Category Archives: Biology

Enzymes & their Roles

Quite simply:

Enzyme + Substrate = Product

  1. The substrate (AKA reagent) binds with the enzyme’s active site to form Enzyme-Substrate complex.
  2. Enzyme reacts with substrate to produce a Product, which is then released.
  3. Product released, and enzyme ready for more substrate.

Enzymes are:

  • One of more polypeptide chains – so a protein – but that form a structure with an ‘Active Site’.
  • The active site is ‘specific’, which essentially means it only has a few substrates that will fit it, and bind with it.

Enzyme Kinetics

The rate of a reaction depends upon:

  • The ‘speed’ of a single reaction, specified as the rate constant, k
  • The number of reactions occuring, specified by the substrate concentration

We know this from our rate equation, Rate = k[Substrates].

So how do Enzymes speed up (or slow down reactions)?

Enzymes change k by decreasing the activation energy.

Ploidy – Variation of Chromosome Numbers

Ploidy refers to the number of complete sets of chromosomes in a cell. You’ll probably have heard of haploid (n, gametic cells) and diploid (2n, somatic cells) cells in the human body so this is just delving a little deeper.

The number of chromosomes in a cell (it’s genome) = x

Diploid cells (somatic cells) = 2x

Haploid cells (gametes of a diploid organism) = x

We also know: Continue reading


Glucose is a highly adaptable metabolite found in many organisms, offering a free energy of -2830kJ mol when fully metabolised.

This energy is released in small portions via ATP, the body’s universal energy currency. A molecule of ATP holds approx 30kJ mol.

Outline to Glycolysis

Outline to Glycolysis

The diagram above shows the process and points where ATP is released or consumed during Glycolysis. It is important to remember that this pathway is only the first section of a larger process (metabolism), as Pyruvate from this chain is used later in Krebs cycle etc.

Glycolysis Diagram

Molecular structrues of Glycolysis

On this diagram we see the steps again, and highlighted in green are the molecules which differ from the next. I’ll come back and edit this later but for now you’ll have to compare it with the first diagram for enzyme names etc.

The pathway:

  1. Glucose –> Glucose-6-Phosphate (-1 ATP)
    The hydrogen on the alcohol on carbon 6 of glucose is replaced by a phosphate group from the ATP by Hexokinase.
  2. Glucose-6-phosphate –> Fructose-6-phosphate
    Phosphoglucose isomerase changes the glucose structure to fructose by swapping the C=O and alcohol groups on carbons 1&2.
  3. Fructose-6-phosphate –> Fructose-1,6-bisphosphate (-1 ATP)
    Phosphofructokinase replaces the hydrogen on the alcohol group of C1 with another phosphate group.
  4. Fructose-1,6-bisphosphate –> GLAP + DHAP
    Aldolase splits the fructose-1,6-bisphosphate into two 3 carbon molecules, dihydroxyacetone phosphate and glyceraldehyde 3-phosphate.
  5. DHAP –> GLAP
    Triose phosphate isomerase converts DHAP into GLAP by changing the structural configuration.
    From here on there are two molecules at a time (2 x 3 carbon rather than 1 x 6 carbon) and so all ATP & NADH figures have been doubled.
  6. GLAP –> 1,3-bisphosphoglycerate (-2 Pi) (+2 NADH)
    Glyceraldehyde 3-phosphate dehydrogenase replaces a H on C1 with an O and phosphate group.
  7. 1,3-bisphosphoglycerate –> 3-phosphoglycerate (+2 ATP)
    Phosphoglycerate kinase removes the phosphate group from C1.
  8. 3-phosphoglycerate –> 2-phosphoglycerate
    Phosphoglycerate mutase switches C2 & C3.
  9. 2-phosphoglycerate –> 2-phosphoenolpyruvate (+2 H2O)
    Enolase removes the alcohol on C3, forming a C=C between C2 & C3.
  10. 2-phosphoenolpyruvate –> Pyruvate (+2 ATP)
    Pyruvate kinase removes the phosphate group from C2, double bond C=O alters structure below C2.

