Biochemistry and Thermodynamics Lecture Flashcards

Comprehensive practice questions covering bioenergetics, redox chemistry, coenzymes, and protein folding based on the provided biochemistry lecture notes.

According to Page 1, what is the standard free-energy change ($\Delta G^{\circ}$) for the reaction: Glucose + Pi $\rightarrow$ Glucose-6-phosphate?

$$13.8\,kJ/mol$$

Based on Page 1, what is the free-energy change for the total reaction: Glucose + ATP $\rightarrow$ Glucose-6-phosphate + ADP?

$$-16.7\,kJ/mol$$

Using the data on Page 2, what is the value of the equilibrium constant ($K_{eq}$) for the breakdown of ATP to ADP?

$$2.22 \times 10^5\,M$$

Define $\Delta G$ according to the lecture notes on Page 3.

Change in Gibbs free energy.

What are the standard conditions for $\Delta G^{\circ}$ as specified on Page 3?

$25^{\circ}C$ ($298\,K$) and $1\,atm$ pressure.

According to Page 4, is the reaction Glucose + Pi $\rightarrow$ Glucose-6-phosphate ($\Delta G' = 13.8\,kJ/mol$) spontaneous?

No, it is endergonic, unfavored, and not spontaneous.

What is the physiological concentration of glucose in a rat hepatocyte as given on Page 5?

$4.8\,mM$ ($0.0048\,M$).

According to Page 8, what are the physiological concentrations of [ATP] and [ADP] in the hepatocyte?

[ATP] = $3.38\,mM$ and [ADP] = $1.32\,mM$.

In the Ramachandran Plot described on Page 9, which angle describes the X-axis (horizontal)?

Phi ($\phi$).

What is the pKa of Histidine as mentioned in the Pop Quiz on Page 9?

$$6.0$$

How many classes of hairpin turns were described in the course according to Page 9?

$$4$$

According to Page 11, what is the definition of a reductant?

The species that brings about reduction and is itself oxidized in the process.

What is the term for the electromotive force (emf) used in biological energy generation according to Page 12?

The transfer of electrons between chemical species that have differing electron affinities.

In the mitochondria, what potential energy source is used by ATP synthase to synthesize ATP as per Page 13?

The proton-motive force (differential transmembrane pH).

According to Page 14, what is a conjugate redox pair?

The electron donor-acceptor pair in a half-reaction.

List the order of increasing electronegativity for atoms common in organic compounds as provided on Page 15.

H < C < S < N < O

In Methane ($CH_4$), what is the formal oxidation state of carbon according to Page 16?

$$-4$$

According to Page 16, what is the most oxidized formal state for carbon?

$$+4$$

Name the four ways electrons are transferred from a donor to an acceptor per Page 19 and 20.

1. Directly as electrons; 2. As hydrogen atoms; 3. Directly as hydride ions ($:H^-$); 4. Through direct combination with oxygen.

What is a reducing equivalent as defined on Page 20?

A single electron equivalent in a redox reaction, whether as an $e^-$, H atom, $:H^-$ ($2e^-$), or oxygen.

Define the reduction potential ($E$) according to Page 21.

A measure (in volts) of the affinity of an electron acceptor for electrons in a conjugate redox pair.

What reaction is used as the reference (0.0 V) for reduction potential as stated on Page 21?

$H^+ + e^- \rightarrow \frac{1}{2} H_2$ at pH 0.

According to Page 22, in which direction do electrons flow between half-cells?

From the half-cell with the lower $E^{\prime\circ}$ to the half-cell with the higher $E^{\prime\circ}$.

What formula relates standard free energy change ($\Delta G^{\prime\circ}$) to standard reduction potential change ($\Delta E^{\prime\circ}$) on Page 24?

$$\Delta G^{\prime\circ} = -nF\Delta E^{\prime\circ}$$

What is the value of the Faraday constant ($F$) provided on Page 24?

$$96,480\,J/V \cdot mol$$

According to Page 26, what is the $\Delta G^{\prime\circ}$ for the complete oxidation of glucose to $CO_2$?

$$-2,840\,kJ/mol$$

Define 'coenzyme' as used on Page 27.

Low molecular weight compound required for catalytic activity.

