Test 1 Flashcards
Why is water so essential and powerful for biochemistry?
1) Solvent properties: Water is a universal solvent, many of the molecules in living organisms need to dissolve in water to participate in chemical reactions. This allows for the proper functioning of cells, tissues, and organs.
- Water’s polarity allows it to
interact with charged and polar
molecules, helping break bonds
and facilitate the movement and
reaction of ions and molecules.
2) Temperature regulation: Water has a high specific heat capacity, meaning it can absorb and retain a lot of heat without significantly changing its temperature. This is crucial in maintaining a stable internal temperature in organisms, which is essential for enzymes and biochemical reactions to proceed at optimal rates.
3) Structure and Function of Biomolecules: Water helps maintain the secondary, tertiary, and quaternary structures of proteins by forming hydrogen bonds.
Name the types of weak interactions between molecules.
1) Hydrogen Bonding
2) Van der Waal Forces
3) Electrostatic Interactions
4) Hydrophobic Interactions
What is the difference between being polar and non polar?
A polar molecule has an uneven distribution of electron density.
- Polar molecules tend to dissolve
in water
- Tend to be asymmetrical
A nonpolar molecule has a symmetric distribution of electron density, meaning there are no significant regions of partial positive or negative charges.
- Tend to be symmetrical
What is the difference between being hydrophobic and hydrophillic?
Hydrophobic (“water-fearing”). Avoid interacting with water. Usually nonpolar and cannot form hydrogen bonds.
Hydrophilic (“water-loving”) Interact well with water. Often polar and can form hydrogen bonds.
What is Keq?
The equilibrium constant. A number that expresses the ratio of the concentrations of products to the concentrations of reactants for a reversible chemical reaction at equilibrium.
- If 𝐾eq >1: At equilibrium, the concentration of products is greater than that of the reactants, meaning the reaction favors the production of products.
- If 𝐾eq <1: At equilibrium, the concentration of reactants is greater than that of the products, meaning the reaction favors the reactants.
- If 𝐾eq =1: The concentrations of reactants and products are roughly equal at equilibrium.
What is Kw?
The ionization constant for water, also known as the water dissociation constant.
It represents the equilibrium constant for the self-ionization of water, where water molecules dissociate into hydronium (H₃O⁺) and hydroxide (OH⁻) ions.
Kw changes with temperature, affecting the pH of pure water and influencing the balance between H⁺ and OH⁻ in aqueous solutions.
What is Ka?
The acid dissociation constant. It is a measure of the strength of an acid in solution and quantifies how much an acid dissociates into hydrogen ions (H⁺) and its conjugate base when dissolved in water.
The larger the value of Ka, the stronger the acid because it indicates that the acid dissociates more fully in solution, producing more H⁺ ions.
What is pKa?
pKa is the negative logarithm of the acid dissociation constant (Ka). It is a measure of the strength of an acid in solution, providing a more convenient scale for comparing acid strengths.
The lower the pKa value, the stronger the acid, as it indicates that the acid dissociates more readily in solution to release hydrogen ions
What is pH?
pH is a measure of the acidity or basicity of a solution. It quantifies the concentration of protons in a solution. The pH scale ranges from 0 to 14, with values below 7 indicating an acidic solution, values above 7 indicating a basic solution, and a value of 7 indicating a neutral solution.
pH= -log[H+]
What is pI?
The isoelectric point, which is the pH at which a molecule, typically a protein or amino acid, has no net electrical charge
For simple amino acids, the pI is typically the average of the pKa values of the amino and carboxyl groups, assuming no other ionizable groups are involved.
What is a zwitterion?
A zwitterion is a molecule that has both a positive and a negative charge on different parts of the molecule, but the overall charge of the molecule is neutral.
Name all of the amino acids with non-polar, alipathic R groups
GAPVILM
Glycine
Alanine
Proline
Valine
Isoleucine
Leucine
Methionine
Name all of the amino acids with aromatic R groups
Phenylalanine
Tyrosine
Tryptophan
Name all of the amino acids with positively charged R groups
Lysine
Arginine
Histidine
Name all of the amino acids with negatively charged R groups
Aspartic Acid
Glutamic Acid
Name all of the amino acids with polar, uncharged R groups
QCNST
Cysteine
Asparagine
Serine
Threonine
Glutamine
Describe how a titration curve relates to conjugate acid-base pairs
A titration curve shows how the pH of a solution changes as a titrant (usually a strong acid or strong base) is gradually added to a solution containing an acid or base
- The buffer region occurs when the pH changes gradually as the titrant is added, and this is where the acid and its conjugate base (or base and its conjugate acid) are in a buffered equilibrium.
