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What is the Icosahedral Matrices?

What is the Icosahedral Matrices?


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This website introduces the "Icosahedral Matrices".

  1. What are the locations of the other half?

It only shows around 30 numbers of the 60 facets. So how to know the other 30 numbers on the back?

  1. The 60 transformation matrices are shown below in the website. Are they rotational matrices? What are the exact meaning of those 9 numbers for a particular matrix? For example,


Regular icosahedron

In geometry, a regular icosahedron ( / ˌ aɪ k ɒ s ə ˈ h iː d r ən , - k ə -, - k oʊ -/ or / aɪ ˌ k ɒ s ə ˈ h iː d r ən / [1] ) is a convex polyhedron with 20 faces, 30 edges and 12 vertices. It is one of the five Platonic solids, and the one with the most faces.

It has five equilateral triangular faces meeting at each vertex. It is represented by its Schläfli symbol <3,5>, or sometimes by its vertex figure as 3.3.3.3.3 or 3 5 . It is the dual of the dodecahedron, which is represented by <5,3>, having three pentagonal faces around each vertex. In most contexts, the unqualified use of the word "icosahedron" refer specifically to this figure.

A regular icosahedron is a strictly convex deltahedron and a gyroelongated pentagonal bipyramid and a biaugmented pentagonal antiprism in any of six orientations.

The name comes from Greek εἴκοσι (eíkosi) 'twenty', and ἕδρα (hédra) 'seat'. The plural can be either "icosahedrons" or "icosahedra" ( /- d r ə / ).


Mitochondrial Machineries for Protein Import and Assembly

Nils Wiedemann and Nikolaus Pfanner
Vol. 86, 2017

Abstract

Mitochondria are essential organelles with numerous functions in cellular metabolism and homeostasis. Most of the >1,000 different mitochondrial proteins are synthesized as precursors in the cytosol and are imported into mitochondria by five transport . Read More

Figure 1: Overview of the five major protein import pathways of mitochondria. Presequence-carrying preproteins are imported by the translocase of the outer mitochondrial membrane (TOM) and the presequ.

Figure 2: The presequence pathway into the mitochondrial inner membrane (IM) and matrix. The translocase of the outer membrane (TOM) consists of three receptor proteins, the channel-forming protein To.

Figure 3: Role of the oxidase assembly (OXA) translocase in protein sorting. Proteins synthesized by mitochondrial ribosomes are exported into the inner membrane (IM) by the OXA translocase the ribos.

Figure 4: Carrier pathway into the inner membrane. The precursors of the hydrophobic metabolite carriers are synthesized without a cleavable presequence. The precursors are bound to cytosolic chaperon.

Figure 5: Mitochondrial intermembrane space import and assembly (MIA) machinery. Many intermembrane space (IMS) proteins contain characteristic cysteine motifs. The precursors are kept in a reduced an.

Figure 6: Biogenesis of β-barrel proteins of the outer mitochondrial membrane. The precursors of β-barrel proteins are initially imported by the translocase of the outer membrane (TOM), bind to small .

Figure 7: The dual role of mitochondrial distribution and morphology protein 10 (Mdm10) in protein assembly and organelle contact sites. Mdm10 associates with the sorting and assembly machinery (SAM) .

Figure 8: Multiple import pathways for integral α-helical proteins of the mitochondrial outer membrane. The precursors of proteins with an N-terminal signal anchor sequence are typically inserted into.

Figure 9: The mitochondrial contact site and cristae organizing system (MICOS) interacts with protein translocases. MICOS consists of two core subunits, Mic10 and Mic60. Mic10 forms large oligomers th.


Abstract

Virus structures are megadalton nucleoprotein complexes with an exceptional variety of protein–protein and protein–nucleic-acid interactions. Three-dimensional crystal structures of over 70 virus capsids, from more than 20 families and 30 different genera of viruses, have been solved to near-atomic resolution. The enormous amount of information contained in these structures is difficult to access, even for scientists trained in structural biology. Virus Particle Explorer (VIPER) is a web-based catalogue of structural information that describes the icosahedral virus particles. In addition to high-resolution crystal structures, VIPER has expanded to include virus structures obtained by cryo-electron microscopy (EM) techniques. The VIPER database is a powerful resource for virologists, microbiologists, virus crystallographers and EM researchers. This review describes how to use VIPER, using several examples to show the power of this resource for research and educational purposes.


Virus structure

The following three basic components are included in the virus structure. The first two are present in all types of viruses. But the last one viral envelope is present mainly in the animal virus structure.

