BIOC 221 - Midterm #1 Flashcards
What constitutes life?
self-sustaining chemical system capable of darwinian evolution
- metabolism
- self-replication
- adaptation
autotrophs
use CO2 from environment as carbon source
often photosynthetic
heterotrophs
obtain carbon from complex molecules (ex.glucose) not from environment
(obtain c by degrading nutrients from autotrophs)
metabolism
entire set of enzyme catalyzed transformations of organic molecules in living cells;
the sum of anabolism and catabolism
Anabolism
phase of intermediary metabolism concerned with the energy-requiring biosynthesis of cell components from smaller precursors.
Catabolism
the phase of intermediary metabolism concerned with the energy-yielding degradation of nutrient molecules.
(a) Energy containing nutrients –(catabolism)–> (b) Energy-depleted end products
a) carbohydrates, fats, proteins
b) CO2, H2O, NH3
energy releases yields high energy compounds (ATP, NADH, NADPH, FADH2)
(a) Precursor molecules –(anabolism)–> (b) Cell macromolecules
a) proteins, polysachs, lipids, nucleic acids
b) amino acids, sugars, fatty acids, nitrogenous bases
uses high energy compounds
(2) types of metabolic pathways
1) branched
2) linear
(3) non-linear types of metabolic pathways
1) convergent (catabolic)
2) cyclic
3) divergent (anabolic)
In each Metabolic Pathway, a principal ____ is modified by a series of chemical ___ catalyzed by___.
metabolite
reactions
enzymes
The series of reactions that modify a principal metabolite often involve…
cofactors
The end product of a metabolic pathway can have (3) fates
a) used immediately
b) used to initiate another pathway
c) stored by the cell
Primary (Basic) Metabolism:
Metabolic processes that are necessary for the maintenance of life
Primary metabolites:
Intermediates or products of primary metabolism such as amino acids, sugars, lipids, nucleotides, organic acids, polyols, and vitamins
Secondary (specialized) Metabolism:
pathways that are not absolutely required for the survival of the organism. Highly evolvable and pliable.
- derived from primary metabolites
•Unlike primary metabolites, absence of secondary metabolites does not result in ___ ___ , but rather in long-term impairment of the organism’s survivability, reproduction, or aesthetics, or perhaps in no significant change at all.
immediate death
Types of Chemical Transformation in Cells
(4-1) Cleavage/formation of C-C bond
(4-2) Internal rearrangements, isomerizations, and eliminations (including condensation reactions)
(4-3) Group transfers (phosphoryl, methyl, formyl …)
(4-4) Free radical reactions
(4-5) Oxidation-reductions (co-factors – NADH, NADPH, FADH2 - store reducing power)
(4-1) Cleavage/formation of C-C bond
1) homolytic cleavage
2) heterolyic cleavage
(4-1) Nucleophilic Carbon-Carbon bond formation reactions
1) aldol reaction
2) claisen condensation
1) aldol reaction
A nucleophilic carbonyl addition reaction, in which the electrophile is the carbonyl carbon of an aldehyde or ketone
2) claisen condensation
A nucleophilic enolate can also attack the carbonyl carbon of a carboxylic acid derivative in a nucleophilic acyl substitution reaction.
Free energy
portion of total energy of a system that is released
2nd law of thermodynamics:
In all natural processes, the entropy of universe always increases
KNOW AMINO ACID STRUCTURES AND PKA’s
!!!
Why is S more suitable than O for Acetyl-Coenzyme A?
S is larger than O, so S-CoA is better LG (more stable with (-) charge)
Better LG in forward rxn
Better Nu in reverse rxn
heterolytic cleavage
one atom gets both electrons
homolytic cleavage
both atoms get one electron each
(2) criteria for spontaneity
1) ΔG (ΔSuniv > 0)
2 Q/Keq
ΔG = ?
RTlnQ/Keq
ΔG° = ?
Q=1, lnQ=0
so
ΔG° = -RTlnKeq
If Q > Keq
reverse spontaneously
If Q < Keq
forward spontaneously
What does ΔG tell us about rate of reaction?
NOTHING
Reaction rate is governed by?
