Biochem Final
Cosubstrates
1. Loosely bound 2. Regenerated outside active site 3. Continually recycled
What is the direction of the conversation of PEP and pyruvate when blood glucose is high?
PEP to Pyruvate
Glucagon signaling leads to increase in
PEPCK (hormonal induction)
Insulin signaling leads to decrease in
PEPCK induction
name the enzyme: oxaloacetate into PEP
PEPck
name the enzyme: F6P into 1,6 FBP
PFK 1
what are the 2 enzyme that correspond to the F6p to 1,6 FBP reaction (bypass reaction and regular)?
PFK 1 and FBPase 1
If the bifunctional enzyme is dephosphorylated, which molecules if activated?
PFK-2
What does the bifunctional enzyme consist of?
PFK-2 FBPase-2
name the enzyme: G6P into F6P
PGI
name the enzyme: 1,3 BPG into 3PG
PGK
name the enzyme: 3PG into 2PG
PGM
how to solve for PI
PI = 1/2(pK1 + pK2), when amino acid is neutral
phosphoryl
PO3 2-
Glucose-6-phosphate <——x——> Fructose-6-phosphate
Phosphofructokinase ATP ——> ADP
if the entropy of a reaction is positive, the reaction is... exergonic or endergonic
exergonic
α-keratin
formed from 2 α-helices twisted around each other. "Coiled coil". Cross-linked by disulfide bonds.
What makes the reaction catalyzed by citrate synthase highly exergonic?
hydrolysis of thioester
An atom that increases its oxidation number (loses electrons or degree of shared electrons) is said to be
oxidized.
if the free energy of a reaction is negative, the entropy of that reaction is likely... postive or negative
positive
In mixed inhibition, the effect on Km can be
positive, negative, or neutral
Increasing Kc (our k1) would have a -------- effect on affinity and a -------- effect on velocity.
positive, positive
Electrostatic catalysis
preferential binding to and stabilization of the transition state through non-covalent interactions (H-bonds, charge-charge interactions, etc)
substrate-level phosphorylation -
production of ATP through a phosphorylated substrate or intermediate in an enzyme-catalyzed reaction.
endo-peptidases
proteases that hydrolyze (cut) peptide bonds internal to polypeptide chains
Kinetics of Protein folding
protein folding is rapid as partially correct intermediates are retained
globular proteins
proteins that fold into relatively compact shapes
Glycoproteins -
proteins which contain a carbohydrate moiety covalently bound to their surface
weak acids that work in biological reactions
protonated amino and carboxyl groups of amino acids and the phosphate groups of nucleotides
Which of the following is activated by high levels of acetyl-CoA?
pyruvate carboxylase
name the enzyme: Pyruvate into oxaloacetate
pyruvate carboxylase
Which enzyme catalyzes a reaction most similar to that catalyzed by a-ketoglutarate dehydrogenase?
pyruvate dehydrogenase
how does pyruvate enter the TCA/Krebs/Citric acid cycle
pyruvate is converted to acetyl CoA through the pyruvate dehydrogenase complex (PDH) located in the mitochondria
In the relaxed form, key contacts are made within subunits that hold the subunits in a state that either
raises Vmax lowers Km
1. α-amylases "cut" amylose chains
randomly producing maltose (from amylose) as well as limit dextran from amylose (the core chain shown in lower panel).
Multi-step Reactions-kcat is either the
rate-limiting step or a combination of rate constants
adenylate energy charge -
ratio of ATP/ADP, normally kept high in healthy cells to prime ATP-dependent reactions
Transamination -
reaction that involves simultaneous conversion of an alpha-keto, alpha amino acid pair to another alpha-keto, alpha amino pair.
Q ≈Keq these reactions are referred to as
readily reversible
Isomerase
rearrangement of atoms, creating isomers
An atom that decreases its oxidation number (gains electrons or degree of shared electrons) is said to be
reduced.
NADPH is a major
reductant
topology
refers to the order in which the secondary structural features are connected in the protein main chain
Feedforward Activation
regulatory mechanism in which an enzyme in a metabolic pathway is stimulated by an intermediate appearing upstream
dehydrogenation
removal of hydrogen
Acceleration of reaction in a GABC is achieved by
removal/addition of a proton that makes the reaction center more reactive.
Annealing
renature
reducing equivalent
represents a single electron equivalent transferred in a redox reaction
GC content shifts Tm
right
adding reactants or/or removing products pushes the reaction to the
right, and removing reactants and add/or adding products pushes the reaction to the left.
Lipids are fused
ring compounds (includes steroids like cholesterol)
Liver isoform
saturates slowly and is still responsive
Animal fats tend toward more
saturation
Km >> [S] is a __________ order equation.
second
Plant oils are derived mostly from
seeds.
The liver is considered glucose _____?
sensing
Metabolic pathways-
set of connected reactions that occur in cells that extract energy and maintain cellular functions(the products of one reaction become the substrates for the next and so on...).
Flush response -
set of symptoms associated with ethanol intake and acetaldehyde accumulation in humans.
The contours of a protein determine the _______ that its interaction partner must have, whereas the surface chemistry of a protein determines the kinds of chemical interactions that the protein will make with its interaction partner (e.g. Coulombic interactions or _____________).
shape hydrogen bonding
Binding of substrate (homoallosteric effector) or positive effectors (heteroallosteric effector) causes change in
shape that is reflected in a steep increase in reaction rate (due to cooperative binding)
Sticky ends
short single stranded stretches of DNA produced by staggered cuts from a restriction enzyme
Allosteric enzymes display
sigmoidal kinetics
most metabolic disorder caused by _ that disrupts one step of a metabolic pathway
single enzyme deficiency
Rate-determining step -
slowest step of an enzyme reaction or pathway that often serves as a control point for the pathway being on or off
Feedback Inhibition
slowing or stopping an early enzyme in a pathway through allosteric inhibition from a late product
NADH and NADPH act with dehydrogenases as
soluble electron carriers
exergonic means
spontaneous delta G negative entropy positive enthalpy negative
irreversible reactions always proceed
spontaneously in the cell (ie metabolites never reach conditions to turn them off because they lie far from equilibrium)-typically reactions kept at homeostasis
Covalent catalysis
stabilization of a stage of the reaction thru the formation of a covalent bond with the enzyme.
maximal contacts between the enzyme and the substrate which collectively:
stabilize the transition state --and-- reduce the free energy of the transition state
Coiled coil
stable, rodlike protein structure formed when two or more alpha helices twist around each other
Le Chatelier' Principle
states that a system at equilibrium will respond to any perturbation to the equilibrium by moving to re-establish the equilibrium state.
The Law of Mass Action
states that when the rates of the forward and reverse reactions are equal, the system will be at equilibrium.
concentration of pathway intermediates are CONSTANT over time. There must be FLOW through the system (no back ups)
steady state has to do with CONCENTRATION 10 in and 10 out. The rates may be different. Ex: 10 in per 10 seconds vs. 10 in per 100 seconds
evolved-coupling stoichiometry-
stoichiometry which has evolved for survival (an example would be theamount of ATP derived from oxidative metabolism).
lower pKa
strong acid
Glycerophospholipids(10.2) have
strongly polar heads and tails roughly equal in width.
Opposing metabolic cycles in which the substrates and products are reversed are called:
substrate cycles
substrate level phosphorylation vs respiration linked phosphorylation
substrate level: when ATP is formed by the transferral of a phosphate group from a substrate -involves soluble enzymes and chemical intermediates respiration linked: involves membrane bound enzymes and transmembrane gradients of protons
Heterotypic
subunits are different
Which of the following enzymes contains an FAD prosthetic group?
succinate dehydrogenase
Which of the following is an enzyme-associated intermediate that is similar in energy to 1,3-bisphosphoglycerate?
succinyl phosphate
Alditols(sugar alcohols)-
sugar derivatives where aldehyde group (anomeric carbon) is reduced to an alcohol
Cyclization of sugars (ring closure) -
sugars form cyclic compounds through reactions between the aldehyde group and intra-molecular hydroxyl groups (form hem-ketals or hemi-acetals)
Tautomers -
two distinct structures that differ only by the position of a double bond and the position of a hydrogen (may vary in stability)
ketogenic amino acids
tryptophan, leucine, isoleucine, lysine, phenylalanine, tyrosine (PILL TT)
somers-
two molecules withthe same chemical formulabut with unique structures
Orientation of collision
two or more reactants must meet at correct angles
Enzymes that work thru covalent catalysis occur in
two steps and through an intermediate.
ornithine and citrulline
uncommon amino acids that are intermediates in arginine biosynthesis and the urea cycle
specific activity
units of enzyme/mg of protein
Dodecanoic
No double bonds
Why are there steric restrictions to rotations around the bonds that make up the peptide backbone?
No two atoms should approach one another more closely than is allowed by their van der Waals radii
Can [ES] = [Et]
No, its not possible. Practically, the turnover of product that occurs from ES produces a free enzyme E so ES never equals Et.
A muscle biopsy from an individual who was incapable of carrying out prolonged, intense excursive contained a sever deficiency in the glycolytic enzyme phosphoglycerate mutate (PGM) Does this individual suffer from lactic acid build up?
No, pyruvate is not made so lactate cannot be made even in prolonged exercise
Is a transition state an intermediate and why?
No, the transition state is short-lived and unstable. Therefore, it is not considered an intermediate, which is longer-lived and more stable.
14CO2 was bubbled through suspension of liver cels that was undergoing gluconeogenesis from lactate to glucose. Which carbons in the glucose molecule would be radioactive?
None. The CO2 that is fixed comes off in the PEP carboxykinase reaction.
Interactions of __________ side chains in the protein sequence lead to the formation of a tightly packed __________ core. This core is stabilized by a __________ __________ number of __________ . When a mutation occurs, it destabilizes the protein core and weakens__________ leading to misfolding.
Nonpolar Hydrophobic Large van der Waals contacts van der Waals contacts
Nucleophiles
electron rich and attack electron poor
Q >> Keq these reactions are often
"coupled reactions"
T-State
Heme is in high-spin state. H2O is bound to heme.
R-State
Heme is in low-spin state. O2 is bound to heme.
2,3 BPG intermediate regulates
Hemoglobin
Anabolic reactions turn ___ molecules into ___molecules using ___.
Simple Complex ATP
Myoglobin 4° Structure
Symmetric homodimer,
Cholesterol Synthesis
Synthesized from 15 acetyl-CoA through a number of intermediates.
Oxidation reduction reactions involve transfer of
electrons (e-)
Where is succinate dehydrogenase located?
mitochondrial inner membrane
Protein-Protein Interfaces
"Core" and "fringe" of the interfaces. Core is more hydrophobic and is on the inside when interfaced. Fringe is more hydrophilic.
Cardiolipin
"Lipid staple" that ties two proteins (or complexes) together in a membrane. Formed from two phosphoglycerols.
In plants, multiple "strips" of branched starch polymers collapse and associate in
"bundles" called starch granules
"breaking" ATP to produce ADP does not
"produce" energy by releasing the energy of the P-O bond. In fact, from general chemistry, recall that breaking bonds requires energy (it is forming bonds, that releases energy).
Substrate-level phosphorylation -
"substrate" in an enzyme reaction supplies phosphoryl group to produce ATP.
Notations and Naming of fatty acids: naming unambiguously requires indicating
# of carbons and the number and placement of double bonds
Starch consists of a-
(1->4) linkages between glucose monomers
2. α (1à6) glucosidases (debranching enzymes) break
(1->6) linkages exposing core for further amylase attack
understand the concept of phosphoryl group transfer potential
(ATP's is high, forexample)thermodynamically unstable arrangements of phosphates (such as phosphoanhydride linkages) produce more stable products (difference in energy coupled to unfavorable reactions)-this is not true for phosphate esters
Km =
(K-1 + K2) / K1
1/Vo =
(Km + [S]) / Vmax [S] = (Km/Vmax ) * 1/[S]+ 1/Vmax
rate of disintegration is defined by:
(k-1+ k2) [ES]
understand the concept of coupled reactions
(where an uphill reaction is coupled to a downhill reaction) - change in free energies is additive
Limit dextrin
(which retains a-1, 6 linkages)is yellow, sticky, and water soluble (envelope glue).
Charge of Amino at pH 1
+
Charge of Amino at pH 7
+
buffering range
+/- 1 pH unit from the pKa
Charge of Carboxylic Acid at pH 13
-
Charge of Carboxylic Acid at pH 7
-
Charge of Sulfhydryl at pH 13
-
How is glycolysis NAD+ regenerated? 3 different ways
-aerobic: e- pass from NADH to O2 in mitochondrial respiration -anaerobic: e- go from NADH to pyruvate, forming lactate. -Yeast (or other bacteria) use e- from NADH to turn pyruvate into ethanol and CO2
what is an intermediate of glycolysis that signals the beginning of the "payoff" phase
-Glyceraldehyde -3- phosphate
NADPH vs NADH
-NADPH for catabolic reactions, there a is higher ration of NADPH/NADP in cells -NADH carries electrons from catabolic reactions to electron transport chain
DGo' =
-RT ln ([C][D]/ [A][B])eq
sulfhydryl
-SH
thiol
-SH group
what cannot be used as a precursor of glucose
-acetyl CoA, fatty acids cannot make glucose
Features of glycolysis Reaction 1. (Hexokinase)
1. Locks glucose inside cell 2. G-6-P still a branch-point for multiple reactions in cell 3. Point of regulation
glucogenic amino acids
-amino acids that can become glucose all amino acids apart from leucine and lysine can become glucose **alanine and glutamine are particularly important -remove amino groups to get pyruvate (alanine) and alpha- ketoglutarate (glutamine)
transketolase
-carbon assimilation reactions -pentose phosphate pathway
TPP:
-cofactor in the cytoplasm that assists transketolase -in mitochondria for the activity of pyruvate-, oxoglutarate- and branched chain keto acid dehydrogenases
pyruvate decarboxylase
-ethanol fermentation -cleaves C-C bond
important proteins in the mitochondria
-flavoproteins: FADH2 -Ubiquinone: can accept 1 (semi-quinone radical) or 2 (ubiquinol) electrons -cytochrome: has iron prosthetic group, has a signature light absorption spectra in reduced (Fe2+) state, cytochrome c: 550, b: 560, and a: 600 nm -iron sulfur proteins: the iron is reduced in electron transport -e-'s end in O2
pyruvate carboxylase
-gluconeogenesis: converts pyruvate to oxaloacetate -requires coenzyme biotin (B vitamin)
where is oxidative phosphorylation in mitochondria
-inner membrane has respiratory chain and ATP synthase
size exclusion chromatography
-large come out first
pentose phosphate pathway:
-meant to make NADPH and pentoses for biological reactions and convert hexoses and pentoses -begins with glucose 6 phosphate -intermediate is 6-phosphogluconate
hexokinase
-phosphorylates OH group on glucose in glycolysis
mass action ratio (Q)
-ratio of products / substrates in cell at any given time
how does oxaloacetate in gluconeogenesis exit the mitochondria
-reduced to malate by malate dehydrogenase -uses NADH -malate is reoxidized in cytosol and NADH is restored
mitochondria trigger apoptosis
-release apaf: apoptosis protease activating factor
how to get rid of reactive oxygen species in mitochondria:
-superoxide dismutase -glutathione peroxidase -> glutathione is GSH, the reduced form donates e- to H2O2 and is oxidized to GSSG -need NADPH to donate more e-
pyruvate dehydrogenase alpha-ketoglutarate dehydrogenase
-synthesis of acetyl-CoA -citric acid cycle
Gluconeogenesis
-synthesize glucose form non-glucose precursors -brain needs 120 g glucose per day -in liver -first step in mitochondria, then in cytosol starts with pyruvate --> oxaloacetate --> phosphoenol-pyruvate -requires: 6 high energy phosphate groups, 4 from ATP and 2 from GTP and 2 NADH
phosphatase carboxylase
-uses water to cleave a phosphate -adds a carboxyl group *decarboxylase involves loss of CO2
Glycolysis is a pathway that metabolizes _ molecule of glucose to _ molecules of __/__ and generates _ molecules of ATP via substrate-level phosphorylation
1, 2, pyruvate/lactate, 2 ATP via substrate level phosphorylation
14C-labeled glyceraldehyde 3-phosphate was added to a yeast extract. After a short time, fructose 1,6-bisphosphate labeled with 14C at C-3 and C-4 was isolated. What was the location of the 14C label in the starting glyceraldehyde 3-phosphate?
1
Which carbon would need to be labeled in glucose in order for it to be detected in carbon dioxide as an indicator of glucose entry into the pentose phosphate pathway?
1
if a radioactive carbon is the carbon 6 on 1,6 FBP where is the radioactive carbon when it is converted into ethanol?
1
What are the products of gluconeogenesis?
1 glucose 2 CO2
Glycolysis products
1 glucose molecule makes: -2 pyruvate (3 C) -2 NADH -net 2 ATP *in the cytosol
On average, populations of humans that have traditionally relied on a High starch diet, have _______ copies of amylase relative to those that have relied on a Low starch diet.
1 or 2 more
Protein Folding: Two original hypothesis (alternative)
1) Proteins fold with a level of flexibility (unconstrained) 2) Proteins fold to level of inflexibility
Systematic naming -
1)Indicate geometric positions of each double bond (ie cis or trans) 2)Indicate positions of double bonds: D-9, 12 3)Indicate number chain length and number of double bonds as below:
Why do proteins not fold correctly or end up in an unfolded state?
1)Protein fails to reach low energy state 2)Protein becomes denatured ("heat shock") 3)Protein aggregates before it is folded 4)Protein folds correctly but is not assembled in quaternary structure due to other factors 5)Protein does not reach its proper destination
What steps of glycolysis are metabolically irreversible?
1, 3, & 10
Step 7 of Glycolysis
1,3-bisphosphoglycerate + ADP <--> 3-phosphoglycerate + ATP Uses phosphoglycerate kinase enzyme.
What activate Pyk?
1,6 FBP
Early evidence for chemiosmosis in mitochondria:
1. An intact inner membrane is required for oxidative phosphorylation 2. Key electron transport proteins span the inner membrane these proteins are asymmetric (from inside to outside) 3. Uncouplers act by dissipating the proton gradient
Yeast yields alcohol in two steps
1. Decarboxylation 2. Oxidation -reduction
A polynucleptid chain has
1. Directionality 2. Individuality
What happens when you add a strong base to H2O
1. Dissociation of base in solution (OH- increases) 2. H+ from water combines with free OH- H+ levels fall, pH rises
Water is polar due to
1. Electronegativity difference between H and O 2.asymmetric distribution of polar bonds
Features of glycolysis Reaction 7. Phosphoglycerate kinase
1. First example of substrate-level phosphorylation 2. Energy of "combustion" now in the form of ATP 3. Produces 2 ATP molecules per glucose (initial investment recovered)
An enzyme reaction is viewed in two steps
1. Formation of the enzyme-substrate complex, which is quick 2. Conversion of the enzyme-substrate complex to product, which is slow
Common Principles of globular structure
1. Hydrophobic Interior & Hydrophilic exterior 2. Structure is devoid of symmetry 3. Very little empty space (tightly packed) 4. The polypeptide chain can turn corners 5. Not all parts can be classified as a-helix, B-sheet, or turns some irregulary structure regins
Cellular metabolism can be subdivided into three stages:
1. Interconversion of polymers and complex lipids with monomeric intermediates. 2. Interconversion of monomeric sugars, amino acids and lipids with still simpler organic compounds. 3.Ultimate degradation to or synthesis from inorganic compounds (such as CO2, H2O and NH3.
Enzyme assay graphs show three distinct regions
1. Mixing period (level) 2. Linear portion "initial rate" (velocity - V0) 3. Equilibrium w/ reverse reaction
Features of glycolysis Reaction 8. Phosphoglycerate Mutase
1. Mutases - moves functional groups within molecules 2. Some classes of this enzyme begin with phosphorylated enzyme
Features of glycolysis Reaction 6. GAPDH
1. Oxidation-reduction reaction - converts aldehyde to carboxylic acid 2. Oxidation of fuel used to drive synthesis of NADH 3. Creates acrylic phosphate (high phosphorl group transfer potential) thru successive high energy bonds in mechanism
Features of glycolysis Reaction 9. Enolase
1. Product has high phosphoryl group transfer potential 2. Product locks molecule in high energy (less stable tautomer) form
Features of glycolysis Reaction 3. (PFK-1)
1. Rate-determining reaction of glycolysis 2. Most highly regulated step in glycolysis (allosteric)
General Properties of Polymerases
1. Read DNA 3' to 5', build new strands 5' to 3 2. Require primer (3'OH) 3. Are processive (ie don't fall off) 4. Generally have proofreading function
Why do proteins typically evolve quaternary structure? In other words, what benefits are gained by having multiple subunits in a protein's structure?
