The Structure of Amino Acids Flashcards
Functional groups
Small group of atoms bonded together in a precise configuration and exhibiting particular chemical properties that it imparts to any organic molecule in which it occurs.
Phosphate group
A functional group characterized by a phosphorus atom bonded to 4 oxygen atoms, 3 single and one double bond. If the atom is not bonded to another atom its a phosphate ion. Has 2 negative charges in its oxygen atoms
Carbonyl group
organic functional group composed of a carbon atom double bonded to an oxygen atom. Polar cause oxygen has a strong attraction for electrons
Sulfhydryl group
Sulfur and hydrogen bond
Carboxyl group
combination of two functional group attached to a single carbon atom, namely they’re hydroxyl (OH) and carboxyl (double bonded O) groups.
Hydroxyl group
consists of an oxygen atom with two lone pairs bonding to a hydrogen atom. Participate in hydrogen bonding. R-OH
Carbonyl group
chemically organic functional group composed of a carbon atom double bonded to an oxygen atom
Carbon group
anything with carbon
R group
Any group in which hydrogen or carbon atoms are attached to the rest of the molecule
Macromolecules
Large molecules made from monomers
Monomers
Molecular subunit used to build a macromolecule
Polymer
Large number of monomers are bonded together
Polymerization
Process by which many identical or similar small molecules (monomers) are covalently bonded to form a large molecule (polymer)
Condensation reactions (DEHYDRATION)
Synthesis reaction and water leaves. Basuically 2 or more molecules combine to form a larger molecule and lose water.
lysis
breakdown
Hydrolysis
Opoosite reaction where the molecules rae broken down into two molecules. Water is invited to the party.
amino acids
a small organic molecule with central carbon atom bonded to an amino group (-NH3), a carboxyl group (-COOH), a hydrogen atom, and a side chain
Amino acid core structure
1.H-Hydrogen atom
2.NH2-An amino functional group
3. COOH-A carboxyl functional group
4. a distinctive “R-group” (side chain)
R-Group (side chain)
Vary from single hydrogen atom to large structures containing carbon atoms linked into rings. Properties of amino acids vary because their R-groups vary.
hydrophilic
Interacting readily with water. Typically polar compunds containing partially or fully charged atoms
Hydrophobic
Not interacting readily with water.
3 types of Amino acid R groups
Does the R-group have a negative charge? If so, it is acidic and has lost a proton, like aspartate.
Does the R-group have a positive charge? If so, it is basic and has picked up a proton, like lysine.
If the R-group is uncharged, does it have an oxygen atom? If so, then the highly electronegative oxygen will form a polar covalent bond in the R-group, thus making it uncharged polar like serine. (Although somewhat less electronegative, nitrogen atoms can also contribute polarity.) The overall polarity of an R-group is based on the number of highly polar covalent bonds relative to nonpolar bonds.
If it has neither a negative charge, positive charge or oxygen atom. It is a nonpolar amino acid
Peptide bond
Covalent bond formed by condensation reaction between 2 amino acids.
Basically when carboxyl group reacts with the amino group of a second amino acid
Peptide (oligopeptide)
A chain composed of fewer than 50 amino acid residues linked together by peptide bonds. Simply also referred to as peptuide.
Polypeptides (many peptides)
Polymers that contain 50 or more amino acids linked by peptide bonds
Residues
one amino acid
Protein
Chain of amino acids
primary structure
unique sequence of amino acids in a protein
Secondary structure
local folded structures that form within a polypeptide due to interactions between atoms of the backbone. They’re stabilized largly by hydrogen bonding that occurs between the oxygen on the carbonyl group C–O of one amino acid residue and the hydrogen on the amino group N-H group of another.
alpha helix
second structure in proteins formed when the polypetide backbone coils into a spiral shape stabilized by hydrogen bonding
beta pleated sheet
segments of peptide chain bend 180 degrees than fold in the same plane. Secondary structure of proteins
backbone
Refers to the polypeptide chain apart from the R groups
Tertiary structure
Overall three dimensional shape of a single polypeptide. Form using a varoiety of bonds and intereactions between R-groups or between R-groups and the backbone.
5 interactions involving R groups
Hydrogen bonding, Hydrophobic interactions, van der wals interactions, covalent bonds, ionic bonding
Hydrogen bonding
Formed when a hydrogen bond is in between 2 highly electronegative atoms (F, N, O) in the same molecule
Hydrophobic interactions
Interactions between nonpolar molecules in water and in their low solubility. Forces nonpolar sidechains together
van der Waals interactions
weak intermolecular forces that happens when adjacent molecules are close together. Further stabilizes nonpolar sidechains and increase the stability of the protein
Covalent bonding
equal sharing of electrons between 2 atoms to make them both stable.
Disulfide bonds
Covalent bond between two sulfur atoms, typically in the side chains of certain amino acids.
Ionic bonding
bonds that may form between groups that have full and opposing charges.
Quaternary structure
Overall three deminsional shape formed from the combination of two or more polypetide chains.
Macromolecular machines
Complexes of multiple proteins that assemble to carry out a particular function
Denatured
unfolding or breaking up of a protein, modifies the standard three dimensional figure.
Molecular chaperones
faciliates the folding or refolding of a protein into its correct three dimensional shape
Prions
Proteinaceous infectious particles
catalyst
Any substance that increases the rate of a chemical change without itself undergoing any permanent chemical change
enzyme
protein that functions as a catalyst
structural proteins
make up body components such as fingernails and hair
Movement
Motor proteins and contractile proteins are responsible for moving the cell itself
Signaling
Proteins are involved in carrying and receiving signals from cell to cell inside the body
Transport
Proteins allow particular molecules to enter and exit cells or carry them throughout the body
Defense
Proteins called antibodies attack and destroy viruses and bacteria that cause disease.
Substrates
Reactant that interacts with a catalyst such as an enzyme in a chemical reaction
