MRI Scanning

MRI Scanning relies on radio frequency electromagnetic waves, and the fact that some atomic nuclei behave like small magnets in an external magnetic field. The patient lies within this magnetic field.

The property that allows some nuclei to behave like magnets is called Spin. Hydrogen nuclei are used in MRIs, because Hydrogen is present in all tissues. A Hydrogen atom is a Proton. These Protons have small N and S poles, and they are in random directions under normal circumstances (gravitational field).

When a strong magnetic field is used, the protons are forced to align itself with the field with the N facing the S pole of the field. Occasionally, a proton is in a flipped position compared to the rest (S pole to S pole) - this is an unstable higher energy state.


The protons rotate in the direction of the magnetic field rather than align exactly with it. The rotation action is called Precession.

The angular frequency of the precession is known as the Larmor Frequency, which depends on the nucleus' involved and the magnetic flux density of the field (the `frequency` is measured using Radians per second). The stronger the external magnetic field is, the faster the protons precess.

The protons in the external magnetic field are occasionally subject to pulses of (radio frequency) waves. This frequency equals the frequency of the precession, so resonance occurs (nuclear magnetic resonance).

When the RF waves are switched off, the protons gradually revert back to the lower energy states - by releasing RF waves. We can detect these, and the rate of the `relaxation` of the protons can be used to tell us about the environment of the protons. For example, water/watery tissues have a relaxation period of several seconds, fatty tissues last several hundred milliseconds, but cancerous tissues has an intermediate period.

This allows an image of the patient to be built up.

PET Scanning

PET, or Positron Emission Tomography, is a technique using γ-radiation and positrons. The radiopharmaceuticals used emit positrons - β+.

For example -  
  Fluorine-18 (18/9 F) decays into 0xygen-18 (18/8 O) along with β+, V and γ.

When the positron is emitted, it can collide with an electron - which is known as Positron-Electron Annihilation - and two γ-photons are emitted. These photons are emitted at 180 degrees to each other.

  By surrounding the patient with γ detectors, the γ-rays are detected, and the time difference between the two rays helps determine where they were emitted. This can eventually build up a 3D image of the area.

On this image you can see that there would be Gamma detectors surrounding the patient.

Radiopharmaceuticals & Gamma Cameras

  To put it plainly, a Radiopharmaceutical, or Tracer, is a radionuclide (, or radioisotope) attached to a substance that will target a specfic part of a patient's body - for example, cancerous cells have an uncontrolled cell division, so take up more glucose to fuel the divisions. Therefore glucose would be a suitable substance to attach a radioactive marker to if you were looking for cancerous tissue.

  Once ingested or injected into the patient's body (and after a suitable time period so the radiopharmaceutical has `zoned in` on the targeted tissue or area), the patient is screened using a Gamma Camera.

A diagram showing a Gamma Camera taking in Gamma radiation, γ.

The γ-radiation emitted from the patient is projected in every direction. The Collimator, shown on the diagram, ensures only the γ-radiation travelling at the right plane enters the camera. The collimator is usually made from lead to stop other planes of radiation entering.
  The Scintillator, shown in the diagram as the crystal, only detects photons travelling along the axis of the collimator, so any radiation at a slight angle is cut out. The γ-photons that are dead on strike the crystal, and electrons are emitted on the other side (the Photoelectric effect). The electron travels up the photomultiplier tube, and impacts involving the dynode release more electrons. Soon there is a huge number of electrons and an electrical pulse is noticeable.
   Those pulses from the photomultiplier tubes are processed electronically by an attached computer and reassembled to produce an image.

The Lac Operon

The Lac Operon is an example of Enzyme Induction – when bacteria change the synthesis rates of specific enzymes in response to environmental changes. Here, the Lac Operon was theorised after experiments where glucose and lactose were given to E. Coli, which then used glucose before using lactose in two growth phases.

The enzyme E. Coli uses to process lactase is called (Beta) B-Galactosidase and Lactose Permease. B-Galactosidase catalyses the hydrolysis of lactose to glucose and galactose, whereas Lactose Permease transports lactose into cells.

The actual structure of the Lac Operon can be read as I-POZY, where:

I is a regulatory gene, and IS NOT part of the operon and is some distance away. I is used in the Lac Operon description to show the start of the process.

P – The Promoter region. This is DNA that RNA polymerase binds to, to transcribe the genes Z and Y.

O – The Operator region. A length of DNA sitting next to the structural genes (Z and Y). It can switch them on or off. The operator region is seen next to the promoter region in diagrams.

Z and Y – Structural Genes. Z codes for the enzyme B-Galactosidase, and Y codes for Lactose Permease.