- The equivalence point is reached when stoichiometrically equivalent amounts of acid and base have reacted
Describe the level of primary protein structure organization with structural features and explanations and examples.
The primary structure of a protein refers to the linear sequence of amino acids in a polypeptide chain. This sequence is held together by peptide bonds formed through condensation reactions between the amino group of one amino acid and the carboxyl group of another.
The primary structure dictates the chemical properties and functions of the protein. Even a single change in the sequence can lead to a functional change or disease (e.g., sickle cell anemia, where a single amino acid change leads to malformed hemoglobin).
eg. Insulin: The primary structure of insulin is a sequence of amino acids in two chains (A and B chains) connected by disulfide bonds.
Describe the level of secondary protein structure organization with structural features and explanations and examples.
The secondary structure refers to the local folding of the polypeptide chain into regular structures, such as alpha helices and beta sheets, which are stabilized by hydrogen bonds between the backbone atoms (not involving the side chains
- Alpha helix: A right-handed coil, where each amino acid forms a hydrogen bond with the amino acid four positions earlier. It has a helical shape.
- Beta sheet: Composed of parallel or antiparallel strands that are connected by hydrogen bonds. The strands lie flat, forming a sheet-like structure.
eg. Alpha Helix: Found in keratin, the protein in hair, skin, and nails.
Beta Sheet: Found in fibroin, a structural protein in silk.
Describe the level of tertiary protein structure organization with structural features and explanations and examples.
The tertiary structure is the three-dimensional (3D) arrangement of the entire polypeptide chain, formed by the interactions between side chains (R groups). This structure is stabilized by a variety of interactions, including hydrophobic interactions, hydrogen bonds, disulfide bonds, and ionic bonds.
- The tertiary structure is crucial for a protein’s function, as it determines the active site (in enzymes) or binding sites for other molecules.
- Folded proteins achieve a stable structure through these various interactions, with hydrophobic regions generally located in the interior, away from water.
eg. Myoglobin: A small oxygen-binding protein with a tertiary structure, important for oxygen storage in muscles.
Describe the level of quaternary protein structure organization with structural features and explanations and examples.
The quaternary structure refers to the arrangement and interaction of multiple polypeptide chains (subunits) in a multimeric protein. These subunits can be identical or different, and the structure is stabilized by the same types of interactions as the tertiary structure.
- Each subunit has its own tertiary structure, and the quaternary structure is the arrangement of these subunits.
- The subunits may be held together by hydrogen bonds, ionic bonds, and hydrophobic interactions.
- The quaternary structure allows for cooperative interactions between subunits, such as cooperative binding of oxygen in hemoglobin, where the binding of one oxygen molecule increases the affinity for subsequent oxygen molecules.
eg. Hemoglobin: A tetramer (four subunits) that carries oxygen in the blood. It has two alpha and two beta subunits, each with its own tertiary structure.
Explain a conceptual understanding of the free energy changes that occur during protein folding
Protein folding is a spontaneous process in which a polypeptide chain adopts its native 3D structure, and this process is driven by changes in free energy (ΔG).
ΔG (Free Energy Change): For protein folding to be thermodynamically favorable, the change in free energy (ΔG) must be negative. This means that the folded protein is energetically more stable than the unfolded state.
During folding, ΔH (enthalpy AKA heat content) becomes more negative due to hydrophobic interactions and hydrogen bonding, making the folded protein more stable.
ΔS (entropy AKA disorder) becomes more negative (less disorder) due to the ordered nature of the folded protein, but the overall ΔG can still be negative if the enthalpy (ΔH) term is favorable enough.
What is so important about the hydrophobic effect during protein folding?
The nonpolar, hydrophobic side chains of amino acids tend to cluster together in the interior of the protein, away from the aqueous environment. This reduces the surface area of the hydrophobic residues exposed to water, which minimizes the unfavorable interactions between nonpolar groups and water molecules.
- When a protein folds, the hydrophobic residues are typically buried in the core of the protein, forming a more stable, lower-energy configuration.
- The polar and charged residues are typically found on the surface of the protein, interacting with water through hydrogen bonds and ionic interactions.
- This folding pattern results in an overall decrease in the free energy of the system, which is energetically favorable.
Describe the folding process of a protein
The folding process is not random; instead, it follows a specific pathway that ultimately leads to the native conformation of the protein.
Unfolded State: Initially, the protein is in a disordered, extended form.
Collapsed Intermediate: As the protein starts folding, it forms local structures (e.g., alpha helices, beta sheets) in a process that minimizes the local free energy.
Native State: The protein eventually folds into its most stable, lowest-energy conformation, driven by the hydrophobic effect and other stabilizing forces.