1. Repeated Function 2. Functional Diversity 3. Folding Stability 4. Genomic Efficiency
Features of glycolysis Reaction 10. Pyruvate kinase
1. Second example of substrate-level phosphorylation 2. 2 ATP harvested per glucose molecule 3. Final regulated step
Protein-protein interactions form complexes by
1. Self-assembly 2. being held together by: Hydrophobic forces Van der Waals forces Salt bridges Hydrogen Bonding
How is Km used?
1. Substrate concentration at 1/2 Vmax 2. approximates Kd of ES and, therefore, approximates an enzymes "affinity" for its substrate 3. used to compare enzymes (and different forms of the same enzyme under various metabolic conditions)
What is the metabolic significance of the following observations? 1) only the liver form of PyK is inhibited by alanine and 2) only gluconeogenic tissues contain appreciable levels of G6P.
1. The liver is the most active gluconeogenic tissue. Since alanine is an important gluconeogenic precursor, its accumulation in liver is a signal that gluconeogenesis should be activated, with simultaneous inhibition of glycolysis. Also, alanine accumulates in muscle under conditions of high metabolic demand, where glycolysis must still function to provide ATP. 2. The function of glucose-6-phosphatase is production of glucose, for exit from the cell and transport to other tissues. Therefore, the enzyme plays a role only in those tissues (primarily liver) that manufacture glucose for export.
Prosthetic Groups
1. Tightly bound 2. Regenerated inside active site
Features of glycolysis Reaction 2. (Glucose-6-phosphate isomerase)
1. Works through a "protein shuttle". - aldose to ketose conversion 2. Substrate and product are rings, but rxn goes through straight chain
Features of glycolysis Reaction 5. Triose phosphate isomerase
1. Works through a proton shuttle 2. Ketose to aldose conversion 3. Ties branches together (economize pathway) 4. Output from glucose must be doubled from here
Important properties of phosphoric acid
1. always retains at least one negative charge in the cell (strong acid) 2. tri-protic (multiple linkages possible) 3. linkages resistant to hydrolysis
what takes place in mito matrix
1. citric acid cycle 2. fatty acid beta oxidation 3. amino acid oxidation
fates of pyruvate:
1. citric acid cycle: aerobic: glucose is completely broken down, oxidized to the acetyl group of acetyl-coenzyme A, and then the acetyl group is completely oxidized to CO2 by the citric acid cycle -gives off 2 CO2 and 2 Acetyl CoA -next gives off 4 CO2 + 4 H2O 2. lactic acid fermentation: reduction to lactate via lactic acid fermentation. NAD+ must be regenerated, so pyruvate accepts an H from NADH and becomes lactate (typically anaerobic) -gives off 2 lactate 3. ethanol fermentation: pyruvate is converted under hypoxic or anaerobic conditions to ethanol -gives off 2 ethanol + 2 CO2
Proximity and orientation effects-positioning and orienting of substrates toward the reaction. Collectively theseeffects:
1. increases proximity and correct orientation of substrates. 2. serves as an "entropy trap" by decreasing entropy (raising energy) of ES relative to E 3. "effectively raises concentration of substrates".
3 stages of cellular respiration
1. organic molecules such as glucose, FA's, and some amino acids, are oxidized into 2 carbon molecules in the form of the acetyl group of Acetyl Coenzyme A (Acetyl CoA) 2. 2 carbon acetyl groups are fed into the citric acid cycle, where they are enzymatically oxidized to CO2. Energy is released and conserved as NADH and FADH2 3. Reduced coenzymes are oxidized, giving up H+ and e-s. e- goes to O2, via the electron transport chain, which produces a lot of ATP (oxidative phosphorylation!!)
buffering capacity is determined by
1. pK +/-
important properties of phosphoric acid:
1. retains at least one negative charge in the cell and remains inside membrane 2. tri-protic (multiplelinkagespossible) 3. resistant to hydrolysis (protected bynegative charge from OH-
citric acid cycle!
1. the acetyl group from acetyl CoA joins with oxaloacetate to make 6 Carbon citrate 2. citrate becomes isocitrate, still 6 C's *cis-actonitate becomes isocitrate via aconitase 3. Isocitrate is dehydrogenated (- CO2) to become the 5 C alpha-ketoglutarate 4. alpha ketoglutarate loses a CO2 to become succinyl CoA 5. succinyl CoA becomes succinate and one ATP is formed 6. succinate is enzymatically converted into fumarate 7. Fumarate is converted into malate 8. malate is converted into the 4 C oxaloacetate *3 NADH and one FADH2 are made from the oxidation steps *1 ATP and 2 CO2 are made
Le Chatelier's Principle predicts that DG is the driving force of a perturbed reaction to reach equilibrium. So,what determines DG of any single reaction that occurs in a cell?
1. the nature of products/reactants (their inherent stability)-this can be measured (empirically) by starting at a chemical standard state. Example: 1) take molecules 2) put reactants and products at standard conditions (1M) 3) let reaction proceed to equilibrium. 4) determine concentrations at equilibrium 5) yields direction of flow and standard free energy(DGo')
What are the four basic folding patterns in globular proteins?
1. those that are built about a packing of a helices 2. those that are constructed on a framework of B sheets 3. those that include both helices and sheets 4. those that contain little helix or sheet structure
Properties of 2,4 Dinitrophenol
1.A weak acid (see above) 2.Hydrophobic
Protein Glycosylation -Features
1.Is common for secreted and cell-surface (integral) proteins 2.Occurs on proteins translated on the rough ER and / or in the Golgi 3.Can be necessary for proper folding 4.Can play rolesin protein stability and trafficking (and many other roles)
Hydrolysis yields free energy "gain" due to:
1.Less charge repulsion of productsrelative to substrates Note how bridging oxygens become terminal oxygens 2.Greater resonance stability of products relative to substrates 3.Greater solvation of products relative to substrates
what two ways could a catalyst enhance the rate of nucleophilic substitution:
1.increase the nucleophilicity (ie of water below) 2.make a proton available to make (amino nitrogen) a better leaving group
Althoughthe organic starting points and/or ending points (glucose and pyruvate) are the same andsome steps of both pathways are shared,both pathways stand alone as:
1.thermodynamically favorable (downhill) pathways on their own 2.independently (or reciprocally regulated)
If all reduced electron carriers are reoxidized to run oxidative phosphorylation, how many ATP can be generated from the oxidation of one acetyl-CoA?
10
pKa of Tyrosne R-group
10
pKa of Lysine R-group
10.5
In addition, the cell maintains ATP/ ADP ratios (adenylate energy charge) at levels approximately
108 times higher than equilibrium. This allows any reaction coupled to ATP usage to benefit thermodynamically as well.
pKa of Arginine R-group
12.5
how many molecules of G6P are regenerated in PPP from 6 molecules of G6P?
18
During the energy investment phase of glycolysis how many ATP are used/transformed into ADP?
2
How many carbons are transferred during a transketolase reaction?
2
Pyruvate carboxylase requires ___ ATP per glucose produced
2
if a radioactive carbon is the carbon 2 on glucose, where is the radioactive carbon when it is converted into PEP?
2
Glyceraldehyde-3-phosphate + Dihydroxyacetone Phosphate + Glyceraldehyde-3-phosphate dehydrogenase =
2 1,3-Biphosphoglycerate
2 3-Phosphoglycerate + Phosphoglycerate Mutase =
2 2-Phosphoglycerate
2 1,3-Biphosphoglycerate + Phosphoglycerate Kinase =
2 3-Phosphoglycerate
How many ATP/GTP molecules are required to synthesize glucose from each of the following compounds? 2 molecules of OAA
2 ATP when converting 2 pyruvate into 2 OAA and 2 GTP when converting 2 OAA into 2 PEP
For the following molecules is processed by glycolysis to lactate. How much ATP is generated from each molecule? GAP
2 ATP, glycolysis has a net of 4 ATP but 2 are used when converting converted glucose to G6P and F6P into 1,6 FBP.
2 2-Phosphoglycerate + Enolase =
2 H2O + 2 Phosphoenolpyruvate
Uracil
2 O
Thymine
2 O and CH3
2 Phosphoenolpyruvate + Pyruvate Kinase =
2 Pyruvate
What are the products of glycolysis?
2 pyruvate 2 ATP 2 NADH
What inhibits FBPase?
2,6 FBP AMP
What activates PFK?
2,6 FBP AMP ADP
How many ATP/GTP molecules are required to synthesize glucose from each of the following compounds? 1,6 FBP
2- one for glucose to G6P and one for F6P into 1,6 FBP.
Step 9 of Glycolysis
2-phosphoglycerate <--> Phosphoenolpyruvate (PEP) Uses enolase enzyme. Dehydration reaction (loss of water).
Total Energy Produced by Glycolysis
2NADH + 4 ATP
How many carbons are transferred during a transaldolase reaction?
3
Cost of FAS in Eukaryotes
3 ATP's per 2 carbon unit added.
For the following molecules is processed by glycolysis to lactate. How much ATP is generated from each molecule? G6P
3 ATP, glycolysis has a net of 4 ATP but 2 are normally used converted glucose to G6P and F6P into 1,6 FBP, but since we are starting with G6p, the first ATP was never used.
In the citric acid cycle, what reduced cofactors are derived from the oxidation of one molecule of acetyl CoA to two molecules of CO2?
3 NADH and 1 QH2
Net Energy Gain of the Citric Acid Cycle
3 NADH, FADH2, and GTP
precursors of glucose used for gluconeogenesis
3 carbon compounds: pyruvate, lactate, glycerol, certain amino acids (alanine)
Stage 1 of the Calvin Cycle
3 ribulose 1-5-bisphosphate + 3 CO2 --> 6 3-phosphoglycerate. Catalyzed by rubisco
an amphiphilic α helix will have side chains of similar polarity every
3-4 residues.
Nucleic Acid Secondary structure
3-dimensional arrangement of nucleotide residues with respect to one another
Stage 2 of the Calvin Cycle
3-phosphoglycerate --> glyceraldehyde 3-phosphate Requires ATP and NADPH Goes through 1,3-bisphosphoglycerate intermediate
Step 8 of Glycolysis
3-phosphoglycerate <--> 2-phosphoglycerate Uses phosphoglycerate mutase enzyme.
pKa of Aspartate R-group
3.9
yield of ATP from the complete oxidation of glucose
30-32
pKa of Glutamate R-group
4
In an a helix, the Ccarbonyl is hydrogen bonded to the amide ___ residues away
4 i + 4
During the energy generation phase of glycolysis how many ATP & NADH are formed?
4 ATP & 2 NADH
Cost of Gluconeogenesis
4 ATP, 2 GTP, and 2 NADH
Hemoglobin Binding Curve
4 subunits present in hemoglobin that can be either T or R -state. Cooperative binding leads to a sigmoidal curve.
Glucose labeled with 14C at C-6 is added to a solution containing the enzymes and cofactors of the oxidative phase of the pentose phosphate pathway. What is the fate of the radioactive label?
5
if a radioactive carbon is the carbon 2 on pyruvate, where is the radioactive carbon when it is converted into glucose
5
You have a competitive inhibitor. Measurements of Km in the absence of the inhibitor is 2.5mM. Measurements of Km in the presence of 3mM inhibitor is 3.9 mM. What is the Ki of the inhibitor?
5 mM
furanose
5 membered ring
pyranose
6 membered ring
name the enzyme: 6-phosphogluconate into Ru5P
6-phosphogluconate dehydrogenase
pKa of Histidine R-group
6.1
What does gluconeogenesis share with glycolysis?
7 of 10 reaction steps (enzymes) with glycolysis (reversible)
Glycogen
Found in animals. Branched every 8-12 residues and compact. Used as storage of saccharides in animals.
How many electrons are transferred from one acetyl group when it is converted to two carbon dioxide molecules in the citric acid cycle?
8
pKa of Cysteine R-group
8
Energy Consumption of the Calvin Cycle
9 ATP molecules and 6 NADPH molecules for every 3 CO2 molecules that are fixated.
If you incubate 14C-CO2 with liver extracts capable of performing gluconeogenesis, where does the radioactive label end up? Select all that apply. Oxaloacetate (OAA) Glucose Pyruvate PEP 1,3 BPG CO2
A C E
extinction coefficient
A coefficient that indicates the ability of a particular substance in solution to absorb light of wavelength l. The molar extinction coefficient, eM, is the absorbance that would be displayed by a 1.0 M solution in a 1-cm light path.
Inverted Repeat in DNA
Found in double-strands. TTAGCAC|GTGCTAA AATCGTG|CACGATT Forms a cruciform.
absorbance (al)
A dimensionless number that indicates how well a solution of a substance absorbs light of a given wavelength. It is defined as the negative logarithm of the fraction of light of wavelength l that passes through a sample of the solution
a-keratin
A fiber protein that is the principal component of hair, skin, and nails is:
A form DNA
A forms in presence of less water A form the bases are near the backbone and tilted A form does not
hydrolysis reaction
A chemical reaction that breaks apart a larger molecule by adding a molecule of water
heat-shock proteins
A group of chaperonins that accumulate in a cell after it has been subjected to a sudden temperature jump or other stress. They are thought to help deal with the accumulation of improperly folded or assembled proteins in stressed cells.
molten globule
A hypothetical intermediate state in the folding of a globular protein, in which the overall tertiary framework has been established but internal side chains (especially hydrophobic ones) are still free to move about.
proteasome
A large, ATP-dependent protease complex that is found in the cytosol of cells and is involved in the selective degradation of short-lived cytoplasmic proteins.
Enzyme assays are measured as
A loss of substrate or gain of product / time (velocity)
What do enzyme assays take advantage of?
A measurable difference between the substrate and the product
prosthetic group
A metal ion or small molecule (other than an amino acid) that forms part of a protein in the protein's native state and is essential to the protein's functioning; its attachment to the protein may be either covalent or noncovalent.
Feedback inhibition
A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.
ramachandran plot
A plot that constitutes a map of all possible backbone conformations for an amino acid in a polypeptide. The axes of the plot consist of the rotation angles of the two backbone bonds that are free to rotate ϕ and ψ, respectively); each point ϕ, ψ on the plot thus represents a conceivable amino acid backbone configuration.
domain
A portion of a polypeptide chain that folds on itself to form a compact unit that remains recognizably distinct within the tertiary structure of the whole protein. Large globular proteins often consist of several domains, which are connected to each other by stretches of relatively extended polypeptide.
Glycolysis can be seen is often run as an anaerobic fermentation pathway where
A steady-state concentration of NAD+ is maintained
sedimentation equilibrium
A technique for using centrifugation to measure the mass of a large molecule such as a protein. A solution of the substance is centrifuged at low speed until the tendency of the substance to sediment is balanced by its tendency to diffuse to uniform concentration; the resulting concentration gradient is used to measure the molecular mass.
dyad axis
A two-fold axis of symmetry.
B Turn
A type of protein secondary structure consisting of four amino acid residues arranged in a tight turn so that the polypeptide turns back on itself.
Enzyme assay
A way to measure the outcome (and rate) of a specific enzyme reaction
Four nucleotides that make up RNA
A, U, G, C
ß-mercaptoethanol
Breaks disulfide bonds.
What are the properties of ATP that allow it to serve as an energy currency?
A. thermodynamically unstable B. kinetically stable
Fe Binding of O2
Fe2+ binds to O2 reversible. Fe3+ has an additional + charge and binds to O2 irreversibly. Fe3+ rusts in O2 rich environments.
What is the activator of allosteric regulation in bacteria?
ADP (energy charge)
negatively charged amino acids
AG aspartate, glutamate
What is the allosteric regulation of the conversion of Fructose 1,6 Bisphosphatase to Fructose 6 Phosphate?
AMP F2,6BP
What is the activator of allosteric regulation in mammals?
AMP and ADP F 2,6-BP (in liver)
What inhibits PFK?
ATP Citrate
phase 2 glycolysis
ATP generating phase (transform Fructose 1,6 bisphosphate to 2 triose phosphates and output energy (2 NADH, 2 ATP, and 2ATP) produce pyruvate/lactate (red blood cell only produce lactate
The simultaneous oxidation an phosphorylation of GAP by GAPDH forms a covalent thioester bond between a cysteine side chain on the enzyme and the oxidized intermediate. You identified a patient who has a mutation of this highly reactive cysteine to a leucine. How would glycolytic flux and ATP production in red blood cells be altered In this patient? Explain.
ATP production would greatly be reduced becasue if 1,3 BPG is not being made, it cannot get converted into 3PG which is the reaction where 2 ADP is converted to 2 ATP. Thus glycolytic flux would decrease and ATP would be used in the investment phase, but not made in the energy regeneration phase (1,3 BPG into 3PG and PEP into pyruvate).
What is the inhibitor of allosteric regulation in mammals?
ATP, Citrate (feedback inhibitor)
What is the inhibitor of allosteric regulation in bacteria?
ATP, PEP (feedback inhibitor)
Typical Cellular Concentrations of: ATP: ADP: AMP:
ATP: 3-5 mM ADP: 0.2 -1.5 mM AMP: 0.004 -0.03 mM
Anaerobic Ammonia Oxidation (Anammox)
Ability of some bacteria to oxidize NH4+ and NO2- into N2. "Short-circuits" the nitrogen cycle.
DNA UV Absorbtion
Absorbs UV light at 260nm.
Complex I in the ETC
Accepts two electrons from NADH via an FMN cofactor. Transfers 4H+ to Pside and 2H+ to Q
Disulfide bonds require what sort of environment?
An oxidizing environment
Gluconeogenesis is a ____ pathway
Anabolic
In Alcoholic fermentation, pyruvate is cleaved into
Acetaldehyde and CO2
Pyruvate carboxylase is allosterically activated by
Acetyl CoA
What activates pyruvate carboxylase?
Acetyl CoA
What inhibits PyK?
Acetyl CoA cAMP ATP Alanine
Step 1 of the Citric Acid Cycle
Acetyl-CoA + Oxaloacetate --> Citrate Uses citrate synthase enzyme H2O --> CoA
Additional Cost of FAS in Eukaryotes
Acetyl-CoA for lipid synthesis is made in mitochondria and must be transferred into the cytosol via citrate transporter. Costs 2 ATP.
Determine whether the following mutations would promote glycolysis or gluconeogenesis in the liver and explain your reasoning. The allosteric binding site for acetyl-CoA on pyruvate carboxylase is mutated, increasing affinity for acetyl-CoA.
Acetyl-CoA is an allosteric activator of pyruvate carboxylase, so increasing the affinity of acetyl-CoA to the enzyme will result in increased enzyme activity, thus promoting gluconeogenesis.
Citrate <——x——> Isocitrate
Aconitase
Step 3 of Epinephrine Signal Transduction
Activated α-subunit separates from ßɣ-complex and moves to adenylyl cyclase, activating it.
Regulation with fructose 2,6-bisphosphate
Activates PFK-1 encouraging glycolysis. Inhibits FBPase-1 discouraging gluconeogenesis
Iodoacetate
Adds carboxymethyl group on free -SH groups. Blocks disulfide bonding.
ATP full name
Adenosine Triphosphate
Step 4 of Epinephrine Signal Transduction
Adenylyl cyclase catalyzes the formation of cAMP from ATP
How many ATP equivalents are produced in aerobic vs anaerobic glycolysis?
Aerobic - 7 Anaerobic - 2
AKAP
Anchoring protein that binds to PKA, GPCR, and adenylyl cyclase.
Starch
Found in plants. D-glucose polysaccharide. "Amylose chain". Unbranched. Has reducing and non-reducing end.
α-helices
Ala is common, Gly & Pro are not very common. Side-chain interactions every 3 or 4 residues. Turns once every 3.6 residues. Distance between backbones is 5.4Å.
Determine whether the following mutations would promote glycolysis or gluconeogenesis in the liver and explain your reasoning. The allosteric binding site for alanine on pyruvate kinase is mutated, decreasing affinity for alanine
Alanine is an allosteric inhibitor of pyruvate kinase, so decreasing the enzyme's affinity for alanine, would lead to increased PyK activity and therefore promote glycolytic flux.
Fructose-6-phosphate <——x——> Glyceraldehyde-3-phosphate + Dihydroxyacetone Phosphate
Aldolase
_ do not obey Michaelis Menten kinetics. Sigmoidal dependence of reaction velocity on substrate concentration rather than hyperbolic dependence like Michaelis Menten.
