Test One cont Flashcards
what does phenylisothiocyanate do
reacts with the alpha amino group on the amino terminal
mucines are synthesized by
tracheobronchial, GI and genitourinary tract
how does Ion-Exchange chromatography work
uses anion or cation charged beads to attract opposite charge and let other molecules go through solution
thrombin can hydrolyze
peptide bond on carboxyl side of arg
when his is changed to ser in fetus what does it reduce
affinity to 2,3-BPG
what are the two models about states in hemo
concerted and sequential
uncom inhib and Km
decrease
what is a phospatidate
fatty acid, glycerol, phosphate
what type of protein structure is formed when distant amino acids interact through weak bonds
tertiary
glycolipid structure contains what instead of alcohol
sugar unit
glucose or galactose
what are the enzymes called for the assembly of polysaccharides
glycosyltransferases
glycoproteins units are called what
glcosaminoglycans
competitive inhibitors
inhibitor reduces number of enzyme molecules available for substrate
what are the side chain in the structure of hemoglobin
methyl, venyl, and propionate side chains
misfolding in sickle cell anemia causes
aggregation process
who discovered misfolded proteins
prusiner
when Km is low
enzyme has more affinity to substrate
what are glycoconjugates
glycoproteins
proteoglycans
glycolipids
why does the pocket in R state disappear
structural transformation
what are proteolytic enzymes
break peptide bonds using water
also hydrolyze ester bonds
what is replaced in fetus for hemoglobin
beta chain replaced by gamma chain
name of heme group
Fe-protoporphyrin IX
hyalurona ex of
GAG, proteoglycan
non sulfated
part of extracellular matrix
peripheral membrane proteins
bound mostly by electrostatic interactions with H bonds
can enzymes change the equilibrium of the reaction they catalyze
no but they can help reach equilibrium faster
how to determine D or L configuration in aldoses and ketoses
look at last OH group
L for Left side
D for right side
what configuration is all the Aldoses in
D
what enzyme is present if type B blood
glycosol transferase B
what is an intrinsically unstructured protein
no distinct 3D region
assume a definite 3D structure upon interaction with other proteins
erythropoietin
glycoprotein hormone secreted by kidney and stimulate production of RBC when O2 level low
w/o glycosylation, hormone can only function at 10% of activity
more substrate means
faster the enzymatic reaction
epimers
isomers where the H and OH are flipped on one or more carbon atom
why can hemoglobin carry oxygen better than myoglobin
has 4 peptides, myo only one
binds oxygen cooperatively meaning the binding of oxygen to one site will aid in binding to other sites more efficiently
what three interactions help the lipid membranes
hydrophobic
van der waals
hydrogen bonds
Km
is the concentration of the substrate at which the reaction velocity is half of the max
how does the entire glycosylation process take place
attaching entire glycosyl unit on a specialized lipid molecule called dolichol phosphate
penicillin binds to
transpeptidase, inhibits cell wall synthesis
why use SDS in gel electrophoresis
help break non covalent bonds
3 types of membrane lipids
phospholipids
glycolipids
cholesterol
what aa is changed into for hemoglobin in fetus
his to ser
looser packing in lipids means
less hydrophobic
sugars have to be what in order to react
activated
what type of functional group is a sphinosine
amino alcohol
4 components of phospholipids
one or more fatty acids
platform to which fatty acids attach to
phosphate
alcohol
statin
help reduce cholesterol by comp inhib key enzyme in cholestrol biosynthetic pathway
competitive inhibitors and Km
increase Km
function of chromatography
molecules interact differently with the stationary phase and mobile phase, thus can be separated from the rest
what is happening in relaxed state of hemo
looser subunits, more free O can bind but harder to release
what happens to proximal histidine in heme group
oxygen binds to it causing plane to change and overall tertiary structure
uncompetitive inhibitor
bind to enzyme substrate complex, binding site created only on complex
the transition state molecule is the least-_____ but highest in ____
stable
free energy
what type of structure do membranes of lipids have
sheet like, 2 molecules thick
lipid function in cell
fuel
store energy
signal transduction messenger
part of membrane
what are the two structural form of hemoglobins
tense and relaxed
what are the three factors that affect fluidity in membrane
length of fatty acid
degree of unsaturation
cholesterol molecules
first histidine location in heme group is
proximal
ex of uncomp inhibitor
lithium and phosphoinositide cycle
what does the enzyme not affect
difference in free energy between substrate and product
function of enzymes
