Midterm #2 Flashcards
(343 cards)
1
Q
how do we isolate one type of cell and a particular part of the cell? (subcellular fractionation)
A
differential centrifugation
2
Q
In differential centrifugation, what determines what remains in the pellet?
A
spin speed
3
Q
when molecules are exposed to enormous acceleration, they begin to ?
A
sediment according to size and shape
4
Q
Ultracentrifugation - sucrose gradient
Seperation/Analysis
A
density gradient established with sucrose , each molecule moves through the gradient by shape/size
- larger [c] of sucrose will represent more dense molecules
5
Q
To isolate one protein from all other substances we crack open cells by:
A
i) osmotic lysis
ii) mechanical
iii) detergents
iv) lysozyme
6
Q
i) osmotic lysis
ii) mechanical
iii) detergents
iv) lysozyme
A
i) hypotonic soln - cells burst
ii) good if cells have cell wall- crush/grind by pressure or sonic
iii) used if protein is in lipid membrane (org solv. may denature protein)
iv) for bacterial cell walls - breaks down cell wall
7
Q
Protein must be stabilized in these ways:
A
i) pH - appropriate buffer
ii) temp - reduce rxns and unfolding
iii) proteases - must be inhibited (cut amide bonds of proteins)
iv) absorption - keep prot. soln concentration to avoid denaturing at surface
v) oxidation - minimize foaming to reduce this
vi) storage under inert gas or frozen
8
Q
Protein Purification - Salting In
A
addition of salt at low ionic strength, can increase solubility
9
Q
Protein Purification - Salting out
A
addition of salt at high ionic strength, can decrease solubility
by engaging all water surrounding protein for its hydration shell - prot precips.
then we isolate by centrifugation
10
Q
Chromotography - Paper
A
sample is seperated by differences b/w aq phase which is attracted to paper and organic phase
11
Q
Column Chromotography makes use of 2 things
A
stationary phase and mobile phase
12
Q
Chromotography - Size Exclusion (gel filtration)
A
resin made up of porous beads equilibrated with low salt buffer
proteins move through resin based on size & shape
smaller proteins - slowed down
13
Q
Chromotography - Ion exchange
A
resin is polymer of - or + charged groups
seperates based on ionic charge of protein
salt gradient elutes protein
14
Q
affinity of protein for charged group on column is affected by (2)
A
1) pH
2) concentration of competing free salt ions in soln
15
Q
Chromotography - Ion exchange
2 things we must know about the protein
A
1) pI
2) pH optimum - where its most stable
need to know how to relate the two
16
Q
Chromotography - affinity
A
resin is covalently linked molecule which is also used for elution
specific interactions retard the protein of interest
17
Q
Chromotography methods enhanced by use of:
A
HPLC: smaller columns, high P, faster run times
limits diffusional spread - increases resolution
FPLC: some prot. denature with P, we can use this (adds pump)
18
Q
Electrophoresis - SDS page
Matrix?
A
seperates according to [charge] of proteins attracted to anode (+)
- matrix is polyacrylamide gel (PAGE)
SDS coats protein giving them equivalent charge (-) to mass ratio
19
Q
SDS PAGE seperates proteins according to ?
A
size
migration of charged proteins in electric field
20
Q
SDS PAGE Is what kind of method?
A
analytical method
- denaturation of protein
21
Q
SDS PAGE - interpretation of bands
A
smaller proteins migrate further, proteins with known MW are used to make up molecular weight markers
log Mr vs distance - plot d for unknown protein and extrapolate MW
22
Q
Isoelectric focusing IEF PAGE
pI values are determined similar to SDS PAGE
A
used to determine pI (seperates proteins according to pI)
- proteins migrate to pH of their pI
ampholytes distribute across electric field based on their pKa creating pI gradient
23
Q
2D PAGE
A
1st - IEF PAGE seperates protein based on pI
2nd - IEF gel slotted into SDS PAGE - seperated by size
24
Q
some enzymes require no chemical groups other than their aa residues and others…
A
require additional chemical component called a cofactor (one or more inorganic ions) or complex organic metallorganic molecule (coenzyme)
25
what lowers the Ea making life possible?
peptide-substrate complex
26
Enzymes make rxns more ?
energetically favorable
27
in order to catalyze a reaction, an enzyme must be complementary to ?
the reaction TRANSITION STATE
28
much of the catalytic power is ultimately derived from free energy released in forming many ____ ___ and ___ b/w enzyme and substrate.
weak bonds and interactions
29
__ __ is a major source of free energy used by enzymes to lower Ea of rxns
binding energy
30
covalent interactions b/w enzyme and substrate lower Ea by providing...
alternate lower energy rxn path
31
weak interactions are optimized when?