  1. A nucleic acid genome
  2. A protein capsid that covers the genome. (Genome plus protein capsid is called the nucleocapsid).
  3. Lipid envelop (In many animal viruses)

All the intact virus is called a virion. Detail of these components is right below.

A- Viral genomes:

Although the genomes of all known cells are made up of double-stranded DNA, the genomes of viruses can be made up of single-stranded or double-stranded DNA or RNA. Viruses vary greatly in their size, ranging from approximately 5-10 kb (Papovaviridae, Parvoviridae, etc.) to even more than 100-200 kb (Herpesviridae, Poxviridae). Different structures of virus genomes are given below.

  • Double-stranded – linear or circular
  • Single strand – linear or circular
  • Other structures – gapped circles

2- RNA: double-stranded – linear

Single-stranded linear structure: These single-chain genomes can be positive-sense single-stranded RNA or negative-sense single-stranded RNA or ambisense. The positive-sense single-stranded RNA can directly serve as mRNA and encode proteins, so for these viruses, viral RNA is infectious. The negative-sense single-stranded RNA is not infectious, as it must be copied into the + sense strand before it can be translated. In an Ambisense virus, some part of genome is sense strand and some part is the antisense.

The genome of some RNA viruses is segmented, which means that a virus particle contains several different RNA molecules, like different chromosomes.

B: Protein capsid

Protein capsid is an essential component of virus structure. Viral genomes are surrounded by shells of proteins known as capsids. An interesting question is how the capsid proteins recognize viral RNA or DNA, but not cellular DNA. The answer is that there is often some kind of “packaging” signal (sequence) in the viral genome that the capsid proteins recognize. A capsid is composed of repetitive structural subunits that are arranged in one of two symmetrical structures, a helix or an icosahedron. These “subunits” may consist of a single polypeptide, in simplest cases. However, in many cases, these structural subunits (also called protomers) are made up of various polypeptides. The detail of helical and icosahedral virus structures is described below.

1) Helical capsids: The first and best example studied is the plant tobacco mosaic virus (TMV), which contains a single-stranded RNA genome and a protein coat made up of a single 17.5 kd protein. This protein is arranged in a helix around the viral RNA, with 3 nucleotides of RNA fitting into a groove in each subunit. The helical capsids can also be more complex as they involve more than one protein subunit.

A Helix can be defined by two parameters, its diameter, and pitch. This structure is very stable and can be easily disassociated and re-associated by changing the ionic strength, pH, temperature, etc. The interactions that hold these molecules together are not covalent and involve H bonds, salt bridges, hydrophobic interactions, and Vander Waals forces.

Several families of animal viruses contain helical nucleocapsids, for example, Orthomyxoviridae (influenza), Rhabdoviridae (rabies) and Paramyxoviridae (bovine respiratory syncytial virus). These are all enveloped viruses.

Different capsid types in virus structure

2) Icosahedral capsids: In these structures, the subunits are arranged in the form of a hollow, quasi-spherical structure, with the genome inside. An icosahedron is defined as consisting of 20 equilateral triangular faces arranged around the surface of a sphere. They exhibit 2-3-5 symmetry.

  • 2-fold rotational symmetry through the edges.
  • 3-fold rotational symmetry through the center of each triangular face.
  • 5-fold symmetry through the center of each corner.

These corners are also called vertices, and each icosahedron has 12.

Since proteins are not equilateral triangles, each side of an icosahedron contains more than one protein subunit. The simplest icosahedron is made using 3 identical subunits to form each face, so the minimum number of subunits is 60 (20 x 3). Remember that each of these subunits could be a single protein or, more likely, a complex of multiple polypeptides.

Many viruses have a genome too large to be packaged within an icosahedron made up of only 60 polypeptides (or even 60 subunits), making them even more complicated. But in these, the total number of subunits is always a multiple of 60.

Apparent clusters or “Lumps” are often seen on the surface of the particle, when viral nucleocapsids are viewed under the electron microscope, These are generally protein subunits grouped around an axis of symmetry and have been called “morphological units” or capsomeres”

C: Viral Envelope

In some animal viruses, the nucleocapsid is surrounded by a membrane, also called an envelope. This envelope is made up of a lipid bilayer and is made up of lipids from host cells. It also contains virus-encoded proteins, often glycoproteins that are transmembrane proteins. These viral proteins serve many purposes, such as binding to receptors in the host cell, playing a role in membrane fusion and cell entry, etc. They can also form channels on the viral membrane.

