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Medicinal chemistry and molecular biology Flashcards

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1
Q

What is a Solenoid ?

A

A solenoid is formed when the DNA is wrapped around the histones to form nucleosomes. The nucleosomes are then packed densely to form solenoids. These go onto form chromatin and then packed to form chromosomes.

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2
Q

What does the endoplasmic reticulum do? Which other organelle carries out a similar process

A

The ER is responsible for the transportation and maturation of proteins and other molecules. It does so by budding off a part of the organelle to form endosomes. An organelle which has a similar function is the Golgi apparatus.

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3
Q

Where can ribosomes be found within a eukaryotic cell ?

A

They can either be found lying loosely in the Cytosole or attached to the surface of endoplasmic reticulum to form Rough endoplasmic reticulum.

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4
Q

What do ribosomes consist of ?

A

Proteins and rRNA

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5
Q

What is the function of the nucleolus?

A

The nucleolus is where rRNA is produced which is used to form the large and small ribosomal sub units

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6
Q

As well as transportation, what else does the Golgi apparatus do ?

A

It participates in the formation of lysosomes

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7
Q

What do lysosomes do and what do they consist of to aid their mission?

A

Lysosomes help to digest and breakdown foreign materials in a cell or old material such as organelles . To do so it uses the aid of A low pH within its structure and many hydrolase enzymes to break down bonds within a material.

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8
Q

How does foreign material or damaged material get to the lysosome in the first place ?

A

The foreign material is transported to the lysosome by the endosomes produced by the golgi apparatus

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9
Q

Mitochondria have their own DNA. how much of it is inherited from each parent ?

A

All of the mitochondrial DNA is inherited from the mother.

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10
Q

How does the prokaryotic cell differ from the eukaryotic cell ?

A

Prokaryotic cells have no nucleus , DNA is compacted by DNA binding proteins to form a nucleoid, have extra small circular DNA called plasmids, a flagellum to support their movement.

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11
Q

How can bacterial cells be arranged and how are they named accordingly ?

A

Bacterial cells can be arranged in the following way and are called:

  • Two bacterium next to each other = diplo-
  • Bacterium forming a grape-like bunch = staphylo-
  • Bacterium arranged in a straight line - strepto
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12
Q

State the difference in structure for a gram positive vs gram negative bacterium

A
  • gram positive bacterium = Has a lipid bilayer cell membrane covered in a large block of peptidoglycan. This is anchored on to the membrane by lipoteichoic acid
  • gram negative bacterium have to outer membranes which are separated by a small gap known as the periplasmic space.
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13
Q

What is the difference between RNA and DNA

A
  • The nucleotide bases in DNA lack a hydroxyl group at the 2’ position and instead just have a hydrogen atom in place.
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14
Q

Which bases are purines and which bases are pyrimidines ?

A

Purines= Adenine and guanine

Pyrimidines - thymine , cytosine and uracil.

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15
Q

How many hydrogen bonds form when the complimentary bases come together ?

A

Adenine and thymine = 2 Hydrogen bonds

Guanine and cytosine = 3 hydrogen bonds

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16
Q

Why are peptide bonds between amino acids so strong ?

A
  • There is further stabillisation present due to conjugation giving the C-N bond some double bond character
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17
Q

What type of bonds join different secondary structures together in a polypeptide bond?

A

Disulfide bonds

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18
Q

What happens when our polypeptide chains are not able to fold into their correct conformation?

A

Chaperons help the chain and stabilise folding . However it can also unfold the chain or maintain the unfolded state to allow the entrance of the chain through passages through membranes .

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19
Q

Where are proteins made if they are to be exported out of the cell or to the cell membrane ? What about for the internal organelles of the current cell ?

A
  • The Rough endoplasmic reticulum produces proteins for export.
  • ribosomes which lay freely in the cytosol produce proteins for the cell it is currently in and it’s organelles .
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20
Q

What does N-linked glycosylation entail? Is this co or post translational ?

A
  • The attachment of an oligosaccharide to the protein via the amide nitrogen of Asparagine (Asn). This is a co -translational modification
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21
Q

Is O-linked glycosylation a post or co translational process and how are the molecules attached ?

A
  • This entails the attachment of oligosaccharides to the protein via the hydroxyl groups found on serine (ser) and threonine (Thr) residues . This is a post translational modification.
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22
Q

If a protein was produced for the mitochondria in the cell how would this work ?

A
  • The protein would be produced by the free flowing ribosomes in the cytosol. The protein would then be marked by a +vely charged amphiphilic alpha helix so it can be recognised by mitochondrial receptors. Chaperons help to unfold the proteins allowing them to enter the mitachondria
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23
Q

What removes damaged or useless proteins from cells? What marks proteins for protein degradation ?

