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Chapter 1: Outline. The Living World Bacteria, Archaea, Eukarya, (Viruses) Biomolecules Functional Groups Major Classes of Biomolecules Biochemical Processes (We are here.) Reactions, Energy, Metabolism, Order Genetic Information Processing. 1.3 Biochemical Processes.

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chapter 1 outline
Chapter 1: Outline
  • The Living World
    • Bacteria, Archaea, Eukarya, (Viruses)
  • Biomolecules
    • Functional Groups
    • Major Classes of Biomolecules
  • Biochemical Processes (We are here.)
    • Reactions, Energy, Metabolism, Order
  • Genetic Information Processing
1 3 biochemical processes
1.3 Biochemical Processes
  • Metabolism is the sum of all biochemical reactions.
  • Functions of metabolism are:
  • Synthesis of biomolecules.
  • 2. Transport of ions and molecules across cell membranes.
  • 3. Production of force and movement.
  • 4. Removal of metabolic waste and other toxic substances.
bio rxns by mechanism 1
Bio Rxns: By Mechanism-1
  • Nucleophilic Substitution-acyl

Sulfur nucleophile attacks C=O


Bio Rxns: By Mechanism-1

Nucleophilic Substitution-alkyl

  • Sulfur nucleohile attacks alkyl C
bio rxns by mechanism 2
Bio Rxns: By Mechanism-2

Addition occurs at C=C

  • Addition: two molecules combine to give one.
  • One molecule usually multiple bonded.
bio rxns by mechanism 3
Bio Rxns: By Mechanism-3

Water is lost to form


  • Elimination- a molecule loses atoms usually in the form of a small molecule like water.
bio rxns by mechanism 4
Bio Rxns: By Mechanism-4
  • Isomerization: molecule rearranges atoms

3-phosphoglycerate to 2-phosphoglycerate

bio rxns by mechanism 5
Bio Rxns: By Mechanism-5
  • Hydrolysis: water cleaves (splits) a covalent bond and inserts itself.

Hydrolysis of a fat

Hydrolysis is a variant of acyl substitution.

bio rxns by redox nature
Bio Rxns: By Redox Nature
  • Redox reactions involve the transfer of electrons.
  • Oxidation: a loss of electrons
  • Reduction: a gain of electrons
  • Oxidizing agent: the electron acceptor
  • Reducing agent: the electron donor
  • Note: Reactions may fall into both classification categories, mechanism and redox.
bio rxns by redox nature 2
Bio Rxns: By Redox Nature-2
  • In biochemistry redox reactions are usually recognized by the following changes:
  • Oxidation occurs when a molecule loses two hydrogens and/or gains an oxygen.
  • Reduction occurs when a molecule gains two hydrogens and/or loses an oxygen.
bio rxns by redox nature 3
Bio Rxns: By Redox Nature-3


Lactate is oxidized.

NAD+ is oxidizing agent.

bio rxns by redox nature 4
Bio Rxns: By Redox Nature-4


The double bond

is reduced.

NADPH is the

reducing agent.

  • Classify the reactions: by mechanism and by redox character.

Mech: addition

Not redox

(add 2H and 1 O)

Mech: elimination


(remove 2H)

  • Energy is the capacity to do work.
  • Cells generate most of their energy from redox reactions.
  • When electrons are transferred to an electron deficient molecule, energy is lost. Several redox reactions provide enough energy for ATP synthesis.
  • The ultimate source of energy used by most organisms on earth is the sun.
  • Metabolism is the sum of all the enzyme- catalyzed reactions in a living organism.
  • In anabolic (biosynthetic) pathways large complex molecules are synthesized from smaller molecules.
  • In catabolic pathways large complex molecules are degraded into simpler products. A portion of the energy produced drive anabolic reactions.
biological order
Biological Order
  • Processes can be classified in the following categories.
  • Synthesis of biomolecules
    • Many reactions are integrated into carefully regulated pathways. Energy is supplied either directly or indirectly by breaking phospho-anhydride bonds of ATP.
biological order 2
Biological Order-2
  • 2. Transport across membranes.
    • Cell membranes regulate the passage of ions and molecules from one compartment to another.
    • Much of this is accomplished by membrane bound proteins.
  • 3. Cell movement
    • Examples include cell division, organelle movement and even movement of enzymes along a DNA strand.
biological order 3
Biological Order-3
  • 4. Waste removal
    • Excess CO2, H2O, and NH3 must be removed.CO2 is exhaled, H2O is excreted by the kidneys, and NH3 is converted to urea.
    • Hydrophobic molecules such as the steroid hormones are converted to water soluble derivatives.
1 4 genetic information
1.4 Genetic Information
  • “Central dogma” of molecular biology
  • The chemical information in a gene (DNA) directs the assembly of amino acids into polypeptides (proteins).
information flow
Information Flow

Transcription: RNA is made on a DNA


Translation: Protein is synthesized

from AAs and the three RNAs.

  • DNA RNA Protein
  • RNA polymerases and proteins copy the coded instructions in genes into RNA molecules.
  • The nucleotide base code of messenger RNA binds to ribosomes where it is decoded into the amino acids sequence of proteins.