Proteins

Question 1

How does protein structure relate to function?

Answer 1

The three-dimensional shape of a protein determines its function by dictating how it interacts with other molecules.

Question 2

Describe the structure of a generic amino acid at pH 7.

Answer 2

At pH 7, an amino acid exists as a zwitterion, which has both a positive charge (on the amino group) and a negative charge (on the carboxyl group), resulting in a neutral overall charge.

Question 3

What is pKa, and how does it relate to amino acid ionization?

Answer 3

pKa is a measure of the strength of an acid. A lower pKa value indicates a stronger acid. The pKa of an amino acid’s side chain determines its ionization state at a given pH.

Question 4

How does pH affect the ionization state of amino acids?

Answer 4

As the pH of the environment changes, the ionization state of amino acids can shift.
* When pH is below the pKa of a group, the group will be protonated (HA).
* When pH is above the pKa, the group will be deprotonated (A-).

Question 5

What is chirality in amino acids, and what is its significance?

Answer 5

Chirality refers to the property of a molecule being asymmetric, meaning it cannot be superimposed on its mirror image. Amino acids, with the exception of glycine, are chiral molecules, existing as L- and D-stereoisomers. Only the L-form is incorporated into proteins.

Question 6

What are the major categories of amino acid side chains?

Answer 6

• Nonpolar (hydrophobic): Characterized by mainly hydrocarbon side chains and a lack of reactive functional groups.
• Polar (uncharged): Possess reactive functional groups containing electronegative atoms, making them polar.
• Charged (very polar): Side chains that are either positively or negatively charged at physiological pH

Question 7

What are the characteristics of nonpolar amino acid side chains?

Answer 7

○ Lack reactive functional groups
○ Primarily composed of hydrocarbon chains
○ Participate in hydrophobic interactions

Question 8

Non-polar aa’s

Answer 8

■ Glycine (Gly) - the smallest amino acid
■ Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile) - aliphatic R groups, highly hydrophobic
■ Phenylalanine (Phe), Tryptophan (Trp) - aromatic R groups, highly hydrophobic
■ Methionine (Met) - aliphatic R group with a sulfur-containing side chain (thioether)
■ Proline (Pro) - aliphatic side chain with a distinctive cyclic structure, secondary amino group, “imino acid” (obsolete terminology)

Question 9

What are the characteristics of polar, uncharged amino acid side chains?

Answer 9

○ Possess reactive functional groups
○ Polar due to the presence of electronegative atoms (e.g., oxygen, nitrogen)
○ Can form hydrogen bonds

Question 10

Polar, uncharged aa

Answer 10

■ Serine (Ser), Threonine (Thr) - contain hydroxyl groups, can be phosphorylated
■ Tyrosine (Tyr) - aromatic R group with a hydroxyl group, can be phosphorylated, weakly acidic (pKa ~10.5)
■ Cysteine (Cys) - sulfur-containing side chain (thiol group), can form disulfide bonds with other Cys residues, weakly acidic (pKa ~8.5)
■ Asparagine (Asn), Glutamine (Gln) - amide-containing side chains (carboxamide functional group)
■ Histidine (His) - imidazole ring (aromatic), can act as both an acid and a base (pKa ~6.0)

Question 11

What is the significance of disulfide bond formation in proteins?

Answer 11

○ Disulfide bonds form when two cysteine residues undergo oxidation, creating a covalent bond between their sulfur atoms (cystine).
○ These bonds provide stability to protein structures, particularly in extracellular proteins or proteins in oxidizing environments.
○ They are not typically found in cytosolic proteins due to the reducing environment of the cytosol.

Question 12

Describe the characteristics of charged amino acid side chains

Answer 12

○ Carry either a positive or negative charge at physiological pH.
○ Acidic amino acids (negatively charged at pH 7):
■ Aspartate (Asp) - second carboxyl group (pKa ~4.0)
■ Glutamate (Glu) - second carboxyl group (pKa ~4.0)
○ Basic amino acids (positively charged at pH 7):
■ Lysine (Lys) - contains two primary amino groups (pKa ~10.0)
■ Arginine (Arg) - contains a guanidinium group (pKa ~12.5), rarely deprotonated under physiological conditions

Question 13

How do polar and nonpolar side chains influence protein structure?

Answer 13

• Polar side chains are typically found on the surface of proteins, where they can interact with water molecules.
• Nonpolar side chains tend to be buried in the protein core, minimizing their contact with water (hydrophobic effect)
• Exceptions to this general pattern can occur depending on the specific protein and its environment.

