Biochemistry Flashcards
steps of the gabriel synthesis
deprotonation to anion
addition of R-Br
amide hydrolysis to a di-carboxyl
L
Leucine
cysteine
Cys
C
secondary structure
alpha helicies and beta sheets
immune system proteins
antigens and antibodies
are the R groups parallel or perpendicular in beta sheets
perpendicular
mannose
C6H12O6
negatively charged amino acids
aspartic acid
glutamic acid
sugars with the formula C3H6O3
glyceraldehyde
dihydroxyacetone
isomerases
rearrangements
charge below the isoelectric point
positive
Glycine
Gly
G
what is the preferred model of enzyme specificity
induced fit
what proton is donated first from an amino acid
COOH
R
arginine
characteristics of amino acids
alpha carbon stereocenter
absolute configuration
R group chemistry
C
cysteine
minerals
inorganic molecules essential for bone formation
isoelectric point of basic amino acid
amine and R group
galactose
C6H12O6
glutamic acid
Glu
E
can enzymes become saturated
yes
x intercept of lineweaver burke plots
-1/Km
T
threonine
ligases
large molecule synthesis
cell adhesion molecules are an example of
binding protein
isoprene
C5H8 with one C=C double bond on the end and one attached to C3
peptide bond formation
dehydration synthesis and acyl substitution
what enantiomer is found in the human body
D
what direction do amino acids flow
N –> C
what filaments are present in actin
thin and microfilaments
non-reducing sugar example
sucrose
charge above the isoelectric point
negative
sucrose
glucose+fructose
pka of acidic R groups
- 7 Asp
4. 5 Glu
lock and key model
active site of an empty enzyme is an exact fit for the substrate
terpenes
mostly conjugated unsaturated polymer of isoprene
polysaccharides
Cn(H2O)x
tertiary structure
geometric 3D folding on alpha helicies and beta sheets to form a globular/ structural protein
V
valine
isoelectric point of neutral amino acid
amine and carboxyl pKa
how is competitive inhibition overcome
increasing substrate concentration
pka of basic R groups
10.7 Lys
12 Arg
where does proline occur in an alpha helix
often the first residue, not found within the helix
what type of isomers are glucose and galactose
epimers
alpha linkages
linked through oxygen on the opposite plane from CH2OH
lipids
hydrophobic biomolecules
asparagine
Asn
N
monosaccharides
(CH2O)n
molten globule
partially folded
what is fibroin and what secondary structure does it have
silk
beta sheets
are coenzymes permanently attached to an enzyme
no
conjugated protein
associated with cofactors by covalent or intermolecular forces
what linkages attach a triacylglycerol
ester linkages
what are kinesins and dyneins used for
vesicles, cell division, cilia and flagella
mixed inhibition
inhibitor has unequal affinity for ES and E, favoring one over the other
lactose
glucose and galactose
what is keratin and what secondary structure does it have
found in hair and nails
alpha helix
transferases
functional group transfer
nonpolar amino acids
proline glycine alanine valine leucine isoleucine methionine
intramolecular nucleophilic substitution
ring closing reaction
how does competitive inhibition change Km
increases
H
histidine
isoelectric point separation
uses a gel with a stable pH gradient and protein moves through an increasing pH and will stop moving when pH is equal to pI
does the non-competitive inhibitor show preference for ES or E?
neither
beta glucose
OH up
how does mixed inhibition change Km
decreases when ES increases over E
increases when E increases over ES
isoelectric point
pH when a molecule has no net charge
[pka(1)+pka(2)]/2
are vitamins organic
yes
hydrolases
hydrolysis
how does competitive inhibition change Vmax
unchanged
M-M saturation curve
graph of reaction velocity versus substrate concentration
characteristics of an active site
contains amino acids that will associate with the substrate
triacylglycerol
glycerol backbone attached to r chain
are the positive amino acids acidic or basic?