TO TURN THE LAC OPERON OFF:

Step 1:

I, the regulatory gene, is transcribed and translated to produce a repressor protein. The protein can bind to lactose and to the operator region.

Step 2:

The repressor protein binds to the O-region, and in doing so covers the promoter region as well. This not only stops the operator region from switching Z and Y `on`, but also prevents RNA Polymerase from binding to P (which in turn stops production of the mRNA that codes for Z and Y).

Step 3:

Without the mRNA the B-Galactosidase and Lactose Permease cannot be created.

TO TURN THE LAC OPERON ON:

Step 1:

As above, the repressor protein is produced and binds to O, covering P also.

Step 2:

Lactose is now present. When lactose binds to the repressor protein they are both removed from O.

This frees O and P to do their own processes – that is, for RNA polymerase to bind to P to begin production of Z and Y, and O switches Z and Y on.

Step 3:

B-Galactosidase and Lactose Permease are now produced, and each act with the Lactose.

 This diagram shows both `on` and `off`.

 This diagram doesn't show the process, but is a good labelled picture of the seperate parts of the Operon. The CAP is the Regulatory Gene, I.

Mitosis

Mitosis is the process of asexual (single organism) division. This is how cells split apart (into four cells).

The process can be split into P-M-A-T, or:

Prophase

Metaphase

Anaphase

Telophase

The starting point is Prophase:

Chromatin condenses and becomes `super-coiled` chromosome/s. The chromosomes come together as homologous pairs to form a Bivalent. Each pair has a maternal and a paternal chromosome, and both chromosomes are identical.

None sister chromatids wrap together at a Chiasma. Sections are swapped (hence some mutations occur).

The nuclear enveloped and nuclear membrane now break down, and spindle fibres form from Centrioles at each end of the cell.

Metaphase:

The Bivalents (homologous pairs) all line up at the equator (the centre of the cell), and attach to the grown spindle fibres. They are then arranged randomly so each member of a pair face the opposite ends of the cell. The chiasma is still in place.

Anaphase:

The Bivalents are pulled apart (with one chromosome per side) by the spindle fibres towards the centrioles. Any non-sister chromatids entwined at this point are pulled apart (so some chromosomes have different codings as parts of one are attached to another and vice versa).

Telophase:

New nuclear envelopes form around the chromosomes. The chromosomes themselves now uncoil back into chromatin. The two cells are split in the centre by Cytokinesis.

This whole process occurs twice to produce 4 new cells, the second time by the original cell and the new copy.

 This process happens twice - the daughter cells are used in the `second round`.

This shows when Mitosis takes place - during the `M` stage. G1 and G2 are Growth Stages, and S is  the synthesis of new DNA. Go is when a cell stops the cell division cycle.

Protein Synthesis

A protein is synthesised during two processes. The first is transcription.

Transcription begins with the specified DNA strand coding for the gene dipping into the nucleolus. This `unzips` the DNA (by breaking hydrogen bonds between complementary bases). The half-DNA acquired is the template strand . Free floating nucleotides line up and bind to the template strand (via Hydrogen bonds). In the mRNA strand about to be created, the base pairs are complementary to one another, but here U-nucleotides bind to A-Template strand nucleotides. The bindings are catalysed by RNA polymerase.

The mRNA produced is complementary to the nucleotide base sequence on the template DNA strand and is therefore a copy of the base sequence on the coding strand of DNA.  The mRNA is the released and goes through a nuclear pore.

Translation is the second stage of protein synthesis, when amino acids are lined up to create the protein.

The mRNA strand is able to fit into a groove in a ribosome. When this happens one can move along the other. There is space for two amino acid-tRNA complexes on the ribosome, where there are six bases (two codons) to bind to. The first base sequence is always AUG.

An amino acid-tRNA complex attaches to the ribosome. The tRNA has an anti-codon, which can bind to a complementary codon on the mRNA. Another complex binds to the adjacent base sequence. The amino acids bound to the tRNA molecules are placed together using peptide bond. The first tRNA molecule is now free to move (it has given up its Amino Acid), and the Ribosome or mRNA shifts along. Another complex binds to the next codon that’s just been revealed. The new amino acid bind to the other amino acids with a peptide bond. This is repeated till the end of the mRNA strand. The chain of amino acids is the coded protein.

A few pictures showing the full process.

 A picture showing Translation across a Ribosome.

Organelles - A summary

This is a brief summary of some common place organelles:

First, I'll provide some picture references so you can remember which cell (animal/plant) these organelles are most common.

A typical common-place animal cell.