Many enveloped viruses also contain matrix proteins, which are internal proteins that bind the nucleocapsid to the envelope. They are very abundant (that is, many copies per virion) and are generally not glycosylated. Some virions also contain other non-structural proteins that are used in the viral life cycle. Examples of this are replicases, transcription factors, etc. These nonstructural proteins are present in low amounts in the virion.

Enveloped viruses are formed by budding through cell membranes, usually the plasma membrane, but sometimes an internal membrane such as ER, Golgi, or nucleus. In these cases, the assembly of viral components (genome, capsid, matrix) occurs on the inner side of the membrane, the envelope glycoproteins clump together in that region of the membrane, and the virus breaks out. This ability to bud allows the virus to leave the host cell without lysing or killing the host. Conversely, unenveloped viruses and some enveloped viruses kill the host cell to escape.


Morphology

Figure: Example of a virus attaching to its host cell: The KSHV virus binds the xCT receptor on the surface of human cells. This attachment allows for later penetration of the cell membrane and replication inside the cell.

Viruses come in many shapes and sizes, but these are consistent and distinct for each viral family. In general, the shapes of viruses are classified into four groups: filamentous, isometric (or icosahedral), enveloped, and head and tail. Filamentous viruses are long and cylindrical. Many plant viruses are filamentous, including TMV (tobacco mosaic virus). Isometric viruses have shapes that are roughly spherical, such as poliovirus or herpesviruses. Enveloped viruses have membranes surrounding capsids. Animal viruses, such as HIV, are frequently enveloped. Head and tail viruses infect bacteria. They have a head that is similar to icosahedral viruses and a tail shape like filamentous viruses.

Many viruses use some sort of glycoprotein to attach to their host cells via molecules on the cell called viral receptors. For these viruses, attachment is a requirement for later penetration of the cell membrane, allowing them to complete their replication inside the cell. The receptors that viruses use are molecules that are normally found on cell surfaces and have their own physiological functions. Viruses have simply evolved to make use of these molecules for their own replication.

Overall, the shape of the virion and the presence or absence of an envelope tell us little about what disease the virus may cause or what species it might infect, but they are still useful means to begin viral classification. Among the most complex virions known, the T4 bacteriophage, which infects the Escherichia coli bacterium, has a tail structure that the virus uses to attach to host cells and a head structure that houses its DNA. Adenovirus, a non-enveloped animal virus that causes respiratory illnesses in humans, uses glycoprotein spikes protruding from its capsomeres to attach to host cells. Non-enveloped viruses also include those that cause polio (poliovirus), plantar warts (papillomavirus), and hepatitis A (hepatitis A virus).

Figure: Examples of virus shapes: Viruses can be either complex in shape or relatively simple. This figure shows three relatively-complex virions: the bacteriophage T4, with its DNA-containing head group and tail fibers that attach to host cells adenovirus, which uses spikes from its capsid to bind to host cells and HIV, which uses glycoproteins embedded in its envelope to bind to host cells.

Enveloped virions like HIV consist of nucleic acid and capsid proteins surrounded by a phospholipid bilayer envelope and its associated proteins. Glycoproteins embedded in the viral envelope are used to attach to host cells. Other envelope proteins include the matrix proteins that stabilize the envelope and often play a role in the assembly of progeny virions. Chicken pox, influenza, and mumps are examples of diseases caused by viruses with envelopes. Because of the fragility of the envelope, non-enveloped viruses are more resistant to changes in temperature, pH, and some disinfectants than are enveloped viruses.


Complex and Asymmetrical Virus Particles

Complex viruses are often asymetrical or symetrical in combination with other structures such as a tail.

Learning Objectives

Break down the differences between complex and asymmetrical viruses

Key Takeaways

Key Points

  • Viruses can be structurally very different.
  • Some complex viruses are large enough to be visible with a light microscope.
  • The viruses of archaea are unique compared to other viruses.

Key Terms

  • capsid: The outer protein shell of a virus.
  • poxvirus: Any of the group of DNA viruses belonging to the family Poxviridae, which cause pox diseases in vertebrates.

Viruses have many structural shapes, often falling into certain categories. While some have symmetrical shapes, viruses with asymmetrical structures are referred to as “complex. ” These viruses possess a capsid that is neither purely helical nor purely icosahedral, and may possess extra structures such as protein tails or a complex outer walls.

