Biochemistry Lecture 5

What is the tertiary structure of a protein?

The specific 3D shape that a protein folds into, primarily determined by interactions between amino acid R groups.

What are Van der Waals forces in the context of protein structure?

Weak, non-covalent interactions between neutral molecules, essential for protein structure and function, especially during protein folding. They occur between non-polar (hydrophobic) amino acid side chains clustering in the interior, stabilizing the protein and shielding hydrophobic regions from aqueous surroundings.

What is a hydrophobic interaction in a tertiary protein structure?

Interaction between nonpolar R groups like phenylalanine and valine, leading to their clustering in the protein's interior.

What is a disulfide bond?

A covalent bond formed between two cysteine residues, crucial for stabilizing protein tertiary structure.

What is X-ray crystallography?

A technique for determining the 3D atomic and molecular structure of a crystal by exposing it to X-rays and analyzing the resulting diffraction pattern using mathematical techniques (Fourier series).

What is an electron density map in X-ray diffraction?

A map derived from the diffraction pattern of X-rays scattered off a protein crystal, used to build an atomic model of the protein structure.

What is the Protein Data Bank (PDB)?

A database where atomic models of protein structures determined by techniques like X-ray crystallography are submitted.

What is Nuclear Magnetic Resonance (NMR) spectroscopy?

A technique that uses a strong magnetic field and radio waves to probe the magnetic properties of atomic nuclei (e.g., ^{1}H, ^{15}N, and ^{13}C) to outline protein structure and dynamics, often complementing X-ray crystallography.

Describe Myoglobin.

A single polypeptide chain of 153 amino acid residues that stores and transports oxygen in muscle tissue, incorporating a heme in a hydrophobic pocket. It has a compact structure with eight α-helices and lacks β-pleated sheets; its exterior has polar side chains, while its interior is primarily nonpolar.

What does a heme group include?

A prosthetic group found in myoglobin and hemoglobin, including a metal ion, Fe(II), with six coordination sites (five occupied by nitrogen atoms, with oxygen binding at the sixth) and an organic component called protoporphyrin IX.

What is CO poisoning in relation to protein binding?

A condition where carbon monoxide (CO) binds to heme with 25,000x greater affinity than oxygen (O2), thus preventing O2 transport. CO binds linearly, while O2 binds at an angle, and histidine E7 forces CO into a bent configuration, weakening its bond with iron.

At what levels of structure can heme groups be found in proteins?

Heme groups can be found in proteins exhibiting primary, secondary, tertiary, and quaternary levels of structure.

Describe Hemoglobin.

A globular protein that transports oxygen in blood, consisting of four polypeptide chains (two α-chains of 141 amino acids each and two β-chains of 146 amino acids each). Its quaternary structure involves multiple subunits held together by stabilizing interactions.

What is positive cooperativity in hemoglobin?

A phenomenon in hemoglobin where the binding of one O2 molecule alters the protein structure, facilitating the binding of subsequent O2 molecules.

What are the structural levels exhibited by proteins?

Proteins exhibit primary, secondary, tertiary, and often quaternary structural levels.

What is sickle-cell anemia?

A genetic disorder caused by an abnormality in hemoglobin structure where polar glutamic acid is replaced by nonpolar valine. This causes red blood cells to alter from rounded to crescent (sickle) shape, preventing effective oxygen transport and leading to insoluble fibers that clog capillaries.

What is the primary function of myoglobin compared to hemoglobin?

Myoglobin primarily functions in oxygen storage in muscle tissue, binds strongly to O2, and has one heme and one subunit.

What is the primary function of hemoglobin compared to myoglobin?

Hemoglobin primarily functions in oxygen transport in red blood cells, exhibits positive cooperativity for O2 binding, and has four hemes and four subunits.

What is 2,3-Bisphosphoglycerate (2,3-BPG) and its role with hemoglobin?

A molecule produced during glycolysis that binds electrostatically to hemoglobin, decreasing its oxygen-binding capacity and affinity for oxygen, thereby facilitating oxygen release to tissues and crucial for maintaining oxygen supply to the fetus.

