Notes you should have taken in Physics

Relationships, Terminology, Definitions, and Make-You-Smarter Stuff.

Atom

carbon-atom-on-the-future-of-human-evolution-websiteThe basic building block of all matter. The smallest particle of an element that has the same properties as the element. It consists of a central core called the nucleus that is made up of protons and neutrons. Electrons revolve in orbits in the region surrounding the nucleus.

  • A molecule is formed when two or more atoms join together chemically.
  • A compound is a molecule that contains at least two different elements.
  • All compounds are molecules but not all molecules are compounds.
  • An element is a substance that is made entirely from one type of atom. For example, the element hydrogen is made from atoms containing a single proton and a single electron. If you change the number of protons an atom has, you change the type of element it is.

Element

periodic-table-on-the-future-human-evolution-website

The Coolest Periodic Table Ever. Brought to you by the Future of Human Evolution Website, courtesy www.periodictable.com. Enlarge.

  • An element is a substance that is made entirely from one type of atom. For example, the element hydrogen is made from atoms containing a single proton and a single electron. If you change the number of protons an atom has, you change the type of element it is.
  • Some of the atoms in hydrogen have no neutrons, some of them have one neutron and a few of them have two neutrons. These different versions of hydrogen are called isotopes.
  • All isotopes of a particular element have the same number of protons, but have a different number of neutrons. If you change the number of neutrons an atom has, you make an isotope of that element.
  • There are 116 different elements. Some elements, like gold, silver, copper and carbon, have been known for centuries. Newer elements like meitnerium, darmstadtium and ununquadium are more recent.
  • All known elements are arranged on a chart called the Periodic Table of Elements.

The Standard Model

The Standard Model is the name given to the current theory of fundamental particles and how they interact. This theory includes:

  • Strong interactions due to the color charges of quarks and gluons.
  • A combined theory of weak and electromagnetic interaction, known as electroweak theory, that introduces W and Z bosons as the carrier particles of weak processes, and photons as mediators to electromagnetic interactions. Discovery of the Higgs Boson at the LHC solidified the validity of the model (with all of its limitations of course).
  • The theory does not include the effects of gravitational interactions. These effects are tiny under high-energy Physics situations, and can be neglected in describing the experiments.
  • A theory that also includes a correct quantum version of gravitational interactions has not yet been achieved.
  • The Standard Model is a well-established theory applicable over a wide range of conditions.

Elementary Particle

Any of the subatomic particles that compose matter and energy, especially one hypothesized or regarded as an irreducible constituent of matter. Also called fundamental particle or sub-atomic particle.

Sub-Atomic Particle

Any of various units of matter below the size of an atom, including the elementary particles and hadrons.

A particle that is less complex than an atom; regarded as constituents of all matter [syn: elementary particle, fundamental particle]

Nucleus

Discovered by Ernest Rutherford in 1911, the nucleus is the central part of an atom. Composed of protons and neutrons, the nucleus contains most of an atom’s mass.

Neutron-Proton-Electron-on-the-future-of-human-evolution-website

Proton

  • Protons are positively charged particles found within atomic nuclei.
  • Ernest Rutherford discovered protons in experiments conducted between the years 1911 and 1919.
  • A stable, positively charged subatomic particle in the baryon family having a mass 1,836 times that of the electron.
  • A stable particle with positive charge equal to the negative charge of an electron.
  • Experiments done at the Stanford Linear Accelerator Center in the late 1960′s and early 1970′s showed that protons are made from other particles called quarks.
    Protons are made from two ‘up’ quarks and one ‘down’ quark.

Neutron

Neutrons are uncharged particles found within atomic nuclei. James Chadwick discovered neutrons in 1932.

Experiments done at the Stanford Linear Accelerator Center in the late 1960′s and early 1970′s showed that neutrons are made from other particles called quarks. Neutrons are made from one ‘up’ quark and two ‘down’ quarks.

Electron

  • Electrons are negatively charged particles that surround the atom’s nucleus. J. J. Thomson discovered electrons in 1897.
  • The electron is the least massive electrically charged particle, therefore absolutely stable. It is the most common lepton with charge -1.
  • An electron is one of the fundamental particles in nature. Fundamental means that, as far as we know, an electron cannot be broken down into smaller particles (this concept is challenged by physicists looking for other particles).
  • Electrons are responsible for many of the phenomena that we observe in everyday life.
  • Mutual repulsion between electrons in the atoms of the floor and those within the shoes of a person’s feet prevents the person from sinking and disappearing into the floor.
  • Electrons carry electrical current and successful manipulation of electrons allows electronic devices to function.

Quark

Quarks are believed to be one of the basic building blocks of matter. They were first discovered in experiments done at the Stanford Linear Accelerator Center in the late 1960′s and early 1970′s.