Allosteric Enzymes (cooperativity)
Mixed Inhibition Graph
Allosteric inhibitor that binds either E or ES. Pivot point is between X-intercept and Y-intercept.
Metal Ions
Alone or coordinated to organic molecules
Anti-parallel ß-sheet
Alternating sheet directions (C & N-termini don't line-up). Has straight H-bonds.
Phosphatidic Acid
Common precursor to TAGs and phospholipids. Consists of a glycerol 3-phosphate with two acyl groups that are attached via acyl transferases.
Ribozyme
An RNA molecule with catalytic function
Transferase
An enzyme that catalyzes the transfer of a functional group
A one year old child was admitted to the hospital due to consistent sluggishness. When admitted, the child's blood glucose was around 0.8 mM (normal is 4-5 mM), and lactate levels were extremely elevated. Provided on potential enzyme that could be altered in this Child to result in these observations (and its not maleate dehydrogenase). Explain.
An enzyme that could be altered is PEPck. If glucose levels are extremely low and lactate levels are extremely high that means pyruvate levels are increased and being converted to lactate rather than getting converted back into glucose by gluconeogenesis whose enzyme PEPck converts pyruvate into PEP.
Zymogen
An inactive precursor of an enzyme, activated by various methods (acid hydrolysis, cleavage by another enzyme, etc.)
prion
An infectious agent that contains protein but no nucleic acid.
spectrophotometer
An instrument that exposes a sample to light of defined wavelengths and measures the absorbance. Different types of spectrophotometers operate in different wavelength ranges, such as ultraviolet, visible, and infrared
circular dichroism spectrum (cd spectrum)
An optical spectrum obtained using circularly polarized light; it gives the circular dichroism of the substance over a range of wavelengths.
Most hunters know that meat from animals that have been run to death tastes sour. Suggest a reason for this observation.
Animals that have been run to death have used their muscles so much that they have run out of O2 and survived for a while on fermentation to regenerated NAD+ for the GAPDH reaction. While performing high amounts of fermentation, the animals have also accumulated large amounts of lactic acid in their muscle tissue, accounting for the sour taste of the meat.
Step 4 of the Urea Cycle
Arginine --> Ornithine Uses arginase enzyme H2O --> Urea
Step 3 of the Urea Cycle
Arginosuccinate --> Argininine Uses arginosuccinase Produces fumarate byproduct
Tyrosine, Phenylalanine, Tryptophan are
Aromatic
pH and Binding Affinity (Bohr Affect)
As [H+] increases, Histidine group in hemoglobin becomes more protonated and protein shifts to T-state. O2 binding affinity decreases.
Affinity Chromatography
Attach a ligand that binds a protein to a bead. Elute with harsh chemicals or similar ligand.
both physical (involving membranes); example: increase in membrane permeability to glucose in response to insulin secretion
Compartmentation
B form DNA
B forms under high humidity, B form has bases near central axis and roughly horizontal, B form has distinct major and minor grooves,
Hydrolysis of Nucleotides
Base hydrolyzes RNA, but not DNA. DNA is stable in base because of 2' deoxy position.
Why do organisms have to undergo fermentation?
Fermentation occurs when oxygen is not available for the TCA cycle and oxidative phosphorylation to occur. This means the animal needs a way to generate ATP without using oxygen.
Hydrophobic/Reverse Phase Chromatography
Beads are coated with a carbon chain. Hydrophobic proteins stick better. Elute with non-H-bonding solvent (acetonitrile).
why does it make good metabolic sense for PEPck, rather than pyruvate carboxylase, to be primary target for the regulation of gluconeogensis at the level of control of enzyme synthesis?
Because pyruvate carboxylase has two metabolic roles—replenishment of citric acid cycle intermediates and initiation of gluconeogenesis. PEPCK catalyzes the first reaction committed to gluconeogenesis
Why does fermentation of glucose to lactate continue to yield energy to an organism?
Because there is a regeneration of NAD+/NADH when converting pyruvate into lactate using LDH and a net of 2 ATP is still being produced during this cycle thus the body can still produce ATP and NADH without entering the citric acid cycle.
Helix Dipole
Formed from added dipole moments of all hydrogen bonds in an α-helix. N-terminus is δ+ and C-terminus is δ-.
Gluconeogenic Bypass of Step 10
Bicarbonate + Pyruvate --> Oxaloacetate Pyruvate decarboxylate (biotin) ATP --> ADP Oxaloacetate --> PEP PEP carboxykinase GTP --> GDP + CO2
pallor, and hypotension
Big Picture - The primary function of the red blood cell is to deliver _ to the tissues and transport _ back to the lungs where it will be eliminated - When oxygen delivery to tissues is compromised there are physiological consequences due to tissue _. The pathological effect is referred to as _. *Anemia is defined as a (increase or decrease) in the total number of _ _ cells, (increase or decrease) amount Hb in circulation, OR (decrease or increase) circulating red blood cell mass. - sings and symptoms of anemia include f_, Syncope (what is it?), Dyspnea (What is it?), pallor, and (hypo or hyper) tension.
Pyruvate Carboxylase requires
Biotin
Disulfide-bonds
Bonds between two -SH groups that form between 2° and 3° structure.
The first rate-limiting reaction of glycolysis is catalyzed by the hexonkinase isozymes hexonkinase 1 (HK) and hexokinase 4 (glucokinase). Name one way the activity of either the hexokinase isozymes is inhibited.
Build up of G6P is an inhibitor of hexokinase, thus its accumulation will allow its activity to be inhibited.
Cellulose
Comes from plants. Poly D-glucose. Formed from ß-1,4-linkage. Form sheets due to equatorial -OH groups that H-bond with other chains.
Where would 14C have to be located in the starting glucose to ensure that all the 14C activity is liberated as 14CO2 during fermentation to ethanol?
C3 and C4
A protein is found to be a tetramer of identical subunits. Name two symmetries possible for such a molecule. What kinds of interactions (isologous or heterologous) would stabilize each?
C4 symmetry with heterologous interactions D2 symmetrywith isologous
Glucose labeled 14C is on carbon 6 and s added to a solution containing enzymes and cofactors of the oxidative phase of PPP. What is the fate of the radioactive label?
C5 on Ru5P
TPP Cofactor
Common acetaldehyde carrier. Used in pyruvate decarboxylase, pyruvate dehydrogenase, α-ketoglutarate dehydrogenase, and transketolase
[1-14C]R5P is incubated with a mixture go purified transketolase, transaldolase, phosphopentose isomerase, phosphopentose epimerase, and GAP. Predict the distribution of radioactivity in the E5P and F6P that are formed in the mixture.
C-1 and C-3 of fructose-6-phosphate should be labeled. Erythrose-4-phosphate should be unlabeled.
Suppose it were possible to label glucose with 14C at any position or combination. For yeast, fermenting glucose to ethanol, which form or forms of label glucose would give the most radioactivity in CO2 and least in ethanol?
C-3 or C-4. Both become C-1 of pyruvate, which is lost as CO2 in the pyruvate decarboxylase reaction
carbonyl
C=O
carboxyl group
C=O-OH
methyl
CH3
methylene bridge
CH3-CH2-CH3
carboxyl
COOH
ß-Barrel Membrane Protein
Can act as a large door. Whole proteins can fit inside.
Glycoproteins
Carbohydrates attached to a protein. Common outside of the cell. Attached at Ser, Thr, or Asn residues.
Anomeric Carbon
Carbon that is cyclized. Always the same as the aldo or keto carbon in the linear form.
Acetyl-CoA + Citrate Synthase =
CoASH + Citrate
What happens to collagen over time?
Collagen becomes more crosslinked, and therefore more brittle, with age.
K2(cat)
Catalytic rate constant
FAS (Fatty-acid Synthetase)
Catalyzes condensation, reduction, dehydration, and reduction of growing fatty acid chain. Requires activation by acetyl-CoA or malonyl-CoA
Glutamine Synthetase Regulation in Nitrogen Metabolism
Catalyzes conversion of glutamate to glutamine. Inhibited by Gly, Ala, and endpoints of glutamine metabolism. Additive effectors.
F0 Domain of Mitochondrial ATP Synthase
Causes rotation of γ-subunit via a half channel and H+ gradient
Salting Out (Purification)
Changes soluble protein to solid precipitate. Protein precipitates when the charges on the protein match the charges in the solution.
Step 2 of the Citric Acid Cycle
Citrate <--> Isocitrate Uses aconitase enzyme H2O <--> H2O
Acetyl-CoA ——x——> CoASH + Citrate
Citrate Synthase
Step 2 of the Urea Cycle
Citrulline --> Arginosuccinate Uses arginosuccinate synthetase 1) ATP --> ADP 2) Aspartate --> AMP
Competitive inhibition
Classical-inhibitor competes for active site (substrate binding site)
Chymotripsin
Cleaves proteins on C-terminal endof Phe, Trp, and Tyr
A-form DNA
Condensed form of DNA. Deeper major groove and shallower minor groove.
ETC (Electron Transport Chain)
Consists of 4 functional protein complexes.
Ketone bodies
Consists of Acetoacetate, Acetone, and D-ß-hydroxybutryate. Formation begins from condensation of 2 acetyl-CoA --> Acetoacetyl-CoA (+ CoA) D-ß-hydroxybutryate can be broken into 2 acetyl-CoA and used as fuel.
Mitochondrial ATP Synthase
Consists of F1 and F0 domains
Ribonucleotide Reductase
Contains two types of allosteric regulatory sites for activity and specificity. Converts ribonucleotides to deoxyribonucleotides.
Why are subunits often arranged symmetrically?
Contributes to low free energy of complexes
The energy of redox is coupled to proton translocation (below):
Converging pathways below show the electron flow from NADH / QH2. This flow leads to a buildup of protons in the intermembrane space.
Mutarotation
Conversion from α to ß forms of the sugar at the anomeric carbon.
Folding Funnel Model
Corresponds the width of a funnel to number of conformation states at a given value of free energy
Restriction Enzyme
Cuts DNA at specific restriction sites.
Cofactors fall into various categories:
Metal Ions Coenzymes: -Cosubstrates -Prosthetic Groups
coulombs law
F = k(q1q2)/r^2
What other molecule can act as a soluble electron carrier?
FAD
enzyme: pyruvate into ethanol
PDC ADH
name the enzyme: fructose 1,6 bisphosphate into F6P
FBPase 1
Give the sign for DH and DS as DNA anneals
DH = (-) and DS = (-)
Palindrome
DNA sequence that reads the same in both directions (both 5' to 3')
Transcription
DNA to RNA implies chemical language is same
If the bifunctional enzyme is phosphorylated, which molecules if activated?
FBPase-2
Determine whether the following mutations would promote glycolysis or gluconeogenesis in the liver and explain your reasoning. Insulin secretion is increased.
Decreased P-of bifunctional enzyme activation of PFK-2 increase of F2,6-BP activate PFK1 and inhibit F1,6-BPase increased glycolysis and decreased gluconeogenesis insulin decreases the increase transcription of PEPCK
Processes at equilibrium
Delta G = 0
Melting
Denature
Where does the body utilize glucose from first?
Diet and Insulin secretion
Step 5 of Glycolysis
Dihydroxyacetonephosphate <--> glyceraldehyde 3-phosphate Uses triose phosphate isomerase enzyme.
Uncompetitive Inhibition Graph
Does not change slope. Changes Km and Vmax. Results in vertical shift up and down. Y-intercept becomes α'/Vmax X-intercept becomes -α'/Km
Features of Purines
Double Rings Can form H-Bonds Conjugated (planar)
CO2 binding in Hemoglobin
Forms carbonic acid that shifts hemoglobin to T-state. O2 binding affinity decreases. Used in the peripheral tissues.
What makes the total enzyme Et
E and ES together
Positive control would be predicted for
E on E6 and H on E8
Pyruvate Dehydrogenase
E1 domain of the PDH complex. Contains TPP cofactor. Releases CO2.
Dihydrolipoyl Transacetylase
E2 domain of the PDH complex. Catalyzes formation of Acetyl-CoA. Has oxidized, acyl, and reduced lipoyllysine.
Dihydrolipyl Dehydrogenase
E3 domain of the PDH complex. Catalyzes regeneration of the lipoyllysine using FAD --> FADH2
energy of a photon, plancks law
E=hv=hc/lambda
What form of the enzyme turns over product?
ES
Uncompetitive Inhibitor only binds the
ES complex
FDNB (1-fluoro-2,3-dinitrobenzene)
FDNB reacts with the N-terminus of the protein to produce a 2,4-dinitrophenol derivative that labels the first residue. Can repeat hydrolysis to determine sequential amino acids.
enzyme: pyruvate into Acetyl CoA
PDH
ß-sheet
Either parallel or anti-parallel. Often twisted to increase strength.
High-Spin Fe
Electrons are "spread out" and result in larger atom.
Low-Spin Fe
Electrons are less "spread out" and are compacted by electron rich porphyrin ring.
ß-oxidation in plants
Electrons are passed directly to molecular oxygen releasing heat and H2O2 instead of the respiratory chain.
Lineweaver-Burke Equation
Found by taking the reciprocal of the Michaelis-Menton Equation.
Translation occurs in the
Endoplasmic Reticulum
First Law of Thermodynamics
Energy cannot be created or destroyed
What are the 2 phases of glycolysis?
Energy investment Energy generation
2 2-Phosphoglycerate <——x——> 2 H2O + 2 Phosphoenolpyruvate
Enolase
Glutamine amidotransferase
Enzyme that catalyzes the transfer of the amino group from glutamine to an amino group acceptor. Forms glutamate. Used in biosynthetic pathways.
HMG-CoA Reductase
Enzyme that converts ß-hydroxy-ß-methyl glutaryl-CoA to mevalonate in cholesterol metabolism.
Step 1 of Epinephrine Signal Transduction
Epinephrine binds to its specific receptor
True or False: A biochemical reaction is at equilibrium if ΔG = 15 kJ/mole. True False
False
True/False: Phosphofructokinase-1 is very active in the presence of high ATP. True False
False
Step 1 of ß-oxidation
Fatty acyl-CoA --> trans-Δ2-enoyl-CoA Uses acyl-CoA dehydrogenase FAD --> FADH2 Results in trans double-bond
CAM plants
Fix CO2 into PEP to form oxaloacetate (via PEP carboxykinase) that is converted to malate at night and stored until the day time.
C4 Plants
Fix CO2 into PEP to form oxaloacetate (via PEP carboxykinase) that is then converted to malate that carries CO2 to rubisco. Bypasses O2 binding.
Cooperativity in protein folding
Folding promotes more folding Unfolding promotes more unfolding
Cooperative Protein Folding
Folding transition is sharp. More reversible.
denaturation
For a nucleic acid or protein, the loss of tertiary and secondary structure so that the polymer becomes a random coil. For DNA, this change involves separation of the two strands. Denaturation can be induced by heating and by certain changes in chemical environment.
apoprotein
For a protein with a prosthetic group (which see), the polypeptide portion of the molecule without the prosthetic group.
INSR (Insulin Receptor Protein)
Form of RTK. Catalytic domains undergo auto-phosphorylation.
Non-Competitive Inhibition Graph
Form of mixed inhibition where the pivot point is on the x-axis. Only happens when K1 is equal to K1'.
α-oxidation
Form of oxidation of branched FA's. Produced propionyl-CoA that must be converted to succinyl-CoA for use in the CAC
Steady state means
Formation of the ES complex = rate of disintegration of the ES complex
Malonyl-CoA
Formed from Acetyl-CoA and HCO3 via the Acetyl-CoA carboxylase (ACC). Serves as a regulator of FA catabolism and precursor in FA synthesis.
Glyoxylate Cycle
Found in plants. Produces succinate from 2 acetyl-CoA. Allows oxaloacetate in the CAC to be used in gluconeogenesis. Uses 3 steps from the CAC.
Mirror Repeat in DNA/RNA
Found in single-strands. TTAGCAC|GTGCTAA Forms a hairpin
Reducing Sugar
Free aldehydes can reduce FeIII or CuIII. Aldehyde end is the "reducing" end.
Electrons can transfer as
Free electrons (e-) or H atoms or H: -ions
Gluconeogenic Bypass of Step 3
Fructose 1,6-bisphosphate + H2O --> Fructose 6-phosphate + Pi Uses FBPase-1 (coordinated with PFK-1)
Step 4 of Glycolysis
Fructose 1,6-bisphosphate <--> dihydroxyacetone + glyceraldehyde 3-phosphate. Uses aldolase enzyme.
Step 3 of Glycolysis
Fructose 6-phosphate --> Fructose 1,6-bisphosphate Uses PFK-1 (phosphofructokinase-1) enzyme. ATP --> ADP
Fructose-6-phosphate + phosphofructokinase =
Fructose-1,6-biphosphate
Glucose-6-phosphate + phosphoglucose isomerase =
Fructose-6-phosphate
Fumarate ——x——> Malate
Fumarase H2O
Succinate + Succinate Dehydrogenase =
Fumarate
Step 7 of the Citric Acid Cycle
Fumarate <--> L-Malate Uses fumarase enzyme 1) OH- 2) H+ -->
Reciprocal regulation (ie one pathway turned on while the opposing pathway is turned off) avoids metabolic waste. Running in both directions is referred to as a:
Futile cycle
Negative control would be predicted for
G on E4 and I on E7
DG reaction =
G products -G reactants
DNA Base-paring
G-C base pairs have 3 H-bonds A-T base pairs have 2 H-bonds
The following questions involve the fate of glucose 6-phosphate (G6P). When the cellular demand for NADPH is greater than the cellular demand for ribose-5-P and ATP, how is G6P metabolized?
G6P will go through oxidation and nonoxidation PPP and not into glycolysis.
The following questions involve the fate of glucose 6-phosphate (G6P). When the cellular demand for NADPH and ATP are high compared to ribose-5-P, how is G6P metabolized?
G6P will go through oxidative PP and reobtain GAP and F6P in the carbon shuffle then go to glycolysis and it could go through the nonoxidative phase and get GAP and F6P to do glycolysis.
G6P concentration activates what?
G6Pase
name the enzyme: G6P into Glucose
G6Pase
nonpolar amino acids
GAP VLIM: glycine, alanine, proline (ring), valine, leucine, isoleucine, methionine
name the enzyme: GAP into 1,3 BPG
GAPDH
Hydrogen Bonding
GC bases - 3 H bonds AT bases - 2 H bonds
Lactose
GalB (1 --> 4) Glc
Amylopectin
Has α-1,4-linkages. Has periodic α-1,6-linkages that cause branching. Branched every 24-30 residues. Has reducing and non-reducing end.
fusion proteins
Genetically engineered proteins that are made by splicing together coding sequences from two or more genes. The resulting protein thus combines portions from two different parent proteins.
Cellobiose
GlcB (1 --> 4) Glc
Gentiobiose
GlcB (1 --> 6) Glc
a,a-Trehalose
Glca (1 --> 1) Glca
Sucrose
Glca (1 --> 2) FruB
Maltose
Glca (1 --> 4) Glc
Fructose 1,6 bisphosphatase favors
Gluconeogenesis
PFK-1 and FBPase-1 are major regulatory enzymes. Decide whether glycolysis or Gluconeogenesis is stimulated under these conditions: Phosphorylation of the bifunctional enzyme (PFK-2/FBPase-2)
Gluconeogenesis
Phase I glycolysis-
Glucose (input 2 ATP) make high energy molecule Fructose 1, 6-bisphosphate
Sucrose
Glucose + Fructose
Lactose
Glucose + Galactose
Step 1 of Glycolysis
Glucose --> Glucose 6-phosphate. Uses hexokinase enzyme. ATP --> ADP
name the enzyme: G6P into 6-phosphogluconolactone
Glucose 6 phosphate dehydrogenase
Gluconeogenic Bypass of Step 1
Glucose 6-phosphate + H2O --> Glucose + Pi Uses glucose 6-phosphatase.
Step 2 of Glycolysis
Glucose 6-phosphate <--> Fructose 6-phosphate Uses phosphohexose isomerase enzyme.
What is the 3 reactions that have to be bypassed in gluconeogenesis?
Glucose to G6P F6P to 1,6 FBP PEP to Pyruvate
What is the net formation in glycolysis?
Glucose —> 2 Pyruvate 2 ADP —> 2 ATP 2 NAD+ —> 2 NADH
Step 6 of Glycolysis
Glyceraldehyde 3-Phosphate + Pi <--> 1,3-biphosphoglycerate. Uses G3P dehydrogenase enzyme. NAD+ <--> NADH
Stage 3 of the Calvin Cycle
Glyceraldehyde 3-phosphate --> Ribulose 1,5-bisphosphate Requires 3 ATP and uses transketolase (TPP). Only uses 8 of the 9 G3P's produced. One G3P is used to make starch/sucrose.
