Biochem 1 Flashcards
in an amino acid, a N-terminus is a nucleophile or electrophile? how about the C-terminus
n: nucleophile
c: electrophile
most amino acids are _____-conformation
what are the 2 exceptions to this rule
S-conformation
glycine and cysteine
what is the N terminus in an amino acid
the H3N+
what is the C terminus in an amino acid
the double bonded O and the single bonded O-
what is the R group in an amino acid
it is the one that determines the amino acid chemistry
how a protein folds
whether a substrate binds in an active site
reaction mechanisms in the enzyme packet
what is the difference between an amino acid and amino acid residue
AA: contains both N and C terminus; it is a stand alone
AA residue: contains R group; does not contain both N/C terminus; part of a polypeptide chain
what are the acidic polar amino acids
aspartate (Asp) and glutamate (Glu) (aspartic acid and glutamic acid)
what is the pka of the acidic amino acids
4
what are the basic amino acids, with their pka
histidine (H) - 6
arginine (R) - 12
lysine (K) - 11
think: H,R,K (hritik is basic)
what are the polar uncharged amino acids
serine
threonine
asparagine
glutamine
what are the normal hydrophobic amino acids
phenylalanine
tyrosine
tryptophan
nonpolar amino acids are?
all aliphatic amino acids, methionine, tryptophan and phenylalanine
neutral polar amino acids are?
alcohols, amides, cysteine, tyrosine
cysteine
asparagine
tyrosine
threonine
glutamine
serine
what is the difference between essential and nonessential amino acids
essential: AA that body CANNOT synthesize
nonessential: AA that body CAN synthesize
what is a zwitterion amino acid
AA with a + and - charge
what is the isoelectric point
the pH at which a protein/polypeptide is electrically neutral (positive charges = negative charges)
if the isoelectric point is neutral, what does that mean in terms of basic and acidic amino acid
equal amount of acidic and basic amino acids
if the isoelectric point is acidic, what does that mean in terms of basic and acidic amino acid
there are more acidic amino acids than basic AA
if the isoelectric point is basic, what does that mean in terms of basic and acidic amino acid
there are more basic amino acids than acidic AA
think in terms of hydrolysis: what is trypsin and chymotrypsin?
t: hydrolyzes after basic AA (R,H,K)
C: hydrolyzes after aromatic AA (F,W,Y)
what role does acid play as a denaturing agent
affects the charge state of charged AA
what role does heat play as a denaturing agent
breaks H bonds and discipline bonds
what role does urea play as a denaturing agent
competes with and disrupts H bonds in proteins
what role does mercaptoethanol play as a denaturing agent
disrupts disulfide bonds
what happens to mesophilic proteins at high temperatures
they become denatured due to a loss of hydrogen bonding
the PDH (pyruvate dehydrogenase complex) is naturally inhibited by ATP because: (what causes the feedback inhibition)
PDH product generates ATP via citric acid cycle
what does acetylcholine control in behavior
voluntary muscle control, parasympathetic nervous system, attention, and alterness
what do epinephrine and norepinephrine control in behavior
fight-flight responses, wakefulness, alertness
what does dopamine control in behavior
smooth movements, postural stability
what does serotonin control in behavior
mood, sleep, eating, dreaming
what does GABA control in behavior
brain ‘stabilization’
what do endorphins control in behavior
natural painkillers
are aliphatic amino acids polar or nonpolar?
nonpolar
are aliphatic amino acids hydrophobic or hydrophilic?
hydrophobic
what is the sentence used for aliphatic amino acids?
what are they?
Glaciers in Alaska Valiantly Locate Isolated Prowlers
Glycine, Alanine, Valine, Leucine, Isoleucine, Proline
what are the aromatic amino acids
tryptophan, phenylalanine, tyrosine
what is the term used to remember the alcohol amino acids?
what are they?
alcohol is a Serious Threat
Serine, Threonine
what is the term used to remember the basic amino acids?
what are they?
basically, His Lost kid Always returned
Histidine, Lysine, Arginine
what is the term used to remember sulfur-containing amino acids?
what are they
Methodically Check for sulfur
Methionine, Cysteine
what are the acidic amino acids
glutamic acid, aspartic acid
glutamte/aspartate
what are the amide amino acids
asparganine and glutamine
what does a phosphate do
enzyme that removes a phosphate group from its substrate
which amino acids can be phosphorylated
serine and threonine
the alcohols
Which amino acid contains an unbranched alkyl side chain?
alanine
which amino acid is not chiral
glycine
do humans have more L or D amino acids
L is more naturally occuring
what is the average weight of an amino acid
110Da
what does a Hill’s coefficient tell you
(less than 1 or greater than 1)
less than 1 or equal to 1: does not demonstrate cooperativity
greater than 1: demonstrates cooperativity
in the citric acid cycle, how many molecules of NADH and FADH2 are generated
2 molecules of NADH and one molecule of FADH2 are generated
looking at Km, which would have the highest catalytic efficiency?
ex. 10^-6
10^-5
10^-4
10^2
10^-6
the highest catalytic efficiency = low Km bc the efficiency would be Kcat/Km
synthetase vs synthase
synthases do not use energy from nucleoside triphosphates (such as ATP, GTP, CTP, TTP, and UTP), whereas synthetases do use nucleoside triphosphates
what is the result of the pentose phosphate pathway
NADPH
catabolism vs anabolism
c: breaking down of a bigger molecule into smaller ones (releases energy)
a: builds molecules required for the body’s functionality (requires energy)
is NADPH utilized in anabolic or catabolic? how about NADH?
which is oxidative/reductive
NADH is mainly involved in catabolic reactions whereas NADPH is involved in anabolic reactions.
NADH is less abundant in the cell, while NADPH is more abundant in comparison to their oxidized forms. (NADPH-reductive, NADH-oxidative)
If there a sugar that needs to be classified as D or L, how do you know which is it
There should be an OH group (most bottom one)
if that is on the left, its L
if that is on the right, its D
if delta G is negative, is the reaction exothermic or endothermic
exothermic
if delta G is positive, is the reaction exothermic or endothermic
endothermic
which amino acids are positively charged
HRK (basic)
which amino acids are negatively charged
D,E (acidic)