Three families of quarks are known to exist. Each family contains two quarks.

  • The first family consists of Up and Down quarks, the quarks that join together to form protons and neutrons.
  • The second family consists of Strange and Charm quarks and only exists at high energies.
  • The third family consists of Top and Bottom quarks and only exists at very high energies. The Top quark was finally discovered in 1995 at the Fermi National Accelerator Laboratory.

For more on quarks:

Hadron

Any of a class of subatomic particles that are composed of quarks and take part in the strong interaction.

Any particle made of quarks and gluons, i.e. a meson or a baryon. All such particles have no strong charge (i.e are strong charge neutral objects) but participate in residual strong interactions due to the strong charges of their constituents.

Hadrons are colourless objects that consist of three quarks of different colour (baryons), or of a quark-antiquark pair (mesons).

Gluon

The carrier particle of the strong interaction. There are 8 different gluons with colour charge 2, i.e. the gluons are by themselves strongly interacting particles. Gluons bind quarks inside proton and other hadrons.

Meson

A hadron with the basic structure of one quark and one antiquark.

Mesons are color-neutral particles with a basic structure of one quark and one antiquark. There are no stable mesons. Mesons have integer (or zero) units of spin, and hence are bosons, which means that they do not obey Pauli exclusion principle rules.
For more on mesons, see:
Stanford Linear Accelerator Center: www2.slac.stanford.edu

Baryon

A hadron made from a basic structure of three quarks. The proton and the neutron are both baryon. The antiproton and the antineutron are antibaryons.

The proton is the only baryon that is stable in isolation. Its basic structure is two up quarks and one down quark.

Neutrons are also baryons. Although neutrons are not stable in isolation, they can be stable inside certain nuclei. A neutron’s basic structure is two down quarks and one up quarks.

Lepton

A fundamental matter particle that does not participate in strong interactions. The charge leptons are the electron, the muon, the tau and their antiparticles. Neutral leptons are called neutrinos.

neutrino-detector-on-the-future-of-human-evolution-website

Neutrino Detector

Neutrino

A fundamental particle with neutral charge and near-zero mass supposedly produced in massive numbers by the nuclear reactions in stars; they are very hard to detect since the vast majority of them pass completely through the Earth without interacting.

A lepton with no electric charge. Neutrinos participate only in weak and gravitational interactions and are therefore very difficult to detect. There are three known types of neutrinos (electron-, muon- and tau-neutrino), one for each family of elementary particles,all of which are very light but could have a non-zero mass as indicated e.g. by the solar neutrino deficit.

Photon

The carrier particle of the electromagnetic interaction.

  • A photon is one of the fundamental particle in nature and it plays an important role involving electron interactions.
  • Depending on its frequency (and therefore its energy) photons can have different names such as visible light, X rays and gamma rays.
  • Photons are the most familiar particles in everyday existence.
  • When we talk about “photons” we generally think of uncharged particles without mass that carry energy (there are other similar kinds of particles).
  • Low-energy forms are called ultraviolet rays, infrared rays, and radio waves.
  • Light, radiant heat and microwaves make use of photons of different energies.
  • An x-ray is a name given to the most energetic of these particles.

Interaction

A process in which a particle decays or it responds to a force due to the presence of another particle (as in a collision).

Ion – Atomic particle, atom, or chemical radical bearing an electrical charge, either negative or positive.

Ionization – The process by which a neutral atom or molecule acquires a positive or negative charge.

Decay – Any process in which a particle disappears and in its place two or more different particles appear.

Forces and Interactions – All forces between objects are due to interactions. All particle decays are due to interactions. The four types fundamental interaction processes responsible for all observed processes are:

Strong interactions, responsible for forces between quarks and gluons and nuclear binding – The interaction responsible for binding quarks and gluons to make hadrons. Residual strong interactions provide the nuclear binding force. In nuclear physics the term strong interaction is also used for this residual effect. (As a parallel, the force between electrically charged particles is an electromagnetic interaction, the force between neutral atoms that leads to the formation of molecules is a residual electromagnetic effect.)

Electromagnetic interactions, responsible for electric and magnetic forces.

Weak interactions, responsible for the instability of all but the least massive fundamental particles in any class.

Gravitational interactions – responsible for forces between any two objects due to their energy (which, of course, includes their mass).

Electron Accelerator

Everyday

Electrons carry electrical charge and successful manipulation of electrons allows electronic devices to function.

The picture and text on old-school video terminals used to be caused by electrons being accelerated and focused onto the inside of the CRT screen, where a phosphor absorbed the electrons and light was produced. A classic television screen is a simple, low-energy example of an electron accelerator (LCD and Plasma have almost completely replaced this application of accelerating electrons).  A typical medical electron accelerator used in medical radiation therapy is about 1000 times more powerful than a color television set.