Fructose-1,6-biphosphate + aldolase =
Glyceraldehyde-3-phosphate + Dihydroxyacetone Phosphate
Glyceraldehyde-3-phosphate + Dihydroxyacetone Phosphate <——x——> 2 1,3-Bisphosphoglycerate
Glyceraldehyde-3-phosphate dehydrogenase 2 Pi + 2 NAD+ ——> 2 NADH + 2 H+
because of the position of resin in the periodic table, arsenate (AsO4-3) is chemically simian to inorganic phosphate and is used by phosphate-requiring enzymes as an alternative substrate. Organic arsenates are quite unstable, however, spontaneously hydrolyzed. Arsenate is known to inhibit ATP production in glycolysis. Identify the target enyzme and explain the mechanism of inhibition.
Glyceraldehyde-3-phosphate dehydrogenase. The acyl arsenate analog of 1,3-bisphosphoglycerate spontaneously hydrolyzes.
Glycine Ramachandran Plot
Glycine can adopt more angles. (H's for R-group).
Phosphofructokinase favors
Glycolysis
RTKs (Receptor Tyrosine Kinases)
Have tyrosine kinase activity that phosphorylates a tyrosine residue in target proteins
Enthalpy
Heat content of the system
Why isn't gluconeogenesis simply the reverse of the reactions in glycolysis?
Glycolysis has 3 rate limiting steps which are irreversible when in reverse (Glucose to G6P, F6P to 1,6 FBP, and PEP to pyruvate) For these steps, gluconeogensis needs a large amount of energy to reverse them since each have a very large negative free energy. These 3 exergonic reactions just be bypassed in gluconeogenesis.
Predict the effect of each of the following mutations on the pace of glycolysis and gluconeogenesis in liver cells. Explain your reasoning. Addition of glucose 6-phosphate (G6P)
Glycolysis is not effected, do to G6P inhibiting hexokinase 1 in muscle cells not hexokinase 4 Gluconeogenesis increases because G6P stimulates G6Pase
Predict the effect of each of the following mutations on the pace of glycolysis and gluconeogenesis in liver cells. Explain your reasoning. Loss of the allosteric site for ATP in phosphofructokinase
Glycolysis would increase due to their not being a feedback inhibition thus keeping PFK-1 active no effect on gluconeogenesis
Furanosides
Glycosidic bond to anomeric carbon of 5 membered ring.
Pyranosides
Glycosidic bond to anomeric carbon of 6 membered ring.
BPG (2,3-bisphosphoglycerate)
Greatly reduces hemoglobin's affinity for O2 by binding allosterically. Stabilizes T-state. Transfer of O2 can improve because increased delivery in tissues can outweigh decreased binding in the lungs.
Birds evolved for sustained flight would contain more _____ in their muscle compared to birds evolved for occasional and short bursts of flight.
H
enthalpy- and entropy-driven processes
H - negative T/S - negative both favor
enthalpy-driven processes
H - negative (favors) T/S - positive S- negative (opposes)
entropy-driven processes
H - positive (opposes) S - positive (favors)
what are the 2 enzyme that correspond to the Glucose to G6P reaction (bypass reaction and regular)?
HK and G6Pase
Which hexokinase is inhibited by G6P
HK1 (HK4 is not)
Amylose Chain
Has α-1,4-linkages that produce a coiled helix similar to an α-helix. Has a reducing and non-reducing end.
F1 Domain of Mitochondrial ATP Synthase
Hexamer of 3 αß dimers. Catalyze ADP + Pi --> ATP via binding-change model
Glucose ——x——> Glucose-6-phosphate
Hexokinase ATP ———> ADP
The first rate-limiting reaction of glycolysis is catalyzed by the hexonkinase isozymes hexonkinase 1 (HK) and hexokinase 4 (glucokinase). How would the flux through glycolysis compare in muscle and liver when blood glucose levels are normal (4-5 mM)? Explain based on what you know about Km of hexokinase and glucokinase.
Hexokinase 1 is used in muscle cells and hexokinase 4 is used in liver cells. The muscle cells will utilized the glucose because it can only utilizes that intermediate where as the liver cells can use other precursers from glycolysis such as G6P or F6P. Due to hexokinase 4 having a higher km, it is Able to adjust its rate of glucose utilization in response to varying blood glucose levels. Where as hexokinase utilizes glucose immediately created a lower Km. If levels were to increase past 5, hexokinase 4 activity would increase where as hexokinase 1 is already at vmax and cannot respond to increase in blood glucose levels.
Km of Isoenzyme M
High
Mechanism of Denaturants
Highly soluble, H-binding molecules. Stabilize protein backbone in water. Allows denatured state to be stabilized.
Chitin
Homopolymer of N-acetyl-ß-D-glucosamine. Have ß-1,4-linkages. Found in lobsters, squid beaks, beetle shells, etc.
Step 2 of Epinephrine Signal Transduction
Hormone complex causes GDP bound to α-subunit to be replaced by GTP, activating α-subunit
Maximal velocity would be a function of
How close the concentration of ES is to the concentration of Et
What general class of enzyme is a protease?
Hydrolase
Ionophore
Hydrophobic molecule that binds to ions and carries them through cell membranes. Disrupts concentration gradients.
Amino sugars-
Hydroxyl groups in sugars can also be replaced by amines. Amino sugars are common in the repeating units of certain polysaccharides.
lambert beer law
I0/I = Absorbance
INSR cross-talk
INSR causes a kinase cascade that alters gene expression and phosphorlates ß-adrenergic receptor causing its endocytosis.
INSR signalling cascade
INSR phosphorlates IRS-1 that causes a kinase cascade.
how to determine isoelectric point
Identify the amino charge at the extreme ends of pH Average the pKas to find the iP
Explain how the pentose phosphate pathway can respond to a cell's need for ATP, lipid synthesis, and nucleotide synthesis.
If a cell needs to synthesize lipids, the nonoxidative and oxidative reactions of the PPP will take place to generate NADPH and then regenerate glucose 6-phosphate to start the PPP again. If nucleotides are needed, the oxidative reactions can be bypassed and glycolytic intermediates can be converted into the intermediates of the nonoxidative pathway of PPP. The PPP does not have a significant effect on the cell's supply of ATP.
The simultaneous oxidation an phosphorylation of GAP by GAPDH forms a covalent thioester bond between a cysteine side chain on the enzyme and the oxidized intermediate. You identified a patient who has a mutation of this highly reactive cysteine to a leucine. describe how the GAPDH mechanism would be altered in this patient.
If there is a mutation in the GAPDH eye, it is unable to to convert the 2 molecules of GAP into 2 molecules of 1,3 BPG. This is because the 2,3 BPG intermediate is unable to be formed since leucine has a NH3+ R group instead of the S-H R group required so the thioester bond will be unable to form.
Step 10 of Glycolysis
PEP + ADP --> Pyruvate + ATP Uses pyruvate kinase enzyme.
RuBisCo (Ribulose 1,5-bisphosphate carboxylase/oxygenase)
Incorporates CO2 into ribulose 1,5-bisphosphate and cleaves the 6C intermediate into 2 3-phosphoglycerate.
GAPs (GTPase activator proteins)
Increase activity of GTPase activity in α-subunit of GPCR.
Phosphorylated enzyme: as kinase energy decreases, bisphosphatase activity ___________, resulting in a
Increases; decrease in F2,6BP
Unphosphorylated enzyme: As bisphosphatase activity decreases, kinase activity __________, resulting in an
Increases; increase in F2,6BP
ionization of weak acid
Indole-3-acetic acid (auxin) is a weak acid: forms ions in solution that alos tend to recombine to form the acid.
Regulation of HMG-CoA Reductase
Inhibited by AMPK (AMP dependent kinase), glucagon, and oxysterol. Activated by insulin.
Regulation of Pyruvate Kinase
Inhibited by ATP, Acetyl-Coa, Alanine, long-chain FA's.
ACC (acetyl-CoA carboxylase) Regulation
Inhibited by PKA in glucagon chain and activated by pjhosphatase in INSR chain.
V0 is the
Initial rate of the reaction
Oxaloacetate is both an
Intermediate in gluconeogenesis and precursor to citric acid cycle
Citrate + Aconitase =
Isocitrate
Different Steps in the Glyoxylate Cycle
Isocitrate --> Glyoxylate (+ succinate) Uses isocitrate lyase Glyoxylate (+ acetyl-coA) --> Malate Uses malate synthase
Step 3 of the Citric Acid Cycle
Isocitrate --> α-ketoglutarate Uses isocitrate dehydrogenase NAD(P)+ --> NAD(P)H + CO2
Isocitrate ——x——> a-Ketoglutarate
Isocitrate Dehydorgenase NAD+ ——> NADH + CO2
The first rate-limiting reaction of glycolysis is catalyzed by the hexonkinase isozymes hexonkinase 1 (HK) and hexokinase 4 (glucokinase). G6P made by hexokinase can either continue through glycolysis or enter the PPP. How is the entrance of G6P into PPP regulated?
It is sensitive to the NADP+/NADPH ratio of the cell. G6PDH Is regulated by the availability of NADP+. If NADPH is high, G6PDH activity will be inhibited by it and the pathway will not divert G6P from glycolysis. If NADPH levels are low, it will stimulate flux through G6PDH regenerating the necessary NADPH.
Ka for Binding
Ka = [PL] / [P][L]
rate enhancement =
Kcat/ Knon
Enzymatic rate enhancement
Kcat/Knon
Vmax =
Kcat[Et]
Kd for binding
Kd = [L] when 50% bound to protein. Kd = 1/Ka
Q =
Keq then DGAct= 0 and the reaction is at equilibrium(there will be no net flow in either direction)
What is the rate limiting step in gluconeogenesis?
Phosphoenolpyruvate carboxykinase
Km in Michaelis-Menton
Km = [S] when V0 = 0.5(Vmax)
Step 8 of the Citric Acid Cycle
L-Malate <--> Oxaloacetate Uses malate dehydrogenase enzyme NAD+ <--> NADH
Ammonia (NH4+) Transportation
L-glutamate is converted to L-glutamine via glutamine synthetase. ATP + NH4+ --> ADP + Pi L-glutamine can be converted back to L-glutamate in the liver.
Step 3 of ß-oxidation
L-ß-hydroxy-acyl-CoA --> ß-ketoacyl-CoA Uses ß-ketoactyl-CoA dehydrogenase NAD+ --> NAD+
positively charged amino acids:
LAH: lysine, arginine, histidine
enzyme: pyruvate into lactate
LDH
avidin is protein that binds extremely tightly to biotin, so avidin is a protein inhibitor of biotin-requiring enzyme reactions. Consider glucose biosynthesis from each of the following and predict which of these pathways would be inhibited by avidin. a) lactate b) OAA c) Malate d) F6P e) PEP
Lactate because lactate is the only substrate that must go through the biotin-requiring pyruvate carboxylase reaction
Homolactic fermentation occurs in many bacteria and produces
Lactic acid as an end-product
PDH (Pyruvate Dehydrogenase Complex)
Large complex that converts pyruvate + Coa --> Acetyl-Coa + CO2 Uses pyruvate dehydrogenase, dihydolipoyl transacetylase, and dihydrolipoyl dehydrogenase. Inhibited by phosphorylation by ATP.
Z-form DNA
Left-handed helical form of DNA
nt
Leigh's disease is the quintessential oxidation phosphorylation disease - clinically characterized by P_ regression, O_ atrophy, tremors, A_, Apnea, Cardiomyopathy. - Leigh's disease caused by a deficiency in Complex _, Complex _, or Complex _. - Treatment include cofactors _, antioxidants _ _, and drugs _ _. Explain first two. - Other therapies include gene replacement, exercise to (increase or decrease) number of mitochondria, cornstarch to provide a (reduced or constant) fuel.
α/ß Protein Folding
Less distinct areas of α and ß folding.
Enzyme tetramers enriched in the ____ isozymes would be most active under anaerobic conditions, whereas tetramers enriched in the ____ isozymes would be less likely to produce lactic acid in the absence of oxygen.
M H
Q (Ubiquinone/Coenzyme Q) Function
Lipid soluble electron carrier. Carries 2 electrons with 2 H+.
Km of Isoenzyme H
Low
Lactic acid producing bacteria have evolved to survive conditions of
Low pH
Entropy of Folded Proteins
Lower Conformation Entropy ΔS = (-) More favorable solvation ΔS = (+)
TAGs (Triacylglycerols)
Made from phosphatidic acid by removing phosphate with phosphatase and adding an acyl group with acyl transferase.
Pi-Triose Phosphate Anti-porter
Maintains Pi balance in cytosol/chloroplast due to G3P export to the cytosol. Also exports ATP and NADH to the cytosol.
Fumarate + Fumarase + H2O =
Malate
Malate <——x——> Oxaloacetate
Malate Dehydrogenase NAD+ ——> NADH
Trans-fats are created by the partial hydrogenation (removal of cis-double bonds) of unsaturated plant oils.Drawbelowtrans-D9-octadecenoateand predict its melting temperature?
Melting temperature may be closerto stearic acid
Membrance Fluidity
Membrane must be fluid. Cis fats increase fluidity, trans fats decrease fluidity.
Type III Integral Membrane Protein
Membrane protein that contains connected protein helices
Type IV Integral Membrane Protein
Membrane protein that contains unconnected protein helices
Type I Integral Membrane Protein
Membrane protein with C-terminus inside and N-terminus outside
Type II Integral Membrane Protein
Membrane protein with N-terminus inside and C-terminus outside
liposomes
Membrane-bound droplets that form when lipids are added to water.
Primary Functions of Lipids:
Membranes and Energy storage
cofactors.
Metal ions or organic molecules bound to enzymes and aid in carrying out reactions (and not part of the polypeptide chain)
a helix favor what amino acids
Methionine Alanine Leucine Glutamate Lysine (MALEK)
σ-hole
Methyl group has area of diminished electron density in center; attracts electronegative groups
what element serves as a cofactor for most glycolysis enzymes
Mg2+
Which of the following properties relate exclusively to carriers(not channels)that accomplish passive transport. a) selectivity filters that act as substrate collection stations b) binding of substrates to the transporter on only one (membrane) side c) Michaelis-Menten kinetics d) movement of molecules or ions down a concentration gradient
Michaelis-Menten kinetics
Fermentation's are pathways that evolved when
Microbes survived before oxygen became plentiful
Temperature Denaturation of Protein
Midpoint of reaction is Tm.
Where does the citric acid cycle occur?
Mitochondria
Tyrosine, Tryptophan are
More Polar Aromatic
Enzyme Km and Substrate Concentration
Most enzymes have a Km that is near the concentration of the substrate.
Charge of Amino at pH 13
N
Charge of Carboxylic Acid at pH 1
N
Charge of Hydroxyl at pH 1
N
Charge of Hydroxyl at pH 13
N
Charge of Hydroxyl at pH 7
N
Charge of Sulfhydryl at pH 1
N
Charge of Sulfhydryl at pH 7
N
Chitin-monomer is
N-acetylglucosamine (amino sugar)
helical dipole moment
N-terminus partial (+) C-terminus partial (-)
Antiparallel β sheet
N-terminus to C-terminus orientations of the two strands are in opposite directions. 1:1, stable 90°
Parallel β sheet
N-terminus to C-terminus orientations of the two strands are in the same direction. 2:1, Less stable
what does the lactic acid cycle regenerate
NAD+ (generates 2 NAD+) -gives off 2 ATP as well
NADH produced in glycolysis is re-oxidized to
NAD+ in fermentation pathways
Does Isoenzyme M inhibit pyruvate
No
NADH is equal to how much ATP
NADH = 2.5 ATP equivalents
what are the products of PPP besides glycolytic intermediates?
NADPH for lipid and cholesterol synthesis Nucleotides (R5P)
amino
NH2
Cytosine
NH2 and O
Production of carbamoyl-phosphate
NH4+ --> Carbamoyl Phosphate Produced by carbamoyl phosphate synthetase I 2 ATP + HCO3 --> 2ADP + Pi
Aspartate, Glutamate are
Negative (Acidic)
Fructose 2,6-bisphosphate
Not a glycolytic intermediate. Interconverts between fructose 2,6-bisphosphate and fructose 6-phosphate using PFK-2 and FBPase-2
Loops
Not highly structured. Not necessary highly flexible, but can occasionally move. Very variable in sequence.
Each residue in a polypeptide chain has two backbone bonds: ________, about which rotation is permitted. The angle of rotation about the _______ bond is referred to as ϕ (phi) and that about the ________ bond is called ψ (psi).
N−Cα−C N−Cα Cα−C
final electron acceptor of electron transport chain
O2
O2 Binding Event
O2 binds to T-state and changes the heme to R-state. Causes a 0.4Å movement of the iron.
Oxygenase Activity in Rubisco
O2 competes with CO2 and reacts to form 2-phosphoglycerate
a anomer
OH down
B anomer
OH up
hydroxyl
OH-
Oxidation reduction reactions involve transfer
Of electrons
Avidin, a protein found in egg whites, binds to biotin so strongly that it inhibits enzymes that require biotin. What is the effect of avidin on glycolysis? On gluconeogenesis? On the pentose phosphate pathway?
Of the 3 processes, only gluconeogenesis involves an enzyme that requires biotin. The enzyme in question is pyruvate carboxylase, which catalyzes the conversion of pyruvate to oxaloacetate, an early step in glucogeogenesis, so the presence of avidin would inhibit gluconeogenic flux.
Dodecenoic
One Double Bond
Paralogs
Similar "paired" genes in the same organism
Oxidoreductases
One substrate becomes oxidized and one substrate becomes reduced
DNA Double-Helix
Opposite strand direction. 3.4Å distance between complementary bases. 36Å for one complete turn.
Step 1 of the Urea Cycle
Ornithine (+ carbamoyl phosphate) --> citrulline Uses ornithine transcarbamoylase enzyme Only step to occur in the mitochondria
Malate + Malate Dehydrogenase =
Oxaloacetate
if Q > Keq then
P/R is greater than at equilibrium and the reaction cannot proceed spontaneously in the forward direction (DGAct> 0)
if Q < Keq then
P/R is less than at equilibrium and the reaction will go spontaneously in the forward direction (DGAct<0)
aromatic amino acids
PTT: phenylalanine, tyrosine, tryptophan
NADH produced in glycolysis is re-oxidized to NAD+ in fermentation pathways by
Passing electrons to an abundant electron acceptor
2 1,3-Bisphosphoglycerate <——x——> 2 3-Phosphoglycerate
Phosphoglycerate Kinase 2 ADP ——> 2 ATP
2 3-Phosphoglycerate <——x——> 2 2-Phosphoglycerate
Phosphoglycerate mutase
Step 6 of Epinephrine Signal Transduction
Phosphorylated PKA causes an enzyme cascade causing response to epinephrine
Determine whether the following mutations would promote glycolysis or gluconeogenesis in the liver and explain your reasoning. The serine that is phosphorylated on pyruvate kinase is mutated to alanine.
Phosphorylation of PyK by PKA inactivates PyK, so preventing that phosphorylation will increase PyK enzyme activity and therefore promote glycolytic flux.
If 32P-labelled inorganic phosphate were introduced to red blood cells undergoing glycolysis, would you expect to detect 32P in glycolytic intermediates? If so, which glycolytic intermediates would be radioactive? Explain your reasoning.
Pi is used by GADPH to add a phosphate to the first position of GAP to produce 1,3-BPG. Since that first phosphate is removed by PGK to make ATP, the only radiolabeled glycolytic intermediate would be 1,3-BPG (and ATP).
Glutamine, Serine, Asparagine, Threonine are
Polar, uncharged
Lysine, Arginine, Histidine are
Positive (basic)
Where is rotation possible in a peptide amide group?
Possible only about the two bonds adjacent to the a-carbon in each amino acid residue
Assume the GAPDH was inhibited with idoacteate, which reacts with its active site cysteine sulfhydryl group. Which glycolytic intermediate would you expect to accumulate most rapidly and why?
Probably F1,6BP. As triose phosphate began to accumulate, the unfavorable equilibrium for the forward reaction might drive both DHAP and GAP back to F1,6BP. Of course, GAP would accumulate first, but probably not to significantly increased levels
PCR (Protein Chain Reaction)
Process by which DNA is replicated. Has melting step, annealing step, replication step.
Glycolate Cycle
Process of converting 2-phosphoglycerate to 3-phosphoglycerate in chloroplast, peroxisome, and mitochondria.
