memory Flashcards
(268 cards)
1
Q
what is constant about covalent bonds connecting monomers
A
directionality
2
Q
what bond connects amino acids
A
peptide bond (Amide(ketone+N))
3
Q
what bond connects nucleotides
A
phosphodiester bonds (PO4)
4
Q
what bond connects monosaccharides
A
glycosidic bond
5
Q
carbonyl vs carboxyl
A
ketone vs carboxylic acid
6
Q
what is thio group
A
RSH
7
Q
which atom is the donor in hydrogen bonding
A
the one attached to the hydrogen
8
Q
which atom is the acceptor in hydrogen bonding
A
the one using lone pair
9
Q
how many h-bonds do ice and water molecules make
A
4 in ice and usually 2-3 in water
10
Q
when do dipole dipole interactions take place and how strong are they relativly
A
between polar non charged groups
weaker than h bonds but stronger than London dispersion
11
Q
when do London dispersion forces take place and how strong are they relatively
A
between non polar molecules
weaker than dipole dipole
12
Q
what is required for an H bond to happen
A
permanent dipoles involving H and F,O,N
13
Q
what is the hydrophobic effect
A
non polar compounds stick together in aqueous solution. (no bond)
sticking together increase entropy of the water which is favoured.
14
Q
what are amphiphilic/amphipathic molecules
A
both hydrophobic and hydrophilic.
15
Q
what facets of cellular life are nucleotides involved in
A
redox reaction
energy transfer
intracellular signal
biosynthetic reaction
genetic info
enzyme
16
Q
what are nucleotides composed of
A
phosphate(s)
sugar
nitrogen aromatic base
17
Q
what sugars can be found in nucleotides
A
deoxyribose
ribose
18
Q
describe pyrimidine and what bases are part of it
A
aromatic ring with 2 nitrogen
cytosine and thymine/uracil
19
Q
how to tell apart cytosine, thymine/uracil
A
thymine has 2 carbonyl groups. uracil is like thymine but without the methyl group
20
Q
describe purine and what bases are part of it
A
6 and 5 aromatic ring with 4 nitrogen.
adenine and guanine
21
Q
how to tell apart adenine and guanine
A
guanine has the carbonyl group
22
Q
which lone pairs cannot accept hydrogen bonds
A
resonance in ring. not allowed because they are delocalized and not available.
23
Q
which nitrogen of the bases does the 5 carbon sugar attach to to for nucleosides
A
pyrimidines N1 - C1’.
purines N9 (5 ring) - C1’
24
Q
how are deoxyribose and ribose different
A
deoxyribose is lacking an oxygen from its 2 carbon
25
what is the difference between a phosphoester bond and a phosphodiester bond
1 r
2 r
26
what is a phosphoanhydride bond
joins two phosphates together
27
which parts of the nucleotide is polar and non polar
the base is non polar
sugar and phosphate are polar
28
what is the difference between RNA and DNA backbones
RNA backbone is more polar
29
when is the bis and tris prefixes used in nucleotide nomenclature
phosphates attached to MULTIPLE carbon or hydroxide groups
30
what is the spontaneous alkaline hydrolysis of phosphodiester bonds in RNA
why does this not happen in DNA
the hydrolysis of the phosphodiester bond results in the phosphate group forming an unstable 5 sided ring that either forms an 2' or 3' phosphate group.
in DNA because the 2' carbon of deoxyribose is missing an oxygen, it cannot undergo this reaction
31
why is using thymine instead of uracil an advantage in DNA
cytosine can delaminate to form uracil spontaneously which can cause mutations.
because uracil is not supposed to be in DNA, repair mechanism will recognize and remove uracil
32
how can ultraviolet light absorption give info on DNA concentration and purity
electron delocalization due to aromatic bases absorb UV light.