Some bacteriophages, such as Enterobacteria phage T4, have a complex structure consisting of an icosahedral head bound to a helical tail, which may have a hexagonal base plate with protruding protein tail fibers. This tail structure acts like a molecular syringe, attaching to the bacterial host and then injecting the viral genome into the cell.

T4 Bacteriophage: T4 is a bacteriophage that infects E. coli and is referred to as a complex virus. Although it has an icosahedral head, its tail makes it asymmetrical, or complex in terms of structure.

The poxviruses are large, complex viruses that have an unusual morphology. The viral genome is associated with proteins within a central disk structure known as a nucleoid. The nucleoid is surrounded by a membrane and two lateral bodies of unknown function. The virus has an outer envelope with a thick layer of protein studded over its surface. The whole virion is slightly pleiomorphic, ranging from ovoid to brick shape.

Mimivirus is the largest characterized virus, with a capsid diameter of 400 nm. Protein filaments measuring 100 nm project from the surface. The capsid appears hexagonal under an electron microscope, therefore the capsid is probably icosahedral. In 2011, researchers discovered a larger virus on the ocean floor off the coast of Las Cruces, Chile. Provisionally named Megavirus chilensis, it can be seen with a basic optical microscope.

Some viruses that infect archaea have complex structures unrelated to any other form of virus. These include a wide variety of unusual shapes, ranging from spindle-shaped structures, to viruses that resemble hooked rods, teardrops, or even bottles. Other archaeal viruses resemble the tailed bacteriophages, and can have multiple tail structures.


Human Immuno-Deficiency Virus (HIV) | Microbiology

In this article we will discuss about:- 1. Structure of HIV 2. Genome Organization of HIV-1 3. Steps of Entry 4. Replication 5. Assembly.

Structure of HIV:

HIV is different in structure from other retroviruses. HIV is of 100-120 nm diameters containing an protein envelope to which spicules of glycoprotein are attached. The envelope encloses an icosahedral capsid core that possesses identical macromolecules of RNA as genetic material. Three dimensional structure of the viral envelope appears like a sphere made up from an assembly of 12 pentamers and 20 hexamers (Fig. 17.41).

The capsid is conical and composed of 2,000 copies of the viral protein p24. The two copies of positive single-stranded RNA are tightly bound with nucleocapsid proteins, p7 and enzymes such as reverse transcriptase, proteases, ribonuclease and integrase. These are required for the develop­ment of the virion. Matrix is composed of viral protein p17 which surrounds the capsid. Hence, the integrity of the virion particle it maintained.

In turn, the matrix is surrounded by the viral envelope which is composed of two layers of phospholipids of host cell which originates at the time of budding from the cell of newly formed virus particles. The host cell proteins and about 70 copies of a complex HIV proteins are embedded in the viral envelope that protrude through the surface of the virus particle. This protein is called Env which constitutes spikes.

It consists of a cap which is made up of three molecules of glycoprotein (gp) 120, and a stem of three gp41 molecules that anchor the spike into the viral envelope. The virus attaches to host cell with glycoprotein and gets fused with target cells to initiate the infectious cycle. Both of these surface proteins (especially gp 120) have been considered as targets of future treatments or vaccines against HIV.

Genome Organization of HIV-1:

The RNA genome consists of at least 7 structural landmarks (LTR, TAR, RRE, PE, SLIP, CRS, INS) and nine genes (gag, pol, and env, tat, rev, nef, vif, vpr, vpu, and tev) encoding 19 proteins (Fig. 17.42). The open reading frames for various polypeptides are shown as rectangles.

Multiple-spliced mRNA transcripts encoding various proteins are shown with splice-sites together with 5′-cap and 3′ poly A tails. Major translated polypeptides from these mRNAs are initially processed to produce 15 protein molecules. In addition, there is a third type of nucleic acid present in all particles which is a special type of tRNA (usually trp, pro or. lys). It is required for replication.

Three of the nine genes (i.e. gag, pol, and env) contain the information which is required to synthesise the structural proteins for new virus particles. For example, env codes for a protein called gpl60 which, after getting broken by a viral enzyme, forms gp120 and gp41. Structure of different regions is given in Fig. 17.43.

Structure and function of these regions are given as below:

It is a short (18-250 nucleotides) sequence which forms a direct repeat at both ends of the genome therefore, it is ‘terminally redundant’. The R region is present at both the ends.