Balancesheet: 2 ATP + 2 NADH – however 1 NADH produces 3 ATP when oxidised by the electron transport chain so glycolysis indirectly produces another 6 ATP. This means glycolysis has a net ATP production of 8 ATP.

Anaerobic Respiration

In anaerobic conditions we find only 2 ATP’s are produced for every glucose molecule converted to 2 lactate molecules.

This is because the cell needs to reoxidise the NADH, and one such way of doing this is reducing the pyruvate by lactate dehydrogenase with the NADH, producing lactate. All pyruvate must be converted to lactate to allow ATP synthesis to continue; and the lack of oxygen means no energy is gained from the oxidation of NADH.

The Kidneys and the Ionic Composition of the Extracellular Fluids

The regulation of homeostasis within the body involves the renal system – which comprises of 2 kidneys connected to a urinary bladder by independant ureters. From the bladder, urine passes out of the body via the Urethra.

The urine from the bladder can tell us many things about the condition of the body – from ionic content to water content to illnesses and disease. There are 4 different properties to look at:

  1. Colour – eg Red/Black might indicate red blood cells present & therefore Malaria
  2. Clarity – is it opaque, translucent…
  3. Odour
  4. Taste – eg A sweet taste might indicate glucose presence and therefore Diabetes

Kidney Function

The kidney allows homeostatic regulation of the water and ion content in the blood. This iincludes:

  • Regulation of extracellular fluid (ECF)
  • Regulation of blood osmolarity
  • Regulation of ion concentrations – eg keeping Na+, K+, Cl-, Ca2+ within normal ranges.
  • Regulation of blood pH with H+/HCO3-

Following the regulation of these systems the waste fluids and substances (such as urea) are excreted. The renal system is also involved in the production of some hormones such as Vitamin D hormone.

To do all of this, the Kidney is highly specialised and first filters substances out of the blood before selectively reabsorbing what is needed by the body. Anything not reabsorbed is excreted.

Kidney Structure

The functional unit within the kidney is the nephron, which spans the cortex and medulla of the kidney.

Diagram of a Kidney with Nephron closeup

Diagram of a Kidney with Nephron closeup – From HowStuffWorks

Looking at the Kidney above, we have:

A – Renal Vein
B – Renal Artery
C – Ureter
D – Cortex/Medulla
E – Renal Pelvis
F – Capsule

In fact, this illustration is not great – all of the tissue between the pelvis and capsule forms the medulla and cortex. The medulla surrounds the pelvis with a structure containing Renal Pyramids (shown in red on the picture above). Surrounding this is the thinner cortex which does not share this unique structure.

Spanning the medulla & cortex there are millions of nephrons. And looking at the nephron (listed in the order filtrate passes through):

5 – Renal corpuscle, comprised of the glomerulus and the bowmans capsule
4 – Prominal Convoluted Tubule
2 – Descending loop of Henle
1 – Ascending loop of Henle
6 – Distal Convoluted Tubule
3 – Renal Capillaries – these do surround all of the above but are only illustrated surrounding several areas.

The distal convoluted tubule then leads on to the collecting duct which also has an important role in Kidney function. The collecting duct leads to the ureter.


Filtration of substances out of the blood happens at the Renal Corpuscle.

Renal Corpuscle

Renal Corpuscle – Modified from original: Gray’s Anatomy figure 1130

The entire unit is the renal corpuscle, which areas in red are the glomerulus and pink the bowmans capsule.

A – Afferent Arteriole
B – Efferent Arteriole (leaving the glomerulus)
C – Fenestrated Endothelium of Glomerular Capillary
E – Basal Lamina
D – Bowman’s Capsule Epithelium
F – Beginning of Proximal Convoluted Tubule

The blood enters the glomerulus and molecules/fluid are filtered out of the blood along a net filtration gradient (~17mmHg). This is driven by the high (60mmHg) hydrostatic pressure which is resisted by the capsule fluid pressure and glomerular osmotic pressure. This net filtration pressure forces molecules through 3 barriers:

  • Glomerular Capillary Endothelium
  • Basal Lamina
  • Bowman’s Capsule Epithelium

This means molecules are sieved and have to be able to ‘fit’ through ‘slits’ in the bowman’s capsule epithelium – so larger molecules like cells and larger proteins (eg red blood cells) stay in the blood. The standard glomerular filtration rate is 125ml/min or 180L/day.

