The distinction between prokaryotes and eukaryotes is considered to be the most important distinction among groups of organisms. Eukaryotic cells contain membrane-bound organelles, such as the nucleus, while prokaryotic cells do not. Differences in cellular structure of prokaryotes and eukaryotes include the presence of mitochondria and chloroplasts, the cell wall, and the structure of chromosomal DNA.
Prokaryotes were the only form of life on Earth for millions of years until more complicated eukaryotic cells came into being through the process of evolution.

Comparison chart

 
Eukaryotic Cell versus Prokaryotic Cell comparison chart
Eukaryotic CellProkaryotic Cell
NucleusPresentAbsent
Number of chromosomesMore than oneOne--but not true chromosome: Plasmids
Cell TypeUsually multicellularUsually unicellular (some cyanobacteria may be multicellular)
True Membrane bound NucleusPresentAbsent
ExampleAnimals and PlantsBacteria and Archaea
Genetic RecombinationMeiosis and fusion of gametesPartial, undirectional transfers DNA
Lysosomes and peroxisomesPresentAbsent
MicrotubulesPresentAbsent or rare
Endoplasmic reticulumPresentAbsent
MitochondriaPresentAbsent
CytoskeletonPresentMay be absent
DNA wrapping on proteins.Eukaryotes wrap their DNA around proteins called histones.Multiple proteins act together to fold and condense prokaryotic DNA. Folded DNA is then organized into a variety of conformations that are supercoiled and wound around tetramers of the HU protein.
Ribosomeslargersmaller
VesiclesPresentPresent
Golgi apparatusPresentAbsent
ChloroplastsPresent (in plants)Absent; chlorophyll scattered in the cytoplasm
FlagellaMicroscopic in size; membrane bound; usually arranged as nine doublets surrounding two singletsSubmicroscopic in size, composed of only one fiber
Permeability of Nuclear MembraneSelectivenot present
Plasma membrane with steroidYesUsually no
Cell wallOnly in plant cells and fungi (chemically simpler)Usually chemically complexed
VacuolesPresentPresent
Cell size10-100um1-10um

Source:https://www.diffen.com/difference/Eukaryotic_Cell_vs_Prokaryotic_Cell