Exam 1 Flashcards
Describe the importance of carbon in the chemical composition of organisms
4 covalent bonds - tetrahedral bonding pattern
Catenation
Carbon-containing compounds, such as carbohydrates and lipids, are used for storing and releasing energy in living organisms
fundamental component of the four major classes of macromolecules - carbohydrates, proteins, lipids, and nucleic acids
relatively stable, which is essential for the formation and maintenance of biological structures
Differentiate between types of weak, noncovalent interactions and provide examples of each
Hydrogen - covalent bond between electronegative atom and hydrogen leads to unequal sharing of electrons (oxygen and nitrogen are most common)
Ex. Hydrogen bonds hold two strands of DNA together by connecting the nitrogenous bases (adenine with thymine, and guanine with cytosine)
Ionic/electrostatic - Interactions between distinct electrical charges on atoms or molecules (ions). Electrostatic attractions between oppositely charged ions
Ex. Salt bridges in proteins, where positively charged amino acids (like lysine) interact with negatively charged amino acids (like glutamate)
Van der Waals - nonpolar and uncharged molecules can interact electrostatically. Depends on transient asymmetry in electrical charge (temporary dipoles)
Ex. Imagine a helium atom. At any moment, the electrons might be closer to one side of the atom than the other, creating a temporary dipole. This temporary dipole can induce a dipole in a neighboring helium atom, resulting in a weak attraction between the two atoms.
Describe the hydrophobic effect and explain its significance in forming membranes
nonpolar substances aggregate in aqueous solutions and exclude water molecules. This effect occurs because water molecules prefer to form hydrogen bonds with each other rather than with nonpolar molecules
- Lipid Bilayers: Phospholipids, which have hydrophilic (water-attracting) heads and hydrophobic (water-repelling) tails, spontaneously arrange themselves into bilayers in water. The hydrophobic tails face inward, away from the water, while the hydrophilic heads face outward, interacting with the water. This creates a stable barrier that separates the cell from its environment.
- Membrane Proteins: Integral membrane proteins have hydrophobic regions that interact with the lipid bilayer’s interior, anchoring them within the membrane. Peripheral membrane proteins, on the other hand, interact with the hydrophilic surfaces of the membrane or with integral proteins.
- Cell Function: The membrane’s structure, influenced by the hydrophobic effect, is essential for various cell functions, including maintaining the cell’s integrity, facilitating communication, and enabling selective transport of molecules.
Know the different functional groups in biochemistry and what types of weak interactions they can form
- Hydroxyl Group (-OH)
Example: Alcohols
Weak Interactions: Hydrogen bonding with other polar molecules and water. - Carbonyl Group (C=O)
Example: Ketones and Aldehydes
Weak Interactions: Dipole-dipole interactions and hydrogen bonding with water and other polar molecules. - Carboxyl Group (-COOH)
Example: Carboxylic acids
Weak Interactions: Hydrogen bonding and ionic interactions when deprotonated (forming -COO^-). - Amino Group (-NH2)
Example: Amines
Weak Interactions: Hydrogen bonding and ionic interactions when protonated (forming -NH3^+). - Phosphate Group (-PO4^3-)
Example: Phosphates in nucleotides and ATP
Weak Interactions: Ionic interactions and hydrogen bonding. - Sulfhydryl Group (-SH)
Example: Thiols
Weak Interactions: Hydrogen bonding and disulfide bond formation (covalent) in proteins. - Methyl Group (-CH3)
Example: Alkyl groups in lipids and methylated DNA
Weak Interactions: Hydrophobic interactions.
Describe how the pKa of a weak acid relates to its dissociation at different pH (mention Henderson-Hasselbalch equation)
The pKa is the pH at which half of the acid molecules are dissociated (ionized) and half are undissociated
When the pH of a solution is:
Equal to the pKa: The weak acid is 50% dissociated, meaning half of the acid molecules have donated a proton (H+) to form its conjugate base.
Below the pKa: The solution is more acidic, so the concentration of H+ ions is higher, leading to less dissociation of the weak acid (more molecules remain in their protonated form).
