Ch 4-5 Protein Structure Flashcards
What is the main factor that contributes to localized charges on proteins?
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.
At physiological pH (7.4), what is the net charge of the polypeptide chain Lys - Glu - Cys - Asp?
-1.
This is calculated based on the pK values of the groups in the chain.
What is the charge of the N-terminus at pH 9.0?
+1.
The N-terminus has a pK value of 9.0.
What is the primary structure of a protein?
The amino acid sequence of the protein.
It determines the 3-D structure of the protein.
What are the two main types of secondary protein structure?
- α-Helix
- β-Sheet
Fill in the blank: The _______ structure of a protein is the final 3-D arrangement of all the amino acids.
tertiary
What stabilizes the tertiary structure of proteins?
Interactions such as H-bonding and disulfide bonds.
What defines the quaternary structure of a protein?
The interaction of multiple polypeptide chains.
Individual polypeptides are termed subunits.
What is the charge of carboxylate groups like those in Asp and Glu at neutral pH?
-1.
What is the significance of the 3-D structure of a protein?
Structure determines function.
True or False: The peptide bond allows for free rotation.
False.
What is the amino acid sequence of a protein referred to?
Primary structure (1°).
What type of protein structure is defined as the local conformation of the peptide backbone?
Secondary structure (2°).
In an α-helix, how many residues are present in one complete turn?
3.6 residues.
What type of bonds stabilize the α-helix structure?
Hydrogen bonds.
What is the role of His E7 in myoglobin?
Acts as a gate for O2 entering.
What is the characteristic of a fibrous protein?
Long, extended structures; often structural.
What is the difference between parallel and anti-parallel β-sheets?
Parallel sheets run in the same direction; anti-parallel sheets run in opposite directions.
What is the charge of lysine (Lys) at pH 7.4?
+1.
What is the significance of the heme group in myoglobin?
It binds O2 through coordination with iron (Fe).
Fill in the blank: The _______ end of a peptide or protein is the free amino terminus.
N-terminal
Fill in the blank: The _______ end of a peptide or protein is the free carboxyl terminus.
C-terminal
What is the primary function of hemoglobin?
Carries oxygen from lungs/gills to tissues
Hemoglobin is found in red blood cells and makes up about 35% of their content.
What is the quaternary structure of hemoglobin composed of?
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.
How many heme groups does hemoglobin contain?
4 heme groups
Each subunit of hemoglobin has one heme group.
What is the effect of cooperative binding in hemoglobin?
When one O2 molecule is bound, it increases the affinity for the next O2 molecule
This makes hemoglobin an allosteric protein.
What type of O2 binding curve does myoglobin exhibit?
Hyperbolic
Myoglobin binds O2 at low pressure and becomes saturated at low O2 amounts.
What type of O2 binding curve does hemoglobin exhibit?
S-shaped
This shape is due to cooperativity in binding.
What is the Bohr effect?
Lower pH reduces O2 affinity of hemoglobin
The effect is due to increased H+ concentration from actively respiring cells.
How does the oxygenated form of hemoglobin compare to the deoxygenated form in terms of pKa?
Oxygenated hemoglobin has a lower pKa
This indicates that oxygenated hemoglobin is a stronger acid.
What happens to O2 affinity as pH decreases?
O2 affinity for hemoglobin decreases
This facilitates the release of O2 to actively respiring cells.
What are the two main structural types of proteins?
Fibrous proteins and globular proteins
Fibrous proteins provide structure, while globular proteins often have functional roles.
What structural feature characterizes fibrous proteins?
Repeating amino acids forming secondary structures like α-helices and β-sheets
Examples include collagen and keratin.
What is the primary function of collagen?
Provides structural support in connective tissues
Collagen forms a triple helix and is the most abundant protein in the body.
What mutation causes sickle-cell anemia?
Glutamate to Valine mutation in hemoglobin
This mutation affects oxygen binding efficiency.
What role do chaperone molecules play in protein folding?
Help misfolded proteins recover their native conformation
If recovery fails, proteins are usually degraded.
What are the consequences of protein misfolding in neurodegenerative diseases?
Aggregation of misfolded proteins forms amyloid deposits
Diseases include Alzheimer’s and Parkinson’s.
What is the role of the amyloid precursor protein (APP) in Alzheimer’s disease?
Incorrectly clipped to form amyloid beta, leading to neuron death
This accumulation occurs over decades.
What is the infectious agent in prion diseases?
A misfolded protein
The prion protein converts normal proteins into prions.
Fill in the blank: The process of respiration plays an important role in _______.
buffering your blood
What is the primary structural difference between collagen and keratin?
Collagen forms a triple helix; keratin adopts a left-handed twist
Both are types of fibrous proteins.
What types of interactions are involved in protein folding?
- Hydrophobic interactions
- Salt (electrostatic) interactions
- Hydrogen bonds
- Disulfide bonds
These interactions help stabilize the protein’s structure.
True or False: All proteins are inherently flexible.
True
What happens to proteins that cannot be salvaged after misfolding?
They are usually degraded to their component amino acids
This process helps prevent accumulation of dysfunctional proteins.
