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Biochem summer > Test One cont > Flashcards

Test One cont Flashcards

1
Q

what does phenylisothiocyanate do

A

reacts with the alpha amino group on the amino terminal

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2
Q

mucines are synthesized by

A

tracheobronchial, GI and genitourinary tract

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3
Q

how does Ion-Exchange chromatography work

A

uses anion or cation charged beads to attract opposite charge and let other molecules go through solution

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4
Q

thrombin can hydrolyze

A

peptide bond on carboxyl side of arg

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5
Q

when his is changed to ser in fetus what does it reduce

A

affinity to 2,3-BPG

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6
Q

what are the two models about states in hemo

A

concerted and sequential

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7
Q

uncom inhib and Km

A

decrease

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8
Q

what is a phospatidate

A

fatty acid, glycerol, phosphate

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9
Q

what type of protein structure is formed when distant amino acids interact through weak bonds

A

tertiary

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10
Q

glycolipid structure contains what instead of alcohol

A

sugar unit

glucose or galactose

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11
Q

what are the enzymes called for the assembly of polysaccharides

A

glycosyltransferases

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12
Q

glycoproteins units are called what

A

glcosaminoglycans

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13
Q

competitive inhibitors

A

inhibitor reduces number of enzyme molecules available for substrate

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14
Q

what are the side chain in the structure of hemoglobin

A

methyl, venyl, and propionate side chains

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15
Q

misfolding in sickle cell anemia causes

A

aggregation process

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16
Q

who discovered misfolded proteins

A

prusiner

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17
Q

when Km is low

A

enzyme has more affinity to substrate

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18
Q

what are glycoconjugates

A

glycoproteins
proteoglycans
glycolipids

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19
Q

why does the pocket in R state disappear

A

structural transformation

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20
Q

what are proteolytic enzymes

A

break peptide bonds using water

also hydrolyze ester bonds

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21
Q

what is replaced in fetus for hemoglobin

A

beta chain replaced by gamma chain

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22
Q

name of heme group

A

Fe-protoporphyrin IX

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23
Q

hyalurona ex of

A

GAG, proteoglycan
non sulfated
part of extracellular matrix

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24
Q

peripheral membrane proteins

A

bound mostly by electrostatic interactions with H bonds

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25
Q

can enzymes change the equilibrium of the reaction they catalyze

A

no but they can help reach equilibrium faster

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26
Q

how to determine D or L configuration in aldoses and ketoses

A

look at last OH group
L for Left side
D for right side

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27
Q

what configuration is all the Aldoses in

A

D

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28
Q

what enzyme is present if type B blood

A

glycosol transferase B

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29
Q

what is an intrinsically unstructured protein

A

no distinct 3D region

assume a definite 3D structure upon interaction with other proteins

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30
Q

erythropoietin

A

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

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31
Q

more substrate means

A

faster the enzymatic reaction

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32
Q

epimers

A

isomers where the H and OH are flipped on one or more carbon atom

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33
Q

why can hemoglobin carry oxygen better than myoglobin

A

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

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34
Q

what three interactions help the lipid membranes

A

hydrophobic
van der waals
hydrogen bonds

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35
Q

Km

A

is the concentration of the substrate at which the reaction velocity is half of the max

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36
Q

how does the entire glycosylation process take place

A

attaching entire glycosyl unit on a specialized lipid molecule called dolichol phosphate

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37
Q

penicillin binds to

A

transpeptidase, inhibits cell wall synthesis

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38
Q

why use SDS in gel electrophoresis

A

help break non covalent bonds

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39
Q

3 types of membrane lipids

A

phospholipids
glycolipids
cholesterol

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40
Q

what aa is changed into for hemoglobin in fetus

A

his to ser

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41
Q

looser packing in lipids means

A

less hydrophobic

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42
Q

sugars have to be what in order to react

A

activated

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43
Q

what type of functional group is a sphinosine

A

amino alcohol

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44
Q

4 components of phospholipids

A

one or more fatty acids
platform to which fatty acids attach to
phosphate
alcohol

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45
Q

statin

A

help reduce cholesterol by comp inhib key enzyme in cholestrol biosynthetic pathway

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46
Q

competitive inhibitors and Km

A

increase Km

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47
Q

function of chromatography

A

molecules interact differently with the stationary phase and mobile phase, thus can be separated from the rest

