Author Archives: dave

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

Bases, Acid Base Reactions and Equilibriums

So we’ve heard of Ka/pKa, the acid dissociation constant – but what is there for bases? There is such a thing as a base dissociation constant Kb but more commonly the reverse of Ka is used.

A base would normally be indicated by a high pKa – meaning there is very little dissociated H+. Kb is simply the opposite as shown below.

Base Dissociation Constant

Base Dissociation Constant

So if we were to look at Ammonia (NH3):

Kb for Ammonia

Kb for Ammonia (NH3)

But…seeing as we aren’t using Kb/pKb we simply need to rearrange our base dissociation formula to fit into Ka/pKa:

Ka of Ammonia (NH3)

Ka of Ammonia (NH3)

From this you may notice it’s the other way round for the Ka for acids, as there the top line holds the base NH3 while in acids the acid is found on the bottom line (eg HCl).

Acid Base Reactions – and Equilibrium

Acid base reactions have an equilibrium, and to calculate it we simply combine the Ka of the acids with the Ka of the bases.

Consider the reaction between HCl and NaOH, producing NaCl and H2O. Their Ka equations would be as follows:…

Acids and Bases – pKa, Equilibrium Constant and logs

The best place to start is at acids – and as we know acids can give up a proton to become deprotonated.

Acid and Conjugate Base

Acid and Conjugate Base (& charges)

The acid will dissociate into a proton (H+) and cunjugate base (A-). Note that this is in equilibrium – there is a mixture of both sides of the equation present. The constant for this equilibium (the acid dissociation constant, Ka) tells us the position of the equilibrium. Ka is the concentration of the products over the concentration of the reagents:

Ka = Products Concentrations / Reagent Concentrations

Ka = Products Concentrations / Reagent Concentrations

therefore, for Hydrochloric Acid (HCl):

Acid Dissociation Constant for HCl

Acid Dissociation Constant for HCl

Simple, huh? What Ka tells us is a numeric value for the strength of an acid in solution. The larger the value, the smaller the extent of dissociation.

To illustrate, a strong acid like HCl has a Ka value of 1×10^7, which clearly shows a large bias towards products. Acetic acid on the other hand has a Ka value of 1.7×10^-5 – which strongly favours reagents.

So, what’s all this ‘log’ stuff?

We use logs to convert long numbers into a user friendly scale – as the numbers we often get are on a huge scale (see HCl and Acetic Acid above). To do this we put p into our acid dissociation constant Ka.

pKa & Log of the Concentrations

pKa & Log of the Concentrations

Simply, p = – log, so the result is the logarithm of negative Ka.

Going back to HCl & Acetic Acid:

HCl Ka = 1×10^7; – log Ka = -7, therefore pKa = -7.

Acetic Acid Ka = 1.7×10^-5; – log Ka = -4.76, therefore pKa = 4.76.

So stronger acids have lower pKa‘s (or have higher Ka‘s).

We can easily convert back into Ka:

Converting between pKa and Ka

Converting between pKa and Ka

pH and pKa

If the pH of a solution = the pKa, then the acid is in equilibrium – it is half dissociated. This scale goes either way – if pH is less than pKa then it’s mainly protonated acid; if pH is more than pKa it’s mainly deprotonated.

pH and pKa - Equilibrium & Protonation

pH and pKa - Equilibrium & Protonation

In the next post I’ll look at the equilibrium constant for bases & for acid base reactions.

Glycolysis

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

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.

Reabsorption

Rates of Reactions, Chemical Kinetics & Orders

NOTE: Formatting needed–

One of the most important things to note with chemical reactions is that the molar concentrations of the substrates are often proportional to the rate of the reaction.

So if we take the simplest rate constant for an equation:

A + B –> C

We could might find the rate law to be:

Rate = k[A][B]

The coefficient k is called the rate constant and is dependant on temperature – this is independant of the concentrations of the substrates; so the larger the value of k, the faster the rate of the reaction. Also important is that the units of k will convert the product of the concentrations into a rate – so change in concentration per unit of time, often expressed as mol.dm-3.s-1.

While temperature increases increase the rate constant and rate of reaction in most cases, reactions with a large activation energy will have small rate constants as considerable temperature rises may be required for the reaction to occur at all.

Consider this theoretical example:

Rate = k[A][B] where k = 5 dm3 mol^-1; [A] = 1 mol.dm-3; [B] = 2 mol.dm-3

Therefore Rate = 5 dm3.mol-1.s-1 x 2 mol^2.dm^-6

The units all cancel to leave us with a rate of: 10 mol.dm-3.s-1

So the units for k in that example were dm3.mol-1.s-1. In another rate law, eg: Rate = k[A] we would find the units for k to be simply s-1.

Once we know the rate law and rate constant for that reaction we can go on to predict the reaction rate for any concentration of substrates.

