Bmb 401 Exam 1 (4)

Front 1

What is the equation for Gibbs free energy?

Back 1

∆G = ∆H - T∆S

Front 2

What equation predicts whether chemical reactions, or changes of physical state, would occur spontaneously at constant pressure and volume?

Back 2

Gibbs free energy

Front 3

What is the acronym for remembering the equaton for Gibbs free energy?

Back 3

Fish is Hell without Tartar Sauce

Front 4

If ∆G < 0, the reaction is energetically ___ (favorable/unfavorable) and ___ (will/will not) proceed spontaneously

Back 4

Favorable, will

Front 5

If ∆G > 0, the reaction is ___ (favorable/unfavorable) and ___ (will/will not) proceed spontaneously

Back 5

Unfavorable, will not

Front 6

At what ∆G value is the reaction at equilibrium?

Back 6

0

Front 7

Reactions are more favorable when there is sufficient ___ (increase/decrease) in enthalpy and ___ (increase/decrease) in entropy

Back 7

Decrease in enthalpy, increase in entropy

Front 8

Reactions are more favorable when ∆H is ___ (greater than/less than) 0 and ∆S is ___ (greater than/less than) 0

Back 8

∆H less than 0, ∆S greater than 0

Front 9

Reactions are more favorable when heat is ___ (absorbed/given off) and randomness of the products is ___ (higher/lower) than that of the reactants

Back 9

Given off, higher

Front 10

The Gibbs free energy equation allows one to determine the energy available in a given reaction for the purposes of doing what?

Back 10

Work

Front 11

Is there a time variable in thermodynamics?

Back 11

No!

Front 12

___ (Endergonic/Exergonic) refers to a reaction that is non-spontaneous, and ∆G is ___ (greater than/less than) 0

Back 12

Endergonic, greater than 0

Front 13

The higher the entropy, the ___ (greater/less) the disorder

Back 13

Greater

Front 14

___ (Endergonic/Exergonic) refers to a reaction that is spontaneous, and ∆G is ___ (greater than/less than) 0

Back 14

Exergonic, less than 0

Front 15

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

Back 15

Will

Front 16

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

Back 16

Will not

Front 17

___ (∆G°/∆G°') is the free energy of a reaction carried out under standard-state conditions

Back 17

∆G°

Front 18

___ (∆G°/∆G°') is the free energy of a reaction carried out under standard-state conditions in biologic systems

Back 18

∆G°'

Front 19

Give the corresponding values for the standard-state conditions: 1. Temperature (°C) 2. Pressure (atm) 3. Amount of each reactant (mole)

Back 19

1. 25°C, 2. 1 atm, 3. 1 mole

Front 20

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

Back 20

1. 25°C, 2. 1 atm, 3. 7, 4. 55.5 M, 5. 1

Front 21

What is the equation for finding ∆G for a given reaction that occurs within a cell?

Back 21

∆G = ∆G° + RT ln [C][D]/[A][B]

Front 22

Natural log, ln, can be converted to log base 10 by multiplying by what number?

Back 22

2.303

Front 23

What are the 3 processes in the central dogma?

Back 23

Replication, transcription, translation

Front 24

What are the 3 sequential products in the central dogma?

Back 24

DNA, RNA, Protein

Front 25

What type of nucleotides are the "language" of DNA?

Back 25

Deoxyribonucleotides

Front 26

What type of nucleotides are the "language" of RNA?

Back 26

Ribonucleotides

Front 27

What is the "language" of proteins?

Back 27

Amino acids

Front 28

Reverse transcription converts ___ (DNA/RNA) into ___ (DNA/RNA)

Back 28

RNA into DNA

Front 29

Deoxyribose contains a(n) ___ (H/OH), while ribose contains a(n) ___ (H/OH)

Back 29

H, OH

Front 30

What is the name for the structure that contains a pentose sugar connected only to a nitrogenous base?

Back 30

Nucleoside

Front 31

What is the name for the structure that contains a pentose sugar connected to a nitrogenous base and a phosphate group?

Back 31

Nucleotide

Front 32

Up to how many phosphate groups can a nucleotide contain?

Back 32

3

Front 33

Adenosine Tri-phosphate (ATP) is a(n) ___ (RNA/DNA) ___ (nucleotide/nucleoside) with ___ (two/three) phosphate groups

Back 33

RNA nucleoside, three

Front 34

What 2 nitrogenous bases are the purines in DNA and RNA?