Which vitamin is used to synthesize NAD+ and NADP+ coenzymes as noted on Page 29?

Niacin (vitamin B3).

Does NAD dissociate from the enzyme after each reaction cycle according to Page 29?

Yes, adenine nucleotide coenzymes (NAD+ and NADP+) dissociate after each cycle.

Which cellular location is NAD+/NADH predominantly located in according to Page 30?

Mitochondria.

According to Page 31, which coenzyme usually functions in anabolism (reduction processes)?

NADPH.

Where is NADP+/NADPH predominantly located in the cell according to Page 31?

The cytosol.

What are the two major flavin coenzymes mentioned on Page 32?

FAD (flavin adenine dinucleotide) and FMN (flavin mononucleotide).

How do FAD and FMN differ from NAD in terms of their association with enzymes per Page 33?

They are tightly bound prosthetic groups that do not dissociate between redox cycles.

What is formed if only one hydrogen atom is transferred to FAD or FMN according to Page 33?

A semiquinone.

According to Page 34, what is the $E^{\prime}$ value for the half-reaction $\frac{1}{2} O_2 + 2H^+ + 2e^- \rightarrow H_2O$?

$$+0.816\,V$$

What is the $E^{\prime}$ value for the NAD+/NADH redox pair as given on Page 38?

$$-0.320\,V$$

What is the $E^{\prime}$ value for the pyruvate/lactate redox pair as given on Page 38?

$$-0.185\,V$$

According to the notes on Page 39, what is the $\Delta G^{\prime\circ}$ for the conversion of pyruvate to lactate?

$$-26.1\,kJ/mol$$

What are the five steps to a functional protein listed on Page 44?

1. Folding; 2. Cofactor binding; 3. Covalent modification; 4. Translocation; 5. Assembly of multi-subunit complex.

Under what condition will proteins spontaneously fold according to Page 45?

When \Delta G < 0 (a downhill process).

What is the primary driver behind protein folding according to Page 45 and 51?

Entropy (specifically the increase in disorder of the surrounding solvent/water).

What is the 'molten globule' as described on Page 48?

The initial collapsed state of a polypeptide where hydrophobic groups are partitioned from water, containing much of the secondary and tertiary structure.

What is the 'native state' of a protein according to Page 48?

The final folded, functional state of the protein.

What is the role of molecular chaperones as described on Page 49?

They assist proteins that become 'trapped' in local free energy wells to reach the native folded state (global minimum).

According to Page 52, what do molecular chaperones add to the stalled folding process?

They add energy to push the protein over the energy barrier into a lower free energy minimum.

What are the two major families of molecular chaperones in eukaryotic cells according to Page 53?

Hsp70 and Hsp60.

What does 'Hsp' stand for as mentioned on Page 53?

Heat shock protein.

What is the bacterial homologue of Hsp70 as stated on Page 54?

DnaK.

Where on a protein does Hsp70 typically bind according to Page 54?

Hydrophobic patches on proteins emerging from the ribosome.

Which small proteins aid Hsp70 in its function according to Page 54?

Hsp40 (DnaJ in bacteria).

What is the bacterial homologue of the Hsp60 system according to Page 56?

GroEL/ES.

What is the maximum polypeptide size that the Hsp60 barrel can accommodate as per Page 58?

~57 kDa (~520 residues).

What is the function of Protein Disulfide Isomerases (PDI) according to Page 59?

They help proteins form correct disulfide bonds by interchanging and shuffling bonds until the native state is reached.

What reaction does Peptide prolyl cis-trans isomerase (PPI) catalyze as per Page 59?

The conversion between trans and cis prolines.

What is the definition of the melting temperature ($T_m$) as provided on Page 60?

The mid-point of the temperature range where cooperative denaturation occurs.

Name two chemical denaturants that disrupt a protein's hydrophobic core as listed on Page 61.

Urea and detergents.

How does pH affect protein structure according to Page 61?

It changes the net charge, leading to electrostatic repulsion and disruption of hydrogen bonds.

What is the function of mercaptoethanol in studying proteins as stated on Page 62?

It reduces the disulfide cross-links between Cys residues.

According to Page 63, what is the approximate weight (in Daltons) for a typical protein per residue?

110 Daltons (number of residues times 110).