Lysosomes are specialized vesicles that bud off of the Golgi apparatus and house digestive enzymes within the cell. Lysosomes have only one outer membrane, made of a phospholipid bilayer, similar to the plasma membrane surrounding the cell.

In contrast, the nucleus, mitochondria, and chloroplasts all have two outer membranes. Each of these is made of a lipid bilayer, for a total of four layers of phospholipids around these structures.

A cell’s cytoskeleton is made up of three types of filaments: microfilaments, intermediate filaments, and microtubules. Microfilaments are made up of actin, whereas microtubules are made up of tubulin. Flagella, cilia, and the mitotic spindle of the cell are made from microtubules. The only filament given that is not made up of tubulin is microfilament.

The question states that the lumen of the organelle contains a high concentration of hydrogen ions. Recall that a high concentration of hydrogen ions results in a low pH. Lysosomes are organelles that contain degradative, hydrolytic enzymes that break down the cell’s waste products. These enzymes need a low pH to be functional, therefore, the lumen of lysosomes has a low pH (around a pH of 5). Lysosomes are known for having a high concentration of hydrogen ions to facilitate this acidic environment.

The other organelle known for sequestering hydrogen ions is the mitochondria. In mitochondria, hydrogen ions are used to create the gradient in the intermembrane space that is used to make ATP.

Recall that the central dogma of molecular biology states that the information flow within a cell involves DNA replication, transcription, and translation. DNA replication involves the formation of two identical DNA molecules from a single molecule and transcription involves synthesis of mRNA from DNA. The DNA molecules can’t leave the nucleus, therefore, both of these processes occur in the nucleus

Translation involves the synthesis of proteins from mRNA molecules. The mRNA molecules exit the nucleus after transcription (through nuclear pores) and enter the cytosol. The ribosomes in the cytosol bind to mRNA and facilitate translation; therefore, translation occurs in the cytosol.

Eukaryotic cells are very resourceful in every way they function. When a cell part becomes worn out or non-functional, these part is broken down and recycled by the cell via lysosomal activation. This process is known as autophagy. The biological monomers produced from the catabolic process can then be used to build new polymers and macromolecules.

Exocytosis is the process by which contents from within the cell are expelled across the membrane. This generally occurs to assist cell signaling, such as the exocytosis of neurotransmitters. Positive selection is the process by which T-lymphocytes are presented by "self" antigens. If the T-cell reacts to the "self" antigen, it is destroyed to prevent autoimmune reactions.

Atoms are the smallest functional unit of matter and are used to construct complex molecules, such as proteins. A protein is composed of numerous smaller atoms.

Ribosomes are composed of ribosomal RNA (rRNA) and proteins, but are smaller than viruses. Viruses are composed of protein coats that house genetic information coded in nucleic acids.

Mitochondria are membrane-bound organelles within the cell. These structures are smaller than the nucleus, but larger than ribosomes. While viruses must be small enough to enter the nucleus through nuclear pores, mitochondria are too large to travel much within the cell.

Cells are the basic functional unit of life. Prokaryotic cells and viruses are both significantly smaller than eukaryotic cells. Eukaryotic cells are relatively large in order to accommodate the various organelles and process that occur within them.

In order from smallest to largest, the answer is atoms, proteins, ribosomes, viruses, mitochondria, a eukaryotic cell.

Lysosomes are membrane-bound organelles in the cell with a low pH internal environment. This low pH environment enables the activity of certain enzymes that reside in the lysosomes. These enzymes, known as hydrolytic enxymes, break down damaged or inactive proteins.

The incorrect answer choices largely outline processes accomplished by other organelles. The smooth endoplasmic reticulum synthesizes lipids. The Golgi apparatus and rough endoplasmic reticulum are responsible for protein modification and packaging prior to export from the cell; frequently, this will include addition of different monomers, such as a monosaccharide or lipid to adjust the protein's identity or function. Transportation of molecules through the cytoplasm is accomplished by the cytoskeleton and microtubule system. 

Ribosomes are found in all cell types and in all three domains. Recall the central dogma of biology: DNA  RNA  protein. Thus, all cells synthesize proteins using ribosomes. Also, note that although prokaryotes have ribosomes, ribosomes are never membrane-bound. Thus it still holds true that prokaryotes do not have any membrane-bound organelles. 

Ribosomes are composed of protein and ribosomal RNA (rRNA). They are made up of 2 subunits—one small and one large.

Glycoproteins are proteins that have been modified by the addition of chains of carbohydrates of varying length. Glycosylation of proteins happens in the endoplasmic reticulum and the Golgi apparatus. Phospholipids are not proteins and are thus not synthesized in the endoplasmic reticulum, rather, they are synthesized in the cytosol. mRNA is the nucleic acid product of transcription, which occurs in the cytosol in eukaryotes, and in the cytosol in prokaryotes. Lumen is the term which means "an opening," e.g., the lumen of a blood vessel is the space where the blood flows, the lumen of the endoplasmic reticulum is the space inside the organelle itself.