260mm absorption/280mm absorption of 1.95 is pure. lower than that decreases the purity. (protein contamination)
absorption at 260mm and DNA concentration has a linear relationship
33
what is the secondary structure of DNA
chains of nucleotides form a right handed double helix shape and bond using hydrogen bonding
34
describe the hydrogen bonding between nucleotides in DNA
a-t has 2 hydrogen bonds
g-c has 3 hydrogen bonds
35
how is b-form DNA stabilized
base stacking (mostly van Der Waals + hydrophobic)
hydrogen bonding stabilized because bases are excluded from h2o
36
why does DNA denaturation happen. how can this be observed
disruption of the non-covalent bonds holding the two strands together.
single strand DNA has higher absorption (hyperchromicity) at 260mm so recording an increase in 260 means there is denaturing happening
37
what is the relationship between 260mm absorption of DNA sample and an increase in temperature.
sigmoidal relationship. cooperative
38
what is Tm of DNA
midpoint of melting DNA
39
what happens when DNA complimentary strands which were denatured are suddenly renatured at a temperature much cooler than their Tm
improper pairing. requires denaturing again to fix
40
why does G-C base pairs have a lower Tm than A-T base pairs
greater base stacking in G-C. NOT DUE TO EXTRA H BOND
41
when denaturing a dsDNA why do some areas separate first.
A-T rich areas go first because of lower Tm
42
If given the percentages of each base pair in a few dsDNA chains, how can you tell which one will denature first
highest A-T content
43
how does pH and salt concentration change Tm of dsDNA
all deviations in pH away from homeostasis decreases Tm
increase in salt increases Tm
decreases in salt decrease Tm
44
if two samples of different dsDNA are both mixed together and denatured and then renatured forming some hybrids what does this mean
there are similar sequences between the two dsDNA
45
what is different when comparing DNA to RNA 3d structures
RNA SS will spontaneously fold on itself and form INTRASTRAND base pairing which is stabilized by hydrogen bonding and base stacking in a manner that is dependant on the nucleotide sequence of the RNA
46
What is unique about the stabilizing forces in RNA secondary structures compared to DNA
contains hydrogen bonds but non Watson crick base pairs are also present.
base stacking is identical with helical right handed structures utilizing hydrophobic and van Der Waals forces to stay together
47
what is the Abs 260/ abs280 for RNA
2.1
48
what is the structure of a DNA RNA double stranded helix
right hand helix with both strands running ANTIPARALLEL
49
how is the RNA melting curve different from DNA
since RNA structures are already partially single stranded, they start at a higher absorption
50
what are the functions of proteins in the body
structure, movement, catalysis, communication, transport
51
what is a zwitterion
neutral ion with equal pos and neg charges
52
how is the ionization state of amino acids altered by pH changes?
whenever the pH is greater than the pka then the base is favoured over the acid, reverse applies too.
this can result in the amino acid gaining a hydrogen at pH below 2 and having a positive charge
amino acid at a pH above 9.5 can result in a loss of a hydrogen and the charge becoming negative
53
what happens to the concentration of base and acid when pH is greater than pka
base is favoured.
54
what happens to the concentration of base and acid when pH is lesser than pka
acid is favoured
55
Which stereoisomer of amino acids are used in proteins
L-form
56
what are the non polar amino acid mnemonic
Grandma Always Visits London In May For Winston's Party
Glycine (slightly polar) alanine valine leucine isoleucine methionine proline.
draw them out
57
what are the polar amino acids mnemonic
Santa's Team Crafts New Quilts Yearly - polar AA's
Missing glycine
serine threonine cysteine asparagine glutamine
tyrosine
draw them out
58
what are the charged amino acids mnemonic
Dragons Eat Knights Riding Horses - charged AA's
aspartate glutamate lysine arginine
draw them out.
