Biochemistry and Cellular Respiration Flashcards
What are the two forms of energy in chemistry?
- Heat (movement of molecules)
2. Potential (energy stored in chemical bonds)
What is the most important potential energy storage molecule in all cells?
ATP
ATP stores energy in what bonds?
ester bonds between phosphate groups
The first law of thermodynamics states what?
energy of the universe is constant (law of conservation of energy)
When the energy of the system decreases, the energy of the surroundings ______.
increases
What does the 2nd law of thermodynamics state?
entropy of the universe increases
Spontaneous reactions tend to ______ the disorder of the universe.
increase
negative delta S means what?
system lost entropy, disorder decreased
positive delta S?
disorder increased
Gibbs free energy equation?
G = H - TS
Equation for delta H?
H = E - PV
How is enthalpy related to bond energy in the cell?
H = E, since change in volume is negligible
G increases with ______ H and ______ S.
increasing
decreasing
What is favorable, when G is negative or positive?
negative
Favorable G is spontaneous or nonspontaneous?
spontaneous (negative)
Exergonic reactions have a ______ delta G.
negative
Endergonic reactions have a ______ delta G.
positive
Exergonic meaning?
energy exits the system
Endergonic reactions only occur if energy is ______.
added
Reactions with a negative delta H are called?
Exothermic
Reactions with a positive delta H are called?
Endothermic
Most metabolic reactions are _____.
exothermic
signs of thermodynamic quantities are assigned from the point of view of the ______.
system
System always moves in the direction of the _____ free energy.
lowest
Spontaneous reactions move in the direction of the _____ free energy state.
lowest
If the products in a reaction have more entropy than the reactants, and the enthalpy of reactants and products are the same, does the reaction occur spontaneously?
yes
S>0
H=0
G=H-TS
In equation, G’ = -RTlnK, if k=1, what does G equal?
0
ln1=0
K equilibrium constant?
Products/reactants
G = G’ + RTlnK
equation to know
Can you calculate G with only G’?
no you need the concentrations of the materials
Difference between K and Keq?
K- ratio of products to reactants at any time
Keq- ratio of products to reactants at equilibrium
How can G be negative if G’ if positive?
if the ratio of products to reactants if small meaning there is more reactants and the reaction goes forward
Does Keq indicate rate of reaction?
No, only the concentrations at Eq
When Keq is large, which has lower free energy, P or R?
Large Keq means more products are present at Eq, since Eq tends toward the lowest free energy state, so the answer is products
When K is large, which has lower free energy?
None, K doesnt say anything about Eq
If delta G is 0, will the forward or backward reaction be favored?
Neither is favored
When delta G=0, K=Keq, so we are at equilibium
What two factors determine whether the reaction will occur spontaneously(-G) in the cell?
- Intrinsic properties of the reactants and products (G’)
2. Concentrations of reactants and products (RTlnK)
Does spontaneous mean the reaction goes fast?
It says nothing about rate, just that it may proceed without additional energy
Thermodynamics tells you what?
- where a system starts and finishes but nothing about the path traveled to get there or the rate of reaction
- measures the difference in free energy between reactants and products
What is the difference in G for a reaction burning sugar in a furnace as opposed to breaking down sugar in a human?
No difference because the difference in energy between products and reactants will the be the same in both cases.
The study of reaction rates is called ______.
chemical kinetics
Energy required to produce the transient intermediate is called ______.
Activation Energy
What determines the kinetics of a reaction?
activation energy barrier
How would the rate of a spontaneous reaction be affected if the activation energy were lowered?
rate would increase
What does a catalyst do?
lowers activation energy without changing delta G
How does a catalyst lower the Ea?
by stabilizing the transition state
T/F
A catalyst is used up in the reaction.
False
Example of Catalyst?
Enzymes
Will an enzyme affect the concentrations of the reagants at Eq?
No it will only affect the rate that Eq is reached
Example of Nonspontaneous (+G) reaction that occurs in the body?
Biosynthesis of macromolecules such as DNA or protein
How can thermodynamically unfavorable reactions in the cell be driven forward?
reaction coupling
What is the basic idea of reaction coupling? How is it possible?
