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Biochemistry > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

What is Work?

A

w

  • force acting over a distance
    • positive = work is done on the system
    • negative = work is done by the system on the surroundings
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2
Q

Define Catabolism

A
  • breakdown of organic compounds to release free energy
    • exergonic reactions
      • free energy is release and used to make ATP
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3
Q

Define Enzymes

A
  • proteins that carry out chemical reactions
    • accelerate reaction rates by physically interacting with the reactants to promote chemistry
      • increase the likelihood of reactants interacting productively
  • do NOT affect a reaction ΔG value
  • cannot promote a reaction that has a positive ΔG value
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4
Q

What is the 2nd Law of Thermodynamics?

A
  • for a process to be spontaneous, there must be an increase in the entropy (randomness or disorder) of the universe
    • the entropy of the universe is always increasing
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5
Q

What are the 6 major classes of enzymes that are clustered based on the types of reactions they catalyze?

A
  1. Oxidation-Reduction
  2. Group Transfer
  3. Hydrolysis
  4. Addition or Removal
  5. Isomerization
  6. Ligation
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6
Q

There is a negative free energy change if and only if the entropy of the universe increases.

What parameters provide for a spontaneous reaction?

A

ΔG = ΔH – TΔS

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7
Q

What is Heat?

A

q

  • transfer of energy between to objects due to a temperature difference (random molecular motion)
  • 2 types
    • exothermic reaction
      • heat flows out of the system and into the surroundings
    • endothermic reaction
      • heat flows from the surroundings and into the system
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8
Q

Why is water so important?

A
  • due to its polarity
    • oxygen draws electrons away from the hydrogens
      • results in oxygen having a partial negative charge and the hydrogens having a partial positive charge
      • b/c of this, can disolve a variety of substances
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9
Q

Define Phototrophs

A

produce energy by trapping sunlight

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10
Q

What are Endergonic Reactions?

A
  • reactions that require an input of energy to spontaneously proceed
    • often coupled to exergonic reactions in order to proceed
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11
Q

Describe Group Transfer Reaction

A
  • functional groups are transferred to a molecule
    ex) pg 431; phosphate group is being transfered
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12
Q

What is the equation for overall Entropy?

A

deltaSuniverse = deltaSsystem + deltaSsurroundings

where for the reaction to be spontaneous, deltaSuniverse must be greater than zero

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13
Q

Calculate ΔG for a process with a ΔH of 84 kJ and a ΔS of +125 J/K at 298K

A

ΔG = -45,650J or -45.7 kJ

Negative ΔG so this is a spontaneous process

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14
Q

If an exothermic reaction has a ΔHsystem = -100 kJ and ΔSsystem = 285 J/K at 25°C, will this reaction occur spontaneously?

A

ΔSuniverse = 0.621 kJ/K

Since this is an exothermic reaction, heat flowed from the system to the surroundings

ΔSuniverse is positive so yes this is spontaneous

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15
Q

Describe Oxidation-Reduction Reaction

A

Reactions involve the relay of electrons

  • reduction
    • a compound gains electrions
  • oxidation
    • a compound losses electrons

ex) page 236; reduction of pyruvate to Lactate

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16
Q

What do organisms use to speed up the rates of reactions?

A

Biological Catalysts

Enzymes

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17
Q

What is Energy?

A

U

  • capacity to do work or generate heat
  • 2 types
    • potential
      • energy due to position or composition i.e. energy that will be released on occurence of some process
    • kinetic energy
      • energy due to motion
        • KE = 1/2mv2​ where m = mass and v = velocity
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18
Q

Covalent Bonds

A
  • a bond that occurs when two nonmetals share electrons
    • nonmetals will share electrons in order to fully occupy their outer energy level
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19
Q

Ionic Bonds

A
  • the attraction between positively charged metal ions and negatively charged non-metal ions
    • involve the transfer of elections
      • metals readily lose their valence electrons
      • non-metals readily gain electrions
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20
Q

Describe Addition/Removal Reactions

A
  • functional groups are….
    • added to a molecule to remove a double bond
    • removed from a molecule to form a double bond

ex) pg 510

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21
Q

Define Cell

A
  • the lowest level of organization that can perform all activities required for life
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22
Q

Describe Hydrolysis Reaction

A
  • a molecule is broke down and water is added to the bond that is broken
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23
Q

What are some Oxygen-containing functional groups?

A
  • carbonyl
    • aldehyde
  • carbonyl
    • ketone
  • carboxylate
  • hydroxyl
    • alcohol
  • Enol
  • Ether
  • Ester
  • Acetyl
  • Anhydride
    • 2 carboxylic acids
24
Q
A
25
Q

What is a saturated hydrocarbon?

A
  • an organic compound with only carbon and hydrogen that has all single bonds
26
Q

Gibbs Free Energy

A
  • a reaction that is spontaneous will give a negative change in Gibbs free energy

ΔG = ΔH – TΔS

27
Q

In a biochemical reaction, the following enthalpy values are known:

Enthalpy of reactants = kJ

Enthalpy of products = 550kJ

What is the change in enthalpy, and what does this tell you about the reaction?

