The Basics of Protein Structure Part 1: The Levels of Structure

In a previous post, we had explored the characteristics of the 20 amino acids that make up proteins.  These amino acids make up a diverse collection of molecules that can be strung together, making up proteins that have a multitude of functions within the cell.

Amino acids form a protein through the action of the ribosome, which we will discuss in a future post.  At this time, suffice it to say that the ribosome uses an elegant mechanism to read mRNA and translate it into the protein encoded by the mRNA by adding amino acids in a string.  As this string of amino acids is created, it begins to form a structure that will have functions within the cell.

Four levels of protein structure exist:

Primary (1^o) structure:  The order of the amino acids is the primary structure.  Think of the primary structure as the alphabet of the amino acids: MGRYNVPL, for example.  The primary structure describes what order amino acids are in, and even though it might not seem like very much information, even the primary structure of a protein can provide a great deal of information in terms of its function and its potential 3-dimensional shape.

Secondary (2^o) structure:  When amino acids are polymerized, they form local structures, which make up the secondary structure.  Think of secondary structure as the shape of a group of amino acids.  Two primary forms of secondary structure exist:  alpha helices and beta sheets.  Alpha helices result from the coiling of the amino acid string turning about itself.  In contrast, beta sheets are flatter and lack coiling.  There are several types of alpha helices and beta sheets, which we will save for a future post, and these different types of structures have important implications for overall shape of a protein.

Tertiary (3^o) structure:  Protein structure gets exciting when you talk about tertiary structure, which can be described as the overall three-dimensional shape of a protein.  In general, the tertiary structure is the “final” form of a protein, although modifications on the protein, as well as interactions with other proteins can affect this structure.

Quaternary (4^o) structure:  When proteins interact with each other, they can form complexes, which is the quaternary structure of these proteins.  You can think of this structure as the way proteins contact each other.  The bundling of proteins together can be between proteins of the same type (such as is the case with hemoglobin) or other types of proteins.

The drawing attempts to illustrate the concept of the different levels of protein structure.  Again, think of the primary structure as the order; the secondary structure as the local shape; the tertiary structure as the overall shape; and the quaternary structure as the way this tertiary structure of the protein interacts with other proteins.

How protein structure is established is a fascinating question and a field that is actively studied by prominent labs around the world.  Protein folding is the process of a chain of amino acids curling into its final shape, and how this process occurs is complex and not completely understood.  In general proteins fold depending on their environment (exposed to water or not, for example) and with the help of other proteins, called chaperones.  Protein chaperones help to establish a protein’s structure as well as maintain it during times of stress.  Further, modifications on proteins can change their structures, such as when p53, a protein that is involved in regulating many processes within the cell, is phosphorylated – its structure and, consequently, its function is altered slightly. 

The structure of proteins has fascinated scientists since we first learned about proteins.  Thousands of scientists around the world are still working to discover new structures and to learn how proteins fold.  The science behind protein folding has important implications in diseases such as Alzheimer’s, cancers, and infectious diseases.   

The Basics: Prokaryotes versus Eukaryotes

Biology is an amazing complex topic, and this complexity is what makes it fun!

Before jumping into advanced topics, however, it is important to have a solid foundation of the basics, which we usually learn before algebra even.  As a quick review, let's talk about prokaryotes and eukaryotes, the two types of cells that should be familiar to most everyone.

The world of living cells is broken down into two major types of cells: prokaryotes and eukaryotes (also called procaryotes and eucaryotes, depending how you would like to spell).  Evolutionarily, we consider prokaryotes to be the ancestors of eukaryotes, which we will discuss further in the future.

Let's start with the prokaryotic cell and its defining characteristics:

• Cell wall:  Prokaryotes have a cell wall, which are tough boundaries that enclose the cellular contents.  The cell wall is pretty tough, too - its composition gives it rigidity that keeps the prokaryotic cell's shape.  The cell wall is covered on the outside by the outer membrane and on the inside by the plasma membrane.  
• Nucleoid:  DNA in prokaryotes isn't organized quite the same as in eukaryotes.  Rather than being organized in a distinct, membrane-bound portion of the cell, prokaryotes organize their DNA in what is considered the nucleoid.  You can think of the nucleoid as a membrane-less compartment where the organism's DNA is found.  Although in the diagram I have drawn a single linear DNA molecule, prokaryotes have a diversity of types of DNA, from single circular DNA to multiple linear and circular DNA molecules.
• Cytoplasm:  The area within the cell wall and membranes is considered the cytoplasm - the fluid portion of the cell.  By no means is the cytoplasm empty space - it is filled with molecules and many events are taking place constantly within the cytoplasm.

Prokaryotes may seem "simple," but they certainly are not.  The above points are a simplification, but are the general characteristics of prokaryotes.

Eukaryotes can be considered more "complex," though certainly not better.  As with prokaryotes, the below characteristics are general and apply to most eukaryotic cells.

