Biochemistry Quiz on Protein Production and Water

A measure of the amount of energy available in a chemical reaction to do useful work.

A weak electrostatic bond between a hydrogen atom and a more electronegative atom (like oxygen or nitrogen).

Endergonic (non-spontaneous) reaction - the reaction will not happen on its own.

Water is a good solvent because of its ability to form hydrogen bonds with many substances.

Reaction at equilibrium, meaning the forward and reverse reactions are happening at equal rates.

Non-polar molecules cluster together in water to minimize their contact with water, increasing entropy and driving protein folding.

Exergonic (spontaneous) reaction - the reaction will happen on its own.

A reaction that occurs without the input of external energy.

Water molecules surrounding hydrophobic (water-fearing) molecules, forcing them together.

A reaction that requires an input of energy to occur.

Low entropy for the hydrophobic interactions due to the ordered water molecules that surround hydrophobic molecules.

Measure of disorder or randomness in a system.

Minimizes the area of hydrophobic surfaces exposed to water, increasing entropy and decreasing the energy required to drive hydrophobic interactions.

An acid that completely dissociates into ions in a solution.

A measure of the hydrogen ion concentration in a solution, usually expressed on a logarithmic scale.

Unit of concentration, measured as moles of solute per liter of solution.

The form of hemoglobin with low oxygen affinity.

The form of hemoglobin with high oxygen affinity.

Binding of oxygen to one subunit increases the binding affinity of other subunits.

Graphical method to diagnose cooperativity.

A molecule that binds to hemoglobin at a different site from oxygen.

Stabilizes the T-state, increasing hemoglobin's O2 release.

Increased H+ (protons) lowers hemoglobin's oxygen affinity.

Hemoglobin subunits are either in T or R state.

Yeast are easy to genetically modify, grow in bulk, and produce potentially high yields of proteins. Their post-translational modifications, including glycosylation, are also similar to mammalian processes.

Yeast have limited ability to fold complex proteins.

Mammalian cells offer a full range of post-translational modifications, facilitate complicated protein formation and assembly, but they can be difficult to grow in large quantities, and protein yield is potentially lower when compared to yeast.

To identify a protein in a sample, test its activity using an assay – a specific test designed to confirm its presence.

Column chromatography is a common method for purifying proteins in large quantities. A protein mixture is put through a porous material; this material separates and collects proteins based on their chemical properties.

A technique that separates proteins based on their size. Larger proteins elute first because they cannot enter the pores of the stationary phase.

A technique that separates proteins based on their charge. Proteins with opposite charges to the stationary phase bind and are eluted later.

A graph that shows how the overall charge of a protein changes with pH. It reveals the protein's isoelectric point (pI).

The pH at which a protein has no net charge. At pH above the pI, the protein is negatively charged, and at pH below the pI, it's positively charged.

Titration curves help determine a protein's pI, which allows us to select the optimal pH for binding and eluting proteins during ion exchange chromatography.

There are two types of IEX media: positively charged (DEAE cellulose) and negatively charged (CM cellulose).

Proteins can be eluted from an IEX column by changing the pH of the buffer to disrupt charge interactions or by increasing the salt concentration.

A technique that separates proteins based on their hydrophobicity. More hydrophobic proteins bind to the hydrophobic stationary phase and are eluted later.

A small, membrane-bound organelle found in almost all eukaryotic cells. They are responsible for breaking down fatty acids, detoxifying harmful substances, and producing hydrogen peroxide (H₂O₂). Although they contain enzymes, they are not involved in protein synthesis, unlike ribosomes.

A biological membrane composed primarily of phospholipids, forming a bilayer. These membranes are found in cell organelles and help define their structure and function. They regulate what enters and exits the organelle.

Specialized structures within a cell that perform specific functions. They work together to maintain the life of the cell. Examples include the nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, lysosomes, and peroxisomes.

A large, membrane-bound organelle that contains the cell's genetic material (DNA) in the form of chromosomes. It controls cell activities by directing protein synthesis.

Organelles responsible for the production of energy (ATP) through cellular respiration. They are often called the 'powerhouses' of the cell.

An extensive network of membrane-bound tubules and sacs, responsible for protein synthesis, folding, and modification, as well as lipid synthesis. It acts as a major transport system within the cell.

A stack of flattened membrane-bound sacs that modify, sort, and package proteins and lipids from the ER for transport within the cell or secretion outside the cell.

Membrane-bound sacs filled with enzymes. They break down waste materials, damaged organelles, and invading bacteria. They are the 'recycling centers' of the cell.

A weak electrostatic bond between a hydrogen atom and a more electronegative atom, like oxygen or nitrogen. It's essential for water's properties and biomolecules' structure.

They are individually weak but collectively strong, influencing water's properties as a solvent, protein folding, and DNA structure.

Non-polar molecules cluster together in water to minimize contact with water, increasing entropy (disorder) and lowering the free energy (∆G) of the system. It's a key factor in protein folding.

Increasing entropy makes a reaction more spontaneous (∆G decreases). This is because disorder increases, making it more likely for the reaction to proceed on its own.

An acid that completely dissociates (breaks apart) into ions when in solution.