- one very favorable reaction is used to drive an unfavorable one
- free energy changes are additive
What is a favorable reaction that the cell can use to drive unfavorable reactions?
ATP hydrolysis
How does ATP hydrolysis drive unfavorable reactions?
- causing a conformational change in a protein (transmembrane transport)
- transfer of a phosphate from ATP to a substrate
What is the difference between an enzyme in a test tube and the ones in our bodies?
- the enzyme is a catalyst with a kinetic role only
- enzymes control outcomes by selectively promoting unfavorable reactions via reaction coupling
What must an enzyme do to its structure to act as a catalyst?
fold into a three dimensional structure
An enzyme may consist of a single polypeptide chain or several polypeptide subunits held together in a _____ structure.
Quaternary
Why is the folding of an enzyme important for function?
for the proper formation of the active site
What shape are enzymes more likely to have?
Globular to form an active site as a cleft in the sphere
The reactants in an enzyme catalyzed reaction are called ____.
substrates
The active site has amino acid residues that stabilize the ________.
transition state of a reaction
If a transition state intermediate possesses a transient negative charge, what amino acid residues might be found at the active site to stabilize the transition state?
- a positive charge would stabilize the negative charge.
- His, Arg, Lys
- Hydrogen of NH2 group in glutamine or aspargnine
Is it possible that amino acids located far apart from each other in the primary protein sequence may play a role in the formation of the same active site?
Yes, they may be far away in the sequence but may end up close to each other in the final folded protein.
What happens if a positive enzyme that stabilizes the transition state is replaced with a negative enzyme?
Effectiveness would decrease or be destroyed altogether because the transition state would not be stabilized lowering the rate
Stereospecificity?
ability to distinguish between stereoisomers
Is the active site for enzymes highly specific for substrate?
yes
What configuration of amino acids are found in animals?
L amino acids and D sugars
Protease?
protein cleaving enzyme
Examples of proteases?
Trypsin, chymotrypsin, elastase
How do proteases work?
Have an active site with a serine residue whose OH group can act as a nucleophil, attacking the carbonyl carbon of an amino acid residue in a polypeptide chain
Recognition Pocket?
pocket in an enzymes structure which attracts certain residues on substrate polypeptides
Enzymes that act on hydrophobic substrates have ______ amino acids in their active sites while hydrophilic/polar amino acids will comprise the active site of enzymes with ______ substrates.
hydrophobic
hydrophilic
4 ways that enzyme activity is regulated?
- Covalent Modification
- Proteolytic Cleavage
- Association with other polypeptides
- Allosteric Regulation
What is the most common example of covalent modification?
addition of a phosphoryl group from a molecule of ATP by a protein kinase to the OH of Ser, Threonine, or Tyr residues
What do protein phosphoylases use instead of ATP?
free floating inorganic phosphate (Pi)
What can reverse protein phosphorylation?
phosphatases
What is proteolytic cleavage?
enzymes in inactive forms are activated by cleavage by a protease
Allosteric Regulation?
modification of the active site through interaction of molecules with other specific sites on the enzyme called allosteric sites
The binding of the allosteric regulator to the allosteric site is generally ____ and ______.
noncovalent
reversible
Explain negative feedback or feedback inhibition.
An end product shuts off an enzyme early in the pathway
What is feedforward stimulation?
enzyme stimulated by its substrate or by a molecule in the synthesis of the substrate
What is enzyme kinetics?
study of the rate of formation of products from substrates in the presence of an enzyme
The reaction rate in enzyme kinetics is dependent on what?
- the concentration of the subtrates
- enzyme
The rate, V, is ______ proportional to the amount of substrate added.
directly
What is the Vmax?
the reaction rate of an enzyme is saturated meaning that adding more substrate does not increase reaction rate
What is Vmax(1/2)?
linear portion of the curve where V is proportional to S
What is Km?
the substrate concentration at which the reaction velocity is half its maximum
What does a low Km mean?
not very much substrate is required to get the reaction rate to half the maximum rate and thus has a high affinity for this particular substrate
Tense? Relaxed?