A
  • the proteasome.

- ubiquitin marks proteins for protein degradation.

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24
Q

What is the name of the enzyme which actually identifies proteins for marking and therefore degradation ?

A
  • enzyme E3
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25
Q

What is the N-end rule?

A
  • The N- terminal amino acid determines the half life of the protein
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26
Q

What is the codon of the start codon for ever protein and amino acid chain

A

-AUG - which codes for a methionine amino acid

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27
Q

What is the function of amino acyl tRNA synthetase enzyme /

A
  • It charges the tRNA with the corresponding amino acid
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28
Q

Which enzyme is responsible for mRNA synthesis

A

DNA dependant RNA polymerase. (requires single stranded DNA to form the RNA strand in the first place ). It helps to form the phosphodiester bonds in the sequence .

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29
Q

Where does the RNA polymerase enzyme bind to the DNA strand .

A
  • Promoter region on DNA
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30
Q

Why are there little to no mistakes in the RNA sequence ?

A

RNA polymerase is able to backtrack and repair damaged nucleotides or nucleotides with errors in them .

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31
Q

Why is transcription and translation coupled in bacterial cells.

A
  • It allows the bacterial cell to respond to environmental stimuli very quickly.
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32
Q

What are operons and why do bacterium cells have them ?

A
  • Operons group multiple genes together so they can be activated and deactivated all at once by a single promoter. This aids it being able to respond to environmental stimuli in bacterial cells very quickly
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33
Q

Which enzyme is responsible for acetylating histones and what does this do ?

A
  • Histone acetylase

- It prepares the histone for transcription usually by unravelling the histone and DNA complex to reveal the DNA.

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34
Q

What Histone modification is known for “ silencing gene expression” ?

A
  • Histone methylation - it does so by reforming the heterochromatin complex
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35
Q

What is the name of the part of the RNA sequence which does not code for amino acids ?

A

Introns

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36
Q

What is the name of the part of RNA sequence which does code for amino acids ?

A

exons

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37
Q

When RNAP wants to bind to the DNA sequence what does it need to bind to ?

A
  • A promoter
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38
Q

What is the name of the process which removes introns from our RNA sequence ?

A

Splicing

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39
Q

What molecule is responsible for the splicing of RNA

A
  • snRNP’s = small nuclear ribonucleoproteins
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40
Q

There are only 25000 genes present in eukaryotes. So how can we form more than 1 million genes ?

A
  • This is mainly due to post-translational modifications such as methylation and acetylation which promote protein diversity.
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41
Q

How does alternative splicing promote Protein diversity ?

A
  • It combines exons in different ways in order to change protein structure by altering the amino acid sequence order.
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42
Q

What happens in the nucleolus ?

A
  • This is where the ribosomal RNA is processed and the small and large sub units of ribosomes are produced. They are then transported into the cytosole to produce the ribosome for protein synthesis.
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43
Q

What enzyme is most responsible for RNA degredation ?

A
  • Nuclease enzymes
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44
Q

What is the name of the structure of DNA ?

A
  • Double helix
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45
Q

How do we describe the two strands which make up our DNA?

A
  • Anti-parallel strands
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46
Q

What is the difference in the DNA replication of the leading vs the lagging strand ?

A
  • The leading strand undergoes continuous DNA replication.
  • The lagging strand forms small DNA fragments known as okazaki fragments due to discontinuous DNA replication. These fragments are separated by RNA primers which constantly initiate replication on this strand over and over again.
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47
Q

Which enzyme joins the small okazaki fragments together ?

A

DNA ligase enzymes

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48
Q

As the DNA strand is unwound how are supercoils removed from the DNA sequence ?

A
  • This is the job of DNA gyrase enzymes.
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49
Q

How can drugs Stop DNA replication in a bacterial cell by targeting the supercoiling process ?

A
  • They can inhibit the function of DNA Gyrase enzymes
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50
Q

How many pairs of chromosomes does a standard eukaryotic cell have ?

A

-23 pairs

51
Q

In what part of mitosis are the chromosomes aligned across the equator of the cell ?

A
  • The pro-metaphase
52
Q

What pulls chromosomes to opposing poles of the cell ?

A
  • mitotic spindles
53
Q

What is the name of the process in which the cell is split into two ?

A

-cytokinesis

54
Q

What happens in the G1 phase of cell replication ?

A
  • All the other organelles are replicated
55
Q

What is the name given to the process of cell programmed death ?