Activation Energy
(2) ways we can drive forward an unfavorable reaction
1) mass action (product depletion by metabolite channeling)
2) reaction coupling
If a spontaneous process is one that is accompanied by a decrease in free energy, then when is system at equilibrium?
when free energy reaches a minimum, and no further decrease is possible
Why is Q/Keq criteria for free energy?
because when Q/Keq = 1 or Q = Keq, system is in dynamic equilibrium (position of minimum free energy) and ΔG = 0
If S is less stable than P, @ equilibrium…
P > S
Keq > 1
spontaneous forward
If S is more stable than P, @ equilibrium…
S > P
Keq < 1
spontaneous reverse
ΔG’°
free energy change for rxn going from standard conditions
1 M, pH 7, 25°C, 1 atm
ΔG’
free energy change going from set of specific initial conditions to equilibrium
ΔG’ depends on?
Q value
ΔG’° reveals?
how far the initial conditions is from equilibrium of the reaction
Hydrolysis Reactions
- uses H2O to split 2 molecules
tend to be strongly favorable (spontaneous)
How much does Keq vary with small change in ΔG’°?
exponentially
Isomerization Reactions
have smaller free energy changes
ΔG° of Isomerization between Enantiomers?
0
If ΔG° > 0, under what conditions will forward reaction occur spontaneously?
conditions where RT lnQ is overly negative so ΔG becomes negative despite positive ΔG°.
- Q «_space;1
Mass Action
driving reaction forward by altering concentration of S or P
Driving a reaction forward by Mass Action
Q«_space;1 so [S]»[P]
(2) ways for Q «1
1) large [S] - accumulate substrate
2) small [P] - deplete product
Which way is most practical to achieve Q «_space;1 ?
accumulating high [S] is not desirable in cells (E costs)
- PRODUCT DEPLETION
Product Depletion
using product as soon as it is made through metabolite channeling (back to back runs enzymes work together - enzyme complex)
- enzyme of next step ready
Reaction Coupling via Common Intermediate
unfavorable rxn can be driven forward when coupled to a favourable rxn if sum of ∆G values is negative
exergonic
system release free energy (catabolic)
endergonic
system gains free energy (anabolic)
enthalpy
heat of system
∆H
enthalpy change - amount of heat released/absorbed
Entropy
S - measure of randomness, disorder, freedom of motion
What is meant when a reaction is Entropy driven?
a spontaneous, endothermic reaction (∆H >0)
- ∆S is largely (+) so ∆H -T∆S is negative
Factors that contribute to larger free energy?
anything that destabilizes reactant (raise E level of S) and stabilizes product (lower E level of P)
Products are stabilized by?
1) ionization
2) isomerization (tautomerization)
3) resonance
4) solvation
Solvation
an interaction of solute with solvent leading to stabilization of solute species in solution.
in MOST cases, formation of solution is favoured by +∆S by mixing
Isomerization
stabilizes product how?
e delocalization
more than one compound/product can exist so ∆S >0
Resonance
allows for delocalization, in which overall E of molecule is lowered since its electrons occupy a greater volume, more stable
Ionization
ions are surrounded by H2O or solvent
more micro states, higher degree of freedom
increased S by mixing
Chemical basis for large free-E change associated with ATP hydrolysis
1) hydrolysis with relief of charge repulsion
2) resonance stabilization
3) ionization
4) greater hydration of ADP & Pi relative to ATP
ATP Hydrolysis is accompanied by? resulting in?
H+ release
acidification
Mechanical example of coupling reaction
work done raising object ∆G > 0
loss of potential energy of position ∆G < 0
What leads to metabolic acidosis?
glycolysis and ATP hydrolysis
The donation of energy by ATP generally involves?
a covalent participation of ATP in group transfer reactions
raising free E content of product
Why is ATP a suitable energy carrier?
1) despite large ∆G’°, ATP is kinetically stable @ pH 7 (high Ea for hydrolysis so requires an enzyme & therefore rxn can be regulated)
2) [ADP] & [Pi] are much lower than than 1 M so Q/Keq «< 1 so ∆Gp is larger than ∆G°
Why is ATP hydrolysis slow?
has high Ea
(rate constant) k = Ae^(-Ea/kT)
since Ea is large, k will be small
ATP thus serves as the universal energy currency in all living cells. Why?
Because of its intermediate position on
scale of group transfer potential, ATP can carry energy from high E phosphate
compounds produced by catabolism ) to compounds such as glucose,
converting them into more reactive species.
Majority of ATP is synthesized how?
regenerated from ADP
ATP Hydrolysis Equation
ATP(4-) + H2O –> ADP(3-) + Pi(2-) + H+
to ensure large negative ∆Gp, it is important to?
maintain high intracellular [ATP]
How often does a typical ATP molecule shuttle out of mitochondria (site of synthesis) and back into it (as ADP) for recharging?
once per minute
energy used by human cells require hydrolysis of how many mols of ATP daily?
