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Metabolism and Biochemical Pathways, Lecture notes of Biochemistry

An overview of the fundamental concepts of metabolism, including the processes of catabolism and anabolism, as well as the common catabolic pathway involving the citric acid cycle and oxidative phosphorylation. It delves into the key agents and compounds involved in energy storage, electron transfer, and acetyl group transport. The document also explores the three stages of catabolism, focusing on the breakdown and conversion of dietary macromolecules, such as carbohydrates, amino acids, and fatty acids, into a form that can be completely oxidized. Particular emphasis is placed on the glycolysis pathway, its key products, and the rate-limiting steps that control the speed of this process. This comprehensive coverage of metabolic processes and biochemical pathways provides valuable insights for students and researchers in the fields of biology, biochemistry, and related disciplines.

Typology: Lecture notes

2022/2023

Available from 08/26/2024

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JUMALON, JOHN DEXTER A.
Metabolism – sum total of all the
chemical reactions involved in
maintaining the dynamic state of the cell
Metabolic Reactions:
Catabolism – molecules are broken down
to provide the energy need by cells.
Anabolism – synthesize the compounds
needed by cells
Biochemical Pathway
- series of consecutive biochemical
reactions
• Carbohydrates
• Lipids
• Proteins
Common Catabolic Pathway
- convert the chemical energy in food
molecules of ATP
Acetyl – CoA Citric acid
cycle Oxidative phosphorylation
ETC (Electron Transport Chain)
Principal Compounds of the Common
Catabolic Pathway
Agents for Storage of Energy and
Transfer of Phosphate Groups
Adenosine Monophosphate (AMP)
• Adenosine Diphosphate (ADP)
• Adenosine Triphosphate (ATP)
ATP
- contains 5-carbon sugar, three
phosphate groups and an adenine base
- energy is released when the bond
between the 2nd phosphate group and the
3rd phosphate group is broken
Agents for Transfer of Electrons in
Biological Oxidation-Reduction
Reactions
Coenzymes
NAD+ - nicotinamide
adenine dinucleotide (oxidized
form)
FAD+ - flavin adenine
dinucleotide (oxidized form)
NADH – nicotinamide
adenine dinucleotide (reduced
form)
FADH – flavin adenine
dinucleotide (reduced form)
Agents for Transfer of Acetyl Group
• Coenzyme A
• Final principal compound
• Acetyl (CH3CO-) – transporting
molecule
Acetyl group – B-mercaptoethylamine
Pantothenic acid – 3’ – 5’ - ADP
CATABOLISM
Stage I: Hydrolysis of Dietary
Macromolecules into Small Subunits
- to degrade large food molecules into
their component subunits
• simple sugars, amino acids, fatty acids,
and glycerol
• digestive process
(DI NAKO MAHANAP SA GOOGLE ANG
PIC DIRI)
Stage II: Conversion of Monomers into a
form that can be completely oxidized
Sugars
- usually enter the glycolysis pathway in
the form of glucose or fructose
- eventually converted to acetyl-CoA
which can be completely oxidized in the
citric acid cycle
Amino Groups
- are removed from amino acids
- remaining carbon skeletons enter the
catabolic processes at many steps of the
citric acid cycle
Fatty Acids
- are converted to acetyl-CoA and enter
the citric acid cycle in that form
Glycerol
- produced by the hydrolysis of fats
- converted to
glyceraldehyde-3-phosphate (one of the
intermediate of glycolysis)
- enters energy metabolism
Monosaccharides, amino acids, and
glycerol are assimilated into the
pathways of energy metabolism
• Glycolysis
• Citric Acid Cycle (Tricarboxylic Acid Cycle
or Kreb’s Cycle)
Stage III: Complete Oxidation of
Nutrients and Production of ATP
Acetyl CoA
- carries 2-carbon remnants of the
nutrients, acetyl groups, to the citric acid
cycle
- electrons and hydrogen atoms are
harvested during the complete oxidation
of acetyl group to CO2
- used in the process of oxidative
phosphorylation to produce ATP
GLYCOLYSIS
- known as Embden-Meyerhof Pathway
- a pathway for carbohydrates catabolism
that begins with the substrate D-glucose
• Anaerobic process
• 10 steps
3 MAJOR PRODUCTS
• ATP – chemical energy
• NADH – chemical energy
• 2 three-carbon pyruvate
Key points:
• occurs in cytosol
• starts with glucose; ends with 2
pyruvates
• works in aerobic or anaerobic condition
• 2 ATP consumed/glucose
• 4 ATP produced/glucose
• 2 NADH & H+produced/glucose
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JUMALON, JOHN DEXTER A.