A
  • Apoptosis
56
Q

What is the name given to prokaryote cell division ?

A
  • simple binary division
57
Q

When DNA damage is detected which TF is activated ?

A
  • Transcription factor 53 which prevents the progression of the cell cycle from the G1 to the S phase. It is malfunctions in this TF which lead to cancer growth .
58
Q

What are the three apoptosis pathways ?

A
  • P53 induced pathway
  • Death receptor pathway
  • mitochondrial pathway
59
Q

Which two genes determine whether tumour growth will occur or not ?

A
  • Proto-oncogenes

- tumour suppressor genes

60
Q

What factors impact a person’s likelihood of developing cancer ?

A
  • sometimes genetic , but mostly environmental factors.
61
Q

Define metastasis

A
  • The ability for a cancer cell to spread to other parts of the body.
62
Q

define angiogenesis

A
  • Tumours can grow to a stage where they develop their own blood vessels which can feed the tumour oxygen and nutrients directly.
63
Q

What is the job of telomeres in DNA

A

-When cell replication occurs, due to the RNA primer being bound at the terminal of the DNA strand, the DNA strand would continuously get shorter to the point the strand is so short it just triggers apoptosis. Telomeres are attached to the end of chromosomes to counteract this strand shortening. Cancer cells have elevated telomerase activity due to their increased cell division and therefore DNA replication rate.

64
Q

-What molecules found on tumours encourage blood vessels to develop on the tumour ?

A
  • Angiogenic factors
65
Q

The idea of cancer vaccines involves which type of cells ?

A
  • dendritic cells
66
Q
  • What is the general principle of cancer vaccines
A
  • Delivering antigens on to the surface of tumour cells to trigger an immune response
67
Q

What are the results of the gram test with different bacterium ?

A
  • both gram positive and negative are stained purple

- upon decolourisation gram negative appears red , gram positive remains purple

68
Q

define a pro drug

A
  • an inactive compound which metabolises in vivo to produce the active drug
69
Q

What was the main problem with sulphanilamide ? how was this resolved ?

A
  • The main problem was that the drug was too water insoluble . Therefore it would recrystallise out in the kidneys .
  • to resolve this R group was changed to give the molecule more polarity and make it more soluble.
70
Q

What does the sulphanilamide drug target in bacterial cells ?

A
  • They target The dihydropteroate synthase enzymes and act as a competitive inhibitor. This prevents the synthesis of folic acid in bacterium
71
Q

Why would two drugs be used at the same time (combination therapy ) ?

A
  • To prevent resistance and ensure the bacteria are killed.
72
Q

What is the target site of trimethoprim ? what is is it often used in combination with ?

A
  • trimethoprim targets the DHFR enzymes in bacterium as the enzyme has a different structure to human DHFR.
  • It is often used in combination with sulphanilamide
73
Q

Define bacteriostatic

A
  • A drug which inhibits bacterial growth and replication but does not kill the bacterium itself.
74
Q

Define bactericidal

A
  • Drug which directly kills the bacterial cells.
75
Q

What is QSAR ?

A
  • A method of studying the strcture of chemical structures and most useful when analysing drug molecules and identifying essential parts of the drug
76
Q

What is the main functional group in penicillin

A
  • The beta lactam group
77
Q

What resistance mechanism have bacterium developed to gain resistance to penicillin ?

A
  • They have developed beta lactamase enzymes
78
Q

Why are five membered rings more active than six membered rings in a drug ?

A
  • The five membered rings have more bond strain .
79
Q

What is the overall charge on the human cell membrane

A

-it is an overall negative charge

80
Q

-States the difference between gram + and gram - bacterium.

A
  • gram + bacterium have a cell wall comprising of a thick layer of peptidoglycan covering the cell membrane.
  • gram negative bacterium have a double membrane. In between the two cell membranes we have the periplasmic space.
  • The peptidoglycan layer is still present but it is found between the two cell membranes.
81
Q

Where are the beta lactamase enzymes found in bacterium ?

A

The beta lactamase enzymes are found in the periplasmic space of gram negative bacterium.

82
Q

What part of the bacterial cell does the beta lactam antibiotics target ?

A
  • They target the cell wall of bacterium by preventing cross linkage of peptidoglycan molecules . This weakens the cell wall and means the cell wall and therefore the cell ruptures on experiencing high osmotic pressure
83
Q

Why are gram negative bacterium often resistant to beta lactam antibiotics?

