These syllabus statements are basically the HL part of B.2.If you're not familiar with the B.2 content, I suggest you go and refresh your memory so this post makes more sense :) Protein AssaysProtein assays commonly use UV-vis spectroscopy and a calibration curve based on known standards. Determination of the concentration of a protein in solution from a calibration curve using the Beer–Lambert law. Testing for proteinA qualitative test for proteins that you've probably done before is the Biuret's test. A volume of Biuret's reagent is added to the sample to be analysed.  The Biuret's test can be used to measure the concentration of a solution of proteins using colourimetry because of it's purple colour. COlourimetryColourimetry is the determination of the concentration of a solution based on how much light it absorbs. A colourimeter can be used to measure how much light passes through the solution and can then calculate an absorbance value. This technique works for any solution as long as it's not colourless. FINDING THE OPTIMUM WAVELENGTH In order to find the wavelength that is absorbed most by the solution, an absorption spectrum should be plotted. This is basically an absorbance against frequency/wavelength graph that will show how well each wavelength is absorbed. The wavelength with the highest absorption should be chosen  HOW IT WORKS:
CALIBRATION CURVES Calibration curves are absorbance-concentration graphs that are used to compare unknown samples to. Absorbance values for samples of known concentration are taken and plotted on a graph, and a line of best fit is drawn. From this graph, any unknown concentrations can be determined by finding their absorbance values on the line of best fit and tracing back to the concentration.  METHODOLOGY (For finding protein concentration)
THE BEER-LAMBERT LAW  A typical colourimetry setup. An incident beam, a cuvette of solution and a detector. The light source will shine a beam of light through the cuvette of sample. The intensity of that light beam is measured, and given the symbol I0. The beam then passes through the sample in the cuvette, and a portion of the light is absorbed. The remaining light beam is detected at the detector, and it's intensity is given the symbol I. THE MATHS In the data book, you're given the following formula:  What they don't tell you in this formula, is that both sides equal A, the Absorbance of the solution.  Above, I've added the absorbance to the formula and annotated the formula to show what each variable is. THE VARIABLES Io
I
A
ε (Epsilon)
l
c
I think I'll have to split this into 3 parts...There are 3 main parts to the B.7 syllabus statements that require quite lengthy explanations.
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This part of B.2 is mainly about enzymesEnzyme BasicsMost enzymes are proteins that act as catalysts by binding specifically to a substrate at the active site.
Enzymes have an active site where the substrate binds to and where the reaction occurs.  A simple diagram of the mechanism of an enzyme catalysed reaction. More on this later... ENzyme modelsLOCK AND KEY The lock and key model is the most basic model of enzymes, that is shown above.
INDUCED FIT The induced fit model suggests that the enzyme plays a role in forming the shape of the active site. The intermolecular forces from the substrate help mould the shape of the active site so that the substrate fits.  Please praise my simply incredible drawing skills Enzyme ActivityAs enzyme activity depends on the conformation, it is sensitive to changes in temperature and pH and the presence of heavy metal ions. EFFECTS OF PH AND TEMPERATURE ON ENZYMES pH and temperature both have the effect of denaturing the enzyme. Denaturing just means that the active site has been damaged and can no longer function Enzymes all have their own ranges of temperature and pH that they work at. For most enzymes, this is the temperature and pH of most organisms. Each enzyme has a different optimum pH and temperature depending on where they operate in the body. Some examples are:
Heavy metal ionsHeavy metal ions act as non-competitive inhibitors. This is a HL concept from B.7 so I won't include the details in this post but the long and the short of it is that it indirectly destroys the active site. Enzyme activityDeduction and interpretation of graphs of enzyme activity involving changes in substrate concentration, pH and temperature. This is basically the kinetics of enzymes. The graphs you will come across here are graphs of Rate of Reaction against Substrate concentration. Because an enzyme can only work at a certain maximum rate, the graph curves off and a maximum rate of reaction is seen.  From this maximum, a 'half max' can also be calculated a bit like they do for half life in physics (and medicinal chem <3). This 'half max' is used to calculate a constant called the Michaelis constant (Km). Every enzyme has a different Michaelis constant. A small Km value suggests that an enzyme only requires a small concentration on substrate to become saturated, and a large Km value suggests that an enzyme requires a large concentration of substrate to become saturated. Long story short: The smaller the Michaelis constant, the 'worse' an enzyme is at catalysing reactions in that you need a lot more of it to reach the same rate of reaction compared to an enzyme with a larger Michaelis constant. Effect of Ph and temperature (graphs)The graph of Rate of Reaction against pH looks like a bell curve, with the largest value for the Rate of Reaction indicating the optimum pH  Enzyme activity plotted against pH for 2 different enzymes The graph of Rate of Reaction against temperature looks different. This is because at low temperatures it does not denature unlike when the pH is low.  Chromatography and ElectrophoresisChromatography separation is based on different physical and chemical principles. Explanation of the processes of paper chromatography and gel electrophoresis in amino acid and protein separation and identification. ChromatographyHopefully you remember this from GCSE. Chromatography is the separation of different substances based on their solubility in a solvent.  Chromatography also doesn't necessarily need to be done using paper, it can also be done using a gel :) Enzyme ChromatographyAn unknown mixture of enzymes can be analysed using chromatography and matching up the different 'spots' from that mixture with samples of known enzymes. The enzymes will travel at different speeds with the solvent depending on how soluble their R group is in water. Sometimes however, some enzymes will travel exactly the same distance in a solvent. In this case, chromatography is done twice along the 2 planes of the paper.
