Biochem

%%Block 8 - Receptors- Chan%%

Explain receptor types & functions
- Major types:
  - Cell surface: TM proteins formed by hydrophobic aa arranged in helical structure

hormone binds receptor → change shape → hormone-receptor complex → response * Function: utilize secondary messenger system/signaling cascade * GPCR * Receptor tyrosine kinases (*intrinsic enzymatic activity) * Amino acid derived hormone receptor (ex. bind epinephrine via GPCR) * Peptide/protein hormone receptor (ex. bind insulin via RTK) * Intracellular: cross PM w/o help; receptor-hormone complex → bind hormone response element on DNA → influence transcription of specific genes * Function: bind to HRE & directly influence transcription of specific genes * Lipid derived/steroid (intracellular)

Described receptor types: transmembrane localization, subunit structure and function; enzymatic activity, intracellular receptors
- @@GPCR:@@ 7 TM protein made from a single polypeptide chain (NH3 outside of cell, carboxyl end is cytoplasmic), 700+ genes in human genome
  - Ligands: photons to proteins
  - Subunits: heterotrimeric, alpha, beta, gamma subunits
  - Function: same signaling molecule can interact w/ different receptors & trigger distinct responses
  - Enzymatic activity:
  - alpha s → + AC → increase cAMP ==> stimulatory
  - alpha i --| AC → decrease cAMP ==> inhibitory (phospholipase, phoshodiesterases)
  - alpha q → PLC: PIP2 → DAG & IP3 → SR release of Ca++ → + PKC ==> stimulatory
  - Classes
  - A: Rhodopsin-like (makes up 85%): largest group & most studied
  - B: Secretin receptor family
  - C: Metabotropic glutamate/pheromone
- ==RTK==: single TM protein, 58 genes; ligand activated enzymatic activity = autophosphorylation → signaling cascade
Properly use terms related to ligand-receptor interactions, agonists/antagonists
- Agonist: molecule that activates a receptor to create a biological response (some agonists elicit stronger responses than the endogenous ligand)
- Antagonist: blocks the action of the agonist
- Inhibitor: blocks the receptor-ligand interaction
Understand post receptor signaling pathways
- GPCR: AC → increase cAMP → PKA→ CREB
- RTK: bind protein ligands w/ high affinity → autophosphorylation → + activate/recruit of effectors to generate signaling cascade → change cellular processes
- PIP3: important lipid second messenger which regulates many cellular processes
  - Class 1 PI3 Kinase: phosphorylates inositol ring of PIP2 @ 3rd position → PIP3
  - Reaction reversed by PTEN (tumor suppressor)
Apply knowledge of receptors to drugs and drug design
- Humira (adalimumab) = biologic monoclonal antibody; used to treat RA, psoriatic arthritis, ankylosing spondylitis, Crohn’s, UC [has been a top selling drug for the past 7 years]
- Diabetes mellitus: insulin
  - insulin → + insulin R → IR kinase enzymes → cascade (bovine → human insulin 1980s)
- Chronic myelogenous leukemia/CML: too many myeloblasts in the blood & bone marrow
  - Philadelphia chromosome (translocation between 9 & 22)
  - progressive disease
  - Sx: fever, fatigue, easy bleeding, anemia, infection, splenomegaly, arthralgia
  - Tx: Gleevec 2001, first kinase inhibitor drug (inhibits BCR - ABL)
- Steps in drug discovery chemical drugs

1. Basic research

2. Drug discovery: screening chemical drug libraries using several assays (testing drug & target, repeat and validate)

3. Preclinical research

4. Clinical research

5. FDA approval of drug

Applying drugs to new diseases, ex. COVID-19

1. Basic research: viral mechanism, viral entry infection, immune response

2. Drug discovery: providing therapeutic options (vaccines, anti-virals, antibody, anti-toxin, enhance immunity)

Questions: Slide 20

Is she trying to say that PIP3 or PI3K is an oncogene?

