Macro Metabolism Exam 1

transcription vs. translation

• transcription: process where a gene’s DNA is converted into mRNA (happens in nucleus)

  • uses RNA polymerase

• translation: converting genetic information in mRNA and using it to build an amino acid chain (happens in cytoplasm at ribosome)

  • uses ribosomes and tRNA

Anabolic response

• Anabolic: to build up or store

• energy requiring (endothermic) (consume ATP to do chemical work)

• primary purpose: energy storage, tissue growth, repair, and cellular maintenance

Short term vs. Long term regulation (know examples)

SHORT term: immediate adaptability to a stressor

→ Ex: change from fatty acid metabolism to glucose metabolism, turning enzymes on/off, removing a phosphate group from a protein

LONG term: physiological adaptations because of stressors applied over time (hours to days)

→ Ex: transcription and translation - gene transcription, changes in diet, physical activity levels, toxin exposure, and health status

 

Phosphorylation (PTM)

the addition of a phosphate group

• can increase or decrease the activity of an enzyme

Glycosylation (PTM)

adding a sugar to an “N” or an “O” in an amino acid side chain

Ubiquitination (PTM)

adding ubiquitin to lysine residue (used to target proteins for degradation)

Disulfide Bonds (PTM)

covalently links “S” atoms of two different cystine residues (happens after translation)

Acetylation (PTM)

adds an acetyl group to an N-terminus of a protein or at lysine residues

Lipidation (PTM)

attaches a lipid to a protein chain

Methylation (PTM)

adds a methyl group usually at lysine or arginine residues

Hydroxylation (PTM)

adds an -OH group to a side chain of a protein

What percentage of total daily energy expenditure does sleeping metabolic rate take up?

~25-35% daily EE

What percentage of total daily energy expenditure does arousal take up?

~5-10% daily EE

What percentage of total daily energy expenditure does basal metabolic rate (BMR) take up?

~65% daily EE

What percentage of total daily energy expenditure does the thermic effect of food take up?

~5-10% daily EE

→ fats take the least amount of energy to digest and proteins take the most (bc protein synthesis costs ATP)

What percentage of total daily energy expenditure does spontaneous physical activity and thermogenesis (NEAT) take up?

20-35% daily EE

→ usually lower than 20% if sedentary and higher than 35% if highly active

Contributions to BMR/RMR

• LEAN MUSCLE MASS (more mass = higher BMR)

• genetics

• stress levels

• hormones (especially thyroid hormone)

• age

• gender

Glycolysis is an example of a(n) _____ pathway (anabolic or catabolic)

catabolic

How to calculate BMI

weight in kg / (height in meters)²

→ lb to kg: divide lbs by 2.2

→ in to m: multiply in by 0.0254

Where does oxidative phosphorylation occur?

inside the mitochondria

Each NADH is equivalent to ___ ATP

2.5

Each FADH₂ is equivalent to ___ ATP

1.5

PTM’s are what kind of bonds?

Covalent

True or False: PTM’s are permanent additions to a protein

flase

transcription factor

a specialized protein that binds to specific DNA sequences to turn genes on or off, controlling the rate at which genetic information is transcribed into RNA

Allosteric regulation

regulates enzymes by binding an effector molecule at a site other than the enzyme’s active site

→ the place the effector molecule binds is called the allosteric site

→ positive effector = allows substrate/co-enzyme to bind easier

→ negative effector: = makes it harder for substrate/co-enzyme to bind

→ allosteric effectors are usually products of the enzyme reaction that feedback on the enzyme but can also be upstream substrates or downstream products of metabolic pathway

How many protons are pumped for the two electrons donated by NADH?

10

How many protons are pumped for the two electrons donated by FADH₂?

6

How many protons are pumped at complex I?

4

How many protons are pumped at complex III?

4

Oxidation

→ loss of electrons, oxidized (LEO)

→ loses energy

→ macronutrients are broken down and oxidized to release energy

→ ex: glucose loses hydrogen atoms and electrons as it breaks down into CO₂

Reduction

→ gain of electrons, reduction (GER)

→ gains energy

→ Coenzymes like NAD+ and FAD accept electrons/hydrogens to become NADH and FADH₂

Krebs Cycle (AKA TCA or Citric Acid Cycle) Purpose

used to generate energy ATP through oxidation of Acetyl-CoA, synthesis of NADH, and production of amino acids

→ takes place in mitochondria

1st regulatory step of Krebs (TCA) cycle

Step 1: Citrate Synthase (The Entry Gate)

→ What it does: Combines a 4-carbon molecule (oxaloacetate) with a 2-carbon molecule (acetyl-CoA) to form 6-carbon citrate. This brings new fuel into the cycle.

• How it’s regulated:

  • Inhibited by: NADH, Succinyl-CoA, and Citrate.