• Nucleus:  Unlike prokaryotes, eukaryotes have a define space for their DNA - the nucleus.  The nucleus is surrounded by the nuclear membrane, which is surrounded by the endoplasmid reticulum (discussed next).  The nucleus is a hub of activity in the eukaryotic cell and by its enclosure in the nuclear membrane, distinct events can occur here and not in the cytoplasm.
• Endoplasmic reticulum:  Surrounding the nucleus is the endoplasmic reticulum (ER), which is a compartment involved in moving molecules in and out of the nucleus, as well as regulating gene expression.  The ER can be broken down into the smooth and rough ER.  The rough ER is where proteins are made on the membrane.  In contrast, the smooth ER can be considered where pieces of the membrane are exchanged with the Golgi apparatus (next).
• Golgi apparatus:  The Golig consists of a stack of membrane-bound vesicles, which are mainly involved in protein trafficking.  Here, a number of modifications can be made to proteins to target them to specific parts of the cell, such as the membrane or lysosomes.
• Secretory vesicles:  Some molecules in the cell need to be sent outside the cell, and they can exit through secretory vesicles.  These vesicles often originate in the Golgi, after which they fuse with the plasma membrane and dump their contents in the extracellular space.
• Lysosome:  The trash compactor of the cell, the lysosome is involved in recycling the contents of the cell.  Lysosomes have contents that break down molecules into their components so that the cell can reuse them.  Additionally, lysosomes can be used to destroy invading bacteria and to break down molecules that can be harmful to the cell.
• Mitochondria:  "The powerhouse of the cell" - the mitochondria (singular mitochondrion) are involved in energy production, yes, but they also function is several other aspects, such as cell death.  Mitochondria themselves are like miniature cells within the eukaryotic cell, and they have their own DNA (mtDNA).  Mitochondria have many interesting aspects that will be discussed in a future post.
• Plasma membrane:  Similar to prokaryotes, the plasma membrane in eukaryotes acts as a boundary, separating the cell from the outside.  Unlike prokaryotes, however, eukaryotes (generally) do not have a cell wall.  The plasma membrane is a very dynamic part of the cell - signaling, budding, engulfing.  

As mentioned, the above characteristics are an incredible simplification of prokaryotes and eukaryotes, but let this serve as a starting point into learning about each type of cell.  Both types have their own special attributes and many mysteries that remain to be solved.

Immunology II: Lymphoid Organs and Cells

As mentioned in the last post, several types of cells derive from lymphoid progenitor cells.  These cells are generated in the bone marrow in general, but only B cells mature there (hence the name B cells).  In contrast, T cells migrate to the thymus where they mature.  After full maturation of both B and T cells, they circulate in the blood system and then enter the peripheral lymphoid organs.  The central lymphoid organs are the bone marrow where the lymphocytes are generated, whereas the peripheral lymphoid organs are where T cells mature and where the adaptive immune responds to various stimuli.

The peripheral lymphoid organs

First, we will consider the components of the peripheral lymphoid system.  The lymph nodes are glands right near each armpit that is where fluid collects from the lymph system.  Lymph drains into the lymph nodes via lymphatic vessels and consists of the extracellular fluid filtered from the blood.  Thus, lymph is kind of a surveillance system for the body.  The afferent lymphatic vessels carry lymph and cells from infected tissues and drain into the lymph node.

The lymph node itself has a unique structure, illustrated to the right.  The follicles are where B lymphocytes set up shop, and T cells exist in paracortical areas (T-cell zones).  Germinal centers within the lymph node are where B cells proliferate after they have been stimulated by T cells.  Several additional tissues are organized similar to the lymph node drawn to the right, and this structure facilitates interaction between B and T cells.

The spleen is another peripheral lymphoid organ that mostly works to break down dead red blood cells.  This destruction occurs in the red pulp of the spleen, but the spleen also has white pulp where lymphocytes enter and exist within the spleen.  Within the white pulp is the periarteriolar lymphoid sheath (PALS) that contains T cells and a B-cell corona.

The digestive system is a major route for infection and has several gut-associated lymphoid tissues (GALT).  Some of these tissues include the tonsils, adenoids, and the appendix.  The intestine also has its own GALT, namely the Peyer's patches, which collect antigen directly from inside the intestine using multi-fenestrated (M) cells.

Similar to the digestive tract, the respiratory tract has its own lymphoid tissue, called the bronchial-associated lymphoid tissue (BALT).

The basics of immunology

Immunology scares me. I'm not ashamed to admit this fact. I find the topic intimidating and overwhelming, especially when I listen to talks given by prominent immunologists. The terminology is difficult, and the concepts seem very intertwined. I've always perceived that breaking into understanding immunology required a lot of work but that it would (and should) make sense... eventually.

 The next few blog posts are going to focus on immunology, not only because I need to learn this information, but also because it is fascinating and a challenging topic.