– The Order of a Reaction

Reactions can usually be defined as either zero order (0), first order (1) or second order (2). The order of a reagent or the overall reaction depends on the effect varying the concentrations of substrates has on the rate of the reaction. So:

  • Zero Order – rate is not related to reactant A – rate is proportional to [A]0
  • First Order – rate is doubled as concentration of reagent B doubles – rate is proportional to [B]1
  • Second Order – rate is quadrupled as concentartion of reagent C doubles – rate is proportional to [C]2

Combining the above information, rate is proportional to [A]0[B]1[C]2 – therefore Rate = k[B]1[C]2 – so the reaction is 3rd order ( 1+2=3). Third order tells us the reaction is made of several parts.

– Measuring Rate & Integrated Rate Equations

0. Zero Order:

As a zero order reaction has a rate which is independant of any reagents, we can assume that Rate = k.

To identify a zero order reaction plot concentration of a reagent against time and you would see a straight line. The integrated rate equation is:

Integrated Rate Equation - Zero Order

Which means that the gradient (from y=mx+c) equals -k. This allows us to determine k from the graph.

Another feature of a zero order reaction is a decreasing half life as the reaction continues. The half life equation for zero order reactions is:

Half Life Equation for Zero Order Reaction

Where [A]0 is the initial concentration. Shows a decreasing half life as concentration falls.

1. First Order:

First order reactions have a rate proportional to the concentration of only one reagent. Any other reagents present will not affect the rate.

To identify a first order reaction plot In(concentration) against time to give a straight line. The integrated rate equation is:

Half Life Equation for Zero Order Reaction

Which means that as with zero order, k is the -ve of the gradient.

The half life of a first order reaction is constant thoughout the reaction:

Half Life Equation for First Order Reaction

This half life is dependant only on k as the half life remains constant regardless of concentration.

2.Second Order:

Second order reactions have a rate proportional either to 1 or 2 reagents (eg 2 x first order reagents or 1 x second order reagents).

To identify a second order reaction, plot 1/concentration against time to give a +ve straight line. The integrated rate equation is:

Integrated Rate Equation for Second Order Reactions

Which means that k = gradient (so the opposite of what we find in zero and first order reactions).

The half life of a second order reaction increases throughout the reaction:

Half Life of a Second Order Reaction

Shows an increasing half life with decreasing concentration.

2(1). Psuedo First Order:

Psuedo first order approximation is used when carrying out some second order reactions. It is useful as it is difficult to effectively control the concentrations of more than one reagent at the same time, and the psuedo technique simply places one reagent in excess at a constant level; essentially limiting the reaction rate the other reagent (you only control the concentration of one reagent).

Rate Order of a Psuedo First Order Reaction

The equation above illustrates that by putting [B] in excess we have essentially removed it from the rate reaction, allowing us to calculate the psuedo rate constant k‘.

Preparation & Reactions of Aldehydes and Ketones, RHO & ROR'

A couple of key points:

  • Aldehydes and Ketones both contain a carbonyl group, but are also less reactive than acid chlorides.
  • They do NOT react with organocopper reagents and weak hydride donors (as these weak reagents are involved in their own synthesis).
  • The reactions are addition rather than substitution as there is no leaving group.
  • They have one less bond to an electronegative atom than acid chlorides (no chlorine!).
Aldehyde & Ketone

Aldehyde & Ketone

They can be formed through reduction of Acid Chloride:

Aldehyde & ketone synthesised with Bu3SnH and R'2CuLi

Aldehyde & ketone synthesised with Bu3SnH and R

If an aromatic ring is being substituted then we must use friedel crafts acylation.

For Acid Chloride to Aldehyde we use Bu3SnH as a source of weak Hydride ions which displace a Cl-. We do not use a more obvious source such as LiAlH4 as this will result in the over reduction of the aldehyde into a primary alcohol.

For Acid Chloride to Ketone we use R’2CuLi as a source of nucleophilic R’ group.

and via reactions with Alcohols:

Simply, Primary alcohols lead to Aldehydes and secondary alcohols lead to Ketones when reacted with PCC. This is oxidation.

Aldehyde & Ketone synthesised from Alcohols

Aldehyde & Ketone synthesised from Alcohols

and finally with Alkanes:

Alkanes are just as simple as alcohols – just add O3 then PPh3 for an easy reaction!

Simple alkenes lead to aldehydes and more complex lead to ketones.

Aldehyde  Ketone synthesised from Alkenes

Aldehyde Ketone synthesised from Alkenes

Synthesis Summary:

In short:

REDUCTION
From Acid Chloride to Aldehyde – Bu3SnH (as a source of H-)
From Acid Chloride to Ketone – R2CuLi (as a source of R)

OXIDATION
From Alcohol to Aldehyde/Ketone – PCC
From Alkene to Aldehyde/Ketone – O3 then PPh3

– Reactions with Carbon Nucleophiles and Hydride Donors

As mentioned earlier, aldehydes and ketones do not react with weak hydride donors (eh Bu3SnH) or organocopper reagents (eg R2CuLi) – they need more powerful reagents.

These come in the form of Grignard reagents (eg RMgBr) and powerful halide donors (eg LiAlH4).

TBF

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.