in the transition state
32
this binding energy contributes to ___ as well as to ___
specificity as well as to catalysis
33
binding energy holds __ in ___ ___ to __ which is a substantial contribution to ___
substrate in specific orientation to react
| catalysis
34
why is binding energy a substantial contribution to catalysis?
holding substrate in specific orientation means substrate is precisely aligned on enzyme - constrained motion - increase rxn rate
35
desolvation and substrate and enzyme
E-S interactions replace most/all H bonds b.w substrate and water that would otherwise impede rxn
36
active site is lined with?
aa residues w/ substituent groups that bind with substrate and catalyze its chemical transformation
37
induced fit
initial interaction b/w enzyme & substrate is relatively weak, but these weak interactions rapidly induce conformational changes in enzyme that strengthen binding.
38
functional groups of aa side chains, and/or cofactors interact w/ substrate to favor the?
transition state
39
Enzymes act by one or more of the following mechanisms:
1) proximity
2) general acid base catalysis
3) hydrolytic cleavage
40
proximity
accelerating rxn b/w species by holding them in appropriate orientation
41
general acid base catalysis, covalent catalysis, metal ion catalysis are distinct from binding energy b/c they?
generally involve transient covalent interaction w/ substrate or group transfer to or from substrate
42
general acid base catalysis refers to ?
H+ transfer mediated by weak acids and bases other than water
43
when does the presence of other H+ donors/acceptors increase the rate of rxn?
when H+ transfer to or from H2O is slower than rate of breakdown of intermediates
44
In active site of enzyme, water may not be available as H+ donor/acceptor. What mechanism becomes crucial?
general acid base catalysis
45
how does general acid base catalysis occur in active site?
a # of aa side chainds can and do take on role of H+ donors/acceptors
- - precisely positioned in enzyme active site to allow H+ transfer
rate enhancement of 10^2 - 10^5
46
General Acid Base Catalysis
1) what is transferred in acid base rxns?
2) what impedes rxns involving unstable intermediates?
in acid base rxns, H+ is transferred.
| Many rxns involve unstable intermediates that breakdown to constituent reactive species impeding rxn
47
In order to avoid having an unstable charged intermediates in the reaction...
an enzyme has appropriately located functional groups readily to donate a proton or accept a proton to stabilize the transition state
- allows time for product synthesis
48
General Acid Base Catalysis makes a potentially reactive group more reactive by?
increasing its e-phillic or n-phillic character by removing or adding H+
49
Hydrolytic Cleavage
instability of (-) charge on substrate (carbonyl group) leads to collapse of intermediate, reformation of double bond with carbon (and oxygen) displaces bond b/w c and amide group of peptide linkage, breaking peptide bond
50
what changes do metal ions make possible?
metal ions make changes in charge distributions possible
| stabilize charge distribution in transition states
51
Hydrolytic Cleavage
| accelerates rxn rate through?
transient formatin of catalyst-substrate covalent bond
52
Metal Ion catalysis
| - how their interactions orient or stabilize...
ionic interactions b/w enzyme bound metal and substrate can help orient substrate for rxn or stabilize charged rxn transition state
53
Metals can also mediate ox-reduc rxns by?
reversible changes in metal ions oxidation state
54
prosthetic group
coenzyme or metal ion tightly or covalently bound to enzyme protein
55
2D electrophoresis is used to separate proteins in 2 ways
seperate proteins of identical MW but diff pI
or
proteins w/ similar pI but diff MW
56
6 main classes of enzymes
1) oxidoreductases
2) transferases
3) hydrolases
4) lyases
5) isomerases
6) ligases
57
1) oxidoreductases
1) transfer of electrons (hydride ions or H atoms)
58
2) transferases
group transfer rxns
59
3) hydrolases
hydrolysis rxn (transfer of functional groups to water)
60
4) lyases
addition of groups to double bonds or formation of double bonds by removal of group
61
5) isomerases
transfer of group within molecule to yield isomeric form
62
6) ligases
formation of C-C, C-S, C-O, and C-N bonds by condensation rxns coupled to ATP cleavage
63
cofactors
additional molecules required by many enzymes for their activity
64
apoenzyme
an enzyme lacking an essential cofactor (protein part)
65
holoenzyme
intact enzyme w/ bound cofactor (complete catalytically active enzyme together w/ bound coenzyme and/or metal ions)
66
effective catalysts enhance rxn rates by factors of
10^5 to 10^17
67
enzymes are characterized by?
formation of enzyme substrate complex often in active site
68
__ __ provide significant amounts of energy used for rate enhancement
weak bonds
69
calmodium won't function without calcium, therefore its is an ____ on its own and it is __.
apoenzyme
| inactive
70
Calcium makes calmodium functional - a ____.
haloenzyme
71
a key factor affecting the rate of rxn catalyzed by enzyme is?
concentration of substrate
72
enzyme reaction
E + S ES E + P
73
enzyme kinetics
determination of the rate of rxn and how it changes in response to change in experimental parameters
74
at relatively low [S] , Vo?