Block 9: Metabolism & bioenergetics - Potter

Describe anaerobic reactions: Immediate energy sources, stored ATP and fast energy source of glycolysis ending in lactate
- Anaerobic reactions: Glycolysis & TCA
- Immediate energy sources: glycolysis is anaerobic → 2 ATP, 2 NADH
- Stored ATP: high concentrations of ATP signifies cells are at high energy state
Describe aerobic reactions
- Pyruvate oxidation, TCA and ETC are all aerobic
- Inner mitochondrial membrane: ATP synthase converts ADP + Pi → ATP → oxidative phosphorylation
Described sustained energy sources: glycolysis ending in pyruvate and beta oxidation of fats $??$
- Oxidation-reduction reactions indirectly provide much of the energy needed to make ATP
Describe cellular metabolic programs: growth and burning of energy
- Cells can either be burning energy via aerobic respiration or growing (can’t do both at the same time)
- When cells are in rapid growth → rely on glucose & are depleted of mitochondria
Describe nutrient-sensing enzymes that control metabolic programs
- AMPK (master regulator)→ tells mitochondria to burn energy from glucose; stimulated by metformin [anti-cancer, anti-aging, --| FA synthesis → also weight loss drug]
  - AMPK very sensitive to levels of AMP (high AMP → cell low energy → need more mitochondria to function)
  - Fructose/glucose → methylglyoxal (MGO) → bind active site of AMPK & inactivate it
- PI3K → determines whether the cell opens up the glucose flood gates and allows 400x more glucose to enter
- mTOR → determines whether cells will live or die
Describe metabolism, anabolic and catabolic reactions
- Catabolism: involves all of the metabolic processes that break down biomolecules
- Anabolism: all of the metabolic processes that synthesize biomolecules
- Catabolic pathways deliver chemical energy in the form of ATP, NADH, NADPH, and FADH2. These energy carriers are used in anabolic pathways to convert small precursor molecules into cellular macromolecules.
  - Converging = catabolic || Diverging = anabolic
Describe bioenergetics
- Describes the transfer & utilization of energy in biologic systems
- Concerns only the initial and final energy states of reaction components
- Predicts if a process is possible (vs. kinetics which measures how fast the reaction occurs)
- Changes in free energy & types of energy/matter organisms exchange → predict if a reaction will take place
- Important to know

1. Energy is not created nor destroyed 2. Disorder (entropy) is always increasing in the universe

Describe enthalpy of formation and Hess’ Law
- Enthalpy of formation: how much energy is required to form a compound in its elemental form
  - If energy must be added, delta H is positive {endothermic}
  - If energy is released, delta H is negative {exothermic}
- Hess’s law of constant heat summation - total enthalpy change for the entire reaction is the sum of each individual change
Describe the role of ATP
- Energy currency of the cell: carrier and storage unit of free energy
- High ATP → high energy
  - First phosphate bond of ATP usually broken to fuel endergonic reactions (positive delta G)
- ATP hydrolysis liberates free energy
1. Describe the roles of oxidation and reduction in metabolism
- Oxidative reactions will tend to release energy
- Reductive reactions will tend to require an input of energy
- Converting ethanol to acetylaldehyde involves oxidation reaction
1. Describe the role of electron carriers
- NAD+ and FAD = coenzymes specialized for carrying electrons
- Electron carriers absorb electrons →ring arrangement
  - NAD+ (oxidized form) → NADH (reduced form)
  - FAD (oxidized form) → FADH2 (reduced form)

==B10 - TCA & Electron Transport Chain - Panavelli==

Describe the CAC and where electrons and carbons go
- Electrons ??? electron carriers ??
- Carbons
  - Pyruvate (3 C) → acetyl CoA (2C) + 4C OAA → citrate (6C) → isocitrate (6C) → alpha-ketoglutarate (5C) → succinyl coA (4C) → succinate (4C) → fumarate (4C) → malate (4C) → OAA (4C)
Describe how electrochemical gradients are produced
- ETC: H+ pumped through complex I, III, and IV; complex II receives electrons from FADH2 → the passage of electrons results in the formation of a proton gradient
Explain how ATP is produced during chemiosmosis
- Chemiosmotic theory:
  - As electrons pass through the ETC, protons are pumped into the inter-membrane space → proton motive force created
  - Protons move back across the membrane via ATP synthase (ATP formation)
- Chemiosmotic coupling: how ox phos links ETC and ATP synthesis
Describe the theoretical energy yield for cellular respiration
- 30-32 ATP (glycolysis, pyruvate oxidation, Kreb’s and oxidative phosphorylation)
Identify entry points of fats and proteins in cellular respiration
- Proteins → amino acids (different processes) → acetyl co A
- Fats → fatty acids → acetyl CoA via Beta oxidation
Describe key intermediates, key regulators, and negative feedback mechanism of cellular respiration
- Pyruvate = key intermediate
  - via ALT w/ B6→ alanine (cytosol)
  - Cahill cycle: allows for recycling of hepatic glucose from skeletal muscle alanine via ALT & for detoxification of NH4+ from proteolysis via the hepatic urea cycle
  - --| glycolysis by inhibiting PK & → + gluconeogenesis
  - Pyruvate → alanine → glucose (in the liver)
  - via pyruvate carboxylase + biotin (B7) + bicarb → OAA (mitochondria)
  - PC = first enzyme of gluconeogenesis
  - Activated by acetyl CoA
  - via PDH (E1,2,3 + 5 cofactors) → acetyl CoA (mitochondria)
  - via LDH + niacin (B3) NADH + H+ → lactate (cytosol)
  - Cori cycle: anaerobic conditions
  - Pyruvate + NADH + B3 → lactate → glucose (liver)
  - Key intermediates of TCA
  - Citrate: allosteric effector
  - alpha-ketoglutarate: nitrogen metabolism
  - succinyl CoA: heme synthesis (vampires succ blood)
  - succinate: odd chain fatty acid synthesis
  - fumarate: nucleotide metabolism (running on fumes)
  - OAA: gluconeogenesis
    - Glyoxylate cycle: anabolic pathway similar to TCA in prokaryotes/fungi
    - citrate, isocitrate, succinate, fumarate, malate, OAA
      - IC OAA SFMate (I C Odd SF Mate)
    - Amino acid metabolism: (ScOAK)
      - Alpha ketoglutarate
      - Succinyl CoA
      - OAA
    - Shuttle system: Citrate & malate (Corvette & Maserati)
  - Negative feedback of TCA
    - ATP and NADH inhibit isocitrate DH & alpha ketoglutarate DH (succinyl CoA also inhibits A-KG-DH)
    - ATP also inhibits glycolysis & pyruvate oxidation