59
what are some of the properties of peptide bonds
planar and rigid
resonance delocalized lone pairs prevents h-bonds
alpha carbon to carbon bond can rotate
60
what is a secondary protein structure
spacial orientation of polypeptide backbone
61
what is a tertiary protein structure
3d structure of polypeptide including side chains
62
what is a quaternary protein structure
spacial arrangement of polypeptide chains in a protein with multiple subunits
63
what is the primary protein structure
AA sequence
64
why is the rotation of peptide bonds limited and what does this result in
steric interference
results in shapes that maximize H bonds and minimize steric hinderance
alpha helix
beta sheet
65
what are some characteristics of the alpha helix
right hand helix
carbonyl oxygen forms H bond with NH3 4 residues down if it can.
close enough for van Der Waals contact
66
what is the difference between regular and irregular protein structures
regular means local repeating shapes like alpha helix and beta sheet
irregular is everything else
67
what is the difference between the two main protein classes
fibrous
-insoluble in aqueous
-elongated shape
-usually forms structural or connective proteins
Globular
-soluble in aqueous
-fold into compact structures
68
where are hydrophobic side chains most likely to be found in a globular protein
inside
69
why are irregular secondary structures primarily found on the outside of the protein
non polar interior cannot satisfy H bond needs
70
describe the forces involved in protein folding
primarily hydrophobic effects bunching all the non polar side chains together
ionic interactions and H bonds also help fine tune the shape
disulphide bonds add rigidity to the structure
71
what is a protein domain
a domain a folded compact part of a tertiary structure that is recognizable and noticeable a little separate.
like a sleeve is to a shirt. a component
72
What is a protein motif
a short part of poly peptide with a recognizable pattern.
73
what is a protein prosthetic group
non peptide part that is permanently incorporated into protein. they provide structure and functional chemical groups
74
how does heat denature globular protein
disrupts H bonds and hydrophobic interactions
75
how does changes in pH denature globular protein
disrupted ionic interactions and h bonding
76
how does changes in salt concentration denature globular proteins
disrupts ionic interactions
77
how does detergent denature proteins
disrupts hydrophobic interactions by bonding to hydrophobic regions
78
what is the nomenclature for quaternary protein structures
Dimer, trimer, tetramer, pentamer
homodimer, heterodimer
79
what forces stabilizes quaternary structure
hydrophobic interactions bring it together. hydrophobic sides of each subunit comes together.
h-bonds and ionic interactions fine tune structure
80
what is protein Kd
equilibrium constant for protein ligand bonding.
Kd is the concentration of ligand at 50% saturation
lower kd is steeper slope
81
describe the structure of myoglobin
monomer consisting of 8 alpha helices and a heme prosthetic group
82
describe the structure of heme
heme is a circular and planar structure with 4 nitrogens surrounding a Fe2+
83
how is heme kept in myoglobin
heme is held in place by hydrophobic interactions and the proximal histidine in the Heme's 5th position
proximal histidine also prevents the oxidation of the iron atom in heme
84
what goes in the 6th position on heme
an oxygen molecule
85
what is the role of the distal histidine in myoglobin
E7His
increases oxygen boding affinity
increases specificity for carrying oxygen by physically excluding other molecules
86
how is ligand affinity and specificity related
relative affinity is related to specificity, If a ligand is has more affinity it is more likely to bind to that protein
87
what type of plot best describes o2 saturation curve of myoglobin
hyperbolic. Constant affinity.
88
describe the quaternary structure of hemoglobin
heterotetramer
2 alpha subunits
2 beta subunits
total 4 Heme prosthetic groups.
89
why are the alpha, beta subunits from hemoglobin and myoglobin considered homologous
probably share a common ancestor due to very similar structures
90
what are some differences between homologous proteins
usually have similar or identical AA in critical locations
these similar AAs are called conservative substitutions. AA is replaced with a similar structure AA
91
what are critical substitutions in proteins
AA substitutions that change structure and function significantly
92
what are the products of spontaneous hydrolysis of phosphodiester bonds in an RNA
5’OH bottom RNA + either 2’ or 3’ nucleoside monophosphate
93
what type of curve is indicative of constant affinity
hyperbolic. Kd does not change
94
what type of curve is indicative of cooperative binding affinity
sigmoidal
affinity changes as more binds
95
how does Hb change its affinity for O2
changing from the low affinity T state to the high affinity R state
96
what are the physical shape differences between T and R state Hb
T has larger central cavity while R has a smaller one
97
what is a homoallosteric vs heteroallosteric
homoallosteric means binding of an effector affects the further binding of the same compound
heteroallosteric means binding of an effector affects the binding of a different compound
98
what is a homoallosteric activator of Hb
O2
99
what is the homoallosteric activator of Mb
none. constant affinity
100
what happens when the first O2 binds to Hb
o2 binds
Fe2+ moves into plane of heme
drags proximal (f8) histadine, f helix then whole subunit with it.