A
  • the outer membrane of the bacterium is negatively charged and can repel away the negatively charged drug molecules.
  • even if this barrier is surpassed, the periplasmic space has beta lactamase enzymes which can break down and deactivate the beta lactam antibiotics.
84
Q

What do beta lactamase inhibitors such as sulbactam and clavulanic acid do ?

A

They inhibit beta lactamase enzyme activity in the periplasmic space of gram negative bacteria .

85
Q

What are penicillin and beta lactam antibiotics used in combination with ?

A
  • Beta lactamase inhibitors such as sulbactam and clavulanic acid
86
Q

define MIC

A
  • The minimum inhibitory concentration
  • The smallest concentration of a drug/ antibiotic required to prevent the growth of bacterium on a petri dish.
    The lower the MIC the more effective the antibiotic
87
Q

Why are cephalosporins less reactive, have a slower mode of action and not as toxic compared to penicllins?

A
  • The ring expansion means they have a larger ring with less bond strain and therefore making cephalosporins less reactive.
88
Q

Why can’t the bacterium destroy the pores created by gramacidin A drugs on the cell membrane ?

A
  • This is because the amino acids which stack up on the cell membrane to form a pore in the cell cytoplasm, are not naturally made by the bacterial ribosome. So the proteasomes released by the bacteria cannot break down the stack of amino acids forming the pore on the cell membrane of the bacterial cell
89
Q
  • How does gramicidin and ionophores work ?
A
  • they form pores in the cell membrane of the bacterial cell which causes ions to leak out of the the bacterial cell leading to cell death
90
Q

What is the antibiotic of last resort and what group does it belong to?

A
  • Vancomycin
  • glycopeptide antibiotic
  • it is the last resort drug as it has severe side effects and bacterium could develop resistance if used too much
91
Q

How do drugs like vancomycin actually work?

A
  • They prevent the cross linking of peptidoglycan which weakens the cell wall and can lead to rupturing of the cell membrane under high osmotic pressure.
92
Q

Why is the G-C bond in DNA stronger than the A-T bond

A

The G-C bond consists of three hydrogen bonds whereas the A-T bond only consists of two hydrogen bonds.

93
Q

How do DNA intercalating agents work ?

A
  • They form strong pi to pi covalent interactions between DNA strands keeping the DNA strands together preventing them from separating and forming single strands .This ultimately prevents DNA replication.
  • DNA minor groove binders do the same thing . They however have positively charged groups on each side of the drug allowing it to bind to the phosphodiester bond ionically.
94
Q

Why are major groove binding agents not used in therapeutics just yet ?

A
  • This is because the major groove binding agents are large and therefore are difficult to get to the target site.
95
Q

How do DNA alkylating agents work ?

A
  • They crosslink DNA strands together to prevent transcription from occurring and DNA replication
  • Some can also lead to the cleaving of a nucleotide base which can lead to instant cell death of the target tumour cell.
  • DNA cleaving agents do the same .
96
Q

What are the most common target sites for anti cancer drugs ?

A
  • dihydrofolate reductase and thymidylate
97
Q

How does 5- flouro- uracil function as an anti cancer drug ?

A
  • It forms a similar shape to the intended substrate , binds to the thymidylate synthase enzyme permanently , preventing the dihydrofolic acid synthesis
98
Q

What enzyme does methotrexate target as an anti cancer drug ?

A
  • dihydrofolate reductase
99
Q

What do microtubules in cells do ?

A

They produce the mitotic spindles which attach to chromosomes during metaphase of cell replication.
microtubules consist of tubulin heterodimers which are joined together to form the microtubules.

100
Q

What does the drug paclitaxel do ?

A

-it is a spindle poison and targets the formation of the microtubules preventing their formation.

101
Q

What are the most common form of anti cancer drugs ?

A
  • spindle poisons
102
Q

How does taxol act as an anti cancer drug

A

-it prevents the breakdown of the microtubules after the metaphase so the cell cannot enter the next stage of cell division.

103
Q

What factors must be taken into account for an oral drug ?

A
  • What the formulation is i.e tablet , capsules/ syrup
  • is it able to survive stomach acid and low pH levels.
  • is it in the correct ionisation state ?
  • Does it have the correct hydrophobic/hydrophilic balance (LogP)
104
Q

What does the “Pi” value show us ?

A

= the log of the isoelectric point.

If PI stays between 6-8 it remains ionised and is therefore soluble and can be absorbed

105
Q

What does the LogP value tell us ?

A
  • P = partition coefficient
    Hydrophobic compound = high logP value
    Hydrophillic compound = low logp value
106
Q

State lipinski’s rules

A

For a compound to be orally available and show good absorption of biological tissue it must :
-be of a mw below 500
-have a clogP of less than 5
-have no more than 5 hydrogen bond donors
-have no more than 10 hydrogen bond acceptors
- have no more than five fused rings
// if the drug only misses out on two or less of these requirements , it can still be deemed as effective orally.

