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Nucleus and ribosomes

Structure and function of the nucleus and ribosomes of a cell. How they work together in the production of proteins.

Introduction

Suppose that you have a very precious piece of information. Let’s imagine that this piece of information is a blueprint. In fact, it’s not just a blueprint for a house, or a car, or even a top-secret fighter jet. It’s a blueprint for an entire organism – you – and it not only specifies how to put you together, but also provides the information that enables every cell in your body to keep functioning from moment to moment.
Sounds important, right? You’d probably want to keep information this valuable in a secure spot, perhaps in a protected vault where you can keep an eye on it. In fact, that’s exactly what eukaryotic cells do with their genetic material, placing it in a membrane-enclosed repository called the nucleus.
Eukaryotic DNA never leaves the nucleus; instead, it’s transcribed (copied) into RNA molecules, which may then travel out of the nucleus. In the cytosol, some RNAs associate with structures called ribosomes, where they direct synthesis of proteins. (Other RNAs play functional roles in the cell, serving as structural components of the ribosome or regulating activity of genes.) Here, we’ll look in a little more detail at the structure of the nucleus and ribosomes.

The nucleus

The nucleus (plural, nuclei) houses the cell’s genetic material, or DNA, and is also the site of synthesis for ribosomes, the cellular machines that assemble proteins. Inside the nucleus, chromatin (DNA wrapped around proteins, described further below) is stored in a gel-like substance called nucleoplasm.
Enclosing the nucleoplasm is the nuclear envelope, which is made up of two layers of membrane: an outer membrane and an inner membrane. Each of these membranes contains two layers of phospholipids, arranged with their tails pointing inward (forming a phospholipid bilayer). There’s a thin space between the two layers of the nuclear envelope, and this space is directly connected to the interior of another membranous organelle, the endoplasmic reticulum.
Nuclear pores, small channels that span the nuclear envelope, let substances enter and exit the nucleus. Each pore is lined by a set of proteins, called the nuclear pore complex, that control what molecules can go in or out.
If you look at a microscope image of the nucleus, you may notice – depending on the type of stain used to visualize the cell – that there’s a dark spot inside it. This darkly staining region is called the nucleolus, and it’s the site in which new ribosomes are assembled.
Image credit: OpenStax Biology.
How do you make a ribosome? Some chromosomes have sections of DNA that encode ribosomal RNA, a type of structural RNA that combines with proteins to make the ribosome. In the nucleolus, new ribosomal RNA combines with proteins to form the subunits of the ribosome. The newly made subunits are transported out through the nuclear pores to the cytoplasm, where they can do their job.
Some cell types have more than one nucleolus inside the nucleus. For instance, some mouse cells have up to 6 nucleoli1. Prokaryotes, which do not have a nucleus, don't have nucleoli and build their ribosomes in the cytosol.

Chromosomes and DNA

Now that we have a sense of the structure of the nucleus, let’s have a closer look at the genetic information stored inside it: the DNA. Most of an organism’s DNA is organized into one or more chromosomes, each of which is a very long string or loop of DNA. A single chromosome can carry many different genes.
In prokaryotes, DNA is typically organized into a single circular chromosome (a loop). In eukaryotes, on the other hand, chromosomes are linear structures (strings). Every eukaryotic species has a specific number of chromosomes in the nuclei of its body’s cells. For example, a typical human body cell would have 46 chromosomes, while a comparable fruit fly cell would have 8.
Chromosomes are only visible as distinct structures when the cell is getting ready to divide. When the cell is in the growth and maintenance phases of its life cycle, the chromosomes instead resemble an unwound, jumbled bunch of threads. In this form, the DNA is accessible to the enzymes that transcribe it into RNA, allowing the genetic information to be put to use (expressed).
In both their loose and compact forms, the DNA strands of chromosomes are bound to structural proteins, including a family of proteins called histones (see picture below). These DNA-associated proteins organize the DNA and help it fit into the nucleus, and they also play a role in determining which genes are active or inactive. The complex formed by DNA and its supporting structural proteins is known as chromatin. You can learn more about DNA, chromatin, and chromosomes in the DNA and chromosomes article.
Image credit: OpenStax Biology. Image at right is a modification of work by the NIH; scale-bar data from Matt Russell.
To give you a sense of just how important DNA packing is, consider that the DNA in a typical human cell would be about 2 meters long if it were extended in a straight line. All 2 meters of that DNA are squeezed into a tiny nucleus with a diameter of just 0.006 mm. That's a feat "geometrically equivalent to packing 40 km (24 miles) of extremely fine thread into a tennis ball" 4!