movement changes the T state to R state
101
what type of allosteric effector is 2,3bpg and hydrogen ion for hemoglobin
2,3bpg is a heteroallosteric inhibitor
H+ is a heteroallosteric inhibitor
102
what are the key characteristics of 2,3bisphosphateglycerate
small and highly negative
103
how does 2,3 BPG bind to Hb
2,3 BPG goes into the larger central cavity of T state Hb. Negative charges interact with positive charge groups that are facing the central cavity
104
what is the effect of hydrogen ions on Hb and what is it called
protonations of side chains and functional groups
-distal and proximal histidine excluded
Pronation of groups associated with 2,3 BPG enhances 2,3BPG and decreases o2 binding
bohr effect
105
the proportion of Hb molecules that exists in the T and R state depends on what
Presence of 2,3BPG, concentration of hydrogen ion, partial pressure of O2
106
high pO2 and pH favours which state of Hb
relax
107
low pO2 and pH favours which state of Hb
tense
108
what is the effect of sickle cell mutation
causes a small hydrophobic patch on the surface of the Hb that causes the molecules to form into long fibres/polymers
109
what is the difference between fetal and adult hemoglobin
his143 is replaced with serene
his143 is a central cavity involved in 2,3BPG so replacing it decreases BPG affinity and increases O2 affinity
110
what are the only two ways reactions can be accelerated
adding heat (increases energy of reactants)
adding catalyst (decreases activation energy barrier)
111
what type of biomolecule are enzymes typically
proteins
112
what are the characteristics of enzymes
they accelerate reaction rates
regenerated at the end of reaction (net 0 impact on quantity of enzyme)
increase reaction rate 10^6-10^20
highly specific, no side reactions
113
what distinguishes enzymes from non biological catalysts
enzymes are regulated and flexible
114
what is the rate of a favourable biochemical reaction determined by
size of activation energy barrier
115
how do enzymes reduce the free energy of the transition state
desolvation, removing the substrates from an aqueous environment
proximity and orientation effects -align the parts
taking part in the reaction mechanism
stabilizing the transition form.
116
what structure determines the affinity specificity and rate of enzyme catalysis
active sites
117
what part of the enzyme does catalysis occur
active sites
118
what allows an enzyme have specificity and affinity
complementary active site structures and shape to its substrate.
key and lock
119
how does desolation improve reaction rates
removes water shell
enhances polar interactions
prevents side reactions
120
what is enzyme induced fit
when enzymes change shape during substrate binding to close off the active site from water and bring reactive groups together
121
describe what enzyme proximity and orientation effects are
chemical reactions only occur if substrates come together in the right orientation to react so active sites on enzymes can bring the substrates close together and in the correct orientation to react. This accounts for a thousand fold increase in rates
122
how do enzymes participate in reactions
positioning functional groups near substrates that can act as acid/base, covalent, metal ion catalysts. Amino acids and cofactors can do this
123
which amino acid side chains can act as acid or base catalysts
aspartate glutamate histamine lysine
124
which amino acids side chains can act as nucleophiles in covalent catalysis
serine tyrosine cystine lysine histadine
in deprotonated forms
125
what are cofactors
molecules or compounds that can enhance the reactive potential of polypeptides by providing new functional groups
126
what are the two types of cofactors
metal ions and coenzymes
127
Can coenzymes be consumed in a enzyme catalyzed reaction
no must be regenerated
128
what is the difference between an apoenzyme and a holoenzyme
polypeptide that have a prosthetic group forming a functional tertiary structure is a holoenzyme
apoenzymes are polypeptides without prosthetic groups
129
what is enzyme transition state stabilization
binding to the transition state will lower transition energy barrier .