Question 14

What is a peptide bond, and how does it form?

Answer 14

○ A peptide bond is a covalent bond formed between the carboxyl group of one amino acid and the amino group of another.
○ This bond forms through a condensation reaction, resulting in the release of a water molecule.
○ Peptide bonds are rigid and planar due to partial double-bond character, restricting rotation around the C-N bond.

Question 15

Define the terms: dipeptide, polypeptide, and protein

Answer 15

Dipeptide: Two amino acids joined by one peptide bond.

Polypeptide: A long chain of amino acids joined by peptide bonds. Usually produced naturally.

Protein: A large polypeptide (or multiple polypeptides) with a defined biological function.

Question 16

Describe the key characteristics of the primary structure of a protein.

Answer 16

• The primary structure is the linear sequence of amino acids in a polypeptide chain.
• It is determined by the order of nucleotides in the corresponding gene.
• Every protein has a unique primary structure, which dictates its higher-level structures and function.

Question 17

What are the properties of peptide bonds, and how do they impact protein structure?

Answer 17

○ Rigid: Limited rotation around the C-N bond due to partial double bond character.
○ Planar: The atoms involved in the peptide bond lie in a single plane.
○ H-bond potential: The carbonyl oxygen acts as an H-bond acceptor, and the amide nitrogen acts as an H-bond donor.
○ These properties contribute to the stability and defined geometry of protein structures.

Question 18

What is secondary structure in proteins, and what are the main types?

Answer 18

• Secondary structure refers to local folding patterns within the polypeptide backbone, stabilized by hydrogen bonds between backbone atoms.
• The two main types of regular secondary structures are:
  ■ α-helix: A right-handed helix formed by hydrogen bonds between the carbonyl oxygen of one residue and the amide hydrogen four residues down the chain.
  ■ β-sheet: Formed by hydrogen bonds between backbone atoms of adjacent polypeptide strands, which can be arranged in parallel or anti-parallel orientations

Question 19

Describe the structural features of an α-helix.

Answer 19

○ A right-handed helix stabilized by hydrogen bonds between backbone carbonyl oxygens and amide hydrogens four residues apart.
○ R groups project outward from the helical axis.
○ The helix is solid, with atoms in the polypeptide backbone in van der Waals contact.
○ Proline is generally not found in the middle of an α-helix due to its rigid cyclic structure, which disrupts the helix’s geometry.

Question 20

Compare and contrast parallel and anti-parallel β-sheets.

Answer 20

Both types of β-sheets are formed by hydrogen bonds between backbone atoms of adjacent polypeptide strands.
○ Parallel β-sheets: Strands run in the same direction, with hydrogen bonds angled.
○ Anti-parallel β-sheets: Strands run in opposite directions, with hydrogen bonds perpendicular to the strands.

In both configurations, side chains project above and below the plane of the sheet.

Question 21

What forces stabilize α-helices and β-sheets?

Answer 21

α-helices: Hydrogen bonds between backbone carbonyl oxygens and amide hydrogens within the same helix.

β-sheets: Hydrogen bonds between backbone carbonyl oxygens and amide hydrogens of neighboring strands.

Question 22

Differentiate between regular and irregular secondary structures in proteins.

Answer 22

Regular secondary structures (α-helices and β-sheets) have a repeating, predictable geometry in the polypeptide backbone.

Irregular secondary structures, such as loops and turns, lack a repeating, predictable geometry but are still well-defined and not disordered.

Question 23

Define tertiary structure and describe the two main protein classes based on their tertiary structure.

Answer 23

• Tertiary structure refers to the overall three-dimensional arrangement of all atoms in a single polypeptide chain, including the spatial relationships between secondary structures and the positions of side chains.

○ Fibrous proteins:
■ Elongated, often with repeating structural motifs.
■ Typically insoluble in aqueous solutions.
■ Primarily structural or connective proteins (e.g., collagen).

○Globular proteins:
■ Compact, often spherical shapes with diverse tertiary structures.
■ Typically soluble in aqueous solutions.
■ Exhibit a wide range of functions (e.g., enzymes, transport proteins).

Question 24

Explain the hydrophobic effect and its role in protein folding.

Answer 24

The hydrophobic effect is the tendency of nonpolar molecules to aggregate in an aqueous environment to minimize their contact with water.

In protein folding, hydrophobic side chains tend to cluster in the protein’s interior, while polar and charged side chains are typically exposed on the surface.