- turned off
- turned on
Cooperativity?
binding of one substrate molecule to the enzyme complex enhances the binding of more substrate molecules to the same complex.
How many active sites do cooperative molecules have?
more than one in a quaternary structure
What type of curve results from cooperative binding?
sigmoidal
The leveling off of the cooperativity curve represents what?
saturation, Vmax
Name one protein that is cooperative and is not catalytic?
Hemoglobin has 4 binding sites
Competitive Inhibitors?
compete with substrate for binding at active site
Structurally competitive inhibitors resemble what?
substrate but the most effective resemble the transition state which the active site normally stabilizes
What can overcome competitive inhibitors?
adding more substrate, if the concentration is high enough the substrate will outcompete the inhibitor
Is Vmax affected in competitive inhibition?
no but it requires more substrate
What happens to Km in competitive inhibition?
Km is increased
Where do noncompetitive inhibitors bind?
at the allosteric site
What happens to Vmax and (1/2) Vmax in noncompetitive inhibition?
decreases
What happens to Km in noncompetitive inhibition?
stays the same
Photosynthesis?
process by which plants store energy from the sun in the bond energy of carbs
Photoautotrophs?
use energy from light to make their own food
Chemoheterotrophs?
use energy of chemicals produced by other living things
Three meanings of oxidize?
- attach Oxygen
- remove Hydrogen
- remove electrons
Three meanings of Reduce?
- remove Oxygen
- add Hydrogen
- add electrons
CH3CH3 to CH2CH2 oxidation of reduction?
oxidation
Fe3+ to Fe2+ oxidation or reduction?
reduction
O2 to H2O oxidation or reduction?
reduction
Redox pair?
when one atom gets reduced, another must be oxidized
catabolism?
breaking down molecules
anabolism?
building up metabolism
How do we extract energy from glucose?
oxidative catabolism
what are the 4 steps of oxidative catabolism?
- Glycolysis
- Pyruvate dehydrogenase complex
- Krebs cycle
- electron transport/oxidative phosphorylation
Stoiciometry of glucose oxidation?
C6H12O6 + 6O2 = 6CO2 + 6H2O
What are the two members of the redox pair in glucose oxidation?
C6H12O6 is oxidized to CO2
O2 is reduced to H2O
What type of reaction is cellular respiration?
big coupled reaction
Short summary of Glycolysis?
glucose is partially oxidized while it is split in half into two identical pyruvic acid molecules.
How many carbon molecules does pyruvic acid have?
three because glucose is split in half
What is produced from glycolysis?
2 ATP
2 NADH
Where does glycolysis occur?
in the cytoplasm absent of oxygen
Short summary of PDC?
pyruvate produced in glycolysis is decarboxylated to form an acetyl group. the acetyl group is then attached to coenzyme A that transfers the acetyl group into the Krebs cycle
What is produced from PDC?
2 NADH per glucose, one per pyruvate
Krebs cycle is also known as what?
tricarboxylic acid cycle
citric acid cycle
Short summary of the Krebs cycle?
the acetyl group from the PDC is added to oxaloacetate to form citric acid which is then decarboxylated and isomerized to regenerate the original oxaloacetate
What is produced from the Krebs cycle?
2 ATP
6 NADH
2 FADH2
T/F
PDC and Krebs cycle use oxygen directly.
False
Oxygen is necessary for which stage of cellular respiration?
oxidative phosphorylation
Where do the PDC and Krebs cycle take place?
matrix of mitochondria
All cells from all domains have the ability to perform _____.
Glycolysis
What is needed to start the pathway of Glycolysis?
ATP
Hexokinase?
catalyzes the first step of glycolysis, the phosphorylation of glucose to G6P.
What inhibits hexokinase?
G6P feedback
What catalyzes the third step of glycolysis?
Phosphofructokinase (PFK)
Is the reaction catalyzed by PFK favorable or unfavorable?
favorable so its irreversible
What is the key biochemical valve controlling the flow of substrate to product in glycolysis?
PFK
What is committed step in glycolysis?
converting F6P to F1,6bP
Very favorable reactions are generally subject to _____ regulation.
allosteric
PFK is allosterically regulated by ____.