130
what would happen to the energy barrier if the substrate was stabilized instead of the transition state
increase energy barrier
131
What are transitions state analogs
potent inhibitor for enzymes because they bind to transition state stabilizers at higher affinities than substrates.
132
what is the relationship between reaction velocity and concentration of substrate
hyperbolic
133
what is Km
concentration of substrate that can reach half of max velocity
the same as Kd for ligand binding but instead for enzymes.
134
what are the mechanisms of regulating intrinsic enzyme activity
competitive inhibition
allostery
reversible covalent modificaiton
ionic signals
135
what are the mechanisms of regulating enzyme activity but not having the intrinsic activity
changing the amount of enzyme and changing the substrate location relative to enzyme
136
do competitive inhibitions bind irreversibly to active sites
no. reversible
137
when competitive inhibitors bind what happens to Km
appear to increase Km
138
how can competitive inhibitors be overcome
increasing substrate concentration
139
how does the reaction velocity and substrate concentration curve differ between allosteric and non allosteric enzymes
allosteric will have sigmoidal curve because it has different states with different activity T and R states like hemoglobin
140
what type of effector is the substrate if an enzyme is allosteric
homoallosteric activator
141
what is enzyme reversible covalent modification
when covalent modification of an amino acid residue changes the tertiary structure of a polypeptide
142
what is the most common type of reversible covalent modification
phosphorylation of an AA with an OH (serine, tyrosine, threonine). this will increase size polarity and charge
143
how can reversible covalent modification change the activity of enzyme
it can increase or decrease
144
what catalyzes the phosphorylation of proteins
protein kinase
145
what catalyzes the dephosphorylation of proteins
protein phosphatases
146
what are the substrates for protein kinase
ATP, protein
147
what are the substrates for protein phosphatase
h2o, phosphorylated protein
148
what are fatty acids
long hydrocarbon chain carboxylic acid
amphipathic
either saturated or unsaturated
149
what is the usual conformation of the double bonds in fatty acids
cis bond
150
how does adding double bonds change the melting point of fatty acids
lowers the melting point
151
what is the notation of fatty acids
(#ofCarbons):(#ofDoubleBonds)DELTA
^(locations of double bonds)
152
how does the length effect the melting point of a fatty acid
increasing length high melting temp
less effect than saturation
153
why do unsaturated melt at lower temps
double bonds bending the molecule don't allow the fatty acids to pact efficiently
154
which melt at higher temps, cis unsaturated fatty acid or trans unsaturated fatty acid
trans because trans conformation doesn't have the same bend shape allowing them to pack better
155
what is a triacylglycerol
glycerol + 3*fattyAcid
usually all different fatty acids (mixed)
156
what are the three types of membrane lipids
glycerophospholipids
sphingolipids
cholesterol
157
describe the structure of a glycerophospholipid
glycerol connected to 2 fatty acids and one polar group
158
what are the important characteristics of cholesterol
very weakly amphipathic
rigid ring structure - contributes to membrane rigidity
30% of mammal membranes
159
describe what a lipid bilayer transition/melting temperature is
changes from a ordered crystalline shape to a fluid state. specific temp depends on acyl chain saturation and length
160
what would be the transition temp difference between artificial and biological transition temperature
artificial membranes are usually homologous so the transition temp will be very specific
biological will have a broader transition temp because there will usually be a bigger mix of compounds
161
how to adapt membrane lipid composition for different temperatures?
changing amount of saturation and length
162
how does cholesterol increase membrane rigidity and what does that do
cholesterol is very rigid and planar due to ring structure which limits how much the surrounding acyl tails can move.
This helps maintain rigidity at higher temps and reduce packing at lower temps.
