Protein structure

Question 1

What does the primary structure of an Amino acid consist of?

Answer 1

the amino acids in a linear sequence

Question 2

What does the secondary structure consist of?

Answer 2

It is local spatial arrangment. alpha helix and b-sheets

Question 3

WHat does the tertiary structure consist of?

Answer 3

overall 3d arrangement of atoms in a protein

Question 4

What does the quaternary structure consist of?

Answer 4

individual polypeptides assemble into a larger functional cluster

Question 5

WHat is a native fold? WHat is the entropy cost?

Answer 5

a protein’s functional 3d conformation. ENtropy cost, but favourable interaCTIONS OUTWAYS the cost

Question 6

Phi (Φ)Angle

Answer 6

angle between alpha carbon and amide nitrogen bond

Question 7

Psi (Ψ) angle

Answer 7

angle between a-carbon and carbonyl bond.

Question 8

WHich angles detremine the secondary structure?

Answer 8

phi and psi

Question 9

What is a ramachandran plot? WHat does it reveal?

Answer 9

displays the distribution of phi and psi dehedral angles. Reveals 2nd structure and rehions with unusla backbone structure

Question 10

HOw is an a-helix stabilized?

Answer 10

by hydrogen bonds between n aa and n+4. example: 1 and 1+4 = 5

Question 11

WHich struictures are more liley to adopt helix structures?

Answer 11

small residues like ALa and LEu

Question 12

WHich structures are more helix breakers?

Answer 12

proline because rotaion around C-n is impossible and Glycine because it prefers b-strand

Question 13

WHich is weaker: anti parallell or parallel beta-sheets

Answer 13

paralelle because the h-bonds are bent

Question 14

What are b-turns

Answer 14

when strand in b-sheets change direction

Question 15

What are common b-turn aa?

Answer 15

Proline in position 2 and glycine in position 3

Question 16

WHat is circular dichroism?

Answer 16

spectroscopy measures the molar absoption difference of ledt and right circularly polarized light. Used to determine 2nd structure

Question 17

What type of proteins are fibrous proteins, typically? Why are they classified as such?

Answer 17

• structural
• they are insoluble in water
• they have a high concentration of hydrophobic amino acids, which help stabilize the structure

Question 18

WHat are chaperones? give an example?

Answer 18

help fold proteins properly by bonding to hydrophoibic exposed regions. This stops aggreation. Example is Hsp70

Question 19

WHat are chaperonins? Give an example?

Answer 19

They use ATP hydrolysis to help protein fold.
The GROEL/GroES has a cis chamber that folds the protein properly. That new folded protein is then release from the trans chamber. EL is without the lid with lid is ES

Question 20

WHat isbthe ribonulcease project?

Answer 20

It discovered that when u add urea and 2-mercaptoenthanol, the protein denatures. If u remeove it, it goes back to your native fold. Helped anser Livetjian’s paradox, which was the question of how proteins folded so quickly in such little time. They take the path that is more thermodynamically favourable

Question 21

Chris ANfinsen’s project?

Answer 21

Answerred levinthal paradox

Question 22

What are amyloid fibers

Answer 22

basis of human disease by alzheimer’s and PArkinson’s disease. Misfolded proteins that aggregate

Question 23

How are prion diseases caused?

Answer 23

prions = misfolded proteins.
prions cause other proteins to misfold, causing disease. BSE(mad cow) Bovine spongifomr, chronic wasting disease, kuru and creutzfeldtz

Question 24

What is the melting temperature (T_m)

Answer 24

The temperature where half of the protein has unfolded.

Question 25

What can denature proteins?

Answer 25

Proteins can be denatured by heat or cold, pH extremes, organic solvents, and chaotropic agents(disrupt hydrogen bonds) , such as urea and guanidinium hydrochloride

Question 26

Why is reversible binding of ligand important for protein function?

Answer 26

ALlows proteins to interact with molecules in a transient manner.
ALlows for binding to be regulated, for signal transduction, and because of specificity.

Question 27

WHat does the dissocation rate constant and association rate constant describe?