Vo increases almost linearly with increase in [S]
75
at higher [S], Vo?
Vo increases by smaller and smaller amounts in response to increases in [S]
76
Vmax
close to plateau like Vo region
| a point reached that beyond it increases in Vo are vanishly small as [S] increases
77
slow step of enzyme substrate rxn?
second step: ES E + P
78
Increase [S] at
a) beginning of graph
b) at 1/2 Vmac
c) at plateau-like region of Vo
a) increases rxn velocity
b) increases rxn velocity
c) does NOT increase rxn velocity
(enzyme fully saturated)
79
Vmax is observed when ?
when virtually all enzyme is present as ES complex and [E] is vanishingly small
enzyme is SATURATED with substrate
80
pre-steady state
initial period when enzyme is first mixed with large excess of substrate during which [ES] builds up
- too short to be observed
81
steady state
reaction achieves a state in which [ES] and concentration of any other intermediates remain approx. constant over time
82
Michaels and Menten derived their equation starting from their basic hypothesis that the RDS (RLS) in enzymatic rxns is ?
the breakdown of ES complex to product and free enzyme
83
Micheals Menten Kinetics - point A
[S] << Km, [S] in denominator makes little difference
Vmax & Km constants - replaced by K
Vo = K[S]
84
Micheals Menten Kinetics - point C
[S] >> Km
Km dropped from denominator
Vo=Vmax
85
Micheals Menten Kinetics - velocity is 100% dependant on?
substrate concentration
86
Micheals Menten Kinetics - point B
```
[S] = Km
Vo= Vmax/2 = (1/2)Vmax
```
87
Km has dimensions of?
molarity
88
Km represents?
[S] at which velocity is half-maximal
89
What does Km NOT represent? but rather reflects?
does NOT represent affinity of substrate for enzyme, but rather reflects specific aspects of enzyme mechanism
(# and relative rates of individual steps
90
only when k2 is rate limiting (k-1 much greater than k2) Km becomes a measure of?
measure of affinity of enzyme for its substrate
| - Kd (dissociation constant)
91
In general, high Km indicates? low Km?
| and why?
k2 rate limiting step (k2 << k-1)
Km=(k2+k-1)/k1 = k-1/k1
weak substrate binding
strong substrate binding
92
Sometimes k2>>k-1 and then Km=?
Km= k2/k1
93
Lineweaver-Burke Equation
michaels menton - rearranged as a straight line plot
| - reciprocal
94
greatest advantage of Lineweaver-Burke Equation
great advantage of allowing a more accurate determination of Vmax which can only be approximated by simple plot of Vo vs. [S]
95
Lineweaver-Burke Equation
a) slope
b) x intercept
c) y intercept
a) Km/Vmax
b) -1/Km
c) 1/Vmax
96
it is useful to determine a more general rate constant Kcat to describe?
to describe the limiting rate of any enzyme catalyzed reaction at saturation
97
if rxn has several steps and one is clearly rate limiting, what is Kcat?
Kcat is equivalent to rate constant for that limiting step
98
when several steps are partially rate limiting, Kcat can become?
a complex function of several of the rate constants that define each individual step
99
Turnover number:
combo of all k values in rxn (represented by Kcat) and therefore a measure of how rapidly an enzyme can operate once active site is filled
100
Kcat - what order rate constant? units?
first order - units of reciprocal time
101
Turnover number is equivalent to?
of S converted to P in given unit of time for one enzyme saturated with S
102
Kcat =?
Vmax/[Et]
103
the kinetic parameters: Kcat and Km are useful for the study & comparison of?
different enzymes whether their rxns are simple or complex
104
each enzyme has values of Kcat and Km that reflect?
cellular environment, [S] normally encountered by enzyme, and chemistry of rxn being catalyzed
105
Kcat and Km also allow us to evaluate ?
kinetic efficiency of enzymes
106
two enzymes catalyzing diff rxns may have same kcat (turnover #) yet rates of uncatalyzed rxns may be?
different, thus rate enhancements brought about by enzyme may differ greatly!