163
how can lipids move in a bilayer
they can move freely laterally
but do not move transversely normally. Flipases enzyme can increase the rates
164
what are the types of membrane proteins
integral, peripheral, lipid linked
165
how do integral membrane proteins hold on to the bilayer
hydrophobic interactions
166
how do peripheral membrane proteins hold on to the bilayer
electrostatic
167
how do lipid-linked membrane proteins hold on to the bilayer
lipid prosthetic groups holding on with hydrophobic effect
168
what polarity are the majority of AA in a transmembrane protein
nonpolar
169
what type of protein secondary structures usually crosses membranes
alpha helix
beta sheet
170
what is the fluid mosaic model of membrane structure
lipids and proteins can move laterally
cytoskeleton limits movement of proteins
carbohydrate chains are connected to extracellular surface of some proteins and lipids
171
what molecules can simple diffuse across the lipid bilayer
gases, small polar, hydrophobic
172
what molecules are blocked by the lipid bilayer
large polar and charged molecules
173
what does the rate of simple diffusion rely on
concentration gradient.
size of molecule
lipid solubility
174
can net energy be greater than 0 when cross a membrane
no. even active must consume energy to make it less than 0
175
what are porins
usually water filled pores made from beta sheets.
176
what are ion channels
very selective holes in lipid bilayer
177
what is different between a carrier protein and a channel
transporter has conformation changes and do not have a membrane spanning holeq
178
what is the relationship between transport velocity and concentration gradient
hyperbolic
179
what is the difference between a primary and a secondary active transporter
primary relies on ATP as energy source
secondary relies on an ion gradient as an energy source
180
what type of transporter is Na+ K+ ATPase
primary active antiport transporter.
3Na+ out and 2 K+ in for one ATP
181
what type of transporter is the Na+ glucose transporter
secondary active symport transporter. used Na+ gradient as energy
182
what are the two major purposes of metabolism
obtain usable chemical energy from the environment
make specific molecules needed to live and grow
183
what is the difference between reduction and oxidation
reduction involves making new single bonds and oxidation involves breaking single bonds
184
what is the difference between a reductive agent and a oxidative agent
reductive agent is being oxidized so the other substrate becomes reduced
oxidative agent is being reduced so the other substrate become oxidized
185
what is the end product of carbon oxidization
carbon dioxide
186
what does the little circle above change in energy mean
energy change in standard state
do not mistake for the actual free energy it is not
187
what happens when delta G is greater than 0
nothing in the forward direction
188
what happens when delta G is much smaller than 0
irreversible
189
what happens when delta G is near 0
reversible reaction
190
what steps are usually regulated in metabolism
irreversible
191
what is reciprocal regulation
pathways in the same direction catalyze each other. prevents pathways from running in 2 directions at the same time.
192
when running a metabolic reaction pathway in the opposite direction what reactions must be changed
irreversible
193
what are the types of high energy intermediates
Electron carriers (NADH, NADPH, FADH2)
Nucleosides triphosphates
thioesters
194
what is important about NAD+ and FAD
they can undergo reversible reduction reaction because of nitrogen base which is why they are common (oxidizing agents) cofactors in catabolism
195
what is different about the use of NAD+ and FAD
NAD+ as a cosubstrate can just leave after being reduced.
FAD is a prosthetic group so it is stuck to the enzyme. when it is reduced it must be oxidized before the reaction happens again. usually by CoQ
196
why is ATP a high energy molecule
when inorganic phosphate is released
increased resonance stabilization,
electrostatic repulsion decreased
(not forced together)
solvation effects
197
why are thioesters high energy compounds
same as esters but has no resonance so there is a bigger energy difference
198
which high energy intermediates are involved in glycolysis
phosphoenolpyruvate
1,3 BPG
199
how does phosphocreatine generate energy
hydrolysis of phosphocreatine resulting in phosphate transfer to ADP forming ATP
catalyzed by CREATINE KINASE
200
what is oxidative phosphorylation
2 separate but connected processes
oxidation of FAD and NAD+
phosphorylation of ADP to ATP
linked by proton gradient across mitochondrial membrane
201
what is the structural difference between FMN and FAD
no adenosine
202
what is the role of CoQ in electron transport chain
Lipid soluble molecule that moves electrons from complex 1 or 2 to complex 3
203
what determines the order of compounds that electrons go through in the electron transport chain
lower reduction potential to higher reduction potential
larger reduction potential change means more negative deltaG
This free energy change then used to transport protons across the membrane (primary transport)
204
what path does NADH take through the ETC and how many protons does this move out of the matrix
complex 1
CoQ
COMPLEX3
cytochrome c
COMPLEX4
10 protons
205
what are the important characteristics of Complex 2 of the ETC
succinate dehydrogenase with FAD prosthetic group.