lower activation energy or facilitate the formation of the transition state
uncom inhib and velocity
decrease
who invented chromatography
Mikhail Tsvet
at low pH (high H+) hemoglobin tends to
release oxygen better
what are polysaccharides
glucose homopolymers
disaccharide heteropolymers
trypsin can hydrolyze
peptide bonds for both Arg and Lys
so when glutamine is substituted by val what happens
val will interact with phe and val on beta chain causing misfolding
proteoglycans
carb constitute higher % of total weight
why are misfolded proteins deadly
they are infectious, influence other proteins to misfold
what are monosaccharides
aldehydes and ketones with OH groups
small molecules composed of 3 to 9 carbon
what are metamorphic proteins
exist is different 3D structures that are usually in equilibrium with each other
aspirin binds to
cyclooxygenase, reducing synthesis of signaling molecules
what is happening in tense state of hemo
chains interacting closely, O is hard to bind but easy to release
what are cofactors
helper chemical to enzymes
what type of substitution occurs in sickle cell anemia
hydrophilic to hydrophobic
proteins and phospholipids can mover across membrane by
lateral motion
transversing (only phospholipids) aka flip flop takes a few hours
what enzyme is present in type A blood
glycosol transferase A
structure of hemoglobin
four pyrrole rings linked by methine bridges to form tetra pyrrole ring
Fe in center bound to 4 N from rings
what is reversible inhibition
they dissociate relatively quickly
comp, uncomp, mixed
mucines (mucoproteins)
mostly carb attached to protein through threonine and/or serine
at high CO2 concentration, the pH will be lower so the H+ concentration will be
high
what carb is usually in proteoglycans
GAG
function of mucine
protect cells against different environmental factors such as infection and chemical inhalation
large polymrs
which type of fate has the least hydrophobic interaction
oil
how does chromatography work
protein mixture added to porous gel matrix, small protein move through all the pores being slow and large proteins move faster
protein folding takes place as a what type of process
cooperative
the regulation of oxygen binding by hemoglobin is also regulated by
hydrogen ions and CO2
at high CO2 concentration, hemoglobin is likely to be in what conformation
tense
what type of effector is 2,3-BPG
allosteric, bind to hemo in different site from oxygen
in sickle cell anemia what aa is substituted
glutamine for valine on alpha chain
what denaturants reduce disulfide bonds
beta-mercaptoethanol
can enzymes catalyze impossible reactions
no
what is the function of distal histidine in heme group
prevents superoxide anion from leaving with electron
what does phosphorylating do to sugars
make them anionic, cannot cross membrane, not recognized by transporters
how can the competitive inhibitor be relieved
increase substrate concentration
heparin ex of
proteoglycan, GAG
used for anticoagulant
what is the substrate of prostaglandin H2 synthase-1
arachidonic acid
hydrophobic and cant leave membrane without binding to active site of protein
what is desalting
molecules moving from higher conc to lower conc
large particles stay in tubing
tubing put into buffer solution
what are GAG
large repeating units of modified disaccharides such as amino sugars and uronic acids
resistant to compression
what aa has glycosylation take place on
asparagine
serine
threonine
binding energy
the energy released upon the substrate binding to the active site of enzyme
mixed inhibitors
can bind simultaneously with substrate to enzyme, reduction of amount of functional enzyme
cannot be relieve by adding more sub
what are the membrane proteins
peripheral and integral
what is needed to break disulfide bonds in gel electrophoresis
beta-mercaptoethanol
how does H+ and pH affect oxygen binding i hemoglobin
the imidazole group of histidine either becomes charged or no charge and interacts with aspartate aa
what type of bond connects fatty acid to glycerol back bone
ester bond
furan is involved with
keto-hexoses
at high pH (low H+) hemoglobin tends to
not release oxygen
what are the two cofactors
metals and organic (coenzymes)
what happens when CO2 binds to N termini of peptide bond
forms negatively charged carbamate ion
hurler disease
accumulation of proteoglycans bc they are not degraded
function of agarose gel electrophoresis
DNA standards will allow researchers to estimate the size and concentration of unknown DNA
what does the negatively charged carbamate ion do in hemoglobin
stabilize T state and releases more oxygen
what type of bond is between active site and substrate
non covalent bond
what is phosphorylating sugars
key step in retaining sugars inside the cell
function of ES complex
bring substrate to the optimum orientation for a productive reaction to take place
as proteins move through the lumen of ER they get….