basic
what filaments are present in tubulin
microtubules
solvation layers
layer of water surrounds a dissolved protein interaction with one another and the protein surface
oxidoreductases
redox reactions
example of positive cooperativity
hemoglobin
feedback inhibition
negative feedback
inhibition that applies to a multi-step synthetic pathway where a product later in the chain acts as an inhibitor for an enzyme in an earlier step
two protein separation techniques
isoelectric point
electrophoresis
are the R groups directed into or out of the helix
out of
how does mixed inhibition change Vmax
decreases
how many residues occur between alpha helicies
four
S
serine
strecker synthesis
aldehyde with NH3 and HCN add cyano and NH2 to the C
Add hydrogen ions and water for the amino acid
what type of isomers are D and L
enantiomers
positively charged amino acids
arginine
histidine
lysine
glycogen
alpha linkages, branched
animals
autocrine
self-target
substrate
molecule acted upon by an enzyme
quaternary structure
association of multiple folded proteins into a multi-subunit complex
salt bridges
acidic and basic R groups go through neutralization reactions resulting in salt formation
when is Km equal to [S]
half of Vmax
oligopeptide
small chain of amino acids
non-competitive inhibition
inhibitor binds away from the active site and changes the enzyme shape
triacylglycerol is the same as
triglycerides
transcription factors are an example of
binding protein
sulfur linkage
S-S between cysteines
I
isoleucine
are the negative amino acids acidic or basic?
acidic
forms of tertiary structure (6)
hydrogen bonding disulfide bonds hydrophobic/hydrophilic interactions ionic interactions van der waals interactions proline turns
lineweaver burke plots
double inverse plot of reaction rate (1/v) versus substrate concentration (1/[S])
Vmax
rate of reaction at saturation levels of substrate, theoretical maximum velocity
serine
Ser
S
cofactors
metal ions or small molecules that assist in catalysis
are prosthetic groups permanently attached to an enzyme
yes
what type of isomers are alpha and beta glucose
anomers
tryptophan
Trp
W
fatty acid
carboxyl attached to an R chain
proline
Pro
P
how are vitamins acquired
diet
fat soluble vitamins
A D E K
does a lower or higher pka lose a proton?
lower
positive feedback
product of reaction acts as an agonist to activate a receptor
arginine
Arg
R
histidine
His
H
what is the electrophile in an intramolecular nucleophilic substitution
Carbon with carbonyl
active site
section of the enzyme where the substrate is converted to product
methionine
met
M
glycolipids
sugars attached to lipids
reversible enzyme inhibition
inhibitor is not permanently bound and the enzyme is not completely disabled
ribose
C5H10O5
sphingolipid
fatty acid derivatives of shingosine
lysine
Lys
K
how does non-competitive inhibition change Vmax
decreases
positive cooperativity
ligand affinity increases with the binding of each subsequent ligand
tryosine
Tyr
Y
what filaments are present in elastin
connective tissue
protein folding
hydrophobic r groups fold into the core and hydrophilic are common on the surface
structural proteins
actin, tubulin, keratine, elastin
cellulose
beta linkages
plants
calmodulin is an example of
binding protein
what is the pka of a strong acid
lower
hemoglobin is an example of
binding protein
Km
michaelis constant
relative measure of an enzyme’s affinity for substrate
y intercept of lineweaver burke plots
1/Vmax
competitive inhibition
inhibitor binds at active site, inhibitor resembles substrate
initial velocity is equal to
[VmaxS]/[Km+S]
agonist
activates a receptor to a response
simple protein
contains only amino acids and no non-protein cofactors
uncompetitive inhibition
inhibitor binds only to the enzyme-substrate complex
lysases
cleavage
L configuration
OH on the left
enzyme-substrate complex
formed when the substrate is bound in the activated site and the substrate is catalyzed to product
G
glycine
molten
fully unfolded, denatured
deoxyribose
C5H10O4
alpha glucose
OH down
induced fit
active site changes as the substrate binds, increases affinity for the substrate and for the transition state (lowers Ea)
examples of lipids
fats, oils, waxes, steroids, glycerides
alpha helicies
hydrogen bonding between the carbonyl O and amide H
what are the exceptions of the L/S configuration of amino acids
glycine (not chiral)
cysteine
disulfide bonds
two oxidized cysteine residues (R-S-S-R)
between alpha helicies in keratin makes hair curly or straight
pka of NH3+
9
how does non-competitive inhibition change Km
unchanged
are minerals organic