Rf values
ElectrophoresisElectrophoresis is another technique that can be used to separate and identify proteins and/or amino acids based on their Isoelectric point (pI). Electrophoresis uses a gel or paper soaked in a buffer solution to separate the amino acids. At the buffer pH (usually 6), some amino acids will form positive or negative ions based on their isoelectric points. These ions are then attracted to the electrodes in the electrophoresis setup. MethodElectrophoresis can either be done using paper or a semi-firm gel. The samples to be tested are applied in the centre of a piece of paper or in a cavity in the gel. An electric field is applied over the gel or paper. Due to the electric field, the proteins and amino acids will seperate.
Factors affecting separationThe separation of the amino acids and proteins depends on how they interact with the gel or the paper and solvent. This can be affected by:
Native and Denaturing electrophoresisNATIVE ELECTROPHORESIS
DENATURING ELECTROPHORESIS
That's it for B.2!Next on my list for biochem is B.7, the HL content for enzymes! Comment if you have any questions or suggestions!
B.2 Part 1 - ProteinsB.2 is quite long, so I will split the post up into 2-3 parts.ProteinsProteins are polymers of 2-amino acids, joined by amide links (also known as peptide bonds). WHAT ARE PROTEINS? Proteins are the main building blocks of human tissue. They make up muscles, skin, hair, fingernails and more less obvious things like enzymes. WHAT'S THE CHEMISTRY? All amino acids have a common structure, they have a carboxylic acid group, and an amine group. The 'R' group which you're hopefully familiar with from organic chemistry, determines which amino acid it is. There are 20 different naturally occurring amino acids, the simplest of which is glycine where the R group is just H. This R group be anything though.
This R group vastly affects the properties of the amino acid. Zwitter IonsAmino acids are amphoteric and can exist as zwitterions, cations and anions. Application of the relationships between charge, pH and isoelectric point for amino acids and proteins. Amino acids are amphoteric because of the general structure discussed above. All amino acids have a carboxylic acid group (acidic) and an amine group (basic). This makes amino acids amphoteric because they can react with both acids and bases. LOW PH In a low pH situation, the amine group reacts with H+ to form a cation.  HIGH PH At a high pH, the carboxylic acid group reacts with OH- to form an anion.  ZWITTERIONS Zwitterions (Zwitter ions) are when a molecule is both an anion and a cation at the same time. This can occur with amino acids. At a certain pH, amino acids have both a H3N+ group, and a COO- group.  The pH at which this zwitterion occurs is called the Isoelectric point (pI). Every amino acid has it's own isoelectric point, which is dependant on the R group. An acidic R group leads to a lower pI and a basic R group leads to a higher pI.  An extra COOH group in the R group leads to a low pI  Only a H for the R group leads to a pI of 6  Several NH and NH2 groups in the R group leads to a high pI At a pH higher than that of the isoelectric point, a cation will form and at a pH lower than the isoelectric point, an anion will form. Effect of the R group on amino acid propertiesExplanation of the solubilities and melting points of amino acids in terms of zwitterions. MELTING POINT As you will have learnt in topic 4, melting points are dependant on Intermolecular Forces (IMFs). An R group with a large amount of intermolecular forces will cause the amino acid to have a high melting point. This syllabus statement is basically a repeat of what has already been learnt in topic 4. SOLUBILITY Same as above. A more polar R group will be more soluble, just like you learnt in topic 4. Protein structuresProtein structures are diverse and are described at the primary, secondary, tertiary and quaternary levels. Description of the four levels of protein structure, including the origin and types of bonds and interactions involved. PRIMARY STRUCTURE This is a protein's one dimensional structure. This is just looking at the sequence of amino acids that are joined to each other. SECONDARY STRUCTURE This is looking at proteins on a broader level. Protein chains can fold or coil depending on intramolecular forces in the protein chain. There are two types of secondary structures that proteins can form (besides straight chain). ALPHA HELIX
BETA PLEATED SHEET
TERTIARY STRUCTURE This is an even broader look at a protein. In 1 protein, there's likely to be sections that have an alpha helix structure, and some sections with a beta sheet structure. Looking at the protein chain as a whole is looking at it's tertiary structure.
