3D Structure of Proteins

Question 0

What is a Kinase

Answer 0

Protein that is going to phosphoralate a target

Question 1

What is a Domain?

Answer 1

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.

Question 2

What is a phosphatase

Answer 2

Protein that is going to dephosphorelate a target

Question 3

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

Answer 3

Domains

Question 4

What defines a secondary structure?

Answer 4

Backbone H bonding defines the secondary structure elements

Question 5

What creates backbone H bonding

Answer 5

Carbonyl oxygen bonding with an amide hydrogen. CO-NH

Question 6

What is the sequence of the H bonding backbone?

Answer 6

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

Question 7

What are characteristics of a peptide bond

Answer 7

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

Question 8

What does a partial double bond cause?

Answer 8

No rotation - stays fixed in trans

Question 9

What is another name for peptide bonds?

Answer 9

Amide bonds

Question 10

What are the Phi 0 and Psi Y torsion angles?

Answer 10

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

Question 11

What do the Phi and Psi torsion angles allow?

Answer 11

Allow proteins to fold in many different ways

Question 12

What does the Ramachandrian Diagram show?

Answer 12

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

Question 13

What is steric exlusion?

Answer 13

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

Question 14

True or False?

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

Answer 14

False

Question 15

What is more stable? Alpha helix or beta sheets?

Answer 15

Alpha Helix

Question 16

True or False?

Hemoglobin contains beta sheets?

Answer 16

False. Hemoglobin is all alpha helix

Question 17

Why is Hemoglobin all helix?

Answer 17

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

Question 18

What is the average AA length of Alpha Helix

Answer 18

12 AA residues

Question 19

What is the basic structure of a alpha helix

Answer 19

Slinky

Question 20

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

Answer 20

1.5 Angstroms

Question 21

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

Answer 21

5.4 A

Question 22

How many amino acids per turn around an Alpha Helix?

Answer 22

3.6 A.A

Question 23

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

Answer 23

Every 100 degrees

Question 24

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

Answer 24

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

Question 25

What is a right handed helix?

Answer 25

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

Question 26

What are the torsion angles of Alpha Helix?

Answer 26

-60

Question 27

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

Answer 27

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

Question 28

What does Proline do to a secondary structure?

Answer 28

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

Question 29

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

Answer 29

H bonding is parallel to the axis of the helix

Question 30

What is a 310 Helix?

Answer 30

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

Question 31

What is the major characteristic of beta strands?

Answer 31

Sticky

Question 32

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"?

Answer 32

Not sticky - Hemoglobin - could cause sickle cell if so | Sticky - antibodies - they have beta strands

Question 33

What is Amaloidoses disease?

Answer 33

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

Question 34

What are beta sheets?

Answer 34

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

Question 35

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

Answer 35

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

Question 36

What is a beta barrel?

Answer 36

Sheets that are not flat but rickedy and form a curl

Question 37

Parallel Beta Sheets have oxygens that are ______

Answer 37

Lined up

Question 38

What is the more stable form of beta sheets?

Answer 38

Antiparallel | *Opposite directions caused possibly by a kink made by proline

Question 39

What is the torsion of beta sheets?

Answer 39

180

Question 40

What causes the instability of Beta Sheets?

Answer 40

No tight packing and Sticky H Bonds

Question 41

What are quaternary proteins?

Answer 41

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

Question 42

What are the types of bonds found in quaternary structure?

Answer 42

Hydrogen, Salt bridges, and disulfide bonds

Question 43

What are two major categories of proteins with quaternary structures?

Answer 43

Fibrous and globular

Question 44

What is a fibrous protein compared to?

Answer 44

A baseball bat

Question 45

What is a coiled-coiled protein?

Answer 45

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

Question 46

What is the structure of a coiled-coiled protein?

Answer 46

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

Question 47

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

Answer 47

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

Question 48

What is collagen triple?

Answer 48

It is a helix found in connective tissue/cartilage

Question 49

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

Answer 49

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

Question 50

Is collagen triple left handed?

Answer 50

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

Question 51

What is the structure of a Collagen triple?

Answer 51

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

Question 52

What is Globular compared to?

Answer 52

Baseball

Question 53

What type of structures can Globular proteins have?

Answer 53

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

Question 54

What are major examples of globular proteins?

Answer 54

Insulin, Hemoglobin, and most enzymes

Question 55

What are beta turns?

Answer 55

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.

Question 56

What two amino acids are commonly found in beta turns?

Answer 56

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.

Question 57

Why are H bonds sticky?

Answer 57

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.