Amino Acids & Proteins Flashcards
what gives each amino acid its unique identity/physical & chemical properties?
it’s side chain or variable R group
what are the acidic amino acids that are deprotonated at physiological pH (negative charge)?
glutamic acid Glu E
aspartic acid Asp D
what are the 3 basic amino acids?
lysine Lys K
arginine Arg R
histidine His H
what distinguishes histidine from the other basic amino acids?
it has a pH of 6.5, very close to physiological pH so could be protonated or deprotonated (although 90% deprotonated)
what are the hydrophobic, nonpolar, aliphatic amino acids (5)?
glyince Gly G alanine Ala A valine Val V Leucine Leu L Isoleucine Ile I
what are the hydrophobic, nonpolar, aromatic amino acids? (2)
tryptophan Trp W
phenylalanine Phe F
what are the five polar amino acids (uncharged)?
serine Ser S threonine Thr T tyrosine Tyr Y asparagine Asn N glutamine Gln Q
what are the two sulphur containing amino acids?
cysteine Cys C
methionine Met M
what’s the main difference between Cys and Met?
Cys is polar while Met is nonpolar, and Cys can form disulfide bonds
what class does proline Pro P belong to?
nonpolar side chain, although it has unique consequences due to its bonding and ring structure
what are the 9 essential amino acids
Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan Valine
how are amino acids are amphoteric?
amino acids can act as acids or bases due to acidic carboxylic acid group and basic amino group
what is the state of the acidic group when the pH of the solution is less than the pKa of the acidic group?
the acidic group will be mostly in its protonated form
what is the state of the acidic group when the pH of the solution is greater than the pKa of the acidic group?
the acidic group will mostly be in its deprotonated form
ammonium group
when the amine is protonated or in its acidic group, NH3+ with a pKa between 9-10
zwitterion
a molecule with positive and negative charges in balance
isoelectric point (pI)
the pH at which a molecule is uncharged (zwitterionic)
how do you find the pI (isoelectric point) of an amino acid?
average the pKa’s of the two functional groups
peptide bond
the covalent bond that links amino acids together into polypeptide chains
disulfide bridges
covalent bonds between cysteine R-groups
what is the polypeptide backbone?
N-C-C-N-C-C
residue
an individual amino acid that is part of a polypeptide chain
thermodynamics states that free energy must decrease for a reaction to proceed spontaneously and that such a reaction will spontaneously move toward:
equilibrium
proteolysis/proteolytic cleavage
hydrolysis of a protein by another protein (cutting)
proteolytic enzyme/protease
the enzyme that does the cutting
proteolytic cleavage is a specific means of cleaving:
peptide bonds
where is the reducing environment?
inside of cells because cells possess antioxidants (chemicals that prevent oxidation reactions)
denatured
improperly folded proteins, usually non-functional
denaturation
the disruption of a protein’s shape without breaking peptide bonds
primary structure
the same as sequence
what are the results of the unique side chain or proline in a polypeptide chain?
1) the formation of a peptide bond with proline eliminates the only hydrogen atom on the nitrogen atom of proline, the absence of the NH bond disrupts the backbone hydrogen bonding the polypeptide chain
2) the unique structure of proline forces it to kink the polypeptide chain
due to the broken hydrogen bonding pattern, in which secondary structure is proline always absent?
alpha-helix
which secondary structure is favourable for a hydrophobic transmembrane region?
alpha-helix because all polar NH and CO groups in the backbone are hydrogen-bonded to each other and on the inside of the helix, nonpolar R groups can interact with the hydrophobic membrane interior. good for integral transmembrane proteins the lipid bilayer
are are beta-pleated sheets stabilized?
by hydrogen bonding between NH and CO groups in the polypeptide backbone, unlike in the alpha-helix, hydrogen bonding can occur between residues distance from each other in the chain or even on separate polypeptide chains
what drives the formation of tertiary structures?
interactions of R groups with each other and with the solvent (water)
hydrophobic effect
hydrophobic R groups tend to fold into the interior of the protein and hydrophilic R groups tend to be exposed to water on the surface of the protein
hydrolase
hydrolyzes chemical bonds (includes ATPases, proteases, and others)
isomerase
rearranges bonds within a molecule to form an isomer
ligase
forms a chemical bond (eg. DNA ligase)
lyase
breaks chemical bonds by means other than oxidation or hydrolysis (ex. pyruvate decarboxylase)
kinase
transfers a phosphate group to a molecule from a high energy carrier, such as ATP
oxidoreductase
runs redox reactions
polymerase
polymerization
phosphatase
removes a phosphate group from a molecule
phosphorylase
transfers a phosphate group to a molecule from inorganic phosphate
protease
hydrolyzes peptide bonds
reaction coupling
one very favourable reaction is used to drive an unfavourable one
how can ATP hydrolysis drive unfavourable reactions?