Ribosomes

As mentioned above, ribosomes are the molecular machines responsible for protein synthesis. A ribosome is made out of RNA and proteins, and each ribosome consists of two separate RNA-protein complexes, known as the small and large subunits. The large subunit sits on top of the small subunit, with an RNA template sandwiched between the two. (A ribosome looks a little like a hamburger with a puffy bun on top, an RNA “patty” threading through it.)
In eukaryotes, ribosomes get their orders for protein synthesis from the nucleus, where portions of DNA (genes) are transcribed to make messenger RNAs (mRNAs). An mRNA travels to the ribosome, which uses the information it contains to build a protein with a specific amino acid sequence. This process is called translation. Prokaryotes lack a nucleus, so their mRNAs are transcribed in the cytoplasm and can be translated by ribosomes immediately.
Image credit: OpenStax Biology.
Eukaryotic ribosomes may be either free, meaning that they are floating around in the cytoplasm, or bound, meaning that they are attached to the endoplasmic reticulum or the outside of the nuclear envelope. (In the first diagram in this article, the red dots represent bound ribosomes; endoplasmic reticulum with bound ribosomes is known as rough endoplasmic reticulum.)
Because protein synthesis is an essential function of all cells, ribosomes are found in practically every cell type of multicellular organisms, as well as in prokaryotes such as bacteria. However, eukaryotic cells that specialize in producing proteins have particularly large numbers of ribosomes. For example, the pancreas is responsible for producing and secreting large amounts of digestive enzymes, so the pancreatic cells that make these enzymes have an unusually high number of ribosomes.
Final fun fact: in a testament to the importance of the ribosome, the 2009 Nobel Prize in Chemistry was awarded to three researchers who mapped its structure and movements down to the level of individual atoms using a technique called X-ray crystallography5.

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  • starky seedling style avatar for user Jenny Kim
    Are translation and protein synthesis the same thing?
    (16 votes)
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  • leaf grey style avatar for user Olivia K
    What does RNA do?
    (12 votes)
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    • aqualine seedling style avatar for user SpinosaurusRex
      1. Messenger RNA (mRNA) carries the genetic information copied from DNA in the form of a series of three-base code “words,” each of which specifies a particular amino acid.

      2. Transfer RNA (tRNA) is the key to deciphering the code words in mRNA. Each type of amino acid has its own type of tRNA, which binds it and carries it to the growing end of a polypeptide chain if the next code word on mRNA calls for it. The correct tRNA with its attached amino acid is selected at each step because each specific tRNA molecule contains a three-base sequence that can base-pair with its complementary code word in the mRNA.

      3. Ribosomal RNA (rRNA) associates with a set of proteins to form ribosomes. These complex structures, which physically move along an mRNA molecule, catalyze the assembly of amino acids into protein chains. They also bind tRNAs and various accessory molecules necessary for protein synthesis. Ribosomes are composed of a large and small subunit, each of which contains its own rRNA molecule or molecules.

      Translation is the whole process by which the base sequence of an mRNA is used to order and to join the amino acids in a protein. The three types of RNA participate in this essential protein-synthesizing pathway in all cells; in fact, the development of the three distinct functions of RNA was probably the molecular key to the origin of life. How each RNA carries out its specific task is discussed in this section, while the biochemical events in protein synthesis and the required protein factors are described in the final section of the chapter.