N-glycosylated
what are hemoglobins components
2 alpha helices and 2 beta chains
binding: a1b1-a2b2
I-cell disease
enzymes missing for degradation of lysozome, enzymes were not properly glycosylated, secreted out into blood
debris remains in inclusion bodies
active site
substrate bind to enzyme
collection of different aa from different parts of the enzyme
what is irreversible inhibition
bind tightly to enzyme and dissociate very slowly
penicillin and aspirin
what are the 2 3D structures of lymphotactin
3 beta strands with alpha helix that binds to specific receptor
beta sheet that binds to glycosaminoglycan
holoenzyme
enzyme with cofactor
what are simple sugars
monosaccharide
disaccharide
oligosaccharide
proteins can absorb how much UV light if aromatic aa attached
280 nm
which bacteria has a thick peptidoglycan layer
gram positive
how do cells communicate to environment
proteins
how does the heme group stabilize after O is added to it
adding another histidine that forms H bond with O
what type of coenzymes are there?
prosthetic groups (tightly bound to enzyme) loosely associated with enzyme
what is the transition state
middle molecule between substrate and product
no longer sub but not yet product
mixed inhibitor and Km and Velocity
increase
what size fragments move faster in gel electrophoresis
smaller
fatty acids attach to sphinosine back bone by what bond
amide bond
what state of hemo is strongly favored
T state
why are aldoses reducing sugars
their free aldehyde group in the open configuration
oligosaccharides
monosaccharides linking with each other
alpha helix is characterized by
H bonds b/w amino acids on same strand with R groups projecting outward
what is added to to catabolic enzymes in golgi complex to make it to lysozome
mannose-phosphate
myoglobin is what type of protein
single polypeptide protein
pyran is involved with
aldo-hexoses
2 types of inhibition
reversible and irreversible
what happens with protein glycosylation in golgi complex
O-glycosylation
further modification of carb on protein
elaborating the N-glycosylated proteins
the is enzyme that glycosylate proteins with GlcNAc is called
GlcNAc transferase
what is the predominant acceptable model for membranes
the fluid mosaic model
at pH higher than 7.4 what happens to HIS in hemo
imidazole group loses charge and break interaction between asp aa, hold on to oxygen
membranes have what type of layer
lipid bilayers
what other aa is present in hemoglobin besides histidine
lysine
archea have what in their membrane that allows for harsher environment
ether bond instead of ester
methyl group instead of H (which allows for more interaction b/w fatty acid tails to create stronger bonds)
what does the active site create
a unique microenvironment tailored for specific substrates and specific reactions
what kind of curve is present for hemoglobin
sigmoidal
the Fe in heme group can bind to
histidine
how does PrP misfold
native structure of alpha helices transforms into large beta sheets
what molecules have a hard time getting through lipid membranes
polar
what molecule plays an important role in modulating o binding in hemoglobin
2,3-biphosphoglycerate (2,3-BPG)
where is sphingomyelin found
in myelin sheath
competitive inhibitor and velocity
not affected
methotrexate competes with what enzyme
dihydrofolate and binds to dihydrofolate reductase
Prusiner discovered what protein that is misfolded
PrP
at pH lower that 7.4 what happens to His in hemo
imidazole group becomes charged allowing it to react asp which stabilizes T state and releases O more efficiently
