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pharmacogenomics 4860 > 1. biotechnology basics > Flashcards

1. biotechnology basics Flashcards

1
Q

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

A

biotechnology

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2
Q

most biotechnology based pharmaceuticals are _____ based

A

protein

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3
Q

Most biopharma medications are developed for these three conditions

A
  1. cancers
  2. rare disease
  3. neurological disorders
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4
Q

is DNA synthesized from a single-stranded RNA template in a reaction catalyzed by the enzyme reverse transcriptase. cDNA is often used to express a specific protein in a cell that does not normally express that protein, or to sequence or quantify mRNA molecules using DNA based methods.

A

cDNA (complementary DNA)

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5
Q

this is a series of events that takes place in a cell as it grows & divides

A

cell cycle

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6
Q

an increase in cell mass

A

cell growth

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7
Q

this is DNA that forms a closed loop that has no ends and provides antibiotic resistance to bacteria. e.g. plasmids

A

circular DNA

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8
Q

create copies of a particular gene for downstream applications, such as sequencing, mutagenesis, genotyping or heterologous expression of a protein.

A

gene cloning

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9
Q

the process where the genomes DNA is copied in cells. occurs during cell division

A

DNA replication

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10
Q

a group of enzymes that break the phosphodiester bond present within the polynucleotide chain of a DNA molecule

A

endonuclease

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11
Q

the process by which the information encoded in a gene is turned into a function.

A

gene expressions

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12
Q

is the process of making an RNA copy of a gene’s DNA sequence.

A

gene transcription

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13
Q

a small circular DNA molecule found in bacteria and other microscopic organisms.

A

plasmid

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14
Q

the process in which cells make proteins

A

protein synthesis

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15
Q

what are the building blocks of genetic materials?

A

DNA/RNA -> nucleotides & nucleosides

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16
Q

what are the building blocks of peptides/proteins

A

amino acids

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17
Q

what are the building blocks of oligosaccharides

A

carbohydrate sugars

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18
Q

what are the 5 nucleotides

A

guanine, cytosine, adenine, thymine and uracil

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19
Q

_____ (primary/secondary/tertiary/quaternary) protein structure is sequence of a chain of amino acids

A

primary

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20
Q

___________ (primary/secondary/tertiary/quaternary) protein structure occurs when the sequence of amino acids are linked by hydrogen bonds

A

secondary

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21
Q

________ (primary/secondary/tertiary/quaternary) occurs when certain attractions are present between alpha helices and pleated sheets

A

tertiary_

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22
Q

______ (primary/secondary/tertiary/quaternary) is a protein consisting of more than one amino acid chain

A

quaternary

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23
Q

there are four groups of amino acids: Glu and Asp are a part of what group

A

acidic side chains

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24
Q

there are four groups of amino acids: Lys, Arg and His are a part of what group

A

basic side chains

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25
Q

there are four groups of amino acids: Asn, Gln, See, Thr, Tyr are a part of what group

A

uncharged polar side chains

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26
Q

there are four groups of amino acids: Ala, Val. Leu, Ile, Pro, Phe, Met, Trp, Gly, Cys are a part of what group

A

nonpolar side chains

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27
Q

_____ and ______ are terms used in pharmacy to define how much os the active drug is available for us

A

stability and degradation

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28
Q

true/false: unique protein drugs can retain 100% of the chemical composition of the biologically active protein yet be biologically inactive

A

true

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29
Q

what processes cause degradation of traditional drugs

A

chemical instability
- oxidation
- hydrolysis
- racemizaitopn

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30
Q

what are the two main processes that cause the degradation of protein drugs

A
  • chemical instability
  • physical instability
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31
Q

this is covalent bond modifications of proteins via bond formation or cleavage (e.g. deamination, hydrolysis, oxidation, racemization, beta-elimination

A

chemical instability

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32
Q

this type of chemical instability process affects Amino acids that contain an amide (e.g. asparagine - Asn or glutamine (Gln)
amide gets converted to an acid (OH)