100 - 150 mols
Each ATP molecule is recycled how many times per day?
~ 1000 times per day
(150 mols per day/0.2 mols in body) = 750 times recycled
ATP cannot be stored for long so?
its consumption closely follows its synthesis
Phosphoenolpyruvate (PEP)
structure
what is responsible for its high ∆G’°?
phosphate ester
tautomerization of pyruvate from enol to keto form
keto more stable
1,3-Biphosphoglycerate (1,3-BPG)
structure
what is responsible for its high ∆G’°?
acyl phosphate
ionization (- H+) and resonance of product (3-PG)
3-Phosphoglyceric acid 3-Phosphoglycerate
(loss of H+)
Phosphocreatine (PCr)
structure
what is responsible for its high ∆G’°?
(P)-Arg res - Gly res - CH3
resonance stabilization (between the 2 primary amino groups)
For ALL reactions with phosphate transfer, what contributes to large negative ∆G’°?
resonance stabilization of Pi
Equation of PCr and ATP
PCr(2-) + ADP(3-) + H+ –> Cr + ATP(4-)
PCr function when [ATP] is high and in excess?
PCr is made as E reservoir for rapid buffering and regeneration of ATP in situ
in situ means to ?
examine the phenomenon exactly in place where it occurs
Advantages of PCr as E reservoir?
1) REGULATION
high [ATP] leads to fat synthesis
2) good buffering for H+ produced from ATP hydrolysis
Hydrolysis of Acetyl CoA (rxn)
Ac-CoA + H2O -> acetate + CoA(S-) + H+
Hydrolysis of Acetyl CoA is favored by?
ionization of CoASH to CoAS- + H+
How does ATP react?
displacement by oxygen, nitrogen - transfer of phosphoryl
Adenylyl =?
AMP
(P)-Ribose-Adenine
Phosphoryl Transfer Reactions to Regenerate ATP
2ADP ATP + AMP
GTP +ADP ATP + GDP
ADP + PCr Cr + ATP
Electrons flow from metabolic intermediates to?
Electron Carriers
- NADH, NADPH, FADH2, FMNH2
Pyruvate is ___ to Lactate, subsequently ____ NADH to ____
reduced
oxidizing
NAD+
Oxidation reactions generally ___ energy
release
Oxidation reactions are a big part of?
Catabolism and ATP formation
During Oxidation/Reduction Reactions, electrons are transferred from atom that have ___ ____ for e’s to atoms with a __ ___ for e’s
lower affinity (e donors, high PE) higher affinity (e acceptors, low PE)
PE of e used to do work
Metabolic energy capture occurs largely through?
synthesis of ATP - molecule designed to provide E for biological work
Most biological oxidations don’t involve direct transfer of e’s from S to O. Instead…?
A series of coupled ox-reduc rxns occurs, with e’s passed to intermediate e carriers (ex. NAD+) before they are finally transferred to O
Why are fats more efficient fuel sources than carbohydrates?
carbon in fats is more REDUCED
Dehydrogenase
enzyme that oxidizes substrate by reduction reaction
(4) ways of e transfer from e donor to e acceptor
1) directly as electrons
2) as H atoms (H+ +e-)
3) hydride ion (H-)
4) through direct combo with O
Reducing Equivalent refers to?
any of a number of chemical species which transfers the equivalent of 1 e in redox reactions
Why do we need E carriers?
most bio rxns dont involve direct transfer of e from Substrate to O.
- series of ox-reduc rxns need intermediate e carriers to carry e’s
Why is better to have a series of ox-reduc rxns rather than direct transfer of e’s?
PE stored in organic S is released in small incremements
- easier to control ox. + capture some E as it’s released
SMALL E TRANSFERS WASTE LESS THAN SINGLE LARGE TRANSFER
Why is FADH2 more versatile than NADH or NADPH?
