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CET I > Paper 3 > Flashcards

Paper 3 Flashcards

1
Q

definition of biotech

A

use of a biological organism to generate a product for medical, industrial or agricultural use

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2
Q

three basic requirements of patentability

A

novelty, non-obviousness, industrial utility

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3
Q

lifetime of a patent

A

around 20 years

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4
Q

cost of goods

A

accumulated total of all costs used to create a product or service

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5
Q

what is humulin?

A

a recombinant human insulin protein

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6
Q

which product dominates pharm?

A

monclonal antibodies, followed by hormones, clotting factors, enzymes, vaccines etc

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7
Q

where are mAbs usually produced?

A

CHOs

early mAbs were produced in hybridoma cell lines

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8
Q

where is the current bottleneck for mAb production?

A

downstream purification

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9
Q

what is gene therapy technology

A

replacing/augmenting defective genes with normal copies of the gene

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10
Q

old adage

A

prevention better than cure

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11
Q

covid prevention, detection and treatment

A
  1. vaccine
  2. LFT, PCR, LAMP, sequencing
  3. mAbs, antivirals, dexamethazone - repurposing old drugs - normally used to treat comatose ppl
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12
Q

What did Oró discover in 1961

A

NAs can form spontaneously from HCN in water-ammonia systems under the conditions that are assumed to have existed on the primitive Earth

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13
Q

what has been suggested as the birthplace of life?

A

deep sea hydrothermal vents

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14
Q

was the primitive environment on Earth oxidising or reducing?

A

reducing

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15
Q

conservative mutation

A

letter changes but no change in function

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16
Q

which gene is used as the standard for classification and identification of microbes?

A

16S rRNA

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17
Q

what three main groups are cells classified into?

A

bacteria, archaea, eukaryotes

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18
Q

what is LUCA and LECA

A

last universal common ancestor, last eukaryotic common ancestor

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19
Q

when does a cell duplicate its entire genome?

A

when it divides into two daughter cells

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20
Q

ortholog, paralog and homolog

A

genes in two separate species from the same ancestral gene in the last common ancestor

  1. related genes resulting from gene duplication within a single genome
  2. genes related by descent in either way
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21
Q

properties of eukaryotic cells

A

DNA in nucleus, larger, have a cytoskeleton, don’t have a tough cell wall, have mitochondria unlike prokaryotes

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22
Q

endosymbiont hypothesis

A

early anaerobic cell engulfed an aerobic prokaryotic cell - new cell can live anaerobically and aerobically

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23
Q

could mitochondria have come from a purple photosynthetic bacterium?

A

maybe - mitochondria have similar size to bacteria, have their own DNA and ribosomes, have a double membrane

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24
Q

organotrophic

A

can use anything as food - sugars, amino acids, hydrocarbons, methane etc. e.g. E coli

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25
Q

are yeast unicellular or multicellular?

A

unicellular eukaryotic cells

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26
Q

how can yeast reproduce

A

vegetatively (by simple cell division) or sexually

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27
Q

a similarity btw chloroplasts and mitochondria

A

contain their own genome

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28
Q

important difference btw mitochondria and chloroplasts

A

cplasts: inner membrane not folded into cristae and doesn’t contain electron transport chains
instead the thylakoid membrane contains ETC, photosynthetic light harvesting systems and ATP synthase

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29
Q

E coli

A

gram negative, facultative anaerobic, rod-shaped, coliform bacterium found in the lower intestine of endotherms
20 minute reproduction time

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30
Q

what do most antibiotics inhibit?

A

either bacterial protein synthesis

or bacterial cell wall synthesis

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31
Q

which genus are most antibiotics made of

A

Gram-positive genus Streptomyces

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32
Q

what do penicillins target?

A

cell wall synthesis
cross linking of peptides on the polysaccharide chains is prevented
penicillin is a suicide substrate

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33
Q

three main ways by which a pathogen can develop drug resistance

A
  1. alter the molecular target of the drug so that it is no longer sensitive to the drug
  2. produce an enzyme that destroys the drug
  3. prevent access to the target by e.g. actively pumping the drug out of the pathogen

‘MOTEP’

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34
Q

penicillinases

A

aka beta-lactamases
enzymes produced by structurally susceptible bacteria which render penicillin useless by hydrolysing the peptide bond in the beta-lactam ring of the nucleus

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35
Q

if cells have approximately the same DNA why do they behave differently?

A

different genes are expressed in different cells and at different times

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36
Q

what is special about the 5’ to 3’ direction?

A

it is the direction in which DNA is synthesised

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37
Q

what is cool about RNA?

A

can catalyses so may be the original biomolecule

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38
Q

what does a parental DNA helix do?

A

produce identical daughter DNA helices

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39
Q

how many nucleotide pairs in the human genome?

A

3.2 bn

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40
Q

what rxn does the enzyme DNA polymerase catalyse?

