Lecture 14: Protein Structure and Function Flashcards
What role do proteins play in the body?
Proteins are the workforce of the body, responsible for carrying out essential biological functions.
What are amino acids?
Amino acids are the building blocks of proteins, each containing an amino (NH₂) group, a carboxyl (-COOH) group, and a side chain.
Describe the primary structure of proteins.
The primary structure of proteins refers to the sequence of amino acids, known as residues, that are linked together in a polypeptide chain.
Explain the secondary structure of proteins.
The secondary structure involves the localized folding of the polypeptide, which can form structures such as alpha helices and beta sheets, stabilized by hydrogen bonds.
How do amino acids polymerize to form proteins?
Amino acids polymerize through peptide bonds, linking the amino group of one amino acid to the carboxyl group of another, forming a polypeptide chain with a byproduct of water.
Define the tertiary structure of proteins.
The tertiary structure is the complete three-dimensional folding pattern of a polypeptide, determined by interactions among the side chains of the amino acids.
What is the quaternary structure of proteins?
The quaternary structure refers to the assembly of multiple polypeptide chains into a single functional protein complex, such as hemoglobin, which is a tetramer.
Explain the significance of the hydrophobic effect in protein folding.
The hydrophobic effect describes how non-polar side chains interact with the aqueous environment, leading to their burial in the protein’s interior, which is crucial for proper folding.
Differentiate between globular and fibrous proteins.
Globular proteins are compact, highly folded, and functional, while fibrous proteins are elongated and structural, such as actin and collagen.
Describe the role of hydrogen bonds in protein structure.
Hydrogen bonds are crucial for stabilizing protein structures, particularly in the secondary structure, where they form between the carboxyl oxygen and the N-H donor.
What are the N-terminus and C-terminus of a protein?
The N-terminus is the left-hand side of the polypeptide chain, containing the amino group, while the C-terminus is the right-hand side, containing the carboxyl group.
Identify the forces involved in maintaining protein structures.
Forces involved in maintaining protein structures include hydrogen bonds, electrostatic interactions, disulfide bonds, and the hydrophobic effect.
Explain the characteristics of charged amino acids.
Charged amino acids are hydrophilic, meaning they interact well with water and are often found on the surface of proteins.
How does the sequence of amino acids affect protein function?
The sequence of amino acids determines the protein’s structure, which in turn dictates its specific function in the body.
What is a dimer in the context of protein structure?
A dimer refers to a protein complex formed by the association of two polypeptide subunits.
Describe the role of weak interactions in protein folding.
Weak interactions, such as hydrogen bonds and van der Waals forces, play a significant role in stabilizing the folded structure of proteins.
Explain the function of salt bridges in proteins.
Salt bridges in proteins are bonds between oppositely charged residues that are sufficiently close to each other to experience electrostatic attraction
Define disulfide bonds and their significance in proteins.
Disulfide bonds are covalent bonds formed between the sulfur atoms of two cysteine amino acids, providing structural stability to proteins.
How do hydrophobic interactions influence protein structure?
Hydrophobic interactions cause non-polar side chains to cluster away from water, contributing to the folding and stability of protein structures.
Explain the process of denaturation in proteins.
Denaturation is the process where proteins lose their three-dimensional structure and function, often due to changes in pH, temperature, or salt concentration.
Describe the impact of temperature on protein structure.
Temperature changes can lead to protein denaturation, with the exception of disulfide bonds which remain intact under heat.
How do hydrophobic amino acids behave in aqueous environments?
Hydrophobic amino acids tend to be exposed to water, leading to their clustering and becoming insoluble, which affects protein folding.
Outline the steps involved in the drug discovery pipeline.
The drug discovery pipeline includes
Target Identification & Validation
Drug Discovery & Screening
Lead Optimization
Preclinical Development
Clinical Trials.
What is the role of GWAS in drug discovery?
GWAS (Genome-Wide Association Studies) helps in identifying genetic variants associated with diseases, aiding in target identification and validation in drug discovery.
Explain the concept of high-throughput screening in drug discovery.