107
Experimentally, Km for enzyme tends to be similar to?
cellular concentration of its substrate
108
an enzyme that acts on S present at low [c] in cell usually has a ___ Km than an enzyme that acts on S that is more abundant.
low
109
best way to compare catalytic efficiencies of diff enzymes
| or turnover of diff substrates by same enzyme is to compare the...
ratio kcat/Km for the 2 reactions
| SPECIFICITY CONSTANT
110
Specificity Constant
the catalytic efficiency of the enzyme (M-1 s-1)
| S=Kcat/Km
111
Specificity Constant is the rate constant for the?
| since Kcat represents... and Km is effectively a measure of..
conversion of E + S to E + P
since Kcat represents how fast enzyme can act once active site is filled and Km is effectively a measure of how fast enzyme can associate with substrate
112
Michaels Menton equation with Kcat
Vo = kcat[Et][S]/(Km +[S])
113
when [S] << Km, equation with Kcat becomes?
Vo = (Kcat/Km) [Et][S]
114
when [S] << Km, what order reaction?
second order rate equation b/c it depends on [Et] and [S]
| units of M-1 s-1
115
Upper limit to Kcat/Km imposed by?
rate at which reactants (E and S) can diffuse together in aq soln
116
diffusion controlled limit is ?
10^8 to 10^9 M-1 s-1
117
If enzymes are near the diffusion controlled limit, they are said to have?
achieved catalytic perfection
118
Different values of Kcat and Km can produce the ?
max ratio
119
Inhibitor
any molecule that acts directly on enzyme to lower its catalytic rate
120
2 major types of inhibitors
irreversible
| reversible
121
3 types of reversible inhibitors
a) competitive
b) un-competitive
c) mixed
122
Irreversible inhibitors
- binding
- can result in?
binds tightly, often covalently to functional sites (destroys it) , permanently inactivating enzyme
can result in a change to Vmax, Km, or both
123
Suicide Inactivators (mechanism based inactivators)
special class of irreversible inhibitors
- compounds that are relatively unreactive until they bind to active site of specific enzyme
- undergoes first few chemical steps of normal enzymatic activity but instead of being transformed into normal product, inactivator is converted to very reactive compound that combines irreversibly with enzyme
124
Suicide Inactivators also called mechanism based inactivators because?
they hijack normal enzyme reaction mechanism to inactivate enzyme
125
advantage of suicide inactivators
target single active site, blocks specific pathways with few side effects
126
Reversible Inhibition - competitive
competitive inhibitor competes with S for active site of an enzyme
127
While competitive inhibitor occupies active site, it prevents?
Binding of S to enzyme
128
Many competitive inhibitors - structure compared to S?
structurally similar to S and form EI complex without catalysis
129
Competitive Inhibitors affect on:
1) Vmax
2) Km
1) none
| 2) increases (alphaKm is apparent Km)
130
Reversible Inhibition - uncompetitive
binds at site distinct from substrate active site - binds only to ES complex
changes overall 3D shape, leads to decrease in activity
131
Uncompetitive Inhibitors affect on:
1) Vmax
2) Km
1) decreases
| 2) decreases
132
Competitive Inhibitor
a) increase [S]
b) increase [I]
a) reduced effect of I
| b) less product
133
Mixed Inhibitor
binds at site distinct from substrate active site but binds to either E or ES
changes overall 3D shape, leads to decrease in activity
134
Mixed Inhibitor
a) Vmax
b) Km
changes both
135
Noncompetitive Inhibition is a special case ...
Vmax decreases, Km is unchanged since alpha = alpha'
136
Enzyme Regulation - rates of enzyme-catalyzed rxns are altered by activators and inhibitors which are termed?
effector molecules
137
Feedback (allosteric) regulation)
an enzyme, early in metabolic pathway, is inhibited by an end product
often takes place at committed step of pathway (step which commits a metabolite to a pathway)
138
allosteric enzymes
have more than 1 site, where S binding at one site induces conformational change in enzyme altering its affinity for S
139
Allosteric Activator
increases enzymes rate of activity
140
Allosteric Inhibitor
decreases enzymes rate of activity
141
allosteric enzymes function through?
reversible noncovalent binding of regulatory compounds called allosteric modulators/effectors
142
other enzymes are regulated by?
reversible covalent modification
143
conformational change converts...
relatively inactive conformation (T state) to more active conformation (R state)
144
heterotrophic allosteric enzyme
modulator is molecule other than the substrate
145
relationship b/w enzyme velocity and [S] is sometimes a ____ curve for an allosteric enzyme rather than ___
sigmoidal
| hyperbolic
146
when relationship b/w enzyme velocity and [S] is produces a sigmoidal curve, we NO longer refer to [S] at half Vmax as ? we use?
Km, we use [S]0.5 or K0.5
147
In the case of aspartate transcarbamoylase - CTP ...
