Flashcards in Biochemistry Deck (91):
What is the first law of thermodynamics?
The energy of the universe is constant.
What is the second law of thermodynamics?
The disorder of the universe (entropy) is always increasing.
What is S?
What is Gibbs free energy equation?
(delta)G = (delta)H - T(delta)S
What is H in gibbs free energy?
What is entropy?
What is enthalpy? (eqn)
(delta)H = (delta)E - P(delta)V
Where E = bond energy
P = pressure
V = volume
*for a liquid H~E because the change in volume is negligible.
What is a favorable/spontaneous (delta)G?
G less than zero
What is Keq?
The ratio of products to reactants at equilibrium
What does Go' assume?
All reactants and products are at 1 molar concentrations -> can use Keq instead of Q.
The rate of formation of the product equals the rate of formation of the reactants.
Define Le Chatlier's principle
Removing either the reactant or the product will push the reaction in that direction in an attempt to return to equilibrium.
i.e. removing the PRODUCT will drive the rxn FORWARD (and vice versa if removing reactant)
Does Keq indicate the rate at which a reaction will proceed?
No. Keq only represents the relative concentrations of reactants to products once equilibrium has been achieved.
Which reaction is faster--spontaneous or nonspontaneous?
Trick question! Spontaneity tells you NOTHING about the rate of a reaction.
Where on a graph of a reaction is the transition state?
The highest point (peak of Ea).
What effect does a catalyst have on Ea? on (delta)G?
Lowers Ea, DOES NOT affect deltaG
How does an enzyme increase reaction rate?
By stabilizing the transition state
Are catalysts consumed in reactions?
What is a recognition pocket?
A site adjacent to the active site which helps the substrate bind at exactly the right residue so that cleavage happens in the same place every time.
What is a cofactor/coenzyme?
An organic (coenzyme) or inorganic molecule that interacts with BUT DOES NOT BIND TO an enzyme to IMPROVE function. e.g. Coenzyme A
What two factors can affect enzyme function?
pH and temperature
What is cooperative binding and what does the binding curve look like?
Binding of one substrate increases the affinity for another substrate. Binding curve is sigmoidal.
What effects do competitive inhibitors have on Km and Vmax?
Increase Km, no effect on Vmax
What effects do noncompetitive inhibitors have on Km and Vmax?
They bind allosterically: no effect on Km, decrease Vmax
What is an uncompetitive inhibitor and what effects do they have on Km and Vmax?
Uncompetitive inhibitors bind to Enzyme-Substrate complexes and draw it out of the system/prevent further reaction. This causes an apparent DECREASE (increase in affinity due to Le Chatliers Principle) in Km AND Vmax.
What is mixed-type inhibition?
Inhibitor can either bind just to E or to Enz-Substrate complex, therefore the effect on Km is variable, but Vmax decreases regardless of type.
At a basic chemical level, how do we derive energy from food?
We oxidize (highly reduced) carbohydrate and fat to produce CO2 and ATP.q
What are three ways to oxidation?
1. Lose e-
2. Lose H+
3. Gain O2
What are three ways to reduction?
1. Gain e-
2. Gain H+
4, Lose O2
What is catabolism?
The process of breaking down molecules.
What is anabolism?
Building of molecules (think anabolic steroids BUILD muscle).
How do we gain energy from glucose? What is the basic reaction equation?
Oxidative catabolism (glycolysis, PDC, Krebs, ETC/oxphos!)
Basic eqn = C6H12O6 + 6O2 -> 6CO2 + 6H2O
What are the products of breaking down 1 glucose in glycolysis?
2 NET ATP (4 produced but 2 are given)
Does glycolysis require oxygen
No! This is why just glycolysis runs during anaerobic respiration (fermentation)
What step "traps" glucose in a cell?
Glucose -> G6P by hexokinase/glucokinase
What is the committed step of glycolysis and why?
Formation of F16BP by PFK because it is extremely energetically favorable (and thus going backwards is hard).
What is the most highly regulated enzyme in the glycolytic pathway?
NADH has significant _____ power
What is the primary role of fermentation?
To regenerate NAD+ so glycolysis can continue in the absence of oxygen.
What is the final electron acceptor in fermentation?
Pyruvate! Making lactic acid in mammals and ethanol in yeast.
What happens in the pyruvate dehydrogenase complex?
Pyruvate (3 carbons) is oxidatively decarboxylated to make Acetyl-CoA (2 carbons)
What is a prosthetic group?
A nonprotein molecule covalently bound to an enzyme as part of the active site.
What is the first step of the Kreb's cycle?
Combine Acetyl-CoA (2C) with oxaloacetate (4C) to make citrate (6C)
What are the products of the Kreb's cycle?
What phases of respiration are in the mitochondrial matrix?
PDC and Kreb's cycle
Where is the ETC located?
Inner mitochondrial membrane
What is the principle function of the ETC/oxphos?
Oxidize all the high energy, highly reduced electron carriers (NADH and FADH2) to pump H+ across the innermembrane, generating a gradient which then turns the ATP synthase motor, generating ATP.
What is the final electron acceptor of aerobic respiration?
Oxygen! Oxygen is reduced to H2O
How is oxidative phosphorylation different for prokaryotes?
