BI 255 EXAM QUESTIONS AND ANSWERS
LATEST UPDATE
Polarity
a lack of electrical symmetry in a molecule; charge differences on opposite ends of a
structure; ex. polar molecule H2O, oxygen has partial neg. charge (more E.N.) and
hydrogen has partial pos. charge (less E.N.)
Hydrogen bonds
very weak bonds; occurs when a hydrogen atom in one molecule is attracted to the
electrostatic atom in another molecule
Electrostatic attraction
the force of attraction between opposite electric charges
Hydrophobic interactions
a type of weak chemical bond formed when molecules that do not mix with water come
together to exclude the water; polar groups arrange near the outside of the molecule to
form H-bonds with water; ex. hydrocarbons are nonpolar molecules that "stick together
in polar environments to avoid contact with water in the cell
Ionic bonds
weaker than covalent in presence of water; bonds are strong when dry, weak when wet
(water is always present in cell in biology, so it is weak)
Amino acids
a simple organic compound containing a central carbon atom, R group, a carboxyl (—
COOH) and an amino (—NH2) group; 20 different types of amino acids each with
different chemical properties; at physiological (cellular) pH, the amino and carboxyl
groups are charged; sequence contains all the info. needed for specifying the 3D shape
of a protein
Energetically favorable
hydrolysis; doesn't require ATP (or GTP)
Energetically unfavorable
condensation; requires ATP (or GTP)
Condensation reactions
result in the formation of a covalent bond (peptide bond) between two monomers with
the release of a water molecule; energetically unfavorable, requires ATP; bond is
formed from the oxygen in the carboxyl group and hydrogens in amino group come
together and are released as water, allowing the C-N bond to form
Hydrolysis reaction
a chemical reaction that breaks apart a larger molecule by adding a molecule of water;
energetically favorable and does not require ATP because it releases energy; occurs
when peptide bonds are broken as an H-atom from water attaches to an amino group of
one amino acid, and the hydroxyl group from water attaches to the carboxyl group of the
other amino acid
ATP Energy stored in terminal phosphate
, breakage of the bond between the last two phosphates releases energy which the cell
can use to drive other processes; bond is broken due to enzymes called ATPases which
hydrolyze the terminal phosphates covalent bond
Peptide bond
covalent chemical bond that forms between the carboxyl group of one amino acid (C)
and the amino group of another amino acid (N) to form a protein; sequence of
chemically different side chains makes each protein distinct
Polypeptides
long polymers of amino acids linked by peptide bonds (not flexible); C-C bonds allow
rotation, flexibility of long molecules, very bendy
R groups
produce structural variability; determine folding of the protein, and folding determines its
function; non-polar side chains, polar side chains (mix well with water), electrically
charged side chains (acidic/basic)
Primary structure
unique for each protein, as determined by the gene that encodes that protein
Secondary structure
stretches of polypeptide chain that forms an alpha-helix and beta-sheets that are
common folding patterns; common because they result from hydrogen bonding between
the N-H and C=O in a polypeptide backbone without involving side chains; produce a
rigid structure held together by hydrogen bonds
Tertiary structure
full 3D organization of a polypeptide chain and amino acid interactions result in entire
molecule starting to fold and these interactions (H-bond, ionic bond, hydrophobic
interactions) are what stabilize the folded structure; R group interactions result in tertiary
structure
Quaternary structure
more than 1 polypeptide chain and not every protein has a quaternary structure;
polypeptides are held together by strong and weak bonds
Protein's shape determines function
proteins confirmation can change when it interacts with other molecules in the cell; even
a change of a few atoms in 1 amino acid can sometimes disrupt the structure of the
whole molecule so bad that all function is lost
Alpha-helix formation
formed when a single polypeptide chain twists around itself to form a rigid cylinder; H-
bond forms between every 4th peptide bond, linking C=O to N-H
Humidity alters keratin hydrogen bonds
ex. hair: water around hydrogen bonds start to compete, so water starts to form bonds
with H bonds of keratin in hair which reforms the shape of straightened hair
Question: Why are hair conditioners oil-based?
Oil in hair makes hair less puffy because the oil prevents interaction with water in hair;
oil barrier is non-polar (hydrophobic), so it does not mix well will with polar water, so it
helps maintain hair shape
Hydrophobicity & Hydrophilicity in protein folding
proteins fold into lowest energy conformation; polypeptide folds in aqueous (water-
based) environment; polar side chain is one the outside of the molecule to form
LATEST UPDATE
Polarity
a lack of electrical symmetry in a molecule; charge differences on opposite ends of a
structure; ex. polar molecule H2O, oxygen has partial neg. charge (more E.N.) and
hydrogen has partial pos. charge (less E.N.)