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48
Q

what is happening in relaxed state of hemo

A

looser subunits, more free O can bind but harder to release

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49
Q

what happens to proximal histidine in heme group

A

oxygen binds to it causing plane to change and overall tertiary structure

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50
Q

uncompetitive inhibitor

A

bind to enzyme substrate complex, binding site created only on complex

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51
Q

the transition state molecule is the least-_____ but highest in ____

A

stable

free energy

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52
Q

what type of structure do membranes of lipids have

A

sheet like, 2 molecules thick

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53
Q

lipid function in cell

A

fuel
store energy
signal transduction messenger
part of membrane

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54
Q

what are the two structural form of hemoglobins

A

tense and relaxed

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55
Q

what are the three factors that affect fluidity in membrane

A

length of fatty acid
degree of unsaturation
cholesterol molecules

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56
Q

first histidine location in heme group is

A

proximal

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57
Q

ex of uncomp inhibitor

A

lithium and phosphoinositide cycle

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58
Q

what does the enzyme not affect

A

difference in free energy between substrate and product

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59
Q

function of enzymes

A

lower activation energy or facilitate the formation of the transition state

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60
Q

uncom inhib and velocity

A

decrease

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61
Q

who invented chromatography

A

Mikhail Tsvet

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62
Q

at low pH (high H+) hemoglobin tends to

A

release oxygen better

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63
Q

what are polysaccharides

A

glucose homopolymers

disaccharide heteropolymers

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64
Q

trypsin can hydrolyze

A

peptide bonds for both Arg and Lys

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65
Q

so when glutamine is substituted by val what happens

A

val will interact with phe and val on beta chain causing misfolding

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66
Q

proteoglycans

A

carb constitute higher % of total weight

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67
Q

why are misfolded proteins deadly

A

they are infectious, influence other proteins to misfold

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68
Q

what are monosaccharides

A

aldehydes and ketones with OH groups

small molecules composed of 3 to 9 carbon

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69
Q

what are metamorphic proteins

A

exist is different 3D structures that are usually in equilibrium with each other

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70
Q

aspirin binds to

A

cyclooxygenase, reducing synthesis of signaling molecules

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71
Q

what is happening in tense state of hemo

A

chains interacting closely, O is hard to bind but easy to release

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72
Q

what are cofactors

A

helper chemical to enzymes

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73
Q

what type of substitution occurs in sickle cell anemia

A

hydrophilic to hydrophobic

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74
Q

proteins and phospholipids can mover across membrane by

A

lateral motion

transversing (only phospholipids) aka flip flop takes a few hours

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75
Q

what enzyme is present in type A blood

A

glycosol transferase A

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76
Q

structure of hemoglobin

A

four pyrrole rings linked by methine bridges to form tetra pyrrole ring
Fe in center bound to 4 N from rings

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77
Q

what is reversible inhibition

A

they dissociate relatively quickly

comp, uncomp, mixed

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78
Q

mucines (mucoproteins)

A

mostly carb attached to protein through threonine and/or serine

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79
Q

at high CO2 concentration, the pH will be lower so the H+ concentration will be

A

high

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80
Q

what carb is usually in proteoglycans

A

GAG

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81
Q

function of mucine

A

protect cells against different environmental factors such as infection and chemical inhalation
large polymrs

82
Q

which type of fate has the least hydrophobic interaction

A

oil

83
Q

how does chromatography work

A

protein mixture added to porous gel matrix, small protein move through all the pores being slow and large proteins move faster

84
Q

protein folding takes place as a what type of process

A

cooperative

85
Q

the regulation of oxygen binding by hemoglobin is also regulated by

A

hydrogen ions and CO2

86
Q

at high CO2 concentration, hemoglobin is likely to be in what conformation

A

tense

87
Q

what type of effector is 2,3-BPG

A

allosteric, bind to hemo in different site from oxygen

88
Q

in sickle cell anemia what aa is substituted

A

glutamine for valine on alpha chain

89
Q

what denaturants reduce disulfide bonds

A

beta-mercaptoethanol

90
Q

can enzymes catalyze impossible reactions

A

no

91
Q

what is the function of distal histidine in heme group

A

prevents superoxide anion from leaving with electron

92
Q

what does phosphorylating do to sugars

A

make them anionic, cannot cross membrane, not recognized by transporters

93
Q

how can the competitive inhibitor be relieved

A

increase substrate concentration

94
Q

heparin ex of

A

proteoglycan, GAG

used for anticoagulant

95
Q

what is the substrate of prostaglandin H2 synthase-1

A

arachidonic acid

hydrophobic and cant leave membrane without binding to active site of protein

96
Q

what is desalting

A

molecules moving from higher conc to lower conc
large particles stay in tubing
tubing put into buffer solution

97
Q

what are GAG

A

large repeating units of modified disaccharides such as amino sugars and uronic acids
resistant to compression

98
Q

what aa has glycosylation take place on

A

asparagine
serine
threonine

99
Q

binding energy

A

the energy released upon the substrate binding to the active site of enzyme

100
Q

mixed inhibitors

A

can bind simultaneously with substrate to enzyme, reduction of amount of functional enzyme
cannot be relieve by adding more sub

