Metabolic Pathways Flashcards
1 g of carbohydrate is equal to what kcal
1 kcal
increases the chemical reaction significantly
catalyst
are the biochemicals that come together and interact at the beginning of the
process such that they are converted into one or more different biochemicals
reactants
temporary state wherein they become or processed futher
intermediates
reactants can become ___ if the next step is a branching point
common intermediates
refer to a chemical that participates as one of the starting chemicals in a
chemical reaction that produces other substance(s).
precursor
” is used more specifically to refer to a
chemical compound preceding another in a metabolic pathway.
precursor
e types of proteins that play an important role in metabolism by catalyzing the
individual reactions in metabolic pathways.
enzymes
Enzymes that catalyze the first reaction in a metabolic pathway are sometimes subject to
___ control by the concentration of the end product of the metabolic pathwa
allosteric
” is a word used in chemistry generally (not just biochemistry) to refer to chemicals
that affect the rate (speed) of chemical reactions by participating in the reaction(s) but in
such a way that itis not consumed by the reaction itself.
catalyst
, the presence of a
___ may be necessary for a reaction to occur to any meaningful extent under certain
conditions
catalyst
are compounds that are neither the initial (starting) chemicals in a pathway or
“process”, nor the end-products used directly or secreted by the cell, nor catalysts (that
participate in but are not used-up by the reactions)
intermediates
are compounds
that are formed as temporary “steps” in the overall chemical process
intermediates
are compounds that occur at branching points in metabolic
pathways.
common intermediates
are compounds that are produced by metabolic
reactions that do not go on to participate in a subsequent reaction in the metabolic pathway.
end products
The concentration of the end products of a metabolic pathway often regulates the rate of the
reaction that produces them, i.e. effectively a ___ that prevents over-production
feedback loop
inhibition or activation of an enzyme by a small regulatory molecule that interacts at a site other than the active site
allosteric control
is a form of negative feedback by which metabolic pathways can be controlled.
end product inhibition
Some branching points in metabolic pathways are sometimes called
cross-over points
s refer to a stage in a metabolic pathway at which an intermediate
(usually a molecule or part of a molecule), could proceed to change in more than one
possible way, i.e. it could follow two or more possible “(metabolic) pathways”.
branching points
The “pathway” followed (next change undergone) by the intermediate is usually the one of
most immediate benefit to the cell, that “decision” being determined by the activity of
____ present around the intermediate.
enzyme
is a position at which at least two “paths” intersect
junction
implies that the intersection is particularly important, i.e.
one at which decisions taken about which on-going paths to follow from that point onwards
may change depending on circumstances and have important consequences.
key junction
are substances (usually compounds) that participate in metabolism processes
and are either produced during metabolism reactions or are “constituents of” i.e. parts that
make-up, foods taken into the body - then broken-down via the digestive
processes
metabolites
are therefore among the chemicals included in metabolic pathways.
They are often intermediates between reactants and end-products.
metabolites
metabolites that are molecules that are essential for an organism’s growth, development, and reproduction:
primary metabolites
metabolites that are organic compounds produced by organisms that are not essential for the organism’s growth, development, or reproduction.
secondary metabolites
is the descriptive term used to refer to some metabolic pathways or parts
of metabolic pathways that take the form of repeated ‘cycles’ in which product(s) of the
individual metabolic reactions in the sequence become the reactants, i.e. the “starting
chemicals”, for the next metabolic reaction in the sequence.
metabolic cycles
metabolic cycles include
Krebs TCA Cycle
Calvin cycle
Urea cycle
” is a point at which many “pathways” meet. These could be routes, wires,
lines of communication or similar e.g. as used in the context of air-travel or information
technology
hub
can therefore be thought of as a location at which many metabolic
processes occur, enabling substances such as molecules, e.g. reaction intermediates, to
transfer between reaction processes on an as-needed basis.
metabolic hub
example of metabolic hubs in the body
krebs TCA cycle
liver
generally modify biochemicals via a series of small steps (stages in the process) rather
than a single chemical reaction
metabolic pathways
Minor adjustments can be made to the structure of the molecules.
Energy is released / used in manageable quantities.
what characteristic of metabolic pathway
metabolic pathways generally modify biochemicals via a series of small steps
Many balances - i.e. requirements for specific enzymes - keep the rate of metabolic processes in
check.
what characteristic of metabolic pathways
each step in a metabolic pathway is a chemical rxn that can catalyze a specific enzyme
Benefit: The biochemical reactions at each stage of a metabolic pathway are more likely to proceed (that is,
continue to happen) because the products of that particular reaction do not accumulate because they go on
to participate in the next step in the metabolic pathway … which changes them into other biochemical(s).