107
Q

Why do some molecules not follow Lipinski’s rules and still are able to be absorbed into the body ?

A
  • some biological molecules like vitamins may have their own active transport mechanism which can bypass Lipinski’s rules
108
Q

Which reactions does our body carry out to aid in the excretion of drugs?

A

Phase 1 excretion reactions
- oxidation - adding an OH groups makes drug more soluble so can be excreted via the kidneys .
-reduction - makes molecule more polar and ionised
-hydrolysis
phase 2 excretion
-sulfatase or conjugation can help to make the molecule more polar or ionised . This increases solubility of the drug further so it can be excreted via the kidneys.

109
Q

What are the requirements for a drug to pass the through the blood brain barrier ?

A
  • Has a molecular weight of less than 300
  • Has a clogP of 3 or less
  • Has no more than 3 hydrogen bond donors
  • Has less than 6 Hydrogen bond acceptors.
110
Q

To prevent LevoDOPA being converted into dopamine before it reaches the blood brain barrier , what do we do ?

A
  • We use levodopa and join it with carbiDOPA . carbiDOPA acts as the competitive inhibitor of enzymes which convert levoDOPA into the active dopamine before it gets to the blood brain barrier .
111
Q

How many peptide chains do antibodies consist of ?

A
  • four in total . two heavy chains two light chains
112
Q

What are the advantages of using ADC’s over standard drugs . What is the main problem with ADCs

A
  • antibody drug conjugates mean that the drug will mostly only act on the intended target site . This would make drugs less toxic so less side effects and we can also use higher doses or more toxic substances knowing they will only target the tumour cells.
  • However this makes the drug very large and therefore it cannot passively travel into the cell. Therefore it must enter a tumour cell via active transport.
113
Q

What is the process of using ADEPT therapy

A
  • inject patient with antibody- enzyme conjugate .
  • wait 48 hours to enure the enzyme antibody conjugate reaches the target site
  • inject patient with prodrug which can only be activated by the enzyme. Therefore the enzyme is only activated at the target site.
114
Q

Why are virus cells so difficult to target ?

A
  • They tend to invade human cells and use the human cells mechanism to replicate , not their own.
115
Q

What different modes of transmission are there for viruses ?

A
  • airborne
  • parasites
  • physical contact
  • food/ water bourne
116
Q

Why is the secondary response far quicker and effective compared to the primary immune response?

A
  • Memory cells from the initial exposure to the antigen are present and instantly identify the antigen. They therefore produce antibodies much faster which stimulate the response of macrophages much faster by binding tot he antigens.
117
Q

How do vaccinations work ?

A

-We introduce the body to antigens of the viral cell to stimulate the production of memory cells. This ensures that secondary exposure to the same virus cell is fast and almost instant so symptoms are not experienced by the patient.

118
Q

What does the term “retro virus” mean ? Give an example of a retrovirus

A

This means the virus can stay dormant for long periods of time before becoming active.
-HIV cells

119
Q
  • Why is HIV so dangerous ?
A
  • Because the HIV virus cells target the body’s T cells which are responsible for the immune response. Hence why when HIV infection does emerge the immune system of the patient is compromised
120
Q

Why is it difficult to make vaccines for HIV infections and also why they develop resistance to drug treatment quickly ?

A
  • Their DNA replication has no proof reading mechanism and therefore the HIV cells replicate but also mutate very quickly due to DNA base errors not being checked. So it is very likely they develop resistance to a drug . To prevent this two drugs are used in combination therapy when dealing with HIV.
121
Q

How do nucleoside reverse transcriptase inhibitors work ?

A
  • they replicate the structure of nucleotide bases but lack the hydroxyl group . This prevents them from forming the phosphodiester backbone during DNA replication to prevent the replication HIV cells.
122
Q

What is the difference between classical isosteres and bio isosteres ?

A
  • classical isosteres are atoms or ions which have identical outter shell configurations
  • bio-isosteres are biological compounds which do not necessarily have the same outer electron configuration but have similar biological properties.
123
Q

How many drugs do we often use in combination therapy to treat HIV ?

A
  • Usually use three
124
Q
  • What symmetry does a HIV protease have ?
A

-c2v symmetry unlike other protease enzymes in the human body . So we could improve the selectivity of drugs used to target HIV protease enzymes by developing them with c2v symmetry.

Medicinal chemistry and molecular biology (1 decks)

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