  • Why it makes sense: If the cell already has high NADH or downstream intermediates (succinyl-CoA/citrate) accumulating, it closes the entry gate to avoid wasting fuel.

2nd regulatory step of Krebs (TCA) cycle

Step 2: Isocitrate Dehydrogenase (The First Energy Generator)

• What it does: Converts 6-carbon isocitrate into 5-carbon alpha-ketoglutarate. This step strips off electrons to create the 1st NADH and releases a molecule of CO₂

• How it’s regulated:

  • Inhibited by: NADH and ATP (negative allosteric effectors)

  • Activated by: Ca²⁺

  • Why it makes sense: High ATP and NADH tell the enzyme "we have enough energy, slow down." Conversely, rising Ca²⁺ signals that muscle work is happening and more ATP is urgently needed

3rd regulatory step of Krebs (TCA) cycle

Step 3: alpha-Ketoglutarate Dehydrogenase (The Second Energy Generator)

• What it does: Converts 5-carbon alpha-ketoglutarate into 4-carbon succinyl-CoA. This reaction produces the 2nd NADH and releases another CO2

• How it’s regulated:

  • Inhibited by: NADH and succinyl-CoA (product feedback).

  • Activated by: Ca²⁺

  • Why it makes sense: Just like step 2, product buildup (NADH and succinyl-CoA) backs up the pathway, while Ca²⁺ pushes it forward to meet workload demand

Products of the TCA cycle (1 turn of the TCA cycle per 1 Acetyl Co-A)

3 NADH, 1 GTP, 1 FADH₂, and 2 CO₂

_{→ (per 1 molecule of glucose (2 turns of the TCA cycle)): 6 NADH, 2 GTP, 2 FADH2, and 4 CO2}

Products of aerobic (with oxygen) glycolysis

per 1 molecule of glucose:

→ 2 pyruvate

→ 2 Net ATP

→ 2 NADH

Covalent regulation

the addition or removal of functional groups (like a phosphate group) to an enzyme (increases / decreases enzyme activity)

Transcriptional/Translational regulation

controlling the rate of gene transcription/translation to change enzyme abundance

Rate limiting step in glycolysis

the conversion of fructose-6-phosphate to fructose-1-6-bisphosphate via the enzyme phosphofructokinase-1 (PFK-1)

products of anaerobic (no oxygen) glycolysis

2 lactate and 2 Net ATP

proton motive force (PMF)

the transmembrane electrochemical gradient generated across the inner mitochondrial membrane by the ETC. As electrons travel though complexes I, III, and IV, the released energy is used to pump protons (H+) out of the matrix

HIGH proton motive force (PMF) in mitochondria

• occurs during rest when ATP demand is low (low ADP availability)

• ETC flux slows down causing electron carriers to back up in a reduced state

• trapped electrons react with abundant molecular oxygen causing increased superoxide (O2-), ROS generation, and high potential energy storage

LOW proton motive force (PMF) in mitochondria

• occurs during exercise when ATP demand is high (high ADP availability)

• protons flow rapidly though intermembrane space back into matrix through complex I and IV to reduce oxygen to water

• smooth flow of electrons through ETC = superoxide and ROS production decreases

• ATP synthesis

Coupled vs. uncoupled oxidative phosphorylation (UCPs)

• uncoupled ox phos: UCPs serve as specialized channels in the inner mitochondrial membrane that allow proteins to leak back into the matrix without passing through ATP synthase

• coupled ox phos: electrons that pass through complexes I-IV are pumped out of the matrix into the intermembrane space. Protons return to the matrix through ATP synthase

What do uncoupling proteins do to ETC flux?

they increase ETC flux by dissipating the proton gradient across the inner mitochondrial membrane

Two main components of the electrochemical gradient

• Electrical gradient: the difference in charge across the inner mitochondrial membrane created by pumping positively charged protons -> intermembrane space becomes more positively charge and mitochondrial matrix remains negatively charged

• Chemical gradient/pH difference: the difference in proton concentration across the inner mitochondrial membrane ->  high proton concentration of intermembrane space causes it to have a lower pH and a high pH in the mitochondrial matrix

 

Where does NADH deliver electrons in the ETC and how many total protons are pumped for their delivery?

• Electrons travel through Complex I (4H+) → Complex III (4H+) → Complex IV (2H+)

• Total: 10 protons per ATP = 2.5 ATP

Where does FADH2 deliver electrons in the ETC and how many total protons are pumped for their delivery?

