BLOCK 1 BIO3

Question 1

What is the Levinthal paradox of protein folding?

Answer 1

How does the protein find stable state with the lowest energy with
When algorithmic search for the minimum energy configuration would take immense time, while protein folding in reality happens very quickly, even in the case of most complex structures.
Should be time longer than the age of the universe but is millisecond or even microsecond time scale.

Question 2

How is it resolved?

Answer 2

The posssible solution is “The proetin fodling funnel”
Assumes that folded proteins can become trapped, the folding funnel hypothesis assumes that the native state is a deep free energy minimum with steep walls.

“Golf -> rugged funnel”

Question 3

What are the favourable and unfavourable interactions and energetic
contributions that determine protein folding?

Answer 3

Favourable:Peptide bonds(covalent chemical bond/electrostatic interactions)
Hydrogen bonding, van der Waals forces, hydrophobic interactions, environment (stabilize the folding)

Unfavorable: Environment
ph, temp, chemical and enzymes

Question 4

What are intrinsically disordered proteins?

Answer 4

Are proteins that contain segments that lack definable structure, this gives them the ability to interact and have manny different bidning parteners and often fold upon bidning.

Question 5

In what contexts is the limited solubility of proteins a problem?

Answer 5

Loss of protein solubility, can lead to disease due to loss of function and/or gain of toxic function

Question 6

What are examples of protein misfolding/aggregation diseases?

Answer 6

Type II diabetes, Parkinson and Alzheimer

Question 7

What is liquid-liquid phase separation of proteins ?

Question 8

What is allostery?

Answer 8

Regulation method of a protein by binding an effector molecule to the protein, at a site other than th active site.
Effectors that enhance the protein’s activity (activators) or decrease (inhibitors)

Question 9

What are enzymes?

Answer 9

Enzymes are naturés catalysts, the majority of thousands of biochemcial reactions happens do enzymes catalyze ability.

Question 10

What ways are they superior to non-biological
catalysts?

Answer 10

There advantages are the high level of kinetic control and the specificity and selective nature

Question 11

Be able to provide 2-3 examples of very important enzymes and their roles in biology.

Answer 11

Nitrogenase
-Good as catalyse for reduction of elementary nitrogen

Carbonic anhydrase
-Ability to solublilize carbon dioxide usefull for carbon caputre

Question 12

Be able to interpret simple enzymatic energy landscapes
Be able to give examples for biotechnological applications of enzymes

Answer 12

Green hydrogen production or CO2 caputre
Synthesis of complex sugards and other high value chemicals (biofueles)
Cleaning/degration of stains

Question 13

What is directed evolution and how is it used to improve enzymes?

Answer 13

Directed evolution method by which biological entities with desired traits are created through iterative rounds of genetic alterations
It improves the enzymes
-thermal stability
-binding affinity
-catalytic activity on natural and non-natural substrates

Question 14

What are antibodies and what are their roles in biology and their applications?

Answer 14

Antibodies are larage glycoproteins (proteins with sugars attached) they target pathogens(bacteria) for destruction or inhibit their mechanism

Applications:
-qualivative detection/identification of proteins
-diagnostics of disease
-Bicologial recognition element for biosensors

Question 15

Be able to perform simple stoichiometric calculations of antibody binding to
target.

Question 16

What are nanobodies and why are they better suited for some applications than
classical antibodies?

Answer 16

Nanobodies: A nanobody is a single-domain antibody, it has the same properties as anitbody but they are much smaller than common antibodies and is more robust

Applications:
-Imaginng, diagnostics and targeting

Question 17

What is the key idea of protein display technologies, such as phage display?

Answer 17

The idea is to retrieve the information of the sequence in the protein, this is done by linking the genotype(information) and phenotype(function) such the information can be retrieved
Phage display is a technique that uses bacteriophages (viruses that infect bacteria)
In this technique, a gene encoding a protein of interest is inserted into a phage causing the phage to “display” the protein on its outside while containing the gene for the protein on its inside, resulting in a connection between genotype and phenotype.
A libary of phage display combiations exists

Question 18

What are these protein display technologies mostly used for?

Answer 18

Directed Evolution of Proteins
Protein-Protein Interaction Studies
Drug Discovery

Question 19

Be able to perform simple calculations of amino acid sequence diversity of
peptides

Question 20

Why is it difficult to determine the sequence of proteins, especially at low
quantities?

Question 21

What is proteomics and what experimental method is it mostly based on?

Answer 21

Proteomics is the study of protein.
Techniques and methods of proteomics approach are used for the identification of proteins’ activities and presence in complex mixtures based on comparison with data bases.
Mass spectromery is the powerful method for analysis of proteomes both in large samples and in single cells

Question 22

What are the advantages and disadvantages of chemical synthesis and
recombinant production of proteins?

Question 23

How are proteins degraded?

Answer 23

Protein degradation may take place intracellularly (inside the cell) or extracellularly (outside the cell)

Extracellularly: Food processed in organs or guts when eating, it gets breaking down my enzymes in month.

Intracellularly: Proteins in cells are broken into amino acids, it removes damaged and abnormal proteins and prevents their accumulation, regualte cellualar processes and the amino acids may be reused for synthesis of protein.

Question 24

What are PROTACS?

Answer 24

Proteolysis targeting chimera ( PROTAC)
PROTAC are bi-functional small meolecule drugs that bring a target protein together with an ubiquitin- activating enzyme. Such that the proetin is targeted for degradation by the proteasome.

Question 25

What is self-assembly and what is its role in biology? Be able to give some
examples for structures that form through self-assembly.

Answer 25

Molecular self assembly is the process of finding defined arrangement without gudiance or magament from an outside source
The role it has in biology is such of ribosome formation, protein filament formation

Structures:
Amyloid fibrils

Question 26

Be able to give some examples for sustainable sourcing of food proteins.

Answer 26

Meat cell cultures
Fungal
Insect

Question 27

Be able to give some examples for functional materials generated from proteins.

Answer 27

Plastic
Proteins from peas can be treated with heat and acidic pH conditions to produce films and foils

Spider silk
Produced by recombinant of protein production
Wastewater treatment with proteins

Question 28

Why is a living cells so much more complex than what the DNA alone can
encode?