1) accepts 1 or 2 e’s with one or two H+
2) reduction potential changes based on binding strength
When are group transfer rxns favorable?
when free E of reactants is much higher than that of products (exergonic rxn)
Unfavorable rxns can be made possible by?
chemically coupling a highly favorable rxn to unfavorable rxn
Ox-Reduc-Rxns generally involve?
transfer of e’s from reduced organic compounds to specialized redox cofactors (serve as source of E for ATP synthesis or used in biosynthesis (NADPH))
Diabetes is the..
altered ability to regulate glucose metabolism
Type 1 Diabetes
no insulin production in pancreas
Type 2 Diabetes
can develop at any age
insulin resistance in fat,muscle, liver cells
Active Transport
from intestinal lumen into gut epithelial cells
Kinases
enzymes that catalyze phosphoryl group transfers with ATP as donor
How does glucose get into cell?
glucose is actively transported into cell by Na+ driven cotransporters
- Na+ gradient provides E : [high] -> [low]
since glucose is moving from [low] ->[high]
How does glucose get released into bloodstream?
passive transport
- down concentration gradient
Glucose Oxidation
chemical process that provides E for organism to carry out all required activities
During GLUCOSE OXIDATION, what happens to glucose?
glucose is broken down (fully oxidized) into CO2 + H2O
Glucose Oxidation releases energy which is..
stored in chemical form for the cell to use (ATP, NADH)
(3) Stages of GLUCOSE OXIDATION
1) glycolysis
2) citric acid cycle
3) electron transport chain
Why is Glucose central to metabolism? (5)
1) past
2) relative stability
3) energy?
4) storage
5) conversion
1) one of several monosach that can be formed from formaldehyde (HCHO) under prebiotic conditions
2) most stable among common sugars
3) relatively rich in E (good fuel)
4) easily polymerized (low osmolarity) for storage (glycogen)
5) virtually all sugars can be converted to glucose so process of glycolysis is central to carb metabolism
How many steps of glycolysis
10
For cells that lack mitochondria, how do they generate ATP?
rely on glycolysis to generate ATP
(4) fates of glucose
1) Synthesis of structural polymers (ECM & cell wall polysach)
2) Storage (glycogen, starch)
3) ox. via glycolysis
4) ox. via PPP
GLYCOLYSIS: step 1
glucose –> glucose-6-phosphate
phosphorylation
HEXOKINASE
ATP - phosphoryl donor
First Energy Consuming Reaction of GLYCOLYSIS? why? (3)
Step 1
1) retention of 9 intermediates (no transporters for sugar-(p)
2) E released by ATP is partially conserved in G6P
3) P group provides binding E for formation of ES complex & increases specificity of E+S binding
1) specific acid-base catalysis
2) general acid-base catalysis
1) specifically H+ and OH- (rxn rate dependant on pH)
2) involves a molecule besides water that acts as H+ donor or acceptor
conformational change in Hexokinase after glucose binding …
creates binding site for ATP and excludes H2O frm active site
GLYCOLYSIS: step 2
G6P –> Frucose-6-Phosphate
Conversion/Isomerization
(general acid base catalysis - Glu res)
PHOSPHO(Hexose/Glucose) ISOMERASE
glucose opens into chain form
aldose to ketose (on C2)
Purpose of Step 2 of GLYCOLYSIS
1) provides C1-OH for additional phosphorylation in step 3
2) C2 carbonyl allows step 4 (splitting of 6C into 2 3C’s)
GLYCOLYSIS: Step 3
F6P –> Fructose 1,6-Biphosphate
PHOSPHOFRUCTOKINASE-1 (PFK-1)
C1 phosphorylated by ATP
rate limiting step
- important control point
GLYCOLYSIS: Step 4
Cleavage of F-1,6-BP –> DHAP + G3P
reversible aldol rxn
ALDOLASE
driven by low Q (mass action)
GLYCOLYSIS: step 5
DHAP G3P
Isomerization
TRIOSE PHOSPHATE ISOMERASE
-driven by mass action (product G3P depletion)
During Prep Phase..
2 ATP molecules invested mainly for metabolic retention
C6 -> C3 + C3
Prep Phase (which steps?)
