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.
Where does protein folding occur?
In the lumen of the rough ER
Describe the role of chaperone proteins during protein folding
Chaperones are helper proteins that assist other proteins in achieving their correct 3D structure and prevent misfolding or aggregation. They are crucial for ensuring the proper folding of newly synthesized proteins and refolding of denatured proteins.
- Chaperones bind to exposed hydrophobic regions of nascent or unfolded proteins, preventing aggregation.
- They bind and release the protein in an ATP-dependent manner, providing an environment conducive to correct folding.
- Once the protein has folded correctly, the chaperone releases it, allowing it to achieve its native structure.
Describe/define the native state of a protein
The native state of a protein refers to its functional three-dimensional (3D) structure that is thermodynamically stable under physiological conditions
This is the lowest-energy conformation that the protein adopts where it has properly folded into its most stable form, held together by a variety of non-covalent forces (hydrogen bonds, ionic interactions, van der Waals forces, and the hydrophobic effect) and, in some cases, disulfide bonds.
Describe/define a breathing protein
The term “breathing” in proteins refers to the dynamic flexibility of proteins, particularly their ability to undergo small, conformational changes while still maintaining their overall structure. These conformational fluctuations are essential for many biological functions, as they allow the protein to interact with other molecules, bind substrates, or undergo changes in structure in response to environmental factors.
1) Side-chain movements: Small adjustments in the position of the amino acid side chains, particularly those on the surface of the protein, can alter interactions with other molecules or substrates.
2) Domain movements: In larger, multi-domain proteins, different structural domains might move relative to each other.
3) Loop fluctuations: Loops connecting secondary structure elements (such as alpha helices and beta sheets) can flex and move, allowing the protein to change shape.
What make transmembrane proteins unique?
Transmembrane proteins span the entire width of the cell membrane, from the extracellular space to the cytoplasm.
Hydrophobic regions are found within the lipid bilayer, hydrophilic outside of it.
integral membrane proteins, they are tightly associated with the membrane and cannot be easily removed without disrupting the membrane structure.
Many have the shapes of alpha helices or beta barrels.
Many are essential for the transport of substances across the membrane, including ions, small molecules, and larger macromolecules via ion channels
What does structure dictate?
Function
What is X-ray crystallography used for?
Used to determine the three-dimensional structure of a molecule, typically proteins, nucleic acids, and other complex biological macromolecules
How does x-ray crystallography work?
The crystal is exposed to an x-ray beam and rotated to capture multiple diffraction patterns from different angles.
As the X-rays pass through the crystal, they are diffracted by the periodic arrangement of atoms, creating a series of spots on a detector (like a CCD camera or film). Each spot represents a different reflection, which carries information about the atomic positions in the molecule.
The diffraction data is collected and used to generate a set of diffraction intensities
From these intensities, the phase information (which is lost during data collection) needs to be estimated
Computational methods are used to combine the diffraction data with the phase information and produce a three-dimensional electron density map of the molecule.
Once the electron density map is generated, it is used to build an initial model of the molecular structure
What is a protein family?
Protein families refer to groups of proteins that share a common evolutionary origin, and therefore, have similar sequences and structural features. Members of a protein family usually have similar functions and are often involved in related biological processes.
What is a core motif in a protein family?
A protein family is defined by the sharing of a common core motif or structural feature, typically a specific arrangement of secondary structure elements
- Core motifs are structurally conserved regions that are usually located in the interior of the protein, where they are shielded from the surrounding aqueous environment.
- These motifs typically consist of helices, beta sheets, or loops that are critical for the protein’s folding and function.
What is a peripheral structure of a protein family?
peripheral structures refer to regions that are more flexible and often involved in interactions with other molecules. These structures can be less conserved across family members.
- often responsible for protein-protein interactions, ligand binding, or cellular signaling.
Explain the tertiary vs primary structure of a protein family (think myoglobin and hemoglobin)
- The primary structure of a protein refers to its amino acid sequence, which determines the protein’s eventual 3D shape and its function.
