Biochemistry Exam 1 Lecture 3

Front 1

What is the shape of a protein specified by?

Back 1

Amino Acid sequence

Front 2

What are amino acid residues?

Back 2

The side chains

Front 3

What are the restrictions on protein folding?

Back 3

Peptide bond is planar by resonance, bonds at both sides of the alpha carbon can rotate but not freely. All polar groups on the polypeptide chain can hydrogen bond with eachother somewhere. Betasheets are stabilized by hydrogen bonds in polypeptide backbone.

Front 4

What are the two conformations peptide bonds can take, and which form is taken more often?

Back 4

Cis and trans. The majority takes Trans conformations except for proline

Front 5

What is the exception to the rule about confirmations and why? Also, how does this impact proteins?

Back 5

X-Proline is 50% cis and 50% trans because both confirmations kind of suck because both have steric interactions.

HOWEVER!

most proteins cannot handle the cis confirmation. We need PPlase to fix this.

Front 6

What mediates cis-trans conversions?

Back 6

(Peptidyl-prolyl isomerase) PPlase

Front 7

How does PPlase work?

Back 7

Some proteins need a cis conformation, so there needs to be something to fix this. The detailed mechanism is still unclear, however it interacts with misfolded protein peptide bonds via hydrophobic spots between X and proline and releases the product (it’s randomized for cis or trans, and if it works then yay).

Front 8

What is an example of a protein that requires a cis conformation?

Back 8

RNaseA

Front 9

What are two possible angles that the terminals can rotate called?

Back 9

Ψ and ϕ

Front 10

What is the ϕ side?

Back 10

N-C

Front 11

What is the Ψ side?

Back 11

C-C=O

Front 12

Are all angles of Ψ and ϕ possible for all protiens?

Back 12

Nope! It depends on the side chains. The less bulky your side chains, the more freedom

Front 13

What has more freedom, Ψ or ϕ?

Back 13

Ψ

Front 14

What angle is disfavored between Ψ and ϕ?

Back 14

90˚

Front 15

What is a right handed helix called and how is it stabilized?

Back 15

It’s called an alpha helix and it’s stabilized by the hydrogen bonds in the polypeptide backbone

Front 16

In an alpha helix, is there really a tube in the center?

Back 16

No it’s so stable and tight that there’s no space inside.

Front 17

In an alpha helix, where are the hydrophillic groups?

Back 17

Sequestered inside the helix

Front 18

What does it mean for an alphahelix to have one side hydrophillic and one side phobic?

Back 18

It can be transmembrane

Front 19

What amino acids favor an alpha helix?

Back 19

Glu, Ala, Leu, Met, Gln, Lys, Arg, His

Front 20

How many aminoacids/coil are in an alpha helix?

Back 20

3.6 Amino acids /coil

Front 21

How many Angstrums/coil are in an alpha helix?

Back 21

5.4 A/coil

Front 22

What is the distance between amino acid residues in an alpha helix?

Back 22

1.5 Angstrums/residue

Front 23

How are beta sheets stabilized?

Back 23

Hydrogen bonds

Front 24

What is the conformation of beta sheets?

Back 24

Antiparallel typically. Parallel sometimes but it’s more unstable.

Front 25

How does a beta sheet look?

Back 25

Fully extended and accordion like

Front 26

Where are the amino acid side chains in a beta sheet?

Back 26

Sticking out from either side of the sheet, alternatively

Front 27

Where does hydrogen bonding occur within a beta sheet?

Back 27

Between strands within a chain

Front 28

What residues promote a beta sheet?

Back 28

Val, Ile, Tyr, Cys, Trp, Phe, Thr

Front 29

What residues have a role in terminating alpha helicies and beta sheets, and making turns?

Back 29

Asp, Asn, Gly, Pro, Ser

Front 30

What are the levels of organization of proteins?

Back 30

Primary, secondary, tertiary,

Front 31

What is the primary structure of proteins?

Back 31

Amino acid sequence

Front 32

What is the secondary structure of proteins?

Back 32

Alpha helix or beta sheets

Front 33

What is the tertiary structure of proteins?