It is a unique, non-coding region of 75-250 nucleotides which is the first part of the genome to be reverse transcribed forming the 3′ end of the provirus genome.

iii. Primer Binding Site (PBS):

It is 18 nucleotide-long and complementary to the 3′ end of the specific tRNA primer used by the virus to begin reverse transcription.

It is a relatively long (90-500 nucleotides) non-translated region downstream of the transcription start site therefore it is present at the 5′ end of all virus mRNAs.

v. Polypurine Tract (PPT):

It is a short (-10 nucleotides) run of A/G residues which is responsible for initiating the synthesis of (-n) strand during reverse transcription.

It is a unique non-coding region of 200-1,200 nucleotides which forms the 5′ end of the provirus after reverse transcription. It contains promoter elements which are responsible for transcription of the provirus (Fig. 17.44).

The other six genes e.g. tat, rev, nef, vif, vpr, and vpu (of in the case of HFV-2) are the regulatory genes. These genes enc proteins that control the ability of HIV to infect cells, produce virus particles or cause disease. The two Tat proteins (e.g. pi6 pi4) act as the transcriptional trans activators for the LTR promoter.

They activate transcription by binding the TAR RNA element. Rev protein (p19) binds to the RRE RNA element and start shutl of RNAs from the nucleus and the cytoplasm. AP0BEC3G is a protein which deaminates DNA: RNA hybrids and/or interferes with the Pol protein. The Vif protein (p23) prevents the action of APOBEC3G.

The Vpr protein (P14) inhibits cell division at G2/M stage. CD4 as well as the MHC class I and class It molecules. The Vpu protein (p16) helps the release of newly synthesised virus particles from infected cells. The ends of each strand of HIV RNA contain a sequence of repeated nucleotides called ‘R0region’ or the ‘long terminal repeat’ (LTR).

Regions in the LTR act as switches to control production of new viruses. The LTR regions can be triggered by proteins from either HIV or the host cell. The Gag and Rev Proteins recognize the Psi element which is involved in viral genome packaging. The in the Gag-Pol reading frame required to make functional Pol. Frame shifting is carried out by the SLIP element (TTTTTT).

Steps of Entry of HIV:

The infectious particle first binds to target cells using semi-or non-specific interactions between the viral envelope and cell surface glycans or adhesion factors. Then the envelope glycoprotein gpl20 interacts with the CD4 antigen. This initiates a conformational change in gpl20 that facilitates its binding to a co-receptor molecule (Fig. 17.45).

Further conformational changes in the gpl20-gp41 complex then lead to exposure of the fusion-peptide region of gp41 and its insertion into the host cell membrane. The viral and cell membranes fuse, the viral uncoating is done and viral RNA plus virion proteins enter the cytosol. Within this reverse transcription complex (viral RNA and virion proteins), reverse transcriptase catalyses the synthesis of complementary DNA.

Replication of HIV:

The resulting complex containing viral cDNA (pre-integration complex) is transported to the host cell nucleus where the viral integrase enzyme catalyses integration of viral cDNA within host cell DNA to form the proving (Fig. 17.46).

In some instances, viral cDNA that is translocated to the nucleus circularizes to form episomes containing one or two long terminal repeats (LTR). These circular forms of viral cDNA are dead-end products of viral replication.

The ends of the LTRs consist of inverted repeats of 4-6 bp. These are brought together to form a cleavage site for IN and are cleaved to form a staggered cut. This process is catalysed by TN polypeptide which is a part of the reverse transcriptase complex. Then this molecule is inserted into the host cell DNA.

The net result of the integration process is that:

(i) The integrated provirus contains 1 or 2 less bases at the end of each LTR,

(ii) The ends of the integrated LTRs always have the same sequence: 5′ – TG…CA – 3′ , and

(iii) 4-6 bp of host cell DNA flanking the integrated provirus are duplicated. A staggered cut (5′ overhang) is introduced into both the ends of the LTRs and the host cell DNA, followed by joining of the cut ends and repair of the free 3′ ends.

Integration is a highly specific reaction with respect to the provirus, but random with respect to host cell DNA. Earlier, it was thought that the 2-LTR circle was the substrate for integration, but it is now believed that the linear form (i.e. the direct product of reverse transcription) is the actual substrate used. After integration, the provirus is present for the lifetime of the cell. There is no specific mechanism for excision of the provirus.

Assembly of HIV:

Assembly of capsid/nucleocapsid occurs in the cytoplasm (or at the cell surface) which later on buds out through the cell membrane, acquiring the envelope during this process (Fig. 17.46). If assembly occurs at cell surface, thickened patches begin to form in the membrane (Env proteins on outer surface. Gag proteins inside).