1) cause a conformational change in a protein
2) transfer a phosphate group from ATP to a substrate
how can enzyme catalyze unfavourable reactions?
by reaction coupling (a selective process)
active site
the region in an enzyme’s three-dimensional structure that is directly involved in catalysis (generally globular)
substrates
the reactants in an enzyme-catalyzed reaction
active site model
“lock and key” : substrate and active site are perfectly complementary
induced fit model
substrate and active site differ slightly in structure and the binding of the substrate induces a conformational change in the enzyme
how do enzymes accelerate the rate of a given reaction?
by helping to stabilize the transition state
recognition pocket
a pocket in the enzyme’s structure which attracts certain residues on substrate polypeptides
what is the nature of amino acids in the active site of enzymes that act on hydrophobic substrates?
the amino acid in the active site is also hydrophobic
what is the nature of amino acids in the active site of enzymes that act on hydrophilic substrates?
the amino acid in the active site is also hydrophilic
how does temperature influence enzymatic function?
as temperature increases, the thermal motion of the peptide and surrounding solution destabilizes its structure. if the protein denatures, it will lose its orderly structure and not be able to bind to the enzyme
how does pH influence enzymatic function
ionizable R groups can change charge depending on pH, this can decrease the affinity of a substrate for the active site, and if the pH deviates sufficiently, the protein can denature
cofactors
metal ions or small molecules that are required for the activity in many enzymes
coenzyme
when a cofactor is an organic molecule, these often bind to the substrate during the catalyzed reaction
covalent modification
groups that are covalently attached to proteins can regulate their activity, lifespan in the cell, or cellular location ex. kinase (activate or inactivate the enzyme), phosphorylase, phosphatase
proteolytic cleavage
many enzymes and other proteins are synthesized in inactive forms that are activated by cleavage by a protease
association with other polypeptides
some enzymes have catalytic activity in one polypeptide subunit that is regulated by association with a separate regulatory subunit
constitutive activity
means continuous or unregulated activity
allosteric regulation
the modification of active-site activity through interactions of molecules with allosteric sites on the enzyme
how can enzyme activity be regulated?
1) covalent modification
2) proteolytic cleavage
3) association with other polypeptides
4) allosteric regulation
what kind of bond binds the allosteric regulator to the allosteric site?
generally a noncovalent and reversible bond
enzyme kinetics
the study of the rate of formation of products from substrates in the presence of an enzyme
reaction rate V
the amount of product formed per unit time (mol/s)
what does reaction rate depend on?
concentration of substrate [S] and enzyme
if there is only a little bit of substrate, what is V proportional to?
the amount of substrate added
saturated
the point at which there is so much substrate, every active site is continuously occupied and adding more substrate doesn’t increase the reaction rate at all (V max)
what is V max a property of?
V max is specific to each enzyme at a particular concentration of that enzyme
Michaelis constant Km
the substrate concentration at which the reaction velocity is half of V max, it is unique for each enzyme-substrate pair and gives information on the affinity of the enzyme for its substrate
what does it mean if enzymes are said to bind substrates cooperatively?
it means that in such enzymes, the binding of substrate to one subunit modulates the affinity of other subunits for substrate
positive cooperativity
binding of a substrate to one subunit increases the affinity of the other subunits for substrate
negative cooperativity
the binding of a substrate to one subunit reduces the affinity of the other subunits for substrate
what is a quality all cooperative enzymes must have?
more than one active site
what kind of curve results from positive cooperative binding?
a sigmoidal curve
tense state
enzyme complex has a low affinity for substrate
relaxed state
when enzyme has grater affinity for substrate
what kind of interaction is cooperativity?
a special kind of allosteric interaction, but instead of an allosteric site, an active site acts like an allosteric regulatory site for the other active sites
competitive inhibitors
molecules that compete with substrate for binding at the active site
how can one overcome competitive inhibition?
by adding more substrate
describe the curve for competitive inhibitor
V max does not change, Km increases
noncompetitive inhibitors
bind to an allosteric site, no matter how much substrate you add, the inhibitor will not be displaced from its site of action
describe the curve for noncompetitive inhibitors
V max diminishes, does not alter Km; substrate can still bind to active site, but inhibitor prevents catalytic activity
uncompetitive inhibitor
binds to the allosteric site on the enzyme-substrate complex, and cannot bind before the substrate has been bound
describe the curve for uncompetitive inhibitor
decreases V max (limits the amount of available enzyme-substrate complex which can be converted to product) and decreases Km (enzymes and substrate cannot readily dissociate)
mixed-type inhibition
inhibitor can bind to either the unoccupied enzyme or the enzyme-substrate complex,
1) if enzyme has greater affinity for the inhibitor in its free form, the enzyme will have a lower affinity or the substrate (Km increases)
2) if enzyme-substrate complex has greater affinity for the inhibitor, the enzyme will have greater affinity for the substrate (Km decreases)
3) if enzyme has equal affinity towards inhibitor in both forms, it would actually be a noncompetitive inhibitor
* in each situation, V max decreases because inhibitor binds to an allosteric site and additional substrate cannot overcome inhibition
