Biochemistry Notes PDF

27 Fatima Omar Saja shawar Nafith Abu-Tarboush Enzymes • What are enzymes? 1. They are specialized proteins, but are all enzymes proteins? NO, MOST of them are proteins but most aren’t. Note: Ribozymes are the exception (they are mainly made from RNA). 2. They differ from other proteins because t...

27 Fatima Omar Saja shawar Nafith Abu-Tarboush Enzymes • What are enzymes? 1. They are specialized proteins, but are all enzymes proteins? NO, MOST of them are proteins but most aren’t. Note: Ribozymes are the exception (they are mainly made from RNA). 2. They differ from other proteins because they act as biological catalysts (they speed up/accelerates chemical reactions) without being consumed, there is no change in enzymes at the STARTING and END points of the reaction (will be discussed later in page 5 in this sheet) 3. They are found in small concentrations because a single enzyme can catalyze a huge number of reactions. So, if you find a molecule in high concentrations, you know it is not an enzyme nor a hormone. 4. We cannot measure the concentration of enzymes between the starting and end points (during reaction), because they are in complex form (enzyme + something else), if we want to measure its concentration, they must be in simple form (only enzyme) 5. Enzymes are the most efficient catalysts known. • General properties of proteins When we want to study the binding process of the enzyme in biochemistry we have to know two concepts: 1. Affinity: The strength of binding between a protein and another molecule. It is a scale that indicates bond strength and can be translated into numbers. (the term is not specific for proteins only; it includes the strength of binding between any 2 molecules). ‫ز‬ ‫ر‬ ‫زز‬ ‫ر‬ ‫ز‬ ‫ز‬ 2. ‫األفينين بتكون‬ ‫يعن‬ ‫*الدكتور طرح مثال انو ممكن اينايم معي يكون بقدر يرتبط بمركب بقوة اكن من مركب ي‬ ‫ي‬ ‫تان ف ي‬ .‫اعىل ألله‬ 3. Specificity: The ability of a protein to bind one molecule in preference to other molecules. The doctor explained it as follows: It is how much I am specific for you, do I bind other molecules or not regardless of how much the STRENGTH of binding between me and you. The two concepts before intersecting each other, they are close to each other; so you would predict if the affinity increases, specificity increases. But that doesn’t mean it doesn’t bind to another molecule. In other words, even if the affinity (bond strength) of one molecule to another is high this molecule can still bind to another molecule. ‫ز‬ ‫ر‬ ‫ز‬ ‫ز‬ ‫يعن انو مارح يرتبط ب مواد تانية غنه‬ ‫ لمركب معي عالية هذا ال ي‬affinity‫يعن حن لو كانت ال‬ ‫ي‬ • From slides: • Are enzymes important? − In human bodies, almost every metabolic process involves the use of enzymes. − Enzymes are used for production of a lot of things such as in fertilization, industry, and science. Examples on enzymes applications: 1. Green tea: − Green tea contains many polyphenols (phenol is an aromatic ring with a hydroxyl group). − Free radicles are found in our body, they are bad because they have a free electron which makes the molecule unstable and wants a molecule to take this electron. − Due to the resonance structure of aromatic rings, phenols are capable and have much more capacity to carry the free radicle. − So, aromatic rings can work as antioxidants − Polyphenols can be oxidized, but in order to be oxidized by the enzyme (polyphenoloxidase) inside cells in the tea, it requires molecular oxygen in air. ‫ احسن من أي مركب‬radical ‫االشكال الحلقية الها قدرة على تعامل مع‬ − When we dry out the green tea after exposed to the air, the plant cells will . ‫تاني‬ start to be broken down exposing the enzyme to the air (now O2 is present), thus the enzyme will start to oxidize polyphenols into tannins (black tea) which give the dark color and the characteristic flavors. 2. Sweets and candies: − Honey gives a sweet taste, and the right structure, texture, and consistency to candies. − But honey is relatively expensive and rare, so corn syrup (a honey like substance that has the same consistency of natural honey) can be used as an alternative. − Corn syrup is enzymatically driven and cheaper than honey. 3. Chocolate: • How is chocolate hard from the outside and soft from the inside? − On the inside, there is an enzyme called sucrase which breaks down sucrose into monosaccharides (fructose + glucose) which makes it more soluble. − On the outside, sucrase enzyme is absent, that’s why it is harder. 