Above the pKa: The solution is more basic, resulting in a lower concentration of H+ ions, which promotes more dissociation of the weak acid (more molecules donate protons and exist as their conjugate base).
pH = pKa + log(A-/HA)
This equation helps predict the degree of dissociation of a weak acid at a given pH and allows for the calculation of the pH of a buffer solution. It is widely used in biochemistry to understand enzyme activity, drug formulation, and the behavior of biological systems under different pH conditions.
Explain how buffers function to maintain stable pH in biochemical systems
composed of a weak acid (HA) and its conjugate base (A-)
Neutralizing Added Acids: When a small amount of a strong acid (e.g., HCl) is added to the buffer solution, the conjugate base (A-) of the buffer reacts with the added H+ ions to form the weak acid (HA). This minimizes the increase in the concentration of H+ ions, thereby maintaining the pH
Neutralizing Added Bases: When a small amount of a strong base (e.g., NaOH) is added to the buffer solution, the weak acid (HA) of the buffer donates H+ ions to react with the added OH^- ions, forming water and the conjugate base (A-). This minimizes the increase in the concentration of OH- ions, thereby maintaining the pH
The effectiveness of a buffer, known as buffer capacity, depends on:
- Concentration: Higher concentrations of the buffer components (weak acid and conjugate base) result in a higher buffer capacity.
- Ratio of Components: The buffer is most effective when the ratio of [A^-] to [HA] is close to 1, meaning the pH is close to the pKa of the weak acid.
basic chemical structure of an amino acid
- Alpha Carbon (Cα): The central carbon atom.
- Amino Group (-NH2): Attached to the alpha carbon.
- Carboxyl Group (-COOH): Attached to the alpha carbon.
- Hydrogen Atom (H): Attached to the alpha carbon.
- R Group (Side Chain): Variable group attached to the alpha carbon, which differs among different amino acids and determines their unique properties.
How to calculate net charge of an amino acid at different pH
- Identify the Ionizable Groups:
- Commonly, amino acids have at least two ionizable groups: the amino group (-NH3^+/NH2) and the carboxyl group (-COOH/COO^-).
- Some amino acids have ionizable side chains (R groups), like the acidic side chains of Aspartic acid (Asp) and Glutamic acid (Glu) or the basic side chains of Lysine (Lys), Arginine (Arg), and Histidine (His). - Determine the pKa Values:
- Find the pKa values for each ionizable group in the amino acid. You can find these values in biochemistry reference materials. - Compare pH with pKa:
- For each ionizable group, compare the pH of the solution with its pKa value to determine its protonation state.
- If the pH < pKa, the group is protonated.
- If the pH > pKa, the group is deprotonated. - Assign Charges:
- Assign the appropriate charge to each group based on its protonation state.
- Amino Group (NH2/NH3^+):
- Below pKa (~9-10): NH3^+ (Charge: +1)
- Above pKa: NH2 (Charge: 0)
- Carboxyl Group (COOH/COO^-):
- Below pKa (~2-3): COOH (Charge: 0)
- Above pKa: COO^- (Charge: -1)
- Ionizable Side Chains (e.g., Asp, Glu, Lys, Arg, His):
- Assign charges based on their individual pKa values and the pH of the solution.
Sum the Charges:
- Add up the charges of all the ionizable groups to determine the net charge of the amino acid at the given pH.
Differentiate between the four levels of protein structure
- Primary Structure: linear sequence of amino acids in a polypeptide chain
- Peptide bonds link the amino acids together
- sequence determines the protein’s properties and function
- Peptide bonds link the amino acids together
- Secondary Structure: folded structures that form within a polypeptide due to hydrogen bonding between the backbone atoms
- Alpha helix: A right-handed coil where the backbone forms hydrogen bonds with the amino acids four residues
- Beta sheet: consists of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a sheet-like arrangement- Provides structural stability and contributes to the overall shape of the protein
- Alpha helix: A right-handed coil where the backbone forms hydrogen bonds with the amino acids four residues
- Tertiary structure: 3D shape of a single polypeptide chain, resulting from interactions between the R-groups of amino acids
- Hydrogen and ionic bonds, hydrophobic interactions, disulfide bonds (covalent bonds between cysteine residues)- determines the protein’s functional domains and its ability to interact with other molecules
- Quaternary Structure: arrangement of multiple polypeptide subunits into a single functional protein complex
- Similar to the bonds and interactions in Tertiary structure but occurring between different polypeptide chains
- Facilitates the formation of protein complexes that perform specific biological functions, such as hemoglobin’s ability to transport oxygen
What 3-D structures, if any, can be present at each level of protein structure? What types of bonds are present in the 3-D structures?
