polymers and life Flashcards
What does it mean for an amino acid to be amphoteric?
An amino acid is amphoteric, meaning it has both acidic and basic properties. It can donate a proton (H⁺) from the carboxyl group (acidic) or accept a proton (H⁺) at the amino group (basic).
What is a zwitterion in amino acids?
A zwitterion is a molecule that has both a positive and negative charge, but an overall neutral charge. In amino acids, this occurs when both the carboxyl group and amino group are ionized, usually at the isoelectric point.
How does the amino acid behave at high pH?
At high pH (alkaline conditions), the carboxyl group of the amino acid is ionized, losing a proton to form a carboxylate ion (-COO⁻).
How does the amino acid behave at low pH?
At low pH (acidic conditions), the amino group of the amino acid becomes protonated (NH₂ → NH₃⁺).
How can amino acids be identified?
Amino acids can be identified using paper chromatography. The sample is sprayed with ninhydrin, and the Rf values (ratio of the distance traveled by the compound to the distance traveled by the solvent) are compared against known values.
What is a protein in terms of its chemical structure?
A protein is a condensation polymer made of amino acids linked by peptide bonds. This forms a polypeptide chain.
What are the different levels of protein structure?
Primary structure: The sequence of amino acids in the polypeptide chain.
Secondary structure: The folding of the chain into structures like alpha-helixes or beta-pleated sheets.
Tertiary structure: The 3D shape of the protein formed by interactions between different parts of the polypeptide chain.
What types of bonds contribute to the tertiary structure of proteins?
Ionic bonds between charged side groups.
Hydrogen bonds between polar side chains.
Disulfide bonds (formed between cysteine amino acids).
Induced dipole-induced dipole (id-id) interactions between nonpolar side chains.
What is DNA?
DNA (Deoxyribonucleic acid) is a polymer of nucleotides, each consisting of a pentose sugar, a phosphate group, and a nitrogenous base. It forms a phosphate-sugar backbone with ester links, and the strands are held together by hydrogen bonds between complementary bases.
What are the base pairs in DNA?
Adenine (A) pairs with Thymine (T) via 2 hydrogen bonds.
Guanine (G) pairs with Cytosine (C) via 3 hydrogen bonds.
What is DNA replication?
In DNA replication:
The hydrogen bonds between base pairs break, unwinding the DNA.
Free nucleotides align with complementary bases on the template strand.
DNA polymerase catalyzes the formation of a new phosphate-sugar backbone.
Two identical DNA molecules are formed.
What are codons in genetic code?
Codons are sequences of three bases in mRNA that code for a specific amino acid during protein synthesis.
What is mRNA?
mRNA (messenger RNA) is a single-stranded RNA molecule that carries the genetic information from DNA to the ribosome for protein synthesis. It is a reverse copy of the DNA strand, with uracil (U) replacing thymine (T).
What is the process of translation in protein synthesis?
During translation:
mRNA binds to the ribosome.
The ribosome moves along the mRNA, reading codons.
tRNA with the correct anticodon binds to the codon and carries the corresponding amino acid.
Amino acids are joined by peptide bonds to form a polypeptide chain.
What is the lock and key model of enzyme action?
In the lock and key model, the enzyme’s active site has a specific shape that exactly matches the substrate, allowing it to bind and catalyze a specific reaction.
What is the reaction order of an enzyme-catalyzed reaction?
The reaction order of an enzyme-catalyzed reaction can be 0 or 1. If substrate concentration increases past the enzyme concentration, the reaction becomes zero-order, meaning it is no longer affected by substrate concentration.
What is a pharmacophore?
A pharmacophore is the part of a drug molecule that interacts with a receptor to produce a therapeutic effect. The fit of the pharmacophore depends on size, shape, bonding, and orientation of the isomer.
What are optical isomers (enantiomers)?
Optical isomers are non-superimposable mirror images of each other. They have chiral centers—carbons with four different groups attached—and may exhibit different properties due to their 3D arrangement.
What is the difference between primary, secondary, and tertiary amines?
Amines are classified based on the number of carbon groups bonded to the nitrogen:
Primary amine: Nitrogen bonded to one carbon.
Secondary amine: Nitrogen bonded to two carbons.
Tertiary amine: Nitrogen bonded to three carbons.
How are amines neutralized?
Amines, being basic, can accept protons (H⁺) and neutralize acids to form ammonium salts.
What are amides, and how do they differ from amines?
Amides have a carbonyl group (C=O) bonded to nitrogen, pulling electrons away from the nitrogen. Primary amides have one carbon bonded to nitrogen, and secondary amides have two carbons bonded to nitrogen.
What happens during the hydrolysis of amides under acidic conditions?
Under acidic conditions, amides can be hydrolyzed by heating with dilute acid to form a carboxylic acid and an ammonium salt.
What happens during the hydrolysis of amides under basic conditions?
Under basic conditions, amides are hydrolyzed by heating with dilute alkali to form a carboxylate ion and ammonia gas.
Why are carboxylic acids weak acids?
Carboxylic acids only partially dissociate into carboxylate ions (RCOO⁻) and H⁺ ions, making them weak acids.
How are esters named?
Esters are named by combining the name of the alcohol (derived from the alkyl group) and the carboxylic acid (derived from the parent acid). For example, ethyl acetate (from ethanol and acetic acid).
What is the difference between addition and condensation polymers?
Addition polymers are formed by the polymerization of alkenes (where the double bond opens up).
Condensation polymers are formed from monomers with at least two functional groups, and each linkage releases a small molecule, such as water.
What are polyamides and polyesters?
Polyamides (e.g., nylon) are formed from a dicarboxylic acid and a diamine.
Polyesters are formed from a dicarboxylic acid and a diol.
What are nylons, and how are they named?
Nylons are polyamides made from a dicarboxylic acid and diamine monomers. They are named based on the number of carbons in the diamine (X) and dicarboxylic acid (Y) components, e.g., Nylon 6,6.
How do uncharged radicals appear in mass spectrometry?
Uncharged radicals are not detected in mass spectrometry because only charged particles are detected.
What is high-resolution mass spectrometry?
High-resolution mass spectrometry measures the m/z (mass-to-charge) ratios of ions to four decimal places for greater accuracy in identifying compounds.
What is NMR spectroscopy?
NMR spectroscopy involves placing a sample in a strong magnetic field and exposing it to radio waves. The nuclei absorb energy based on their environment, providing information about the molecular structure.
What does chemical shift mean in NMR spectroscopy?
The chemical shift is measured relative to tetramethylsilane (TMS), which has a chemical shift of 0. The shift provides information about the environment of the hydrogen or carbon atoms.
What information can be obtained from H NMR spectroscopy?
The number of hydrogen environments is determined by the number of peaks.
Spin-spin coupling (splitting of peaks) indicates the number of adjacent hydrogens.
The height of peaks corresponds to the relative number of hydrogens in that environment.