4. Amoxicillin & p-hydroxyphenylglycine: − Amoxicillin is the most used antibiotic in the world, and it is synthesized by enzymes. *the doctor didn’t mention anything about p-hydroxyphenylglycine* 5. Other uses: − Enzymes such as peptidases and proteases break down proteins into smaller molecules. Those enzymes can be added to meat to make them softer. − In contact lenses solution. − Washing powder. − In research and experiment labs. • The biological catalysts; Enzymes ▪ What do we mean by biological catalysts? By biological we mean that they work in biological systems (living organisms), they are being produced by living organisms & work inside it. ▪ Since we call it a biological catalyst this means there are other enzymes that aren’t biological in their nature (chemical reactions); they are not produced inside a living organism. ▪ How can I produce an enzyme? Enzyme is a protein, so we need a cell, mRNA, a process of translation to make the enzyme. − What are enzymes? (specialized proteins, small amounts, acceleration, no change) *Was discussed in the beginning of the sheet* ▪ In a reaction, enzymes are only found at the beginning and end of the reaction, and the concentration is constant. But why can’t we find them in the middle of the reaction? And why can’t we measure their concentration? This is because when an enzyme bind to a molecule (substrate) bonding between them occur causing conformational change huge change in the enzyme chemical structure ( new chemical structure=not enzyme anymore ) :‫*مثال للتوضيح‬ ‫ز‬ ‫إذا عندي تفاعل ز‬ ‫بي جلوكوز و فوسفات‬ glucose 6 phosphate.‫واعطان‬ ‫ي‬ ‫ثم طلبت منك تحسبىل تر ز‬ ‫تحسبىل إياه‬ ‫ رح تقدر‬،‫ فعليا‬،‫كن الجلوكوز ز يف التفاعل‬ ‫ي‬ ‫ي‬ ‫ز‬ ‫اش اسمو‬ ‫يف بداية التفاعل بس ما رح تقدر تحسبو خالل التفاعل النو بطل عندي ي‬ ‫ز‬ .‫ثان مختلف‬ ‫جلوكوز وصار عندي مركب ي‬ ▪ So enzymes convert reactants to products and remain unchanged in the end of the reaction. ▪ Enzymes are the most efficient catalysts known. ▪ They usually speed up chemical reactions in the range of 10^6 to 10^14. ▪ Non-enzymatic catalysts though, from 10^2 to 10^4. ‫ الدكتور قال انو مرة جاب‬.‫*الفكرة هون إنك الزم تكون فاهم قديش األنزيم برسع التفاعل‬ ‫ وبعدين ضفنا انزيم‬،‫ومعط المتفاعالت والنواتج ورسعة هاد التفاعل‬ ‫سؤال انو ز يف تفاعل‬ ‫ي‬ ‫ كم بتتوقع رسعة التفاعل رح تصن؟ الموضوع مش محتاج حسابات وبس‬،‫عىل هاد التفاعل‬ ‫ز‬ .‫مبن عالفهم والجواب الرقم الموجود فوق‬ ‫ي‬ ▪ The actions of enzymes are fine-tuned (‫ )مضبوطة بدقة‬by regulatory processes. ▪ Example: (catalase 108, carbonic anhydrase 107) − Hydrogen peroxide (H2O2) is a toxic material which is produced inside the body by oxidases enzymes. − Catalase enzyme works on H2O2 to break it down into water and oxygen gas (the 1st reaction). − This reaction can happen without needing any catalysts, but it may take hours, days… − So, for example, if we use chemical catalyst like platinum surface, it will speed up the reaction ~10 thousand times. − And if we use biological catalyst like catalase, it will speed up the reaction ~100 million times!! So, you can see the effectiveness of enzymes in speeding up reactions. • How to express an enzymatic equation? − In enzymatic reactions, reactants are known as substrates. − We can simply express an enzymatic reaction using this formula. where E is the free enzyme; S is the free substrate, ES is the enzymesubstrate complex; P is the product of the reaction; and EP is the enzymeproduct complex before the product is released. We can’t calculate enzyme concentration here because there is no enzyme in this phase. (discussed before) − This reaction occurs in a specific place on the enzyme called the active site. • Active sites of enzymes − This is the part of the protein that makes it function as an enzyme. Hemoglobin for example is a protein that can’t function as an enzyme because it doesn’t have an active site. − A specific three-dimensional shape which includes a region where the biochemical reaction takes place (they are globular proteins) − Contains a specialized amino acid sequence that facilitates the reaction. − An active site has special characteristics that makes it act as an active site like: 1. It is found inside (interior not exterior) the enzyme; you can’t find it on the surface of the enzyme. ▪ This is because the process of changing the structure of the substrate into a product, I have to change the energy, and the changing of the bond’s energy is not an easy process. So you need to produce pressure on the substrate and enclose it so it could be very close to the enzyme. 2. They look like canals, and have a base that has a lining, amino acids backbone form this lining, while the R groups either project towards the space (active site) or towards the inside of the sphere. The R groups that project towards the space bind to the substrate. Those R groups must be polar (charged or uncharged polar A.A) to bind to the substrate. But do active sites have non-polar A.A? Actually yes, they may have nonpolar A.A, and if present, they are responsible for the binding since they can form hydrophobic interactions (not true bonds) with the substrate. Note: active site must have polar A.A, but it may have non-polar A.A. Due to the three-dimensional structure, different parts of the polypeptide chain project to the active site. For example, an active site can have A.A number 3 and the A.A next to it might be A.A 317 and the next to it 17 and so on.(the amino acids are driven from different types proteins That's why they don't have a consecutive numbering ) End of sheet 27