The genome is packaged when the particle has budded out through the membrane. In both types, ‘maturation’ is accomplished with the catalysis and cleavage events by viral protease which results in budding of the particles.

During this process, considerable structural changes occur which results in completely rearrangement of the smooth gag shell of the immature particle that lead to condensation of the core visible in mature particles.


Understanding the structure of viruses

Photo by CDC on Unsplash

Viruses are infectious particles existing in nature. As discussed in the previous post, viruses come in a variety of sizes.

In this post, we will look at the basic structural components of a virus particle.

Although viruses are not as complex as other living organisms and they lack the ability to reproduce on their own, their structures do not lack any sophistication.

All viruses carry their viral genomic materials in the form of nucleic acid (DNA or RNA). They act as the blueprint for making more viral proteins essential for their propagation inside the host cell. The DNA or RNA in a virus particle is packaged inside a protein shell called a capsid. On top of that, viruses can be enclosed by an envelope layer. But not all viruses have an envelope.

ENVELOPE

The envelope layer is composed of a lipid bilayer. The lipid bilayer is like that of a cell membrane. Very often viruses get their lipid bilayers from the host cells’ cell membrane during their release from the host cells. This process is called budding.

A virus particle’s lipid bilayer can be embedded with various viral proteins. These envelope proteins are also called matrix proteins. For example, coronaviruses develop spikes, made of matrix proteins called glycoproteins. Together with the envelope, they form the “crown” like the outer layer, a trademark of coronavirus. There are two main types of virus particles. They are either “enveloped” or “nonenveloped”. Take a look at the schematic of a typical “enveloped” and “nonenveloped” viruses. Virus lacking the envelope layer is sometimes called a “naked virus”.

Credit: Reference [1]

CAPSID

Capsid is the protective shell that encloses the viruses’ genomic materials. Together, it is called a nucleocapsid. This protective shell is made up of viral structural proteins. A basic subunit of the capsid is called a capsomere. Multiple capsomers together make up the capsid. Capsid can come in two basic structures: spherical (icosahedral or polygon-shaped) or helical.

Example of helical virus
Left: Model of Tobacco Mosaic Virus (TMV) Right: Electron micrograph of TMV. The white bar represents 100nm
Credit link Molecular models of icosahedral viruses
Credit: Reference [2]

There is a third structure: complex or head-tail. Complex capsids are a kind of hybrid between both helical and icosahedral capsids. For example, a T4 bacteriophage, a virus that infects bacteria has an elongated icosahedral head, helical body, and tail structures.

Credit: Adapted by Petr Leiman (Purdue University) from a drawing by Fred Eiserling (UCLA)

What is a T number?

First described in 1962 by Caspar and King, the T (triangular) number is used to explain the size and complexity of icosahedral capsids. Over the years, this concept has evolved as more icosahedral capsids are discovered and analyzed. For example, a virus with a T number of 1 (for example, a parvovirus) represents a simple icosahedral assembly of 20 triangular faces and 60 structural subunits.

Examples of large and small icosahedral capsids.
Credit: Reference [2]

Three main functions of a capsid

  • Protects the viral nucleic acids
  • Aids in the attachment of the virus particle to a host cell
  • Delivers the viral genome by penetrating the host cell membrane

The assembly and stability of the capsid structure are very important. The capsid must be able to protect the nucleic acids from harmful radiation such as UV, environments of varying pH, temperature and exposure to enzymes that can break down proteins and nucleic acids.

For naked viruses, they lack the envelope layer for additional protection. The capsid serves as the main protective layer as well as aiding in the penetration of the host cell membrane.

Check out this video on the self-assembly of the virus capsid using 3D printed model

NUCLEIC ACID

Nucleic acids in the form of DNA and RNA contain important genetic blueprint for the synthesis of all the viral proteins that are required in the assembly and making of new virus particles. They are safely packaged inside the capsid. Once inside a host cell, they are released.

Generally, DNAs are double-stranded (ds) while RNAs are single-stranded(ss). However, in viruses, there are many potential combinations: dsDNA, dsRNA, ssDNA, or ssRNA.

How are viruses classified?

Generally, viruses are classified based on the organisms they infect. They are further classified into families, subfamilies, genera, and species based on 3 main conditions:

  • Viral genome (size and type of nucleic acids, ss or ds)
  • Presence of envelope
  • Size and shape of the capsid

Other considerations such as the physicochemical properties, proteins, lipids, antigenic and biological properties, and genomic replication strategies also influence the classification of viruses.

