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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
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.
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:
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.
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.
Fructose-6-phosphate –& Fructose-1,6-bisphosphate (-1 ATP)
Phosphofructokinase replaces the hydrogen on the alcohol group of C1 with another phosphate group.
Fructose-1,6-bisphosphate –& GLAP + DHAP
Aldolase splits the fructose-1,6-bisphosphate into two 3 carbon molecules, dihydroxyacetone phosphate and glyceraldehyde 3-phosphate.
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.
GLAP –& 1,3-bisphosphoglycerate (-2 Pi) (+2 NADH)
Glyceraldehyde 3-phosphate dehydrogenase replaces a H on C1 with an O and phosphate group.
1,3-bisphosphoglycerate –& 3-phosphoglycerate (+2 ATP)
Phosphoglycerate kinase removes the phosphate group from C1.
3-phosphoglycerate –& 2-phosphoglycerate
Phosphoglycerate mutase switches C2 & C3.
2-phosphoglycerate –& 2-phosphoenolpyruvate (+2 H2O)
Enolase removes the alcohol on C3, forming a C=C between C2 & C3.
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 s and the lack of oxygen means no energy is gained from the oxidation of NADH.
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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 concentratio 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:
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:
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:
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:
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:
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:
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 essentially limiting the reaction rate the other reagent (you only control the concentration of one reagent).
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‘.
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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
They can be formed through reduction of Acid Chloride:
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
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.
Ketone synthesised from Alkenes
Synthesis Summary:
From Acid Chloride to Aldehyde – Bu3SnH (as a source of H-)
From Acid Chloride to Ketone – R2CuLi (as a source of R)
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).
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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
Cell Structure
membrane bound organelles
Eukaryotes,
Unicellular & Multicellular
Eukaryotes,
Unicellular & Multicellular (Yeast)
Eukaryotic,
M Large Vacuoles
Eukaryotic,
Multicellular
Polysaccharide
Autotrophic, Aerobic
Heterotrophic
Autotrophic,
Hetrotrophic
Heterotrophic
Autotrophic
(Photosynthetic)
Heterotrophic,
Digestive System
Reproduction
Binary Fission
Seeds/Spores, Some
asexual while some sexual
Develop from embryo
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:
Large White Butterfly
Arthropoda
Lepidoptera
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 th 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)
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.
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Acid Chlorides:
Highly Reactive Carboxylic Acid Derivatives such as Acid Chlorides can be easily formed:
Easy preparation of acid halides from Carboxylic Acids
Acid Chlorides are:
Highly reactive functional groups.
Mainly involved in nucleophilic substitution reactions.
Have identical reactions to acid bromides and acid anhydrides (so I will only focus on the Chlorides).
Flash animation showing the Step-by-step mechanism of the formation of an Acid Chloride from Thionyl Chloride and a Carboxylic Acid. Click to launch.
Acid Chlorides undergo a fair number of useful reactions. Below is a table illustrating them:
Paths to common, useful products of Acid Chlorides
The mechanism for all of these substitution reactions begins with the addition of Nu- or :NuH to the δ+ carbon atom of the carbonyl. This then creates an tetrahedral intermediate which then collapses to eject the chlorine (Cl-). The only difference with :NuH is an additional step where a base (such as pyridine) removes the H+ from the nucleophile.
Nucleophilic Substitution using Nu- and :NuH on Acid Chloride
Acid Chlorides can be converted into Ketones using organocopper reagents such as Me2CuLi and Ph2CuLi. This can be extremely useful in increasing chain length, amongst other things. The reason we used organocopper reagents instead of Grignard reagents (which we already know work) is down to how far the reaction goes. Grignard reagents are capable of converting Ketones into tertiary alcohols, and so tend to follow this route to completion.
The reactions involving Hydride ions are all run using weaker sources of H- than LiAlH4 (which would normally be the obvious choice). This is because the LiAlH4 will continue the conversion from an Aldehyde to a primary alcohol.
Addition of Aromatic Rings (Friedel Crafts Acylation):
Aromatic rings have no direct route for attack. They are poor nucleophiles (due to their stability) and as such require the Acid Chloride to be activated (made into a better electrophile) so they can be pulled in.
This activation can be achieved by using a Lewis acid such as AlCl3 or FeBr3. This reaction type is know as a Friedel Crafts Acylation. The animation below shows the mechanism and reaction scheme for this activation, and joining.
Friedel Crafts Acylation Mechanism - Addition of an Aromatic Ring to form Ketone. Click to launch animation.
If you’re wondering why the product does not reach further, simply consider the properties of the carbonyl group. The carbonyl group has electron withdrawing properties and as such reduces the available of electrons in the aromatic ring…requiring stonger conditions to instigate a second acylation reaction.
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One of the most important functional groups is the Carbonyl group.
Source: Wikipedia. Shows C=O and two additional atoms.
A couple of points about the carbonyl group:
It is Planar (flat).
Bond angles are 120 degrees.
The Carbon = Oxygen double bond is the result of overlapping Pi and s orbitals.
Both the Oxygen and Carbon atoms are sp2 hybridised.
Oxygen has 2 lone pairs of electrons not involved in bonding.
Oxygen is electronegative relative to Carbon and therefore the bond is polarised.
There are 2 ways to represent the polarisation of the carbonyl. Delta-notation to show partial charges, or Resonance forms to show the individual structures which contribute to the bonding sturture.
Resonance Forms
Reactivity:
There are three main loci of reactivity – with electrophiles, nucleophiles and bases.
Reactions with Electrophiles, E+
The Oxygen atom is electron rich and interacts with the Electrophile. One lone pair is used to form a new Sigma bond.
Reactions with Nucleophiles, Nu-
The carbon atom is electron deficient and so attracts the nucleophile.
Reactions with Bases, BASE-
A hydrogen on a neighbouring carbon is removed by strong bases, creating a resonance stabilised anion.
The reactivity of carbonyl compounds is influenced by the atoms attached.
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