Proline Ramachandran Plot
Proline adopts fewer angles. Amino group is incorporated into a ring.
Biotin Function
Prosthetic group that serves as a CO2 carrier to separate active sites on an enzyme
exo-peptidases
Proteases that hydrolyze (cut) peptide bonds from one end of a polypeptide chain
TFP (Trifunctional Protein)
Protein complex that catalyzes the last three reactions of ß-oxidation. Hetero-octamer (α4ß4)
fibrous proteins
Proteins of elongated shape, often used as structural materials in cells and tissues. Compare globular proteins.
chaperonins
Proteins that are involved in managing the folding of other proteins. Some of them help proteins to fold correctly; some prevent premature folding; and some prevent polypeptides from associating with other polypeptides until they have folded properly.
globular proteins
Proteins whose three-dimensional folded shape is relatively compact. Compare fibrous proteins.
ß-adrenergic receptor
Prototype for all GPCR's. Bind adrenaline/epinephrine to stimulate breakdown of glycogen.
Adenine
Purine with NH2
Guanine
Purine with O & NH2
Adenine, Guanine
Purines (two nitrogenous bases)
name the enzyme: PEP into Pyruvate
PyK
what are the 2 enzyme that correspond to the PEP to pyruvate reaction (bypass reaction and regular)?
PyK and pyruvate carboxylase and PEPck
Pyranose vs. Furanose
Pyranose is a 6-membered ring. Furanose is a 5-membered ring.
Cytosine, Uracil, Thymine
Pyrimidines (one nitrogenous base)
Ethanol Fermentation
Pyruvate --> Acetalaldehyde --> Ethanol Uses pyruvate decarboxylase (TPP) and alcohol dehydrogenase. NADH --> CO2(TPP) + NAD+
Lactic Acid Fermentation
Pyruvate --> L-Lactate NADH --> NAD+ Regenerates NAD+ for use in glycolysis
2 Phosphoenolpyruvate ——x——> 2 Pyruvate
Pyruvate Kinase 2 ADP ——> 2 ATP
Glucose-Alanine Cycle
Pyruvate can be converted into Alanine via alanine aminotransferase (PLP). Adds a NH4+ group from glutamate to pyruvate. Alanine can travel to the liver and be reconverted back into pyruvate needed for gluconeogenesis.
A one year old child was admitted to the hospital due to consistent sluggishness. When admitted, the child's blood glucose was around 0.8 mM (normal is 4-5 mM), and lactate levels were extremely elevated. Explain why lactate levels are increased in this child.
Pyruvate is building up becasue it cant be converted back into glucose. the body is converting it to lactate and regenerating ATP and NADH.
What is the direction of the conversation of PEP and pyruvate when blood glucose is low?
Pyruvate to PEP
S =
Q/T
Upon binding of one substrate molecule to a subunit, other subunits are more likely to shift to
R form
aldehyde
R-C=O-H
acyl phosphate
R-C=O-O-OPO32-
ketone
R-C=O-R
Translation
RNA to Protein Implies chemical language is different
Second Order Enzyme Assay
Rate here dependent on enzyme finding substrate and turnover
What determines the rate of the overall reaction?
Rate-limiting reaction
Kcat
Rate-limiting step in any enzyme-catalyzed reaction at saturation. Known as the "turn-over number". Kcat = Vmax/Et
Chargaff's Rule
Ratio of A:T and G:C are always equal or close to 1
What is the rate determining reaction of glycolysis?
Reaction 3. PFK-1
Orthologs
Similar genes in different organisms
ω-oxidation
Similar to ß-oxidation but occurs simultaneously on both ends of the molecule.
Xu5P is an intermediate in the PPP. Xu5P levels rise in response to excess glucose shunting through the PPP, does flux through glycolysis increase of decrease?
Recall that xylulose-5-phosphate also plays a regulatory role—it is a specific activator of protein phosphatase 2A (PP2A) in liver. PP2A dephosphorylates PFK-2/FBPase-2 (see Figure 12.19), leading to increased levels of fructose-2,6-bisphosphate, which in turn activates the glycolytic enzyme phosphofructokinase (PFK-1). Thus, as xylulose-5-phosphate levels rise in response to excess glucose via the pentose phosphate pathway, flux through glycolysis also increases.
GABC in Oxidation-Reduction Reactions
Redox reactions usually involve an increase or decrease in the number of C-H bonds or C-O bonds (often involve single to double or double to single bond conversions)
In Alcoholic fermentation, pyruvate is cleaved into acetaldehyde and CO2 and the acid aldehyde is then
Reduced to ethanol
DTT (dithiothreitol)
Reduces disulfide bonds.
Non-Oxidative Pentose Phosphate Pathway
Regenerates glucose 6-phosphate from ribose 5-phosphate. Uses transketolase and transaldolase enzymes.
Regulation of the Citric Acid Cycle
Regulation occurs at Steps 1, 2, 4, and 5. High energy molecules (ATP, Acetyl-CoA, NADH) inhibit while low-energy molecules (ADP, AMP, CoA, NAD+) activate these steps
Collagen
Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil". Contains gly core.
Ethanol Metabolism Features
Requires the enzyme cofactor thymine pyrophosphate for non-oxidative decarboxylation
Oxidation of Odd-numbered FA's
Results in propionyl-CoA formation. Propionyl-CoA can be converted to succinyl-CoA and used in the CAC
D
Right
Animals lack "cellulase" enzymes to digest b-(1->4) linkages. Cellulose is digested innature by animals like:
Ruminants (using bacteria) Termites (using protozoa)
sodium glucose transporters (Where are they located? What do they do?)
SGLT (co transports Glucose with Na+) pulls in to cell (requires energy) create concentration gradient Located on the APICAL side
polar, uncharged amino acids:
ST CAG: serine, threonine, cysteine, asparagine, glutamine
Parallel ß-sheet
Same sheet directions (C & N-termini line up). Has angled H-bonds.
Compare and contrast classical and non-classical competitive inhibition.
Same: both bind free enzyme, compete for free enzyme Different: non-classical binds another site (allosteric), whereas classical binds to the active site
When substrate concentration goes up, enzymes will become
Saturated and the rate of the reaction will level off
cAMP
Secondary messenger in GPCR signalling. Formed from ATP by adenylyl cyclase. Activates PKA (protein kinase A).
Amphiphilic
Secondary structures that display a predominantly hydrophobic face opposite a predominantely hydrophilic face
α-hemolysin
Secreted as a monomer. Assembles to punch holes in membranes.
Ion-Exchange Chromatography
Separates sample based on charge. CM attracts +, DEAE attracts -. May have repulsion effect on like charges. Salt or acid used to remove stuck proteins.
Size-Exclusion Chromatography
Separates sample based on size with smaller molecules eluting later.
Homologs
Shares 25% identity with another gene
Folding Funnel
Shows 3D version of 2D energy states. Lowest energy is stable protein. Rough funnel is less cooperative.
Ramachandran Plot
Shows favorable phi-psi angle combinations. 3 main "wells" for α-helices, ß-sheets, and left-handed α-helices.
Ramachandran plot
Shows favorable phi-psi angle combinations. 3 main "wells" for α-helices, ß-sheets, and left-handed α-helices.
intercellular control, often exercised through action of a second messenger (the hormone is the first messenger)
Signal transduction
If 2 molecules of glucose were oxidized to pyruvate and then those same pyruvate molecules are used in gluconeogenesis, what is the net production/ utilization of ATP?
Since 2 molecules of glucose are being oxidized to pyruvate that means there is a Total of 4 pyruvate molecules that will used for gluconeogenesis. 4 ATP would be used at the 3 bypasses. 2 ATP used converted Pyruvate into oxylaoacetate and into PEP. Then 2 ATP used when converted 3PG into 1,3 BPG. There is then a net total of 4 ATP left over.
Features of pyrimidines
Single Ring Can Form H-Bonds Conjugates (planar)
FMN
Single electron transfer.
FADH2
Single-electron transfer
Lineweaver-Burke Graph
Slope = Km/Vmax Y-intercept = 1/Vmax X-intercept = - 1/Km
Competitive Inhibition Graph
Slope changes by factor of α. Slope becomes αKm/Vmax. X-intercept becomes 1/αKm Y-intercept does not change. Vmax does not change.
How does respiration work?
Slow oxidation of fuels Harvest energy through formation of high-energy linkages
Genomic Efficiency
Smaller units require less coding and produce less errors in txn, tsln
SDS
Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative charge.
What is necessary to stabilize a regular folding?
Some kind of noncovalent bonding, like hydrogen bonds
Features of glycolysis Reaction 4. Aldolase
Splits into two 3-carbon products - represents the branch point of glycolysis and the transition from hexose sugars to triode sugars
Mg2+ in Rubisco
Stabilizes negative charge in intermediate and held by Glu, Asp, and carbamoylated Lysine residue
Rate-limiting Step of the Citric Acid Cycle
Step 1 Acetyl-Coa + Oxaloacetate --> Citrate
ATP Consuming Steps of Glycolysis
Step 1 and 3. Glucose --> Glucose 6-phosphate Fructose 6-phosphate --> Fructose 1,6-bisphosphate
First Committed Step of Glycolysis
Step 3 of Glycolysis. Fructose 6-Phosphate --> Fructose 1,6-bisphosphate. (PFK-1)
GTP/ATP Producing Steps of the Citric Acid Cycle
Step 5 Succinyl-CoA <--> Succinate Using succinyl-Coa synthetase
NADH Producing Step of Glycolysis
Step 6 G3P <--> 1,3-bisphosphoglycerate
FADH2 Producing Steps of the Citric Acid Cycle
Step 6 Succinate <--> Fumarate Using succinate dehydrogenase enzyme
First Energy Yielding Step of Glycolysis
Step 6 of Glycolysis. G3P + Pi <--> 1,3-bisphosphoglycerate
First ATP Yielding Step of Glycolysis
Step 7 of Glycolysis. 1,3-bisphosphoglycerate <--> 3-phosphoglycerate
Bypass Reactions in Gluconeogenesis
Steps 1,3, and 10 must be bypassed.
CO2 Producing Steps of the Citric Acid Cycle
Steps 3 and 4 Isocitrate --> α-ketoglutarate α-ketoglutarate --> Succinyl-CoA
NADH Producing Steps of the Citric Acid Cycle
Steps 3, 4, and 8. Isocitrate --> α-ketoglutarate α-ketoglutarate --> Succinyl-CoA L-Malate --> Oxaloacetate
ATP Producing Steps of Glycolysis
Steps 7 and 10. 1,3-bisphosphoglycerate <--> 3-phosphoglycerate PEP --> Pyruvate
What can be measured from V0 = kcat [ES]
Substrate Concentration Velocity of the reaction (change in product over time) Sometimes the total enzyme concentration (only for pure enzymes)
First Order Enzyme Assay
Substrate easily found so rate here is dependent only on turnover
Enzyme substrate complex
Substrate reversible bound to the enzyme (before any chemistry takes place)
Step 6 of the Citric Acid Cycle
Succinate <--> Fumarate Uses succinate dehydrogenase FAD <--> FADH2
Succinate ——x——> Fumarate
Succinate dehydrogenase Q ——> QH2
Complex II in the ETC
Succinate dehydrogenase. Accepts two electrons electrons from succinate via an FAD group. Q --> QH2
Step 5 of the Citric Acid Cycle
Succinyl-CoA <--> Succinate Uses succinyl-CoA synthetase enzyme GDP + Pi <--> GTP + CoA
Succinyl-CoA <——x——> Succinate
Succinyl-CoA synthetase GDP + Pi ——> GTP + CoASH
Methionine, Cysteine are
Sulfur containing groups
Thioesters
Sulfur not electronegative enough to provide resonance stability to the carbonyl
Upon binding of one inhibitor molecule (negative effector) to a subunit, other subunits are more likely to shift to
T form
In the absence of substrate, all enzyme subunits are typically in the
T form (low affinity, low activity)
Name the enzyme: DHAP into GAP
TPI
Hemoglobin 4° Structure
Tetramer. Dimer of dimers. α2ß2 tetramer.
What is the second bypass of gluconeogenesis?
The conversion of Fructose 1,6 Bisphosphatase to Fructose 6 Phosphate
What is the third bypass of gluconeogenesis?
The conversion of Glucose 6 phosphate to Glucose.
What is the first bypass of gluconeogenesis?
The conversion of pyruvate to Phosphoenolpyruvate
The concept of uncoupling
The simple experiment to the left shows that oxygen is also used without ATP production if 2, 4 -Dinitrophenol is added This suggests the two processes are now uncoupled.
How do allosteric enzymes work?
The enzyme has two subunits, one with the substrate active site and the other with the allosteric site, where the effector binds (there may be more than one of these). The enzyme can alternate between an active form, which reacts with the substrate, and an inactive form, which does not. The effector can be an activator or inhibitor of the enzyme: the activator stabalises the active form, and the inhibitor stabalises the inactive form.
How is PyK regulated?
The enzyme is allosterically inhibited by ATP, acetyl-CoA, and long-chain fatty acids accumulation of fructose 1,6-bisphosphate triggers its activation Accumulation of alanine allosterically inhibits slowing the production of pyruvate by glycolysis. The liver isozyme (L form) is also regulated hormonally Glucagon activates cAMP-dependent protein kinase (PKA), which phosphorylates the pyruvate kinase L isozyme, inactivating it When the glucagon level drops, a protein phosphatase (PP) dephosphorylates pyruvate kinase, activating it This mechanism prevents the liver from consuming glucose by glycolysis when blood glucose is low; instead, the liver exports glucose The muscle isozyme (M form) is not affected by this phosphorylation mechanism.
Primary Structure
The first level of protein structure; the specific sequence of amino acids making up a polypeptide chain.
lock and key model
The model of the enzyme that shows the substrate fitting perfectly into the active site
Quaternary Structure
The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits.
induced fit hypothesis.
The idea of substrate bond strain and a shape change of the enzyme upon substrate binding
chaotropic
The property of being able to disrupt the hydrogen bonding structure of water. Substances that are good hydrogen bonders, such as urea or guanidine hydrochloride, are chaotropic. Concentrated solutions of these substances tend to denature proteins because they reduce the hydrophobic effect.
How should the bond lengths and bond angles behave in regular conformations of a polypeptide chain?
They should be distorted as little as possible from those found through X-ray diffraction studies
TPP
Thiamine pyrophosphate - helps in fermentation
fluorescence
The phenomenon by which a substance that absorbs light at a given wavelength reradiates a portion of the energy as light of a longer wavelength.
circular dichroism
The property of absorbing right circularly polarized light and left circularly polarized light to different extents. Stereoisomers exhibit circular dichroism. Also, some types of secondary structure, such as a helices and b sheets in proteins, exhibit a predictable circular dichroism at specific wavelengths.
Secondary Structure
The second level of protein structure; the regular local patterns of coils or folds of a polypeptide chain.
The concept of chemiosmotic coupling:
The simple experiment to the left shows that oxygen is only used in the ETC when the substrate for ATP production is supplied to mitochondria. This suggests the two processes are coupled.
How should the six atom sin the peptide amide group behave in regular conformations of a polypeptide chain?
The six atoms in the peptide amide group must remain coplanar with the associated a-carbons in the trans configuration.
concentration gradient.
The spatial difference in solute concentration (from top to bottom -upper left)
Tertiary Structure
The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain.
[E], or free enzyme is equal to
The total amount of enzyme [Et] minus the amount of enzyme in the ES complex
These relationships arehow can we tell which reactions in a cell will occur and when (ie under what conditions)?
Things to consider: 1) thermodynamics(ie free energy change) 2) kinetics(ie rate) 3) concentrations of intermediates (substrates and products)
if Km = [S] then Vo = Vmax [S]/ ([S]+[S]) =
Vmax / 2 so Km = the [S]at one-half the maximal velocity
If Km = [S] then V0 =
Vmax [S] / ([S] + [S])
(DGAct) >> 0
These are "uphill" reactions that do not occur spontaneously in the forward direction. These reactions must be coupled to other "downhill" reactions including those that use energy currencies such as ATP.
(DGAct) << 0
These are irreversible, generally at the beginning and / or end of pathways, serve as regulatory points and are controlled kinetically (thru access to an active enzyme).
(DGAct) approximately = 0
These are near equilibrium, readily reversible, generally internal to pathways and controlled by fluctuations in concentrations of substrates and products.
The differences reflect the differences in "quick" energy demand between animals and plants.
They are relatively simple but have a large surface area to volume ratio (fractal -like).
Acyl-phosphates
This arrangement is known as a "mixed" anhydride.
Which molecules represent the most potential energy?
Those that have the most carbons that can undergo the greatest increase inoxidation state.
ATP description
Three phosphates, phosphodiester bond to ribose sugar, N-glycosidic bond to Adenine base
ß-turns
Tight u-turns with specific phi-psi angles. Must have gly at position 3. Proline may also be at ß-turn because it can have a cis-omega angle.
Km and Vmax for General Inhibitors
Vmax [S] / aKm + a' [S] where a is a function of concentration of the inhibitor and the inhibitor binding constant to the free enzyme
if Km = [S] then Vo =
Vmax [S]/ ([S]+[S])
Transaldolase
Transfers a three-carbon aldo group
Transketolase
Transfers a two-carbon keto group
Complex IV in the ETC
Transfers electrons from cytochrome c to O2. Four electrons are used to reduce on O2 into two H2O molecules. Transfers 4H+ to Pside
Complex III in the ETC
Transfers two electrons from QH2 to cytochrome c via the Q-cycle. Transfers 4H+ to Pside.
Rubisco Activase
Triggers removal of ribulose 1,5-bisphosphate or 2-carboxyaarabinitol 1-phosphate so Lys can be carbamoylated.
Glyceraldehyde-3-phosphate <——x——> Dihydroxyacetone Phosphate
Triose phosphate isomerase
if Km >> [S] then Vo =
Vmax [S]/ Km Vo = (kcat/Km) [ET][S]
if [S]> Km then Vo =
Vmax [S]/ [S]Vo = Vmax or Vo = kcat[ET]
kcat =
Vmax/[E]t
Reaching Vmax means
Turning over product as quick as possible
Hill Plot
Turns sigmoid into straight lines. Slope = n (# of binding sites). Allows measurement of binding sites that are cooperative.
α+ß Protein Folding
Two distinct areas of α and ß folding.
Dodecadienoic
Two double bonds
Bacteriorhodopsin
Type III integral membrane protein with 7 connected helices.
Membrane Translayer Flip-Flop
Typically slow, but can be sped up with Flippase, Floppase, or Scramblase.
turn over #
Vmax/active sites
v =
Vmax[S]/Km + [S]
Kinetics of Allosteric Enzymes
Vo vs [S] plots are sigmoidal due to cooperative substrate binding
N-acetylglutamate
Upregulates the production of carbamoyl phosphate and the urea cycle. Formed from acetyl-CoA and glutamate.
ßARK and ßarr
Used in desensitization. ßARK phosphorylates receptors and ßarr draws receptor into the cell via endocytosis
FMOC Chemical Synthesis
Used in synthesis of a growing amino acid chain to a polystyrene bead. FMOC is used as a protecting group on the N-terminus.
Malate-Aspartate Shuttle
Used to maintain gradient of NADH inside of the mitochondria. Involves transport of malate or aspartate; aspartate aminotransferase; and malate dehydrogenase.
Nitrogenase Complex
Uses ATP hydrolysis and ATP binding to overcome activation energy. Has a FeMo cofactor. Is an α2ß2 homodimer. Fixes N2 into NH4+
SDS-PAGE
Uses SDS. Gel is made from cross-linked polyacrylamide. Separates based off of mass with smaller molecules moving faster. Visualized with Coomassie blue.
Circular Dichroism
Uses UV light to measure 2° structure. Can be used to measure destabilization.
Amidotransferase
Uses a PLP group to transfer amino group from an amino acid to α-ketoglutarate to form L-glutamate and an α-ketoglutarate.
Oxidative Pentose Phosphate Pathway
Uses glucose 6-phosphate to produce 2 NADPH and ribose 5-phosphate used for biosynthesis
In aerobic glycolysis, NAD+ is regenerated by
Utilization of the electron transport chain
Michaelis-Menton Equation
V0 = (Vmax[S]) / (Km + [S])
Isoelectric Focusing
Variation of gel electrophoresis where protein charge matters. Involves electrodes and pH gradient. Protein stops at their pI when neutral.
Hydrophobic
Water fearing
B-form DNA
Watson-Crick model DNA. Deep, wide major groove.
π-π Ring Stacking
Weird interaction where aromatic rings stack on each other in positive interaction.