CTP, the end product of the rxn, decrease rate of enzyme activity - allosteric inhibitor
ATP increases rate of enzyme activity - allosteric activator
148
many effectors work together to regulate the pathway
push-pull mechanism
149
Reversible Covalent Modification of aa residues...
alters activity
150
Reversible Covalent Modification - when aa residue in enzyme is modified...
a novel aa with altered prperties has been added into protein
151
Reversible Covalent Modification - introduction of a charge can alter...
local properties of enzyme and induce a change in conformation
152
Reversible Covalent Modification - introduction of hydrophobic group can trigger?
association with membrane
153
Reversible Covalent Modification - changes are often ___ and can be critical to __ of altered enzyme
substantial and can be critical to function of altered enzyme
154
Reversible Covalent Modification
the making and breaking of covalent bond b/w a non protein group and enzyme that affects its activity
155
hyperbolic curve only seen for...
non-regulatory enzymes
156
Phosphoryl groups cause a change in?
3D structure enhancing or inhibiting enzyme activity
157
Enzymes are phosphorylated by a ___ ___ and dephosphorylated by a ___.
protein kinase
| phosphatase
158
Adenylation
transfer of adenylate by ATP
159
ADP-ribosylation
transfer of an adenosine diphosphate-ribosyl moiety from NAD+
160
Uridylylation and Methylation
transfer groups
161
Proteolytic Activation
enzymes are synthesized as larger inactive precursor forms called proenzymes or zymogens
162
Proteolytic Activation
| - activation involves? resulting in?
IRREVERSIBLE hydrolysis of one or more peptide bonds, resulting in an active form of the enzyme
163
the amount of a particular enzyme present in cell changes according to ?
rates of its synthesis and degredation
164
Synthesis can be controlled at what level?
genetic level, where the production (transcription) of mRNA from a gene may be induced or repressed
165
Rates of enzyme synthesis and degradation
a) synthesis (transcription of RNA
b) rate of mRNA degradation
c) enzyme degradation (reflected by its half-life) time taken for 50% of protein to be degraded
166
Labile enzymes
termed this - most enzymes important in metabolic regulation have short half lifes
167
monosaccharides
simple sugars - polyhydroxyl aldehyde or ketone (D-glucose)
168
disaccharides
consist of two monosach. subunites most abundant in nature (i.e. sucrose)
169
oligosaccharides
short chains of monos units joined by glycosidic bonds or linkages
170
2 < 20 unit sugars are glycoconjugates
attached to protein or lipids
171
polysaccharides
> 20 monosac. units
may have 1000s, linear or branched
ex. starch, glycogen have same subunit (D-glucose) but different linkages
172
Carbohydrate formula
Cn(H2O)n
173
Carbohydrates are produced how in plants?
produced from CO2 and H2O via photosynthesis
174
Carbohydrates
| variety of functions
energy source & storage
structural component of cell walls & exoskeleton
informational molecules in cell-cell signaling
175
aldose
contains aldehyde functionality
| -carbonyl group at the end of the chain
176
ketose
contains ketone functionality
| - carbonyl group NOT at end of chain
177
Enantiomers
stereoisomers that are nonsuperimposable mirror images
178
In sugars that contain many chiral centers, which is designated as D (right) or L (left)?
only the one that is most distant from carbonyl carbon
179
D and L isomers of a sugar are..
enantiomers
180
most hexoses in living organisms are __ stereoisomers
D
181
some simple sugars occur in the L-form, such as
L-arabinose
182
Diastereomers:
stereoisomers that are not mirror images
183
Diastereomers have different ...
physical properties
184
Epimers
two sugars that differ only in the configuration around one carbon atom
185
Ribose is ...
the standard five-carbon sugar
186
Glucose is...
the standard 6-carbon sugar
187
Galactose is ...
an epimer of glucose
188
Mannose is...
epimer of glucose
189
Fructose is...
the ketose form of glucose
190
Aldehyde and ketone carbons are?
electrophilic
191
Alcohol oxygen atom is?
nucleophilic
192
When aldehydes are attacked by alcohols...
hemiacetals form
193
When ketones are attacked by alcohols...
hemiketals form
194
Pentoses and hexoses readily undergo ?
intramolecular cyclization
195
anomeric carbon
former carbonyl carbon becomes new chiral center called ANOMERIC CARBON
196
former carbonyl oxygen becomes? position of this group determines?
a hydroxyl group, position of this group determines if anomer is α or β
197
If hydroxyl group is opposite side (trans) of ring as CH2OH moiety, configuration is?
α
198
If hydroxyl group is same side (cis) of ring as CH2OH moiety, configuration is?
