Biochemistry and Cell Structure Review

Vocabulary flashcards covering cellular structure, organelle functions, metabolic classifications, stereochemistry, and reaction thermodynamics.

Universal Cell Components

Structures shared by all cells, consisting of a plasma membrane, cytoplasm, ribosomes, and a DNA-containing region (nucleoid or nucleus).

Three Domains of Life

The three evolutionary lineages descended from a last universal common ancestor: Bacteria, Archaea, and Eukarya.

Six Kingdoms of Life

Taxonomic classification comprising Bacteria and Archaea (unicellular prokaryotes), Protista (unicellular eukaryotes), Fungi (unicellular or multicellular eukaryotes), and Plantae and Animalia (multicellular eukaryotes).

Peptidoglycan

The structural material composing the bacterial cell wall that provides mechanical support.

Bacterial Cell Membrane

A membrane composed of lipid and protein that functions as a permeability barrier.

Bacterial Nucleoid

A non-membrane-bound region in bacterial cells containing DNA and protein to store genetic information.

Bacterial Pili and Flagella

Protein structures on bacterial cells responsible for adhesion and conjugation (pili) or motility (flagella).

Nucleolus

A structure within the eukaryotic nucleus responsible for synthesizing rRNA.

Mitochondrion

A eukaryotic organelle dedicated to ATP production.

Chloroplast

A eukaryotic organelle in plant cells responsible for photosynthesis.

Rough Endoplasmic Reticulum

A eukaryotic organelle responsible for protein synthesis.

Smooth Endoplasmic Reticulum

A eukaryotic organelle involved in lipid synthesis and drug metabolism.

Golgi Apparatus

A eukaryotic organelle that functions in protein processing and sorting.

Lysosome

A eukaryotic organelle in animal cells that degrades debris.

Peroxisome

A eukaryotic organelle that oxidizes fatty acids.

Plant Vacuole

A eukaryotic organelle in plants that degrades and recycles macromolecules, stores metabolites, and maintains cell rigidity.

Chemoautotroph

An organism that obtains energy from chemical sources and carbon from $CO_2$ (e.g., S-, Fe-, and N-oxidizing bacteria).

Chemoheterotroph

An organism that derives energy from chemical sources and carbon from organic compounds (e.g., animals, most fungi, and bacteria).

Photoautotroph

An organism that uses light for energy and $CO_2$ as a carbon source (e.g., plants, algae, cyanobacteria).

Photoheterotroph

An organism that uses light for energy and organic compounds as a carbon source (e.g., green/purple nonsulfur bacteria).

Bulk Elements

Essential chemical elements required by organisms in large amounts: C, H, O, N, P, S.

Trace Metal Ions

Essential metal ions required in smaller amounts: $K^+$, $Na^+$, $Ca^{2+}$, $Mg^{2+}$, $Zn^{2+}$, $Fe^{2+}$.

Cellular Structural Hierarchy

The organizational levels of biomolecules: monomers $\rightarrow$ macromolecules $\rightarrow$ supramolecular complexes $\rightarrow$ organelles/cell.

E. coli Molecular Composition

The overall chemical breakdown of E. coli: $70\%$ water, $15\%$ protein, $6\%$ RNA, $3\%$ polysaccharides, $2\%$ lipids, and $1\%$ DNA.

Tetrahedral Carbon

A carbon atom bonded to 4 single substituents forming bond angles of $\sim 109.5^\circ$.

Geometric Isomers

Isomers (cis/trans) defined by a fixed arrangement around a double bond, resulting in different physical properties and biological activities.

Enantiomers

Chiral stereoisomers that are non-superimposable mirror images; they have identical physical properties (except in polarized light) but often different biological activities.

Diastereomers

Stereoisomers that are not mirror images of one another, featuring distinct physical properties and biological activities.

Chiral Center

A carbon atom bound to 4 different substituents, yielding 2 possible stereoisomers whose interconversion requires breaking a covalent bond.

Stereospecific Binding

The spatial property where biological macromolecules possess 3D binding pockets accommodating only one specific stereoisomer.

Conformations

Molecular shapes formed by rotation around single bonds without breaking any covalent bonds (e.g., $\sim 12\,kJ/mol$ rotation barrier in ethane).

Energy Transductions

Cellular processes in which light or nutrient energy is converted into chemical work (synthesis, mechanical work, gradients, signaling) with heat released.

Adenosine Triphosphate (ATP)

The primary energy currency of the cell, providing energy through reactions such as $ATP \rightarrow ADP + P_i$ or $ATP \rightarrow AMP + PP_i$.

Four Ways to Acceleration Reaction Rates

Methods to speed up chemical reactions in cells: higher temperature, higher reactant concentration, coupling to a favorable reaction, or catalysis (lowering activation energy).