Energy and Thermodynamics

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Questions and Answers

During DNA replication, what is the primary role of single-stranded binding proteins (SSBs)?

  • To prevent the separated DNA strands from re-annealing. (correct)
  • To degrade incorrectly incorporated nucleotides.
  • To initiate the unwinding of the DNA double helix.
  • To catalyze the formation of phosphodiester bonds.

What is the significance of the major and minor grooves in DNA structure?

  • They provide structural stability to the DNA double helix.
  • They provide access points for proteins to bind and interact with the DNA sequence. (correct)
  • They are the sites where DNA polymerase binds during replication.
  • They determine the overall length of the DNA molecule.

Which of the following is a key difference between eukaryotic and prokaryotic DNA replication?

  • Eukaryotic chromosomes are linear and have telomeres, while prokaryotic chromosomes are circular without telomeres. (correct)
  • Prokaryotic DNA replication requires a primer, while eukaryotic replication does not.
  • Prokaryotic replication involves multiple origins of replication, while eukaryotic replication involves a single origin.
  • Eukaryotic DNA replication occurs in the cytoplasm, while prokaryotic replication occurs in the nucleus.

What event typically triggers the termination phase of DNA replication in prokaryotes?

<p>The binding of termination proteins to specific sequences on the DNA. (C)</p> Signup and view all the answers

What is the role of the centromere during cell division?

<p>To serve as the attachment point for spindle fibers during mitosis and meiosis. (D)</p> Signup and view all the answers

According to Chargaff's rule, if a double-stranded DNA molecule contains 28% adenine (A), what percentage of guanine (G) would it be expected to contain?

<p>22% (A)</p> Signup and view all the answers

Which of the following best describes the difference between continuous and discontinuous replication?

<p>Continuous replication synthesizes one strand in a long, uninterrupted sequence, while discontinuous replication synthesizes the other strand in short fragments. (D)</p> Signup and view all the answers

Mitochondrial DNA differs from nuclear DNA primarily in which aspect?

<p>Its structure and mode of inheritance (D)</p> Signup and view all the answers

Which of the following is NOT a component of a nucleotide?

<p>An amino acid (A)</p> Signup and view all the answers

Mutations in mismatch repair genes can lead to which of the following outcomes?

<p>Increased genomic instability and cancer predisposition (A)</p> Signup and view all the answers

Flashcards

Nucleotide Components

A nucleotide is composed of a sugar, a phosphate group, and a nucleobase.

Chargaff's Rule

States that DNA from any cell of all organisms should have a 1:1 ratio (base Pair Rule) of pyrimidine and purine bases.

Major and Minor Grooves

The deep groove is called the major groove, and the shallow groove is called the minor groove.

Centromere's Role

Attachment point for the mitotic spindle during cell division, ensuring proper chromosome segregation.

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DNA Replication

The process by which a double-stranded DNA molecule is copied to produce two identical DNA molecules.

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Continuous vs. Discontinuous Replication

Continuous replication proceeds smoothly, while discontinuous replication involves Okazaki fragments.

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Role of SSBs

SSBs prevent the single strands of DNA from re-annealing or forming secondary structures during replication.

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Main Enzymes in DNA Replication

DNA polymerase synthesizes new DNA strands, ligase joins DNA fragments, and helicase unwinds DNA.

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DNA Polymerase Role

DNA polymerase adds nucleotides, proofreads, and removes primers during replication.

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Mismatch Repair

Mismatch repair corrects errors in DNA replication to maintain genetic stability.

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Study Notes

Energy

  • The capacity to do work, existing as heat, light, electricity, and chemical forms.
  • Kinetic energy (KE) is the energy of motion, defined as $KE = 1/2 \cdot mv^2$.
  • Potential energy (PE) is stored energy, defined as $PE = mgh$.
  • Energy is measured in Joules (J), where $1 J = 1 kg \cdot m^2/s^2$, or in calories (cal), where $1 cal = 4.184 J$.

