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CPE423 Synthetic Biology > Control Systems > Flashcards

Control Systems Flashcards

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1
Q

What three things must be understood in order to build biological systems?

A

How information in stored, how it flows and how that flow is controlled

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2
Q

How is information stored in biology?

A

DNA

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3
Q

How does information flow in biology?

A

Transcription and translation (DNA to RNA).

The central dogma of molecular biology.

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4
Q

What is the equation for the consumption of glucose and lactose?

A

glucose+lactose>CO2+H2O (+ethanol and H2)

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5
Q

How does the bacterium behave when breaking down glucose an lactose?

A

Glucose metabolism is switched on first, and then when glucose is depleted, glucose metabolism is switched off and lactose metabolism is then switched on.

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6
Q

Describe the diauxic shift in glucose and lactose metabolism

A

This is when diauxy growth kinetics are seen and bacterial density increases with glucose usage, then plateaus while the switch is taken to lactose metabolism, and then increases again.

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7
Q

Why do organisms develop the diauxy mechanism?

A

So that they are not using resources and energy to carry out certain functions and make proteins when they are not needed.

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8
Q

Give an example of industrial biotechnology and how this is different to synthetic biology

A

The production of penicillin, this is mass produced using the original organism that produces penicillin by growing it on a large scale and then purifying the product.

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9
Q

Give an industrial example of synthetic biology

A

Insulin. Waiting for 1000 pigs to grow will give you too little insulin. This would not make a profit.
Using synthetic biology, we took the ‘device’ from pigs that produces insulin and inserted it into ecoli, and now we have ecoli that can produce insulin.

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10
Q

Define modularisation

A

The ability to break up a system into component devices and parts

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11
Q

What comparison can we make to a normal chemical plant for biological processes switching on and off?

A

Similar to a valve on a pipe stream or inlet or outlet.

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12
Q

Are all enzymes proteins?

A

Yes

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13
Q

Are all proteins enzymes?

A

No

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14
Q

How does a device operate?

A

As a collection of proteins (pathways)

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15
Q

What are constitutive devices?

A

Devices that are always switched on

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16
Q

What are inducible devices?

A

Devices that can be switched on and off

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17
Q

What happens if there is an enzyme present that can act on multiple pathways?

A

There may be a chance of cross-reacting where not intended.

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18
Q

What happens if you try and make a modification to an organism that is not helpful to it growing and surviving?

A

There will be a reduction in the number of those organisms available as there will be a decrease in growth rate.

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19
Q

What is a permease?

A

A protein that makes a small hole in the cell so that molecules can travel through it.

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20
Q

What parts make up an operon?

A

Promotor, operator, parts that code for proteins, terminator.

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21
Q

What is the more common name for an operon?

A

A gene

A device

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22
Q

What do we control to control the amounts of proteins being made?

A

The flow of information at intermediate steps in the pathway.

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23
Q

What are the four levels of control?

A

Transcriptional control (control of conversion of DNA to mRNA)
Translational control (control of the conversation of mRNA to proteins)
RNA control
Post translational control

24
Q

What is the primary control step?

A

Transcription

25
Q

What is transcription catalysed by?

A

An enzyme complex made up of several proteins called RNA polymerase

26
Q

What are the DNA parts that code proteins called?

A

Protein coding sequence (coding DNA)

27
Q

What are the DNA additional parts called?

A

Control elements (non-coding DNA)

28
Q

What is a promotor?

A

The stretch of DNA where RNA polymerase binds, upstream from the coding DNA sequence, that acts as a genetic switch

29
Q

Describe how RNA polymerase works.

A

RNA polymerase (promiscuous) includes a sigma factor which provides specificity and helps the RNA polymerase identify promotors (the genetic switch). Contact between RNA polymerase and the operator starts transcription (mRNA production)

30
Q

Define an operon

A

a cluster of protein coding sequences that produce proteins for a particular function whose production is controlled simultaneously

31
Q

What is RNA polymerase made up from?

A

Alpha and beta parts, plug a sigma factor than can dissociate.

32
Q

Which part of RNA polymerase do you need to change in order to get it to recognise a different promotor?

A

The sigma factor as it needs to be able to recognise the promotor.

33
Q

Where can different sigma factors be found?

A

In the chassis of your engineered system and is synthesized by another piece of DNA

34
Q

What does CAP stand for?

A

Catabolite activator protein

35
Q

What is an operator?

A

It is a piece of DNA to which a protein called a repressor binds

36
Q

What is the function of a repressor?

A

It blocks the movement of the RNA polymerase

37
Q

What are the two types of transcription factor?

A

Activators (increase gene expression)

Repressor (decrease gene expression)

38
Q

What stops a represser from binding to the operator?

A

If something else binds to it first with a higher affinity

39
Q

What does a catobolite activator protein do?

A

Binds to the CAP site (when the molecule that is required is present) and gives the RNA polymerase a ‘push’ so that transcription is stronger

40
Q

What does a terminator do?

A

Terminates transcription

41
Q

Describe an amplifier.

A

If the input is present, then the output is present. If the input is not present, then the output is not present.
(eg. when only a promotor, operon and terminator are the parts of a device, so it is always on)

42
Q

Describe a NOT gate.

A

When the input is present, then the output is not present. When the input is absent, then the output is present.
(eg. when a represser is present, mRNA is NOT produced and vice versa)

43
Q

Describe an AND logic gate.

A

The output is only present when all required inputs are present.

44
Q

Describe an OR logic gate.

A

The output is present when either or both/all of the inputs are present. The output it nor present if none of the inputs are present.

45
Q

Describe a NAND gate.

A

The output only is present when both of the inputs are not present.

46
Q

Describe an ANDN gate.

A

The output is only present when one specific input is present (eg. activator and not repressor).

47
Q

Describe an NOR gate

A

One of two repressors is required to be present for the output to not be present.

48
Q

Describe a ORN gate

A

The output is present when A is on, or when B is off, or when both A and B are on or off together.

49
Q

Describe a XOR gate.

A

This is an ‘exclusively OR’ gate. The output is present if A is on OR B is on, but not both or neither.

50
Q

Describe a XNOR gate.

A

The output is present if both A and B are present OR not present, but not if only one is present.

51
Q

On mRNA, which nucleotide is replaced with a U?

A

T

52
Q

What is the key mediator of translation?

A

The ribosome

53
Q

How is control achieved in translation?

A

The amount of protein produced is controlled by the affinity of the ribosome to the RBS (ribosome binding site). The tighter the interaction, the stronger the RBS, the more protein is produced. This affinity is determined by the nucleotide sequence of the RBS.

54
Q

What is the half-life of an mRNA molecule?

A

2 minutes

55
Q

What does the strength of the RBS depend on?

A

It depends on the code for the protein that follows the ribosome binding site on the mRNA. If the mRNA is bent (like a hairpin as the open pairs are looking for stability so fold to make pairs with other nucleotides on the mRNA) the ribosome cannot attach and this is therefore a weak binding site. If there are no folds or hairpins close to the RBS then it will be a strong RBS.

56
Q

On what principle does the RBS calculator work?

A

Free energy difference between mRNA structure and mRNA bound to a ribosome

CPE423 Synthetic Biology (5 decks)

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