Medical Biochemistry w/ Borgon Exam 2 Review

What is the most highly oxidized compound in living systems?

Carbon dioxide

In the _______________________ reaction from lactate to pyruvate, _____ electrons and _____ hydrogen ions are removed from lactate to form pyruvate. Electrons are transferred to ______.

Dehydrogenation; two; two; NAD

What are some ways redox reactions can occur?

- Direct electron transfer
- As a hydrogen atom (H+ and e-)
- As a hydride ion (H+ and 2e- = H-)
- Direct combination with oxygen

Check slides for examples

_________________________ applies to biochemistry, and organic chemistry principles are still valid.

Thermodynamics

Building complex structures that are low in entropy is only possible when energy from the _________ is spent in the process.

Sun

Some biomolecules like ATP are "high energy" with respect to their hydrolysis and group transfers, and energy can be stored in reduced organic compounds can be used to reduce cofactors such as __________ and __________, which serve as universal electron carriers.

NAD+ and FAD

True or false: Anabolic reactions are energy-producing (exergonic) and break molecules down.

False;

Catabolic reactions are energy-producing (exergonic) and break molecules down.

Anabolic reactions are energy-consuming (endergonic) and are biosynthetic.

Determine if the following represents a catabolic or anabolic reaction:

1. Amino acids -> Proteins
2. Carbohydrates -> CO2
3. Fatty acids -> Lipids
4. Nitrogenous bases -> Nucleic acids
5. Proteins -> NH3

1. Anabolic
2. Catabolic
3. Anabolic
4. Anabolic
5. Catabolic

To maintain organization, living systems extract useable energy from their surroundings, release useless energy (_________), and increase ___________ in the universe.

Heat; entropy

Free energy is the energy available to do ______, expressed as _____, which measures enthalphy (______), entropy (_____), and movement of a system.

Work; ΔG; ΔH; ΔS

What is the free energy equation?

ΔG = ΔH - TΔS

A positive ΔH represents an _________________ reaction and a negative ΔH represents an _________________ reaction.

A positive ΔS means ______ disorder and a negative ΔS means _______ disorder.

A positive ΔG represents an ________________ reaction and a negative ΔG represents an __________________ reaction.

Endothermic; exothermic;
More; less;
Endergonic; exergonic

In terms of ΔH and ΔS, when will a reaction always be spontaneous?

A negative ΔH, a positive ΔS

In terms of ΔH and ΔS, when will a reaction never be spontaneous?

A positive ΔH, a negative ΔS

If you have a positive ΔH and a positive ΔS, when will the reaction be spontaneous?

At high temperatures

Note: If you have a negative ΔH and a negative ΔS, the reaction will be spontaneous at low temperatures.

True or false: Systems move toward equilibrium, where ΔG= 0.

True

At chemical equilibrium, the ________________ and ______________ rates are equal.

Forward; reverse

Free energy tells the _____________ of a reaction.

Direction

Note: Free energy and the equilibrium constant measure the direction of processes.

True or false: Negative free energy is not favorable.

False;

Negative free energy is favorable and spontaneous; the reaction will move forward.

Positive free energy is unfavorable.

True or false: ΔG tells you how fast a reaction proceeds.

False;

ΔG tells direction of reactants as they go towards equilibrium

kcat tells you how fast a reaction proceeds.

Reaction rates can be sped up by increasing temperature, increasing _____________ concentration, decreasing _____________ concentration, enzyme catalysis, or activation via _______.

Reactant; product; ATP

Note: [ ] represents concentration

True or false: ΔG° is the biochemical standard state, where pH = 7, and [H2O] = 55.5 M

False;

ΔG° = -RTlnKeq, equal to standard conditions of 1M reactants and products; 298 K, 1 atm, pH 0

ΔG'° = biochemical standard state, where pH = 7, and [H2O] = 55.5 M

When Keq is greater than 1, ΔG is ____________ and the reaction proceeds ___________.
When Keq is equal to 1, ΔG is _____________ and the reaction ___________________.
When Keq is less than 1, ΔG is ____________________ and the reaction ______________________.

Negative; process forward
Zero; is at equilibrium
Positive; proceeds in reverse

The actual ΔG determines a reaction's direction in __________.

Cells

For a reaction at concentrations other than "standard", ΔG can be calculated by using the ______________.

Concentrations

Reactions that are not spontaneous can occur is the concentrations of reactants or products is changed from ______.