- Primary Structure
3-D Structures: None. It’s linear
Bonds: Peptide bonds (covalent) between amino acids - Secondary Structure
3-D Structures: Alpha (coil with a helical structure) and Beta (forms sheet-like structures
Bonds: hydrogen bonds between the backbone amide hydrogen and carbonyl oxygen atoms - Tertiary Structure
3-D Structures: includes folds and twists forming the overall globular or fibrous shape. Includes alpha-beta barrels, helix-turn-helix motifs
Bonds & Interactions:
- Hydrogen bonds between side chains
- Ionic bonds between positively and negatively charged side chains
- hydrophobic interactions among nonpolar side chains
- Disulfide bonds (covalent) between cysteine residues
- van der Waals forces - Quaternary Structure
3-D structures: arrangement and interaction of multiple polypeptide subunits to form a single functional protein complex (ex. hemoglobin and DNA polymerase)
Bonds and Interactions: Hydrogen, ionic, and disulfide bonds, hydrophobic interactions, van der waals forces
Calculate net charge of a short polypeptide at pH 7
peptide sequence: Ala-Glu-Lys-His
- Identify Ionizable Groups:
Amino terminus (N-terminus)
Carboxyl terminus (C-terminus)
Side chains of Glutamic acid (Glu), Lysine (Lys), and Histidine (His) - Determine pKa Values (Approximate):
- N-terminus (amino group): pKa ≈ 9.6
- C-terminus (carboxyl group): pKa ≈ 2.1
- Glutamic acid (side chain carboxyl group): pKa ≈ 4.1
- Lysine (side chain amino group): pKa ≈ 10.5
- Histidine (side chain imidazole group): pKa ≈ 6.0 - Compare pH with pKa and Assign Charges:
- N-terminus: pH 7 < pKa 9.6 → NH3^+ (Charge: +1)
- C-terminus: pH 7 > pKa 2.1 → COO^- (Charge: -1)
- Glutamic acid: pH 7 > pKa 4.1 → COO^- (Charge: -1)
- Lysine: pH 7 < pKa 10.5 → NH3^+ (Charge: +1)- Histidine: pH 7 > pKa 6.0 → N (Charge: 0)
- Sum the charges:
N-terminus: +1
C-terminus: -1
Glutamic acids: -1
Lysin: +1
Histidine: 0
Net charge=0
Describe the Anfinsen experiments and summarize the general conclusions from said experiments
- Denaturation: Anfinsen first denatured ribonuclease A using urea and mercaptoethanol, which disrupted its native structure and rendered it inactive.
- Renaturation: He then removed the denaturants, allowing the protein to refold spontaneously. Remarkably, ribonuclease A regained its enzymatic activity, indicating that it had refolded into its correct 3-D structure
Anfinsen concluded that the primary structure (amino acid sequence) of a protein contains all the information necessary for it to fold into its native, functional 3-D structure. This principle is known as Anfinsen’s dogma or the thermodynamic hypothesis.
These experiments were pivotal in demonstrating that protein folding is a self-assembly process driven by the intrinsic properties of the amino acid sequence, without the need for external templates or factors
Explain how the protein folding funnel is a model for proteins to obtain their native tertiary structure
- Energy Landscape:
- The funnel represents the energy landscape of a protein, with the vertical axis showing free energy and the horizontal axis showing the conformational space.
- The top of the funnel corresponds to high-energy, unfolded states, while the bottom represents the low-energy, native folded state. - Folding Pathways:
- As the protein folds, it moves down the funnel, sampling different conformations and decreasing its free energy.
- The narrowing shape indicates fewer possible conformations as the protein approaches its native state. - Stabilizing Interactions:
- Various interactions like hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals forces guide the folding process.