ATP
What effect would high concentration of ATP have on PFK activity?
it would slow glycolysis because ATP binds to the allosteric site of PFK to inhibit it
Lowering the amount of ATP will _____ reaction rate in glycolysis.
increase
Two molecules of ____ are reduced in glycolysis per glucose catabolized, forming 2 NADH.
NAD+
NADH is an ______ carrier.
electron
What is NADH responsible for?
shuttling energy in the form of reducing power
Aerobic? Anaerobic?
- with oxygen
- without oxygen
What is the problem with oxidative metabolism under anaerobic conditions?
no oxygen so electron transport cannot function and a limited supply of NAD+ becomes entirely to NADH
Would a limited supply of NAD+ stimulate or inhibit glycolysis?
inhibit because NAD+ is needed as a substrate to produce NADH.
What is the purpose of fermentation?
to regenerate NAD+ in anaerobic conditions, allowing glycolysis to continue without oxygen
What does fermentation use pyruvate for?
acceptor of the high energy electrons from NADH
Two examples of fermentation?
- reduction of pyruvate to ethanol (yeast makes beer)
2. reduction of pyruvate to lactate in human muscle cells
What happens to the lactate in human muscle cells after a period of strenuous exercise?
Cori Cycle- lactate is exported from muscle to liver. Liver converts it back to pyruvate when oxygen is available while making NADH from NAD+. It utilizes NADH to make ATP in oxidative phosphorylation
Oxidative decarboxylation?
happens in PDC and Krebs, molecule is oxidized to release CO2 to produce NADH
In oxidative decarboxylation, pyruvate is changed from a 3-carbon molecule to a ______, while _____ is given off and ______ is produced.
2 carbon molecule
CO2
NADH
In PDC, an acetyl unit is activated and is attached to ______.
Coenzyme A
What is produced by the hydrolysis of ATP during metabolism?
AMP
What is the role of acetyl-CoA?
it is high energy, transfers acetyl fragment into Krebs cycle
What effect would a high level of AMP have on the activity of pyruvate dehydrogenase?
stimulates PDC, increasing the rate of entry into the Krebs cycle
PDC is composed of three enzymes, why is this more efficient than three independent enzymes?
intermediates are passed from active site to active site without having to diffuse
Prosthetic group?
nonprotein molecule covalently bound to an enzyme as part of the active site
What prosthetic group does PDC contain?
thiamine pyrophosphate (TPP)
What is thiamine in TPP?
vitamin B1
Vitamins are often _______.
prosthetic groups
NAD+ is a ______.
cofactor
cofactor?
various substances that are necessary to the function of an enzyme but never actually interact with the enzyme
What would a thiamine deficiency do?
shutdown the PDC and Krebs cycle because it is required as a TPP prosthetic group, ATP production would fall. Glycolysis would increase to make up for lower levels of ATP
What starts the Krebs cycle?
2 carbon acetyl unit from acetyl CoA
what is released when the 2 carbon acetyl unit is combined with oxaloacetate?
CO2
What is the first intermediate produced in the Krebs cycle?
citrate
What does citrate possess?
three carboxylic acid functional groups
What is a molecule with three carboxylic acid groups ready for?
oxidative decarboxylation
What is stage 1 of the Krebs cycle?
the two carbons in the acetate fragment of acetyl CoA are condensed with the 4 carbon compound oxaloacetate to make citrate
How many chiral carbons are present in citrate?
none, the C’s dont have 4 unique substituents
If pyruvate is radiolabeled on its number one carbon, where will it end in the Krebs Cycle?
CO2
What is stage 2 of the Krebs cycle?
citrate is further oxidized to release CO2 and to produce NADH from NAD+ with each oxidative carboxylation
How many carbons from the CoA component of acetyl CoA enter the Krebs?
none, CoA assists in catalysis so it is not consumed but regenerated as CoA-SH
What is stage 3 of the Krebs?
