Amino acids, peptides, and protein III LO

Question 1

what forms a tertiary structure?

Answer 1

interactions between secondary structures

Question 2

what are the 2 major classes of tertiary structures?

Answer 2

fibrous and globular proteins

Question 3

what is a quaternary structure?

Answer 3

multiple polypeptide chains that come together to form a functional protein

Question 4

what are the common amino acids in loops and turns?

Answer 4

glycine and proline

Question 5

what is the difference between a loop and a turn?

Answer 5

turn is shorter and loop is longer sequence of AA

Question 6

why are glycine and proline the amino acids that are present in turns and loops?

Answer 6

• glycine has small R group with no side chains to react with other AA
• proline cannot hydrogen bond due to covalent bond between nitrogen and alpha carbon

Question 7

what are the characteristics of a beta turn?

Answer 7

• 180 degree turn over 4 amino acids
• stabilized by H bond from carbonyl O of 1st AA and amide of 4th AA
• proline in position 2 or glycine in position 3 are common

Question 8

why are loops and turns important in a proteins function?

Answer 8

because it determines the 3D structure of the protein which ultimately determines its function

Question 9

what is Kd?

Answer 9

dissociation constant

Question 10

what does the Kd represent in a protein-ligand binding scenario?

Answer 10

concentration at which 50% of ligand is bound to protein

Question 11

what is the relationship between Kd and the affinity of the protein for the ligand?

Answer 11

small Kd = more tightly bound ligand due to high affinity for protein

Question 12

as Kd increases, what must happen to the amount of ligand in the solution to achieve 50% binding?

Answer 12

more ligand must be present

Question 13

what is the equation for calculating Kd?

Answer 13

Kd = [protein][ligand] / [ligand-protein complex]

Question 14

what are the characteristics of fibrous proteins?

Answer 14

insoluble, made from a single secondary structure (a helix or b sheet)

Question 15

what are the characteristics of globular proteins?

Answer 15

water soluble globular proteins and lipid soluble membranous proteins

Question 16

what type of tertiary proteins are most common within the body?

Answer 16

globular proteins

Question 17

what is the function of loops in the V regions of antibodies and what is the significance of this?

Answer 17

binds antigens

shows that loops can have functions that aren’t just associated with protein folding

Question 18

what are the 4 characteristics similar between protein and ligand that achieve high specificity?

Answer 18

1. size
2. shape
3. charge
4. hydrophobic/hydrophillic character

Question 19

what are the 2 models for binding specificity?

Answer 19

1. lock and key model

2. induce fit model

Question 20

who developed the lock and key model?

Answer 20

emil fisher

Question 21

who developed the induced fit model?

Answer 21

daniel koshland

Question 22

what is the lock and key model?

Answer 22

there is complementarity that is preformed between ligand and protein and this is why they fit together

Question 23

what is the induced fit model?

Answer 23

• proteins affinity for the ligand increases once the ligand binds due to conformational change
• ligand and protein can both change their conformations to induce this high specificity
• can increase the affinity of the protein for a second ligand

Question 24

how is heme situated with myoglobin in order to bind oxygen?

Answer 24

• located deep within the protein in the cyclic porphyrin ring
• contains divalent iron molecule coordinated with histidine and oxygen
• this configuration ensures that iron doesn’t become oxidized thus losing it’s affinity for oxygen

Question 25

what binds better to heme than oxygen?

Answer 25

carbon monoxide

Question 26

why is carbon monoxide poisoning bad?

Answer 26

carbon monoxide binds tighter than oxygen and once bound does not dissociate from heme. oxygen can therefore not be transported in the body because CO is bound instead

Question 27

what cellular aspect of mitochondria does CO also affect?

Answer 27

cytochromes in the electron transport chain

Question 28

what subunits is hemoglobin made up of?

Answer 28

2 alpha and 2 beta subunits

Question 29

what is positive cooperativity?

Answer 29

when one oxygen molecule binds to hemoglobin, the other 3 sites increase their affinity for oxygen (opposite for negative cooperativity)

Question 30

how can positive cooperativity be recognized on paper?

Answer 30

sigmoidal binding curves

Question 31

what state is hemoglobin in when it has no oxygen bound?

Answer 31

T state (tense state)

Question 32

what state is hemoglobin in after the 1st oxygen molecule binds?

Answer 32

R state (relaxed state)

Question 33

what drives oxygen to leave hemoglobin?

Answer 33

concentration and partial pressure gradients

Question 34

what is a one word answer to explain why hemoglobin makes a good transporter of oxygen?

Answer 34

cooperativity

Question 35

how does pH affect the binding of oxygen to hemoglobin?

Answer 35

- high pH increases affinity | - lower pH decreases affinity

Question 36

what increases the oxygen transfer efficiency?

Answer 36

Bohr Effect

Question 37

what is the Bohr Effect?

Answer 37

there is a pH difference between the lungs and tissues

Question 38

how is carbon dioxide carried back to the lungs?

Answer 38

as bicarbonate in blood or attached as carbamate on amino terminal residues of each hemoglobin subunit

Question 39

what is the most important part of x-ray cyrstallography in identifying proteins?

Answer 39

crystallizing the protein

Question 40

what are 2 reasons that we as clinicians need to know what the structures of protein are?

Answer 40

1. understand how proteins work | 2. structure-based or structure-guided drug design