1-5
The C3 fragments will be oxidized to…
capture E in the form of ATP and NADH
GLYCOLYSIS: Step 6
(2) G3P -> (2) 1,3-Biphosphoglycerate
GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE (GAPDH)
Oxidation
reduction of NAD+ to NADH
Inorganic Phosphate
G3P –> 1,3-BPG
carbonyl C oxidized to mixed anhydride C
reduction of NAD+ to NADH (e released stored in NADH & high-E anhydride linkage to phosphate)
PHOSPHOROLYSIS
Inorganic Pi attacks carbonyl C releasing S from E
(nonspontaneous)
GLYCOLYSIS: Step 7
1,3-BPG -> 3-Phosphoglycerate
3-PHOSPHOGLYCERATE KINASE
High E phosphoryl transfer (generates 2 ATP)
(spontaneous)
GLYCOLYSIS: Step 6 + 7
step 6 & 7 are coupled
intermediate (1,3-BPG) is channeled (product depletion)
Glyceraldehyde-3-phosphate dehydrogenase AND 3-Phosphoglycerate kinase form Enzyme complex
SUBSTRATE CHANNELING
GLYCOLYSIS: Step 8
3-PG -> 2-PG
PHOSPHOGLYCERATE MUTASE
conversion
Mutase
an enzyme of isomerase class that catalyzes shifting of functional groups from one position within same molecule
Step 8 Mechanism
Phosphoglycerate Mutase has P group attached to HIS res.
- E transfers P to 2C
intermediate: 2,3-BPG - P from C4 transferred to His res of E
Logic of Step 8
necessary prep for next step (dehydrogenation) which generates high E PEP
- makes C2 more acidic allowing dehydration
GLYCOLYSIS: Step 9
2-PG -> Phosphoenolpyruvate
ENOLASE
dehydration - loss of H2O
Glycolysis: Step 10
PEP -> Pyruvate
PYRUVATE KINASE
tautomerization enol to keto form of pyruvate
(ATP) Energy-Expending Steps of Glycolysis
1 (glucose -> G6P)
3 (F6P -> F-1,6-P)
(ATP) Energy-Forming Steps of Glycolysis
7 (1,3-BPG -> 3-PG)
10 (PEP -> pyruvate)
Net gain of GLYCOLYSIS
2 ATP + 2 NADH
Most steps are close to ___ where ∆G is almost zero.
Which steps have largest negative ∆G?
Steps 1, 3, 10
1- glucose to G6P
3- F6P to F-1,6-P
10 - PEP to pyruvate
Step 8: Isomerization of 3PG to 2PG
What if this step was skipped?
3PG would be converted to a compound, which is then transformed to more stable keto form, forming a β-keto acid - (less stable than α-keto acid) which is unstable due to decarboxylation producing acetaldehyde (hangover molecule)
Why is Arsenate (AsO4 3-) a bad substitute for step 6?
the product of the reaction is unstable and decomposes in water to product 3-phosphoglycerate without generating ATP
(G3P is oxidized but phosphorylation isnt coupled with it)
(1) Fate of G6P other than glycolysis
PPP
- ribose & NADPH
(2) Fates of pyruvate other than CAC
1) Fermentation (ethanol & CO2)
2) Lactate
Pyruvate’s Fate: AEROBIC CONDITIONS
imported into mitochondria
oxidized to acetate (Ac-CoA)
then completely oxidized by CAC & ox. phos. to CO2 + H2O
How is NAD+ ultimately reoxidized?
by passing its e- to O2 in mitochondrial respiration
What is the limiting factor of GLYCOLYSIS?
reduced NAD+ level
Aerobic Conditions equation
pyruvate + CoA + NAD+ -> Ac-CoA + CO2 + NADH
Pyruvate’s Fate: ANAEROBIC CONDITIONS or HYPOXIA
NADH can’t be reoxidized by O2 to NAD+
LACTATE FERMENTATION
Lactate Fermentation
Under Anaerobic Conditions/Hypoxia (low O2)
Pyruvate –> Lactate (reduction)
oxidizes NADH to NAD+ (for glycolysis)
best buffering for H+ produced during ATP hydrolysis + catabolism
Glucose -> Pyruvate
Glucose + 2NAD+ + 2ADP + 2Pi -> 2Pyruvate + 2ATP + 2NADH + 2H+ + 2H2O
Pyruvate -> Lactate
2 Pyruvate + 2NADH + 2H+ -> 2Lactate + 2NAD+
Glucose –> Lactate
Glucose + 2ADP + 2Pi –> 2Lactate + 2ATP + 2H2O
After Lactate Fermentation?
can accumulate during strenuous exercise
- eventually diffuses into bloodstream and is reconverted to glucose in liver (gluconeogenesis)
Does Lactate Fermentation cause Metabolic Acidosis?
NO! in fact, it alleviates it.
What causes Metabolic Acidosis?
Glycolysis and ATP hydrolysis
Alcohol Fermentation
Pyruvate converted to acetaldehyde, then reduced to ethanol by NADH regenerating NAD+ for glycolysis
