Introduction

Question 1

Proteins are [3]

What is interesting about proteins?

Answer 1

Proteins are diverse, complex, central to life

Integral membrane proteins; antibodies; hormones; enzymes; oxygen carriers; structural proteins; viral capsid self-assembly

Different structure = different function

Question 2

Give 4 examples of globular proteins.

Answer 2

IgG - antibody that binds antigens and elicits immune response
Insulin - hormone
Pepsin - enzyme
alpha-amylase - enzyme

Question 3

Describe muscle proteins and how they work together.

Answer 3

Titin - connects the Z disc to the M line in the sarcomere;
Myosin - thick filaments, M-line
Actin - thin filaments, Z-line

Question 4

Give an example of a scaffolding/structure protein.

Answer 4

Structure of skin, hair, nails, horns, feathers, scales, etc.

Keratin

Question 5

Describe the hagfish’s defensive slime.

Answer 5

Cold-set hydrogel, expands by 10,000x

Defensive mechanism of the hagfish slime made of keratin-like proteins

Question 6

Give examples of proteins as sensory receptors.

Often these are membrane-bound

Answer 6

Question 7

Describe the human visual cycle.

Answer 7

Signal transduction via G-protein coupled receptors which occurs due to conformational change in rhodopsin induced by interaction with light

Question 8

What is shown here?

Answer 8

Kinesin (motor protein), stepping along microtubules (cell scaffolding), carrying a vesicle

A nanomachine!

Question 9

Aside from kinesin, give an example of a nanomachine.

Answer 9

Salmonella flagella

Question 10

What is an amyloid fiber?

Answer 10

Aggregates of proteins; proteins clumping together in a uniform fashion.

E. coli uses amyloid fibers to adhere to target and as a protective mechanism, as an example.

Question 11

Give an example of protein self-assembly.

Answer 11

Viral capsid domains

Viruses are just protein capsids enclosing nucleic acids.

Question 12

What is a spike protein?

Answer 12

Note the significant glycosylation, which may play a role in virality.
Also note this protein is membrane bound - palmitoylated cysteine residues.

Question 13

Describe the flow of biological information.

Answer 13

DNA → protein

Recall: Transcriptomics; proteomics; genomics

Question 14

What are the grand challenges of the ‘protein folding problem’? [7]

Answer 14

• Predict structure from sequence
• Design sequence to get structure
• Predict function from structure
• Predict binding partners
• Biocatalysts
• Drug design
• Tailored protein nanomaterials

Question 15

What is CASP?

Answer 15

Critical Assessment of Techniques for Protein Structure Prediction

Question 16

Describe how structure prediction is improving.

Answer 16

• Latter improvements are due to AlphaFold2

AI-based program

Question 17

Desribe the evolution of corn.

Answer 17

• Single amino acid change in TGA1 protein caused loss of seed coat
• Lys → Asn
• Seed coat → no seed coat

Evidence that the origin of naked kernels during maize domestication was caused by a single amino acid substitution in TGA1 (Wang et al., 2015).

Teosinte glume architecture 1 (TGA1)

Question 18

What does functionality in foods refer to?

Answer 18

The physical and chemical properties that influence the performance of proteins in food systems during processing, storage, preparation, and consumption.

Question 19

What are the physical and chemical properties of proteins in foods? [3] What about other important functions? [3]

Answer 19

Physical/chemical

• Provide structure (bulk; texture; viscosity)
• Stablize gels; foams; emulsions
• Adds flavour and aroma (amino acids)

Other

• Nutrition
• Bioactivity (hormones; allergens)
• Enzyme activity (spoilage; processing; assays for safety/quality)

Question 20

What is the mechanism of protein solubility?

Answer 20

Hydrophilicity

e.g., whey proteins

Question 21

What is the mechanism of protein viscosity?

Answer 21

Water binding; hydrodynamic size and shape

e.g., gelatin

Question 22

What is the mechanism of protein water binding?

Answer 22

Hydrogen bonding; ionic hydration

e.g., muscle proteins; egg proteins

Question 23

What is the mechanism of protein gelation?

Answer 23

Water entrapment and immobilization; network formation

e.g., muscle proteins; milk & egg proteins

Question 24

What is the mechanism of protein cohesion-adhesion?

Answer 24

Hydrophobic; ionic; hydrogen bonding

e.g., muscle proteins; egg proteins; whey proteins

Question 25

What is the mechanism of protein elasticity?

Answer 25

Hydrophobic bonding; disulfide crosslinks ## Footnote e.g., muslce proteins; cereal proteins

Question 26

What is the mechanism of protein emulsification?

Answer 26

Adsorption and film formation at interfaces ## Footnote e.g., muscle proteins; egg & milk proteins

Question 27

What is the mechanism of protein foaming?

Answer 27

Interfacial adsorption and film formation ## Footnote e.g., egg and milk proteins

Question 28

What is the mechanism of protein fat and flavour binding?

Answer 28

Hydrophobic bonding; entrapment ## Footnote e.g., milk proteins; cereal proteins; egg proteins

Question 29

Which proteins provide the most functionality in foods, traditionally?

Answer 29

Animal based proteins & gluten

Question 30

What are potential issues with sustainability of meeting the growing demand for protein?

Answer 30

* Land * Water * Energy * Greenhouse gases

Question 31

Will we meet our future needs for food?

Answer 31

Yield predicted < Yield needed

Question 32

What are the main drivers of increased demand for protein foods? [3]

Answer 32

1. Growing population 2. Increased meat/dairy as affluence rises 3. Biofuels use

Question 33

How do we meet our future needs for foods?

Answer 33

* Reduce waste * Increase plant consumption * Maximize yield * Precision fermentation; vertical farming; animal-product analogues. * Eat more recombinant proteins (& fats) * Cell cultured meat

Question 34

What are the top reasons for wanting to incorporate more plant protein?

Answer 34

* Improve overall health and nutrition * Weight management * Wanting to eat clean * Due to health concerns * To save money * Concerns about environmental protection

Question 35

How do we get plant proteins to act like meat? ## Footnote The traditional way

Answer 35

* Extract proteins in water * Boil them to denature them * Have them form a gel by adding calcium

Question 36

How do we get plant proteins to act like meat? ## Footnote Newer way

Answer 36

* Extrusion (heat; pressure) ## Footnote Considered 'stereotypical' now to make plant-based meat analogues.

Question 37

What are the market opportunities associated with plant-based analogues?

Answer 37

* Sustainability * Flexitarian diet * Health * Culture ## Footnote 40% of Americans are looking to consume more plant protein

Question 38

How is the Beyond Burger made to look like meat?

Answer 38

* A big part of the flavour of meat is the saturated fat - hence adding coconut oil to this product; finding suitable fats for these products is one of the limiting factors associated with scaling these products up

Question 39

How is the Impossible burger made?

Answer 39

* Also uses coconut oil like Beyond for the saturated fat source * They use soy leghemoglobin to add pigment; also hemoglobin is important to attribute 'meat-like' flavours; they use yeast to make the soy leghemoglobin

Question 40

Describe a company making recombinant egg white protein.

Answer 40

Question 41

Describe recombinant milk proteins. ## Footnote whey & caseins

Answer 41

Nobody cares about the welfare of microbes, so we can use them instead of cows to make dairy proteins.

Question 42

Describe cell-cultured meat.

Answer 42

* Just want the meat, not the whole animal.

Question 43

What are alternative proteins? [3]

Answer 43

* Plant-based * Fermentation * Cultivated ## Footnote Technologies that aim to recapitulate the organoleptic properties of animal-based food products.