1 M

Do all individual steps in biosynthetic pathway need to be favorable?

No, but the overall pathway must have a negative free energy change.

The conversion of L-malate to oxaloacetate (through malate dehydrogenase) is not a favorable reaction because ΔG'° is _____________.

However, oxaloacetate _____________________ is kept very low by ___________ _____________.

Positive; concentration; citrate synthase

True or false: Hydrolysis reactions tend to be strongly favorable.

True;

Note: In hydrolysis reactions, water is consumed.

Isomerization reactions have ____________ free-energy changes (ΔG° = 0 between enantiomers)

Smaller

The complete oxidation of reduced compounds is strongly favorable, and is _________________ and controlled.

Stepwise

Most organic molecules, including the reduced fuels, are in the singlet spin state (all electrons paired). On the other hand, molecular oxygen is in the _______________ spin state (with _____ electrons unpaired). This makes oxygen ___________________ (slightly magnetic).

Triplet; two; paramagnetic

Electron transfer between organic molecules and oxygen is quantum-mechanically ______________________. Direct oxidation (spontaneous combustion) of biomolecules does not occur readily, as most are singlet state, but it can react with ________________ (radicals).

Unfavorable; doublets

A few ______________, such as transition metal ions and FAD, can catalyze consecutive ___________-electron transfers needed for the utilization of O2.

Cofactors; single

True or false: Heterolytic bond cleavage is rare.

False;

Homolytic bond cleavage is rare.

Vitamin B12 synthesis is an example of a ____________________ bond cleavage.

Homolytic

Homolytic: electrons __________ and generate ______________

Heterolytic: electrons remain with one fragment; products are highly ______________ and reactive; gives rise to __________________ groups (e.g. protons, nucleophiles/electrophiles)

Split; radicals

Unstable; transferable

What are some chemical reactions in the cell?

- Cleavage and formation of C-C bonds (e.g. pyruvate -> acetaldehyde)
- Cleavage and formation of polar bonds
- Internal rearrangements (glucose 6-phoshpate -> fructose 6-phosphate)
- Eliminations (without cleavage)
- Group transfers
- Oxidation- reductions; e- transfers (acetaldehyde -> ethanol)

Check slides for further insight.

__________ ____________ involve moving a group from one molecule to another.

Group transfers

What is a very common group transfer reaction?

Proton transfer

Match the following proton transfers to their respective characteristics:

A. Acyl transfer
B. Glycosyl transfer
C. Phosphoryl transfer

1. Activates metabolites or signal transduction (nucleophilic displacement)
2. Attachment of sugars
3. Biosynthesis of fatty acids

A- 3
B- 2
C- 1

Note: Don't forget proton and methyl transfers!

Several phosphorylated compounds have large ΔG'° for hydrolysis.
Electrostatic _______________ within the reactant molecule is ________________.
The products are stabilized via __________________, or by more favorable solvation.
The product undergoes further _______________________.

Repulsion; relieved;
Resonance;
Tautomerization

When you look at the standard free energy table, you notice that ADP is more thermodynamically favorable than ATP. However, reactions typically use ATP. Why?

With ATP, we can cleave the phosphoanhydride bond and continue moving forward in the reaction.

However, with ADP, if you cleave the bond, it causes the reaction to go both forward and backward.

True or false: AMP has a high energy bond.

False;

AMP does not have a high energy bond (phosphoester)

How many phosphoanhydrides does ATP have?

Two;

Note: They are high energy, weak

ATP hydrolysis can be coupled to other reactions.
Hydrolysis reactions are often written as a single step, but are actually ________ steps, and ___________ is omitted.

Two; water

Note: Reactions involving ATP create a highly unstable transition state.

____________________ is an important donor of acyl groups in fatty acid biosynthesis.

Acetyl-CoA

True or false: Thioesters are high energy, while oxygen esters are low energy.

True;

Note: This is due to less resonance stabilization in thioesters; thioesters are localized from the S-CoA group.

Oxidation-reduction reactions involve ___________________ transfer. These are used in energy-producing/consuming reactions.

Electron

True or false: A higher reduction potential (E) means a higher affinity for electrons.

True;

Note: Electrons are transferred from a lower to higher E for a negative ΔG

______________ binding to cofactors like FAD can shift reduction potentials to allow them to participate in a range of reactions.

Proteins;

This is how FAD can receive electrons from ubiquinone.