A

addition of a deoxyribonucleotide tot he 3’ end of a polynucleotide

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41
Q

4 levels of protein structure

A

1 amino acids
2 folding e.g. alpha helix/beta sheet
3 how it folds in 3D
4 multiple domains

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42
Q

three mechanisms of proof-reading

A

DNA, exonucleolytic and mismatch repair

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43
Q

transcription

A
  1. unwind small portion of DNA double helix to expose bases on each DNA strand
  2. one of the two strands of the DNA double helix then acts as a template for the synthesis of an RNA molecule
  3. nucleotide sequence of the RNA chain determined by the complementary base pairing btw incoming nucleotides and the DNA template
  4. RNA polymerase is responsible for unwinding the DNA helix just ahead of the active site for polymerisation.
  5. growing RNA chain extended one nucleotide at a time in the 5’ to 3’ direction

UNTECOPO 5

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44
Q

how many transcripts per hour can be made from a single gene?

A

over a thousand

45
Q

do RNA polymerases need to be as accurate as DNA polymerases?

A

no, bc don’t PERMANENTLY store genetic info in cells

46
Q

differences in transcription btw eukaryotes and prokaryotes

A

bacteria 1 type of RNA polymerase, eukaryotes 3
bacterial RNA polymerase only needs one sigma factor, euk need many transcription factors
initiation harder for euk
in euks, RNA molec resulting from transcription has both INTRONS AND EXONS

47
Q

alternative splicing

A

different introns can be removed for different gene products, or exons can be of different lengths

48
Q

for translation, in which direction is the codon read?

A

5’ to 3’ direction

49
Q

what do aminoacyl tRNA synthetases do?

A

they have a two step mechanism which ensures that the correct amino acid is bound to the correct tRNA molecule

50
Q

how many binding sites does a ribosome have for tRNA?

A

3: E P A

exit, peptidyl, aminoacyl

51
Q

three main steps in translation

A

initiation, elongation and termination

52
Q

why has the ribosome been a frequent target of antibiotic molecs?

A

prok and euk ribosomes quite different, w/o ribosome protein synthesis is screwed

53
Q

how does covid replicate?

A

has RNA and needs to make lots of copies - does that using a polymerase. Uses error prone replication - not concerned with high fidelity copying bc will have an evolutionary advantage if it mutates a lot. changes in spike protein mean undetectable. proof-reading leads to cumulative mutations. delta to omicron 100 mutations

54
Q

lac operon

A

a polycistronic transcript which can make multiple proteins from one mRNA transcript

55
Q

what can incorrectly folded proteins lead to?

A

neurodegenerative diseases e.g. Alzheimer’s or Parkinson’s

56
Q

are lipid bilayers thicker for saturated or unsaturated lipids?

A

saturated lipids

57
Q

why are exosomes an interesting therapeutic product?

A

diagnostics, precision medicine

can easily cross cell barriers so could deliver NA based therapies

58
Q

what does covid do?

A
  1. binds 2. fuses with cell membrane 3. uncoats and NA released. 4. NA processed by viral proteases 5. Viral RNA which can code for 9 to 11 proteins is synthesised 6. Virus encapsulated 7. Virus buds from vesicles 8. Virus emerges from cell membrane
    bifunc rena pro cabudem
59
Q

what are the opportunities for developing antivirals

A

specifically target RNA genome replication bc virus has an RNA polymerase specific to itself

60
Q

is inside or outside of a cell more positive

A

outside of a cell

61
Q

what are the two major classes of membrane transport proteins?

A

transporters and channels

62
Q

sth that is amphiphillic

A

transmembrane protein

63
Q

what is the equilibrium potential for an ion?

A 
voltage gradient (membrane potential) at which equilibrium is reached. It is given by V in the Nernst equation
at eq /\Gconc+/\Gvolt = 0
64
Q

what does the transporter GLUT4 do?

A

allows glucose to pass from cells to blood via simple diffusion. Type II diabetes mellitus - cells don’t insert GLUT4 into their membranes so high BGC so heart disease/stroke/kidney failure

65
Q

why does ATP => ADP + Pi release energy?

A

release of terminal phosphate removes an unfavourable repulsion btw adjacent negative charges. When released, the inorganic phosphate is stabilised by resonance and by favourable bond formation with water.

66
Q

is NADH an intermediate in anabolic or catabolic rxns

A

catabolic

67
Q

what is glycolysis?

A

glucose to two pyruvates, releasing two ATPs and 2 NADHs

68
Q

why are reactive oxygen species contained within mitochondria?

A

oxygen is toxic

69
Q

what does PCR do?

A

enable amplification of the number of DNA copies

70
Q

when did recombinant DNA tech really take off?

A

In 1978 when Genentech made synthetic human insulin

71
Q

why do we need the Taq polymerase for PCR?

A

PCR based on thermocycle. Need 90 deg to separate two DNA strands, but this destroys DNA polymerase which likes 37 deg C. So need a heat resistant DNA polymerase, i.e. Thermophilus aquaticus.

72
Q

is DNA charged?

A

Yes, negatively

73
Q

what does bla do?

A

codes for amphicillin resistance

74
Q

lac repressor

A

catabolyte repression to maximise bacterial growth

75
Q

what is good about yeast expression vectors compared to plasmids?