Back 33

The entire structure of a single polypeptide side chain

Front 34

In RNaseA, How does the structure fold?

Back 34

It can fold into the correct structure by itself via thermodynamics.

Front 35

How do you know you have the correct protein structure?

Back 35

The structure is the energetically most stable.

Front 36

What is Anfinsen’s experiment?

Back 36

Use urea to break non-covalent bonds. Use reducing agents to break SS bonds to denature proteins. Removing these reagents in the correct order will spontaneously reactivate renaturing activity. However, if you remove the reducing agent first, incorrect SS bonds are produced and prevent renaturation. SS bonds are random and is created in the deactive structure and can keep it innactive.

Front 37

What do non-polar side chains tend to create?

Back 37

Hydrophobic core

Front 38

What are the three models for protein folding?

Back 38

Framework, hydrophobic collapse, and Nucleasion-condensation mechanism

Front 39

What is the framework model for protein folding?

Back 39

Secondary structure is created first, then you get the folded conformation

Front 40

What is the hydrophobic collapse model for protein folding?

Back 40

Hydrophobic collapse occurs first, then the growth of a secondary structure occurs. Then you get your folded conformation

Front 41

What is the nucleasion condesnation mechanism model for protein folding?

Back 41

You get a folding nucleus, and by hierarchial assembly you get a folded conformation

Front 42

If you make a mistake in an early step of protein folding, what must occur?

Back 42

You must unfold it and start over. Typically this is done via chapperones

Front 43

What are chaperones?

Back 43

Proteins that help protein folding during and after translation.

Front 44

What are the two heat shock proteins?

Back 44

Hsp70 and GroEL/ES (Hsp60-like) system

Front 45

What is similar between Hsp 70 and 60?

Back 45

Both recognize exposed hydrophobic regions as bad folding. Both bind to the hydrophobic region and partially unwind it. Both hydrolyze ATP and leave the protein to refold. Both don’t really know what the right «structure» is

Front 46

What are the differences between Hsp70 and 60?

Back 46

HSp70 are the cute little chaperones that are small and work in the middle of protein translation. Hsp60 is the large complex that works after translation

Front 47

How does Hsp work?

Back 47

It uses PDI to make the SS bond in the ER.

Front 48

How does PDI work?

Back 48

PDI uses its own cystine to make SS intermediate and will release the protein to give a 2nd change to make the correct SS bond.

Front 49

Do chaperones know the correct confirmation? Explain?

Back 49

No. It just reduces at random using hydrophobic side chains. It grabs onto the hydrophobic ends and twists it to get it unexposed. It goes for the most stable confirmation (which typically will activate the protein)

Front 50

If there are two possible protein conformations, will one be refolded?

Back 50

Only if one has less hydrophobic side chains exposed. Otherwise both can exist

Front 51

How does the hsp70 system work during translation?

Back 51

Hsp70 will bind to the exposed hydrophobic region of the protein as it’s being translated. Then 70 will hydrolyze ATP and release the protein in the ‘correct’ folding

Front 52

How does hsp 60 work?

Back 52

The h-phobic side chains are contacted and extended at the lid. Then the lid closed to put the denatured polypeptide into the hydrophilic barrel. It gives the peptide a second chance to fold.

Front 53

What is the lid on a HSP60 complex?

Back 53

GroES

Front 54

Are proteins inactivated by hsp proteins?

Back 54

Pretty much no

Front 55

Can some proteins recover activity by simple renaturation?

Back 55

Yes

Front 56

What do all chaperones basically do?

Back 56

Hlpe the protein take the most energetically stable conformation and sucessfully ‘activate’ the proteins.

Front 57

What is the Delta S for cytochrome C?

Back 57

-27J/K*mol

Front 58

What is Delta S for myoglobin?

Back 58

+170 J/K*mol

Front 59

If delta S <0, what does it mean?

Back 59

It is conformational

Front 60

If delta S>0 what does it mean?

Back 60

Hydrophobic

Front 61

For folding what do Delta G and Delta H have to be?

Back 61

Less than zero

Front 62

What is modeling?

Back 62

If you know the structure of one protein, you can model a related protein after it to help you get a starting point to try to find the protein structure.