- The primary amino acid sequence contains all the information needed to reach the native conformation.
Importance:
- Efficiency: The funnel model explains how proteins fold efficiently without sampling all possible shapes.
- Predictive Power: Helps predict folding mechanisms and intermediate states, aiding in understanding protein folding diseases.
Differentiate between IDP and metamorphic proteins
IDPs are flexible and unstructured, enabling versatile interactions, while metamorphic proteins switch between distinct stable structures, each with specific functions
Intrinsically Disordered Proteins (IDPs)
- Structure: Lack a fixed or stable 3D structure under physiological conditions. They exist as dynamic ensembles of conformations
- Function: Highly versatile, often involved in signaling, regulation, and interactions with multiple partners. Their flexibility allows them to adapt to different binding partners
Metamorphic Proteins:
- Structure: can adopt multiple, distinct, stable conformations under physiological conditions. These conformations are not in dynamic equilibrium but are stable states
- Function: Different conformations typically have different functions or interact with different molecules, allowing participation in multiple biochemical pathways or processes
Differentiate between endergonic and exergonic reactions, given ∆G
endergonic reactions require energy input (positive ∆G), while exergonic reactions release energy (negative ∆G)
Endergonic Reactions
∆G: positive
Energy: require an input of energy to proceed
Spontaneity: non-spontaneous under standard conditions
Ex. Photosynthesis
Exergonic Reactions
∆G: negative
Energy: release energy during the reaction
Spontaneity: spontaneous under standard conditions
Ex. Cellular respiration
Explain the relationship between Keq and ∆G°’ of a reaction at equilibrium. How does altering the concentrations of reactants and products affect the spontaneity of a reaction?
Keq and ∆G°’ determine the standard spontaneity of a reaction, while altering reactant and product concentrations affects the actual spontaneity (∆G) under given conditions
Keq > 1: ∆G°’ is negative (reaction is exergonic and spontaneous under standard conditions).
Keq < 1: ∆G°’ is positive (reaction is endergonic and non-spontaneous under standard conditions).
Keq = 1: ∆G°’ is zero (reaction is at equilibrium with no net change)
Q < Keq: ∆G is negative (reaction is spontaneous in the forward direction).
Q > Keq: ∆G is positive (reaction is non-spontaneous in the forward direction, but spontaneous in the reverse direction).
Q = Keq: ∆G is zero (reaction is at equilibrium).
Describe how enzymes accelerate the rate of chemical reactions. Explain what the transition state is and its energetic relationship to the substrate and product.
enzymes lower the activation energy by stabilizing the transition state, making reactions more efficient
Enzymes are biological catalysts that speed up the rate of chemical reactions by lowering the activation energy (Ea) required for the reaction to proceed
1. Stabilizing the Transition State: Enzymes provide an active site that stabilizes the transition state, reducing the energy needed to reach it
2. Orientation and Proximity: Enzymes bring substrates into close proximity and the correct orientation, facilitating effective collisions
3. Induced Fit: The enzyme’s active site can change shape to better accommodate the substrate, enhancing catalytic efficiency
4. Providing a Favorable Microenvironment: The active site may have a unique pH or polarity that favors the reaction
The transition state is a high-energy, unstable intermediate state that occurs during the transformation of reactants into products. It represents the point at which old bonds are breaking, and new bonds are forming
Energetic Relationship:
- Substrate (S): The reactant(s) that bind to the enzyme’s active site
- Transition State (TS): The highest-energy state during the reaction; it has the highest free energy.
- Product (P): The final molecule(s) formed after the reaction
- In the presence of an enzyme, the activation energy (Ea) required to reach the transition state is significantly lowered, making the reaction proceed faster.