QUATERNARY STRUCTURE
Effect of shape on functionA protein’s three-dimensional shape determines its role in structural components or in metabolic processes. GLOBULAR PROTEINS Haemoglobin is an example of a globular protein. Globular proteins usually have complex tertiary and quaternary structures, and are usually somewhat spherical. Because of their complex structure, they are more heat sensitive. The protein chain in a globular protein usually has it's polar R groups exposed, and is therefore more soluble in water. FIBROUS PROTEINS Fibrous proteins have little or no tertiary or quaternary structures at all, and form long fibres. This structure makes them much 'stronger' than globular proteins. Their polar R groups are not exposed like in globular proteins, making them insoluble. Examples of fibrous proteins would be in hair, skin and bones, where insolubility and structure are needed. Part 2 coming soonAs in as soon as I learn it...What is Metabolism?Metabolic reactions take place in highly controlled aqueous environments. Metabolism is the general name given to chemical reactions that occur inside the body in order for organisms to grow, reproduce and for homeostasis to occur. These reactions are generally catalysed by enzymes, which we'll talk about later. What the syllabus means by "Highly controlled aqueous environments" is that these reactions take place in the cytoplasms of cells, which is roughly 90% water (aqueous). The conditions in the cytoplasm is strictly controlled by homeostasis. Things that are controlled: - pH (by buffers) - Concentrations of substances (by active transport and diffusion) - Temperature (sweat etc) Anabolic and Catabolic reactionsReactions of breakdown are called catabolism and reactions of synthesis are called anabolism. Catabolic reactions are reactions where molecules are decomposed or 'broken down' to produce energy. Examples: - Respiration (glucose to H2O + CO2) - Breakdown of Proteins into amino acids - Breakdown of Lipids into fatty acids - Breakdown of starch into glucose (digestion in humans) Anabolic reactions are the opposite of catabolic reactions. They use energy to synthesise larger molecules from smaller ones. Examples: - Photosynthesis (CO2 + H2O into glucose) - Synthesis of proteins from amino acids - Synthesis of glucose into starch and cellulose (growth and energy storage in plants) Photosynthesis and (Aerobic) respirationPhotosynthesis is the synthesis of energy-rich molecules from carbon dioxide and water using light energy. Respiration is a complex set of metabolic processes providing energy for cells. Because this is chemistry and not biology, we only need to know the basics of this, which is some very basic biology, and the formula.  The reactions for photosynthesis and aerobic respiration are opposites of each other. This being said, they do not occur via the same reactions. Both are complex and have a huge number of steps and intermediates. The use of summary equations of photosynthesis and respiration to explain the potential balancing of oxygen and carbon dioxide in the atmosphere. All this statement is saying is that because plants use carbon dioxide to do photosynthesis and produce oxygen, and we use oxygen to do respiration and produce carbon dioxide, it's a kind of equilibrium. There's no net production of oxygen or carbon dioxide, it's balanced and the concentrations of the gases in the air remains the same. ANAEROBIC respirationANIMALS Anaerobic respiration is respiration, but in the absence of oxygen. This is what happens when in animals when they don't have enough oxygen to create the amount of energy needed in that short period of time during physical activity. In this case, glucose is broken down into lactic acid to release energy.  Once we return to normal aerobic respiration, our body metabolises (gets rid of) this acid. PLANTS In plants and microorganisms however, anaerobic respiration produces ethanol and carbon dioxide instead of lactic acid. Sound familiar? This is how many alcoholic drinks such as beer are brewed from yeast.  Condensation and Hydrolysis reactionsExplanation of the difference between condensation and hydrolysis reactions. Condensation reactions are reactions where two molecules combine together to form a larger molecule (common in organic chem) with the elimination of a small molecule which is commonly water. Examples: - Amino acids forming proteins - Glucose forming starch (monosaccharides forming polysaccharides) Hydrolysis reactions on the other hand, are the reverse of condensation reactions. A molecule is hydrolysed when a water molecule (often in the presence of acid or base) breaks a bond in a larger molecule to form 2 smaller molecules. Examples: - Proteins forming amino acids - Starch forming glucose (polysaccharides forming monosaccharides) That's all for B.1I'm trying out a new layout on my new posts, I'm going to try and structure my posts based on the syllabus statements. I think it helps give my posts more structure and easy readability. let me know in the comments if this new layout is better!This topic will be split up into seperate posts because of it's length. This post covers syllabus statements 5.1 and 5.3What is energetics?Energetics is basically the study of energy in a reaction I guess, the amount of energy required or produced by reactions and more. It's quite a vital part of chemistry and links to almost every other topic in IB Chemistry. The BAsicsJust a couple of basic things that you should know before you even begin this topic.
