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Biochemistry CVM 6110 > Proteins, Protein Folding and Modifications > Flashcards

Proteins, Protein Folding and Modifications Flashcards

1
Q

What are the 4 non-covalent forces involved in Protein Folding?

A

Hydrophobic Interactions

Hydrogen bonds

Ionic or electrostatic interactions

van der Waals Forces

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2
Q

Besides contributing to protein folding what else do the 4 non-covalent forces do?

A

prevent protein degredation

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3
Q

Why did Dr. Dickerson equate the 4 non-covalent protein folding forces to Velcro?

A

Because they all work together and you can change one of them and not necessarily compromise its stability! Like pulling up the corner on a piece of velcro - it still sticks together

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4
Q

What drives Hydrophobic Interactions?

A

Water!

Not nonpolar hydrophobic groups

It would rather interact with itself than hydrophobic groups that would cause it to form an ordered structure…and water likes chaos!

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5
Q

True or False

A polar substance in water will dissolve very easily

A

True

It has a better interaction with water than water has with itself!

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6
Q

Which bond type is the biggest player in secondary and tertiary structure?

A

Hydrogen Bonds - surprise!

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7
Q

Is a hydrogen bond stronger or weaker when it’s bent?

A

weaker

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8
Q

Is a hydrogen bond stronger or weaker when it’s linear?

A

stronger

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9
Q

How do electrostatic interactions work?

A

Interactions between charged groups (pos and neg that attract) - important for stabilization and binding of charged ligands and substrates

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10
Q

In Electrostatic Interactions why are the charged groups located on the outer surfaces of the protein?

A

so they can interact with water molecules

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11
Q

Why are non-charged or non-polar groups located on the innermost portion of a protein?

A

Because they don’t want to interact with water

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12
Q

What is the weakest of the noncovalent forces?

A

Van der Waals Forces

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13
Q

What is the purpose of Van der Waals Forces?

A

to contribute to the folded structure

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14
Q

Why wouldn’t you want Van der Waals forces in secondary structure?

A

Because they are weak forces and you need strong hydrogen bonding to stabilize alpha helices and beta sheets!

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15
Q

What are chaperones?

A

Helper proteins that help to fold and unfold using ATP - one chaperone on one side helps to unfold and the other on the other side may help to fold again…

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16
Q

Does protein folding happen without chaperones?

A

Yes but they faciliate the process they don’t catalyze it

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17
Q

Clinical Correlation

What is a prion?

A

a protein that acts as an infectious agent in it’s misfolded form

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18
Q

What are Transmissible Spongiform Encephalophaties caused by?

A

Bad Prions - the bad prions act as a template and convert good prions to bad prions - that’s why it happens so quickly and the nervous system shuts down.

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19
Q

How does one develop bad prions to begin with?

A

Infectious agent/process (most common)

Can be hereditary

Spontaneous mutation

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20
Q

Structurally how does a bad prion differ from a good prion or what does it change a good prion to?

A

Changes it from an alpha helix to a beta sheet - these beta sheets form plaques which then lay down on the neurons and shut down the nervous system

21
Q

Name the Transmissible Spongiform Encephalophathies

A

Mad Cow (BSE)

Scrapie

Creutzfeldt-Jakob

22
Q

What did scientists determine about Scrapie in different breeds of sheep?

A

some breeds are more susceptible than others - that’s why they are trying to breed the TSE out of them by getting rid of those genes

23
Q

What is the structure of the mature Collagen?

A

triple helix encompassing 3 different polypeptide chains - superhelix!

24
Q

Which 2 amino acids are abundant in Collagen?

A

glycine and proline!

25
Q

Roughly what percent of collagen is glycine?

A

33%

26
Q

Roughly what percent of collagen is proline?

A

13%

27
Q

Why are there so many different genes that code for different collagen proteins?

A

That’s what allows the range of collagen structures - from very rigid to very flexible - allows for tissue specific forms of collagen to form

28
Q

9% of collagen is a modified amino acid…which one?

A

hydroxyproline

29
Q

What’s significant about gene families?

A

members code for proteins of closely-related structure and function - different gene family members may be expressed at different times during development or in different tissues

All members of gene families have similar DNA sequences and similar amion acid sequences

30
Q

Which is the most abundant derived amino acid that helps with collagen structure?

A

4-hydroxyproline

31
Q

2 of these amino acids come together to form allysine which is used in collagen crosslinking

A

lysine

32
Q

What does proline do for the collagen structure?

A

it causes it to twist and the peptide bond becomes perpendicular not parallel

33
Q

Which is more prevalent in collagen: inter chain h-bonding or intra chain h-bonding?

A

interchain - between 2 different chains!

34
Q

Due to the nature of collagen and it’s glycine and twisting from proline what happens to hydrogen bonding?

A

Hydrogen bonds are non-existent - h-bonding is pushed to the outside

35
Q

What does crosslinking do for collagen structure?

A

provides structure and rigidity

36
Q

What is a defect of collagen that we discussed in class?

A

Ehlers-Danlos Syndrome - defect in making collagen

37
Q

What does HERDA stand for and what is it?

A

Hereditary Equine Regional Dermal Asthenia

An autosomal recessive skin disorder of collagen - some animals it’s severe - some need to be put to sleep - causes loose, hyperextensible, fragile skin

38
Q

How does HERDA work?

A

it’s a mutation in the collagen enzyme that causes the proline to not have a conformational change - isoproline isomerism

39
Q

What are lipoproteins?

A

complexes of lipids and proteins that transport lipids from tissue to tissue and participate in lipid metabolism

40
Q

What are lipoproteins composed of?

A

Apoproteins and a lipid complex

41
Q

Which level of structure is an apoprotein?

A

alpha helices - allowing them to associate with lipids in fatty interior of cells - that interior is polar!

Outer edge of helix has positive charges

inner edge has negative charges

Aromatics on inside of the helices hydrophobic

42
Q

What does a Glycoprotein do?

A

It helps with cell signalling and interaction

Cell recognition

43
Q

Are glycoproteins good or bad?

A

both - they participate in both normal and disease related functions

44
Q

Which linkages are most common in glycoproteins?

A

N-glycosidic and O-glycosidic linkages

N-linkage on asparagine

O-linkage on serine or theronine and hydroxylysine

45
Q

What is clinical significance of Glycosylated Hemoglobin?

A

HbA1c=glycosylated hemoglobin

This value is monitored in diabetics to assess their level of control. It reflects the lifespan of a RBC.

46
Q

If HbA1c or glycosylated hemoglobin is high is there a high average content of glucose in that individual or a low average?

A

high

increased HbA1c due to an increase in glucose

47
Q

Are structures of proteins set in stone?

A

no, they are changing all the time

48
Q

What happens when you change the structure of proteins

A

Disease processes in most cases

Biochemistry CVM 6110 (8 decks)

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