A

deamination

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33
Q

this type of chemical instability process affects peptide bonds of amides, especially when Pro is next to Asp

A

hydrolysis/proteolysis

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34
Q

this type of chemical instability is a major degradation pathway of proteins both in solution and lyophilized formulations. occurs in the presence of atmospheric oxygen

A

oxidization

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35
Q

______ containing amino acids are common targets of oxidation. this is due to the attraction of the nucleus to the valence electrons of _____ is not strong therefore easier to give up electrons for oxidation (e.g. cysteine and methionine)

A

sulfur

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36
Q

true/false: unpaired cysteines can be oxidized to form cysteine disulfide

A

true

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37
Q

this type of chemical instability is a reduced a SH on one cysteine can undergo exchange with another disulphide bond

A

disulfide exchange

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38
Q

true/false: a change in disulfide bonding will dramatically change the protein structure `

A

true

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39
Q

why would disulphide exchange or oxidation of an unpaired cysteine create a problem for proteins?

A

because such modifications will create new protein structures

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40
Q

all amino acids, except for ____, in mammalian biology are the L-amino acids

A

Gly

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41
Q

this process is the conversion of L-amino acids to D,L mixtures of amino acids.

A

racemization

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42
Q

what are the two labile amino acids that undergo deamination and racemization?

A

Asn, Gln

43
Q

what is a labile amino acid that undergoes proteolysis and racemization

A

Asp

44
Q

what are the five amino acids that under go oxidation

A

Met, Cys, His, Top and Tyr

45
Q

what are the three amino acids that undergo beta-elimination and racemization

A

Ser, Thr, Cys

46
Q

what is a labile amino acid that undergoes disulfide exchange and oxidation

A

Cys

47
Q

this type of instability results in changes in protein secondary, tertiary and quaternary structures. no chemical bond formation or cleavage. predominant in large proteins

A

physical instability

48
Q

true/false: peptides of >20 amino acids will degrade only by chemical instability since they have a complex secondary and tertiary structure

A

false -> peptides of < 20 AA will degrade only by chemical instability since they DO NOT have complex secondary and tertiary structures

49
Q

what are the four types of physical degradation

A
  • denaturation
  • adsorption to surfaces/interfaces
  • aggregation
  • precipitation
50
Q

this type of physical degradation is known as the disruption of secondary and/or tertiary structures. may or may not be reversible. is caused by heat, extreme pH and chemicals. typically involves the unfolding of proteins

A

protein degradation

51
Q

when a protein is degraded, is it water soluble or water insoluble?

A

water insoluble - because the hydrophobic components become exposed when the protein is denatured

52
Q

this type of physical degradation is the preference of molecules to localize at an interface (e.g. solid-liquid, air-liquid)

A

adsorption

53
Q

proteins are ______ molecules which have both hydrophilic and hydrophobic amino acid residues

A

amphiphilic

54
Q

true/false: larger proteins tend to adhere to surfaces more than smaller proteins

A

true

55
Q

disulfide linked proteins are ___ (more/less) likely to unfold and will be less surface active

A

less

56
Q

proteins may desorb, which is the removal of the protein from the surface and return it to the solution. once the protein desorbs, its hydrophobic residues/domains will be exposed to the water which will lead to either ________ or ________

A

aggregation or precipitation

57
Q

________ results from the interactions between the hydrophobic portions of DIFFERENT denatured protein molecules

A

aggregation

58
Q

immunogenicity is a complex immunological phenomenon affected by various factors. __________ have the potential to trigger an immune response in a patient, which can:
- decrease a drugs effectiveness
- cause harmful side effects

A

protein aggregates (or denatured proteins)

59
Q

what are some additives used for prevent protein adsorption?

A

surfactants, other proteins (e.g. albumin), phospholipids

60
Q

true/false: surfactants, proteins (e.g. albumin) and phospholipids are all amphillic and/or have surface activity

A

true

61
Q

why is albumin used to prevent/minimize other protein adsorption?