5 14C glucose with only 5 radioactivity labelled is given in metabolically active liver cells in culture. The cells are isolated after a short time and the G6P of the cells is analyzed. The G6P contains the 14C label in the carbon 5 and carbon 2 positions. Explain.
When glucose with the 5 radioactive carbon goes through glycolysis and 1,6 FBP is converted into DHAP and GAP using aldolase. The 5-14C is on GAP, but when it is DHAP is converted to another GAP its creates 2 molecules of GAP with the Carbon 2 labeled. When GAP is converted back into DHAP in gluconeogenesis, the Carbon is now present in in both molecules 2nd carbon. When gluconeogenesis continues, DHAP and GAP is converted back into 1,6 FBP using FBPase 1, carbon 2 and 5 are now radioactively labeled.
Binding Cooperativity
When one subunit of hemoglobin changes from T to R-state the other sites are more likely to change to R-state as well. Leads to sigmoidal graph.
Explain how the 2 phosphates in 1,3-BPG provide the energy necessary to generate ATP.
When the first phosphate in 1,3-BPG is added by GAPDH, the phosphate bond to the carbon is a high-energy bond. When 2-PG is converted into PEP by enolase, enolase produces a C-C double bond which increases the phosphoryl group transfer potential of PEP compared to 2-PG. By breaking the phosphate bonds in both 1,3-BPG and PEP, enough energy is release to power the endergonic reaction of adding a phosphate to ADP to make ATP.
In eukaryotes, when does an oxidizing environment for proteins occur?
When they are synthesized on rough ER and inserted into the ER membrane
van der waals forces
When two molecules approach very closely, their charge fluctuations tend to localize an area of partial positive charge on one molecule next to an area of partial negative charge on the neighboring molecule, producing a net attractive force.
Homotropic Regulation of Binding
Where a regulatory molecule is also the enzyme's substrate.
Heterotropic Regulation of Binding
Where an allosteric regulator is present that is not the enzyme's substrate.
hydrophobic effect
With respect to globular proteins, the stabilization of tertiary structure that results from the packing of hydrophobic side chains in the interior of the protein.
condensation reaction
a chemical reaction in which two or more molecules combine to produce water or another simple molecule
pyridoxal phosphate PLP
a coenzyme containing vitamin B6 (pyridoxine), function in amino group transfer
During strenuous activity, the demand for ATP in muscle tissue is vastly increased. During extended periods of physical exertion, muscles rely on anaerobic fermentation as their main source of ATP. What would be the consequence of the following mutations on the ability of muscle to carry out strenuous physical activity? Explain your reasoning. b)Total loss of function mutation in lactate dehydrogenase
Without LDH functioning, Pyruvate would never be Able to be converted to lactate and no ATP would be made for the muscles. Without ATP for the muscles, the individual would not be able to carry out strenuous physical activity.
Formula for a hyperbola
Y= ax/(b+x)
Does Isoenzyme H inhibit pyruvate
Yes
''steady state conditions"
[ES] and [E] are constant during a large portion of the reaction
Fermentation is a/an _____________________ process that converts _____________ into carbon dioxide and _____________________. anaerobic, pyruvate, ethanol eukaryotic, glyceraldehyde 3-phosphate, ethanol anaerobic, lactate, ethanol prokaryotic, lactate, propanol
a
Glycolysis Catabolism Anabolism Both
a
Which of the following catalyzes a unique reaction of gluconeogenesis? Pyruvate carboxylase Aldolase Pyruvate kinase Enolase
a
Which of the following is a reason why there are additional steps in gluconeogenesis that are not in glycolysis: The ΔG for some of the reactions are too negative for them to be reversible The ΔG for the reactions are too positive for them to be reversible There are a lack of those particular molecules in the cell There isn't a reaction to reform the glucose
a
when a compound has an increase in Os and decrease in Hs: Oxidized reduced
a
Amylopectin-
a branched polymer with alpha 1-6 linkages
protein folding is resisted by
a change in conformational entropy
Rossman Fold
a common domain structure for an important class of enzymes that bind a nicotinamide adenine dinucleotide (NAD) cofactor and carry out reactions critical to the production of ATP in metabolic processes
A muscle biopsy from an individual who was incapable of carrying out prolonged, intense excursive contained a sever deficiency in the glycolytic enzyme phosphoglycerate mutate (PGM) What is the explanation for the inability of this individual to exercise intensively? Make sure fermentation is in your answer.
a deficiency in PGM causes a decrease in 3PG an all following steps including pyruvate production and fermentation into lactate. This causes less NAD+ to be produced as a product of fermentation.
subunit
a distinct polypeptide chain
transition state
a higher energy state thru which reactants must pass to become a product
The reaction catalyzed by fumarase is _____.
a hydration of an alkene
the release of heat to the surroundings, ultimately leads the surroundings to
a less ordered state.
phosphagens contain
a linking nitrogen in an unfavorable resonance
domains
a local part of the protein providing a partial function an independently-folded or independently-evolved portion of the protein
active site
a location that binds the substrate, product and shows a high degree of specificity
Semi-conservative replication
a mode of replication of DNA seen in nature in which each strand serves as a template for two newly synthesized strands.
amphiphilic
a molecule with both polar and nonpolar portions
ketose
a monosaccharide with one ketone (R-C=O-R)
boat conformation
a nonplanar conformation of a cyclohexane ring in which carbons 1 and 4 of the ring are bent toward each other
nucleation
a nucleus of secondary structure
A comparison in the arrangement of the terminal phosphate of ATP to the hydrolyzed product, Pi. The hydrolysis of ATP is an example of
a phosphoryl group transfer (to water). Note that in many biochemical reactions the phosphate is not hydrolyzed, but rather transferred to another intermediate. ATP is said to be a high energy molecule (with high phosphoryl group transfer potential).
oxyanion hole -
a pocket inside the active site of serine proteases which provides H-bond stabilization to the oxyanion transition state.
If DG = 0,
a reaction will be at equilibrium
If DG> 0,
a reaction will go (backward) spontaneously
If DG < 0,
a reaction will go (forward) spontaneously
What indicates cooperativity?
a sigmoidal curve S-shaped
futile cycle-
a substrate cycle that requires more energy equivalents to occur in one direction than are output from the reactions in the opposing direction
Reducing sugar-
a sugar with an open chain aldehyde orketone group
Le Chatelier'Principle states that
a system at equilibrium will respond to any perturbation to the equilibrium by moving to re-establish the equilibrium state.
understand the concept of a co-substrate-
a type of cofactor-acts as a common substrate for lots of cellular reactions-typically exist in two forms (high and low energy_-made in catabolic reactions, spent in anabolic reactions-appears as "circular half arrows" in biochemistry reactions
Product inhibition-
a type of feedback inhibition when the product of a reaction also serves as an allosteric inhibitor
"effectively raises concentration of substrates" refers to
a) productive collisions less likely to occur due to high entropy b) favorable enzyme-substrate interactions lower entropy in active site of enzyme
The two most dire consequences of mis-folded proteins are:
a)The protein function is absent(lack of function) b)The protein aggregates, removing other functional proteins in the process
Substrate-level phosphorylation requires:
a)a higher energy moleculeb)a source of phosphate
Transition state analogues:
a)approximate the transition state, not the substrate.b)bind non-covalently to the conformation of the enzyme that binds the transition state.
Which of the following can be converted into glutamic acid in a single enzyme-catalyzed step?
a-ketoglutarate
a-Ketoglutarate ——x——> Succinyl-CoA
a-ketoglutarate dehydrogenase NAD+ + CoASH ——> NADH + CO2
how many high-energy phosphates are generated or consumed in converting a) 1mole of glucose to lactate? b) 2 moles of lactate to glucose?
a. 2 generated (glycolysis) b. 6 consumed (gluconeogenesis requires ATP)
Considering the enthalpy term, ΔH of folding is made negative by all the factors below:
a.Charge-Charge interactions (salt bridges) b.Internal hydrogen bonds c.Van der Waal's forces contribute to both the packing of atoms in proteins as well as the space between atoms in a protein.
Why may some proteins be more likely to fail to reach low energy states?
a.Protein is large b.Protein relies on non-local interactions c.Protein has mutation (variant) from gene sequence d.Protein in crowded cellular environment
Open System
able to exchange both energy and matter
Closed System
able to exchange energy, but not matter
axial
above and below
axial-
above and below the approximate plane of a "puckered" sugar ring -large groups generally destabilizing
Feed-forward activation
accelerating a late enzyme in a pathway through allosteric activation from an early substrate in the pathway
Hemi-acetals or hemi-ketals can react with nucleophiles to form
acetals or ketals.
Which of the following condenses with oxaloacetate to form citrate?
acetyl-CoA
Ka
acid dissociation constant base / acid
AMPK
activated by 5' AMP, generally shifts metabolism away from biosynthesis and toward energy production
Typically, allosteric enzymes are the regulated steps in enzyme pathways (allosteric regulation). In other words they have two different states (on or off) and rate curves and they can conditionally be
activated or inhibited by outside effectors.
mutations frequently increase the _.
activation energy. fewer molecules have enough energy to reach the transition state, will get fewer product.
activity vs specific activity
activity: total units of enzymes specific activity: # of enzyme units per mg of total protein, a measure of enzyme purity
reduction is normally the...?
addition of Hs
triose
aka glyceraldehyde -3- phosphate **hence the name of the enzyme that makes it: triose phosphate isomerase
Allosteric inhibitors of pyruvate kinase
alanine, ATP, Acetyl CoA
What are the 3 fates of pyruvate?
alcohol fermentation homolactic fermentation citric acid cycle
galactose
aldohexose C2 right C3 & 4 left C5 right
glucose
aldohexose C3 points left
mannose
aldohexose C2 & 3 left C4 & 5 right
name the enzyme: fructose 1,6 bisphosphate into GAP and DHAP
aldolase
Ribose
aldopentose All OH to right
erythrose
aldotetrose
Glyceraldehyde
aldotriose
hydrogen bonds
an interaction between a hydrogen atom covalently bonded to another atom
Sequential (two subtypes)-
all substrates bind before first product produced, no enzyme-substrate intermediate
Homotypic
all subunits are the same
Hexokinase IV (aka glucokinase) contributes toward the role of the liver as a "glucostat"... how?
allows the liver to adjust its rate of glucose utilization in response to varying blood glucose levels
alpha helix vs beta sheet phi and psi angles
alpha helix: phi: -57 psi: -47 beta sheet: phi: -139 psi: +135 parallel is smaller
As the upstream metabolites increase, they (metabolites preceding the defective enzyme) are more likely to enter _ pathways that have _ Km values. Explain
alternate, high, this means that they will enter other pathways where the enzyme has lower affinity for the substrate, (enter an inefficient pathway)
a β strand in an amphiphilic β sheet will have
alternating polar and nonpolar side chains
free energy barrier -
amount of input free energy needed for a substrate to become a product
polyprotic acid
an acid species in which more than one proton dissociates
The oxidation of succinate to fumarate is best characterized as an oxidation of _____.
an alkane to an alkene
metalloenzyme-
an enzyme that employs a metal ion as part of its catalytic mechanism
If the cell has a high energy charge, it is likely to engage in anabolic / catabolic reactions.
anabolic
Glycogen-glucose homo-polysaccharide -
animal energy storage polymer
Chitin-N-acetylglucosamine homopolysaccharide (similar to glucose) -
animal/fungi structural polymer
Central pathways (such as glycolysis and the citric acid cycle)
are common to all organisms and carry the most metabolic traffic.
Central pathways (suchas glycolysis and the citric acid cycle)
are common to all organisms and carry the most metabolic traffic.
Glycosides -
are sugar molecules (glycones) condensed to diverse non-carbohydrate moieties (aglycone).
Intermediary metabolites(intermediates)
are the molecules interconverted in the process of generating and storing metabolic energy (ie in energy metabolism).
Cyclic Symmetry
around a central axis
understand the role of ATP
as a currency and its hydrolysis as a universal coupling agent for cellular reactions (for example, in ATPase pumps or other anabolic reactions)
Q << Keq these reactions are referred to
as irreversible reactions
Vmax (maximal rate)
attained when catalytic sites on the enzyme are saturated with substrate. Describes a STEADY STATE equilibrium of the REACTION catalyzed by the enzyme when the enzyme is substrate saturated.
Which of the following promote pyruvate kinase activity in glycolytic tissue? Long-chain fatty acids F16BP ATP Alanine
b
Which of the following statements about gluconeogenesis in animal cells is true? A rise in the cellular level of fructose-2,6-bisphosphate stimulates the rate of gluconeogenesis. The conversion of fructose 1,6-bisphosphate to fructose 6-phosphate is not catalyzed by phosphofructokinase-1, the enzyme involved in glycolysis. The conversion of glucose 6-phosphate to glucose is catalyzed by hexokinase, the same enzyme involved in glycolysis. An animal fed a large excess of fat in the diet will convert any fat not needed for energy production into glycogen to be stored for later use. The conversion of phosphoenol pyruvate to 2-phosphoglycerate occurs in two steps, including a carboxylation.
b
hich of the following steps in glycolysis also reduces NAD+ to NADH? Glucose to Glucose 6-phosphate Glyceraldehyde 3-phosphate to 1,3-Bisphosphoglycerate 3-Phosphoglycerate to 2-phosphoglycerate Phosphoenolpyruvate to Pyruvate
b
when a compound has an increase in Hs and decrease in Os: Oxidized reduced
b
With all other factors being equal, rank the plant cells below in their tendency to draw the most water into the cell? Hint: use the symbols <, =, and or > a) A cell with 10 glucose molecules b) A cell with 100 glucose molecules c) A cell with a starch molecule 1000 glucose units in length d) A cell with 10 starch molecules each 1000 glucose units in length
b > a =d > c
y-intercept is
b or 1/Vmax
The correct expression for the comparison of the amount of energy contained in each of the macromolecules listed (per gram) would be a) Fats > Carbohydrates > Protein b) Fats > Carbohydrates = Protein c) Carbohydrates > Fats > Protein d) Carbohydrates = Fats > Protein
b) Fats > Carbohydrates = Protein
Cellulose-
b-(1->4) linkages between glucose monomers
nucleoside
base + sugar
glutamate titration curve
begins at +1, ends at -2
histidine titration curve
begins at +2, ends at -1
Esters are condensation bonds
between acids (in yellow) and alcohols.
what buffers blood plasma?
bicarbonate system -carbonic acid (acid) and bicarbonate (base) -dissolved CO2 affects this system, determines concentration of H2CO3 -blood is pH 7.4, and much more HCO3- is present than H2CO3
2) Substrate or effectors alter
binding of substrates or effectors stabilizing T (off) and R (on) forms.
Mixed Inhibitor
binds free enzyme and ES complex
Glycosidic bond
bond between the (cyclic) anomeric carbon and an alcohol, thiol, or amino
hydrolysis/condensation reactions are reactions in which
bonds are broken/formed through addition/subtraction of water
Energy of collision
bonds have potential energy, reactants have kinetic energy and various types of motion. Not all reactant energies are equal.
Glycogen-more highly branched
branches occur approximately every 10 glucose residues as opposed to every 25 glucose residues
During glucose respiration, hydrogen bound to carbon is gradually replaced
by oxygen bound to carbon.
readily reversible reactions sometimes are shared
by pathways that go in opposite directions
The major products of the pentose phosphate pathways are which of the following? Ribose and ATP Xylulose and NADH Ribulose and NADPH Glyceraldehyde 3-phosphate and GTP
c
Which of the following steps in gluconeogenesis converts NADH to NAD+? Fructose 6-phosphate to Fructose 1,6-bisphospate 3-Phosphoglycerate to 1,3-Bisphosphoglycerate 1,3-Bisphosphoglycerate to Glyceraldehyde 3-phosphate 2-Phosphoglycerate to 3-Phosphoglycerate
c
Which of the following steps in glycolysis forms ATP? 3-Phosphoglycerate to 2-phosphoglycerate Glucose 6-phosphate to Fructose 6-phosphate 1,3-Bisphosphoglycerate to 3-Phosphoglycerate Dihydroxyacetone phosphate to Glyceraldehyde 3-phosphate
c
Step 7 of Epinephrine Signal Transduction
cAMP is degraded, reversing activation of PKA. α-subunit hydrolyzes GTP to GDP and becomes inactivated.
Step 5 of Epinephrine Signal Transduction
cAMP phosphorylates PKA, activating it
zwitterions
can act as either acid or base, neutral
Unlike combustion of glucose, the oxidation of glucose in respiration is a step-wise process. It allows
capture and storage of the energy of oxidation along the way
what happens to the blood when stored fatty acids are used as energy
carboxylic acid build-up: beta-hydroxybutyric acid and acetoacetic acid cause acidosis (lowering of blood pH)
Uronic acids are oxidized to
carboxylic acids at the terminal alcohol.
ion exchange chromatography:
cation exchange: the column contains anionic groups, binds positive proteins anion exchange: the column contains cationic groups, bind negative proteins
Regulation -
cellular control of a reaction or pathway through various means such as control of enzyme activities at key entry points or exit points
Binding of negative effectors (heteroallosteric effector)causes
change in shape that is reflected in a steep decrease in reaction rate (due to cooperative binding)
pancreatic amylases
chop carbohydrates into mono or disaccharide in the duodenal lumen
Which of the following is an intermediate between citrate and isocitrate in the citric acid cycle?
cis-aconitate
what intermediates from the citric acid cycle can undergo gluconeogenesis
citrate, isocitrate, alpha-ketoglutarate, succinyl-CoA, succinate, fumarate, and malate
CATH
class, architecture, topology, and homologous superfamily
Lyase
cleave C-C, C-O, C-N, and C-S bonds by means other than hydrolysis or oxidation
Hydrolase
cleaves bonds on molecules with the addition of water (hydrolysis)
Reversible processes
close to equilibrium Delta G close to 0
competitive and noncompetitive inhibition on Vmax and Km
competitive inhibition: changes Km, not Vmax noncompetitive: changes Vmax, not Km
Therefore, a protein will only bind to molecules that have the appropriate shape and chemistry (i.e. only those that are __________ the protein).
complementary to
Catabolic reactions turn ___ molecules into ___molecules creating ___.
complex simple ATP
protein components of the mitochondrial electron transport chain
complex number: 1. NADH dehydrogenase (e- go NADH--> Ubiquinone) 2. succinate dehydrogenase *only complex in Citric acid cycle (e- go succinate --> ubiquinone, makes fumarate) 3. Ubiquinone: cytochrome c oxidoreductase, Cytochrome c (e- go ubiquinone --> cytochrome c) 4. cytochrome oxidase (cytochrome c --> O2) e- donors: NADH (1) and succinate (2)
Km
concentration of substrate at which half the active sites are filled. It provides a measure of the substrate concentration required for signifiant catalysis to occur. It reflects the AFFINITY of the enzyme for the substrate (or substrate for enzyme)
How does the reaction catalyzed by malate dehydrogenase proceed despite a DG°¢of 29.7 kJ/mol?
concentrations of oxaloacetate are kept very low by rapid use in the subsequent step
Anhydride-
condensation product of two acids (phosphoric)
anhydrides
condensation products of two acids
hydrophobic collapse
condenses into tight globule bombardment with water
Keq-
equilibrium constant -ratio of products / substrates at equilibrium
Polyunsaturated fatty acids (PUFAs) -
contain multiple double bonds.
unsaturated-
contains double bonds (unconjugated)-usually in cis-geometry
fibroin
contains long regions of stack antiparrallel B sheets, with the polypeptide chains running parallel to the fiber axis
Heteropolysaccharide-
contains more than one type of monomer
saturated-
contains no double bonds
Homopolysaccharide -
contains single type of monomer
irreversible reactions are typically
control points in pathways
mutarotation-
conversion of alternate anomeric forms of monosaccharides through a straight chain intermediate
What needs to happen to OAA in order for it to leave the mitochondria?
converted to Malate
When does the CO2 leave in glucneogenesis?
converting OAA into PEP
Which of the following describes the isomerization of citrate to isocitrate?
converts a tertiary alcohol, which cannot easily be oxidized, to a secondary alcohol that can be oxidized
Pyruvate Carboxylase
converts pyruvate to oxaloacetate
binding of substrate to one site modifies binding of another substrate to another side.
cooperativity
reactions that are not spontaneous based on Gibbs Free Energy at Standard state can be made spontaneous via
coupling two reactions
Disulfide bonds
covalent bonds formed by the concurrent oxidation of two nearby cysteine side chains to form a cysteine
Blunt ends
cuts from a restriction enzyme with no single stranded overlap
amino acids with Sulfur
cysteine, methionine
Where does glycolysis occur?
cytosol
In an anaerobic muscle preparation, lactate formed from glucose labeled in C-3 and C-4 would be labeled in: all three carbon atoms. only the methyl carbon atom. the methyl and carboxyl carbon atoms. only the carbon atom carrying the OH. only the carboxyl carbon atom.
d
The products of the pentose phosphate pathway are used for which of the following? Production of glucose None of the above Formation of ADP Lipid synthesis
d
Which of the following events will allow hexokinase IV to enter the nucleus? Increased levels of glucose Increased levels of hexokinase I Increase levels of glucose 6-phosphate Increased levels of fructose 6-phosphate
d
Which of the following does not represent a fatty acid? a) R-COOH b) 16:1D9 c) Myristate d) (CH2O)12
d) (CH2O)12
Would the loss of binding site for fructose 1,6-bisphosphate in pyruvate kinase increase or decrease the rate of glycolysis?
decrease
Activation of FBPase-2 causes what?
decrease in 2,6 FBP increase of FBPase-1 decrease in PFK-1 increase of gluconeogenesis decrease in glycolysis
low levels of ATP causes?
decrease in glycolysis
Predict the effect of each of the following mutations on the pace of glycolysis and gluconeogenesis in liver cells. Explain your reasoning. Increase in glucagon secretion
decrease in glycolysis and increase in glyconeogenesis. Glucagon increased PKA which phosphorylates the bifunctional enzyme, decreasing 2,6 FBP, increasing FBPase 1 and decreasing PFK 1. The PyK is inhibited by ATP, Alanine, Acetyl CoA, and cAMP produced from the activation of PKA. 1,6 FBP is inhibited. Glucagon also promotes activity of PEPck and increased levels of Acetyl CoA increases Pyruvate carboxylase activity.
