Exam 1 Flashcards
What is Work?
w
- force acting over a distance
- positive = work is done on the system
- negative = work is done by the system on the surroundings
Define Catabolism
- breakdown of organic compounds to release free energy
- exergonic reactions
- free energy is release and used to make ATP
- exergonic reactions
Define Enzymes
- 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
- accelerate reaction rates by physically interacting with the reactants to promote chemistry
- do NOT affect a reaction ΔG value
- cannot promote a reaction that has a positive ΔG value
What is the 2nd Law of Thermodynamics?
- 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
What are the 6 major classes of enzymes that are clustered based on the types of reactions they catalyze?
- Oxidation-Reduction
- Group Transfer
- Hydrolysis
- Addition or Removal
- Isomerization
- Ligation
There is a negative free energy change if and only if the entropy of the universe increases.
What parameters provide for a spontaneous reaction?
ΔG = ΔH – TΔS
What is Heat?
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
- exothermic reaction
Why is water so important?
- 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
- oxygen draws electrons away from the hydrogens
Define Phototrophs
produce energy by trapping sunlight
What are Endergonic Reactions?
- reactions that require an input of energy to spontaneously proceed
- often coupled to exergonic reactions in order to proceed
Describe Group Transfer Reaction
- functional groups are transferred to a molecule
ex) pg 431; phosphate group is being transfered
What is the equation for overall Entropy?
deltaSuniverse = deltaSsystem + deltaSsurroundings
where for the reaction to be spontaneous, deltaSuniverse must be greater than zero
Calculate ΔG for a process with a ΔH of 84 kJ and a ΔS of +125 J/K at 298K
ΔG = -45,650J or -45.7 kJ
Negative ΔG so this is a spontaneous process
If an exothermic reaction has a ΔHsystem = -100 kJ and ΔSsystem = 285 J/K at 25°C, will this reaction occur spontaneously?
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
Describe Oxidation-Reduction Reaction
Reactions involve the relay of electrons
- reduction
- a compound gains electrions
- oxidation
- a compound losses electrons
ex) page 236; reduction of pyruvate to Lactate
What do organisms use to speed up the rates of reactions?
Biological Catalysts
Enzymes
What is Energy?
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
- energy due to motion
- potential
Covalent Bonds
- a bond that occurs when two nonmetals share electrons
- nonmetals will share electrons in order to fully occupy their outer energy level
Ionic Bonds
- 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
- involve the transfer of elections
Describe Addition/Removal Reactions
- functional groups are….
- added to a molecule to remove a double bond
- removed from a molecule to form a double bond
ex) pg 510
Define Cell
- the lowest level of organization that can perform all activities required for life
Describe Hydrolysis Reaction
- a molecule is broke down and water is added to the bond that is broken
What are some Oxygen-containing functional groups?
- carbonyl
- aldehyde
- carbonyl
- ketone
- carboxylate
- hydroxyl
- alcohol
- Enol
- Ether
- Ester
- Acetyl
- Anhydride
- 2 carboxylic acids
What is a saturated hydrocarbon?
- an organic compound with only carbon and hydrogen that has all single bonds
Gibbs Free Energy
- a reaction that is spontaneous will give a negative change in Gibbs free energy
ΔG = ΔH – TΔS
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?
deltaH = Hproducts - Hreactants = -250 kJ
The overall change in enthalpy is negative meaning heat was lost to the surroundings
Exothermic Reaction
What are some Sulfar-containing functional groups?
- sulfhydryl
- disulfide
- thioester
What is the equation to calculate the deltaS of surroundings?
deltaSsurroundings = -deltaHsystem/T
deltaH is from the system
if deltaH is negative, then heat flowed from the system to the surroundings (exothermic)
What are the two ways organisms can obtain energy?
Chemically (Chemotrophs)
Light (Phototrophs)
Describe Isomerization Reaction
- 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
What do all cells contain?
- 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
What are some Nitrogen-containing function groups?
- amino
- protonated
- amido
- imine
- N-substituded imine
- Schiff base
- guanidinum
- imidazole
True or False
Biochemistry is organized around carbon, which makes up about 1/2 the dry weight of cells
True
What are some examples of things organisms need to do to live?
- 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.
What is the 1st Law of Thermodynamics?
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
Entropy
S
- a measurement of the randomness of disorder
- unitis J/K
Define Enthalpy
- 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
Define Chemotrophs
produce energy by oxidizing a carbon source from their environment
What is a Spontaneous Process?
- 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
True or False
Thermodynamics in Biochemistry tells you how fast the reaction will go (reaction rates)
False
Thermodynamics tells you nothing about reaction rates
Only whether or not a reaction will occur spontaneously
Define Unsaturated Hydrocarbons
- molecules that do not contain the maximum number of hydrogen atoms
- Alkenes = double bond
- Alkynes = triple bond
The foundation of Biochemistry is based on what four organic biological macromolecules?
- Proteins
- Nucleic Acids
- DNA & RNA
- Carbohydrates
- Lipids
Describe Ligation Reaction
- 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
- the ATP in these reactions serves as an energy source for the reaction
ex) 824
Hydrogen bond donor vs. Hydrogent bond acceptor
- 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
Define Anabolism
- 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
- endergonic reactions
What are the 4 types of Noncovalent Bonds?
- hydrogen bonds
- electrostatic interactions
- van der Waals interactions
- hydrophobic interactions
What is the equation of enthalpy when a system undergoes a change at constant pressure?
deltaH = deltaU + PdeltaV
PdeltaV = expression for work done by expansion of gas
- pressure during chemical reactions is constant
- volume changes in most biochemical reactions is insignificant
- PdeltaV = 0
What are some Phosphate-containing functional groups?
- phosphoryl
- phosphoanhydride
- mixed anhydride
- carboxylic acid and phosphoric acid
- also called acyl phosphate
- carboxylic acid and phosphoric acid
Define Steroisomers
- compounds that have the same molecular formula and some order of atomic connections but differ in molecular arrangement
What is Internal Energy?
- the sum of all the energy of a system
- can be changed by the flow of work, heat or both
- deltaU = q + w
What are Exergonic Reactions?
- spontaneous reactions that release free energy
Chiral vs. Achiral
- Chiral
- a molecule that is not identical in all respects with its mirror image
- it is superimposable
- a molecule that is not identical in all respects with its mirror image
- Achiral
- a molecule that is identical with its micco image
- superimposable
- a molecule that is identical with its micco image
True of False
Enzymes only accelerate a reaction that can occur spontaneously
True
Positive ΔG
What are Functional Groups?
- give organic compounds diversity
- provide compounds with diverse physical and chemical properties
- double and triple bonds are functional groups