A

deltaH = Hproducts - Hreactants = -250 kJ

The overall change in enthalpy is negative meaning heat was lost to the surroundings

Exothermic Reaction

28
Q

What are some Sulfar-containing functional groups?

A
  • sulfhydryl
  • disulfide
  • thioester
29
Q

What is the equation to calculate the deltaS of surroundings?

A

deltaSsurroundings = -deltaHsystem/T

deltaH is from the system

if deltaH is negative, then heat flowed from the system to the surroundings (exothermic)

30
Q

What are the two ways organisms can obtain energy?

A

Chemically (Chemotrophs)

Light (Phototrophs)

31
Q

Describe Isomerization Reaction

A
  • the bonds of a molecule are rearranged
    • the product formed will have the same molecular formula but the atoms will be bonded differently

ex) 458

32
Q

What do all cells contain?

A
  • contain a nucleus or nucleoid that contains their DNA (genome; genetic code)
  • contain a cytoplasm where a variety of metabolic processes occur
  • contain a plasma membrane that serves as the boundary or barrier for the cell
33
Q

What are some Nitrogen-containing function groups?

A
  • amino
    • protonated
  • amido
  • imine
  • N-substituded imine
    • Schiff base
  • guanidinum
  • imidazole
34
Q

True or False

Biochemistry is organized around carbon, which makes up about 1/2 the dry weight of cells

A

True

35
Q

What are some examples of things organisms need to do to live?

A
  • maintain their genetic code
    • replicate and protect
  • reproduce
    • pass on the genetic code from generation to generation
  • metabolize
    • produce energy which allows organisms to move, breath, fight off infections etc.
36
Q

What is the 1st Law of Thermodynamics?

A

Conservation of Energy

  • energy can be converted from one form to another, but the energy of the universe is constant
    • energy can be neither created nor destroyed
37
Q

Entropy

A

S

  • a measurement of the randomness of disorder
    • unitis J/K
38
Q

Define Enthalpy

A
  • a thermodynamic term that is equivalent to the heat absorbed at constant pressure (units in J)

H = U + PV

H = enthalph

U = energy

P = pressure

V = volume

39
Q

Define Chemotrophs

A

produce energy by oxidizing a carbon source from their environment

40
Q

What is a Spontaneous Process?

A
  • a reaction will occur without the input of any additional energy from outside the system
    • 2nd Law says that a spontaneous reaction results in an increase in the disorder of the universe
41
Q

True or False

Thermodynamics in Biochemistry tells you how fast the reaction will go (reaction rates)

A

False

Thermodynamics tells you nothing about reaction rates

Only whether or not a reaction will occur spontaneously

42
Q

Define Unsaturated Hydrocarbons

A
  • molecules that do not contain the maximum number of hydrogen atoms
    • Alkenes = double bond
    • Alkynes = triple bond
43
Q

The foundation of Biochemistry is based on what four organic biological macromolecules?

A
  1. Proteins
  2. Nucleic Acids
    1. DNA & RNA
  3. Carbohydrates
  4. Lipids
44
Q

Describe Ligation Reaction

A
  • two molecules are joined together at the expense of ATP to form one compount
    • the ATP in these reactions serves as an energy source for the reaction
      • ATP is not added to the molecule

ex) 824

45
Q

Hydrogen bond donor vs. Hydrogent bond acceptor

A
  • donor
    • group (O, N, S) that is covalently bonded to the hydrogen
  • acceptor
    • nearby group (O, N, S) that has a negative charge due to a dipole
46
Q

Define Anabolism

A
  • Small molecules are used to make larger, more complex molecules
    • endergonic reactions
      • require the input of free energy (ATP) to occur b/c reactions result in an increase
47
Q

What are the 4 types of Noncovalent Bonds?

A
  1. hydrogen bonds
  2. electrostatic interactions
  3. van der Waals interactions
  4. hydrophobic interactions
48
Q

What is the equation of enthalpy when a system undergoes a change at constant pressure?

A

deltaH = deltaU + PdeltaV

PdeltaV = expression for work done by expansion of gas

  1. pressure during chemical reactions is constant
  2. volume changes in most biochemical reactions is insignificant
    1. PdeltaV = 0
49
Q

What are some Phosphate-containing functional groups?

A
  • phosphoryl
  • phosphoanhydride
  • mixed anhydride
    • carboxylic acid and phosphoric acid
      • also called acyl phosphate
50
Q

Define Steroisomers

A
  • compounds that have the same molecular formula and some order of atomic connections but differ in molecular arrangement
51
Q

What is Internal Energy?

A
  • the sum of all the energy of a system
  • can be changed by the flow of work, heat or both
  • deltaU = q + w
52
Q

What are Exergonic Reactions?

A
  • spontaneous reactions that release free energy
53
Q

Chiral vs. Achiral

A
  • Chiral
    • a molecule that is not identical in all respects with its mirror image
      • it is superimposable
  • Achiral
    • a molecule that is identical with its micco image
      • superimposable
54
Q

True of False

Enzymes only accelerate a reaction that can occur spontaneously

A

True

Positive ΔG

55
Q

What are Functional Groups?

A
  • give organic compounds diversity
  • provide compounds with diverse physical and chemical properties
    • double and triple bonds are functional groups

Biochemistry (5 decks)

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