β
199
Pyranoses
six membered oxygen containing rings
200
Furanoses
5 membered oxygen containing rings
201
anomeric carbon is usually drawn on ....
right side
202
The ring forms exist in...
equilibrium with the open-chain forms
203
Aldehyde can reduce both Cu2+ and Ag+, which allows detection of?
reducing sugars such as glucose
204
Colorimetric Glucose Analysis - enzymatic methods are used to quantify ...
reducing sugars such as glucose
205
The enzyme glucose oxidase catalyzes the conversion of ... to..
glucose to glucono-δ-lactone and hydrogen peroxide
206
Hydrogen peroxide oxidizes organic molecules into ...
highly colored compounds
207
Concentrations of such compounds is measured
colorimetrically
208
Electrochemical detection is used in
portable glucose sensors
209
Two sugar molecules can be joined via a ...
glycosidic bond between an anomeric carbon and a hydroxyl carbon
210
The glycosidic bond (an acetal) between monomers is less reactive than the ...
hemiacetal at the second monomer
211
Second monomer, with the hemiacetal, is?
reducing
212
Anomeric carbon involved in the glycosidic linkage is?
nonreducing
213
maltose
The disaccharide formed upon condensation of two glucose molecules via 1 → 4 bond is called
214
Nonreducing Disaccharides - Two sugar molecules can be also joined via ..
a glycosidic bond between two anomeric carbons
215
nonreducing disacch. - two sugar molecules joined via glycosidic bond b/w 2 anomeric carbons - product has...
two acetal groups and no hemiacetals
216
Nonreducing Disaccharides - have no...
reducing ends - nonreducing sugar
217
Trehalose
constituent of hemolymph of insects
| provides protection from drying
218
Polysaccharides - Natural carbohydrates are usually found as
polymers
219
homopolysaccharides
monomeric species
220
heteropolysaccharides
two or more types of monomers
221
polysach. can be (4)
homopolys.
heteropolys.
linear
branched
222
Polysach MW
don't have a defined MW - no template used to make polysac.
223
Glycogen
branched homopolysaccharide of glucose
224
Glycogen: Glucose monomers form..
(α1 → 4) linked chains
225
Glycogen - Branch-points with ...
(α1 → 6) linkers every 8–12 residues
226
Glycogen - Functions as ?
the main storage polysaccharide in animals
227
Starch
a mixture of two homopolysaccharides of glucose
228
Amylose
is an unbranched polymer of (α1 → 4) linked residues
229
Amylopectin
is branched like glycogen but the branch- points with (α1 → 6) linkers occur every 24–30 residues
230
Starch is the...
main storage polysaccharide in plants
231
In aqueous solutions, which carbohydrates occur predominantly as cyclic (ring) structures?
aldotetrose and all monosaccharides with 5 or more carbon atoms in backbone
232
How is this cyclic carbohydrate formed? what kind of bonding?
Carbonyl group forms covalent bond with oxygen atom of hydroxyl group along chain
233
Addition of one alcohol molecule to a:
a) aldose
b) ketose
a) hemiacetal
| b) hemiketal
234
addition of 2 alcohol molecules to a
a) aldose
b) ketose
a) acetal
| b) ketal
235
The reaction with the first molecule of alcohol creates an additional?
chiral center (carbonyl carbon)
236
Two epimers of D-glucose
D-mannose
| D-galactose
237
Anomers
isomeric forms of monosachs that differ in their configuration about the hemiketal or hemiacetal carbon atom
238
Mutarotation
the process of interconversion of alpha and beta anomers in aq. solns
239
How can a reaction produce either of two stereoisomeric configurations? (α and β)
because alcohol can attack either front or back of carbonyl atom
240
Which anomer of D-glucose is more predominant in solutions?
2/3 β-D-glucose
1/3 α-D-glucose
so β form more predominant
241
Ribose
1) part of?
2) derivates?
3) central role in?
1) part of RNA backbone
2) phosphorylated derivatives - ATP & NADPH
3) metabolism
242
Gum Arabic
1) complex mixture of?
2) historically the source of?
1) glycoproteins & polysachs
| 2) source of sugars arabinose and ribose
243
Xylose
1) added to __ and __ in proteoglycan type O -glycosylation
2) 1st sacharide in biosynthesis of?
1) serine and threonin
| 2) polysachs such as heparin sulfate and chondroitin sulfate
244
Mannose
1) important in?
2) with is associated with mutations in enzymes involved in mannose metabolism
1) glycosylation of certain proteins
| 2) congenital disorders
245
Galactose
1) ___sacharride
2) combined with something to form...?
1) monosach.
| 2) combined with glucose through condensation rxn to form disach LACTOSE
246
DHAP
| key element in (2)?
pentose phosphate pathway and triglyceride synthesis
247
D-Erythulose
| 1) part of...
PPP
248
Pentose Phosphate pathway generates? for?
reducing equivalence (NADP -> NADPH) for fatty acid synthesis or other metabolic processes
249
D-fructose
| found in what cycle
ketose form of glucose
| - krebs cycle
250
D-Ribulose
in what pathway?
key to formation of ? production of?
