Ch 4-5 Protein Structure

Question 1

What is the main factor that contributes to localized charges on proteins?

Answer 1

The side chains of amino acids.

Side chains of Asp and Glu are normally deprotonated at pH 7, while those of Lys and Arg are normally protonated.

Question 2

At physiological pH (7.4), what is the net charge of the polypeptide chain Lys - Glu - Cys - Asp?

Answer 2

-1.

This is calculated based on the pK values of the groups in the chain.

Question 3

What is the charge of the N-terminus at pH 9.0?

Answer 3

+1.

The N-terminus has a pK value of 9.0.

Question 4

What is the primary structure of a protein?

Answer 4

The amino acid sequence of the protein.

It determines the 3-D structure of the protein.

Question 5

What are the two main types of secondary protein structure?

Answer 5

• α-Helix
• β-Sheet

Question 6

Fill in the blank: The _______ structure of a protein is the final 3-D arrangement of all the amino acids.

Answer 6

tertiary

Question 7

What stabilizes the tertiary structure of proteins?

Answer 7

Interactions such as H-bonding and disulfide bonds.

Question 8

What defines the quaternary structure of a protein?

Answer 8

The interaction of multiple polypeptide chains.

Individual polypeptides are termed subunits.

Question 9

What is the charge of carboxylate groups like those in Asp and Glu at neutral pH?

Answer 9

-1.

Question 10

What is the significance of the 3-D structure of a protein?

Answer 10

Structure determines function.

Question 11

True or False: The peptide bond allows for free rotation.

Answer 11

False.

Question 12

What is the amino acid sequence of a protein referred to?

Answer 12

Primary structure (1°).

Question 13

What type of protein structure is defined as the local conformation of the peptide backbone?

Answer 13

Secondary structure (2°).

Question 14

In an α-helix, how many residues are present in one complete turn?

Answer 14

3.6 residues.

Question 15

What type of bonds stabilize the α-helix structure?

Answer 15

Hydrogen bonds.

Question 16

What is the role of His E7 in myoglobin?

Answer 16

Acts as a gate for O2 entering.

Question 17

What is the characteristic of a fibrous protein?

Answer 17

Long, extended structures; often structural.

Question 18

What is the difference between parallel and anti-parallel β-sheets?

Answer 18

Parallel sheets run in the same direction; anti-parallel sheets run in opposite directions.

Question 19

What is the charge of lysine (Lys) at pH 7.4?

Answer 19

+1.

Question 20

What is the significance of the heme group in myoglobin?

Answer 20

It binds O2 through coordination with iron (Fe).

Question 21

Fill in the blank: The _______ end of a peptide or protein is the free amino terminus.

Answer 21

N-terminal

Question 22

Fill in the blank: The _______ end of a peptide or protein is the free carboxyl terminus.

Answer 22

C-terminal

Question 23

What is the primary function of hemoglobin?

Answer 23

Carries oxygen from lungs/gills to tissues

Hemoglobin is found in red blood cells and makes up about 35% of their content.

Question 24

What is the quaternary structure of hemoglobin composed of?

Answer 24

4 polypeptides: 2 identical α subunits and 2 identical β subunits

Each α subunit has 141 amino acids, and each β subunit has 146 amino acids.

Question 25

How many heme groups does hemoglobin contain?

Answer 25

4 heme groups ## Footnote Each subunit of hemoglobin has one heme group.

Question 26

What is the effect of cooperative binding in hemoglobin?

Answer 26

When one O2 molecule is bound, it increases the affinity for the next O2 molecule ## Footnote This makes hemoglobin an allosteric protein.

Question 27

What type of O2 binding curve does myoglobin exhibit?

Answer 27

Hyperbolic ## Footnote Myoglobin binds O2 at low pressure and becomes saturated at low O2 amounts.

Question 28

What type of O2 binding curve does hemoglobin exhibit?

Answer 28

S-shaped ## Footnote This shape is due to cooperativity in binding.

Question 29

What is the Bohr effect?

Answer 29

Lower pH reduces O2 affinity of hemoglobin ## Footnote The effect is due to increased H+ concentration from actively respiring cells.

Question 30

How does the oxygenated form of hemoglobin compare to the deoxygenated form in terms of pKa?

Answer 30

Oxygenated hemoglobin has a lower pKa ## Footnote This indicates that oxygenated hemoglobin is a stronger acid.

Question 31

What happens to O2 affinity as pH decreases?

Answer 31

O2 affinity for hemoglobin decreases ## Footnote This facilitates the release of O2 to actively respiring cells.

Question 32

What are the two main structural types of proteins?

Answer 32

Fibrous proteins and globular proteins ## Footnote Fibrous proteins provide structure, while globular proteins often have functional roles.

Question 33

What structural feature characterizes fibrous proteins?

Answer 33

Repeating amino acids forming secondary structures like α-helices and β-sheets ## Footnote Examples include collagen and keratin.

Question 34

What is the primary function of collagen?

Answer 34

Provides structural support in connective tissues ## Footnote Collagen forms a triple helix and is the most abundant protein in the body.

Question 35

What mutation causes sickle-cell anemia?

Answer 35

Glutamate to Valine mutation in hemoglobin ## Footnote This mutation affects oxygen binding efficiency.

Question 36

What role do chaperone molecules play in protein folding?

Answer 36

Help misfolded proteins recover their native conformation ## Footnote If recovery fails, proteins are usually degraded.

Question 37

What are the consequences of protein misfolding in neurodegenerative diseases?

Answer 37

Aggregation of misfolded proteins forms amyloid deposits ## Footnote Diseases include Alzheimer's and Parkinson's.

Question 38

What is the role of the amyloid precursor protein (APP) in Alzheimer's disease?

Answer 38

Incorrectly clipped to form amyloid beta, leading to neuron death ## Footnote This accumulation occurs over decades.

Question 39

What is the infectious agent in prion diseases?

Answer 39

A misfolded protein ## Footnote The prion protein converts normal proteins into prions.

Question 40

Fill in the blank: The process of respiration plays an important role in _______.

Answer 40

buffering your blood

Question 41

What is the primary structural difference between collagen and keratin?

Answer 41

Collagen forms a triple helix; keratin adopts a left-handed twist ## Footnote Both are types of fibrous proteins.

Question 42

What types of interactions are involved in protein folding?

Answer 42

* Hydrophobic interactions * Salt (electrostatic) interactions * Hydrogen bonds * Disulfide bonds ## Footnote These interactions help stabilize the protein's structure.

Question 43

True or False: All proteins are inherently flexible.

Answer 43

True

Question 44

What happens to proteins that cannot be salvaged after misfolding?

Answer 44

They are usually degraded to their component amino acids ## Footnote This process helps prevent accumulation of dysfunctional proteins.