Both myoglobin and hemoglobin share a common primary structure in that they are both globins and are composed of alpha-helices arranged in a specific sequence. - The amino acid sequence of myoglobin is almost identical to one of the subunits of hemoglobin (the α-globin chain). However, the primary structure is what distinguishes myoglobin (a single polypeptide chain) from hemoglobin (which has four subunits, two α-globins and two β-globins).
In myoglobin, the tertiary structure consists of a single polypeptide chain folded into a compact globular shape, with a heme group embedded in a pocket of the protein. The tertiary structure of myoglobin allows it to bind oxygen tightly and effectively in muscles.
In hemoglobin, the tertiary structure is more complex. It has four subunits (two α-globin and two β-globin chains), each containing a heme group. These subunits are arranged in a tetrameric structure. The quaternary structure of hemoglobin involves interactions between the subunits, allowing for cooperative binding of oxygen.
Explain how Protein to ligand binding is reversible, transient, and drives cellular function
Reversible binding means that the interaction between the protein and ligand is not permanent. After binding, the ligand can dissociate from the protein
The binding equilibrium between the protein and ligand is governed by a balance between the association rate (how fast the protein and ligand bind) and the dissociation rate (how fast the ligand leaves the protein). This equilibrium can be influenced by factors such as concentration of the ligand, temperature, and affinity (how strongly the protein binds to the ligand).
The dissociation constant (Kd) describes how tightly a ligand binds to a protein.
- A low Kd indicates strong binding, whereas a high Kd suggests weak binding.
Reversibility means that ligands can bind and unbind repeatedly, which allows proteins to interact with multiple ligands over time, facilitating continuous cellular processes.
Explain Binding regulation: homo vs heterotropic modulation
Homotropic modulation occurs when the binding of a ligand to one site of a protein (such as an enzyme or receptor) affects the binding of the same type of ligand at another site on the same protein. In other words, the modulator (the ligand) is identical to the molecule the protein normally binds to.
Heterotropic modulation occurs when the binding of a ligand to one site of a protein affects the binding affinity for a different type of ligand at a separate site. In this case, the modulator is a different molecule than the one the protein normally binds to.
Explain Sickle cell: genetic mutation -> protein sequence changes -> alterations in structure and function
caused by a mutation in the hemoglobin gene that leads to significant changes in structure and function
located on chromosome 11, this mutation is a single nucleotide substitution that changes the sixth codon of the beta-globin gene (the protein subunit of hemoglobin) from glutamic acid (Glu) to valine (Val).
The glutamic acid is a negatively charged, hydrophilic amino acid, whereas valine is a nonpolar, hydrophobic amino acid.
his hydrophobic interaction between the valine residues on different hemoglobin molecules is key to the changes in the protein’s structure and behavior
LEads to polymerization, conformational change, and sickle shaped cells which are prone to block blood flow.
Explain Cooperativity: concerted vs sequential
Cooperativity refers to the phenomenon where the binding of a ligand to one site on a protein affects the binding of subsequent ligands at other sites on the same protein.
The Concerted Model suggests that the protein exists in two distinct conformational states, R (relaxed) and T (tense) states, and that all subunits of the protein must be in the same conformation at any given time.
The Sequential Model proposes that the conformational change in a protein occurs one subunit at a time, rather than all subunits shifting simultaneously
- The protein has both high-affinity (R) and low-affinity (T) states for each subunit.
- When one subunit binds a ligand, it induces a local conformational change in that subunit, which increases the affinity of the adjacent subunits for the ligand, but not necessarily for all subunits at once.
- As more ligands bind, each subunit individually undergoes a sequential conformational change, gradually increasing the overall affinity of the protein for the ligand.
What is the Hill equation?
A mathematical formula used to describe the cooperative binding of ligands to a multimeric protein
Explain the Bohr Effect
The physiological phenomenon where the binding affinity of hemoglobin for oxygen (O₂) is influenced by changes in pH and carbon dioxide (CO₂) concentration.
It describes how hemoglobin’s oxygen-binding affinity decreases in the presence of lower pH (more acidic conditions) and higher CO₂ concentration, both of which are commonly associated with active tissues.