This arrangement minimizes the disruption of water’s hydrogen bonding network and contributes significantly to the stability of globular proteins.

Question 25

What types of interactions contribute to the stability of tertiary structure in proteins

Answer 25

Hydrophobic interactions: The major driving force behind protein folding, resulting from the clustering of nonpolar side chains in the protein’s interior.

Hydrogen bonds: Form between polar side chains and backbone atoms, contributing to the precise positioning of secondary structures and stabilizing the overall fold.

Ion pairs (salt bridges): Electrostatic interactions between oppositely charged side chains, further stabilizing the tertiary structure.

Disulfide bonds: Covalent bonds between cysteine residues, providing additional stability, particularly in extracellular proteins.

Question 26

What are protein domains and motifs?

Answer 26

○ Domain: A distinct structural unit within a polypeptide chain that folds independently and often has a specific function.
○ Motif: A short, recurring pattern of secondary structures (e.g., α-helices and β-sheets) that may be associated with a particular function.
○ Both domains and motifs contribute to the complexity and diversity of protein structures.

Question 27

What are prosthetic groups, and how do they contribute to protein structure and function?

Answer 27

○ Prosthetic groups are non-peptide components that are permanently associated with a protein.
○ They can play roles in:
■ Structure: E.g., Zn²⁺ ions in zinc finger motifs, which bind to DNA.
■ Function: E.g., heme in hemoglobin, which binds to oxygen

Question 28

How can proteins be denatured

Answer 28

Denaturation is the loss of a protein’s native three-dimensional structure, leading to a loss of function.

Question 29

what factors can cause denaturation in proteins

Answer 29

■ Heat: Disrupts weak interactions like hydrogen bonds and hydrophobic interactions.
■ Changes in pH: Alter the ionization states of amino acid side chains, affecting electrostatic interactions.
■ High salt concentrations: Interfere with ionic interactions and can lead to protein precipitation.
■ Detergents: Disrupt hydrophobic interactions.
■ Reducing agents (e.g., DTT): Break disulfide bonds.

Question 30

What is quaternary structure, and what forces stabilize it?

Answer 30

○ Quaternary structure refers to the arrangement of multiple polypeptide chains (subunits) in a protein complex.
○ It is stabilized by the same forces that stabilize tertiary structure:
■ Hydrophobic interactions
■ Hydrogen bonds
■ Ionic interactions (salt bridges)
■ Disulfide bonds (in some cases)

Question 31

Describe the structure and function of hemoglobin

Answer 31

• Hemoglobin is a tetrameric protein found in red blood cells.
• It consists of two α-globin subunits and two β-globin subunits, each containing a heme group that can bind oxygen.
• Hemoglobin’s primary function is to transport oxygen from the lungs to tissues throughout the body.
• The tetrameric structure allows for cooperative binding of oxygen, resulting in a sigmoidal oxygen-binding curve.

Question 32

Describe the structure and function of myoglobin.

Answer 32

• Myoglobin is a monomeric, globular protein found in muscle tissue.
• It consists of 8 α-helices, a heme prosthetic group, and a hydrophobic pocket between helices E and F where the heme binds.
• Myoglobin’s primary function is to bind and store oxygen, facilitating oxygen diffusion through muscle tissue and acting as a reserve during intense exercise.
• The heme group contains an iron atom (Fe²⁺) that binds to oxygen.
• The proximal histidine (His F8) coordinates with the iron atom, preventing its oxidation and anchoring the heme in the binding pocket.
• The distal histidine (His E7) assists in oxygen binding and increases the specificity for oxygen over other ligands, such as carbon monoxide.

Question 33

What is a ligand, and what is Kd?

Answer 33

Ligand: A molecule that binds reversibly to a protein.
○ Kd (dissociation constant): A measure of the affinity of a ligand for its binding site on a protein.
■ A lower Kd value indicates a higher affinity.

Question 34

Describe the oxygen binding curves for myoglobin and hemoglobin.

Answer 34

○ Myoglobin: Exhibits a hyperbolic oxygen binding curve, indicating a constant affinity for oxygen.
○ Hemoglobin: Exhibits a sigmoidal oxygen binding curve, characteristic of cooperative binding.
■ The sigmoidal shape reflects a change in binding affinity as more oxygen molecules bind to the hemoglobin molecule.

Question 35

Explain cooperative binding in hemoglobin.