Differentiate between classes of enzymes based on enzymatic function
- Oxidoreductases: transfer electrons between molecules (ex. dehydrogenases, oxidases)
- Transferases: Move functional groups (e.g., methyl, phosphate) between molecules (ex. kinases, transaminases)
- Hydrolases: cleave bonds with the addition of water (ex. proteases, lipases)
- Lyases: remove atoms to form double bonds or add atoms to double bonds (ex. decarboxylases, synthases)
- Isomerases: move functional groups within a molecule (ex. epimerases)
- Ligases: join two molecules at the expense of ATP (ex. DNA ligase, synthetases)
Identify common characteristics shared by enzyme active sites
- Specificity: active sites are highly specific to their substrates
- 3-D Shape: active site’s unique 3D structure complements the substrate
- Microenvironment: The active site provides a specific microenvironment that make differ from the surrounding solution
- Amino Acid Residues: may contain specific ones that participate directly in the catalytic process through various interactions
- Induced fit: Some enzymes exhibit an induced fit mechanism, where the active site undergoes a conformational change upon substrate binding, enhancing the enzyme’s catalytic activity
- Binding Sites: active sites have binding sites that hold the substrate in place, aligning it properly for the catalytic reaction
- Transition stabilization: active sites stabilize the transition state of the reaction, lowering the activation energy and increasing the reaction rate
Differentiate between classes of enzymatic reactions with multiple substrates
Sequential Reactions: Both substrates bind before any product is released, and can be ordered or random.
Ping-Pong Reactions: One substrate binds and a product is released before the second substrate binds, involving an enzyme intermediate state.
- Sequential Reactions (Single-Displacement)
Definition: Both substrates bind to the enzyme before any product is released.
Types:
Ordered Sequential: Substrates bind to the enzyme in a specific order.
Random Sequential: Substrates can bind in any order. - Double-Displacement
Definition: One substrate binds to the enzyme and a product is released before the second substrate binds. The enzyme alternates between different states
Outline the Michaelis-Menten model of enzyme kinetics. How does enzyme activity vary as a function of substrate concentration?
E + S <-> ES -> E + P
Low [S]: At low substrate concentrations, the reaction velocity increases linearly with [S] because there are many free enzyme molecules available.
Intermediate [S]: As substrate concentration increases, the reaction velocity begins to level off and follows a hyperbolic curve. This is due to the enzyme molecules becoming increasingly saturated with substrate.
High [S]: At high substrate concentrations, the reaction velocity approaches Vmax and becomes independent of [S], as all enzyme active sites are occupied.
Explain the relationship between KM, substrate concentration, and reaction velocity
Low [S]: v increases linearly with [S].
[S] = Km: v is half of Vmax.
High [S]: v approaches Vmax and becomes independent of [S].
Km:
- It indicates the affinity of an enzyme for its substrate.
- A low Km value means high affinity (the enzyme binds substrate tightly).
- A high Km value means low affinity (the enzyme binds substrate loosely).
Explain how temperature and pH can alter enzyme activity
Optimal Temperature: Each enzyme has an optimal temperature at which it functions most efficiently. For many human enzymes, this is around 37°C (98.6°F).
Increased Temperature: As temperature increases, enzyme activity generally increases due to higher kinetic energy, which leads to more frequent collisions between enzyme and substrate. However, if the temperature exceeds the optimal range, the enzyme can denature (lose its structure), resulting in a sharp decline in activity.
Decreased Temperature: Lower temperatures reduce enzyme activity as molecular motion slows down, leading to fewer collisions between enzyme and substrate.
Optimal pH: Each enzyme has an optimal pH at which it exhibits maximum activity. This varies widely among different enzymes.
Deviation from Optimal pH: Changes in pH can affect the ionization of the enzyme’s active site and the substrate, which can alter the enzyme’s shape and function. Extreme pH values can lead to enzyme denaturation.
Differentiate between the four major catalytic strategies of enzymes
- Covalent Catalysis: The enzyme forms a transient covalent bond with the substrate, creating a reactive intermediate that helps to lower the activation energy
- Ex. Chymotrypsin uses a serine residue to form a covalent bond with the substrate during peptide bond hydrolysis - Acid-Base Catalysis: The enzyme donates or accepts protons (H⁺) to stabilize the transition state or intermediates, facilitating the reaction
- Metal Ion Catalysis: Metal ions in the enzyme stabilize negative charges, participate in redox reactions, or enhance the binding of substrates
- Proximity and Orientation Effects: The enzyme brings substrates into close proximity and the correct orientation to increase the likelihood of productive collisions