A
  • it is very water soluble because it is highly charged
  • contains several disulphide bonds (very stable)
  • competitor for inter-surface phenomenon (decreased chances of intermolecular interactions of the protein interested)
62
Q

true/false: protein solutions should be shaken

A

false!!! air bubbles provide a new interface for proteins to adhere to

63
Q

list some agents that are used to prevent protein aggregation

A
  • sugars and salts (favour a compact state of the protein)
  • polyols, PEGs and other polymers
  • free amino acids (arginine)
64
Q

_______ may aggregate/precipitate in the reservoir of _____ pumps; precipitates may block/obstruct the intake of the drug and therefore the patient will not receive the correct dose of ______

A

insulin

65
Q

what are some reasons aggregation of insulin pumps may occur?

A
  • body temperature
  • agitation of insulin in reservoir with air
  • adsorption of insulin to hydrophobic surfaces of air and PVC
66
Q

true/false: total protein content (by protein assay) may not reflect its biological activity as its conformation can not be revealed by its protein contents. therefore, must perform a bioassay as well in addition to assaying for total protein

A

true

67
Q

true/false: both chemical and physical degradation result in a loss go biological activity

A

true

68
Q

k is known as the first order rate constant; the _______ (smaller/larger) the magnitude of k, the faster the degradation of active drug

A

larger

69
Q

this type of degradation (physical or chemical) is assayed by a measure of the amount of intact protein using electrophoresis

A

chemical degradation

70
Q

this type of degradation (physical or chemical) is harder to measure; measure the biological activity of protein (e.g. clot lysis assay to t-PA)

A

physical degradation

71
Q

this drug is a tissue plasminogen activator (rt-PA). its indications include acute M.I. and pulmonary embolism

A

Activase (altepase)

72
Q

true/false: degradation is additive

A

true

73
Q

are most protein based drugs in the lyophilized form or solution form

A

most in lyophilized form b/c degradation reaction is accelerated when proteins are in solution

74
Q

what are some methods used to enhance protein stability

A
  • pH (buffer)
  • decrease temperature
  • light
  • oxygen content (nitrogen flushing)
  • excipients (antioxidants, chelating agents, ionic strength)
  • lyophilization
75
Q
  • genetic engineering
  • replace certain chemical reactive amino acids with those that are less reactive
  • replace/intorduce certain amino acids to stabilize protein conformations
  • biological activity must be retained
A

enhancement of in vivo protein stability

76
Q

what are some ways that amino acids can be used for mutagenesis

A
  • replace asparagine (undergoes deamination) with serine (avoids deamination)
  • introduce additional Cys to enhance disulphide bridges and stabilize conformation
  • introduce amino acids that improve hydrophobic packing to maximize hydrogen bonding
  • introduce salt bridges
  • replace Glycerol & Pro by Ala to reduce the conformational freedom of Gly and Pro
77
Q

these two amino acids are alpha helical breakers

A

proline and glycine

78
Q

this amino acid tends to break or kink helices because
- it cannot donate an amide hydrogen bond (having no amide hydrogen)
- its side chain interferes sterically
- its ring structure also restricts its backbone

A

proline

79
Q

this amino acid tends to disrupt alpha helices because
- its high conformational flexibility (due to its small size) makes it entropically expensive to adopt the relatively constrained alpha helical structure

A

glycine

80
Q

what are some challenges with protein drug delivery?

A
  • poor oral bioavailability
  • protein denaturation in the digestive system
  • acid hydrolysis in the stomach
  • enzymatic degradation
  • poor absorption due to size
  • poor absorption due to polar charge/distribution
81
Q

what are some different example of parenteral delivery?

