Synthetic Biology

Question 1

What did Fred Sanger​ do?
What did Har Gobind Khorana​ do ?
What did Kary Mullis​ do?
What did Hamilton O. Smith​ and Daniel Nathans​ do?
What did Emmanuelle Charpentier​ and Jennifer Doudna​ do?
What did Joe Ecker​ do?

Answer 1

Reading genes​
Writing genes​
Copying genes​
Cutting and pasting genes​
Gene editing​
RNAi​

Question 2

Putting the Engineering into Genetic Engineering​

Answer 2

Synthetic biology takes well characterised genetic parts and re-assembles them to make a new whole​

Parts may be from any organisms​

Question 3

Describe the Repressilator​

Answer 3

This synthetic network may reach a steady, or if you get the control right, may show oscillatory behavior.​

Outcome depends on: ​
repressor concentration​
translation rate​
decay rates of mRNA and protein​

Question 4

What’s oscillatory behavior?

Answer 4

Oscillations are favoured by strong promoters coupled to efficient ribosome-binding sites, tight transcriptional repression (low `leakiness’), cooperative repression characteristics, and comparable protein and mRNA decay rates ​

“A general obstacle to the design of biochemical networks is uncertainty about the values of parameters that characterize the interactions between different components.”​

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Question 5

Genetic circuits​

Answer 5

Logical arguments as used in electronics are very useful in understanding the function of genetic elements​

Combinations of well-characterised genetic elements may be used to build logical arguments in a cell​

Applications in computing as well as in bioproduction of useful molecules​

Question 6

BioBricks​

Answer 6

The parts used in synthetic biology are often called “BioBricks”​

Drew Endy (right) is one of the founders of the BioBricks Foundation ​

iGEM is a competition that is giving students across the world experience with BioBricks and synthetic biology​

Well-understood parts can be expressed in a “chassis” organism for construction of new pathways​

Question 7

Synthetic biology for biofuels​ (expand)

Answer 7

Escherichia coli​
Cinnamomum camphora​
Photorhabdus luminescens​
Bacillus subtilis​
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Question 8

A minimalist approach​

Answer 8

The reductionist approach in science is key to understanding molecular biology, genetics and synthetic biology​

The idea is that reducing complex phenomena to their constituent parts and then understanding those parts is sufficient to understand the whole.​

This has been a powerful approach in biology​

Emergent properties are those which arise from the parts when assembled together. Systems biology is concerned with these emergent properties​

Question 9

A minimal genome​

Answer 9

Craig Venter was one of the main drivers behind the Human Genome Project​
His industrial approach forced it to get finished years before it otherwise might​
A feature of Synthetic Biology is the involvement and easy relationship that exists between industry and academia​

Mycoplasma genetallium was chosen as it had the smallest genome known at the time (1079 kb, 525 genes)​

Venter and his team transplanted a fully synthesised minimal genome grown in yeast cells into a recipient M. capricolum cell (531 kb, 473 genes, including 149 genes of unknown function!)​

Question 10

summary

Answer 10

In order to re-engineer a system, it is necessary to understand it.​

Think of:​

Khorana’s chemical synthesis​

Likewise, the characterisation of parts since the repressilator teaches us about genetic control​

The repressilator itself teaches us about how oscillatory mechanisms may evolve in cells​

The Minimal Genome Project​
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We’ve talked about;​

Synthetic biology’s origins in chemical biology, engineering, reductionism​

Synthetic biology’s relation to minimal genome engineering and engineering of parts represent two main branches, which are separate in their approach and goals, but complementary​