Product accumulation
decreases the rate at which the reaction occurs in the forward direction
Nature of lipids-
definition based on solubility, which is marginal in water. Solubility is primarily in organic solvents or oils.
lysosomes
degradation proteins and contains lysocylic enzymes
Aconitase catalyzes the _____ of citrate to aconitate followed by the _____ of aconitate to isocitrate.
dehydration; hydration
deltaG
deltaG=DeltaG' +RTlnQ
When insulin levels are high, what happens to the bifunctional enzyme and the ultimate effect?
dephosphorylate it activate PFK-2 increase in 2,6 FBP decrease of FBPase-1 increase in PFK-1 decrease of gluconeogenesis increase in glycolysis
reaction coordinate
describers the overall progress of the reaction thru time
Reaction coordinate
describes the overall progress of the reaction thru time
Tautomers-
differ by position of hydrogenand double bond(anomeric carbon)-interconvert (but slowly)
free energy of activation-
difference in free energy between the substrate and the transition state in an enzyme-catalyzed reaction.
In many biochemistry reactions in which carbon molecules are oxidized (losing electrons), the electrons are transferred to an
electron "carrier".
Zwitterion
dipolar ions that can be overall neutral despite local, opposite charges
entropy means
disorder
The muscle is considered glucose _____?
disposal
Ka and pKa
dissociation constant: Keq=[H+][A-]/[HA]=Ka pKa = -log[Ka]
Nucleophile
donates electrons
Oxidation reactions often involve forming
double bonds from single bonds -this is made easier by base catalysis
As [OH-] goes up [H+] goes
down
How does the nuclear binding inhibitor protein associated with HK4 help regulate its activity?
draws hexokinase IV into the nucleus when the fructose 6-phosphate concentration in liver is high and releases it to the cytosol when the glucose concentration is high
Why is there such a large free-energy change associated with ATP hydrolysis?
due to the -3 charge not happy next to each other so they repulse if the bond is broken it is more stable
1) Multi-subunit enzymes
each has active sites (substrate binding) and regulatory (effector binding) sites and shows cooperative binding of substrate and effectors
Glycolysis investment phase(hexose phase)-
early phase of glycolysis in which ATP is used twice to phosphorylate six carbon sugars.
Electrophiles
electron poor and attack electron rich
catabolic -
energy liberating, complex molecules recycled toprecursors
anabolic -
energy requiring, precursors built into complex molecules
Waxes also play an
energy storage role and density modulator in certain aquatic organisms like plankton. They may be the major source of ocean-derived petroleum.
Catabolic reactions (pathways) -
energy-liberating reactions (pathways) that generally breakdown complex molecules and yield small molecules. These reactions (pathways) are often oxidative in nature.
Anabolic reactions (pathways)-
energy-requiring reactions (pathways) that generally build precursors (small molecules) into complex molecules. These reactions (pathways are often reductive in nature).
name the enzyme: 2PG into PEP
enolase
General Acid base catalysis (GABC)
enzyme acts as a general acid or general baseto facilitate a reaction.
three factors that affect reaction rate
enzyme concentration, substrate concentration, and inherent speed of the enzyme
when [ES]= [Et]
enzyme operating at Vmax [ES] means enzyme + substrate, Et means total amount of enzyme
electrostatic catalysis -
enzyme's remove the solvation sphere of a substrate or substrates. This can eliminate an energy barrier imposed by ordered solvent molecules and also eliminate water's diminishing effect on ionic interactions between the substrate and the enzyme
Electron carriers "save" the energy of oxidation for cellular use. They do this by
existing in two energy states (high and low). The reduced form of these carriers (or cofactors) are high in potential energy.
Transition state theory
explains reaction rates by assuming an equilibrium between reactants (substrates) and those reactants (substrates) activated to the transition state.
Irreversible processes
far from equilibrium Delta G very negative
Glyoxylate cycle
fatty acids enter and are converted into succinate for the citric acid cycle
Tropocollagen
fibrous protein consisting of three strands twisted together and containing large amounts of glycine, proline, and hydroxyproline
[S] > Km is a __________ order equation.
first
irreversible reactions are reactions that often are the
first (or last) steps in a pathway
pyruvate enol and keto
first appears in enol form, then tautomerizes to keto form, which predominates at pH 7
The Ping-Pong Mechanism (double-displacement) -
first product produced before all substrates bind, goes thru enzyme-substrate intermediate
henderson hasselbalch equation
fits titration curve of all weak acids -at the midpoint of titration, pH=pKa can use as pH=pKa + log[conjugate base]/[acid]
condensation reaction and hydrolysis reaction
formation of ATP from ADP and inorganic phosphate (water is a product) hydrolysis: using water to cleave, water is a reactant --> carried out by hyrdolases
Annealing
formation of complimentary base pairs that causes DNA to "zipper" into a double helix
helical symmetry
formed by rotation of each unit by 360/n degrees (with n units per turn)
delta G is
free energy
G0A=
free energy of the average reactant molecule in a population
Classical Inhibitors only bind
free enzymes
So, the energy of hydrolysis of ATP, comes
from the difference in free energy between substrates and products.
how is the efficiency of the enzyme calculated
from the ratio of kcat to KM
allosteric activator of pyruvate kinase
fructose-1,6-bisphosphate
The structure of a protein dictates the partners with which it can interact. Therefore, the structure of a protein is directly related to its
function
Flux -
general term for fluctuation or movement of molecules through enzyme steps or pathways that leads to addition or subtraction of substrates or products from specific reactions.
What activates PEPck?
glucagon
Starch(plants) and glycogen(animals) are very similar to one another. They are both
glucans(composed of glucose).
G6P promotes?
gluconeogenesis
PFK-1 and FBPase-1 are major regulatory enzymes. Decide whether glycolysis or Gluconeogenesis is stimulated under these conditions: Decrease [fructose 2,6 bisphosphate]
gluconeogenesis
When ATP and citrate levels are high, what does it promote?
gluconeogenesis
if glucagon, ATP, Alanine, cAMP, and acetyl CoA levels are high, what does it promote?
gluconeogenesis
name the enzyme: 6-phosphogluconolactone into 6-phosphogluconate
gluconolactone
glycolysis equation
glucose + 2NAD+ + 2ADP + 2Pi--> 2pyruvate +2ATP + 2NADH + 2H + +2H2O *aerobic
Glucose + Hexokinase =
glucose-6-phosphate
An individual with chronic hypoglycemia was suspected of having a defect in one of the enzymes unique to gluconeogenesis. To identify the defective enzyme, tissue samples from a normal liver were compared to samples from the patient's liver biopsy, using a biochemical assay that measures glucose production from glycerol or malate. It was found that incubation with glycerol produced normal amounts of glucose in both the control and biopsied liver samples; however, incubation with malate did not lead to glucose production in the liver biopsy, even though it did lead to glucose production in the control liver sample. On the basis of these observations, which of the 4 main gluconeogenic enzymes is most likely defective in this individual? Explain your reasoning and what data you used to rule out enzymes.
glycerol to DHAP to GAP all the way to glucose is so it is not G6Pase or FBPase 1 since the path follows Pyruvate into maleate into OAA is working so pyruvate carboxylase is not defective. this leaves the reaction where OAA converts to PEP by PEPck, since there is no glucose being made this has t be defective.
glycogen breakdown and synthesis
glycogen phosphorylase a is catalytically active breaking down glycogen this is inhibited by phosphoprotein phosphatase 1 and becomes the inactive glycogen phosphorylase b which can be restored to active state by adding phosphate with phosphorylase b kinase -glucagon and epinephrine activate phosphorylase b kinase synthesis: -glycogen synthase a is active, becomes inactivated by glycogen synthase kinase (GSK-3) (which adds phosphates) and is reactivated by phosphoprotein phosphatase 1 (PP
If insulin and 1,6 FBP levels are high, what does it promote?
glycolysis
PFK-1 and FBPase-1 are major regulatory enzymes. Decide whether glycolysis or Gluconeogenesis is stimulated under these conditions: Activation of PFK-2
glycolysis
PFK-1 and FBPase-1 are major regulatory enzymes. Decide whether glycolysis or Gluconeogenesis is stimulated under these conditions: Activation of the insulin receptor
glycolysis
PFK-1 and FBPase-1 are major regulatory enzymes. Decide whether glycolysis or Gluconeogenesis is stimulated under these conditions: Decrease [ATP]
glycolysis
When AMP, ADP, and 2,6 FBP levels are high, what does it promote?
glycolysis
What is the breakdown of sugar of sugar into pyruvate?
glycolysis (no krebs, no electron transport, no pdc cycle)
Predict the effect of each of the following mutations on the pace of glycolysis and gluconeogenesis in liver cells. Explain your reasoning. Loss of the phosphatase domain of the bifunctional enzyme that controls the level of fructose 2,6-bisphosphate
glycolysis increases due to 2,6 FBP stimulating PFK 1 Gluconeogenesis deceases due to 2,6 FBP inhibiting FBPase 1
How much does the rate change in each tissue when blood glucose goes from 12 mM to 15 mM?
greater in liver than in generic tissue
Anti-codon
group of three bases on a tRNA molecule that are complementary to an mRNA codon
Electron Transport Chain-
harvesting the energy of reduced cofactors through a series of redoxreactions (oxidative phosphorylation)
amphoteric
having an acid-base nature
enthalpy means
heat
name the enzyme: Glucose into G6P
hexokinase
G6P inhibits what?
hexokinase 1
Which hexokinase contributes to glycolysis and gluconeogensis?
hexokinase 4
Low Km (Kd) means ______ affinity
high
the muscle has a ____ affinity for glucose
high
Phosphoanhydride
high energy bonds between phosphates
If the reaction is regulated in the liver with high blood glucose, explain how it Is regulated?
high glucose causes release of insulin release of insulin causes decrease of PKA inhibitor of PKA causes the dephosphorylation of PyK activating it inhibition of PKA also decreases levels of Acetyl-CoA, ATP, Alanine, and cAMP These decreased levels contribute to the activation of PyK insulin activates PEPck 1,6 FBP is activated whole thing activates glycolysis
Molecules (like ATP) that favorably transfer phosphoryl groups are said to have
high phosphoryl group transfer potential.
high dielectric constant
high polarity of the molecule water dissolves many things
In order to allowmetabolic flow that can generate energy (catabolic pathways) and do biosynthesis, cells would need to maintain ratios of NAD+ / NADH that are (high/low) and ratios of NADPH/NADP+that are (high/low).
high, high
Entropy of unfolded proteins
higher conformational entropy ΔS = (+) less favorable solvation ΔS = (-)
Because it is more reduced than glucose, palmitic acid has a
higher energy density
Which of the following amino acids participates in the transfer of a phosphate groupin the reaction catalyzed by succinyl-CoA synthetase?
histidine
what amino acid can act as a buffer for proteins
histidine, has midpoint at pH 6
General Acid-Base catalysis relies on polar ionizable residues such as:
histidine, serine, tyrosine, cysteine, lysine, arginine, glutamate, aspartate
rate enhancement indicates
how much faster a reaction proceeds in the presence of an enzyme
Saponification -
hydrolysis of fats under conditions of strong base (sodium hydroxide)-makes soaps (detergents)
3' end
hydroxyl group
what decides whether glucose-6-phosphate enters glycolysis or pentose phosphate pathway?
if NADP+ is high, enters pentose phosphate pathway - can synthesize nucleotides and nucleic acids by making ribose
The following questions involve the fate of glucose 6-phosphate (G6P). When the cellular demand for ribose-5-P is greater than NADPH and ATP, how is G6P metabolized? How would this change if NADPH levels were high?
if NADPH levels are low, needs to go thaw the oxidative phase to obtain both NADPH and R5P. IF levels of NADPH are high, NADPH will recognize the high levels and inhibit G6P from going into PPP and going back into glycolysis.
In humans and most/all organisms examined to date), the mutation that leaves this pathway non-functional occurs in the gene for the same enzyme step of the pathway, the last step. From an evolutionary perspective, this is best explained by the fact that
if Vitamin C is present in the diet, there is no cost to this mutation.
The operational relationship between pKa and pH is that:
if pH = pKa, the compound in question will be half protonated and half deprotonated
overcome competitive inhibition
if substrate concentration supersedes competitive molecule (molecule competing for active site) by a lot
anomers -
if they differ spatially at a chiral carbon formed from a ring closure
conformational -
if they have the same chemical formula and arrangement of functional groups, but develop different three-dimensional shapes in space
constitutional-
if they have the same chemical formula, but they have unique arrangement of functional groups
diesteromers-
if they have the same formula and arrangement of functional groups, are unique spatially, but not as non-superimposable mirror images of one another
enantiomers
if they have the same formula and arrangement of functional groups, but they are non-superimposable mirror images of one another
epimers-
if theyhave the same formula and arrangement of functional groups, but they are unique spatially at a single carbon position
stereo-isomers-
if theyhave the same formula andarrangement of functional groups, but they are unique spatially
Readily reversible reactions can go
in either direction depending on the flux of products and reactions. The enzymes are not typically controlled because the concentrations of products and reactants control the reaction.
phosphofructokinase 1 (PFK-1)
in glycolysis, converts fructose-6-phosphate to fructose 1,6 bisphosphate **bisphosphate means two phosphates in different locations -this is the first committed (irreversible) step in glycolysis
enolase
in glycolysis, removes water from 2-phosphoglycerate to make phosphoenolpyruvate (PEP)
ketone bodies
in the liver, acetyl-CoA (derived from fatty acid breakdown) is converted to ketone bodies acetoacetate or beta-hydroxybutyrate -can be used as fuel, important for the brain when glucose in unavailable *too many ketone bodies lowers blood pH and is called ketoacidosis
hormone synthesis location
in the mitochondria! -catalyzed by cytochrome p-450
zymogen-
inactive precursor of (typically) a digestive enzyme including serine proteases.
Would the loss of allosteric site for ATP in phosphofructokinase increase or decrease the rate of glycolysis?
increase
Would the loss of binding site for citrate in phosphofructokinase increase or decrease the rate of glycolysis?
increase
Would the loss of phosphatse domain of the bifunctional enzyme that controls the level of fuctose 1,6-biphosphate increase or decrease the rate of glycolysis?
increase
initially a competitive inhibitor does what to the Km value of the enzyme
increase (no longer has as high affinity for substrate b/c there is another molecule competing for active sites)
Activation of PFK-2 causes what?
increase in 2,6 FBP decrease of FBPase-1 increase in PFK-1 decrease of gluconeogenesis increase in glycolysis
high levels of ATP causes?
increase in gluconeogenesis
low levels of AMP causes?
increase levels of gluconeogenesis (still inhibiting but not as much)
high levels of AMP causes?
increase levels of glycolysis (increased activation)
Classical-inhibitor can be titrated by
increased S concentration
Effects of concentration on reaction rates
increases in reactant(s) concentration increases likelihood of collisions
If [S]>>KM,v is
independent of [S]
Uncompetitive inhibition
inhibitor binds only once the ES complex has formed (it cannot bind to the free enzyme)
inhibition
inhibitor binds the free enzyme and the ES complex after it has formed
2-carboxyarabinitol 1-phosphate
inhibits carbamoylated rubisco. Synthesized in the dark and is broken down by rubisco activase or light.
Animal fats tend toward more saturation and serve a variety of functions such as:
insulation and / or.....energy and heat production.
What inhibits PEPck?
insulin
Which of the following hormones causes liver cells to be a "sugar sink"in mammals? a) epinephrine b) insulin c) glucagon d) eicosanoids
insulin
induced dipole interactions
interactions of polarizable molecules
charge-charge interactions
interactions that involve the attraction of + and - charged ions or the repulsion
Co-substrates typically have two forms (energy states, like ATP and ADP)that are
interconverted in many cellular reactions. They are often represented differently in biochemistry equations.
intermediary metabolites (intermediates) are the molecules
interconverted in the process of generating and storing metabolic energy (ie in energy metabolism). They are small in number (25-50)and generally kept at fairly constant cellular concentrations.
Readily reversible reactions are typically
internal to pathways
alcohol dehydrogenase
involved in ethanol fermentation, catalyzes oxidation of ethanol in the liver
transketolase
involved in pentose phosphate pathway: -transfers a 2C molecule from a ketose to an aldose acceptor
how can you identify aromatic amino acids:
light diffraction, signature peak at 280 nm (tyrosine and tryptophan- highest)
chemiosmotic
involving simultaneous transport and a chemical reaction
The molecule (ion) above (shown in purple) that forms a complex (intercalates)with starch to turn starch-containing substances a dark purple color is
iodine
oxidative decarboxylation
irreversible oxidation of pyruvate in which the carboxyl group is removed and acetaldehyde and CO2 are formed --> goes to ethanol -enzyme: pyruvate decarboxylase and TPP coenzyme
The respiratory quotient
is another measure of how much free energy a molecule contains. Lower numbers mean higher free energy content.
reducing equivalent
is the amount of a reducing compound capable of donating the equivalent of 1 hydrogen atom.
Which of the following is activated by ADP?
isocitrate dehydrogenase
How does aconitase demonstrate both of the meanings of the term domain described in class?
it has independently folded regions and separate regions for different activities.
amylose -
linear polymer with helical twist
If [S]<<KM,v is
linearly dependent on [S]
Equation for dissociation of ES complex is
k-1 (ES) = k1 (E) (S) or (k-1/ k1) = (E) (S) / (ES)
rate of formation of the enzyme-substrate complex =
k1[A][B]
Rate of formation is defined by:
k1[E][S]
V0 =
k2(cat)[ES]
Consider the enzyme-catalyzed reaction with Vmax=164 (μmol/L)min−1 and KM=32 μmol/L. If the total enzyme concentration was 9 nmol/L, how many molecules of substrate can a molecule of enzyme process in each minute? Calculate kcat/KM for the enzyme reaction. Is this a fairly efficient enzyme?
kcat = 1.82 x 10^4 min-1 or 302 s-1 kcat/KM = 9.5 x 10^6 M-1 s-1 Yes, this is a very efficient enzyme, it is operating near the diffusion limit.
The second order rate constant is
kcat/Km
Fructose
ketohexose C3 left
xylulose
ketopentose C4 points left
ribulose
ketopentose C4 points right
dihydroxyacetone
ketotriose
irreversible reactions are controlled
kinetically, not thermodynamically
Fatty acids have
large (wide) head group and narrow tail
What does Km value tell us about substrate affinity? Give in terms of small or large value
large value Km the substrate doesn't bind tightly or doesn't have high affinity for enzyme. Low value Km the substrate binds tightly and has a strong affinity for enzyme
Glycolysis payoff phase(triose phase)-
late phase of glycolysis in which net ATP is harvested from three carbon units producing organic acids.
productive collision
leads to a chemical rxn
% mismatch shifts Tm
left
L
left
You have a competitive inhibitor. Measurements of Km in the absence of the inhibitor is 2.5mM. Measurements of Km in the presence of 3mM inhibitor is 3.9 mM. This inhibitor binds
less tightly than the substrate and only to the free enzyme.