A

can be used to express euk proteins needing post-translational modifications
also allows cloning of v large DNA molecs

76
Q

cDNA

A

for cloning eukaryotic genes
cDNA produced from fully transcribed mRNA found in the nucleus and therefore only contains the EXPRESSED genes of an organism

77
Q

protein purification methods

A

three main types of column chromatography: ion-exchange, gel-filtration, affinity

78
Q

isoelectric point

A

pH at which a protein has no net charge

if pH > pI, protein has net positive charge

79
Q

what dye is used for SDS PAGE?

A

Coomassie blue

80
Q

how can you kill a tumour without using chemotherapy?

A

use the patient’s OWN T cells in treatment to minimise chance of rejection. Genetically modify them to form a chimera (mixture of two things). So get specific killing of tumour, no need for chemotherapy

81
Q

what are clones in the context of cells?

A

cells derived from a common ancestor cell

82
Q

type I diabetes

A

immune rxns against insulin-secreting cells in the pancreas kill these cells, leading to severe insulin deficiency, high BGC and body wasting
i.e. beta cells destroyed by autoimmune rxn

83
Q

what is the major class of immunoglobulin in the blood?

A

IgG

84
Q

polyclonal antibodies

A

cheap, rapid, large quantities of non specific anitbodies, recognise multiple epitopes on an antigen, different batches vary in composition

85
Q

uses of enzymes

A

Textiles: catalase to remove H2O2
Food and drink: Fungal alpha amylase for dough improvement
Pulp: Cellulase for pulp refining

86
Q

specific activity

A

number of units of enzyme activity per mg of total protein present (including impurities)

87
Q

what does lysozyme do?

A

destroys bacterial cell walls by HYDROLYSING the sugar linkages between NAM and NAG in peptidoglycan.
Glu 35 and Asp 52 are the catalytic residues in lysozyme
substrate is an oligosaccharide of six sugars.
final products are an oligosaccharide of four sugars and a disaccharide, produced by hydrolysis

88
Q

which vitamin is the precursor of the coenzyme NAD+?

A

niacin

89
Q

issues with Lineweaver Burk plot

A

need a lot of data points at low substrate concentration

90
Q

what can lead to enzyme inactivity?

A

active site blockage, inactivation of catalytic groups, change in the shape of the active site

91
Q

examples of post-translational modifications

A

methylation, acetylation, glycosylation

92
Q

effect of immobilisation on rmax

A

rmax decreases

93
Q

which gene regulatory protein is regularly mutated in cancers?

A

p53 - for detecting DNA damage in cell cycle control and arresting the cycle

94
Q

meiosis

A
  1. meiotic S phase
    then two rounds of chromosome segregation
    meiosis I segregates the homologs
    meiosis II segregates the sister chromatids
95
Q

mitosis vs meiosis

A

mitosis: homologs don’t pair up and the sister chromatids segregate in a single division

96
Q

insulin production

A

insulin is a peptide hormone of 51 amino acids (A chain and B chain which are linked by disulfide bonds). Synthesised as a larger protein (proinsulin) then cleaved by proteolytic enzymes. PTM of proinsulin to insulin only occurs in the beta cells of the islets of Langerhans

97
Q

RQ

A

CO2 made/O2 used in mol/s for both

98
Q

what does a high degree of reduction imply?

A

a low degree of oxidation

99
Q

oxygen utilisation rate

A

O2 used/S used in mol/s for both

100
Q

when are secondary metabolites starting to be produced?

A

in the stationary phase, e.g. penicillin

vs e.g. alcohol as a primary metabolite in the growth phase

101
Q

what type of rxn is cell growth?

A

autocatalytic - catalyst is product of rxn

102
Q

generation time

A

time required to double the cell concentration

103
Q

maintenance energy

A

substrate consumed for non-growth functions
e.g. repair, osmotic balance, motility
essential for homeostasis

104
Q

directly growth associated

A

related to energy generation, rate of product formation prop to growth rate of cells
growth associated products formed as a result of the primary metabolic functions of the cells
e.g. ethanol production by the anaerobic fermentation of glucose by yeast

105
Q

what phase do cells need to be in for a chemostat to work?

A

exponential growth phase

106
Q

how do adaptor molecs enable ribosomes to translate mRNA sequences into protein sequences?

A

The adaptor molecs are tRNAs. These short RNA molecs have an anti-codon which is a 3-base nucleotide sequence which complements and base pairs with a specific codon in the mRNA. so each codon (apart from the three stop codons) needs a complementary tRNA. the corresponding amino acid is covalently linked to the other end of the tRNA molec by a specific enzyme (an amino acyl tRNA synthetase) to form an amino acyl (or charged) tRNA. Ribosomes move along the mRNA reading one codon at a time and a specific amino acyl tRNA binds to the ribosome according to which codon is being read.

107
Q

difference between synthetic biology and genetic engineering

A

synthetic bio involves many more genes

synthesis of poliovirus genome from nucleotide monomers (7741 bases)

108
Q

what about a CSTR is better than a PFR?

A

PFR: poorer T ctrl, undesired thermal gradients and shutdown cleaning more difficult and dear. To deal with exothermic nature of a rxn, CSTR cd have a cooling jacket

CET I (5 decks)

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