The classification of viruses is complex and constantly evolving as more and more viruses are discovered.

If you are curious about the different kinds of viruses and virus taxonomy, Viralzone is a great website for you to explore.

Looking for something to do while self-isolating, how about making some origami icosahedrons?


21.1 Viral Evolution, Morphology, and Classification

In this section, you will explore the following questions:

  • How were viruses first discovered and how are they detected?
  • What three hypotheses describe the evolution of viruses?
  • What is the basic structure of a virus?
  • How are viruses classified?

Connection for AP ® Courses

The first organisms that originated about 3.5 billion years ago were prokaryotes that possessed the structures and metabolic processes associated with cells (refer to the Cell Structure chapter). As discussed in the chapter on cell structure, prokaryotic cells are much smaller than eukaryotic cells and inhabit just about every square inch of our planet, from the most inhospitable environments to the surface of the skin. Viruses are much smaller than prokaryotes and much simpler in structure. They must reproduce inside a host cell. Their origin is still a mystery to us, but we do know that they can make us very sick.

Viruses have a basic structure: a DNA or RNA core surrounded by an outer capsid of proteins. Some viruses have an outer phospholipid envelope. As we will explore in more detail, many viruses use some sort of glycoprotein to attach to their host cells. Viruses infect all known cell types and use the host cell’s replication proteins and metabolic machinery to replicate. Classification of viruses is challenging, but one method categorizes them based on how they produce their mRNA. Retroviruses (also called RNA viruses) use the enzyme reverse transcriptase to transcribe DNA from RNA. (In the Genes and Proteins chapter we learned that the usual flow of genetic information is from DNA to RNA to protein.) Common viruses include bacteriophage T4, adenovirus, and HIV retrovirus.

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP ® Biology Curriculum Framework. The AP ® Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP ® Biology course, an inquiry-based laboratory experience, instructional activities, and AP ® exam questions. A learning objective merges required content with one or more of the seven science practices.

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes.
Enduring Understanding 3.A Heritable information provides for continuity of life.
Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information.
Science Practice 6.5 The student can evaluate alternative scientific explanations.
Learning Objective 3.1 The student is able to construct scientific explanations that use the structures and mechanisms of DNA and RNA to support the claim that DNA and, in some cases, that RNA are the primary sources of heritable information.

The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards:
[APLO 2.20][APLO 3.3][APLO 3.29][APLO 3.30][APLO 2.22][APLO 2.26][APLO 1.31][APLO 1.27][APLO 1.30]

Discovery and Detection

Viruses were first discovered after the development of a porcelain filter, called the Chamberland-Pasteur filter, which could remove all bacteria visible in the microscope from any liquid sample. In 1886, Adolph Meyer demonstrated that a disease of tobacco plants, tobacco mosaic disease, could be transferred from a diseased plant to a healthy one via liquid plant extracts. In 1892, Dmitri Ivanowski showed that this disease could be transmitted in this way even after the Chamberland-Pasteur filter had removed all viable bacteria from the extract. Still, it was many years before it was proven that these “filterable” infectious agents were not simply very small bacteria but were a new type of very small, disease-causing particle.

Virions, single virus particles, are very small, about 20–250 nanometers in diameter. These individual virus particles are the infectious form of a virus outside the host cell. Unlike bacteria (which are about 100-times larger), we cannot see viruses with a light microscope, with the exception of some large virions of the poxvirus family. It was not until the development of the electron microscope in the late 1930s that scientists got their first good view of the structure of the tobacco mosaic virus (TMV) (Figure 21.1) and other viruses (Figure 21.2). The surface structure of virions can be observed by both scanning and transmission electron microscopy, whereas the internal structures of the virus can only be observed in images from a transmission electron microscope. The use of these technologies has allowed for the discovery of many viruses of all types of living organisms. They were initially grouped by shared morphology. Later, groups of viruses were classified by the type of nucleic acid they contained, DNA or RNA, and whether their nucleic acid was single- or double-stranded. More recently, molecular analysis of viral replicative cycles has further refined their classification.

Evolution of Viruses

Although biologists have accumulated a significant amount of knowledge about how present-day viruses evolve, much less is known about how viruses originated in the first place. When exploring the evolutionary history of most organisms, scientists can look at fossil records and similar historic evidence. However, viruses do not fossilize, so researchers must conjecture by investigating how today’s viruses evolve and by using biochemical and genetic information to create speculative virus histories.