OAA is regenerated so the cycle can continue
Up til the Krebs in glucose metabolism, most of the energy produced is from ______.
high energy electron carriers, not ATP
What is the difference between the inner and outer layers of the mitochondrion?
inner layer- impermeable and folded into cristae
outer- contains large pores
Cristae extend into the ______, which is the innermost space of the mitochondria.
matrix
where are the enzymes of the Krebs and PDC located?
matrix
Where are the enzymes for the electron transport chain and ATP synthase involved in oxidative phosphorylation found?
inner mitochondrial membrane
What are the two goals of electron transport/ oxidative phosphorylation?
- reoxidize all the electron carriers reduced in glycolysis, PDC, and Krebs
- store energy in the form of ATP
What needs to be transported into the mitochondria for oxidative phosphorylation to begin? What is already there?
- NADH from glycolysis
- other NADH, FADH2
What is different in prokaryotes with cellular respiration?
everything is located in the cytoplasm because there are no organelles so they do not have to shuttle into the mitchondrial matrix like in eukaryotes
How do prokaryotes carry out oxidative phosphorylation?
establish a proton gradient, so they need a membrane impermeable to protons
What membrane is used for oxidative phosphorylation in Eukaryotes? Bacteria?
- inner mitochondrial membrane
- cell membrane
Oxidative Phosphorylation?
oxidation of high energy electrons carriers NADH and FADH2 coupled with phosphorylation of ADP to produce ATP
What is the energy released through oxidation of NADH and FADH2 used for in the electron transport chain?
pump protons out of the mitochondrial matrix
What is the proton gradient used as a source for?
energy used to drive phosphorylation of ADP to ATP
How many electron carriers does the electron transport chain have?
5
What is the first large carrier in the electron transport chain?
NADH dehydrogenase (coenzyme Q reductase)
What does NADH dehydrogenase pass its electrons to?
ubiquinone(coenzyme Q)- small carrier
What does ubiquinone pass its electrons to?
cytochrome C reductase- large membrane bound complex
What is the next carrier in the chain of ETC after cytochrome C reductase?
cytochrome C- small hydrophilic
What is the last member of the ETC? Where does it pass its electrons?
- cytochrome C oxidase
- passes its reducing power to O2, reducing it to H2O
What is the pH in the matrix as opposed to the rest of the cell?
much higher because H+ is pumped out of the matrix
high pH= low H+
ATP production is dependent on a ________.
proton gradient
The passage of protons from the intermembrane space through the ________ causes it synthesize ATP from ADP + Pi.
ATP synthase
If the proton gradient is destroyed, what is inhibited first?
muscular contraction because ATP would run out
What has a positive delta G under normal aerobic conditions in the cell?
pumping protons to form a pH gradient
How much ATP is generated per NADH? FADH2? GTP?
2.5
1.5
1
Total ATP generated in cellular respiration from a single molecule of glucose?
30 Eukaryotes
32 Prokaryotes
What is glycogenolysis?
glycogen breakdown
Glycogenolysis occurs in response to ______.
glucagon when blood sugar levels are low, it releases glucose into the blood
How are fatty acids broken down in hepatocyte mitochondria?
Beta oxidation
4 other processes that convert on the Krebs?
Glycogenolysis
Glucogenesis
Beta oxidation
Amino Acid Catabolism
In Eukaryotes, the ultimate yield of ATP from NADH is lower when NADH is produced by _______.
Glycolysis
What category of enzymes irreversibly modifies their substrate?
proteases
In cellular respiration in bacteria, which area has the lowest pH?
extracellular space because protons are pumped out of the cytoplasm to the outside of the cell
Reaction rate changes ____ as substrate concentration is increased when it was originally at low concentration.
linearly
T/F
The effect of estrogen on luteinizing hormone one day before ovulation is an example of feedback inhibition.
False
as ovulation approaches, high levels of estrogen stimulate the release of lutenizing hormone
If the affinity of hemoglobin for oxygen is decreased, the oxygen dissociation curve shifts to the _____.
right
Oxygen binding to the active site of one subunit of the hemoglobin tetramer causes the other subunits to have increased affinity for oxygen. this is an example of ______.
cooperativity
Protein phosphatases regulate the activity of metabolic pathways by ______.
covalent modification
A competitive inhibitor binds to the ____ site and has ____ effect on Vmax.
active
no