A
  • IV administration
  • subcutaneous injection
  • continuous subcutaneous infusion (pumps)
  • continuous intraperitoneal infusion
  • intrathecal
82
Q

what are some alternative formulations used for parenteral routes of protein drugs (alternative to solutions)

A
  • liposomes
  • micro encapsulations coated with polymers
83
Q

what are some alternative routes of delivery of protein drugs besides injection

A
  • inhaler
  • intraocular
  • intranasal
84
Q

is an injection or continuous infection of protein drugs more beneficial

A

continuous infusion because it doesn’t spike out of therapeutic range and cause side effects like an injection would and does waste drug

85
Q

what are the four types of liposomes

A
  • conventional
  • stealth
  • targeted
  • cationic
86
Q

what are some advantages and disadvantages of intra-ocular drug delivery

A

ADVANTAGES
- convenient
- rapid systemic absorption
- bypass first pass metabolism
- dosing controlled precisely

DISADVANTAGES
- low systemic bioavailability

87
Q

what are some advantages of nasal delivery of protein based drugs

A
  • highly vascularized (quick absorption)
  • milder pH (limited metabolism/destruction of protein based drugs)
  • avoidance of first pass metabolism
88
Q

this nasal spray contains calcitonin
it was approved in 2104 to treat certain bone problems (such as Pagets disease, postmenopausal osteoporosis) and to reduce high blood levels of calcium

A

Miacalcin (Salmon Calcitonin) nasal spray

89
Q

what are the FOUR ways calcitonin affects blood calcium levels

A
  • inhibits calcium absorption by the intestines
  • inhibits osteoclast activity in the bones
  • inhibits phosphate reapportion by the kidney tubules
  • inhibits tubular reabsorption box calcium, leading to increased rates of its loss in urine
90
Q

true/false: most proteins are kept at high temperatures

A

false - most kept at cold temperatures
exception is Alteplase

91
Q

most proteins may adhere to either plastic or glass containers. the effectiveness of the products could be reduced by 3-4 fold due to adherence. ________ is added to reduce adherence

A

human serum albumin (HSA)

92
Q

this medication is used for the treatment of cystic fibrosis. it is packaged in protective foil pouches provided by manufacture. stored in original light protective container. light protective pouches for travellers can be obtained from the manufacturer by patients who are going to travel.

A

dornase alfa (PULMOZYME)

93
Q

this medications lyophilized form is light sensitive. solution after reconstitution is not light sensitive

A

Alteplase

94
Q

what are some travel/shipping requirement for protein drugs

A
  • stored in insulated, cool containers
  • ice packs in warmer climates
  • be cautious to protect the protein from freezing in the sub-freezing weather
  • do not place protein products in direct contact with ice
  • avoid using dry-ice
  • place protein products in an insulated package not in a cargo container
95
Q

true/false: when preparing protein drugs, it is important to shake them well

A

false - swirl the container - do not shake

96
Q

true/false: most patients using protein products are immune compromised

A

true

97
Q

what is the general sterility policy for protein drugs after reconstitution in the hospital

A

72 hours

98
Q

what is the general sterility policity for protein drugs reconstituted at home

A

a 7 day expiration date is used, provided the product is stable and kept in the refrigerator

99
Q

this is not recommended as most proteins will adhere to the filter. inline filters for TPN patients: protein products should be infused below the filter

A

filtration

100
Q

what are some education points for those who are using parenteral protein drugs at home?

A
  • make sure they are capable to handle, reconstitute and inject
  • clean area and has a storage facility
  • the patient is rotating the injection site
101
Q

describe the normal clotting process

A

stage 1: blood vessels are damaged and bleeding starts
stage 2: blood vessels contract to slow the flow of blood to the injured area
stage 3: platelets stick to, and spread on, the walls of damaged blood vessels. these spreading platelets release substances that activate other nearby platelets which clump at the site if injury to form a platelet plug
stage 4: the surface of these activated platelets then provides a site for blood clotting to occur. clotting proteins like factor VIII (8) and factor IX (9) circulating in the blood are activated on the surface of the platelets to form a mesh-like fibrin clot

102
Q

what is the difference in clotting between a healthy individual and someone who has a bleeding disorder?

A

HEALTHY INDIVIDUAL
the bleeding starts, vessel’s constrict, platelet plug, fibrin clot formed

BLEEDING DISORDER
the bleeding starts, vessels constrict, incomplete platelet plug, incomplete formation of fibrin clot

103
Q
A

pharmacogenomics 4860 (10 decks)

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