how does T state transform to R state
bonds between 2,3-BPG and hemoglobin must break, more oxygen pressure must exist
what does the specificity depend on for binding in active site
precise arrangement of atoms
hemoglobin and myoglobin bond in what type of manner
cooperative
what is gel electrophoresis
proteins separated by mass only using a detergent
use power source to drive protein from neg to pos side of gel
what does the enzyme affect
amount of free energy needed to initiate conversion of substrate to product
what is a cytokine
class of immune protein that bind to receptors on immune system cells to elicit specific immune responses
ex of membrane anchored protein
prostaglandin H2 synthase-1
function of carb
energy store, DNA and RNA synthesis
cell wall of bact and plant are oligosaccharides
link to protein and lipids to make more diverse
what is maximum velocity
saturation achieve
all enzymes are being occupied
what is the aa sequence for for glycosylation
n-x-s or n-x-t
carb are made of
monosaccharides
where does CO2 bind to hemoglobin
N termini of peptide chain
enzymes can catalyze reactions at a rate of
10^6
integral membrane proteins
interact exclusively with the hydrocarbon core
glycoproteins
proteins constitute higher % of total weight
what denaturants destroy weak bonds
Heat, urea, SDS, pH
glycosylation occurs where
ER
and golgi complex
who described the different parameters of enzymatic reactions
michaelis and menten
when is the maximum binding energy released
when substrate is in transition state
max interactions between active site and enzyme
function of hemoglobin
four polypeptide protein
carries oxygen from lungs to rest of body and CO2 and H+ back to lungs
ex of competitive inhib
methotrexate
dermatan sulfate ex of
proteoglycan, GAG
in skin, heart valves, blood vessels, tendon
preven infection, cardio disease, carcinogens
Lymphotactin is an example of
metamorphic proteins
cytokine
what kind of bonds between membranes of lipids
non covalent
what happens in beta-thalasemia
no beta chains, all alpha chains
alpha chains aggregate and precipitate leading to immature RBC
oxygen binding in hemoglobin is modulated by
CO2 and H+
glycosylation usually works with what
GlcNAc
glycoside mostly form what configuration
circular
apoenzyme
enzyme without cofactor
what are reducing sugars
aldoses
what happens in alpha-thalasemia
alpha chains not produced only 4 beta chains HbH
HbH binds tightly to O2 causing poor delivery to tissues
when Km is high
enzyme has less affinity to substrate
what site is responsible for lowering the activation energy
active site
inhibitors
molecules that can inhibit enzymes by different mechanisms
serve as control for enzymatic activity
where does 2.3-bpg bind in hemo
center during T state
what is the Bohr effect
how pH (h+) and CO2 affected binding of oxygen to hemoglobin
longer saturated fatty acid molecules have more hydrophobic interactions than shorter saturated fatty acid molecules
true
what is the term called that defines the difference between substrate and transition state
activation energy or gibbs free energy of activation
how can molecules pass through membrane
must shed interactions with water and form new ones with lipid core
what are the platforms in phospholipids that fatty acids attach to
glycerol
(phosphoglycerides)
sphingosine
(sphingolipids)
homopolymer
if a polysaccharide is composed of a single sugar
what are enzymes
biological catalyst
catalyze reactions at faster rates
what chemical is needed for edman degradation
phenylisothiocyanate
what does chromatography mean
color writing
