Biochem Final part 1 Flashcards
Hydrophobic
water-fearing
hydrophobic effect
the energetic preference of nonpolar molecular surfaces to interact with other nonpolar molecular surfaces and thereby to displace water molecules from the interacting surfaces
Hydrophilic
water-loving
Amphoteric
they can react either as acids or bases, depending on the circumstances
Isoelectric point
the pH at which the net electric charge is zero
zwitterion
a functional group molecule in which at least one has a positive electrical charge and one a negative electrical charge.
primary structure
covalent bonds linking amino acid residues in a polypeptide chain
secondary structure
recurring structural patterns
-ɑ-helix, β-sheets, β-turn, random coils
tertiary structure
3D folding of polypeptide
-determined by amino acid sequence
-hydrogen bonds between nearby amino acid residues
- salt bridges
quaternary structure
2+ polypeptide subunits
protein domain
part of a polypeptide chain that is independently stable or could undergo movements as a single entity
motif
recognizable folding pattern involving 2+ elements of 2° structures & the connection(s)
b-a-b loop or b barrel
Intrinsic disorder proteins
-Lack of definable structure
-Often lack a hydrophobic core
-High densities of charged residues (Lys, Arg, Glu) and Pro
-Facilitates protein interactions with multiple binding partners
Denaturation
loss of three-dimensional structure sufficient to cause loss of function
- can happen by heat, pH extremes, detergents, strong acids/bases, organic solvents
native conformation
the arrangement of all atoms contained in the protein in a conformation that is stable and functional
thermodynamically the most stable, therefore, lowest free energy
enzyme
A biomolecule, either protein or RNA, that catalyzes a specific chemical reaction
substrate
the molecule that is bound to the active site and acted upon by the enzyme
Active site
provides a specific environment in which a given reaction can occur more rapidly
allosteric site
an effector binding site within enzymes, distinct from the active site, that
allows molecules to either activate or inhibit (or turn off) enzyme activity
Pre-steady state
the initial transient period during which ES builds up
steady state
the period during which [ES] and other intermediates remain constant
Saturation effect
occurs at Vmax, when virtually all the enzyme is present as the ES complex
- Further increases in [S] do not affect rate
Km vs Kcat
Km: Michaelis constant, characteristic of the enzyme and the substrate under s[ecific conditions
Kcat: limiting rate of any enzyme-catalyzed reaction at saturation
V0 vs Vmax
V0: initial velocity
Vmax: maximum velocity
Stereoisomer
each of two or more compounds with the same molecular formula,
differing only in the spatial arrangement of their atoms
enantiomer
stereoisomers that are mirror images
diastereomer
stereoisomers that are not enantiomers (D (OH to the right) and L(OH to the left))
aldose
sugar with the carbonyl group is at the end of the carbon chain (in an aldehyde group)
Hemiacetal (/hemiketal)
Ring formation that occurs because aldehyde and ketone groups react reversibly with hydroxyl groups in an aqueous solution
ketose
sugar with the carbonyl group is at any other position (in a ketone group)
acetal (/ketal)
Glycoside formation: hemiacetals and hemiketals react with alcohols to form the corresponding acetal and metal - no OH instead two OR groups
pyranose
six-membered rings are pyranoses ex: fructose (monosaccharide cyclization)
furanose
Five-membered rings are called furanoses
Anomer (alpha and beta)
The two possible diastereomers that form because of cyclization
are called anomers; up (above ring, β) or down (below ring, ɑ)