How does BPG impact hemoglobin/the bohr effect
BPG is an allosteric effector of hemoglobin that stabilizes the T-state (tense state), thus promoting oxygen release
What is an Ig?
An immunoglobulin. One of the major immune fighting molecules found everywhere in the body. AKA antibodies.
What are the five kinds of Ig?
IgG: Most abundant, protects against bacterial infections
IgA: Surveillance at surface barriers.
IgM: Produced at the first sight of threat
IgE: Determines if you have an allergy
IgD: Least understood, found in blood
Explain a Humoral vs cellular immune defense
Humoral: primarily mediated by antibodies (also called immunoglobulins), which are produced by B cells. It targets pathogens that are outside cells (extracellular pathogens) and involves the secretion of antibodies into bodily fluids such as blood, lymph, and mucosal secretions.
Cellular: mediated by T cells, which are a type of white blood cell that target infected or abnormal cells, such as cells infected by viruses or cancerous cells. Unlike humoral immunity, the cellular immune response involves direct cell-to-cell interactions and is effective against intracellular pathogens (those inside cells)
Describe MHCI vs II
Major Histocompatibility Complex (MHC) molecules are essential components of the immune system that play a central role in antigen presentation to immune cells. MHC molecules help the immune system recognize and respond to foreign pathogens or infected cells.
MHCI present intracellular antigens (e.g., viral peptides) to cytotoxic T cells (CD8+ T cells). These T cells are responsible for killing infected or abnormal cells.
MCHII present extracellular antigens (e.g., bacterial proteins) to helper T cells (CD4+ T cells). These T cells help activate other immune cells and coordinate the immune response.
What is an antigen?
Any substance that is recognized by the immune system as foreign or potentially harmful and triggers an immune response.
What is an epitope?
An epitope is the specific part of an antigen that is recognized by the immune system. It is the small region or molecular structure on an antigen that binds to an antibody or a T-cell receptor (TCR), initiating the immune response.
Describe polyclonal vs monoclonal antibodies
Polyclonal antibodies are a mixture of antibodies that are produced by different B cell clones in response to a particular antigen. They recognize and bind to multiple epitopes (the specific regions of the antigen) on the same antigen.
Monoclonal antibodies are highly specific antibodies that are produced by a single clone of B cells. They recognize a single, specific epitope on the antigen, making them much more uniform than polyclonal antibodies.
Describe Ig general structure: heavy vs light chains
An antibody molecule has a Y-shaped structure, with distinct variable and constant regions on both the heavy and light chains.
2 heavy chains, 2 light chains, each with a variable region and a constant region.
Heavy chains: This region is found at the tip of the Y and determines the antibody’s specificity.
Describe Ig general structure: fab vs fc
Fab (Fragment, Antigen-Binding): Each arm of the Y is formed by one light chain and one heavy chain. The Fab region is responsible for binding to the antigen. The variable regions of both the heavy and light chains together form the antigen-binding site. These regions are highly specific to the shape of the antigen.
Fc (Fragment, Crystallizable): The Fc region is the stem of the Y and is formed by the constant regions of the two heavy chains. This region does not bind antigens but is responsible for mediating immune responses. It interacts with Fc receptors on immune cells (such as macrophages and NK cells) and can activate the complement system. The Fc region determines the isotype of the antibody (IgA, IgG, IgM, etc.) and influences its role in immune defense.
Describe the series of events that happens upon Ig binding antigen
- Antibody binds to the antigen, forming the antigen-antibody complex.
- The Fc region of the antibody is exposed and recognized by Fc receptors on macrophages and other immune cells.
- This binding triggers opsonization, enhancing the ability of macrophages to recognize and bind the pathogen.
- Phagocytosis: Macrophages engulf the pathogen, creating a phagosome.
- The phagosome fuses with a lysosome, and the pathogen is digested and destroyed.
- The complement system is activated, leading to pathogen lysis and further enhanced phagocytosis.
- Macrophages release cytokines and chemokines, activating additional immune cells and promoting inflammation.
- Memory cells are formed, preparing the immune system for future encounters with the same pathogen.
