CHEM 4500 Biochemistry — Vocabulary Flashcards (Video Notes)

Most elements originated in stellar life cycles; heavy elements formed in stars beyond hydrogen and helium.
Life is primarily associated with the elements carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur: $C, H, O, N, P, S$ ; many other elements also play critical roles.
A schematic periodic-table-like figure illustrates tiered abundance and distribution of elements important to biology.

Biochemistry concerns the transmission of genetic information across generations and the molecular processes underlying evolution.
The primordial question: how did life begin?
Common hypothesis: a complex mixture of simple compounds on early Earth (the “primordial soup”) randomly reacted over hundreds of millions of years, yielding self-replicating molecular systems (RNA is a leading candidate).
Experiments (e.g., Miller-Urey) show feasibility of biomolecule formation under prebiotic-like conditions.
Evolution of such systems into living organisms remains unresolved; RNA is suspected to have dual roles as information carrier and catalyst.
Early life was anaerobic (little or no O₂ tolerance).

Evolution of photosynthetic organisms enabled direct use of sunlight as energy.
Oxygen (O₂) is a by-product of photosynthesis; its accumulation was initially toxic to many anaerobic organisms.
As O₂ accumulated, aerobes (organisms that use oxygen in metabolism) came to dominate.

Primitive, unicellular organisms eventually formed symbiotic relationships with other microorganisms.
This endosymbiosis led to the formation of organelles and the rise of eukaryotes (which can be unicellular or multicellular).

Biomolecules span a wide size range: from very small (<$10^2$ Da) to enormous (> $10^9$ Da).
Most biomolecules are small metabolites, but many biopolymers and lipid assemblies exist.
Principal biopolymers to study: carbohydrates, nucleic acids, and proteins.

Polysaccharides: monomeric units are saccharides or monosaccharides; a residue is a monomer unit.
Polysaccharides can be homopolymers (identical monomers) or heteropolymers (two or more monomers).
Nucleic acids: monomeric units are nucleotides; a nucleotide comprises a sugar, phosphate, and a nitrogenous base.
DNA and RNA are polymers of nucleotides; a small example residue is deoxyadenosine monophosphate (dAMP).
A partial depiction shows a DNA segment with one dAMP residue within a polynucleotide chain.
Proteins: monomeric units are amino acids (20 standard amino acids); proteins exhibit vast structural diversity and catalysis (enzymes).

Roles: energy storage, membranes, signaling, and other functions.
Triacylglycerols (TAGs): esters of glycerol and fatty acids; major form of energy storage.
Phospholipids: similar to TAGs but with phosphate-containing head groups; major component of biological membranes; amphipathic molecules with both hydrophobic and hydrophilic regions.
Phospholipids spontaneously form membrane bilayers due to their amphipathic nature and molecular geometry.
Sterols (steroids): important lipid class found in membranes; serve as membrane components and as precursors to other biomolecules.

Life is fundamentally cellular.
Three major cellular domains: eubacteria (bacteria), archaea, and eukarya (eukaryotes).
Nucleic acid sequence data underpin the classification of life into a tree of life.
The tree includes major branches such as bacteria, archaea, and eukaryotes, with further subdivisions (e.g., fungi, animals, plants, etc.).
Eukaryotic cells are generally larger than prokaryotic cells and contain membrane-bound organelles.
Analogy: a cell can be viewed as a factory, with organelles performing specialized functions.

Typical features: pili, capsule, cell wall, plasma membrane, cytoplasm; nucleoid (DNA-containing region) not enclosed by a membrane; ribosomes; flagella.

Features include: nuclear envelope with a nucleus; rough and smooth endoplasmic reticulum; Golgi complex; mitochondria; lysosomes; peroxisomes; cytoskeleton (centrioles, microtubules, microfilaments);
A nucleus with chromatin and nucleolus; basal bodies associated with flagella or cilia.

Three major themes:
- Metabolism: individual reactions, pathways, and their functions.
- Information: instructions encoded in molecules that assemble and drive metabolic pathways.
- Regulation: changing rates of pathways and processes to achieve coordinated function.
Bioinformatics uses computational methods and information science to analyze biological systems.
Genomics: analysis of entire genomes, DNA sequencing, gene expression patterns, etc.
Proteomics: analysis of the total pool of proteins in a cell, their relative abundances, and modifications.
Metabolomics: analysis of the total pool of metabolites (reactants and products) in a cell.

The chemical basis of life connects to topics like kinetics, equilibria, and acid-base chemistry introduced in General Chemistry, which biochemists routinely apply.
The transition from simple molecules to complex biopolymers underpins understanding of metabolism and regulation.
The progression from prokaryotic to eukaryotic organization explains compartmentalization and specialized chemistry within cells.
The origin-of-life scenarios connect chemistry, catalysis, information transfer, and evolutionary theory, highlighting the interdisciplinary nature of biochemistry.