ATP hydrolysis has a negative ΔG; it readily reacts with water, in large part due to its ______________________ bonds

Phosphoanhydride

ATP has a ______________ ____________ as both P=O bonds compete for oxygen's electrons, relieved upon hydrolysis

Hydrolysis (break down by addition of water, thus _____________ a water) of these bonds is accompanied by large -ΔG change

Electrostatic _________________ of the oxygens is relieved, and ADP can form _______________ better H-bonds with water

ADP has ____________ entropy than ATP

Competing resonance;
Consuming;
Repulsion; better;
Greater

Vitamin B12 synthesis is one of the rare reactions where ATP's ________________ is cleaved.

Triphosphate

What is the equation for ATP hydrolysis?

ATP --> ADP + Pi + heat energy

Reactions are coupled using a ________ _____________, which involves exchanging ATP's high energy groups, which raises the ___________ ________ of the target.

Group transfer; energy state

~P transfer to COO- yields COO~P (acylphosphate, _____ energy)
~AMP transferred to an amino acid retains its _______ energy
~P transfer to C-OH produces a phosphoester (____ energy)

High; high; low

True or false: The hydrolysis of thioesters is not strongly favorable.

False;

The hydrolysis of thioesters is strongly favorable.

The end goal in the electron transport chain is to produce ___________, which is at the top of the reduction potential chart.

Water

What only accepts/donates two electrons at a time?

NAD+

(NAD+ + 2e- + 2H+ -> NADH + H+)

True or false: NADH can dissociate from the enzyme after the reaction.

True

NADH is generally involved in _______________ reactions (NAD+ ______, NADH _______) as an ________________ agent as NAD+.

Catabolic; high; low; oxidizing

NADPH is an activated carrier with high energy bonds, involved in generally _________________ reactions (NADP+ _________, NADPH _________) as a ________________ agent as NADPH.

Anabolic; low; high; reducing

What can accept/donate one or two e- at a time?

FAD

(FAD + 2e- + 2H+ -> FADH2)

True or false: FAD cannot work with homolytic reactions.

False;

FAD can work with homolytic reactions

Because _______ can accept/donate one or two e- at a time, this permits the use of molecular ____________ as an ultimate electron ______________, which goes ____ e- at a time.

FAD; oxygen; acceptor; one

Flavin (B2) cofactors are _____________ bound to proteins, even ______________ as in succinate dehydrogenase. This binding allows FAD to participate in this _________________ reaction.

Tightly; covalently; oxidation

Note: Remember that when FAD interacts with protein, it can change its reduction potential to receive electrons.

FADH+ is a __________________, while FADH2 is ___________ _____________.

Semiquinone; fully reduced

The biochemical reactions (metabolism) in the living cell are organized into metabolic pathways:

Extraction of _________
Storage of ________
___________ of important building blocks
____________ of waste materials

Energy;
Fuels;
Synthesis;
Elimination

In the metabolome of growing E. coli, about 50% of metabolites are __________ _________.

Amino acids

Note: Most of the metabolome consists of glutamate.

Organisms maintain ___________ by keeping the concentraions of most metabolites at _________ _________, where the rate of synthesis equals the rate of breakdown.

Homeostasis; steady state

What happens when a steady state is perturbed?

A new steady state will be established

The levels of required metabolites must be altered very rapidly: __________________ glycolysis for action, ___________________ glycolysis after action, _________________ glucogenesis after successful action

Increase; decrease; increase

Blood clotting, oxytocin contractions, and lactation are all examples of ________________ ________________.

Positive feedback

Note: In positive feedback, the product activates its own synthesis

ATP inhibiting glycolysis is an example of _______________ _____________.

Feedback inhibition, or negative feedback

Note: This occurs when ultimate products of metabolic pathways directly or indirectly inhibit their own biosynthetic pathways

What issue might positive feedback cause?

Pathways can get out of control

Do most pathways have negative or positive feedback?

Negative feedback; this makes it safe

True or false: The thyroid feedback loop is an example of positive feedback.

False; this is negative feedback

Note: In the thyroid feedback loop, the hypothalamus releases TRH, which stimulates the anterior pituitary. The anterior pituitary releases TSH, which stimulates the thyroid. The thyroid releases T4, which activates T3, which inhibits further activity from the hypothalamus and the anterior pituitary.

In glycolysis, the activation of pyruvate kinase from high concentrations of fructose 1,6-biphosphate is an example of _______________ ______________.

Positive feedforward

What is reaction rate dependent upon?