Autoregulatory systems ensure the hydrostatic pressure remains constant even when blood pressure or heart rate increases by altering blood flow through the glomerular capillaries. Smooth muscle contracts or relaxes depending on the need.


DNA Mutations and Genetic Diseases

As mentioned, chromosomes select characteristics such as sex (Men have different copies of the sex chromosome, X and Y wheras females have two X chromosomes) but also cause diseases through chromosomal abnormalities:

  • Downs Syndrome – Caused by 3 copies of chromosome 21. This is referred to as trisomy.
  • Turner Syndrome (women) – only 1 X chromosome.
  • Klinefelter Syndrome (men) – YXX (trisomy) rather than YX.
  • Cystic Fibrosis – 3 nucleotides removed in DELTAF508 gene – stopping production of phenylalanine.
  • Sickle Cell Anaemia – A changed to T in gene for haemaglobin.

Materials can be traslocated from one chromosome to another, nucleotides added or removed or bases substituted. These changes can cause diseases and other genetic problems. Usually these are seen during protein synthesis.

– Down’s Syndrome

Downs Syndrome is a genetic disease caused by an extra copy (which may be complete or partial) or chromosome 21 (trisomy 21). The disease is often associated with lessened cognitive ability & physical development and features a common set of facial characteristics. Further implications of Down’s Syndrome vary greatly from one individual to another. Fertility is another affected function, with very few males able to successfully reproduce and only some females when mating with unaffected males. Incidence rates of the disease in their children are much greater at approximately half.

While treatment can be provided to improve a sufferers quality of life there is no cure.

Fig 2 - Trisomy 21 Causing Down's Syndrome (Female Karyotype)

It is estimated 1 in 800-1000 people are born with the disease, with several factors contributing to the likelyhood of a child having it. The most notable of these seems to be the age of the mother, with the chance of the disease increasing as a mother gets older.

The Mutation in Down’s Syndrome

There are several ways Down’s Syndrome has been discovered to occur. About 95% of all cases occur via the first route, Trisomy-21.

  1. Trisomy 21 – 95% of cases – Where the extra chromosome 21 is added to a gamete in nondisjunction (where either homologous chromosomes fail to come apart in meiosis 1 or sister chromatids fail to come apart during meiosis 2 or mitosis) event during production in the parent; then joining with a gamete from the other parent to produce an embryo with 47 chromosomes. The vast majority (~88%) of this mutation occurs in the mother.
  2. Mosiac Down’s Syndrome – 1-2% of cases – Where some of the cells in the embryo (and later body) have Trisomy-21 and some are normal. This can occur as Trisomy-21 above followed by a reversion to normal cells during cell division in the embryo; or the other way around where cell division in a normal embryo somehow change to Trisomy-21.
  3. Robertson Translocation – 2-3% of cases – In the karyotype of one of the parents, the long arm of chromosome 21 is attached to another chromosome (often 14) and following normal disjunctions during cell replication there is a high possibility of a child receiving the extra chromosome. This is also known as familial Down’s syndrome, as it is passed directly down and the parents show a normal phenotype – with this type there is no age effect and males are as likely as females to cause the disease in their offspring.

A final, very rare occurance is the duplication of a portion of chromosome 21, meaning that there are copies of some of the genes. If these are the genes responsible for the effects seen in Down’s syndrome then these effects will be expressed but otherwise the phenotype will be normal.

– Sickle Cell Anaemia

Sickle cell anaemia affects the red blood cells in the body, by producing cells which hold a rigid sickle shape rather than the usual doughnut. As this is a genetic disease based on a recessive allele there is a possibility for offspring to be carriers, suffer the disease or not carry it at all, depending on their parents. Sickle cell disease is caused by having both recessive alleles (SS) while people can also have sickle cell trait which means they are a carrier but do not show the effects of the disease (HbS).

As the cells are more rigid than normal, and combined with their unusual shape there are many complications which can occur within the body. These include blockages of blood vessels, increased destruction of blood cells (and so reduced oxygen capacity), problems with the spleen and a host of other blood & circulation related problems.