PPPathway
formation of many bioactive molecules
NADPH production
251
D-Xylulose
in what pathway?
key to formation of ? production of?
PPPathway
formation of many bioactive molecules
NADPH production
252
of stereoisomers:
a) Ketose
b) Aldose
a) 2^(n-3)
| b) 2^(n-2)
253
G3P
- product of?
used as? rearranged to form?
prime photosynthetic end product
used as nutrient
rearranged to form monosachs such as glucose which can be transported to other cells or packaged for storage as insol polysac such as starch
254
D-mannose and D-galactose are converted to...?
glucose, the primary metabolic fuel
255
α-D-galactose is converted to β-D-galactose
this is an example of what kind of conversion?
through what rxn does this conversion occur?
ANOMERIC conversion through a MUTAROTATION rxn/interconversion
256
Formation of cyclic form of D-glucose
this reaction yields?
the cleavage of the bond requires?
yields H2O
| cleave of bond requires H2O
257
a solution of α-D-glucose and β-D-glucose eventually..
become identical eq. mixtures
| rings open up briefly into linear form and close again
258
Monosaccharides are ___ agents
reducing
259
Reducing Sugar
Glucose and other sugars capable of reducing cupric (Cu2+) ion
260
Disaccharides (such as maltose, lactose, sucrose) consist of?
two monosachs joined covalently by an O-glycosidic bond
261
O-glycosidic bond formed when?
hydroxyl group of one sugar molecule (typically cyclic) reacts with anomeric carbon of the other
262
oxidation of sugar by cupric ion (reducing sugar) occurs only with?
linear form
263
reducing end of polysachs or disachs
the end of the chain with free anomeric C (one not involved in glycosidic bond)
264
Reducing or Nonreducing?
a) Lactose
b) Maltose
c) Sucrose
d) Trehalose
a) reducing
b) reducing
c) nonreducing
d) nonreducing
265
homopolysachs
contain only a single monomeric species
266
heterpolysachs
contain two or more monomeric species
267
Starch and Glycogen - Homo or Heteropolysachs?
homopolysaccharides that serve as storage forms of monosachs
268
most important storage polysachs in:
a) plants
b) animals
a) starch
| b) glycogen
269
starch and glycogen are both heavily hydrated b/c?
they have so many exposed hydroxyl groups available to H bond with water
270
In Starch - strands of amylopectin form __ __ __ with each other and amylose
duoble helical structures
271
glucose residues at non reducing ends of outer branches of starch are?
removed enzymatically during mobilization of starch energy
272
Glycogen and Start often form?
granules in cells
273
Granules contain?
enzymes that synthesize and degrade these polymers
274
Glycogen and Amylopectin have how many reducing ends? how many nonreducing ends?
ONE reducing end
| many nonreducing ends
275
Cellulose
branched homopolysach of glucose
276
Glucose monomers in Cellulose form?
(β1-4) linked chains
277
What forms between adjacent monomers in cellulose?
H bonds
278
H bonds form between adjacent monomers in cellulose, as well as?
between chains
279
the β1-4 bonds in cellulose cause differences in ?
| examples?
structure and physical properties
| - water insoluble and tough structure
280
What makes cellulose a difficult substrate to act on?
fibrous structure and water insolubility
281
what allows fungi, bacteria and protozoa to use wood as a source of glucose?
they secrete cellulase which hydrolyzes β1-4 linkages
282
Chitin
linear polysach of N-acetylglucosamine residues in (β1-4) linkage
283
Chitin forms...
extended fibers similar to those of cellulose
284
Chitin physical properties & structure
hard, insoluble, cant be digested by vertebrates, structure is tough but flexible
285
Chitin is found in?
cell walls in mushrooms, exoskeletons of insects, spiders, crabs, and other arthropods
286
Agar is a complex mixture of?
heteropolysachs containing modified galactose units
287
Agar serves as a component in?
cell walls of some seaweeds
288
One component of Agar
Agarose
289
Agar solutions form? use?
GEL commonly used in the lab as a surface for growing bacteria
290
Agarose solns form? use?
GELS that are commonly used in lab for seperation DNA by electrophoresis
291
Glucosaminoglycans
a family of linear polymers composed of repeating disaccharide unit
292
Glucosaminoglycans
| One monomer is always either....