no
is an enzyme or a general catalyst faster
enzyme
apoenzyme
simple enzyme
what charge will a protein have in a pH below the pI
positive charge
aspartic acid
Asp
D
are saturated or unsaturated molecules healthier
unsaturated
ketose
from a ketone
K
lysine
glutamine
Gln
Q
A
alanine
M
methionine
where are waxes found
coatings on leaves and stems
michaelis menten kinetics
M-M
hydrophobic core
hydrophobic R groups fold into the interior of a globular protein to escape water
troponin is an example of
binding protein
saponification
hydrolysis of an ester using KOH into a glycerol and an acid
what is the difference between kinesins and dyneins
direction
kinesins move from - to +, from the center to the periphery in a cell, from nerve to dendrite
how does uncompetitive inhibition change Km
decreases
pka of histidine
6
fructose
C6H12O6
glyceraldehyde
C3H6O3
Proteins
amino acid polymers
aldose
from an aldehyde
irreversible inhibition
inhibitor binds covalently to the enzyme and active site disabling the enzyme for a prolonged period of time, or permanently
leucine
Leu
L
is cellulose digestible by humans
no
D
aspartic acid
P
proline
how does uncompetitive inhibition change Vmax
increases
what does the strecker synthesis create
alpha-aminonitriles
glucose
C6H12O6
paracrine
immediate vicinity
zwitterion
+ and - functional groups cancel one another out
@ pH of 7.4 the COOH is COO- and NH2 is NH3+
polypeptide
longer chain of amino acids
what type of isomers are epimers
diastereomers
Valine
Val
V
deoxy
-OH is replaced by H
E
glutamic acid
beta linkages
linked through oxygen on the same plane as CH2OH
linkages used to attach glycolipids
glycosidic bond
R-O-CH2 of glycerol backbone
what linkages attach lactose
beta
what is the configuration of almost all amino acids
L and S
exceptions to zwitterion at pH of 7.4
charged R groups
allosteric enzymes
activity is influenced by the reversible, non-covalent binding of another molecule
maltose
glucose+glucose
reducing sugar
can reduce a free aldehyde or ketone group
all monosaccharides
what is the strongest type of protein folding interactions?
disulfide bonds
what is the nucleophile in an intramolecular nucleophilic substitution
OH on the chiral C
phenylalanine
Phe
F
isoleucine
Ile
I
are enzymes universal
no, specific
hydrophilic surface
surface R groups are polar or charged
polar amino acids
serine threonine cysteine asparagine gluamine
electrophoresis
separate based on size with the smallest traveling the farthest
what does mercaptoethanol do
reduce disulfide bonds
F
Phenylalanine
what is Km inversely proportional to?
E-S binding affinity
zymogen
inactive enzyme precursor that when activated, converts to the active form
beta sheets
hydrogen bonding beween the carbonyl O and amide H
how to irreversibly denature a protein
heat
where do resonance bonds form in a protein
carbonyl and nitrogen
why are zymogens important
important for enzymes needed quickly but that would be detrimental if active at all times
Y
tyrosine
N
asparagine
aromatic amino acids
phenylalanine
tryptophan
tyrosine
motor proteins
myosin, kinesins/dyneins
where does proline occur in a beta sheet
at the end to enable the 180° shift to the next row
electrostatic interactions
interactions between charged R groups
dihydroxyacetone
C3H6O3
starch
alpha linkages, branched
plants
vitamins
relatively small, organic molecules that are essential nutrients for metabolism
globule
fully folded
steroids
4 membered ring structures
phospholipids
polar head group (phosphate) attached to a triacylglycerol
protein denaturing agents
acid
heat
urea
mercaptoethanol
isoelectric point of acidic amino acid
R and carboxyl pKa
alanine
ala
A
furanose
5 carbons
D configuration
OH on the right
holoenzyme
enzyme and cofactors
waxes
ester of a long-chain (12-32 C) alcohol and a fatty acid
fatty acid-ester-alcohol
where are sphingolipids found
cell membrane of brain and nervous tissue
are enzymes organic or inorganic
organic
mercaptoethanol structure
HS-C-C-OH
sugars with the formula C6H12O6
glucose
fructose
galactose
mannose
what do alpha-aminonitriles do
intermediates in amino acid synthesis
residues
amino acids
prostaglandins
lipid mediators that have autocrine and paracrine functions in the body
example of a steroid
cholesterol
pyranose
6 carbon
what filaments are present in keratin
intermediate filaments
primary structure
amino acid sequence
pka of COOH
2
Threonine
Thr
T
Q
glutamine
what charge will a protein have in a pH above the pI
negative charge
what is myosin used for
cellular transport
histones are an example of
binding protein
W
tryptophan