What is Cytochrome c?

A small hemeprotein located in the inner mitochondrial membrane, critical for cellular respiration and apoptosis, featuring a porphyrin ring structure.

What is protein denaturation?

The disruption of stabilizing interactions (secondary, tertiary, or quaternary structures) in a protein, leading to loss of its specific 3D shape and biological inactivity, without affecting amide bonds among amino acids.

What are the causes of protein denaturation?

Increased temperature, extreme pH (acidic or basic), introduction of certain organic compounds or heavy metal ions, and mechanical agitation.

What are the consequences of protein denaturation?

Unfolding of globular proteins, disruption of tertiary structure, and loss of biological activity.

How does heat cause protein denaturation?

Denaturation of proteins at temperatures above 50ºC, disrupting hydrogen bonds and hydrophobic interactions. It enhances digestibility but does not alter nutritional value (e.g., autoclaving surgical items).

How does pH cause protein denaturation?

Denaturation caused by changing pH, which breaks hydrogen bonds and disrupts ionic bonds and salt bridges (e.g., tannic acid causing protein coagulation).

How do organic compounds cause protein denaturation?

Denaturation caused by alcohols (e.g., ethanol, isopropyl alcohol) replacing protein's hydrogen bonds with their own and disrupting internal hydrogen bonding, acting as disinfectants by coagulating internal bacterial proteins.

How do heavy metal ions cause protein denaturation?

Denaturation caused by heavy metal ions (e.g., Ag$^+$, Pb^{2+}, Hg^{2+}) bonding with ionic residues or reacting with disulfide bonds in proteins (e.g., AgNO_{3} for gonorrhea).

How does mechanical agitation cause protein denaturation?

Denaturation caused by physical force, like whipping, which stretches polypeptide chains and disrupts stabilizing interactions (e.g., whipped cream or egg whites).

What types of bonds are disrupted by acids and bases during protein denaturation?

Ionic bonds and salt bridges.

What happens to a protein's primary structure during denaturation?

During denaturation, a protein's secondary, tertiary, and quaternary structures are disrupted, but its primary structure (amino acid sequence) remains intact.

What is ß-mercaptoethanol used for in protein studies?

A chemical utilized to break disulfide bridges in tertiary and quaternary protein structures.

What is Urea used for in protein unfolding?

A chemical added to facilitate unfolding of proteins and increase the accessibility of disulfide bonds to reducing agents.

What is protein refolding?

The process by which native protein conformations can potentially be recovered after denaturation by removing agents like ß-mercaptoethanol and urea.

What is meant by incorrect protein folding?

A cellular issue where proteins may fold improperly or associate with others before completing their folding process, which can lead to dysfunction.

What are molecular chaperones?

Proteins that assist in the correct and timely folding of other proteins within the cell.

What is hsp70?

An example of a molecular chaperone, highly conserved across organisms, that assists in protein folding.

What is α-hemoglobin stabilizing protein (AHSP)?

A molecular chaperone that prevents α-chain damage to blood cells and assists in delivering α-chains to ß-chains for hemoglobin assembly.

How is bioinformatics used in predicting protein structure?

The use of computational tools to search databases for known protein structures, establish sequence homology, and predict protein structure through methods like fold recognition, de novo prediction, and modeling algorithms.

What is de novo prediction in protein structure?

A bioinformatics method for predicting protein structure based solely on its amino acid sequence, without relying on known homologous structures.

What is the role of hydrophobic interactions in protein folding?

Significant drivers in protein folding where nonpolar hydrophobic side chains are located internally (away from water) and polar side chains are positioned outside (interacting with the aqueous environment), creating a thermodynamically favorable state.

What are liposomes, and what do they demonstrate?

Spherical aggregates of lipids arranged with polar head groups in contact with water and nonpolar tails oriented inward, away from water, serving as an example of hydrophobic interactions driving structural organization.