High-throughput screening is a method used to quickly assess the biological activity of a large number of compounds, facilitating the identification of potential drug candidates.
Describe the purpose of rational drug design in lead optimization.
Rational drug design aims to optimize the properties of drug candidates based on their molecular structure and biological activity.
What is involved in preclinical development of a drug?
Preclinical development involves testing the safety and efficacy of a drug in vitro (in cell lines) and in vivo (in animal models) before clinical trials.
Explain the significance of clinical trials in drug development.
Clinical trials are essential for evaluating the safety and efficacy of a drug in human subjects, involving patient recruitment, engagement, and regulatory compliance.
What are malic enzymes and their function?
Malic enzymes are enzymes that catalyze the conversion of malate to pyruvate, playing a role in metabolic pathways.
Describe the effectiveness of NPD-389 in breast cancer treatment.
NPD-389 has been shown to decrease cell viability in breast cancer cell lines and is more effective than embonic acid and its analogue, MDSA.
What is structural-based virtual screening (docking)?
Structural-based virtual screening (docking) is a computational method used to predict how small molecules, such as drug candidates, bind to a target protein.
Describe the factors considered in the selection of the top 1000 inspected compounds.
The selection is based on chelating the metal, hydrogen bonding (ideally >3 - 5), cost, new chemical scaffolds, and new binding pockets.
Define the composition of amino acids.
Amino acids are made up of carbons, hydrogens, oxygens, nitrogen, some sulfur, and selenocysteine, which is the only amino acid containing selenium.
How does the shape of an amino acid influence its function?
The function of an amino acid is heavily dependent on its shape, which is determined by the arrangement of its carboxyl group, amino group, and side chain.
Explain the role of the side chain in amino acids.
The side chain determines the properties of the amino acid and is the only part that varies among different amino acids.
Describe the characteristics of hydrophobic amino acids.
Hydrophobic amino acids have carbon-rich side chains that do not interact well with water.
How do charged amino acids interact with other molecules?
Charged amino acids interact with oppositely charged amino acids or molecules.
Define the primary structure of a protein.
The primary structure is the linear sequence of amino acids as coded by DNA, joined by peptide bonds through dehydration reactions.
Explain the process of forming peptide bonds in proteins.
Peptide bonds are formed by joining an amino group to a carboxyl acid, releasing a water molecule each time a bond is formed.
Describe the secondary structure of proteins.
The secondary structure involves localized folding of the polypeptide into structures like alpha helices or beta sheets, stabilized by hydrogen bonds.
What is an alpha helix in protein structure?
An alpha helix is a right-handed coil stabilized by hydrogen bonds between nearby amine and carboxyl groups of amino acids.
Explain what beta sheets are in protein structure.
Beta sheets are formed when hydrogen bonds stabilize two or more strands of amino acids.
Define the tertiary structure of a protein.
The tertiary structure refers to the three-dimensional shape of the protein chain.
How do membrane-bound proteins interact with lipids?
Membrane-bound proteins have their hydrophobic amino acids on their exteriors so that hydrophobic side chains can interact with the lipids in the membrane.
Define the role of charged amino acids in protein interactions.
Charged amino acids allow amino acids to interact with molecules that have complementary charges.
Describe the structure of antibodies in the immune system.
Antibodies have flexible arms that recognize and bind to pathogens to target them for destruction by the immune system.
Explain the structure of insulin as a protein in the bloodstream.
Insulin is a small stable protein that can maintain its shape while traveling through the bloodstream.
What is the function of the enzyme Alpha Amylase?
Alpha Amylase is an enzyme that begins the digestion of starches in our saliva.
Describe the function of the calcium pump in muscle contraction.
The calcium pump is aided by magnesium and powered by ATP to move calcium ions back to the sarcoplasmic reticulum after each muscle contraction.
Explain how Ferritin functions as a storage protein.
Ferritin is a spherical protein with channels that allow iron ions to enter and exit depending on need, storing iron in a non-toxic form.
What structural role does collagen play in the body?
Collagen forms a strong triple helix that is used throughout the body for structural support.
