Lecture 7: The Amino Acids Flashcards
__ are the most versatile biomolecules
proteins
proteins tend to function as __ (enzymes)
catalysts
besides catalysts, provide 3 more functions of proteins
- mechanical support
- generate movement
- control growth
DNA is a relatively __ carrier of information, mostly for genes that code for __
inert; proteins
proteins are __ polymers made of monomers
linear
what are the monomers of proteins?
amino acids
what determines the 3-D shape of proteins?
amino acid sequence
the function of the protein relies on the __ of the protein
shape
aside from shape, what accounts for the wide array of protein functions?
functional groups
proteins can interact with each other to form __
complex assemblies
what is a possible benefit of forming a complex assembly rather than remaining as a single protein?
typically more or different capabilities
what characteristic of proteins makes them good structural elements?
they are rigid
proteins with some flexibility can act as __ , __ or __ involved in protein function or assembly of protein complexes
hinges, springs, levers
the primary structure of proteins
amino acid sequence
the secondary structure of proteins
discrete regions of higher order structure (alpha helix, beta sheets)
the tertiary structure of proteins
higher order folding of secondary structures
the quaternary structure of proteins
multi-protein (subunit) assemblies
why is the chemistry of amino acids relevant (3)
- determines structure, which determines function
- mediate interactions between proteins and molecules
- help catalyze chemical reactions in the active site of enzymes
all amino acids contain an alpha carbon attached to __ (4)
- amino group
- carboxylic acid group
- hydrogen
- side chain
the amino and carboxyl group can be __ depending on the surrounding pH
ionized
at physiological pH: the amino group will be __ and the carboxyl will be __
protonated; deprotonated
amino acids at physiological pH exist mostly in the __ form
zwitterionic
what is a chiral molecule?
not superimpossable on its mirror image and has at least one chiral centre
which chiral isomer is the only one used for making proteins? (R/L)
L
the CORN rule can be used to determine ___ in amino acids
R/L consiguration
using the corn rule, the cw direction is the ___ isomer
D
using the corn rule, the ccw direction is the __ isomer
L
the hydrophobic amino acids have __ R groups
nonpolar
the polar amino acids have __ R groups where the charge is ___ distributed
neutral; unevenly
positively charged amino acids have ___ R groups at pH 7
positively charged (ionic)
negatively charged amino acids have __ R groups at pH 7
negatively charged (ionic)
what three factors are important to consider with side chains?
- are there polar groups
- are they ionizable
- size
what is an ampiphatic molecule?
has both hydrophillic and hydrophobic parts
the larger the hydrocarbon, the ___ hydrophobic
more
hydrophobic R groups are hydrophobic, but Phe, Trp, and Tyr can form ___ interactions
van der waals
protein folding patterns are driven by ___
the hydrophobic effect
the polar neutral side chains contain a ___ that hoards electrons
heteroatom (O,N,S)
most neutral polar side chains are typically ___
unreactive
which neutral polar amino acid has an ionizable OH group?
tyrosine
negatively charged amino acids are also called __ amino acids
acidic
negatively charged amino acids have what type of side chain at pH 7?
deprotonated carboxyl group
positively charged amino acids are also called __ amino acids
basic
histidine has an imidazole group with pka =6, making both forms abundant at pH 7, therefore it is chemically ___
versatile
histidine is often found in the active sites of enzymes where the imidazole ring can bind and ___
release H ions in enzymatic reactions
the 7 amino acids with ionizable side chains play important roles in the active sites of
active sites of enzymes
amino acids which have a direct role in catalysis are called ___ amino acids
catalytic
amino acids that have an accessory role in catalysis are called __ amino acids
active site
when the pH > pka
unprotonated (basic)
when the pH
protonated (acidic)
the hydrophobic side chains are neither ___ nor ___, therefore water molecules cannot interact with them
charged; polar
hydrophobic side chains typically do not take part in __ or __
interactions; chemical reactions
amino acids mediate the interactions between what three pairs?
- protein–protein
- protein–nucleic acid
- Substrate–enzymes
what 4 interaction types are used by amino acids?
van der waals, dipole-dipole, charge-charge, stacking
what are essential amino acids?
amino acids which cannot be made and must be obtained from the diet
