PROTEINS: Study Guide Flashcards
What is the definition of side chain and simple protein
Sidechain: a group of atoms attached to the main part of a molecule and having a ring or chain structure.
Simple Protein: protein that yields only alpha-amino acids or their derivatives by hydrolysis; e.g., albumins, globulins, glutelins, prolamines, albuminoids, histones, protamines.
What is the definition of a conformational isomer?
Any of two or more isomers that differ only in stereochemical configuration. They have the same chemical formula but differ in spatial arrangement.
What is the difference between Protonation and Deprotonation?
Protonation: The addition of a proton (hydrogen ion) to an atom, molecule or ion, normally to generate a cation.
Deprotonation: is the removal (transfer) of a proton (or hydron, or hydrogen cation), (H+) from a Brønsted–Lowry acid in an acid–base reaction. The species formed is the conjugate base of that acid.
What is the difference between acidic and basic AA
Acidic: polar and negatively charged at physiological pH. Both acidic amino acids have a second carboxyl group.
Basic: Basic amino acids are polar amino acids that have a positive charge at the neutral pH.
what is the definition of proteinogenic?
amino acids that are incorporated biosynthetically into proteins during translation. The word “proteinogenic” means “protein creating”.
what is the definition of a salt bridge?
an interaction between two groups of opposite charge in which at least one pair of heavy atoms is within hydrogen bonding distance. Salt bridges can contribute to protein stability, although the effect depends on the environment
what is the definition of an Isoelectric point
the pH at which a particular molecule carries no net electrical charge.
what is the definition of a disulfide bond?
also called an S-S bond, or disulfide bridge, is a covalent bond derived from two thiol groups.
what is the definition of pKa
Therefore, the pKa is a quantitative measure of how easily or how readily the acid gives up its proton [H+] in solution and thus a measure of the “strength” of the acid. Strong acids have a small pKa, weak acids have a larger pKa.
What is the difference between monomorphic and polymorphic
Polymorphism: as related to genomics, refers to the presence of two or more variant forms of a specific DNA sequence that can occur among different individuals or populations. (common variant)
monomorphic: Having but a single form; retaining the same form throughout the various stages of development; of the same or of an essentially similar type of structure;
What is the difference between a beta-turn and helix loop
beta turn: generally occur when the protein chain needs to change direction in order to connect two other elements of secondary structure. The most common is the beta turn, in which the change of direction is executed in the space of four residues.
helix loop: s a protein structural motif that characterizes one of the largest families of dimerizing transcription factors.
what is the difference between glycoprotein and proteolipid
glycoprotein: proteins containing glycans attached to amino acid side chains. Glycans are oligosaccharide chains; which are saccharide polymers, that can attach to either lipids (glycolipids) or amino acids (glycoproteins).
proteolipid: a protein covalently linked to lipid molecules, which can be fatty acids, isoprenoids or sterols.
what is the definition of hydrophobic interaction
the tendency of nonpolar groups or molecules to aggregate in water solution.
what is the definition of the native state
the native state of a protein is it’s properly folded and assembled form with operative structure and function. The native state of a protein needs all four levels of biomolecular structure
what is the definition of the subunit
a protein subunit or subunit protein is a single protein molecule that assembles (or “coassembles”) with other protein molecules to form a multimeric or oligomeric protein
P1: Know the major elements required for life present in all amino acids (AAs).
carbon, oxygen, hydrogen (CHNOPS)
P1: Proteins are considered to be “true polymers”. Why?
- large molecules composed of many repeating monomers (interlinked)
-proteins are polymers comprised of amino acids (monomers)
P1:Be able to identify the alpha carbon within the general structure of a free AA.
- general structure: central alpha carbon, primary/ alpha carboxyl group, side chain, primary amine and hydrogen
-find the amine group connected to the carboxyl- it will be the carbon that they share/ connect with
P1:Know the four groups of AA. Which ones have an overall neutral charge? Which ones are hydrophilic?
Group 1: Hydrophobic amino acids
-nonpolar R groups, overall neutral charge at physiological pH
-the group with the most members
Group 2: Polar amino acids
-polar R groups, overall neutral charge
-some can be phosphorylated (serine/tyrosine)
-cysteines (SH) group can form covalent disulfide bonds
Group 3: Positively charged AA
-positive R groups at physiological pH, hydrophilic
-referred to as basic AA (side chains have nitrogen)
-involved in protein ion channels
Group 4: Negatively charged AA
-negative charged R groups, hyrophillic
-referred as acidic amino acids
-involved in ion channels
-has the least members (2/20)
P1:Be able to identify peptide bonds within a polypeptide chain.
(slide 19) connects two r groups/ in the middle of them
-often connecting a carbon or nitrogen
P1: How do fibrous proteins and globular proteins differ? How are they similar?
-proteins are grouped by shape
-fibrous (simple shape): structural roles (filaments or tubules)/ assist with spatial organization/ serve as anchoring junctions
-globular (complex shape): regulatory or chemical roles/ serve as enzymes or transporters/receptors
P1:How does the hydrophobic effect impact protein folding?
-hydrophilic AA: protein exterior
-hydrophobic AA: protein interior (move inwards to avoid water)
-stabilization relies on noncovalent interactions (hydrogen bonds, salt bridges, van der Waals)
-in a nonpolar environment, the opposite composition
-hydrophobic effect drives the folding
P1:Define “chiral”. Explain why isomer selection matters for pharmaceuticals.
Chiral: asymmetric in that structure and mirror image not superimposable
-the L isomer of AA is slightly more soluble and is easier to bind/transport
-isomer selection means maximizing drug efficacy
-L isomer active versus d isomer is not or harmful
-isomer selection means to minimize undesirable side effects
P1:Know which standard AA is achiral and why.
Glycine is the only AA achiral due to identical hydrogens as the side chains.