%%B11. Glycolysis and Pyruvate Metabolism%%

Describe the process of glycolysis
- Occurs in cytoplasm, glucose → 2x pyruvate + 2 ATP + 2 NADH
- Possible when O2 is low
- Has energy consuming and energy producing phases
Describe Phase 1 of glycolysis → energy consuming
- ATP investment
  - \
  1. First priming reaction, uses up ATP (glucose → G6P via HK)
  - \
  1. First isomerization (G6P → F6P via PHI)
  - \
  1. Second priming reaction, uses ATP (F6P → F16P via PFK-1)
  - \
  1. Cleavage of 6 C sugar → 2 x 3 C sugar phosphates (F16P → DHAP and G3P via aldolase)
  - \
  1. Second isomerization (DHAP → G3P via TPI)
Describe Phase 2 of glycolysis
- 6.) G3P → 1,3 BPG via G3P DH * no ATP, oxidation reaction!
- 7.) 1,3 BPG → 3 PG via PK *__substrate level phosphorylation__
- 8.) 3 PG → 2 PG via PGM (important intermediate is 2, 3 BPG which binds to hgb and favors O2 release)
- 9.) 2 PG → PEP via enolase
- 10.) PEP → pyruvate via PK *makes ATP
Describe enzymes that are regulated in glycolysis

enzyme not fully active, large negative delta G
- Hexokinase
  - Activated by: glucose
  - Inhibited by: G6P (muscle), negative feedback
- PFK-1: $**RDS;**$ 2 binding sites for ATP (lots of ATP bind allosteric site)
  - Activated by: F26BP (liver; strong)
    - increased insulin → activates PFK-2 → F26BP → + PFK-1
  - Inhibited by ATP, low pH (m), citrate (L)
    - increased glucagon --| PFK-2
    - fatty acid synthesis → ATP & citrate --| PFK-1
- Pyruvate kinase: basically irreversible, generates ATP
  - Activated by: F16BP
  - Inhibited by: ATP, alanine, acetyl coA
1. Describe pyruvate metabolism
2. Explain how glycolysis can operate under anaerobic conditions
3. Describe the reason of pyruvate dehydrogenase and its regulation
4. Explain how inhibitors of pyruvate metabolism lead to lactic acidosis

^^B12. Gluconeogenesis and glycogen metabolism - Benmerzouga^^

Discuss gluconeogenesis and its importance in glucose homeostasis
Compare between glycolysis and gluconeogenesis including hormonal regulation of the processes
Describe the metabolism of fructose and galactose
Apply your knowledge of metabolic pathways to clinical scenarios: classical galactosemia, hereditary fructose intolerance, peripheral insulin resistance, etc
Describe the key steps in glycogen synthesis and glycogen degradation
Recognize the two key enzymes involved in glycogen synthesis and the two main enzymes in glycogen degradation
Describe the regulation of glycogen metabolism by insulin, epinephrine, glucagon, glucocorticoids, and growth hormones
Apply the concepts of glycogen metabolism to clinical scenarios