Introduction

Question 1

In addition to enzymes, there are many types of other proteins. Mention some examples.

Answer 1

1. Structural components
2. Transport molecules
3. Signal transduction proteins
4. Regulatory proteins
5. Membrane transporters
6. Hormones
7. Antibodies
8. Enzymes
   Human being: 10.000 different enzymes

Question 2

Why is a virus not a living entity?

Answer 2

It cannot reproduce by itself / without a living cell

Question 3

What are molecular biology research questions?

Answer 3

How is the living cell organized?
How does it function in terms of survival and growth?
How are the metabolic pathways regulated in response to environmental changes?
Can we understand that behavior in quantitative terms?

Question 4

For that you need precise data of..

Answer 4

Structural components , functional components (signal transduction, metabolic pathways), regulation of expression and acticity (genomics, proteomics)

Question 5

How complex is the simplest organism? (how many genes)

Answer 5

400

Question 6

What is the evidence for the least complex genome?

Answer 6

Sequencing + knock outs

Question 7

How do you know it is the networks that matter, not just the individual genes?

Answer 7

If you have 400 genes and you knock out one of them, the 399 other genes need this genes.
They found out by knocking out genes and see with how many are really needed

Question 8

Why do networks matter?

Answer 8

Bc multiple processes can only exist together

Question 9

Possible exam question: provide evidence that networks are crucial for life

Answer 9

The genomes of many organisms were sequenced, smallest genome was sequenced, knock-outs revealed that a certain gene no was acquired in order for the other genes to function. So 299 genes need the 1 other gene in order to function.

Question 10

What is an example of a system in the cell?

Answer 10

Glycolysis.

Question 11

What is flux?

Answer 11

A balancing of production and degradation rates for all internal metabolites. Reaction rates become equal to each other: flux

Question 12

Flux: J. Metabolite concentrations at steady state: Xss. Why is Jss a property of a system?

Answer 12

It only exists at steady state and the rates are all equal.
J = v1ss = v2ss = v3ss = v4ss ..
Flux would not exist if every enzyme is in a seperate test tube

Question 13

What is an example of a component in the cell?

Answer 13

Any reaction of the pathway
Rate vi = v(ei, Si, Pi)
e = enzyme conc, S = substrate, P = product)
It is a component property because you can only understand it in terms of the immideate surroundings of it

Question 14

V = V+ * S/S+Km,s. = michaelis-menten. Hoe krijg je de Vmax?

Answer 14

S heel groot (oneindig) maken. Dan krijg je S/S+Km,s = 1 want de Km,s is dan irrelevant. Dan houd je V+ over. = Vmax

Question 15

How to derive v = v+ * S/S+Km,s from

v = [enzyme] * k+ * (S/Km,s) - (k- * P/Km,p)/1+ (S/Km,s) + (P/Km,P) ?

Answer 15

1) P = 0.
v = [enzyme]* (k+ * S/Km,s) / (1+S/Km,s)
2) [enzyme]*k+ = V+
3) Dan nog *Km,s. Dan krijg je v = v+ =S/S+Km,s

Question 16

What is the difference between system properties and component properties?

Answer 16

System properties: depend on all components, e.g. flux depends on all vi’s.
Component properties: depend on local properties, e.g. P, S,..

Question 17

Why is the first step not the rate-limiting step?

Answer 17

Because of back pressure, product inhibition, feedback inhibition, gene expression (see word document and formule)

Question 18

Laws of physics and chemistry that constitute limitations to biology?

Answer 18

Thermodynamics, diffusion, (cant diffuse faster), electro conductance, elements cannot be synthesized, entropy of the universe