A sickled red blood cell sits among normal cells

It is interesting to note that the disease is found in higher levels in areas where Malaria is more common, as being a carrier (so the sickle cell trait rather than sickle cell disease) is a benefit as sickling of blood cells as they are attacked by malaria halts its spread.

Sickle cell disease is caused by a mutation on the haemoglobin gene – where A is changed to T at position 17 in a base substitution (mis-sense). This changes a glutamic acid on the protein (GAG) to a valine (GTG).

– Types of Mutation in DNA

Fig 1 - Showing different types of chromosomal mutation

Wild Type = Normal Sequence of DNA

  • Point Mutations – Single nucleotide changes in the DNA strand which result in different codons.
    • Miss-sense = Resulting in a different amino acid.
    • Non-sense = Resulting in a STOP codon and possible termination of protein chain.
    • Silent = Codon codes for the same amino acid as wild type so the protein is the same.
  • Frameshift Base Insertions or Deletions = One nucleotide added or removed, resulting in the change of most of the following amino acids.

5- Selection & Evolution

Darwin’s Origin of the Species & Natural Selection

One of the key points of selection and evolution is that of Natural Selection – that some organisms have a better chance of survival than others.

Let’s look at what might happen:

  • Organisms within a population are not identical, varying in both genotypes and phenotypes.
  • While some organisms in the population survive, others die (removing themselves from the gene pool).
  • The surviving organisms then breed, passing on their genes to their offspring. (As the parent organisms survived, it is likely they hold some advantageous genetic characteristics that the organisms which perished did not).
  • This increases the frequency of the advantageous genes in the population, and the cycle can begin again.

Over time, the population is filtered to leave only organisms with characteristics suited to their environment – helping them survive.

5- Classification & Taxonomy

The Five Kingdoms

There are 5 kingdoms in the classification system. Organisms are classified according to their evolutionary relationships (their phylogeny).

Phylogeny is the study of the evolutionary history of organisms, and gives us an insight as to how to group them and their extinct relatives. The base hierarchy in the classification system is the Kindom.

Generally, we can order the Kingdoms by increasing complexity. To help remember the names of the kingdoms, I was taught:

Pretty Polly Finds Parrots Attractive – Prokaryote, Protoctista, Fungi, Plantae, Animalia.

Prokaryotes Protoctista Fungi Plantae Animalia
Cell Structure Unicellular; no membrane bound organelles Eukaryotes, Unicellular & Multicellular Eukaryotes, Unicellular & Multicellular (Yeast) Eukaryotic, Multicellular; Large Vacuoles Eukaryotic, Multicellular
Cell Wall Murein Sometimes Polysaccharide Chitin Cellulose None
Nutrition Autotrophic, Aerobic Heterotrophic Autotrophic, Hetrotrophic Heterotrophic Autotrophic (Photosynthetic) Heterotrophic, Digestive System
Reproduction Binary Fission Fission Spores Seeds/Spores, Some asexual while some sexual Develop from embryo
Example Bacteria Algae, Protozoa Penicillin Mosses, Ferns Humans, Animals


Q. What’s a photosynthetic organism?

A. An organism that gets its energy by absorbing light.

Q. What’s a autotrophic organism?

A. An organism which gets it’s energy from light (photosynthesis) or from chemical interaction (chemosynthesis).

Q. What’s a heterotrophic organism?

A. An organism that relies on complex organic matter for food.

Remember that 4 of the 5 kingdoms feature Eukaryotes! Only Prokaryotae contains Prokaryotes (no surprise there!).

Taxonomy (Breaking it down)

We break down organisms into a total of 7 hierarchical classes (including Kingdom above). That’s a lot of possible choices for organisms, and is know as Taxonomy, or Alpha Taxonomy.

The 7 levels are Kingdom, Phylum, Class, Order, Family, Genus and Species. You could remember this as:

King Penguins Climb Over Frozen Grassy Slopes

Here’s an example of two organisms and their taxonomy:

Humans Large White Butterfly
Kingdom Animalia Animalia
Phylum Chordata Arthropoda
Class Mammalia Insecta
Order Primates Lepidoptera
Family Hominidae Pieridae
Genus Homo Pieris
Species sapiens brassica

As you can see, humans are sapiens of the Genus Homo. AKA Homo sapiens (I bet you’ve heard that before!).