101
Q

what are the membrane proteins

A

peripheral and integral

102
Q

what is needed to break disulfide bonds in gel electrophoresis

A

beta-mercaptoethanol

103
Q

how does H+ and pH affect oxygen binding i hemoglobin

A

the imidazole group of histidine either becomes charged or no charge and interacts with aspartate aa

104
Q

what type of bond connects fatty acid to glycerol back bone

A

ester bond

105
Q

furan is involved with

A

keto-hexoses

106
Q

at high pH (low H+) hemoglobin tends to

A

not release oxygen

107
Q

what are the two cofactors

A

metals and organic (coenzymes)

108
Q

what happens when CO2 binds to N termini of peptide bond

A

forms negatively charged carbamate ion

109
Q

hurler disease

A

accumulation of proteoglycans bc they are not degraded

110
Q

function of agarose gel electrophoresis

A

DNA standards will allow researchers to estimate the size and concentration of unknown DNA

111
Q

what does the negatively charged carbamate ion do in hemoglobin

A

stabilize T state and releases more oxygen

112
Q

what type of bond is between active site and substrate

A

non covalent bond

113
Q

what is phosphorylating sugars

A

key step in retaining sugars inside the cell

114
Q

function of ES complex

A

bring substrate to the optimum orientation for a productive reaction to take place

115
Q

as proteins move through the lumen of ER they get….

A

N-glycosylated

116
Q

what are hemoglobins components

A

2 alpha helices and 2 beta chains

binding: a1b1-a2b2

117
Q

I-cell disease

A

enzymes missing for degradation of lysozome, enzymes were not properly glycosylated, secreted out into blood
debris remains in inclusion bodies

118
Q

active site

A

substrate bind to enzyme

collection of different aa from different parts of the enzyme

119
Q

what is irreversible inhibition

A

bind tightly to enzyme and dissociate very slowly

penicillin and aspirin

120
Q

what are the 2 3D structures of lymphotactin

A

3 beta strands with alpha helix that binds to specific receptor
beta sheet that binds to glycosaminoglycan

121
Q

holoenzyme

A

enzyme with cofactor

122
Q

what are simple sugars

A

monosaccharide
disaccharide
oligosaccharide

123
Q

proteins can absorb how much UV light if aromatic aa attached

A

280 nm

124
Q

which bacteria has a thick peptidoglycan layer

A

gram positive

125
Q

how do cells communicate to environment

A

proteins

126
Q

how does the heme group stabilize after O is added to it

A

adding another histidine that forms H bond with O

127
Q

what type of coenzymes are there?

A 
prosthetic groups (tightly bound to enzyme)
loosely associated with enzyme
128
Q

what is the transition state

A

middle molecule between substrate and product

no longer sub but not yet product

129
Q

mixed inhibitor and Km and Velocity

A

increase

130
Q

what size fragments move faster in gel electrophoresis

A

smaller

131
Q

fatty acids attach to sphinosine back bone by what bond

A

amide bond

132
Q

what state of hemo is strongly favored

A

T state

133
Q

why are aldoses reducing sugars

A

their free aldehyde group in the open configuration

134
Q

oligosaccharides

A

monosaccharides linking with each other

135
Q

alpha helix is characterized by

A

H bonds b/w amino acids on same strand with R groups projecting outward

136
Q

what is added to to catabolic enzymes in golgi complex to make it to lysozome

A

mannose-phosphate

137
Q

myoglobin is what type of protein

A

single polypeptide protein

138
Q

pyran is involved with

A

aldo-hexoses

139
Q

2 types of inhibition

A

reversible and irreversible

140
Q

what happens with protein glycosylation in golgi complex

A

O-glycosylation
further modification of carb on protein
elaborating the N-glycosylated proteins

141
Q

the is enzyme that glycosylate proteins with GlcNAc is called

A

GlcNAc transferase

142
Q

what is the predominant acceptable model for membranes

A

the fluid mosaic model

143
Q

at pH higher than 7.4 what happens to HIS in hemo

A

imidazole group loses charge and break interaction between asp aa, hold on to oxygen

144
Q

membranes have what type of layer

A

lipid bilayers

145
Q

what other aa is present in hemoglobin besides histidine

A

lysine

146
Q

archea have what in their membrane that allows for harsher environment

A

ether bond instead of ester

methyl group instead of H (which allows for more interaction b/w fatty acid tails to create stronger bonds)

147
Q

what does the active site create

A

a unique microenvironment tailored for specific substrates and specific reactions

148
Q

what kind of curve is present for hemoglobin

A

sigmoidal

149
Q

the Fe in heme group can bind to

A

histidine

150
Q

how does PrP misfold

A

native structure of alpha helices transforms into large beta sheets

151
Q

what molecules have a hard time getting through lipid membranes

A

polar

152
Q

what molecule plays an important role in modulating o binding in hemoglobin

A

2,3-biphosphoglycerate (2,3-BPG)