• Electrons enter at Complex II (0H+) → Complex III (4H+) → Complex IV (2H+)

• Total: 6 protons per ATP = 1.5 ATP

Euglycemia

normal, healthy blood glucose levels (90-126 mg/dL)

• occurs between meals

Hypoglycemia

• low blood glucose (below 54 mg/dL)

• occurs during fasting/starvation or after prolonged/intense exercise

Hyperglycemia

elevated blood glucose (above 126 mg/dL)

• occurs immediately after the digestion and absorption of carbohydrates before insulin is released OR in metabolic conditions involving insulin resistance

Catabolic response

• pathway that breaks down complex molecules

• energy releasing (exothermic) (they capture released chemical bond energy to produce ATP, NADH, and FADH2 (and heat as a byproduct)

• primary purpose: generate and deliver ATP to meet immediate cellular demands

How does a high NADH/NAD+ and ATP/ADP ratio affect the rate of TCA cycle flux?

• low energy demand (rest)

• allosteric inhibition of citrate synthase, isocitrate dehydrogenase, and alpha-ketoglutarate dehydrogenase

• overall TCA cycle flux: decreased/slowed

How does a low NADH/NAD+ and ATP/ADP ratio affect the rate of TCA cycle flux?

• high energy demand (exercise)

• relief of inhibition through oxidation of NADH back into NAD+

• overall TCA cycle flux: increased/accelerated

What is mtDNA and does it contribute to mitochondrial proteins?

• mtDNA = mitochondrial DNA located in the mitochondrial matrix (maternally derived)

• provides 13 ETC subunits (within complex I, III, IV, and ATP synthase)

structural differences between amylose, amylopectin, and glycogen

• Amylose: completely linear and unbranched (connected by glycosidic bonds)

• Amylopectin: moderately branched (connected by glycosidic bonds)

• Glycogen: highly branched compact and spherical (connected by glycosidic bonds)

  • extensive branching creates numerous non-reducing ends which allows huge amounts of glucose to be stored compactly in liver and skeletal muscle without causing a massive osmotic influx of water into the cell

slow oxidative vs. fast glycolytic muscle fibers

• slow oxidative: slow contraction speed, high oxidative capacity, low intensity continuous activity

• fast glycolytic: high contraction speed, high glycolytic capacity (low oxidative capacity), high intensity short burst energy

substrate level phosphorylation vs. oxidative phosphorylation

• substrate level phosphorylation: an enzyme directly transfers a phosphate group from a phosphorylated substrate onto ADP to make ATP

  • occurs in the cytosol and mitochondrial matrix

  • energy source: high energy bonds

  • Ex: PCr, Glycolysis, TCA cycle

• oxidative phosphorylation: couples macronutrient oxidation and electron transfer to proton pumping and ATP synthesis

  • occurs in inner mitochondrial membrane and matrix

  • strictly aerobic

  • energy source: electrochemical gradient / PFM

  • ex: ETC (complexes I-IV) paired with ATP synthase

How many ATP are produced from substrate level phosphorylation?

4

How many ATP are produced from oxidative phosphorylation?

26-28 (depending on shuttle choice; Glycerol-3-Phosphate vs. Malate-Aspartate shuttle)

How is PCr timed?

0 to ~10-15 seconds

How is oxidative phosphorylation timed?

dominant after 2 minutes

How is anaerobic glycolysis timed?

15 seconds to ~2 min

Gluconeogenesis

anabolic metabolic pathway that synthesizes glucose from non-carbohydrate carbon precursors (ex: lactate and glycerol)

Where does gluconeogenesis occur?

Tissue Level: mostly in the liver, some in the kidneys

Subcellular: begins in mitochondrial matrix, proceeds through cytosol, and ends in endoplasmic reticulum

What would cause gluconeogenesis to occur?

activated during catabolic states of low glucose

• ex: fasting, starvation. prolonged exercise, low carb diets

How is glycogenolysis different in the muscle vs. the liver?

muscle: enters glycolysis directly (G6P is trapped)

→ supplies ATP for muscle contraction

liver: cleaved to free glucose via Glucose-6-phosphate

→ maintains systemic blood glucose

glycogenolysis

catabolic pathway where stored glycogen is broken down to release free glucose molecules into blood/cells

How are ROS mitigated in the cell?

• Superoxide Dismutase (SOD):

  • SOD1: located in cytosol and cofactor is Cu/Zn → targets superoxide

  • SOD2: located in mitochondria and cofactor is Mn → targets superoxide

• Catalase: cofactor is iron (heme) and targets H2O2 (hydrogen peroxide)

  • located in peroxisomes, cytosol, and mito

• Glutathione System: cofactor is selenium and NADPH and targets H2O2 (hydrogen peroxide)

  • located in cytosol and mito matrix

• Peroxiredoxins and Thioredoxins: cofactors are cystine thiol (-SH) and NADPH → targets hydrogen peroxide and organic peroxides

  • located in cytosol and mito matrix

PCr System

• located in cytosol

• anaerobic

• substrate level phosphorylation

• key enzyme: creatine kinase

• utilized in first 0-15 sec of exercise