The only similarity between these two examples is that they are both in the Animalia kingdom. This means they share a great number of common traits, and so actually tells us a lot about the organisms.

It is also worth bearing in mind that Protoctista is often the ‘Other’ category where organisms who have no clear Kingdom are put. For example, Slime Moulds have fungi characteristics, yet are not quite suitable for classification in the Fungi Kingdom.

The Species

Species is the final tier on the taxonomy hierarchy; and is a group of organisms with similar traits. These include:

  • Morphology (The outside appearance of an organism, including shape, colour, structure and pattern)
  • Physiology (The way in which an organisms works, by looking at it’s biochemical, mechanical and physics functions)
  • Behaviour

BUT most importantly, we can class two organisms as the same species if they can naturally breed together and produce fertile offspring.

The fertility point is an important one, as there are several organisms that can breed together, but produce a sterile offspring which cannot breed any further – such as a horse and a zebra which can produce a hybrid. This hybrid is sterile, so we know what the horse and the zebra are different species.

Protein Purification

– Protein Identification

Protein purification begins with the need to identify the protein we want to purify! There are several methods that can be used to rapidly identify the protein:

  • Enzyme Assay (by catalytic activity) – with certain enzymes we can use colorimetry to detect a product as a reaction progresses. The higher the more enzyme present, the faster the colour or light absorbance will change. An example is testing for Alcohol Dehydrogenase, which will lead to a change in the levels of NADH and NAD+ as Ethanol is converted to Ethanal. This change can be detected by colorimetry at ~340nm.
  • SDS-PAGE Electrophoresis (by size) – this method seperates protein chains by size by electrophoresis. This method denatures the proteins.
    The sample is run at the same time as a molecular mass marker sample, containing proteins of known mass. The marker sample will provide a scale for the mass of your sample. Once you’ve run the gel you will be able to plot the results as above, draw a best fit line and read off the Molecular Mass of your sample protein.
  • Immuno-Assay (by specific antibodies) – Antibodies that fit specifically to the protein you are looking for are added to the sample. When these bind to the target protein they will instigate a colour change or some other noticable change. The presence and concentration of the target protein can be assessed by the extent of the changes – if it was a colour change then the darker the colour goes, the more target enzyme must be present.
  • Western Blotting – A combination of electrophoresis and immuno-assay. The immuno-assay technique is run by electrophoresis. This will be useful if your sample contains several different proteins and you need to identify the target protein. The band of colour (or change) will show you the correct protein, and then you simply need to calculate the approximate molecular mass using the molecular mass markers.

– Protein Purification

I’ve broken the purification methods here into 8 different headers, each a physical-chemical property or biological activity.