Awesome, lets begin!What is an Acid and A Base? (SL)An acid is generally defined as a substance that dissociates to form H+ ions, and a base as a substance that dissociates to form OH- ions. There are 2 main theories you need to know for IB, Bronsted-Lowry and Lewis, but to understand these, you need to meet a new ion, the hydronium ion. In GCSE you were lied to. Unfortunately, the H+ ion does not really exist. For it to exist, water would need to spontaneously just break apart, and that doesn't really make sense.  It makes much more sense for the hydronium ion to exist, and the dissociation of water to look like this  This way, it's just a collision between 2 water molecules that results in a hydrogen (proton) swapping waters. Now, on to our acid base theories Bronsted - Lowry (SL)The Bronsted-Lowry theory of Acids and Bases says that an Acid is a proton donor. Here's an example of an acid 'donating' a proton.  Here, the HCl molecule donates its proton (hydrogen) to water to become Cl-. A base is defined as a proton acceptor in the Bronsted Lowry theory of acids and bases. Here, NH3 accepts a proton from water to form NH4+ and OH-  Lewis (HL)The Lewis theory of acids and bases defines an acid as an electron pair acceptor, and a base as an electron pair donor. There are a couple of examples of this but they're annoyingly complicated and confusing (mostly because I haven't learnt bonding yet) so I'm going to leave them out because I suggest you just memorise those definitions. The pH Scale (SL)pH stands for 'power of hydrogen', and is calculated using only the concentration of H3O+ ions. It is a logarithmic scale, the pH is the number you raise 10 to to get the H3O+ concentration, with the opposite sign. This sounds complicated but it's actually quite simple, to get the H3O+ concentration, just raise 10 to the negative of the pH. If the pH is 3 then the H3O+ concentration is 10 to the power of -3 mol/dm^3  And yes, there is a formula for it
Strong and weak acids and bases (SL)In Chemistry (the superior science), there are such things as strong and weak acids. Strong and weak often get confused with concentrated and dilute - they are NOT the same thing!!! While concentrated and dilute relate to the amount of your acid or base in a certain amount of water, strong and weak relate to the extent of dissociation of acids and bases in water. A strong acid or base fully dissociates in water |
 | Notice that the gradient of the curve before 45 and after 55 ml is very small (it's very flat). This is a way you can tell between a strong and weak acid or base. |
Next let's look at a weak acid and strong base pH curve
 | Now you see that the equivalence point has been shifted up, and the gradient of the graph before the equivalence point isn't as small as before (it's less flat). This is where the buffer zone is. Another thing to note is that when the weak acid has been half neutralised, pH = pKa. |
There are of course different combinations of strong and weak acids and bases, and you should be able to see which is which from the pH curve. Whichever is weak will have a less steep gradient, and the equivalence point will be further from it. For example, a weak base will have the equivalence point lower than 7 (further away from base pH) and the gradient will be steeper on the base side of the equivalence point. I'm not very good at explaining so it's diagram time.
Chemical Indicators (HL)
Here's a video I made last year explaining how they work. It's just a very simple equilibrium!
Calculations:
I'm going to make a video on how to do various calculations in this topic, and I'll put it here for you.
And I'm pretty sure that's it!
I hope this is useful, let me know in the comments if I've missed anything or anything is unclear. Sorry this is so late!
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I'm a 17 year old student who has a huge passion for science!
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