Lehninger Chapter 1
The foundations of biochemistry
Overview of cellular, physical, and genetic background to biochemistry
Biochemistry asks how properties of living organisms arise from biomolecules,
showing that these molecules act solely by the physical and chemical laws of
nature.
• Six distinguishing features of living organisms:
- High degree of chemical complexity and microscopic organization
- Systems for extracting, transforming and using energy from the
environment
- Defined functions for each of an organism’s components and regulated
interactions among them (both macroscopic and microscopic)
- Mechanisms for sensing and responding to alterations in their
surroundings
- Capacity for precise self-replication and self-assembly
- Capacity to change over time by gradual evolution
1.1 Cellular foundations
Plasma membrane: separates the cell contents from the surroundings.
Thin hydrophobic semi-permeable barrier consisting of proteins and
phospholipids. Inorganic ions and charged/polar molecules cannot freely
pass through. Proteins on the surface can allow passage (transport),
transduce signals (receptors) and carry out reactions (enzymes).
Cytoplasm: Internal volume of cell
Composed of concentrated aqueous solution (Cytosol) and suspended
particles. Contains RNA, enzymes, small organic molecules (metabolites),
coenzymes, large supramolecular structures (ribosomes for protein
synthesis, proteasome for protein degradation etc.) and organelles
Nucleus/nucleoid: Organelle that stores the genome (DNA)
Cells of eukaryotes contain a nucleus: a nuclear envelope with double
membrane. Prokaryotes contain a nucleoid that is not separated from the
cytoplasma
Cells of animals and plants: 5-100 µm. Microorganisms: 1-2 µm. Size is limited by
diffusion (metabolites and O2).
- Three distinct domains of life
- Bacteria
- Archaea
- Eukaryotes
Further distinctions can be made in habitats:
- Aerobic organisms need oxygen supply
- Anaerobic organisms do not need oxygen.
And in energy source:
- Phototrophs: trap and use sunlight as energy source
- Chemotrophs: oxidize chemical fuel (
o Lithotrophs can oxidize inorganic fuels
o Organotrophs oxidize organic compounds in their surroundings
, Or in nutrient source
- Autotrophs: use CO2 as nutrient
- Heterotrophs: use organic nutrients
E.coli is most studied bacterium. Bacteria have a thin layer of polymer
(peptidoglycan) on their surface, which constitutes the cell envelope together
with the plasma membrane. DNA in nucleoid is a circular molecule and the
cytoplasm contains smaller circular DNA molecules (Plasmids).
Eukaryotes contain organelles with membranes, such as the nucleus,
mitochondria, endoplasmatic reticulum (ER), Golgi complexes, peroxisomes, and
lysosomes. Plants also contain vacuoles and chloroplasts. Can be separated by
centrifugation. The cytoplasm is organized by the constantly changing
cytoskeleton. Three types are present: Actin filaments, microtubules and
intermediate filaments). Small vesicles of the endomembrane system move
along these fibers to deliver specific metabolites, also outside the cell
(exocytosis) or to take them up (Endocytosis)
Cells contain supramolecular structures (chromosomes, proteins, membranes,
cell walls) build up from small monomers (nucleotides, amino acids,
phospholipids, sugars). Supramolecular complexes are held together by
The foundations of biochemistry
Overview of cellular, physical, and genetic background to biochemistry
Biochemistry asks how properties of living organisms arise from biomolecules,
showing that these molecules act solely by the physical and chemical laws of
nature.
• Six distinguishing features of living organisms:
- High degree of chemical complexity and microscopic organization
- Systems for extracting, transforming and using energy from the
environment
- Defined functions for each of an organism’s components and regulated
interactions among them (both macroscopic and microscopic)
- Mechanisms for sensing and responding to alterations in their
surroundings
- Capacity for precise self-replication and self-assembly
- Capacity to change over time by gradual evolution
1.1 Cellular foundations
Plasma membrane: separates the cell contents from the surroundings.
Thin hydrophobic semi-permeable barrier consisting of proteins and
phospholipids. Inorganic ions and charged/polar molecules cannot freely
pass through. Proteins on the surface can allow passage (transport),
transduce signals (receptors) and carry out reactions (enzymes).
Cytoplasm: Internal volume of cell
Composed of concentrated aqueous solution (Cytosol) and suspended
particles. Contains RNA, enzymes, small organic molecules (metabolites),
coenzymes, large supramolecular structures (ribosomes for protein
synthesis, proteasome for protein degradation etc.) and organelles
Nucleus/nucleoid: Organelle that stores the genome (DNA)
Cells of eukaryotes contain a nucleus: a nuclear envelope with double
membrane. Prokaryotes contain a nucleoid that is not separated from the
cytoplasma
Cells of animals and plants: 5-100 µm. Microorganisms: 1-2 µm. Size is limited by
diffusion (metabolites and O2).
- Three distinct domains of life
- Bacteria
- Archaea
- Eukaryotes
Further distinctions can be made in habitats:
- Aerobic organisms need oxygen supply
- Anaerobic organisms do not need oxygen.
And in energy source:
- Phototrophs: trap and use sunlight as energy source
- Chemotrophs: oxidize chemical fuel (
o Lithotrophs can oxidize inorganic fuels
o Organotrophs oxidize organic compounds in their surroundings
, Or in nutrient source
- Autotrophs: use CO2 as nutrient
- Heterotrophs: use organic nutrients
E.coli is most studied bacterium. Bacteria have a thin layer of polymer
(peptidoglycan) on their surface, which constitutes the cell envelope together
with the plasma membrane. DNA in nucleoid is a circular molecule and the
cytoplasm contains smaller circular DNA molecules (Plasmids).
Eukaryotes contain organelles with membranes, such as the nucleus,
mitochondria, endoplasmatic reticulum (ER), Golgi complexes, peroxisomes, and
lysosomes. Plants also contain vacuoles and chloroplasts. Can be separated by
centrifugation. The cytoplasm is organized by the constantly changing
cytoskeleton. Three types are present: Actin filaments, microtubules and
intermediate filaments). Small vesicles of the endomembrane system move
along these fibers to deliver specific metabolites, also outside the cell
(exocytosis) or to take them up (Endocytosis)
Cells contain supramolecular structures (chromosomes, proteins, membranes,
cell walls) build up from small monomers (nucleotides, amino acids,
phospholipids, sugars). Supramolecular complexes are held together by
