test 2 // isc biochem

enzymes & cellular respiration

what are enzymes?

what specifically do they change the value of?

biological catalysts; usually proteins

lower a reaction’s activation energy (Ea)

where in an enzyme does catalysis occur?

in the active site

what are cofactors and how are they used?

what are some examples?

non-protein molecules that help enzymes during the catalysis reaction in a variety of ways: stabilizing active sites, helping the substrate bind, transferring atoms/electrons

metal ions (minerals) or derived from vitamins

what is the purpose of enzyme regulation?

enzyme regulation controls the speed and timing of the biochemical reactions of catalysis, helping cells maintain homeostasis and use energy in the most efficient way possible

since most enzymes are proteins, what does that make them sensitive to? provide examples

what part of the enzyme is especially affected?

environmental conditions such as pH or temperature, as they impact noncovalent interactions that work to stabilize the enzyme

active site is affected/comprised, preventing substrate binding

allosteric enzymes catalyze ___ reactions, so they are points of ___

irreversible; regulation

what is the overall purpose of cellular respiration?

breaking down glucose to harvest useable energy (ATP)

what are the four parts/pathways of cellular respiration?

1. glycolysis

2. pyruvate oxidation'

3. citric acid/kreb’s cycle

4. oxidative phosphorylation

what are the overall inputs and outputs of cellular respiration?

inputs: glucose and oxygen

outputs: carbon dioxide, water, and ATP

what is the purpose of glycolysis?

breakdown of glucose into two pyruvates, generating 2 ATP and 2 NADH

does glycolysis require oxygen?

no

what are the inputs and outputs of glycolysis? (per glucose molecule)

mention the net gain of energy

inputs:

• 1 glucose

• 2 NAD+

• 2 ATP

outputs:

• 2 pyruvates

• 2 NADH

• 4 ATP

• 2 H2O

net gain of energy: 2 ATP (2→4)

what are the allosteric/regulatory enzymes involved in glycolysis? mention which reaction they are associated with

1. hexokinase (rxn 1)

2. phosphofructokinase (rxn 3)

3. pyruvate kinase (rxn 10)

what is the location of glycolysis in eukaryotes and prokaryotes?

eukaryotes: cytoplasm/cytosol

prokaryotes: cytoplasm/cytosol

what is the purpose of pyruvate oxidation?

converting pyruvate into acetyl-CoA, which is the starting molecule of the kreb’s cycle

what is the location of pyruvate oxidation in eukaryotes and prokaryotes?

eukaryotes: mitochondrial matrix

prokaryotes: cytoplasm/cytosol

what are the inputs and outputs of pyruvate oxidation? (per cycle of cellular respiration aka two pyruvates)

input:

• 2 pyruvates

• 2 NAD+

• 2 CoA

output:

• 2 acetyl-CoA

• 2 NADH

• 2 CO2

what is the regulatory enzyme of pyruvate oxidation?

pyruvate dehydrogenase complex

other than generating energy in the long run, what else is glycolysis useful for?

synthesis of biological monomers, such as amino acids

what is the purpose of the citric acid cycle?

to oxidize the carbons in the various intermediates to carbon dioxide; transfer of high-energy electrons to electron carriers (reduction of the carriers), the energy of which is later used to drive ATP synthesis

what is the location of the citric acid cycle in eukaryotes and prokaryotes?

eukaryotes: mitochondrial matrix

prokaryotes: cytoplasm/cytosol

what are the inputs and outputs of the citric acid cycle?

(per turn of the cycle; *NOTE: two turns of the cycle occur per glucose molecule)

which molecule is regenerated in the cycle and continues to be used throughout the cycle?

inputs:

• 1 acetyl-CoA

• 3 NAD+

• 1 FAD

• 2 H2O

outputs:

• 2 carbon dioxides

• 3 NADH

• 1 FADH2

• 1 GTP/ATP

oxaloacetate is regenerated throughout the cycle

what are the regulatory enzymes associated with the CAC? mention which reactions they are associated with

1. isocitrate dehydrogenase (rxn 3)

2. α-ketoglutarate dehydrogenase (rxn 4)

____ regulates phosphofructokinase

citrate

what is the purpose of oxidative phosphorylation?

produces the majority of ATP during cellular respiration; the high-energy electrons from all of the previous parts of cellular respiration are passed along and as they are, they release their energy to power the PMF that drives ATP synthesis

what is the location of oxidative phosphorylation in prokaryotes and eukaryotes?

mention what the proton gradient is formed between

eukaryotes: inner mitochondrial membrane; the proton gradient is formed between the mitochondrial matrix and the intermembrane space

prokaryotes: plasma membrane; the proton gradient is formed between the cytoplasm and the periplasmic region

what are the electron carriers associated with oxidative phosphorylation?

1. NADH

2. FADH2

3. coenzyme Q

4. cytochrome C

explain how PET scans visualize tumors using fluorodeoxyglucose (FDG)

1. FDG enters a cell using a glucose transporter (resembles glucose enough to do so)

2. FDG is phosphorylated by hexokinase (1st rxn of glycolysis); the product, FDG-6-phosphate, cannot leave the cell and it cannot be processed further (isomerization) through glycolysis, either

Once FDG becomes trapped inside cancer cells, the fluorine attached to it emits positrons/gamma rays as it decays, which is detected by the PET machinery

Explain why fluoroacetate (FA) causes citrate levels to rise

1. FA can be converted into fluorocitrate by citrate synthase (1st step of CAC)

2. fluorocitrate is a suicide inhibitor for aconitase, the enzyme that catalyzes the second step of the CAC; this completely disables the CAC at this step, and regular citrate starts to accumulate due to it

3. accumulated citrate leaves the mitochondria and binds to cytoplasmic phosphofructokinase, acting as an allosteric inhibitor and shutting down glycolysis (and, downstream, cellular respiration as a whole)

which parts of cellular respiration are ATP-generating?

glycolysis, CAC, and oxidative phosphorylation