Thermodynamic Systems

  • A system is the part of the universe of interest.
  • The surroundings are the rest of the universe outside the system.
  • Open systems exchange both matter and energy with surroundings.
  • Closed systems exchange energy but not matter.
  • Isolated systems exchange neither energy nor matter.

State Functions

  • Properties that depend only on the current state, not on how it was achieved, such as energy, pressure, volume, and temperature.
  • Changes in state functions are independent of path: $\Delta U = U_{final} - U_{initial}$.

First Law of Thermodynamics

  • Energy is conserved, meaning it can be converted but not created or destroyed.
  • $\Delta U = q + w$, where
    • $\Delta U$ is the change in internal energy of the system
    • $q$ is heat added to or removed from the system
    • $w$ is work done on or by the system

Enthalpy

  • Measures heat content of a system at constant pressure, defined as $H = U + PV$.
  • Under constant pressure, $\Delta H = \Delta U + P\Delta V = q_p$.
  • Exothermic processes release heat $(\Delta H < 0)$.
  • Endothermic processes absorb heat $(\Delta H > 0)$.
  • Units of enthalpy are Joules (J) or Kilojoules (kJ).
  • Standard enthalpy of formation ($\Delta H_f^\circ$) is the enthalpy change when 1 mole of a compound is formed from its elements in their standard states (1 atm and 298 K).
  • $\Delta H^\circ = \sum n \Delta H_f^\circ (products) - \sum n \Delta H_f^\circ (reactants)$.

Calorimetry

  • Calorimetry measures heat flow using $q = mc\Delta T$.
    • $q$ is heat absorbed or released
    • $m$ is mass
    • $c$ is specific heat capacity
    • $\Delta T$ is change in temperature
  • Bomb calorimeters measure heat at constant volume: $q = C\Delta T$, where $C$ is the heat capacity of the calorimeter.

Hess's Law

  • The enthalpy change of an overall process is the sum of enthalpy changes of its individual steps: $\Delta H_{overall} = \Delta H_1 + \Delta H_2 +...$
  • Reversing a reaction changes the sign of $\Delta H$.

Entropy

  • Measures the disorder or randomness of a system, defined as $\Delta S = q_{rev}/T$.
    • $q_{rev}$ is heat absorbed or released in a reversible process
    • $T$ is absolute temperature
  • Entropy is measured in Joules per Kelvin (J/K).
  • Entropy increases with:
    • Increasing temperature
    • Increasing volume
    • Increasing number of particles
    • Change of state from solid to liquid to gas
  • Standard entropy change: $\Delta S^\circ = \sum nS^\circ (products) - \sum nS^\circ (reactants)$.

Second Law of Thermodynamics

  • The entropy of the universe increases in any spontaneous process: $\Delta S_{universe} = \Delta S_{system} + \Delta S_{surroundings} > 0$.

Gibbs Free Energy

  • Measures the spontaneity of a process: $G = H - TS$ and $\Delta G = \Delta H - T\Delta S$.
  • Spontaneous process: $\Delta G < 0$.
  • Non-spontaneous process: $\Delta G > 0$.
  • Equilibrium: $\Delta G = 0$.
  • Standard free energy change: $\Delta G^\circ = \sum n \Delta G_f^\circ (products) - \sum n \Delta G_f^\circ (reactants)$.

Free Energy and Equilibrium

  • $\Delta G = -RTlnK$, where
    • $R$ is the ideal gas constant (8.314 J/mol·K)
    • $T$ is absolute temperature
    • $K$ is the equilibrium constant
  • If $K > 1$, products are favored $(\Delta G < 0)$.
  • If $K < 1$, reactants are favored $(\Delta G > 0)$.
  • If $K = 1$, equilibrium $(\Delta G = 0)$.

Temperature Dependence of Equilibrium Constant

  • van't Hoff equation relates changes in the equilibrium constant with temperature to changes in enthalpy: $ln(K_2/K_1) = -\Delta H^\circ/R (1/T_2 - 1/T_1)$.

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