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### 75 Cards in this Set

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 What is the equation for Gibbs free energy? ∆G = ∆H - T∆S What equation predicts whether chemical reactions, or changes of physical state, would occur spontaneously at constant pressure and volume? Gibbs free energy What is the acronym for remembering the equaton for Gibbs free energy? Fish is Hell without Tartar Sauce If ∆G < 0, the reaction is energetically ___ (favorable/unfavorable) and ___ (will/will not) proceed spontaneously Favorable, will If ∆G > 0, the reaction is ___ (favorable/unfavorable) and ___ (will/will not) proceed spontaneously Unfavorable, will not At what ∆G value is the reaction at equilibrium? 0 Reactions are more favorable when there is sufficient ___ (increase/decrease) in enthalpy and ___ (increase/decrease) in entropy Decrease in enthalpy, increase in entropy Reactions are more favorable when ∆H is ___ (greater than/less than) 0 and ∆S is ___ (greater than/less than) 0 ∆H less than 0, ∆S greater than 0 Reactions are more favorable when heat is ___ (absorbed/given off) and randomness of the products is ___ (higher/lower) than that of the reactants Given off, higher The Gibbs free energy equation allows one to determine the energy available in a given reaction for the purposes of doing what? Work Is there a time variable in thermodynamics? No! ___ (Endergonic/Exergonic) refers to a reaction that is non-spontaneous, and ∆G is ___ (greater than/less than) 0 Endergonic, greater than 0 The higher the entropy, the ___ (greater/less) the disorder Greater ___ (Endergonic/Exergonic) refers to a reaction that is spontaneous, and ∆G is ___ (greater than/less than) 0 Exergonic, less than 0 In going from reactants at a higher energy to products of a lower energy, the reaction ___ (will/will not) occur without an input of energy Will In going from reactants at a lower energy to products of a higher energy, the reaction ___ (will/will not) occur without an input of energy Will not ___ (∆G°/∆G°') is the free energy of a reaction carried out under standard-state conditions ∆G° ___ (∆G°/∆G°') is the free energy of a reaction carried out under standard-state conditions in biologic systems ∆G°' Give the corresponding values for the standard-state conditions: 1. Temperature (°C) 2. Pressure (atm) 3. Amount of each reactant (mole) 1. 25°C, 2. 1 atm, 3. 1 mole Give the corresponding values for the standard-state conditions in biologic systems: 1. Temperature (°C) 2. Pressure (atm) 3. pH 4. Molar concentration of water (M) 5. Activity 1. 25°C, 2. 1 atm, 3. 7, 4. 55.5 M, 5. 1 What is the equation for finding ∆G for a given reaction that occurs within a cell? ∆G = ∆G° + RT ln [C][D]/[A][B] Natural log, ln, can be converted to log base 10 by multiplying by what number? 2.303 What are the 3 processes in the central dogma? Replication, transcription, translation What are the 3 sequential products in the central dogma? DNA, RNA, Protein What type of nucleotides are the "language" of DNA? Deoxyribonucleotides What type of nucleotides are the "language" of RNA? Ribonucleotides What is the "language" of proteins? Amino acids Reverse transcription converts ___ (DNA/RNA) into ___ (DNA/RNA) RNA into DNA Deoxyribose contains a(n) ___ (H/OH), while ribose contains a(n) ___ (H/OH) H, OH What is the name for the structure that contains a pentose sugar connected only to a nitrogenous base? Nucleoside What is the name for the structure that contains a pentose sugar connected to a nitrogenous base and a phosphate group? Nucleotide Up to how many phosphate groups can a nucleotide contain? 