no protons are moved by complex 2
206
what path does FADH2 take through the ETC and how many protons does this move out of the matrix
Complex 2 (succinate dehydrogenase)
CoQ
Complex 3
Cytochrome C
Complex 4
6 protons
207
what is the proton electrochemical gradient
gradient induced by complex 1,3,4 using primary active transport to move protons to low pH intermembrane space which increases potential energy
208
what is the action of ATP synthase
uses the proton electrochemical gradient for phosphorylation of ADP into ATP
209
what are the two parts of ATP synthase
F0
-transmemebrane
-protons pass through
-triggers a conformational change in F1
F1
-catalytic portion
-makes ATP from ATP and Pi
210
describe the structure of F1 ATP synthase
a wheel that is turned by F0 shaft. 3 active sites making ATP
211
what happens to the ATP after it is created inside the mitochondria by ATP synthase
anti port with ADP to leave the mitochondria.
212
how does the inorganic phosphate needed for ATP synthase get into the mitochondria
Pi - H+ symport.
Pi is moved with H+ gradient.
secondary active
213
how are phosphorylation and oxidation coupled
ATP synthesis and consumption reduce the magnitude of proton electrochemical gradient which is recovered by oxidation of cofactors
-you can only use as much as you make
214
what is the P:O ratio of NADH and FADH2
NADH 2.5
FADH2 1.5
deoxidation of both only make one water.
215
what determines the rate of oxidative phosphorylation
[ADP] determines ATP synthase activity (phosphorylation) which determines H+ EC gradient which determines rate of oxidation
216
how is oxygen consumption rate connected to [ADP]
O2 consumption rate connected to oxidation rate which is a result of ATP synthase activity
217
what happens when there is a decrease in electron transport in ETC
increased concentration of NADH and FADH2 which inhibits PDH and CAC
218
what happens when there is a increase in electron transport in ETC
decreased concentration of NADH and FADH2 which activates PDH and CAC
219
what is another way protons can enter the mitochondrial matrix other than ATP synthase and Pi-H+ symport
uncoupling protein generates heat from H+ crossing instead of ATP.
brown fat way of generating heat
220
what is the effect of an uncoupler on O2 consumption
increase. dissipates gradient separate from ATP synthase
221
what is 2,4-dintrophenol
diet pill that dissipates H+ gradient by converting to kinetic energy.
overheating can be fatal
222
what is glucogenolysis
glycogen ->pyruvate
223
what is gluconeogenesis
pyruvate -> glucose
224
what are the characteristics of the hexokinase reaction
coupled reaction
irreversible
phosphate transfer
regulated.
225
what is a substrate level phosphorylation
when high energy phosphorylated compound transfers phosphate group to ADP
226
Annotate glycolysis pathway with ATP , NADH involvement
check notes.
227
what is the difference between glucose and fructose
aldehexose vs ketohexose
228
what are the characteristics of PFK1 reaction
irreversible
coupled reaction
phosphate transfer
regulated and rate limiting for glycolysis
229
explain how F1,6BP turns into 2 GAP
first split into DHAP + GAP (isomers)
DHAP is then converted into GAP
230
which reactions in glycolysis have energy investment
hexokinase and PFK1
reactions that attach a phosphate to the sugar
231
describe the GAPDH reaction in glycolysis
GAPDH catalyses the reaction that adds an inorganic phosphate into GAP to make 1,3BPG
reversible
energy capture (makes NADH)
phosphate addition (not transfer)
232
which are the high energy intermediates in glycolysis
1,3BPG
phosphoenolpyruvate PEP
233
why does 1,3BPG have such a large transfer potential
can dissociated into two products both with resonance
234
describe the reaction that uses 1,3BPG
1,3BPG and ADP turn into 3PG and ATP
energy capture (ATP)
coupled reaction
reversible
substrate level phosphorylation
235
how many times does phosphate transfer happen in glycolysis for one glucose
6 times.
