Key TERMS Flashcards
What is Quaternary Structure of a protein?
–> Use hemoglobin as an example.
The quaternary structure of a protein refers to the arrangement and interaction of multiple polypeptide chains (subunits) within a protein complex.
The quaternary structure is relevant only for proteins composed of more than one polypeptide chain.
Hemoglobin is an example of a protein that has quaternary structure. It is composed of four polypeptide subunits: two alpha (α) chains and two beta (β) chains. These subunits come together to form the functional hemoglobin protein, allowing it to effectively bind and release oxygen molecules. The specific arrangement of these subunits — α1β1 and α2β2 — is crucial for the protein’s function in transporting oxygen in the blood.
What is the Isoelectric point (pI)?
The isoelectric point, abbreviated as pI, is the pH at which a molecule, particularly an amino acid or a protein, carries no net electric charge. At this specific pH value, the molecule’s positive and negative charges balance each other out, making the overall charge neutral.
–>This was tied to the thing where we would see what the overall net charge of amino acid was (so seeing when the amino group, carboxyl group, and side chain were charged).
In the case of Isoelectric point, we are looking at the overall MOLECULE’s net charge, not just one amino acid.
[The pI value is especially important in biochemistry and molecular biology because it influences the solubility of the molecule and its interaction with other molecules. Proteins, for example, may have different conformations and solubilities at pH values above or below their isoelectric point. ]
what is a globular protein?
A globular protein is a type of protein that is roughly spherical (globular) in shape and is soluble in water.
WHat is an Alpha chain in protein?
–> WHat is a BETA chain in protein?
WHat are the similarities and differences between PROTEIN structures, RNA structures, and DNA structures?
Describe the Phi (ø) and Psi (y) angles.
(those aren’t the accurate symbols)
What is a counterion?
–>How does it impact RNA folding?
A counterion is an ion that accompanies an oppositely charged ion, helping to neutralize the charge.
–> A positively charged counter-ion Neutralizes the Phosphate Backbone: The backbone of RNA consists of repeating phosphate groups, each carrying a negative charge. Counterions, typically cations like Na+, K+, Mg2+, or Ca2+, help neutralize these negative charges. This neutralization is essential for reducing the electrostatic repulsion between phosphate groups, which in turn allows the RNA molecule to fold into its functional three-dimensional structure.
WHat does an Induced Fit Model mean in biochemistry?
The induced fit model is a concept in biochemistry that describes how the binding of a substrate to an enzyme’s active site causes a conformational change in the enzyme that enhances the fit between the enzyme and the substrate. This model expands on the earlier “lock and key” model proposed by Emil Fischer in 1894, which suggested that the enzyme and substrate fit together perfectly without any change in the enzyme’s shape.
The induced fit model underscores the dynamic nature of enzyme-substrate interactions, emphasizing that enzymes are not rigid structures but are flexible and can adapt their shape to fit substrates and catalyze reactions efficiently. This understanding is fundamental in fields like drug design and biotechnology, where the goal is often to create molecules that can specifically and effectively modulate enzyme activity.
What is Glucokinase?
Based off of it’s name, “gluco” means sugar and “kinase” means enzyme that adds phosphate, so we can assume that it’s adding phosphate to glucose (phosphorylation).
Function: Glucokinase catalyzes the phosphorylation of glucose to produce glucose-6-phosphate. This reaction consumes one molecule of ATP and is the first step in both the glycolysis pathway (which generates energy) and glycogenesis (the storage form of glucose). The product, glucose-6-phosphate, is a critical intermediate that can enter various metabolic pathways.
What is Protease?
Protease is a type of enzyme that specializes in breaking down proteins into smaller peptides or individual amino acids. These enzymes play critical roles in many biological processes, including digestion, cell signaling, immune function, and the cell life cycle. Here’s a detailed look at proteases:
Types of Proteases
Proteases can be categorized based on the mechanism they use to cleave peptide bonds in proteins:
Serine Proteases: These use a serine residue to mediate hydrolysis of peptide bonds. An example is trypsin, which specifically cleaves peptide bonds at the carboxyl side of lysine and arginine amino acids.
Cysteine Proteases: These have a cysteine residue in their active site that helps break down proteins. An example is caspase, involved in apoptosis (programmed cell death).
Aspartic Proteases: These enzymes use an aspartate residue to hydrolyze peptide bonds. An example is pepsin, which is used in the stomach to digest proteins.
Metalloproteases: These proteases require a metal ion (usually zinc) to function. An example is matrix metalloproteinase, which plays a role in cell remodeling and repair.
What are the
Define the type of enzyme based on the name ending:
- -kinase
- -phosphotase
- -ease
- -kinase = ADDS a PHOSPHATE
- -phosphotase = Removes a phosphate.
- -ease = digests a protein.