3 Adenosine Tri-phosphate (ATP) is a(n) ___ (RNA/DNA) ___ (nucleotide/nucleoside) with ___ (two/three) phosphate groups RNA nucleoside, three What 2 nitrogenous bases are the purines in DNA and RNA? A and G What 2 nitrogenous bases are the pyrimidines in DNA? C and T What 2 nitrogenous bases are the pyrimidines in RNA? C and U Overall, what 3 nitrogenous bases are pyrimidines? C, T, and U Is thymine found in RNA? No DNA is very ___ (weak/stable) Stable ___ (RNA/DNA) is especially prone to hydrolysis RNA What characteristic makes RNA more prone to hydrolysis than DNA? It's 2' hydroxyl group In hydrolysis of RNA, the 2' OH gets hydrolyzed by H2O and turns into what nucleophile? What does it then attack O-, attacks the phosphate next to it RNAs 2' hydroxyl is ___ (less/more) reactive than DNAs 2' hydrogen More What is the "working copy" of genetic information? RNA DNAs ___ (stability/instability) is excellent for genomes, while RNAs ___ (stability/instability) is excellent for working copies Stability, instability In DNA replication, what is polymerized first? As what? RNA, as a primer In DNA replication, what is polymerized second? DNA In DNA replication, what is the name for the first polymerized structures that act as RNA primers? NTPs In DNA replication, what is the name for the second polymerized structures that add DNA? dNTPs What does DNA ligase require for energy? ATP In the first step of the mechanism for the addition of nucleotides to a DNA strand:Primer, ___ (NTP/dNTP), is added to the DNA template NTP In the second step of the mechanism for the addition of nucleotides to a DNA strand:The second step is that incoming ___ (NTPs/dNTPs) enter dNTPs In the third step of the mechanism for the addition of nucleotides to a DNA strand:The 3' ___ (hydrogen/hydroxyl) makes a nucleophilic attack on the ___ (alpha/beta/gamma)-phosphate of the incoming nucleotide Hydroxyl, alpha In the fourth step of the mechanism for the addition of nucleotides to a DNA strand:The ___ (alpha/beta/gamma) and ___ (alpha/beta/gamma) phosphates leave as pyrophosphate Gamma and beta phosphates In the fifth step of the mechanism for the addition of nucleotides to a DNA strand:___ (Alpha/Gamma/Beta/Pyro)phosphate is immediately ___ (reduced/hydrolyzed) into 2 molecules of ___ (organic/inorganic) phosphate Pyrophosphate, hydrolyzed, inorganic The DNA replication reaction is driven forward by the ___ (loss/gain) of ___ (alpha/gamma/beta/pyro)phosphate by ___ (reduction/hydrolysis) to 2 molecules of ___ (organic/inorganic) phosphate Loss, pyrophosphate, hydrolysis, inorganic Molecules of inorganic phosphate have ___ (zero/several) resonance structures, and are therefore at a ___ (higher/lower) energy state than they would be in a nucleotide triphosphate or pyrophosphate Several, lower Resonance within inorganic phosphates helps to ___ (increase/decrease) the enthalpy of the products compared to the reactants Decrease 2 molecules of inorganic phosphate can orient themselves ___ (structurally/randomly) in solution, contributing to the favorability of this reaction going forward Randomly Replication is carried out by what enzyme? *Hint: Think, what adds new DNA?* DNA polymerase Replication generally occurs ___ (before/after) cell division Before Replication requires a primer with a free ___ (2'/3') hydroxyl 3' What abbreviation is given to pyrophosphate? PPi What abbreviation is given to the 2 inorganic molecules that are produced from the hydrolyzation of pyrophosphate? 2Pi A DNA template, nucleotide triphosphates, and RNA polymerase are the 3 needed materials for what process? Transcription What is the process by which RNA is polymerized? Transcription The mechanism for ribonucleotide addition to a growing RNA chain is similar to DNA replication, but there ___ (is/is no) primer necessary for RNA synthesis Is no primer necessary Is primer necessary for RNA synthesis? No Is primer necessary for DNA replication? Yes In transcription, the nucleotides that are being added are ___ (deoxyribonucleotides/ribonucleotides) Ribonucleotides What is the name of the regions of the DNA that are designed to promote transcription by attracting the DNA polymerase to the start site? Promoters In ___ (bacteria/eukaryotes), promoters are generally comprised of a -35 and -10 region (Pribnow box) Bacteria What is the main eukaryotic promoter? At what position is it located? TATA box, -25 The ___(TATA/CAAT) box is sometimes present in eukaryotes, residing at position ___ (-80/-75/-90) CAAT, -75 The polymerase reaction in DNA replication is catalyzed by a class of enzymes called ___ (DNA/RNA) polymerases DNA