Chapter 4 Flashcards
Thermodynamics
Study for energetics of chemical reactions.
Heat energy
movement of molecules
Potential energy
energy stored in chemical bonds
Entropy
(S) increase in disorder
Enthalpy
(H)
Gibbs free energy
ΔG = ΔH-TΔS
ΔG’s changes
ΔG increases with increasing ΔH (bond energy) and decreases with increasing entropy.
The change in Gibbs free energy of a reaction determines
whether the reaction is favorable (spontaneous, ΔG negative) or unfavorable (non spontaneous, ΔG positive)
Exergonic (ΔG)
energy exists the system
Endergonic (ΔG)
only occur if energy is added
ΔH <0
Liberates Heat; exothermic
ΔH>0
Require input of heat; endothermic
The signs of thermodynamically quantities are assigned from the point of view
of the system, not the surrounding do the universe
Spontaneous means
that a reaction may proceed without additional energy input, but is says nothing about the rate of the reaction
ΔG does not depend on
the pathway a reaction takes or the rate of the reaction; it is only a measurement of the difference in free energy between reactants and products
Chemical Kinetics
study of reaction rates
Activation Energy (Ea)
energy required to produce the transient intermediate.|This barrier prevents many reactions from proceeding even though the ΔG for the reaction may be negative
Transition State (TS)
exists for a short time either moving forward to form product or breaking back down into reactants
Catalyst
lowers the Ea of a reaction without changing the ΔG.|Lowers the Ea by stabilizing the TS, making its existence less thermodynamically favorable. (enzymes are catalysts)
Thermodynamically unfavorable reactions in the cell can be driven forward by
reaction coupling
Reaction coupling
where one very favorable reaction is used to drive an unfavorable on. Free energy changes are additive.
ATP hydrolysis
causes a conformational change in protein. Used to power energy
During ATP hydrolysis there is a transfer of phosphate
from ATP to a substrate
One reaction in a test tube
the enzyme is a catalyst with a kinetic role only. It influences the rate of the reaction, but not the outcome
Many “real life” reactions in the cell
enzyme controls outcomes by selectively promoting unfavorable reactions via reaction coupling
Enzymes are proteins that
must fold into specific three-dimensional structures to act as
catalyst
Active site
the region in the enzyme’s
three-dimensional structure that is directly involved in catalysis
How is the active site’s transition state stabilized
the active site has amino acid residues that stabilize the transition state of the reaction
The active site for enzymes is generally highly
specific in substrate recognition, including stereo specificity
Substrates
reactants in an enzyme
Covalent Modification
proteins can have several different groups covalently attached to them|This can regulate their activity, lifespan of the cell, and or cellular location|Different sites on an enzyme can either activate or inactivate the enzyme
Proteolytic Cleavage
many enzymes are synthesized in inactive forms that are activated by cleavage by a protease
Association with other polypeptides
associations with other polypeptides can affect enzyme activity|Some proteins demonstrate continuous rapid catalysis if their regulatory subunit is removed|There are other proteins that require association with another peptide in order to function
Allosteric Regulation
binding of small molecules to particular sites on an enzyme that are distinct from the active site or on another polypeptide. Non covalent and reversible. An Allosteric regulator can alter the conformation of the enzyme to increase decrease catalysis
Negative Feedback
Enzymes usually act as part of pathways, not alone. In a pathway there are one or two key enzymes that are regulated.
Feedforward stimulation
stimulation of an enzyme by its substrate, or by a molecule used in the synthesis of the substrate
Enzyme Kinetics
the study of the rate of formation of products from substrates in the presence of an enzyme
The reaction rate (V, for velocity)
is the amount of product formed per unit time (mols).
Reaction rate is directly proportional
to the amount of substrate added
Once an enzyme is saturated (Vmax)
there is so much substrate that every active site is continuously occupied and adding more substrate does not affect the rate of the reaction
Michaelis constant (Km)
substrate concentration at which the reaction velocity is half its max
Enzyme inhibitors
can reduce enzyme activity by competitive/non competitive inhibition
Competitive Inhibition
(resembles the TS) molecules compete with substrate for binding at the active site. Inhibition can be overcome by adding more substrate.|Km increases, Vmax stays the same
Non Competitive Inhibitor
binds at an Allosteric site. No matter how much substrate is added the inhibitor will not be displaced from its site of action.
Oxidize
Attach oxygen (or increase the number of bonds to oxygen)|Remove hydrogen|Remove electrons
Reduce
Remove oxygen (or decrease the number of bonds to oxygen)|Add hydrogen|Add electrons
When one atom gets reduced
another one must be oxidized. They are called redox pairs
Oxidation of glucose
ATP and NADH and pyruvate in glycolysis|Pyruvate Dehydrogenase: NADH per glucose (one per Pyruvate)|Krebs Cycle: NADH, FADH and GTP per glucose
Fermentation
regenerates NAD + in anaerobic conditions, this allows glycolysis to continue in the absence of oxygen
Two goals of oxidative phosphorylation: (can be performed by bacteria too)
Reoxidize all the electron carriers reduced in glycolysis, PDC, and the Krebs cycle and store energy in the form of ATP in the process|Eukaryotes use the inner mitochondrial membrane; bacteria just use their cell membrane
Oxidative Phosporilation
oxidation of the high
ATP synthase
large protein complex which contains a proton channel that spans the inner membrane. ATP production is dependent on a proton gradient
High pH
low [H+]
FADH’s function
FADH gives its electrons to ubiquitous instead of NADH dehydrogenase. By bypassing the first proton pump,|FADH is only responsible for the pumping of six protons across the inner membrane
Glycogenolysis
glycogen breakdown. Occurs in response to glucagon, when blood sugar levels are low. Releases glucose into the blood
Glucogenesis
occurs when dietary sources of glucose are unavailable, and when the liver has depleted stores of glucose.|Primarily occurs in the liver and involves converting noncarbohydrate precursor molecules into oxaloacetate and then glucose.
Beta- Oxidation
Generates one NADH and one FADH2 for each 2-carbon group removed. The acetyl-CoA can then enter the Krebs cycle. The glycerol back bone of the TAG can be converted into glucose and can enter cellular respiration at glycolysis.
Amino acid Catabolism
amino acid group is removed and converted into urea for excretion. The remaining carbon skeleton (alpha-keto acid) can either be broken down into water and CO2, or can be converted to glucose or acetyl-CoA.
Photosynthesis
process by which plants and other photo autotrophs utilize light energy to synthesize carbohydrates
Carbon Fixation
Process in which carbon dioxide is incorporated into more complex organic molecules
G–P
can be used to produce glucose and other organic molecules
Light dependent and light independent reactions
are inexorably linked; neither set of reactions alone can produce carbohydrate from CO
The Krebs Cycle and the Calvin Cycle
both series of reactions that regenerate their starting product. They both indirectly need a particular substance. Oxygen in the Krebs cycle and light for the Calvin Cycle. Krebs cycle seeks to oxidize carbohydrates to COS,|while the Calvin cycle seeks to reduce CO to carbohydrates
Where do light dependent reactions occur?
Thylakiod membrane
Where do light independent reactions occur?
stroma
What is the energy production use of light dependent reactions?
produces ATP and NADPH
What is the energy production use of light independent reactions?
uses ATP and NADPH
What is the product of a light dependent reaction?
Oxygen
What is the product of a light independent reaction?
carbohydrate