An acid that only partially dissociates in solution, forming an ionic salt.

The ion product of water, representing the product of the concentrations of hydrogen (H+) and hydroxide (OH-) ions in pure water. It's a constant at a specific temperature.

The weaker the acid, the lower its Ka value. This means it takes more energy to stabilize the weak acid to form the salt (to ionize it).

The side chain of serine is a hydroxyl group (-OH).

The side chain of threonine is a hydroxyl group (-OH) attached to a CH3 group.

The side chain of valine is an isopropyl group (-CH(CH3)2).

The side chain of tryptophan is an indole ring.

The side chain of tyrosine is a phenyl ring with a hydroxyl group (-OH).

The 5 amino acids with charged side chains are: Aspartic Acid (Asp), Glutamic Acid (Glu), Lysine (Lys), Arginine (Arg), and Histidine (His).

The charge on a protein varies depending on the amino acid sequence and pH. For example, Lysine's side chain can change from 0 to +1 based on the pH.

Charged amino acid side chains form ionic bonds, also known as salt bridges, which are strong electrostatic interactions.

Inhibitor competes with substrate for binding in the enzyme's active site. It is usually a substrate analog. Its effect can be overcome with high substrate concentration.

Inhibitor binds to a site other than the active site, affecting enzyme conformation and reducing its activity. Substrate can still bind.

Inhibitor permanently inactivates the enzyme by forming a strong, covalent bond.

Inhibitor can dissociate from the enzyme, allowing the enzyme to regain activity.

Km increases as the inhibitor competes for the active site, but Vmax remains the same at high substrate concentrations.

Km stays the same, but Vmax decreases because the inhibitor reduces the enzyme's maximum activity.

A graphical representation of enzyme kinetics that is used to determine Km and Vmax. It plots the reciprocal of velocity against the reciprocal of substrate concentration.

A280 measures absorbance at 280 nm, which is primarily due to aromatic amino acids (Trp, Tyr, Phe). Enzymes have varying amounts of these amino acids, making A280 insufficient for identifying specific enzyme types.

The 5' triphosphate group on the initiating nucleotide provides energy for RNA synthesis.

RNA polymerase initiates transcription in prokaryotes by binding to the promoter region of the DNA.

Actinomycin D inhibits transcription by intercalating into DNA, blocking RNA polymerase from binding and moving along the DNA.

Rho-dependent termination requires the Rho protein, while Rho-independent termination relies on a hairpin structure in the RNA transcript.

Core RNA polymerase binds to specific sequences in the promoter region of DNA, initiating RNA synthesis.

RNA polymerase recognizes the promoter region by its specific DNA sequence, which serves as a binding site.

Transcription starts when RNA polymerase binds to the promoter region of DNA, unwinding the DNA strands and synthesizing a complementary RNA strand.

Transcription ends when RNA polymerase encounters a termination signal on the DNA, either through the Rho protein or a hairpin structure in the RNA.

RNA polymerase is an enzyme that synthesizes RNA from a DNA template in prokaryotes.

The promoter region is a specific DNA sequence recognized by RNA polymerase, typically at -10 and -35 positions relative to the transcription start site.

Describes the cell membrane as a dynamic structure composed of a phospholipid bilayer with embedded proteins that are constantly moving laterally. It implies that proteins and lipids can move freely within the membrane, contributing to its flexibility and functional diversity.

A sigma factor is a protein required for RNA polymerase initiation that helps identify strong or weak promoters, ensuring correct strand copying and directionality.

The temperature at which a membrane transitions from a more ordered, gel-like state to a more fluid state. This change is influenced by the length of the fatty acid chains and the presence of double bonds.

Certain RNA molecules can act as catalysts, similar to enzymes, by folding into specific structures.

Complex three-dimensional folds in RNA that allow for enzymatic activity, often containing hairpins and bulges.

The movement of lipids and proteins within the plane of the membrane. It allows for dynamic changes in membrane composition and facilitates various cellular processes.

A technique used to study lateral diffusion in membranes. It involves bleaching a small area of the membrane with a laser and observing the rate at which fluorescent molecules return to the bleached area.

The base pairing between adenine (A) and uracil (U) is crucial for maintaining the integrity and stability of RNA structures.

Proteins that are permanently embedded within the lipid bilayer of a membrane. They usually span the membrane, interacting with both hydrophobic and hydrophilic environments, and play a crucial role in various cellular functions.

Rifampicin is an antibiotic that inhibits bacterial RNA polymerase, specifically preventing the initiation of transcription.

DNA methylation is a chemical modification that adds a methyl group to DNA, generally reducing gene expression by inhibiting transcription.

Proteins loosely associated with the surface of a membrane. They can interact with integral proteins or directly with the lipid headgroups, but they are not embedded within the bilayer.

A common secondary structure of integral membrane proteins. The helix is formed by hydrogen bonds between backbone atoms, allowing the protein to span the membrane with its hydrophobic amino acid side chains facing the lipid acyl chains.

Integral membrane proteins have a hydrophobic surface exposed to the lipid acyl chains, allowing them to embed within the lipid bilayer. This hydrophobicity makes them difficult to study outside of their membrane environment.