It occurs across the PM instead of the mitochondria...because they don't have mitochondria!
Does NADH or FADH2 yield more ATP per molecule?
NADH = 2.5 ATP
FADH2 = 1.5 ATP
1 NADH = ____ ATP
How do they NADH from glycolysis differ from the NADH of the Kreb's cycle?
The Kreb's NADH are already located in the mito matrix where as the glycolytic NADH have to be transported in via the glycerol phosphate shuttle. This causes them to bypass the first H+ pump and get treated like FADH2 (only make 1.5 ATP).
How many ATP are generate per molecule of glucose catabolized?
30 for eukaryotes
Can Acetyl CoA or fatty acids be used for gluconeogenesis?
No, but the glycerol backbone of TAGs can
What does the pentose phosphate shunt do? (PP shunt)
Diverts G6P from glycolysis to be made into NADPH and ribose-5-phosphate to eventually be made into a ribonucleotide.
What is the primary regulatory enzyme in the PP shunt?
What process does glucose activate? Inhibit?
Promotes glycolysis, inhibits gluconeogenesis
What is one of the most heavily regulated enzymes of the Kreb's cycle?
What are positive regulators of glycolysis?
F2,6BP and AMP
What is the primary enzyme of gluconeogenesis?
What 2 opposing enzymes regulate glycogenesis?
Glycogen synthase and glycogen phosphorylase
What is the product of Beta-oxidation of fatty acids?
FADH2 and NADH inside the mitochondrion
Where does ketogenesis occur?
What are some ketone bodies? What do they get converted into once they reach their target organ?
Acetone, acetoacetate, and Beta-hydroxybutyrate
All get converted into Acetyl-CoA so that they can enter the Krebs cycle.
How is acetyl-coA activated for fatty acid synthesis? What does it form?
Acetyl-CoA is carboxylated by acetyl-coA carboxylase to form malonyl coA
What molecule does fatty acid synthesis use to build FAs?
reducing power of NADPH
What are three DIRECT mechanisms of enzyme regulation?
1. Peptide hydrolysis
2. Allosteric regulation
How does DNA methylation work?
Methyl group binds to cytosine resulting in methyl-cytosine base pairing with guanine.
Where in the cell does fatty acid oxidation occur?
What are the products of the oxidative pentose phosphate shunt?
Ribulose-5-phosphate and 2 NADPH
During the metabolism of a fatty acid side chain containing 11 carbons, how many water molecules are used and how much FADH2 is produced?
4 molecules of water will be used and 4 FADH2 will be produced during the oxidation of an 11-C fatty acid. Fatty acid metabolism occurs by removal of two carbons per round of β-oxidation until the final two or three carbons are reached, depending on whether the original fatty acid chain had an even or odd number of carbons in total. Since the side chain in the question has a total of 11 carbons, there will be four rounds of β-oxidation, leaving the final three carbons at the end of the process. Each β-oxidation uses one water molecule and produces one FADH2 (as well as one NADH although the question does not ask about NADH).
What 2 hormones have an effect on F26BP and what are their effects?
Insulin activates F26BP which activates PFK, driving glycolysis.
Glucagon deactivates F26BP, doing the opposite.
Do charged things cross the plasma membrane?
Phosphates are _____ charged.
How many carbons are removed from a fatty acid with EACH round of beta oxidation? What are the other products?
2, releasing acetyl-coA. Typically pdts go right into the Krebs cycle
1 FADH2 and 1 NADH (reduced electron carriers)
What is left over after beta oxidation?
A 2 or 3 carbon nub
What is the enzyme used in beta-oxidation of FAs?
Where does fatty acid synthesis occur? What are your starting materials?
Acetyl CoA + HCO3- -> malonyl CoA
What is the reducing power of NADPH often used for?
Fatty acid synthesis
During starvation ____ levels decline and ______ and ______ levels increase
glucose levels decline
acetyl coA (fatty acid oxidation) and ketone bodies (ketogenesis) increase
What does protein breakdown give you and where do the pieces go?
1. Amino group -> make nitrogenous bases or get converted into urea and get excreted.
2. Carbon skeleton -> pyruvate
What are the principle enzymes of gluconeogenesis?
Pyruvate carboxylase, PEP carboxykinase, and F16BPase
What are the different metabolic routes glucose might take?
1. Enter glycolysis (make ATP)
2. Enter glycogenesis (store energy for later)
3. Enter PP shunt (make Ribose-5-P + NADPH)
Which carbon on the pentose does the base and the phosphate bind to?
Base binds to 1' carbon
Phosphate binds to 5' carbon
Describe the P-O (phosphodiester) bond?
Very similar to an ester bond. The 3' OH of one pentose binds to the 5' phosphate on a second pentose...this forms the sugar-phosphate backbone.
What breaks the phosphodiester bond?
How many hydrogen bonds bind C and G?
And A and T?
C and G is connected by 3 H bonds (hence why is is stronger!)
A and T are only connected by 2
What is another name for a restriction enzyme?
What is chromosome capping?
Telomeres at the ends of chromosomes have repetitive sequences and can thus loop around and base pair to itself, protecting the ends of chromosomes.
What is the best way to repair a double stranded DNA break?
Homologous repair and crossing over after replication has occurred. Uses the sister chromatid to repair.