Biochemistry_slides_S1-2

Chapter 1: Biochemistry and the Organization of Cells

What is Biochemistry?

• Biochemistry is the study of the structures, mechanisms, and chemical processes shared by all organisms.

• Key Questions in Biochemistry:

  • How is a biomolecule made in a cell?

  • How is it used in a cell?

  • How is it broken down in a cell?

• Provides the essential science foundation for understanding biological processes and diseases in humans, animals, and plants.

• Applications of Biochemistry:

  • Medicine

  • Veterinary medicine

  • Agriculture

  • Biotechnology

  • Various fields such as neurochemistry, bioorganic chemistry, molecular genetics, etc.

What do Biochemists Do?

• Food Science:

  • Analyze food composition, develop nutritious food sources, extract nutrients, extend shelf life.

• Agriculture:

  • Study herbicide/insecticide interactions, examine growth inhibition, assess toxicity.

• Pharmacology and Clinical Chemistry:

  • Investigate drug action mechanisms, engage in viral research, study organ function, assess health diagnostics.

Chapter Outline

• Basic themes of biochemistry.

• Chemical foundations.

• Origins of biology and classification of organisms.

• Discussion of prokaryotes vs. eukaryotes.

• Concepts of biochemical energetics.

Basic Themes in Biochemistry

• Living organisms utilize the same types of biomolecules and energy.

• Biochemistry is multidisciplinary, integrating biology and chemistry to explore life processes at a molecular level.

Origin of Life on Earth

• Suggests fundamental similarity among all cell types, derived from simple molecules (H2O, CH4, CO2, NH3, N2, H2).

• Simple molecules are theorized to have originated from atoms.

Levels of Structural Organization in the Human Body

• Hierarchy of Life:

  • Atoms (e.g., Oxygen, Hydrogen)

  • Molecules (e.g., Water)

  • Macromolecules (e.g., Proteins)

  • Organelles (e.g., Mitochondria)

  • Cells (e.g., Bone cells)

  • Tissues (e.g., Bone tissue)

  • Organs (e.g., Bones)

  • Organ systems

Biomolecules

• Early Earth Gases:

  • NH3, H2S, CO, CO2, CH4, N2, H2, H2O.

• Experiments show biomolecules like proteins and nucleic acids can form under abiotic conditions.

• Theories suggest reactions occurred in early oceans or clay surfaces.

Chemical Foundations of Biochemistry

• Study of organic compounds focusing on carbon and hydrogen derivatives essential to life.

• Reactions of biomolecules are explained using organic chemistry principles.

Abundance of Important Elements

• Lists abundance of elements in organisms vs. the universe relative to carbon, emphasizing essential elements:

  • Hydrogen, Carbon, Nitrogen, Oxygen, Sodium, Magnesium, Phosphorus, etc.

Functional Groups of Biological Importance

• Overview of key functional groups: Alkenes, alcohols, ethers, amines, and carboxylic acids.

• Examples showcasing their structures and importance in biochemical interactions.

Major Groups of Biochemicals

• Amino Acids:

  • Central carbon atom bonded to carboxyl, amino group, hydrogen, and R group.

• Proteins:

  • Structured in levels: Primary (amino acid sequence), Secondary (sub-structures), Tertiary (3D shape), Quaternary (protein complexes).

• Carbohydrates:

  • Composed of carbon, hydrogen, and oxygen (general formula: (CH2O)n); simplest form is monosaccharides (e.g., glucose).

• Nucleotides:

  • Building blocks of DNA/RNA; energy currency (ATP); composed of sugar, nitrogenous base, and phosphate groups.

• Lipids:

  • Hydrophobic molecules built from long hydrocarbon chains (e.g., palmitic acid).

Role of Functional Groups

• Functional groups are vital for the reactions of organic compounds.

• ATP (adenosine triphosphate) serves as energy currency with important esters and anhydrides.

Biomolecules and Their Formation

• Living cells have large macromolecules:

  • Proteins (from amino acids), nucleic acids (from nucleotides), polysaccharides (from monosaccharides), lipids (from glycerol and fatty acids).

• Polymers:

  • Formed through the bonding of smaller units.

• Key role in life processes for proteins and nucleic acids.

Molecules to Cells

• RNA's role in life and its capabilities for self-catalysis.

• RNA-world theory suggests original RNA encoded and catalyzed its own replication leading to DNA becoming primary genetic material.

Prokaryotes vs. Eukaryotes

• Prokaryotes are single-celled organisms without a nucleus (e.g., bacteria).

• Eukaryotes have defined nuclei and organelles (e.g., plants, animals).

• Differences in organelles mark the distinction between prokaryotic and eukaryotic cells with functions outlined for typical organelles.

Source of Energy in Life Processes

• Sun is the ultimate energy source for life, with photosynthetic organisms synthesizing carbohydrates and non-photosynthetic organisms using them for energy.

Thermodynamic Principles

• Thermodynamics studies energy transformations, with key principles outlining spontaneity based on changes in free energy (∆G).

• ∆G:

  • Negative: Reaction spontaneous (exergonic).

  • Positive: Nonspontaneous (endergonic).

  • Zero: System at equilibrium.

Laws of Thermodynamics

• First and second laws relate changes in free energy (∆G) to enthalpy (∆H) and entropy (∆S).

• Understanding the relationship between energy changes and biological processes is crucial.