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Biochemistry-Jourdan > 3D Structure of Proteins > Flashcards

3D Structure of Proteins Flashcards

0
Q

What is a Kinase

A

Protein that is going to phosphoralate a target

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1
Q

What is a Domain?

A

Functional unit in evolution that is preserved. A conserved part of a given protein sequence that can evolve, function and exist independently of the rest of the protein chain.

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2
Q

What is a phosphatase

A

Protein that is going to dephosphorelate a target

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3
Q

Kinase and phosphatase are examples of what part of a protein structure?

A

Domains

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4
Q

What defines a secondary structure?

A

Backbone H bonding defines the secondary structure elements

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5
Q

What creates backbone H bonding

A

Carbonyl oxygen bonding with an amide hydrogen. CO-NH

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6
Q

What is the sequence of the H bonding backbone?

A

Alpha-C, C, O, N, H, Alpha-C

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7
Q

What are characteristics of a peptide bond

A

They are uncharged bonds and almost all are trans peptide bonds.

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8
Q

What does a partial double bond cause?

A

No rotation - stays fixed in trans

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9
Q

What is another name for peptide bonds?

A

Amide bonds

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10
Q

What are the Phi 0 and Psi Y torsion angles?

A

Phi: N-C.alpha
Psi: C-C.alpha

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11
Q

What do the Phi and Psi torsion angles allow?

A

Allow proteins to fold in many different ways

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12
Q

What does the Ramachandrian Diagram show?

A

Shows the angles of Phi and Psi that are most commonly seen.

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13
Q

What is steric exlusion?

A

Two atoms cant be in the same place at the same time

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14
Q

True or False?

Around the torsion angles there can be complete rotation (360 degrees)

A

False

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15
Q

What is more stable? Alpha helix or beta sheets?

A

Alpha Helix

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16
Q

True or False?

Hemoglobin contains beta sheets?

A

False. Hemoglobin is all alpha helix

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17
Q

Why is Hemoglobin all helix?

A

Needs to be more stable. Red blood cells are bags of hemoglobin that remain in a harsh environment for 120 days

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18
Q

What is the average AA length of Alpha Helix

A

12 AA residues

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19
Q

What is the basic structure of a alpha helix

A

Slinky

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20
Q

What is the linear displacement along the axis of an Alpha Helix?

A

1.5 Angstroms

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21
Q

What is the Angstrom of one complete turn of Alpha Helix?

A

5.4 A

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22
Q

How many amino acids per turn around an Alpha Helix?

A

3.6 A.A

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23
Q

Around an Alpha Helix, how often will an amino acid with an R group be pointed out?

A

Every 100 degrees

24
Q

What happens if an Alpha Helix is projected through a membrane?

A

There will be a cluster of alpha helices and hydrophobic R groups pointed out and hydrophilic R groups pointed inside.

25
Q

What is a right handed helix?

A

When looking down the helix it will be curling in a right handed fashion

26
Q

What are the torsion angles of Alpha Helix?

A

-60

27
Q

What does the torsion angle of 60 do to the structure of the chain

A

Adds to the kinking of the chain to give it the alpha helix structure

28
Q

What does Proline do to a secondary structure?

A

Develops a kink in the alpha helix because it no longer has an amide bonding to participate in the backbone h bonding.

29
Q

What is the orientation of the H bonding to the axis of the helix?

A

H bonding is parallel to the axis of the helix

30
Q

What is a 310 Helix?

A

It is like the alpha helix but wider and tighter. The 3rd amino acid is bonded and there are 10 atoms between the bondings

31
Q

What is the major characteristic of beta strands?

A

Sticky

32
Q

What is an example of a protein we would not want to be “sticky”? What is an example of something we would want to be “sticky”?

A

Not sticky - Hemoglobin - could cause sickle cell if so

Sticky - antibodies - they have beta strands

33
Q

What is Amaloidoses disease?

A

Large sheets of beta strands formed together. Can cause diseases such as alzeimer’s

34
Q

What are beta sheets?

A

At least two beta strands coming together. Form 22 average length

35
Q

What is the orientation of the Backbone H bonding on a beta sheet? Where are the R groups?

A

Bonding is perpendicular to axis sheet and R groups projected up and down

36
Q

What is a beta barrel?

A

Sheets that are not flat but rickedy and form a curl

37
Q

Parallel Beta Sheets have oxygens that are ______

A

Lined up

38
Q

What is the more stable form of beta sheets?

A

Antiparallel

*Opposite directions caused possibly by a kink made by proline

39
Q

What is the torsion of beta sheets?

A

180

40
Q

What causes the instability of Beta Sheets?

A

No tight packing and Sticky H Bonds

41
Q

What are quaternary proteins?

A

They involve the clustering of several individual peptide or protein chains into a final specific shape.

42
Q

What are the types of bonds found in quaternary structure?

A

Hydrogen, Salt bridges, and disulfide bonds

43
Q

What are two major categories of proteins with quaternary structures?

A

Fibrous and globular

44
Q

What is a fibrous protein compared to?

A

A baseball bat

45
Q

What is a coiled-coiled protein?

A

Alpha keratin that is a fibrous protein. Found in skin, nails, and hair.

46
Q

What is the structure of a coiled-coiled protein?

A

Modified alpha helix - 2 right handed alpha helices intertwined to form a left handed super helix. 3.5 residues/turn and every 2 turns we start identically where we started

47
Q

What is the amino acid sequence of coiled - coiled alpha keratin?

A

Heptad sequence - same 7 sequence over and over again. (ends are complicated)

48
Q

What is collagen triple?

A

It is a helix found in connective tissue/cartilage

49
Q

How often is there a glycine and proline in Collagen triple?

A

Every third animo acid is a glycine and every second is a proline

50
Q

Is collagen triple left handed?

A

It is right handed but each chain curls and wraps to the left

51
Q

What is the structure of a Collagen triple?

A

Very strong rope. Gly is so small it can fit in the center of the triple helix. Has Proline kinks and no H bonds within the strand

52
Q

What is Globular compared to?

A

Baseball

53
Q

What type of structures can Globular proteins have?

A

They can have many combinations of both helix and sheets and are mostly clumped into a shape of a ball

54
Q

What are major examples of globular proteins?

A

Insulin, Hemoglobin, and most enzymes

55
Q

What are beta turns?

A

tight loop is formed when the carbonyl oxygen of one residue forms a hydrogen bond with the amide proton of an amino acid three residues down the chain. This hydrogen bond stabilizes the beta bend structure.

56
Q

What two amino acids are commonly found in beta turns?

A

Proline and Glycine are frequently found in beta turns, proline because its cyclic structure is ideally suited for the beta turn, and glycine because, with the smallest side chain of all the amino acids, it is the most sterically flexible.

57
Q

Why are H bonds sticky?

A

Hanging H bonds. H bonds are in the direction opposite of the axis of the strand. H bonds will want to interact with neighbor strands.

Biochemistry-Jourdan (8 decks)

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