Components of the Immune System
All of the cells that comprise the immune system emerge from the bone marrow, where all of them originally come from and where some of them remain for maturation.  The cell type that gives rise to immune cells is the hematopoietic stem cell.  From this pluripotent state, the hematopoetic stem cell can then mature into a myeloid progenitor cell or a common lymphoid progenitor.  Myeloid progenitor cells can differentiate into several more cell types, including granulocyte and macrophage progenitors and megakaryocyte and erythrocyte progenitors.  The granulocyte and macrophage progenitors can then develop into neutrophils, eosinophils, basophils, mast cells, and macrophages.  Megakaryocyte and erythrocyte progenitors generate platelets upon maturation.

Hematopoietic stem cells can also develop into a common lymphoid progenitor, which consists of B cells, T cells, and NK cells.  These types of cells leave the bone marrow and migrate through the lymph nodes.  Dendritic cells also develop from lymphoid progenitor cells but mature in the bone marrow before entering the lymph node.

Basic functions of immune cells

• Macrophages are a common cell type that mature from monocytes (from the myeloid progenitor cells originally).  Monocytes circulate in the blood and continuously differentiate into macrophages when they enter the body's tissues.  Once in the tissues, macrophages can be considered the garge trucks of the body:  they engulf the environment as well as other cells in the process of phagocytosis.  Thus, macrophages can function to neutralize harmful elements within the body.
• Dendritic cells also mature from myeloid progenitor cells, and their main function is to process and display antigen that will then be readable by T lymphocytes.  This antigen display requires the presentation of co-stimulatory molecules, and when dendritic cells encounter a pathogen (or other foreign antigen), they mature and begin expressing these co-stimulatory molecules.
• Mast cells differentiate in body tissues and are involved in mediating mucosal immunity.  They are most well-known for their role in allergic reactions.
• Neutrophils are a type of granulocyte (so called because they have densely-staining and strange-shaped nuclei) that are involved in phagocytosis and increase in numbers upon an immune response.
• Eosinophils respond to parasites.
• Basophils may function similarly to mast cells.
• B cells differentiate into plasma cells and function to secrete antibodies.
• T cells destroy virus-infected cells and also function to activate other immune cells, such as B cells and macrophages.
• NK cells are involved in innate immunity and destroy "weird-looking" cells, such as tumor cells or cells infected with viruses.

References for the interested:

Immunobiology. Janeway, Travers, Walport, Shlomchik.
Basic Concepts of Immunology and Neuroimmunology: Basic Immunology

Basic Immunology: Nuts and Bolts of the Immune System

Introduction to the Immune System

Escaping Anergy

Cancer and Oncogenes

Cancer is a diverse group of diseases with one common characteristic: unchecked cellular replication.  Via several potential mechanisms, cancer cells are able to avoid all of the checkpoints involved in cell growth and division, thus enabling them to divide more frequently or indefinitely.  Many events can lead to the development of a cancer cell, including inheritance of mutated DNA or the activity of a carcinogen, or a chemical agent that leads to the development of cancer.

Gene expression is often deregulated in cancer cells such that some genes are overexpressed, while others are underexpressed.  Genes that can be mutated to lead to an upregulation of activity and lead to the development of a cancer cell are termed proto-oncogenes.  When these proto-oncogenes are actually mutated, they are considered oncogenes.

An oncogene is often a gene involved in regulating cell division and drive the cell cycle.  When they are overexpressed, such as during cancer, they can push the cell to divide more frequently and, with further mutations, transform the cell such that it divides without restriction.

Oncogenes were first discovered in viruses, specifically in Rous Sarcoma Virus (RSV), a retrovirus that encodes a homologue to cellular src kinase (the viral form called v-src).  Tumors in birds caused by RSV are the result of v-src causing unregulated cellular proliferation.  Large amounts of research into this area has identified cellular src kinase as a proto-oncogene that, when mutated to become constitutively active, becomes an oncogene and can drive cancer development.  Interestingly, viruses have highlighted a number of cellular oncogenes and pathways that are improperly regulated in cancer.  Over 20 viral oncogenes have been identified to date.

Cellular proto-oncogenes (the genes before they become oncogenes) can promote cellular proliferation and the development of cancer in several ways.  One of these ways is to be overexpressed and function when the gene product really shouldn't function.  This is the case with proteins such as myc and growth factor receptors.  With overexpression of these proteins, there is the potential for amplified signaling through these pathways that can push the cell to divide more than it normally does, leading to the development of cancer.  An additional mechanism whereby a proto-oncogene can become an oncogene is via mutation that leads to improper regulation, such as constitutive activity.  A classical example of this type of phenomenon is via Ras, which when mutated is constitutively active and cannot hydrolyze an attached GTP to inactivate.  Thus, Ras remains active and cannot be "turned off."  This constant activity of Ras results in  signal transduction to the nucleus of the cell and pushes the cell to divide through transcription of several genes involved in cell division.