N-acetylglucosamine, or N-acetylgalactosamine
293
Glucosaminoglycans
| the other monomer is in most cases ____ or it can be ___
```
uronic acids (c6 oxidation)
sulfate esters
```
294
Glucosaminoglycans
| combo of sulfate grups and carboxylate groups of uronic acid residues give these a ?
very high density of negative charge
295
extended rod form of Glucosaminoglycans provides?
max seperation b/w (-) charged groups
296
Glucosaminoglycans are ___ ___ molecules
extended hydrated
297
the sulfated Glucosaminoglycans are attached to..to form?
extracellular proteins to form proteoglycans
298
Hyaluronan
Glucosaminoglycan
- lubricant
synovial fluid of joints
glassy transparent appearance
299
Choindroitin sulfate
Glucosaminoglycan
| tensile strength of tendons and joints
300
(β1-4) linked D-glucose units have different macroscopic __ __ than (α1-4) units
physical structure
301
Cellulose (β1-4) __ differently than Amylose(α1-4)
folds differently
302
Most stable Amylose structure
α-helix with 6 residues per turn favoring internal H bonding
303
Most stable CELLULOSE structure
each chair turned 180 degrees yielding straight chain and all OH groups available to bond with neihgbouring chains
304
Cellulose can be used as a starting material for?
fermentation to ethanol for gasoline augmentation
305
Heparin
linear polymer 3-40 kDa
| highest (-) charge density biomolecules
306
Heparin Sulfate
is heparin-like polysach but attached to proteins
307
Heparin prevents?
blood clotting by activating protease inhibitor antithrombin
308
Heparin binding to various cells regulates?
development and formation of blood vessels
309
Heparin can also bind to viruses and bacteria and?
decrease their virulence
310
Glycoconjugate
informational carb (via anomeric C) covalently joined to a protein or lipid
311
Glycoprotein
protein with small oligosach attached
312
Glycoprotein - carbohydrate is attached via?
anomeric carbon
313
Sucrose is a major?
product intermediate in photosynthesis
314
In many plants, what is the principle form of sugar transported from leaves to other parts of the plant?
Sucrose
315
Trehalose plays a role in?
energy storage in insects
316
N-glycosyl bonds join...
anomeric carbon of a sugar to a N atom in glycoproteins
317
Glycocalyx
specific oligosachs chains on cell membrane of eukaryotic cells forming a carb layer
318
These oligosach chains found attached to eukaryotic cell membranes are central players in...
cell to cell recognition&adhesion, cell migration during development, immune response, wound healing etc.
- INFORMATIONAL carbn
319
Glycolipid
lipid with covalently bound oligosach
320
Glycoproteins usually found?
on outer face of plasma membrane, in extracellular matrix and in blood
321
Oligosach portion of glycoproteins are very ____ and like ____ are very rich in ___
heterogenous
glycosaminoglycans
information
322
Glycolipids are found on?
exterior membrane
323
Glycolipids allow other cells to
recognize it
| cell to cell surface recognition
324
Proteoglycans
macromolecules of cell surface or ECM in which one or more glycosaminoglycan chains are joined covalently to membrane protein
325
Syndecans
type of proteoglycan
| - proteins have a single transmembrane domain
326
Glypicans
type of proteoglycan
| - protein is anchored to a lipid membrane
327
Glypicans and Syndecans are?
two major families of membrane heparan sulfate proteoglycans
328
Proteoglycan structure...
| how is the glycosaminoglycans linked to core protein?
xylose residue at reducing end is joined by its anomeric C to OH of Ser residue
329
Aggrecan
best studied core protein
330
Some proteoglycans can form ?
proteoglycan aggregates
331
proteoglycan aggregates
enormous supramolecular assemblies of many core proteins all bound to single molecule of hyluranon
332
Hyaluronan and Aggrecan form?
huge noncovalent aggregates
333
Hyaluronan and Aggrecan form huge noncovalent aggregate and hold?
lots of water
| associated water of hydration
334
This proteoglycan aggregate of hyaluronan and aggrecan is very low...
it covers...
```
friction material
joint surfaces (articular cartilage)
```
335
Extracellular Matrix
material outside cell
| - strength, elasticity and physical barrier in tissue
336
Main components of the ECM
- proteoglycan aggregates
- collagen fibres
- elastin (a fibrous protein)
337
Integrins
family of plasma membrane proteins that mediate signaling b/w cell interior and ECM
338
some integral membrane proteins are __
| example?
proteoglycans
| syndecans
339
other integral membrane proteins are ___ for extracellular proteoglycans
example?
receptors
| integrins
340
Integrins
| these proteins link what? transmit..?
link cellular cytoskeleton to ECM and transmit signals into cell to regulate processe
341
Integrins link cellular cytoskeleton to ECM and transmit signals into cell to regulate? (4)
cell..
-growth
-mobility
apoptosis (programmed cell dying)
wound healing
342
association b/w cells and proteoglycan of ECM is mediated by?
membrane protein (integrin) & extracellular protein (ex. fibronectin)
343
Major component of ECM?
proteoglycans