      All credit goes to: https://www.ncbi.nlm.nih.gov/books/NBK21603/
      (34 votes)
  • male robot hal style avatar for user Vish
    can we compare nucleoplasm to cytosol ?
    (10 votes)
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    • piceratops seed style avatar for user Sachin Pillai
      Yes, but there are some differences to keep in mind. Cytosol has enzymes, fatty acids, sugars, and amino acids, all dissolved within it. It is the area of the cell in which organelles are suspended. On the other hand, the nucleoplasm in the nucleus only contains chromatin and the nucleolus. It lacks any of the other macromolecules that could be found in the cytoplasm. Also, there are small differences between the chemical formulas and structures of the two substances.
      (15 votes)
  • blobby green style avatar for user Ambrose Kingston
    What does the 'deoxy' prefix to the full name of DNA signify, in contrast to RNA?
    (4 votes)
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  • aqualine seed style avatar for user Peter Barber
    So if RNA contains Uracil instead of Thymine as a base pair for Adenine as in DNA, but it is sections of DNA that encode RNA production....What process leads to Uracil replacing Thymine in the RNA production process?
    (8 votes)
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  • blobby green style avatar for user Parsa Payandeh
    In one of the pictures above,we can observe a huge amount of ribosomes on the surface of the endoplasmic reticulum.Why?
    (3 votes)
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    • male robot donald style avatar for user Tybalt
      The picture you are referring to is an image of a section of the endoplasmic reticulum known as the "Rough ER". The ribosomes there create proteins to be transported to their respective destinations by the Golgi Body.

      As for your second question, there are, in fact, ribosomes floating freely in the cell. The reason for having both bound and free ribosomes is that the bound ribosomes make proteins that will be transported elsewhere, while the free ones make proteins that will be used for the cell itself.

      Does this help?
      (6 votes)
  • starky ultimate style avatar for user Greacus
    This has always been a bit confusing for me: Do human cells have 46 chromosomes (2 of each) in resting state, or only in duplication states (while mitosis is happening) (so 23 in resting state).
    I always thought it was the second one, but why would we state everywhere that we have 46 chromosomes, while this would only be for the shorter period of the cells lifecycle?
    (4 votes)
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    • duskpin ultimate style avatar for user Daltara Darana
      We do have 46 chromosomes, 22 pairs of homologous chromosomes + sex chromosomes. Many cells are in G0 stage, so mitosis doesn't happen (somatic cells that don't divide anymore, just do their job), if mitosis happens then each chromosome would have 2 identical chromatids (homologous chromosomes aren't 100% identical, they may have different alleles), we could say that some cells have 92 chromosomes, while some 46 and gamettes 23, but it would be a bit confusing.
      And I don't think chromosomes are resting, they are actively transcribed into RNAs.
      (3 votes)
  • blobby green style avatar for user choui003
    When the article says that ribosomes can be bound to the endoplasmic reticulum, does that mean that ribosomes are actually in between the two phospholipid bilayers of the nuclear envelope? And if so, how would the finished proteins exit the endoplasmic reticulum?
    (3 votes)
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    • female robot grace style avatar for user tyersome
      The ribosomes are reversibly attached to the outer surface of the membrane rather than being inserted into the membrane.


      The proteins produced by ER-bound ribosomes start with what are known as a signal sequence§ and are initiated within the cytosol — the signal sequence then directs the complex of peptide, mRNA, and ribosome to dock with the ER.

      The ER-bound ribosomes are thus tethered to the ER by the growing polypeptide during its synthesis. These proteins will eventually be exported, sent to some types of organelles, or remain associated with a cell membrane.

      In contrast, if a protein lacks a signal sequence it will (usually) be translated in the cytosol — many if not most of these proteins will remain in the cytosol, but some will end being imported into mitochondria, chloroplasts, peroxisomes, or the nucleus.


      This process is covered in more detail here:
      https://www.khanacademy.org/science/biology/gene-expression-central-dogma/translation-polypeptides/a/protein-targeting-and-traffic


      Does that help?



      §Note: these signal sequences get cleaved and will not be part of the mature proteins.
      (3 votes)
  • blobby green style avatar for user Rohit Patil
    what is role of rRNAin protein synthesis?
    and is there only three types of RNA or more?
    (3 votes)
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  • blobby green style avatar for user Ambrose Kingston
    Is a protein an enzyme or is an enzyme a type of protein?
    (2 votes)
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