what characteristic of metabolic pathways
chemical equilibrium may never be reached because the products of reactions do not continue to exist in that form due to participation of nexts step
one that is not part of a metabolic pathway but is
considered entirely on its own - the meaning of “isolated”. In that case only a certain proportion of the
reactants may be converted into the products of the reaction due to a natural “equilibrium” situation at which
a certain proportion of the total matter concerned is in the form of the reactants and a certain
(other) proportion in the form of the products of the reaction
isolated chemical rxn
Benefit: Accumulation of concentrations of biomolecules that are the reactants of a step in a metabolic
pathway can help to increase the rate (i.e. the “speed”) of the process. This is related to the above
considerations of “equilibrium”.
what metabolic pathway characteristic
Steps in a metabolic pathway tend to be arranged in physical space such that the product of one reaction is
in the right place to become a reactant (or “precursor”) in the next step in the sequence.
is the metabolic pathway that converts glucose C6H12O6, into pyruvic acid, CH3COCOOH
glycolysis
does glycolysis require oxygen?
no
an ancient metabolic pathway
glycolysis
parallel pathway of glycolysis
pentose phosphate pathway
what metabolic pathway, occur in the oxygen-free conditions of the Archean oceans, also in the absence of enzymes, catalyzed by
metals
glycolysis
pentose phosphate pathway
two phases of glycolysis
investment phase
yield phase
The first step is phosphorylation of glucose by a family of enzymes called ___ to form glucose 6-phosphate (G6P).
hexokinase
This reaction consumes ATP, but it acts to keep the glucose concentration low, promoting continuous transport of glucose into
the cell through the plasma membrane transporters.
conversion of glucose to glucose 6-phosphate
In addition, the conversion of glucose to glucose-6 phosphate blocks the glucose from leaking out because ___
the cell lacks
transporters for G6P, and free diffusion out of the cell is prevented due to the charged nature of G6P
why free diffusion of glucose 6-phosphate is not possible
charged
Glucose may
alternatively be formed from the ____ or hydrolysis of intracellular starch or glycogen.
phosphorolysis
Glucose may
alternatively be formed from the phosphorolysis or hydrolysis of intracellular ___ or ___.
starch
oxygen
is a biochemical process that breaks down chemical bonds in a compound using inorganic phosphate
phosphorolysis
In animals, an isozyme of hexokinase called ___ is also used in the liver, which has a much lower affinity for glucose
(Km in the vicinity of normal glycemia), and differs in regulatory properties
glucokinase
The different substrate affinity and alternate
regulation of this enzyme are a reflection of the role of the liver in maintaining blood sugar levels.
glucokinase
G6P is then rearranged into fructose 6-phosphate (F6P) by what enzyme
glucose phosphate isomerase
can also enter the
glycolytic pathway by phosphorylation at this point.
fructose
The change in structure is an ____ , in which the G6P has been converted to F6P
isomerization
This reaction is freely reversible under normal cell conditions
what step in glycolysis
conversion of F6P to G6P
The change in structure is an isomerization, in which the G6P has been converted to F6P. The reaction requires an enzyme,
phosphoglucose isomerase, to proceed. This reaction is freely reversible under normal cell conditions. However, it is often
driven forward because of a low concentration of ___
F6P
under
conditions of high F6P concentration, this reaction readily runs in reverse. This phenomenon can be explained through what principle
Le Chatelier principle
Isomerization to a keto sugar is necessary for ____stabilization in the fourth reaction step
carbanion
. Because the reaction catalyzed by _____
1 (PFK-1) is coupled to the hydrolysis of ATP (an energetically favorable step)
phosphofructokinase
rate limiting step in glycolysis, a key regulatory point
phosphofructokinase coupled with the hydrolysis of ATP
s necessary to allow the formation of two charged groups (rather than only
one) in the subsequent step of glycolysis, ensuring the prevention of free diffusion of substrates out of the cell.
second phosphorylation event
The same reaction can also be catalyzed by pyrophosphate-dependent ____ (PFP or PPi-PFK), which is
found in most plants, some bacteria, archea, and protists, but not in animals
phosphofructokinase
phosphofructokinase uses what phosphate donor instead of ATP
pyrophosphate
is the conversion using phosphofructokinase reversible?
yes
Destabilizing the molecule in the previous reaction allows the hexose ring to be split by aldolase into two triose
sugars: dihydroxyacetone phosphate (a aldose/ketose), and glyceraldehyde 3-phosphate (an aldose/ketose)
ketose
aldose
two classes of aldolases
class I
class II
aldolases present in animals nad plants
aldolases I
aldolases present in fungi and bacteria
class II aldolases
is a glycolytic enzyme that catalyzes the conversion of fructose 1-6-diphosphate to glyceraldehyde 3-phosphate and dihydroxy-acetone phosphate via the glycolysis metabolic pathway
aldolase
The resulting carbanion is
stabilized by the structure of the carbanion itself via ___ charge distribution and by the presence of a charged ion
prosthetic group.
resonance
rapidly interconverts dihydroxyacetone phosphate with glyceraldehyde-3-phosphate (GADP) that
proceeds further into glycolysis.
triosephosphate isomearase
The second half of glycolysis is known as the
pay-off phase
yield of pay-off phase of glucose
2 NADH
4 ATP
The aldehyde groups of the triose sugars are oxidized/reduced, and inorganic phosphate is added to them, forming 1,3-
bisphosphoglycerate.