While most findings agree that viruses don’t have a single common ancestor, scholars have yet to find a single hypothesis about virus origins that is fully accepted in the field. One such hypothesis, called devolution or the regressive hypothesis, proposes to explain the origin of viruses by suggesting that viruses evolved from free-living cells. However, many components of how this process might have occurred are a mystery. A second hypothesis (called escapist or the progressive hypothesis) accounts for viruses having either an RNA or a DNA genome and suggests that viruses originated from RNA and DNA molecules that escaped from a host cell. A third hypothesis posits a system of self-replication similar to that of other self-replicating molecules, likely evolving alongside the cells they rely on as hosts studies of some plant pathogens support this hypothesis.

As technology advances, scientists may develop and refine further hypotheses to explain the origin of viruses. The emerging field called virus molecular systematics attempts to do just that through comparisons of sequenced genetic material. These researchers hope to one day better understand the origin of viruses, a discovery that could lead to advances in the treatments for the ailments they produce.

Viral Morphology

Viruses are acellular, meaning they are biological entities that do not have a cellular structure. They therefore lack most of the components of cells, such as organelles, ribosomes, and the plasma membrane. A virion consists of a nucleic acid core, an outer protein coating or capsid, and sometimes an outer envelope made of protein and phospholipid membranes derived from the host cell. Viruses may also contain additional proteins, such as enzymes. The most obvious difference between members of viral families is their morphology, which is quite diverse. An interesting feature of viral complexity is that the complexity of the host does not correlate with the complexity of the virion. Some of the most complex virion structures are observed in bacteriophages, viruses that infect the simplest living organisms, bacteria.

Morphology

Viruses come in many shapes and sizes, but these are consistent and distinct for each viral family. All virions have a nucleic acid genome covered by a protective layer of proteins, called a capsid. The capsid is made up of protein subunits called capsomeres. Some viral capsids are simple polyhedral “spheres,” whereas others are quite complex in structure.

In general, the shapes of viruses are classified into four groups: filamentous, isometric (or icosahedral), enveloped, and head and tail. Filamentous viruses are long and cylindrical. Many plant viruses are filamentous, including TMV. Isometric viruses have shapes that are roughly spherical, such as poliovirus or herpesviruses. Enveloped viruses have membranes surrounding capsids. Animal viruses, such as HIV, are frequently enveloped. Head and tail viruses infect bacteria and have a head that is similar to icosahedral viruses and a tail shape like filamentous viruses.

Many viruses use some sort of glycoprotein to attach to their host cells via molecules on the cell called viral receptors (Figure 21.3). For these viruses, attachment is a requirement for later penetration of the cell membrane, so they can complete their replication inside the cell. The receptors that viruses use are molecules that are normally found on cell surfaces and have their own physiological functions. Viruses have simply evolved to make use of these molecules for their own replication. For example, HIV uses the CD4 molecule on T lymphocytes as one of its receptors. CD4 is a type of molecule called a cell adhesion molecule, which functions to keep different types of immune cells in close proximity to each other during the generation of a T lymphocyte immune response.

Among the most complex virions known, the T4 bacteriophage, which infects the Escherichia coli bacterium, has a tail structure that the virus uses to attach to host cells and a head structure that houses its DNA.

Adenovirus, a non-enveloped animal virus that causes respiratory illnesses in humans, uses glycoprotein spikes protruding from its capsomeres to attach to host cells. Non-enveloped viruses also include those that cause polio (poliovirus), plantar warts (papillomavirus), and hepatitis A (hepatitis A virus).

Enveloped virions like HIV, the causative agent in AIDS, consist of nucleic acid (RNA in the case of HIV) and capsid proteins surrounded by a phospholipid bilayer envelope and its associated proteins. Glycoproteins embedded in the viral envelope are used to attach to host cells. Other envelope proteins are the matrix proteins that stabilize the envelope and often play a role in the assembly of progeny virions. Chicken pox, influenza, and mumps are examples of diseases caused by viruses with envelopes. Because of the fragility of the envelope, non-enveloped viruses are more resistant to changes in temperature, pH, and some disinfectants than enveloped viruses.

Overall, the shape of the virion and the presence or absence of an envelope tell us little about what disease the virus may cause or what species it might infect, but they are still useful means to begin viral classification (Figure 21.4).


Watch the video: Icosahedral Symmetry (June 2022).


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