Metabolism – sum total of all the chemical reactions involved in maintaining the dynamic state of the cell Metabolic Reactions: Catabolism – molecules are broken down to provide the energy need by cells. Anabolism – synthesize the compounds needed by cells Biochemical Pathway

  • series of consecutive biochemical reactions
  • Carbohydrates
  • Lipids
  • Proteins Common Catabolic Pathway
  • convert the chemical energy in food molecules of ATP Acetyl – CoA Citric acid cycle Oxidative phosphorylation ETC (Electron Transport Chain) Principal Compounds of the Common Catabolic Pathway Agents for Storage of Energy and Transfer of Phosphate Groups - Adenosine Monophosphate (AMP)
    • Adenosine Diphosphate (ADP)
    • Adenosine Triphosphate (ATP) ATP
    • contains 5-carbon sugar, three phosphate groups and an adenine base
    • energy is released when the bond between the 2nd^ phosphate group and the 3 rd^ phosphate group is broken Agents for Transfer of Electrons in Biological Oxidation-Reduction Reactions - Coenzymes ● NAD+^ - nicotinamide adenine dinucleotide (oxidized form) ● FAD+^ - flavin adenine dinucleotide (oxidized form) ● NADH – nicotinamide adenine dinucleotide (reduced form) ● FADH – flavin adenine dinucleotide (reduced form) Agents for Transfer of Acetyl Group
    • Coenzyme A
    • Final principal compound
    • Acetyl (CH3CO-) – transporting molecule Acetyl group – B-mercaptoethylamine Pantothenic acid – 3’ – 5’ - ADP

CATABOLISM

Stage I: Hydrolysis of Dietary Macromolecules into Small Subunits

  • to degrade large food molecules into their component subunits
  • simple sugars, amino acids, fatty acids, and glycerol
  • digestive process (DI NAKO MAHANAP SA GOOGLE ANG PIC DIRI) Stage II: Conversion of Monomers into a form that can be completely oxidized Sugars
  • usually enter the glycolysis pathway in the form of glucose or fructose
  • eventually converted to acetyl-CoA which can be completely oxidized in the citric acid cycle Amino Groups
  • are removed from amino acids
  • remaining carbon skeletons enter the catabolic processes at many steps of the citric acid cycle Fatty Acids
  • are converted to acetyl-CoA and enter the citric acid cycle in that form Glycerol
  • produced by the hydrolysis of fats
  • converted to glyceraldehyde-3-phosphate (one of the intermediate of glycolysis)
  • enters energy metabolism Monosaccharides, amino acids, and glycerol are assimilated into the pathways of energy metabolism - Glycolysis - Citric Acid Cycle (Tricarboxylic Acid Cycle or Kreb’s Cycle) Stage III: Complete Oxidation of Nutrients and Production of ATP Acetyl CoA
    • carries 2-carbon remnants of the nutrients, acetyl groups, to the citric acid cycle
    • electrons and hydrogen atoms are harvested during the complete oxidation of acetyl group to CO
    • used in the process of oxidative phosphorylation to produce ATP GLYCOLYSIS
    • known as Embden-Meyerhof Pathway
    • a pathway for carbohydrates catabolism that begins with the substrate D-glucose
    • Anaerobic process
    • 10 steps 3 MAJOR PRODUCTS
    • ATP – chemical energy
    • NADH – chemical energy
    • 2 three-carbon pyruvate Key points:
    • occurs in cytosol
    • starts with glucose; ends with 2 pyruvates
    • works in aerobic or anaerobic condition
    • 2 ATP consumed/glucose
    • 4 ATP produced/glucose
    • 2 NADH & H+^ produced/glucose

JUMALON, JOHN DEXTER A.

  • 2 H2O produced/glucose Rate-limiting steps – control speed of glycolysis it has ATP Regenerate ATP – substrate level PKD – pyruvate kinase deficiency
    • Anemia 1,3 – BPG 2,3 – BPG = RBC