Answer 27

kd= It describes the rate at which a ligand-protein complex dissociates
ka = rate at which protein adn ligand assosciate to form the complex

Question 28

“Ligand binding is reversible” what does this imply?

Answer 28

The bind of a ligand to an active site on the protein is transiet, meaning it is not covalent, but non-covakent

Question 29

What crurve deos the bindnig of o2 to myoglobin follow?

Answer 29

follows a hyperbolic binding curve: fraction of binding sites increase as the ligand concentration increase. At a high partial pressure of o2, there is a low probablity that af ree o2 molecule will collide with and bind to myoglobin

Question 30

Why is prosthetic group (heme) necessary for O2 binding by proteins (globins)?

Answer 30

Heme bound to a protein is necessary because protein side chains do lack affinity for O2. Although Transitional metals do have a greater affinity, they can’t be used because they would generate free radicals. Therefore, heme is better, but a free heme will oxidize it’s iron (Fe2+) to Fe(3+) which is very reactive

Question 31

What are key features of a porphyrin and how do they coordinate Fe2+?

Answer 31

the porphyrin ring’s 4 Ns bind to the Fe2+

Question 32

How many potential coordinating groups can Fe2+ in heme have?

Answer 32

The iron atom (Fe2+) in heme can have up to six coordinating groups.
●
Four of these coordination sites are occupied by the nitrogen atoms in the center of the porphyrin ring.
●
A fifth coordination site is occupied by the nitrogen atom in the imidazole ring of a histidine residue (His93) in the protein.
●
The sixth coordination site is available to bind oxygen

Question 33

Why doesn’t heme bind to two O2 molecules?

Answer 33

It is because the binding of first O2 molucle causes a structural change. If it could bind to do, that would mean it would be hard to release O2

Question 34

Which helices and residues are important for heme-protein association and heme-O2 binding?

Answer 34

Residues - proximal histidine residue (His93): forms coordination bond and distal (His64) h-bond with the Oxygen molecule bound to iron in heme (helps stabilize
- alpha helices create a hydrophobic environment favourable for heme binding

Question 35

Benefit of heme group being sequestered in a hydrophobic pocket

Answer 35

●
It prevents the heme from being oxidized.
●
It allows the protein to control the binding of oxygen to the heme group.
●
It helps to prevent the formation of toxic free radicals.

Question 36

Why don’t we all die of CO poisoning, despite CO binding to heme over 20K times more efficiently than O2?

Answer 36

we do not die of CO poisoning because the protein pocket of myoglobin and hemoglobin reduces the affinity of heme for CO by steric hinderance.Also, The distal histine ( Hsp64) that is h-bonded to O2 causes the CO2 bind at an angle, which does weaken the bond

Question 37

How can binding of O2 to heme be measured?

Answer 37

• UV-Vis spectrophotometry
• Heme is a strong chromophore
• when O2 binds to heme(429), the colour changes from a purple (429) colour to red (414)

Question 38

Positive cooperativity

Answer 38

binding of the first ligand increases the affinity of the remaining sites for the ligand. sigmoidal binding curve, which indicates that the protein transitions from a low-affinity state to a high-affinity state as more ligand molecules bind

Question 39

Negative cooperativity

Answer 39

occurs when the binding of the first ligand decreases the affinity of the remaining sites for the ligand. This is a less common phenomenon than positive cooperativity

Question 40

Homotropic regulation and example

Answer 40

• occurs when the normal ligand of the protein is the allosteric regulator.
• For example, the binding of oxygen to hemoglobin is a homotropic allosteric interaction because oxygen is both the ligand and the allosteric regulato

Question 41

Heterotropic regulation
and example

Answer 41

For example, 2,3-bisphosphoglycerate (2,3-BPG) is a heterotropic allosteric regulator of hemoglobin. 2,3-BPG binds to hemoglobin at a site that is different from the oxygen-binding site and decreases the affinity of hemoglobin for oxygen

Question 42

What type of allosteric regulation is cooperativity?

Answer 42

a positive, homotropic allosteric regulation.