Concentration of reactants vs products, substrates vs
competitors

Temperature, pH, cofactors, coenzymes

Activity of the catalyst: intrinsic rate, signal transduction, transcription/translation vs degradation, tissue-specific expression, isozymes, activation vs. inhibition, organelle localization

The elasticity coefficient measures the responsiveness to _______________.

Substrate

True or false: The reaction rate is more sensitive at high substrate concentrations.

False; the rate is more sensitive at low substrate concentrations

Note: Frequency of substrate meeting the enzyme matters

Another note: The rate becomes insensitive at high substrate concentrations as the enzyme is saturated with substrate

Most reactions in the cell operate ________ equilibrium. However, hey enzyme operate _____________ equilibrium, which are highly ___________ to control flux.

Near; far from; regulated

Transcription can regulate enzyme _________________.

Concentrations

Hormones like insulin can control transcription.

True or false: Insulin increases the transcription of many glycolytic enzymes and decreases the transcription of gluconeogenic enzymes.

True

Isozymes are __________

A) multiple enzymes that share the same catalytic function.
B) enzymes that catalyze varied reactions.
C) a group of enzymes that aid in anabolism (synthesis).
D) enzymes that catalyze reverse reactions to those of main enzymes.

A) multiple enzymes that share the same catalytic function

Note: These isozymes have different kinetics and regulation

Hexokinase I is expressed in ______ tissues at different levels.
Hexokinase IV is only expressed in the ________. It converts glucose into G6P for glycogen, as it has a higher _____ so it can function at higher glucose concentrations.

All;
Liver; Km

Phophorylation is catalyzed by protein ___________, which add a phosphate to Ser, Thr, and Tyr.
Dephosphorylation is catalyzed by protein ____________________.

Kinases; phosphatases

Phosphorylation can affect protein ____________ or interface with binding partners.

Surface

Binding of regulatory protein subunits affects enzyme _____________.

Specificity

Note: Hexokinase IV moves from cytoplasm to nucleus and binds to regulatory proteins to prevent glycolysis.

____________________ is an important degradative process.

Ubiquitination

Note: Proteins have a finite lifespan and have a range of half-lives.

Another note: Ubiquitin goes to E1 activating enzyme to E2 conjugating enzyme to target protein and the E3 ligating enzyme to make ubiquitinated protein. This can then go to the proteasome, which will degrade the protein.

True or false: Glucose 6-phosphate inhibits production of hexokinase.

True;

Note: This is an example of negative feedback

A 10% decrease in [ATP] leads to a _________ increase in [AMP], a more potent _______________ regulator.

600%; allosteric

AMP kinase is an important regulator of _______________, which activates energy-producing pathways when high levels of _________ were detected.

Homeostasis; AMP

Note: Higher levels of AMP and lower levels of ATP as well as exercise activates AMP kinase.

AMP kinase activates food intake, fatty acid uptake, glucoe uptake, mitochondrial biogenesis, glycolysis

AMP kinase inhibits fatty acid synthesis, cholesterol synthesis, and insulin secretion.

______________________ converts glucose -> glucose 6-phosphate. It is sequestered into the ___________ when F6P high, and released into _____________ when glucose concentration is high.

_________ allosterically inhibits hexoknase (not in active site).

Hexokinase; nucleus; cytosol

G6P

Fructose 6-phosphate -> fructose 1,6-biphospohate is the ________________ step in glycolysis, catalyzed by _________.

Committed; PFK-1

True or false: Glycolysis is only activated when ATP is high.

False

Note: ATP is a substrate and also an allosteric negative effector, so glycolysis is only activated when ATP is low.

Another note: Citrate has negative feedback

PFK-2/FBPase-2 activates glycolysis if AMP is _______, glucogenesis if AMP is _____.

High; low

Fructose 6-phophate _____________ glycolysis, while fructose 2,6-biphophate __________________ glycolysis.

Serine 32 (kinase domain) _______________ glycolysis, while serine 32-P (phophatase domain) ______________ glycolysis.

Decreases; increases

Increases; decreases

_____________ ____________ is allosterically ______________ by fructose 1,6-biphosphate to increase glycolysis (feedforward)

Allosterically ____________ by high-energy markers (ATP, acetyl-CoA, fatty acids, and alanine)

____________________ in response to glucose depletion in the liver, so it will send glucose to the ____________

Pyruvate kinase; activated

Inhibited

Inactivated; brain