Answer 35

○ Cooperative binding occurs when the binding of one ligand molecule (e.g., oxygen) to a protein complex (e.g., hemoglobin) affects the affinity of other binding sites for the same ligand.
○ In hemoglobin, the binding of oxygen to one subunit induces a conformational change that is transmitted to the other subunits, increasing their affinity for oxygen.
○ This positive cooperativity is essential for efficient oxygen transport, allowing hemoglobin to load up with oxygen in the lungs (high oxygen partial pressure) and release it in tissues where oxygen is needed (low oxygen partial pressure).

Question 36

What are the two conformational states of hemoglobin, and how do they differ in their affinity for oxygen?

Answer 36

• Tense state (T state): Deoxyhemoglobin (without oxygen bound) exists in the T state, characterized by a lower affinity for oxygen.
• Relaxed state (R state): Oxyhemoglobin (with oxygen bound) exists in the R state, characterized by a higher affinity for oxygen.
• The transition from the T state to the R state is triggered by the binding of oxygen and involves subtle structural rearrangements within the hemoglobin molecule.

Question 37

Define allostery and describe the types of allosteric effectors.

Answer 37

Allostery: The regulation of protein activity by the binding of a molecule (effector) to a site other than the active site.
- Types of allosteric effectors:
■ Homoallosteric: Affect further binding of the same ligand.
■ Heteroallosteric: Affect further binding of a different ligand.
■ Activators: Increase binding affinity.
■ Inhibitors: Decrease binding affinity.

Question 38

What are the allosteric effectors of hemoglobin, and how do they influence oxygen binding?

Answer 38

○ Oxygen (O2): Homoallosteric activator. Binding of oxygen to one subunit increases the affinity of other subunits for oxygen.
○ 2,3-Bisphosphoglycerate (2,3-BPG): Heteroallosteric inhibitor. Binds to the central cavity of deoxyhemoglobin (T state), stabilizing this low-affinity state and promoting oxygen release.
○ Hydrogen ions (H+): Heteroallosteric inhibitor (Bohr effect). Lowering pH (increasing H⁺ concentration) promotes protonation of key amino acid residues, stabilizing the T state and facilitating oxygen release in tissues where metabolic activity is high.

Question 39

Explain the Bohr effect and its physiological significance

Answer 39

○ The Bohr effect describes the influence of pH on hemoglobin’s oxygen binding affinity.
○ Lowering pH (increasing H⁺ concentration) decreases hemoglobin’s affinity for oxygen, promoting oxygen release in tissues where metabolic activity is high and pH is lower due to the production of CO₂ and lactic acid.
○ This effect enhances oxygen delivery to tissues that need it most.

Question 40

Describe how 2,3-BPG modulates hemoglobin’s oxygen affinity

Answer 40

2,3-BPG is a small, negatively charged molecule that binds to the central cavity of deoxyhemoglobin (T state).

This binding stabilizes the T state, decreasing hemoglobin’s affinity for oxygen and promoting oxygen release in tissues.

The central cavity of oxyhemoglobin (R state) is too small to accommodate 2,3-BPG

Question 41

Compare and contrast the properties of fetal hemoglobin and adult hemoglobin.

Answer 41

Fetal hemoglobin (HbF): Composed of two α subunits and two γ subunits. Has a higher affinity for oxygen than adult hemoglobin due to a lower affinity for 2,3-BPG.

Adult hemoglobin (HbA): Composed of two α subunits and two β subunits.

The higher oxygen affinity of HbF allows it to efficiently extract oxygen from maternal blood across the placenta.

Question 42

Explain the molecular basis of sickle cell anemia.

Answer 42

• Sickle cell anemia is a genetic disease caused by a single amino acid substitution in the β-globin chain of hemoglobin (Glu6 to Val).
• This substitution creates a hydrophobic patch on the surface of deoxyhemoglobin, leading to the formation of long, fibrous aggregates that distort red blood cells into a sickle shape.
• These sickled cells are less flexible and can block blood vessels, causing pain and tissue damage.

Question 43

Summarize the specific roles of histidine residues in hemoglobin function.

Answer 43

His F8 (proximal histidine): Anchors the heme group to the globin chain and prevents oxidation of the iron atom.

His E7 (distal histidine): Facilitates oxygen binding and enhances specificity for oxygen over other ligands.

Four His residues in the central cavity: Bind to 2,3-BPG, contributing to the stabilization of the deoxyhemoglobin (T) state.

His residues at the subunit interface: Contribute to the conformational changes associated with the T-to-R state transition upon oxygen binding.