” - RS-SR’ + R”SH

43
Q

How can disulfide exchange or oxidation of an unpaired cystein create a problem for proteins?

A

these will create new protein structure

44
Q

Racemization does what?

A

Conversion of L-amino acids to D

45
Q

Undertsadn beta-elimination

A

slide 42

46
Q

Whats a labile aa

A

unstable aa

47
Q

Primary reaction of Asn and Gln

A

deamidation, racemization

48
Q

Primary reaction of Asp

A

hydrolysis, racemization

49
Q

Primary reaction of Met, Cys, His, Trp, Tyr

A

Oxidation

50
Q

primary reaction of ser, thr, cys

A

beta elimination and racemization

51
Q

primary reaction for cys

A

disulfide excahnge and oxidation

52
Q

What does physcial instability do to structure?

A

it disrupts secondary, tertiary, and quaternary structures

53
Q

if proteins are more then 20 aa how will they degrade?

A

physical

54
Q

if proteins are less than 20 aa how will they degrade?

A

chemical

55
Q

Where are the polar and non-polar regions in a folded protein?

A

hydrophobic on the inside

hydrophilic on the outside

56
Q

What are the 4 types of physical degradation?

A

denaturation
absorption to surfaces/interfaces
aggregation
precipitation

57
Q

What does proetin denaturation do to bonds?

A

disruption of secondary and tertiary bonds

58
Q

is physcial degradation reversible?

A

may or may not be reversible

58
Q

what can cause physcial degradation?

A

heat, extreme pH, chemcials (organic solvents)

59
Q

why are denatured portain usualy insoluble?

A

because hydrophobic regions folded inside are now exposed to the outside environemnt

60
Q

Why do molecules localize to interfaces?

A

molecules are amphiphilic so they have both hydrophobic and hydrophilic components so at the interface both parts can be happy

61
Q

Since moleculesAbsorption to surfaces/interfaces implies what? where do proteins adhere?

A

Proteins adhere to the walls of the doage form containers or the delivery device

62
Q

larger or smaller proteins adhere more?

A

larger proteins adher more

63
Q

What kind of proteins are less likely to unfold?

A

disulfide linked proteins

64
Q

what happens when absorption at an interface happens?

A

proetin denaturation

65
Q

what is the removal of a protein from the surface and return to the solution called?

A

protein desorption

66
Q

what happens when a protein desorbs?

A

it’s hydrophobic regions are exposed to water and aggregation or precipitation occurs

67
Q

Explain protein aggregation

A

interaction between hydrophobic regions of DIFFERENT denatured protein molecules

68
Q

What steps preceed precipitaion formation?

A

protein in native conformation - aggregates - precipitation

69
Q

why can protein aggregation be dangerous for drugs?

A

it has the potential to trigger an immune response which could lead to decreased drug effectiveness or even harmful side effects

70
Q

what can we do to prevent protein absorption?

A

surfactants
other proteins albumin
phospholipids

  • these all are amphilic or have surface activity
71
Q

how do surfactants work to prevent protein aggregation?

A

refer to pictures on slides 61-63

72
Q

Why is albumin used to prevent portein absorption?

A
  • water soluble, highly charges
  • conatins serveerla disulfide bonds ( very stable )
  • a competitor for inter-surface phenomenon ( decreased chances of intermolecular interactions of the protein interested)
73
Q

should we shake protein solutions? why?

A

no - precipitation provides interfaces for proteins to adhere to

74
Q

is precipitation accelerated in large or small air-water interfaces?

A

large

75
Q

what are some agents that can prevent protein aggregation?

A
  • sugars and salts
  • polyols, PEG and other polymers
  • free AA (arginine, glutamate, glycine, etc)
76
Q

What is the effect of aggregation in insulin pumps?

A

precipates may blcok/obstruct the intake of the drug and pateint may not recive enough insulin

77
Q

Aggregation in insulin pumps may be due to:

A
  • body tempertaure changes
  • agitation of insulin in reservoir with air
  • adsorption of insulin to hydrophobic surfaces of air and PVC
78
Q

rate constant describes what?

A

the kinetics of degradation

active drug -k-> inactive drug

79
Q

as a drug decays what does it lose?

A

biological actvity

80
Q

Rate constant is association with what order of kinetics? a unit of whta?

A

first order rate constant
a unit of time 1/time

81
Q

as the magnitude of k increase what happens to degration?

A

degradation of the active drug gets faster

82
Q

what can assays be used to measure?

A

the function, presence or amount of a substance

83
Q

how do we assay chemiacl degrdation? and what are we meauring?

A

the amount of intact prptain via electrophoresis

84
Q

how do we assay physcial degrdation? and what are we meauring?

A

physical degradation is harder to measure however we can meausr ethe biological activity a proetin such as thru clot lysis assay for t-PA

85
Q

roles of fibrin and plasminogen in actue M.I or pulmonary embolism

A

fibrin - clot

plasminogen - cardiac repaire

86
Q

What is activase/altepase?

A

indicated for acute M.I and pulmonary embolism

87
Q

How does activase work?

A

t-PA (tissue plasmonogen activator) is an endogenous proetin that works by binding to fibrin an d activating plasminogen

this results in fibrinolysis or the dissolution of the fibrin clot

88
Q

are different forms of degrdation additive?

A

yes

89
Q
A

Pharmacogenomics (2 decks)

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