  1. Stability (Heat). Some proteins are more heat tolerant than others and can survive heating while others denature. If your target protein is heat stable at above 60C and your contaminants are not, then simply heating your mixture to 60C for 30 minutes will denature most of the contaminents. This will leave you with a much higher concentration of your target protein in your mixture.
  2. Solubility (Seperate by pI). Proteins are least soluble at the pH equal to their isoelectronic point. When helped by the addition of salts to the solution this can lead to their precipitation. As the salt concentration increases, different proteins will precipitate.
  3. Size. Proteins can be seperated by Gel Permeation Chromatography (Gel filtration). The proteins are run through a buffered, porous, cross linked resin. While small molecules are able to fit into the pores in the resin, the larger proteins cannot and so travel ahead, with the small molecules lagging behind.
    This is due to a larger volume of buffer available to the smaller molecules, meaning more buffer must pass down the column for them to elute, compared to the relatively smaller volume of buffer required to elute the larger, excluded proteins.
  4. Density (Centrifuge). By centrifuging the sample in a test tube containing a sucrose density gradient, the centrifugal forces will force the proteins down the tube until they reach a concentration where the density of the sucrose solution is the same as their own. This level is known as it’s isopycnic level.
  5. Charge. There are several different methods of purification by charge:
    1. Gel Electrophoresis – Based on movement of a protein through a cross linked gel called polyacrylamide. This would occur at a pH where the protein has a charge (not at it’s pI). The size of the pores can be altered by changing the concentration of cross linking reagent, and the speed at which a protein travels is equal to its charge:mass ratio. (This method does not tell us anything about the protein’s molecular weight).
    2. SDS PAGE – This cannot really be used for purification because SDS detergent (Sodium Dodecylsulphate) is used which denatures the protein. It unfolds the protein and surrounds it with -ve charge sulphate groups which means all the proteins have a uniform charge:mass ratio. SDS has a 12 carbon hydrocarbon chain, and then a hydrophilic sulphate group. The Sulphate groups surrounding the protein form a miscelle.
      The sample is now allowed to run on a gel, from -ve to +ve, and as they all have the same mass to charge ratio, their rate is determined only by their size. The smaller protein molecules move faster and the larger molecules move slower through the gel.
    3. Isoelectric Focusing – Very similar to (1) above, but instead of an electric charge, there is a pH gradient along which the proteins can move until they are at a point where they  have no net charge (at their pI).
    4. Ion Exchange Chromatography. Essentially, both columns and proteins become charged at different pH’s, and by altering the pH we can hold on to some proteins while others are eluted.
      Diethylaminoethyl-Cellulose (DEAE-Cellulose) has a +ve charge below pH 9.5 wheras CarboxyMethyl-Cellulose (CM-Cellulose) has a -ve charge above pH 3.0. Therefore:
      – Proteins with a +ve charge at pH7 will bind to a column of CM-Cellulose, while
      – Proteins with a -ve charge at pH7 will bind to a column of DEAE-Cellulose.
      We can then alter the pH of the solution to release certain proteins or to pick up others. Another way of dispersing ionic interactions between the column and proteins is to increase the salt concentration.
  6. Hydrophobicity. Proteins nearly always feature hydrophobic areas or side chains and these allow the proteins to bind to resins with hydrophobic groups attached. This means the proteins can be eluted with a gradient of buffer (eg an organic solvent such as ethanol). The proteins forming the strongest interactions with the resin column will require higher concentrations of ethanol to elute.
  7. Biological Function. If a protein has a high affinity for a substrate (eg. ADH has a high affinity for NAD+) then we can use affinity chromatography. If we immobilise the substrate (eg. NAD+) then the protein will bind to that substrate, immobilising itself – allowing other proteins to run free of the column. By releasing free NAD+ throught he column the substrate will gradually release the immobilised NAD+ in favour of the free NAD+ and run free of the column.
    This method can purify a protein in one step, and works best if the protein has a high affinity for the bound ligand.
  8. Fusion Proteins. This involves the addition of a gene to a protein that essentially ‘tags’ the protein. An example would be a tag containing histidine residues, which would bind to metal ions in the column.
    Here, the imidazole rings on the histidine residues stick to the immobilised metai ions allowing other proteins to elute the column. Then, like the method above, add free imidazole to release the fusion proteins and then use a protease to cut the tag away. Run the column again and only the tags will bind, allowing the protein of interest to run free.

Proteins – Quaternary Structure & Overview

The quaternary structure of a protein involves the association of folded polypeptide chains into a mature, active protein.

  • This can be a single polypeptide chain (monomer), 2 chains (dimer), 3 chains (trimer), 4 chains (tetramer) and so on…
  • The associated chains can be identical or different.

Some quaternary structure require additional polypeptide chains (which were removed during production) in order to achieve a working protein state (eg. Mature insulin). There are also structures which will revert to their original shape once broken, as the order is set in the primary structure of Amino Acids.

With Insulin, a helper amino acid strand is used to ‘hold’ two sequences in place, allowing the formation of disulphide bridges. I’ve tried to illustrate before and after:

S is the signal chain, while B acts as a support structure during disulphide bridge formation between A and C.

– An Overview

  • Primary Structure – The sequence of Amino acids on a chain.
  • Secondary Structure – The 3D relationship between Amino Acids – leading to α helix, β pleated sheet etc.
  • Tertiary Structure – The 3D relationship between parts of the above structure.
  • Quaternary Structure – The number of and relationship between amino acid chains (seperate tertiary structures).