oxidized
Hydrogen atom balance and charge balance are both maintained because the phosphate (Pi) group actually exists in the form
of a h
hydrogen phosphate anion
an anion akin to inorganic phosphate may replace phosphate as a substrate to form 1-arseno-3-
phosphoglycerate.
arsenate
As a consequence of bypassing this step, the molecule of ATP generated from 1-3
bisphosphoglycerate in the next reaction will not be made, even though the reaction proceeds. As a result, arsenate is an
___ of glycolysis
uncoupler
This step is the enzymatic transfer of a phosphate group from 1,3-bisphosphoglycerate to ADP by
phosphoglycerate kinase
what enzyme is used to turn G3P to 1,3-bisphosphoglycerate
gylceraldehyde 3-phoshpate dehydrogenase
. This step, one of the two substrate-level phosphorylation steps,requires ADP; thus, when the cell has plenty of ATP (and little ADP), this reaction does not occur.
glycolysis reaching a breakeven point of 2 ATP molecules synthesized
enzyme to convert 1,3-bisphosphoglycerate to 3-phosphoglycerate
phosphoglycerate mutase
next converts 2-phosphoglycerate to phosphoenolpyruvate
enolase
This reaction is an elimination reaction involving an
elimination mechanism.
reaction of 2-phosphoglycerate to phosphoenolpyruvate
A final substrate-level phosphorylation now forms a molecule of pyruvate and a molecule of ATP by means of the
enzyme
pyruvate kinase
e, is a series of chemical
reactions that release stored energy through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins.
citric acid cycle
e is used by organisms that respire (as opposed to organisms that ferment) to generate energy, either
by anaerobic respiration or aerobic respiration
TCA cycle
Its central importance to many biochemical
pathways suggests that it was one of the earliest components of metabolism and may have originated abiogenically.
krebs cycle
The cycle consumes ___(in the form of acetyl-CoA) and water, reduces NAD+
to NADH, releasing carbon dioxide.
acetate
The cycle consumes acetate (in the form of acetyl-CoA) and water, reduces NAD+
to NADH, releasing ___ ___
carbon dioxide
In eukaryotic cells, the citric acid cycle occurs in the
matrix of mitochondrion
In prokaryotic cells, such as bacteria, which
lack mitochondria, the citric acid cycle reaction sequence is performed in the
cytosol
In prokaryotic cells, such as bacteria, which
lack mitochondria, the citric acid cycle reaction sequence is performed in the cytosol with what gradient
proton gradient
The
overall yield of energy-containing compounds from the TCA cycle
3 NADH
1 FADH2
one GTP
is a key metabolic pathway that connects carbohydrate, fat, and protein metabolism.
citric acid cycle
One of the primary sources of acetyl-CoA is from the breakdown of sugars by glycolysis which yield pyruvate that in turn is
decarboxylated by the ___ ___ complex generating acetyl-CoA
pyruvate dehydrogenase
is the starting point for the citric acid cycle. A
acetyl coA
e. Acetyl-CoA may also be obtained from
the oxidation of __ ___
fatty acids
The citric acid cycle begins with the transfer of a two-carbon acetyl group from acetyl-CoA to the four-carbon
acceptor compound (____) to form a six-carbon compound (citrate)
oxaloaceatate
The citric acid cycle begins with the transfer of a two-carbon acetyl group from acetyl-CoA to the four-carbon
acceptor compound (oxaloacetate) to form a six-carbon compound (____)
citrate
The citrate then goes through a series of chemical transformations, losing two carboxyl groups as ___
CO2
enzyme for conversion of Oxaloactetate + Acetyl coA + H2O to Citrate + CoA-SH
citrate synthase
how many carbons does oxaloacetate have
4C
citrate has how many carbons
6C
enzyme for Citrate > isocitrate
aconitase
enzyme for isocitrate > ketoglutarate
isocitrate dehydrogenase
how many carbons does ketoglutarate have
5
enzyme for ketoglutarate > succinyl coA
a-ketoglutarate dehydrogenase
how many c does succincyl CoA have
4
enzyme for succinyl coA to succinate
succinyl CoA synthethase
enzyme for succinate > fumarate
succinate dehydrogenase
enzyme for fumarate > malate with the help of H2O
fumarase
enzyme for malate > oxaloacetate
malate dehydrogenase
Mitochondria in animals, including humans, possess ___ succinyl-CoA synthetases: one that produces GTP from GDP, and
another that produces ATP from ADP
two
what are the products of succinyl coA synthethases in animals
GTP from GDP
ATP from ADP
. Plants have the type that produces what kind of succincyl coA synthethase
ATP
The GTP that is formed by GDP-forming succinyl-CoA synthetase may be utilized by ___ ___ ____to form
ATP (the catalyzed reaction is GTP + ADP → GDP + ATP).
nucleoside disphosphate kinase