153
Q

where is sphingomyelin found

A

in myelin sheath

154
Q

competitive inhibitor and velocity

A

not affected

155
Q

methotrexate competes with what enzyme

A

dihydrofolate and binds to dihydrofolate reductase

156
Q

Prusiner discovered what protein that is misfolded

A

PrP

157
Q

at pH lower that 7.4 what happens to His in hemo

A

imidazole group becomes charged allowing it to react asp which stabilizes T state and releases O more efficiently

158
Q

how does T state transform to R state

A

bonds between 2,3-BPG and hemoglobin must break, more oxygen pressure must exist

159
Q

what does the specificity depend on for binding in active site

A

precise arrangement of atoms

160
Q

hemoglobin and myoglobin bond in what type of manner

A

cooperative

161
Q

what is gel electrophoresis

A

proteins separated by mass only using a detergent

use power source to drive protein from neg to pos side of gel

162
Q

what does the enzyme affect

A

amount of free energy needed to initiate conversion of substrate to product

163
Q

what is a cytokine

A

class of immune protein that bind to receptors on immune system cells to elicit specific immune responses

164
Q

ex of membrane anchored protein

A

prostaglandin H2 synthase-1

165
Q

function of carb

A

energy store, DNA and RNA synthesis
cell wall of bact and plant are oligosaccharides
link to protein and lipids to make more diverse

166
Q

what is maximum velocity

A

saturation achieve

all enzymes are being occupied

167
Q

what is the aa sequence for for glycosylation

A

n-x-s or n-x-t

168
Q

carb are made of

A

monosaccharides

169
Q

where does CO2 bind to hemoglobin

A

N termini of peptide chain

170
Q

enzymes can catalyze reactions at a rate of

A

10^6

171
Q

integral membrane proteins

A

interact exclusively with the hydrocarbon core

172
Q

glycoproteins

A

proteins constitute higher % of total weight

173
Q

what denaturants destroy weak bonds

A

Heat, urea, SDS, pH

174
Q

glycosylation occurs where

A

ER

and golgi complex

175
Q

who described the different parameters of enzymatic reactions

A

michaelis and menten

176
Q

when is the maximum binding energy released

A

when substrate is in transition state

max interactions between active site and enzyme

177
Q

function of hemoglobin

A

four polypeptide protein

carries oxygen from lungs to rest of body and CO2 and H+ back to lungs

178
Q

ex of competitive inhib

A

methotrexate

179
Q

dermatan sulfate ex of

A

proteoglycan, GAG
in skin, heart valves, blood vessels, tendon
preven infection, cardio disease, carcinogens

180
Q

Lymphotactin is an example of

A

metamorphic proteins

cytokine

181
Q

what kind of bonds between membranes of lipids

A

non covalent

182
Q

what happens in beta-thalasemia

A

no beta chains, all alpha chains

alpha chains aggregate and precipitate leading to immature RBC

183
Q

oxygen binding in hemoglobin is modulated by

A

CO2 and H+

184
Q

glycosylation usually works with what

A

GlcNAc

185
Q

glycoside mostly form what configuration

A

circular

186
Q

apoenzyme

A

enzyme without cofactor

187
Q

what are reducing sugars

A

aldoses

188
Q

what happens in alpha-thalasemia

A

alpha chains not produced only 4 beta chains HbH

HbH binds tightly to O2 causing poor delivery to tissues

189
Q

when Km is high

A

enzyme has less affinity to substrate

190
Q

what site is responsible for lowering the activation energy

A

active site

191
Q

inhibitors

A

molecules that can inhibit enzymes by different mechanisms

serve as control for enzymatic activity

192
Q

where does 2.3-bpg bind in hemo

A

center during T state

193
Q

what is the Bohr effect

A

how pH (h+) and CO2 affected binding of oxygen to hemoglobin

194
Q

longer saturated fatty acid molecules have more hydrophobic interactions than shorter saturated fatty acid molecules

A

true

195
Q

what is the term called that defines the difference between substrate and transition state

A

activation energy or gibbs free energy of activation

196
Q

how can molecules pass through membrane

A

must shed interactions with water and form new ones with lipid core

197
Q

what are the platforms in phospholipids that fatty acids attach to

A

glycerol
(phosphoglycerides)
sphingosine
(sphingolipids)

198
Q

homopolymer

A

if a polysaccharide is composed of a single sugar

199
Q

what are enzymes

A

biological catalyst

catalyze reactions at faster rates

200
Q

what chemical is needed for edman degradation

A

phenylisothiocyanate

201
Q

what does chromatography mean

A

color writing

Biochem summer (12 decks)

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