BIO7/8 - Biocomputing

Question 1

• What is a biological circuit?

Answer 1

A biological circuit is like a tiny machine inside a cell made of biological parts (like DNA and proteins). It works together to control how the cell behaves, like turning genes on or off based on certain signals. It’s similar to how an electronic circuit controls devices.

Question 2

• Are there biological circuits in natural biological cells?

Answer 2

Yes, natural cells have biological circuits. Examples include:

The Lac Operon in bacteria, which controls the digestion of lactose based on its availability.

Quorum Sensing in bacteria, where cells communicate to coordinate behavior like biofilm formation.

Question 3

• Can yeast cells be re-programmed?

Answer 3

Yes, yeast cells can be re-programmed by modifying their DNA using synthetic biology tools. Scientists insert synthetic genetic circuits, often involving promoters (regions where RNA-polymerase attaches), regulatory genes, and reporter genes (Genes that reports if a gene upstream is transcribed, could be fluorescent), to control or alter yeast behavior. Applications include producing biofuels, medicines, or industrial enzymes

Question 4

• What is meant with the term “living pill”?

Answer 4

A “living pill” refers to engineered cells, like bacteria, that are designed to function as a medicine. These cells can detect specific signals in the body (e.g., biomarkers of disease) and respond by producing therapeutic molecules or performing actions like reducing inflammation

Question 5

• What is biological circuit design?

Answer 5

Biological circuit design is the process of creating synthetic networks of genes and molecules to control cellular behavior. It involves designing genetic circuits that can sense inputs, process them using logic (like AND/OR gates), and produce specific outputs, such as protein production or chemical signaling

Question 6

• Describe the analogy of biological circuits to that of electrical circuits.

Answer 6

Components: DNA, RNA, and proteins in biological circuits act like resistors, transistors, and capacitors in electrical circuits.

Inputs and Outputs: Biological inputs (e.g., molecules or signals) correspond to electrical signals (voltage/current).

Logic: Both use logical operations like AND, OR, and NOT to process information.

Control: Biological circuits regulate cell behavior, just as electrical circuits control devices

Question 7

• How does an electronic transistor work?

Answer 7

A transistor is like a tiny switch. When a small signal is sent to one part (the base), it allows a bigger signal to pass through the other two parts (the collector and emitter). This lets it turn things on/off or make signals stronger.

Question 8

• How is the binary ’0’ and ‘1 ́ represented in an electronic computer?

Answer 8

The 0 is represented with the absence (low amount) of an electronic signal

The 1 is represented with the presence (high amount, often 5 or 3.3 volts) of an electronic signal

Question 9

• Describe the four modules of a biological circuit and explain their function.

Answer 9

The four modules of a biological circuit are:

Sensors: Detect specific inputs (e.g., molecules, light, temperature) and trigger a response.

Logic Gates: Process the input signals using rules (like AND/OR/NOT) to make decisions.

Actuators: Produce the desired output, such as synthesizing a protein or releasing a chemical.

Communication Modules: Enable interaction between cells or within parts of a circuit, like signaling molecules for coordination.

Question 10

• Explain the process of transcription.

Answer 10

Transcription is the process where genetic information in DNA is copied into RNA:

Initiation: Helicase unwinds the DNA at the promoter region, separating the two strands.

Binding: RNA polymerase attaches to the exposed DNA strand.

Elongation: RNA polymerase moves along the DNA, reading the template strand and synthesizing a complementary RNA strand.

Termination: Transcription stops when RNA polymerase reaches a termination signal, releasing the RNA molecule.

Question 11

• Explain the process of translation.

Answer 11

Translation converts mRNA into a protein:

Initiation: The mRNA moves into the cytoplasm and binds to a ribosome.

Reading Codons: The ribosome reads the mRNA in groups of three nucleotides (codons).

tRNA Matching: Transfer RNA (tRNA) molecules, each carrying a specific amino acid, match their anticodons to the mRNA codons.

Chain Formation: The ribosome links the amino acids carried by tRNA into a growing protein chain.

Termination: The process ends when a stop codon is reached, releasing the complete protein.

Question 12

• Explain how reaction rates may be estimated.

Answer 12

Question 13

• What is the role of an enzyme in a biochemical reaction?

Answer 13

An enzyme speeds up a biochemical reaction by lowering the activation energy needed for the reaction to occur. It acts as a catalyst, binding to specific reactants (substrates) and helping convert them into products more efficiently, without being consumed in the process.

Question 14

• Describe the ODE of the simple reaction A -> B with rate k1.

Answer 14

Question 15

Explain the reactions involved in constitutive gene expression.

Answer 15

Constitutive gene expression is the continuous and unregulated production of RNA and proteins from a gene. Unlike regulated genes, these genes are always “on,” ensuring a constant supply of essential molecules needed for basic cellular functions.

Question 16

• How is flow of information (binary signals) carried out?

Answer 16

In biocomputing, the flow of information (binary signals) is carried out using molecules:

Inputs: Biological signals, like the presence or absence of a molecule, represent binary states (e.g., 1 for presence, 0 for absence).

Processing: Genetic logic gates (e.g., AND, OR, NOT) process these signals by controlling gene expression or enzymatic reactions.

Outputs: The result is a measurable change, like protein production, fluorescence, or metabolite release, representing the final binary state.

This molecular interaction mimics the flow of electronic binary signals.

Question 17

• What is meant by gene expression?

Answer 17

Gene expression refers to whether a gene is actively transcribed into RNA and, subsequently, whether that RNA is translated into a protein. It determines if and how much of a gene’s product is made in a cell.

Question 18

• How can signals (small molecules) external to the cell trigger expressions inside the cell?

Answer 18

External signals can trigger cell responses by binding to receptors on the membrane or inside the cell. They can also activate or modify transcription factors, that in turn activate DNA sequences.

Question 19

• What is meant by cooperative gene expression and why is it important?

Answer 19

Cooperative gene expression occurs when multiple molecules, such as proteins or transcription factors, work together to regulate a gene. The binding of one molecule enhances the likelihood of others binding, creating a stronger or more precise response. This would be equivalent to a biological AND gate.

Question 20

• What are transcription factors and how can they be used in biological circuits?

Answer 20

Transcription Factors are proteins that regulate gene expression by binding to specific DNA sequences near genes. They can act as activators (turning genes on) or repressors (turning genes off).

Use in Biological Circuits:

Logic Gates: Combine multiple transcription factors to create AND, OR, or NOT gates for processing biological signals.

Signal Response: Use transcription factors to sense environmental or cellular signals and trigger specific outputs.

Question 21

• What is the Hill function and why is it interesting?

Answer 21

Question 22

• What is the function of a DNA-binding protein?

Answer 22

Much like transcription factors, DNA-binding proteins bind to a DNA sequence and regulate gene expression. However, they can do so in a multitude of ways that does not necessarily involve inhibiting/activating transcription.

Question 23

• In nature, cell communicate through small molecules, can this be used for biological circuits?

Answer 23

Yes, cell communication through small molecules can be used in biological circuits. These molecules act as signals for information transfer between cells or within a circuit.

Question 24

• Explain why there is a limit of how complex biological circuits we can build in a cell.

Answer 24

“The limiting factor is how many unique non-interfering molecules we can handle in a single cell.”