The Ultimate Scientific Experiment

The Large Hadron Collider (LHC) is the world’s largest and most powerful particle accelerator. It first started up on 10 September 2008, and remains the latest addition to CERN’s accelerator complex. The LHC consists of a 27-kilometre ring of superconducting magnets with a number of accelerating structures to boost the energy of the particles along the way.

large-hadron-accelerator-on-the-future-of-human-evolution-website

The Large Hadron Collider: Unlocking secrets to benefit the Future of Human Evolution.

Inside the accelerator, two high-energy particle beams travel at close to the speed of light before they are made to collide. The beams travel in opposite directions in separate beam pipes – two tubes kept at ultrahigh vacuum. They are guided around the accelerator ring by a strong magnetic field maintained by superconducting electromagnets. The electromagnets are built from coils of special electric cable that operates in a superconducting state, efficiently conducting electricity without resistance or loss of energy. This requires chilling the magnets to ‑271.3°C – a temperature colder than outer space.

Accelerators at CERN boost particles to high energies before they are made to collide inside detectors. The detectors gather clues about the particles – including their speed, mass and charge – from which physicists can work out a particle’s identity. The process requires accelerators, powerful electromagnets, and layer upon layer of complex subdetectors.

Particles produced in collisions normally travel in straight lines, but in the presence of a magnetic field their paths become curved. Electromagnets around particle detectors generate magnetic fields to exploit this effect. Physicists can calculate the momentum of a particle – a clue to its identity – from the curvature of its path: particles with high momentum travel in almost straight lines, whereas those with very low momentum move forward in tight spirals inside the detector.

 

Molecular Biology Series: Proteins and Amino Acids

Structurally, proteins are polymers of amino acids. Amino acids are carbon compounds consisting of two side chains: basic amine (NH2) and acidic carboxylic acid (COOH) groups. The variable R-group is what gives amino acid its distinctive characteristic i.e. amino acids differ only due to the R-group. There are 20 different types of amino acids which makeup all the proteins in the body. An amino acid joins with another amino acid through a peptide bond i.e. a bond between carboxylic group of one and amine group of the next amino acid. Thus a polymer of amino acid is formed called polypeptide. Longer polypeptides eventually fold and a structural protein is formed.

The content and precise sequence of amino acids in a protein is encoded by the precise sequence of bases in the DNA. This precise sequence of amino acids is then responsible to determine the biological function of the protein. The sequence of amino acids also determines how the protein folds to make a 3D structure which is a prerequisite for its biological function. For e.g. many enzymes catalyze certain chemical reactions by binding with the substrate molecule. This binding is only possible when protein folds into a precise 3D structure which makes it possible for it to bind to the substrate in the precisely needed fashion. Just a little mistake and the precise binding does not possible thus the reaction fails to proceed. The field of protein folding, structure and stability has been one of the most important research fields for many years and still remain one of the unsolved mysteries.

<insert structure of amino acid image>

Structure of amino acids: Every amino acid consists of a basic amino and an acidic carboxyl group connected to a central Carbon molecule. The R-group attached to the central Carbon is what gives individual amino acid its identity.

<insert polypeptide chain image>

A polypeptide chain: Peptide bond between adjacent amino acids i.e. between carboxyl group from one and amine group from the other amino acid forms a polypeptide.

<insert folding polypeptide chain image>

 

Folding of a polynucleotide chain: A polypeptide chain of more than 100 amino acids can fold into a protein which has precise 3D structure and is biologically active


Next Article >

Central Dogma of Molecular Biology (Series)

DNA is found inside the nucleus in the chromosomes whereas the site of protein synthesis is outside the nucleus in the cytoplasm. Thus, direct production of protein from the DNA sequence is not possible. Exceptions exist, for example prions or prion-like proteins. The lack of exist of cellular machinery that can synthesize proteins directly from DNA maybe also due to the fact that RNA evolved before DNA. In fact, convincing evidences can be found which suggest that DNA is result of evolution of RNA to store the information in a safer manner i.e. for survival. In any case, central dogma of molecular biology is the backbone of molecular biology upon which today’s science exists. It shows the flow of information from DNA to protein. First postulated by Francis Crick (co-receiver of Noble prize in physiology and medicine for discovering the structure of DNA), the central dogma states that sequence of bases in DNA determine the sequence of bases in RNA (which is also a polymer of ribose nucleotide different from DNA) by a process called transcription, this sequence of RNA polymer then determine the sequence of amino acids in a protein. Protein is a polymer of amino acids.  There have been many modifications to the central dogma. For e.g. reverse transcription i.e. formation of DNA from RNA has been found and so on. However, the basic principle is still among the most widely seen phenomenon.