Carbohydrates are directional molecules-
linked chains of carbohydrate monomers can often be distinguished by an anomeric (reducing) and non-anomeric (non-reducing) ends
micelles
lipid molecules orient with polar (hydrophilic) head toward water and nonpolar (hydrophobic) tails away from water
lipoate
lipoic acid, in microorganisms, an intermediate carrier of hydrogen atoms in acyl groups in alpha keto acid dehydrogenase
Hexokinase 4 is located where
liver
Transcription starts with
localized melting
Lipids are open chain structures(polar head groups) with
long non-polar tails includes: fatty acids, triacylglycerols (triglycerides), phosphoacylglycerols (glycerophospholipids), sphingolipids, glycosphingolipids
Nucleic Acid Tertiary Structure
longer range interactions in 3 dimensions
oxidation is normally the...?
loss of Hs
the liver has a ____ affinity for glucose
low
Tissue isoform
low Km Saturates quickly and is not responsive
If the reaction is regulated in the liver with low blood glucose, explain how it Is regulated?
low glucose causes release of glucagon release of glucagon causes PKA pathway to occur PKA causes the phosphorylation of PyK inactivating it PKA also increases levels of Acetyl-CoA, ATP, Alanine, and cAMP These increased levels contribute to the inhibition of PyK Acetyl CoA activates pyruvate carboxylase Glucagon activates PEPck 1,6 FBP is inhibited whole thing activates gluconeogenesis
Kd of a transition state analogue would be expected to be
lower than a Kd of a substrate analogue
In the tense form, key contacts are made within subunits that hold the subunits in a state that either
lowers Vmax raises Km
amino acids involved in glycolysis
lysine, cysteine, histidine
slope of line =
m or Km/Vmax
Phosphate esters -
major participants in metabolic pathways
first step of glycolysis:
make glucose - 6- phosphate with hexokinase
Which of the following is an equilibrium-controlled step within the mitochondria?
malate dehydrogenase
semi-conservatively,
meaning each opposite parent strand serves as a template for new daughter strand synthesis
Entropy
measure of how energy is dispersed within the system
Cooperativity
melting promotes more
When a metabolic disorder is caused by a single enzyme deficiency, the disruption usually leads to the accumulation _
metabolites preceding the defect
Metal ion catalysis
metal ions within the enzyme's active site that participate in catalysis.In the reaction below, for example, the zinc ion stabilizes an electron rich transition state.
If [1-14C]glucose (glucose labeled at C-1 with 14C) is used as a substrate, what is the location of 14C in the product ethanol?
methyl group
oxidize fuels occurs
mitochondria
buffer
mixture of weak acid (proton donor) and conjugate base (proton acceptor) ex: acetic acid and acetate, H2PO4 1-/HPO4 2-, NH4+/NH3 -each buffer has a characteristic buffer zone
Nucleoside
molecule containing a sugar in a glycosidiclinkage with a-N-base
Nucleotide
molecule containing a sugar-phosphate in a glycosidic linkage with a-N-base
competitive inhibitor
molecule that looks like substrate and sits in the active site of the substrate, competes for active site of enzyme with substrate
aromatic
molecule with benzene ring
Ampholytes
molecules that contain groups with both acidic and basic pKas
B-keratin
more B-sheet structure found mostly in birds and reptiles
collagen
most abundant single protein in most vertebrates built from triple helices of polypeptides rich in glycine and proline
chair conformation
most stable conformation of cyclohexane
most and least likely amino acids to be in alpha helix
most: alanine, arginine least: proline, glycine
Allosteric enzymes are often
multi-subunit and exhibit cooperativity (Hill coefficients > 1) between subunits:
Repeated function (Quaternary)
multiple binding or active sites
Folding Stability (Quaternary)
multiple subunits allow maximum functional diversity while minimizing folding problems
Functional Diversity (Quaternary)
multiple subunits allow mixing and matching of functions
hexokinase 1 is located where
muscle
how does fructose enter the muscles and kidney? how about the liver?
muscles and kidney: hexokinase phosphorylates C6 liver: liver enzyme fructokinase phosphorylates C-1
B Strand (parallel) n, h, p
n = 2.0 h = 3.2 p = 6.4
B Strand (antiparallel) n, h, p
n = 2.0 h = 3.4 p = 6.8
3-10 helix n, h, p
n = 3.0 h = 2.0 p = 6.0
Polypeptide II helix n, h, p
n = 3.0 h = 3.1 p = 9.3
a helix n, h, p
n = 3.6 h = 1.5 p = 5.4
An hydrogen attached to an amino nitrogen from amino acid n forms a hydrogen bond with amino acid
n-4
Proton shuttle -
name for isomerase reaction mechanism used in steps 2 and 5 of glycolysis and the reverse of these reactions in gluconeogenesis. Results in aldose to ketose or ketose to aldose conversions.
a reaction is favorable when its free energy is
negative
When an upstream enzyme in a pathway is defective, then what occurs in regards to steady state, flux, and metabolite concentration?
new steady state occurs, flux (output) is REDUCED and concentration of downstream metabolites is REDUCED
When an downstream enzyme in a pathway is defective, then what occurs in regards to steady state, flux, and metabolite concentration?
new steady state occurs, flux (output) is REDUCED and the concentration of Upstream metabolites is INCREASED
polyproline II helix
no stabilizing hydrogen bonds between main-chain groups left-handed 1/3 Prolines Often contains glycine
Increasing Kr would have ------ effect on affinity and a ---- effect on velocity.
no, positive
if the free energy of a reaction is positive, the reaction is... spontaneous or non spontaneous
non spontaneous
endergonic means...
non spontaneous delta G postive entropy negative enthalpy positive
3) Effectors bind
non-covalently to enzymes and modify Km and or Vmax
coenzyme
non-protein compound required for the functioning of an amino acid
Phenylalanine (description)
nonpolar aromatic
Glycine, Alanine, Proline, Valine, Leucine, Isoleucine are
nonpolar, aliphatic
Valine, Leucine, Isoleucine are
nonpolar, aliphatic, branched
Glycine, Alanine, Proline are
nonpolar, aliphatic, straight chained
Isolated System
not able to exchange energy or matter
What kind of a inhibitor protein is associated with HK4?
nuclear binding
transcription occurs in the
nucleus
Catalytic rate constant
number of molecules of substrate converted to product per unit of time or turnover number
The energy produced in the form of ATP by oxidative metabolism is an example
of evolved-coupling stoichiometry. In other words, evolution has chosen the amount of ATP derived from metabolism. Efficiency is only one consideration. Another consideration is that the process is driven forward, even when fuels are in low supply.
GABC in Nucleophilic substitution reactions
one group (the nucleophile) is substituted for another (the leaving group).
point group symmetry
one point is fixed
how to determine the Km of an enzyme in a multi substrate enzyme reaction
one substrate is put at a saturation velocity level in order to determine the km of the other
lactone
organic compound containing an ester group
tertiary structure
overall course of the polypeptide chain
Which of the following explains the proper binding of the two substrates for citrate synthase?
oxaloacetate binds, then acetyl-CoA
During the oxidation of isocitrate, the intermediate that is decarboxylated to form α-ketoglutarate is _____.
oxalosuccinate
NAD+ is a major
oxidant
What are the 2 phases of PPP?
oxidative non-oxidative
Free straight chain monosaccharides can be
oxidized (to aldonicacids (or lactones) and uronic acids) or reduced (to alditols(sugar alcohols).
Henderson-Hasselbach Equation
pH = pKa + log ([A-] / [HA])
Henderson-Hasselbalch equation
pH = pKa + log [A-]/[HA]
pKr:
pK values of the amino acid R group
Double bonds of fatty acids affect melting point -
packing of fatty acids due primarily to VanderWaal's forces (longer chains pack better, unkinked chains pack better).
Glucagon-
pancreatic hormone secreted under conditions of low blood glucose.
initial rate (Vo)-
period of time measured in a typical MM enzyme assay after the mixing period and before product builds up.
B strand phi and psi
phi = -150 to -100 psi = +120 to +160
3-10 helix phi and psi
phi = -70 to -60 psi = -30 to -10
a helix phi and psi
phi = -70 to -60 psi = -50 to -40
Polypeptide II helix phi and psi
phi = -80 to -60 psi = +130 to +160
5' end
phosphate group
Nucleotides consist of
phosphate, sugar, and nitrogen base
if the enthalpy of a reaction is positive, the free energy of that reaction is likely... positive or negative
positive
name the enzyme: Ru5P into Xu5P
phosphopentose epimerase (ribose-5-phosphate epimerase)
name the enzyme: Ru5P into R5P
phosphopentose isomerase
Glucose labeled 14C is on carbon 6 and s added to a solution containing enzymes and cofactors of the oxidative phase of PPP. If you wanted the radioactive label to end up in S7P, what enzymes would you need to add to the solution mentioned?
phosphopentose isomerase phisphotpentose epimerase transketolase
When glucagon levels are high, what happens to the bifunctional enzyme and the ultimate effect?
phosphorylate it activate FBPase-2 decrease in 2,6 FBP increase of FBPase-1 decrease in PFK-1 increase of gluconeogenesis decrease in glycolysis
what triggers glycolysis for hexoses?
phosphorylation!
Base Stacking
pi stacking (resonance stability) and van der Walls forces optium when bases are stacked
enzymes that work thru covalent catalysis are called
ping-pong reactions
Cellulose-glucose homo-polysaccharide -
plant (mostly) structural polymer
Starch-glucose homo-polysaccharide -
plant energy storage polymer
equatorial
point away
equatorial-
point away from approximate plane of a "puckered" sugar ring -large groups generally not destabilizing
Aldoses
polyhydroxy aldehydes
Ketoses
polyhydroxy ketones
DX Naming-
position of double bonds from the carboxyl group
Hydrophobic effect
positions non-polar bases to the interior, polar backbone to exterior (water layer)
synthases and synthetases
synthases: catalyze condensation reactions and do not use ATP synthetases: catalyze condensation reactions and do use ATP (also ligases)
Ligase
synthesizes bonds coupled to the cleavage of phosphate bonds
bilayers
tails of phospholipids facing each other
Effects of temperature on reaction rates
temperature increases the average kinetic energy (movement)of molecules as is shown in the graph below:
Tm
temperature of DNA where 50% is melted, 50% is annealed
Phosphagens are
temporal energy buffers in animal muscle
coheviseness
tendancy of water to stick to itself
adhesiveness
tendency for water to stick to other polar or charged substances
reduction potential:
tendency of an molecule to accept electrons in an redox reaction -a positive # means it will gain the electron
Why are we short one 6C molecule in PPP?
the CO2 lost during the oxidative phase
Self-replication
the ability of DNA to replicate based on the duplicate nature of the information contained in base-pairing rules
If pKa > pH
the acid form predominates
If pKa = pH
the acid is half dissociated
thiamine pyrophosphate TPP
the active coenzyme form of vitamin B1 involved in aldehyde transfer reactions
respiration
the aerobic process of glucose breakdown to CO2 and H2O
A reducing equivalent is
the amount of a reducing compound capable of donating the equivalent of 1 hydrogen atom.
H donors
the atom to which the hydrogen is covalently bonded
H acceptors
the atom with the nonbonded electron pair
free energy barrier
the barrier that must be overcome for a reaction to occur
Cooperative binding
the binding of substrate (or activator or inhibitor)to one active site increases the likelihood that another substrate (or activator or inhibitor) will bind to other sites
effect of angle on H bond strength
the bond is the strongest when the angle defined by the donor atom and the acceptor atom is 180
effect of distance on H bond strength
the closer the stronger the bond
gene expression
the combination of transcription and translation
Triacylglycerols(triglycerides)-
the common storage form of lipidsin plants and animals.They areoften what we refer to commonly as "fat". Triacylglycerols are tri-esters of fatty acids and glycerol (see below).
if pKa < pH
the conjugate base form predominates
The energy of hydrolysis of ATP, comes from
the difference in free energy between substrates and products
Second Law of Thermodynamics
the entropy of an isolated system will tend to increase to a maximum value (ie delta G < 0 )
(ES <-> ESI) Positively affects formation of .
the enzyme-substrate complex, therefore, Km App goes down, affinity goes up. ES turnover to E + P is altered (slowed), therefore, Vmax goes down
In general, which enzyme establishes the flux of a metabolic pathway
the first enzyme
The development of a hydrophobic core during protein folding is primarily due to
the hydrophobic effect
protein folding is promoted by
the hydrophobic effect (the favorable entropy change of the solvent due to the release of water from clathrates which occurs when hydrophobic side chains are buried within the molecule)
Reversible inhibition involves
the non-covalent binding of an inhibitor to an enzyme.
ATP coupling coefficient -
the number of ATP s either generated in or required for a reaction or set of reactions (pathway) to occur
The osmotic concentration (solute particles per liter solution) depends on
the number of dissolved particles, not their mass.
Pasteur effect-
the observation that significantly less glucose is used during aerobic glycolysis in comparison to anaerobic glycolysis. This is due to the fact that more ATP is produced in the complete oxidation of glucose, which feeds back and slows the cycle. It is evidenced by buildup of intermediates that precede the PFK-1 step.
isoelectric point
the pH at which the positive and negative charges are equal, the molecule has a net neutral charge
what buffer system is in the cytoplasm of cells
the phosphate buffer system H2PO4- is proton donor, HPO4 2- is e- acceptor has a pKa of 6.86, resists pH changes from 5.9-7.9
pKa
the pka of an ionizable weak acid group is the pH at which half of the ionizable weak acid group is protonated and half of the ionizable group is deprotonated
The upper limits of the catalytic proficiency constant are constrained only by
the rate of diffusion
conjugate base
the species that results when an acid donates a hydrogen ion
obligate-coupling stoichiometry-
the stoichiometry of biochemical pathways, which is fixed by the biochemical nature of the process(ie molecules used in the cell)
Reduction potential -
the tendency of a chemical species to accept electrons
Standard reduction potential
the tendency of a chemical species to accept electrons under standard (ized) conditions
chemiosmotic theory
the theory that says that ATP synthesis in the mitochondria is driven by a proton gradient across a membrane -the energy from the flow of electrons to O2 is used to pump H+ out, H+ coming back across the membrane spins ATP synthase and generates ATP
phosphoryl group transfer potential-
the thermodynamic potential a phosphorylated molecule has to "push" the phosphate to ADP to produce ATP.
catalytic triad-
the three amino acid residues that take part in the catalytic mechanism of serine proteases (asp, his, ser)
ionization of water
the transfer of a proton from one water molecule to another to produce a hydroxide ion and a hydronium ion
What are the most frequently observed secondary structures of polypeptides?
the α helix and the β sheet
Metastability
theoretically thermodynamically unstable, but so long-lived as to essentially be stable
malonyl CoA
there is enough energy, don't break down FA's
Oxygen has a marked tendency to attract electrons. Therefore, oxidation is a
thermodynamically favorable (downhill) in both processes. .
coupled reactions would not occur in the forward direction unless
they are "coupled" with a second thermodynamically favorable reaction. can be coupled to ATP hydrolysis can be linked in sequence with other reactions
codon
three-nucleotide sequence on messenger RNA that codes for a single amino acid
Polymerization of nucleic acids occurs
through the formation of phosphate esters (depicted below).An ester bond is a bond formed between an alcohol and an acid.
Upon binding of one activator molecule (positive effector) to a subunit, other subunits are more likely to shift
to R form
Why do enzymes relatively weak bonds to the substrate
to avoid a thermodynamic pit
Electrons are "obligately coupled"
to or transferred to electron carriers (NAD+and FAD). These same electron carriers transfer electrons to oxygen in reactions catalyzed by the electron transport chain. Oxygen is the terminal electron acceptor in this process.
Osmotic concentration is directly related
to osmotic pressure (the pressure to resist water flow across a semi-permeable membrane).
Step 2 of ß-oxidation
trans-Δ2-enoyl-CoA (+ H2O) --> L-ß-hydroxy-acyl-CoA Uses enoyl-CoA hydratase
name the enzyme: S7P + GAP into E4P + F6P
transaldolase
last step in glycolysis:
transfer phosphate from phosphoenolpyruvate to ADP, done by pyruvate kinase
name the enzyme: R5P + Xu5P into S7P + GAP
transketolase
name the enzyme: Xu5-P + E4-P into GAP + F6P
transketolase
tRNA (transfer RNA)
translator moleculecontains important sites for: amino acid attachment 3'OHanticodon (reads code)
What are collagen fibers built from?
triple helices of polypeptides rich in glycine and proline
True/False: The active form of FBPase-2 is when it's phosphorylated. True False
true
Transition state-
unstable arrangement (highest free energy level) midway between substrate and product where some chemical bonds are being broken (short lifetime) and some are being formed.
carboxylation
uses CO2 to make carboxylic acid
circular dichroism
uses polarized light and molar extinction coefficient to distinguish alpha helix and beta sheets
Michaelis-Menten equation
v = (vmax [S])/(Km + [S])
Waxes are
very long chain fatty acids and very long chain alcohols (40 -60 carbons in length) with maximal stacking and high melting points(semi-solids) and an effective water shield for skin, feather, fur and leaf.
Biotin -
vitamin (cofactor) involved in a variety of carboxylation reactions in the cell including pyruvate carboxylase
hydrolysis:
water attacks --> how glycosidic linkages are broken down
water high specific heat
water has high specific heat --> water resist change in temperature because its harder to break H bonds
Hydrophilic
water loving
Glycogen has an increased
water-solubility (does not crystallize) quicker digestion (target) -animals Stored primarily in liver, muscle
dipole-dipole
weak attractions between groups that are polar, but not actually carrying a full charge
noncovalent bonds
weak bonds that play important roles in the attraction/repulsion of neighboring molecules and shapes of many macrimolecules
Triglycerides have
weakly polar head,multiple interactions between tails.
fructose 2,6 bisphosphatase
when fructose 2,6 bisphosphate (F26BP) levels are high, glycolysis is stimulated through fructose 1,6 bisphosphate with PFK-1 when they are low, gluconeogenesis is stimulated through fructose 6 phosphate formulation with FBPase 1
14C-labeled glyceraldehyde 3-phosphate was added to a yeast extract. After a short time, fructose 1,6-bisphosphate labeled with 14C at C-3 and C-4 was isolated. Where did the second 14C label in fructose 1,6-bisphosphate come from?
when going through gluconeogenesis, the 1 GAP molecule was converted to DHAP using TPI. This isomerization caused the 1 C of this molecule to be labeled as well. When DHAP and GAP form together using aldolase, then 1,6 FBP is created showing how C3 and C4 and labeled.
The Law of Mass Action states that
when the rates of the forward and reverse reactions are equal, the system will be at equilibrium.
DGAct= -RT ln Keq + RT ln Q
where Q or mass action ratio-actual ratio of cellular[product]/[reactant]
Aldonic acids-sugar derivatives
where aldehyde group (anomeric carbon) is oxidized to a carboxylic acid (ring closure results in a lactone, cyclic ester)
The consequence of cooperative binding of allosteric enzymes:
within small substrate concentrations, can see large fluctuations in reaction rate
Co-substrates are molecules that
work with enzymes (Ch 8). They are not permanently bound to enzymes, but are involved in the enzyme reaction.They act more like substrates (except they are shared in a variety of cellular reactions).
During strenuous activity, the demand for ATP in muscle tissue is vastly increased. During extended periods of physical exertion, muscles rely on anaerobic fermentation as their main source of ATP. What would be the consequence of the following mutations on the ability of muscle to carry out strenuous physical activity? Explain your reasoning. a)Constitutively active mutation in PFK
would be able to perform but lactic acid would build up and eventually make the individual ill
unproductive collision
wrong angle or insufficient energy
If [S]=KM,v is
½ of Vmax
Step 4 of ß-oxidation
ß-ketoacyl-CoA (+ CoA) --> Fatty acyl-Coa (shorter) Uses thiolase enzyme
ΔGtransport Equation
ΔGtransport = RTln([S]out / [S]in) + ZFΔΨ
α vs. ß sugars
α form has -OR/OH group opposite from the -CH2OH group. ß form has -OR/OH group on the same side as the -CH2OH group.
GPCR (G-protein coupled receptor)
α-helical integral membrane proteins. Is a αßɣ heterotrimer.
Step 4 of the Citric Acid Cycle
α-ketoglutarate --> succinyl-CoA Uses α-ketoglutarate dehydrogenase complex CoA + NAD+ --> NADH + CO2
ϴ-value in Binding
ϴ = (bound / total)x100% ϴ = [L] / ([L] + 1/Ka)
