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The plasma membrane in bacteria

The plasma membrane

Like bacteria and archaea, eukaryotic cells have a plasma membrane, a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment. The plasma membrane controls the passage of organic molecules, ions, water, and oxygen into and out of the cell. Wastes (such as carbon dioxide and ammonia) also leave the cell by passing through the plasma membrane, usually with some help of protein transporters.

Figure 2. The eukaryotic plasma membrane is a phospholipid bilayer with proteins and cholesterol embedded in it.

As discussed in the context of bacterial cell membranes, the plasma membranes of eukaryotic cells may also adopt unique conformations. For instance, the plasma membrane of cells that, in multicellular organisms, specialize in absorption are often folded into fingerlike projections called microvilli (singular = microvillus); (see figure below). The “folding” of the membrane into microvilli effectively increases the surface area for absorption while minimally impacting the cytosolic volume. Such cells can be found lining the small intestine, the organ that absorbs nutrients from digested food.

An aside: People with celiac disease have an immune response to gluten, a protein found in wheat, barley, and rye. The immune response damages microvilli. As a consequence, afflicted individuals have an impaired ability to absorb nutrients. This can lead to malnutrition, cramping, and diarrhea.

Figure 3. Microvilli, shown here as they appear on cells lining the small intestine, increase the surface area available for absorption. These microvilli are only found on the area of the plasma membrane that faces the cavity from which substances will be absorbed. Credit: “micrograph”, modification of work by Louisa Howard

The cytoplasm

The cytoplasm refers to the entire region of a cell between the plasma membrane and the nuclear envelope. It is composed of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals (see figure below). Even though the cytoplasm consists of 70 to 80 percent water, it nevertheless has a semisolid consistency. It is crowded in there. Proteins, simple sugars, polysaccharides, amino acids, nucleic acids, fatty acids, ions and many other water-soluble molecules are all competing for space and water. 

The nucleus

Typically, the nucleus is the most prominent organelle in a cell (see figure below) when viewed through a microscope. The nucleus (plural = nuclei) houses the cell’s DNA. Let’s look at it in more detail.

Figure 4. The nucleus stores chromatin (DNA plus proteins) in a gel-like substance called the nucleoplasm. The nucleolus is a condensed region of chromatin where ribosome synthesis occurs. The boundary of the nucleus is called the nuclear envelope. It consists of two phospholipid bilayers: an outer membrane and an inner membrane. The nuclear membrane is continuous with the endoplasmic reticulum. Nuclear pores allow substances to enter and exit the nucleus.

The nuclear envelope

The nuclear envelope, a structure that constitutes the outermost boundary of the nucleus, is a double-membrane—both the inner and outer membranes of the nuclear envelope are phospholipid bilayers. The nuclear envelope is also punctuated with protein-based pores that control the passage of ions, molecules, and RNA between the nucleoplasm and cytoplasm. The nucleoplasm is the semisolid fluid inside the nucleus where we find the chromatin and the nucleolus, a condensed region of chromatin where ribosome synthesis occurs.

Chromatin and chromosomes

To understand chromatin, it is helpful to first consider chromosomes. Chromosomes are structures within the nucleus that are made up of DNA, the hereditary material. You may remember that in bacteria and archaea, DNA is typically organized into one or more circular chromosome(s). In eukaryotes, chromosomes are linear structures. Every eukaryotic species has a specific number of chromosomes in the nuclei of its cells. In humans, for example, the chromosome number is 23, while in fruit flies, it is 4. 

Chromosomes are only clearly visible and distinguishable from one another by visible optical microscopy when the cell is preparing to divide and the DNA is tightly packed by proteins into easily distinguishable shapes. When the cell is in the growth and maintenance phases of its life cycle, numerous proteins are still associated with the nucleic acids, but the DNA strands more closely resemble an unwound, jumbled bunch of threads. The term chromatin is used to describe chromosomes (the protein-DNA complexes) when they are both condensed and decondensed.

Figure 5. (a) This image shows various levels of the organization of chromatin (DNA and protein). (b) This image shows paired chromosomes. Credit (b): modification of work by NIH; scale-bar data from Matt Russell

The nucleolus

Some chromosomes have sections of DNA that encode ribosomal RNA. A darkly staining area within the nucleus called the nucleolus (plural = nucleoli) aggregates the ribosomal RNA with associated proteins to assemble the ribosomal subunits that are then transported out to the cytoplasm through the pores in the nuclear envelope.


Discuss amongst yourselves. Use the Design Challenge rubric to consider the nucleus in more detail. What “problems” does an organelle like the nucleus solve? What are some of the qualities of a nucleus that may be responsible for ensuring its evolutionary success? What are some of the trade-offs of evolving and maintaining a nucleus? (Every benefit has some cost; can you list both?) Remember, there may be some well-established hypotheses (and it is good to mention these), but the point of the exercise here is for you to think critically and to critically discuss these ideas using your collective “smarts”.


Ribosomes are the cellular structures responsible for protein synthesis. When viewed through an electron microscope, ribosomes appear either as clusters (polyribosomes) or single, tiny dots that float freely in the cytoplasm. They may be attached to the cytoplasmic side of the plasma membrane or the cytoplasmic side of the endoplasmic reticulum and the outer membrane of the nuclear envelope (cartoon of cell above).

Electron microscopy has shown us that ribosomes, which are large complexes of protein and RNA, consist of two subunits, aptly called large and small (figure below). Ribosomes receive their “instructions” for protein synthesis from the nucleus, where the DNA is transcribed into messenger RNA (mRNA). The mRNA travels to the ribosomes, which translate the code provided by the sequence of the nitrogenous bases in the mRNA into a specific order of amino acids in a protein. This is covered in greater detail in the section covering the process of translation.

 Figure 6.Ribosomes are made up of a large subunit (top) and a small subunit (bottom). During protein synthesis, ribosomes assemble amino acids into proteins.