A typical common-place plant cell.

The Nucleus:

The nucleus is the largest organelle, and contains almost all of the genetic data. The data is organised into chromatin, and is used in protein synthesis, cell division and other processes. Chromatin consists of DNA strands and proteins, and contains the `codes` for proteins. During cell division the chromatin condenses into Chromosomes.
The Nucleolus in the centre creates Ribosomes and RNA, used in creating proteins (protein synthesis).
Molecules may pass through the Nuclear Pores.

Endoplasmic Reticulum (ER):
There are two types of ER - Rough ER and Smooth ER. The difference is that the Rough ER has Ribosomes bound to it whereas the Smooth ER doesn't.

Rough ER transports proteins that were attached to Ribosomes. The Smooth ER is involved in making lipids.

The Golgi Apparatus:

The Golgi Apparatus is a pile of membrane coated sacs, flattened together. It receives proteins and modifies them, maybe adding sugar molecules, then packages the proteins in vesicles.

Mitochondria:

The Mitochondria is responsible for producing ATP (Adenosine Triphosphate) - the `universal energy carrier`, during respiration.

Chloroplasts:

Mainly found in plant cells. The membrane surrounding the Grana (plural of Granum) is the Thylakoid Membrane (more specifically, the Thylakoid stack to produce Granum, therefore the Thylakoid Membrane coats the Grana). Chloraphyll is present on the Thylakoid Membrane and in the intergranal membranes. The chloroplast is involved in Photosynthesis.

Ribosomes:
Ribosomes are very small organelles. They float freely in the Cytosol (the Cytosol is the fluid in the cell, the Cytoplasm is the fluid plus the organelles), and are also attached to the Rough ER. They consist of two subunits. Ribosomes are involved in Protein Synthesis.

Centrioles:
Small protein `microtubules` (fibre strands) either side of the nucleus. They're involved in cell division.

Electron Microscopes

Electron Microscopes are split into two types: Transmission Electron Microscopes (TEM) and Scanning Electron Microscopes (SEM). An Electron Microscope involves using a beam of Electrons rather than light. This beam has a much smaller wavelength (0.004nm) than light, so the resolution is much greater than when using a Light Microscope. Magnets are used rather than lenses. Electrons are not visible to humans, so the image produced is projected onto a screen (no colour) as an Electron Micrograph. Colour is sometimes added for visual aid. Staining is still used, but metal particles/salts are used instead.

Transmission Electron Microscopes, or TEM:
The TEM is when electrons pass through a very thin sample there is contrast in the denser parts, because the electrons don't pass through as easily. A 2D image is produced. The largest magnification possible with the TEM is x500,000.

 
The Scanning Electron Micrscope, or SEM:

The electron beam is fired at the sample, but doesn't pass through - they're reflected away to give a 3D image. The highest magnification with the SEM is around x100,000.

Summary:
The Electron Microscope has a much higher resolution than a ligh microscope (0.1nm!). We can also use the TEM to view the organelles inside cells, rather than the top layer of the specimen. The SEM can provide a unique 3D image when required. Some of the troubles involved in using an Electron Microscope are that the microscope is a difficult piece of equipment to master, and that the microscope must have a vaccuum (so the Electrons don't rebound off air particles etc) - greatly increasing the cost of the microscope.

Light Microscopes

Light Microscopes utilise multiple lenses to magnify an image to appear larger than it actually is, using light from a bulb underneath the specimen.
A light microscope normally consists of four objective lenses - a x4, x10, x40, and a x100 lens. The x100 lens is usually an oil immersion lens.  The eyepiece lens also adds x10 to the microscope.

Those numbers are the magnification that the light microscope can show you. Magnification is a measure of how big an image is seen to be compared to how big it actually is. The highest magnification that the light microscope will provide you with is x1500.
Resolution is the ability to distinguish between two seperate points. The higher the resolution, the better the detail. The highest resolution a light microscope will give is around 200nm - because of the wavelength of light. Any closer and the objects will appear as one point.

To prepare a specimen for viewing using the light microscope, it is often `stained` or `sectioned`. Staining the specimen is using a chemical to add colour (by binding to other chemicals on the specimen or otherwise). For example, Acetic Orcein stains DNA dark red. Sectioning involves embedding the specimen in wax, so it can then be cut into strips for viewing. This is to help with soft, delicate pieces of tissue.

Staining:

Sectioning:

A sectioned kidney (not the best example to use with a microscope).

A formula to use with magnification is:    

Actual size of specimen = Image size (measured via microscope measuring utensil or using an image provided)  / Magnification of image

Or     I=AM