Back 34

A and G

Front 35

What 2 nitrogenous bases are the pyrimidines in DNA?

Back 35

C and T

Front 36

What 2 nitrogenous bases are the pyrimidines in RNA?

Back 36

C and U

Front 37

Overall, what 3 nitrogenous bases are pyrimidines?

Back 37

C, T, and U

Front 38

Is thymine found in RNA?

Back 38

No

Front 39

DNA is very ___ (weak/stable)

Back 39

Stable

Front 40

___ (RNA/DNA) is especially prone to hydrolysis

Back 40

RNA

Front 41

What characteristic makes RNA more prone to hydrolysis than DNA?

Back 41

It's 2' hydroxyl group

Front 42

In hydrolysis of RNA, the 2' OH gets hydrolyzed by H2O and turns into what nucleophile? What does it then attack

Back 42

O-, attacks the phosphate next to it

Front 43

RNAs 2' hydroxyl is ___ (less/more) reactive than DNAs 2' hydrogen

Back 43

More

Front 44

What is the "working copy" of genetic information?

Back 44

RNA

Front 45

DNAs ___ (stability/instability) is excellent for genomes, while RNAs ___ (stability/instability) is excellent for working copies

Back 45

Stability, instability

Front 46

In DNA replication, what is polymerized first? As what?

Back 46

RNA, as a primer

Front 47

In DNA replication, what is polymerized second?

Back 47

DNA

Front 48

In DNA replication, what is the name for the first polymerized structures that act as RNA primers?

Back 48

NTPs

Front 49

In DNA replication, what is the name for the second polymerized structures that add DNA?

Back 49

dNTPs

Front 50

What does DNA ligase require for energy?

Back 50

ATP

Front 51

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

Back 51

NTP

Front 52

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

Back 52

dNTPs

Front 53

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

Back 53

Hydroxyl, alpha

Front 54

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

Back 54

Gamma and beta phosphates

Front 55

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

Back 55

Pyrophosphate, hydrolyzed, inorganic

Front 56

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

Back 56

Loss, pyrophosphate, hydrolysis, inorganic

Front 57

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

Back 57

Several, lower

Front 58

Resonance within inorganic phosphates helps to ___ (increase/decrease) the enthalpy of the products compared to the reactants

Back 58

Decrease

Front 59

2 molecules of inorganic phosphate can orient themselves ___ (structurally/randomly) in solution, contributing to the favorability of this reaction going forward

Back 59

Randomly

Front 60

Replication is carried out by what enzyme? *Hint: Think, what adds new DNA?*

Back 60

DNA polymerase

Front 61

Replication generally occurs ___ (before/after) cell division

Back 61

Before

Front 62

Replication requires a primer with a free ___ (2'/3') hydroxyl

Back 62

3'

Front 63

What abbreviation is given to pyrophosphate?

Back 63

PPi

Front 64

What abbreviation is given to the 2 inorganic molecules that are produced from the hydrolyzation of pyrophosphate?

Back 64

2Pi

Front 65

A DNA template, nucleotide triphosphates, and RNA polymerase are the 3 needed materials for what process?

Back 65

Transcription

Front 66

What is the process by which RNA is polymerized?

Back 66

Transcription

Front 67

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

Back 67

Is no primer necessary

Front 68

Is primer necessary for RNA synthesis?

Back 68

No

Front 69

Is primer necessary for DNA replication?

Back 69

Yes

Front 70

In transcription, the nucleotides that are being added are ___ (deoxyribonucleotides/ribonucleotides)

Back 70

Ribonucleotides

Front 71

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?

Back 71

Promoters

Front 72

In ___ (bacteria/eukaryotes), promoters are generally comprised of a -35 and -10 region (Pribnow box)

Back 72

Bacteria

Front 73

What is the main eukaryotic promoter? At what position is it located?

Back 73

TATA box, -25

Front 74

The ___(TATA/CAAT) box is sometimes present in eukaryotes, residing at position ___ (-80/-75/-90)

Back 74

CAAT, -75

Front 75

The polymerase reaction in DNA replication is catalyzed by a class of enzymes called ___ (DNA/RNA) polymerases

Back 75

DNA