Hydrogen bonds
very weak bonds; occurs when a hydrogen atom in one molecule is attracted to the
electrostatic atom in another molecule
Electrostatic attraction
the force of attraction between opposite electric charges
Hydrophobic interactions
a type of weak chemical bond formed when molecules that do not mix with water come
together to exclude the water; polar groups arrange near the outside of the molecule to
form H-bonds with water; ex. hydrocarbons are nonpolar molecules that "stick together
in polar environments to avoid contact with water in the cell
Ionic bonds
weaker than covalent in presence of water; bonds are strong when dry, weak when wet
(water is always present in cell in biology, so it is weak)
Amino acids
a simple organic compound containing a central carbon atom, R group, a carboxyl (—
COOH) and an amino (—NH2) group; 20 different types of amino acids each with
different chemical properties; at physiological (cellular) pH, the amino and carboxyl
groups are charged; sequence contains all the info. needed for specifying the 3D shape
of a protein
Energetically favorable
hydrolysis; doesn't require ATP (or GTP)
Energetically unfavorable
condensation; requires ATP (or GTP)
Condensation reactions
result in the formation of a covalent bond (peptide bond) between two monomers with
the release of a water molecule; energetically unfavorable, requires ATP; bond is
formed from the oxygen in the carboxyl group and hydrogens in amino group come
together and are released as water, allowing the C-N bond to form
Hydrolysis reaction
a chemical reaction that breaks apart a larger molecule by adding a molecule of water;
energetically favorable and does not require ATP because it releases energy; occurs
when peptide bonds are broken as an H-atom from water attaches to an amino group of
one amino acid, and the hydroxyl group from water attaches to the carboxyl group of the
other amino acid
ATP Energy stored in terminal phosphate
, breakage of the bond between the last two phosphates releases energy which the cell
can use to drive other processes; bond is broken due to enzymes called ATPases which
hydrolyze the terminal phosphates covalent bond
Peptide bond
covalent chemical bond that forms between the carboxyl group of one amino acid (C)
and the amino group of another amino acid (N) to form a protein; sequence of
chemically different side chains makes each protein distinct
Polypeptides
long polymers of amino acids linked by peptide bonds (not flexible); C-C bonds allow
rotation, flexibility of long molecules, very bendy
R groups
produce structural variability; determine folding of the protein, and folding determines its
function; non-polar side chains, polar side chains (mix well with water), electrically
charged side chains (acidic/basic)
Primary structure
unique for each protein, as determined by the gene that encodes that protein
Secondary structure
stretches of polypeptide chain that forms an alpha-helix and beta-sheets that are
common folding patterns; common because they result from hydrogen bonding between
the N-H and C=O in a polypeptide backbone without involving side chains; produce a
rigid structure held together by hydrogen bonds
Tertiary structure
full 3D organization of a polypeptide chain and amino acid interactions result in entire
molecule starting to fold and these interactions (H-bond, ionic bond, hydrophobic
interactions) are what stabilize the folded structure; R group interactions result in tertiary
structure
Quaternary structure
more than 1 polypeptide chain and not every protein has a quaternary structure;
polypeptides are held together by strong and weak bonds
Protein's shape determines function
proteins confirmation can change when it interacts with other molecules in the cell; even
a change of a few atoms in 1 amino acid can sometimes disrupt the structure of the
whole molecule so bad that all function is lost
Alpha-helix formation
formed when a single polypeptide chain twists around itself to form a rigid cylinder; H-
bond forms between every 4th peptide bond, linking C=O to N-H
Humidity alters keratin hydrogen bonds
ex. hair: water around hydrogen bonds start to compete, so water starts to form bonds
with H bonds of keratin in hair which reforms the shape of straightened hair
Question: Why are hair conditioners oil-based?
Oil in hair makes hair less puffy because the oil prevents interaction with water in hair;
oil barrier is non-polar (hydrophobic), so it does not mix well will with polar water, so it
helps maintain hair shape
Hydrophobicity & Hydrophilicity in protein folding
proteins fold into lowest energy conformation; polypeptide folds in aqueous (water-
based) environment; polar side chain is one the outside of the molecule to form