twice for investment
four times for payout (2x2)
236
what is the rate of metabolic processes regulate by
substrate availability
change of enzyme activity
change of enzyme quantity
compartmentation
237
which are the regulated enzymes in glycolysis
hexokinase
PFK1
pyruvate kinase
238
how is hexokinase regulated
product inhibition. glucose 6 phosphate
239
what is PFK1 regulated by
inhibited by citrate, ATP, PEP(feedback inhibition)
activated by AMP
240
what is pyruvate kinase regulated by
Fructose 1,6 phosphate feed forward activation
ATP product inhibition
PEP homoallosteric activation
241
what type of enzyme is pyruvate kinase
allosteric enzyme
sigmoidal curve
PEP is a homoallosteric activator
242
why is it important that both PFK and PK is inhibited by ATP
synchronous regulation of irreversible reactions helps maintain intermediates steady state
243
which is the oxidation reaction in glycolysis
GAPDH
244
what are the fates of pyruvate
ethanol
lactate
acetyl CoA
245
how many NADH is produced from one glucose
2
246
describe the production of lactate
pyruvate + NADH + H <---> lactate +NAD
247
what happens to lactate after production
exported by a lactate proton symport
then can be reformed into pyruvate and used as fuel for cardiac tissue
248
how can lactate export from cell be beneficial during intense exercise
symport with proton can lead to decrease in pH of blood which reduces affinity for O2. increase O2 release at muscle
249
what effect does lactate production have on pH
production consumes a proton
increase pH
250
what happens when ethanol is created from pyruvate
anaerobic fate for yeast
decarboxylation and reduction reaction
produces CO2, ethanol and NAD+
251
what links glycolysis to CAC
PDH reaction
252
where does PDH reaction occur
mitochondria matrix
253
which metabolic processes happen inside mitochondria matrix
PDH
CAC
oxidative phosphorylation (ETC)
beta oxidation
254
how does pyruvate get into mitochondria matrix for PDH
outer membrane has porins that are easy to pass though
inner membrane passed using (pyruvate translocase) symport with hydrogen ion. active secondary transport
255
describe the PDH reaction
pyruvate +HSCoA+ NAD ----> Acetyl CoA+ CO2+NADH
oxidative decarboxylation
irreversible
transacetylation (acetyl group moves to CoA)
256
describe the structure of Acetyl CoA
acetyl group attached to CoA with thioester bond
257
Describe the structure of PDH/ PDC and it's advantages
multiezyme complex
-speeds up reaction times
-limits side reactions
-multiple ezymes controlled together
258
what is the structural difference between active and inactive PDH
inactive PDH has a phosphate group attached.
attached by kinase. detached by dehydrogenase
259
how many CO2 is produced in the CAC
2 per Actyl CoA
260
how is FADH2 deoxidized in succinate dehydrogenase
reduced Q into QH2
261
which enzymes are regulated in CAC
isocitrate dehydrogenase
a-ketoglutarate dehydrogenase
262
is the CAC catabolic or anabolic
both. amphibolic
this is because CAC intermediates can also be used to synthesize AA, Carbohydrates, fats, nucleotides and others
263
what are anaplerotic reactions?
reactions that replenish CAC intermediates
264
what is the pyruvate carboxylase reaction
pyruvate carboxylase catalyzes the reaction that converts pyruvate into oxaloacetate
an anaplerotic reaction
activated by acetyl CoA
inhibited by ADP
265
how many ATP does the CAC generate for each acetyl CoA
3NADH x 2.5 = 7.5 ATP
1 FADH x1.5 = 1.5 ATP
1GTP = 1 ATP
10 total
266
what is the function of the CAC
provide biosynthetic precursor (NADH FADH2)
267
how many ATP is produced by complete aerobic oxidation of glucose
32 ATP
268
why is lactate a metabolic fuel in aerobic metabolism
Lactate converted into pyruvate then acetyl coA into the CAC