<insert central dogma molecular biology image>

Central Dogma: DNA can duplicate (replication), make RNA (transcription), this RNA is transported to the cytoplasm where it is used by the cellular machinery for translation (synthesis of protein)


Next Article >

Molecular Biology Series: The Structure of DNA

Being a deoxyribose nucleic acid, a strand of DNA is made up of by the repetition of nucleotides each of which consists of a deoxyribose sugar, attached to one of the four nucleic acid bases (adenine, guanine, cytosine and uracil). Each sugar-base combination is joined with each other by a phosphodiester linkage between the sugar molecules thus forming a polynucleotide.

DNA is a double helical molecule; there are two strands running in anti-parallel direction i.e. opposite in polarity. These two strands are held together by weak hydrogen bonds between the bases.

This pairing between the bases is made possible by the specific structure and meticulous precision of the specificity of possible pairing between the 4 bases. Adenine can pair only with thymine but not with other bases and vice versa. Similarly, cytosine can pair with guanine and not any other bases and vice versa. This means that the number of adenine must be equal to the number of thymine and the number of cytosine must be equal to the number of guanine in a stretch of DNA. This is often called Chargaff’s rule named after its discoverer.

Since DNA is a polymer of deoxyribose nucleotide the sequence of the bases which appear in a certain stretch of DNA determines the information it codes for. Human genome consists of about 3 billion bases. Not all DNA in the chromosome encode for a protein, some DNA sequences encode a protein (called genes), others encode only RNAs but those never form proteins. These two are called structural DNA. Other DNA sequences either function as regulatory DNA to regulate the production of RNA and/or protein or are vestige of evolution. Surprisingly, structural DNA sequences make up less than 2% of the human genome. Most of it consists of what was previously considered to be “junk DNA” i.e. DNA stretches without function. Today it is known that “junk DNA” is not junk after all. Everyday scientists are discovering specific roles for these non-structural DNA elements especially related to regulation of production of RNA/proteins. Thus the “information” about an organism or its “blue print” is encoded in the DNA but for that information to manifest as a visible trait or phenotype either as physical appearance, behavior or mental state, that information needs to transfer into proteins. After an enormous complexity of regulation and interaction with the environment, protein is formed and it gets involved in its specific function. At an instant of time, enormous amounts of genes continuously produce proteins which continuously perform their functions to keep a cell alive. A group of working cells make tissues, group of tissues make organs and a proper combination of functional organs make up an organism.

<insert image nucleotide pairing>

Schematic diagram showing the base pairing: Due to the structure of the bases adenine can only base pair with thymine and cytosine can base pair only with guanine. This hydrogen-bond is what holds the two strands of DNA together.

<insert nucleotide structure image>

Structure of a nucleotide: The sugar (deoxyribose) pairs with one of the bases to form a nucleotide.

<insert polynucleotide structure image>

Structure of a polynucleotide: Adjacent nucleotides join to form a DNA strand. Nucleotides connect through a phosphodiester bond between phosphate group (P) of one nucleotide and the deoxyribose sugar (D) of another.

<insert double helix dna structure image>

Double helical structure of a DNA: Two strands of DNA (polynucleotides: colored red and blue) are helically coiled around each other and held together by weak hydrogen bonds between the bases of each nucleotide.

Next Article >

Molecular Biology Series: Cells, Proteins, & DNA

A cell is similar to a car in many aspects. A car is made up of different parts each with a specialized function. It has wheels, an engine, steering wheel, brakes and a body that form a functioning car. Likewise, humans (and all complex living things) consist of parts made up of specialized cells each with their own functions.  While there are approximately 10,000,000,000,000 (1023) number of cells in each of us, there are only about 200 different cell types i.e. liver cells, nerve cells, skin cells, blood cells and so on.  DNA carries instructions on which, and how many, cells to make to complete the creation and maintenance of a human body.  Furthermore, every cell type has its own specialized functions and needs different types, numbers, and amounts of various proteins. The types, numbers and amounts of proteins in each cell are also controlled by DNA. Thus to understand the working of a cell (and therefore the human organism) it becomes necessary to understand how DNA directs the production of proteins.

DNA in a cell is made up of four different parts called nucleotides that appear in different sequences and patterns in a long string. Each nucleotide consists of a sugar (deoxyribose) bound on one side to a phosphate group and bound on the other side to a nitrogenous base.

<insert cells proteins dna image>

Proteins are the workhouse of a cell. They play a vital role in the maintenance, growth, division of cells and in communication between cells. The human genome, a complete set of human genes, comes in 23 separate pairs of chromosomes. Chromosomes are densely packed structures containing DNA and proteins. DNA in the chromosomes consist of genes (functional DNA), regulatory DNA (which regulates the function of genes) and other nucleotides (repeating units base pairs). Coiled DNA in the chromosome is bound with certain chromosomal proteins belonging to the “DNA-bound” family of proteins. The function of these proteins is to package the DNA and control its function.

 Next Article