Level 1 Biology - Molecules, Genes and Cells Lecture Notes PDF

Level I Biology MOLECULES, GENES AND CELLS: LECTURE NOTES WEEK ONE IDEAS AND UNDERSTANDING: 1. Differentiate living from non-living objects by understanding the minimum necessary attributes of homeostasis,...

Level I Biology MOLECULES, GENES AND CELLS: LECTURE NOTES WEEK ONE IDEAS AND UNDERSTANDING: 1. Differentiate living from non-living objects by understanding the minimum necessary attributes of homeostasis, organisation, metabolism and reproduction. They can also undergo evolution. 2. Explain how life is thought to have evolved from simple chemical processes over vast time frames. The research of Stanley Miller provided the first clear evidence for this mechanism. The conditions on early earth were very different to the current environment. 3. Describe how life can be classified into 3 kingdoms; Archaea, Prokaryotes and Eukaryotes. We can trace back through the fossil record and morphological data as well as using modern molecular methods to generate phylogenetic trees to show the evolutionary relationships of living organisms through time. Complex multicellular organisms evolved from simple single celled organisms. WHAT IS LIFE? There is no good strict definition to what defines a living object. However, it must follow these characteristics: Homeostasis – Regulate internal processes (includes temp, pH etc). Organisation – Show organised, and often symmetrical, cellular structures. Metabolism – Transform energy. Evolve (Not an absolute necessity) Reproduction – Able to duplicate themselves or pass-on heritable properties (traits). HOW DID LIFE BEGIN? The Earth is over 4.5 Ga years old. The hypothesised early world’s conditions were: High temperatures CO2, N2, H2O vapour, and H2 gas Hydrogen compounds (e.g. Hydrogen sulphide H2S, ammonia NH3, and methane CH4) No (or very low) oxygen – reducing conditions Possible energy sources include planetary heat, UV radiation, volcanoes, lightning, meteorites. The first evidence suggesting life was possible in early Earth came from Stanley Miller who was a PhD student in Harold Urey’s lab. Harold Urey won a Nobel prize in 1934 for discovering deuterium; however, Urey was heavily interested in early lifeforms. He gave a seminar which Miller saw, inspiring him to join Urey’s lab. Stanley Miller was eager to prove how simple biological molecules came from these conditions. Miller set up a sealed system in a glass flask with water, ammonia gas, methane, and carbon dioxide. He boiled the flask to produce water vapour and would strike the flask with electricity to simulate lightning strikes. After a week of stewing the experiment, a brown sludge was left in the flask. He  isolated what was in the sludge and found a few amino acids were formed. In a revolutionary 1953 science paper, he revealed to the public it is possible to make simple biological molecules from inorganic material. Since this time, the experiment had repeated by many more scientists. More amino acids have been found in repetitions. In order to study evolution, shared derived characteristics are studied to understand how organisms are related to each other. This is the study of Phylogeny where phylogenetic trees and other methods are used. Carl Linnaeus came up with the classification system that help in the categorisation of life. All life is based on the three domains: Bacteria, Archaea, and Eukarya. Animals are then categorised by Kingdom, Phylum, Class, Order, Family, Genus, and Species. In this semester of biology, the latter two is focused on particularly. When writing a name, the Genus goes first, followed by the Species (e.g. Panthera pardus) and must be written in italics (if hand-written, underline it). IDEAS AND UNDERSTANDING: 1. Information flow of Gene (DNA) to RNA to protein is a central unifying dogma of biology. 2. Differentiate prokaryotic cells from eukaryotic cells. 3. Distinguish between the Gram-positive and Gram-negative bacteria based on their structure (cell walls and cell membranes), and their differential staining using gram staining. 4. Differentiate between animal and plant cells based on their structural components. 5. Structure and function of the endomembrane system within eukaryotic cells, particularly the nucleus, the smooth and rough endoplasmic reticulum, the Golgi body, lysosome and vacuole. 6. Differentiate between the structures and functions of the mitochondrion and the chloroplast. In particular, the photosynthetic role of chloroplast in plants and the respiratory role of mitochondria in both plants and animal cells. 7. Evidence for the endosymbiotic theory of the evolution of the chloroplast and mitochondria. THE PROKARYOTIC CELL Evolution relationships suggest Archaea and Eukaryotes diverged further away from the domain of Bacteria. It is an interesting complex that Archaea and Bacteria are both Prokaryotes, yet Archaea and Eukaryotes are more closely related. Prokaryotes most commonly come in three different forms; spherical (coccus), rod shaped (bacillus), spiral. Prokaryote genetic information is contained within a single circular chromosome composed of double-stranded DNA and live within the nucleoid region (not membrane enclosed). Also, many prokaryotes possess circular bits of DNA known as plasmids, which exist and replicate independently of the chromosome. Plasmids have relatively few genes (fewer than 30) and can be transferred between bacteria in a process called conjugation or horizontal transfer (this is essentially bacteria’s having sex!). This is an important method of sharing genetic information within large populations of bacteria. Other parts of the prokaryote include: Ribosomes, Organelles, Cytoskeleton, Flagella, and Exoskeleton. Bacteria tend to fall into two classes which can be differentiated through the Gram stain: The Gram-positive have a thick cell wall rich with peptidoglycan. The crystal violet enters the cell, where it forms a complex with iodine in the stain. Since the complex is too big to pass through the cell wall, alcohol rinse will not remove it. RESULT: Crystal violet masks the red safranin dye. The Gram-negative have a thin cell wall with little peptidoglycan, which is located between the plasma membrane and an outer membrane. The crystal violet-iodine complex can pass through this thin cell wall and hence is  removed by the alcohol rinse. RESULT: Safranin dye stains cell pink/red. THE EUKARYOTIC CELL Eukaryotes possess a clearly defined nucleus. Eukaryotic chromosomes are found inside a membrane bound nucleus, they are larger, they contain large amounts of internal memory, and have a diverse and dynamic cytoskeleton. Compartmentalisation of organelles offer two key advantages: 1. Incompatible chemical reactions can be separated. 2. Chemical reactions become more efficient. So, what are the main compartments? (Bold are a part of the Endomembrane System) Nucleus: The nucleus contains the chromosomes, and functions as the information and storage processing centre. It is enclosed by a membrane called the nuclear envelope. The RNA molecules are synthesised and found within the very central part, which is the nucleolus. Rough Endoplasmic Reticulum: The Endoplasmic Reticulum surrounds the nuclear envelope. It is rough because ribosomes attach to the membrane. The RER is the site of protein synthesis, protein processing, and carbohydrate synthesis. Smooth Endoplasmic Reticulum: The Smooth Endoplasmic Reticulum is free from ribosomes. It is the site of lipid synthesis, carbohydrate synthesis, and chemical detoxification. Golgi Apparatus: The Golgi apparatus consists of flattened membranous sacs called cisternae, which are stacked on top of one another. This is the site of protein sorting, carbohydrate synthesis, and protein processing Lysosomes: Lysosomes function as digestive centres in animal cells; it degrades and recycles. They contain about 40 different enzymes, specialised in breaking up different macromolecules. It can occur by three different processes; autophagy, phagocytosis, receptor-mediated endocytosis. Vacuoles: The vacuole is a large “storage bubble” that contains proteins, pigments and toxins. ▪ Mitochondria: The mitochondria synthesise ATP and aids metabolism. Chloroplasts: Most algae and plant cells possess chloroplast. The chloroplast has a double membrane and has flattened vesicles in the interior which is called thylakoids. They are responsible for converting light into energy. Cytoplasm: Everything within the plasma membrane, excluding the nucleus. HOW DID THE EUKARYOTE EVOLVE? Along the evolutionary line, there was infolding of the plasma membrane in a prokaryote cell. As time went on, these infoldings became more complex and eventually formed a nuclear envelope. This early form of a eukaryotic cell more than likely engulfed an aerobic bacterium that can produce large amounts of ATP. The early eukaryote gained an energy source while the bacterium, now known as a mitochondrion, gained protection. This is a symbiotic relationship. This cell is now known as an animal cell. An early animal cell would have engulfed a chloroplast, this is where plant cells would have diverged from animal cells. The proof for the endosymbiotic theory includes: Membranes: Mitochondria and chloroplasts have their own cell membranes, just like a prokaryotic cell does. DNA: Each mitochondrion and chloroplast have its own circular DNA genome, like a bacteria's genome, but much smaller. This DNA is passed from a parent to its offspring and is separate from the "host" cell's genome in the  nucleus. Reproduction: They multiply by pinching in half — the same process used by bacteria. Every new mitochondrion/chloroplast must be produced from a parent in this way; if a cell's mitochondria/chloroplasts are removed, it can't build new ones from scratch. Function: The organelles cannot function without creating their own proteins and enzymes from their own DNA. IDEAS AND UNDERSTANDING: 1. Identify individual functional groups within a molecule and predict how the combination of functional groups will influence the properties of the molecule. 2. Recognise a chiral centre (carbon) and explain the significance of stereoisomers (or enantiomers) on the 3- dimensional structure of molecules. All amino acids except glycine contain a chiral centre but proteins only contain one of the two possible enantiomers of each amino acid. (i.e. only the "L" form, e.g. L-alanine). 3. Recognise the chemical structures for the four major classes of biological molecules. 4. Explain how the dehydration reaction can be used in a "uni-directional" repetitive fashion to enable the synthesis of large complex (polymeric) molecules of polysaccharides, nucleic acids and proteins from individual (monomeric) precursor molecules of carbohydrates, nucleotides and amino acids respectively. 5. Describe the structural and functional differences between the glucose polymers starch and cellulose and the impact these differences have on the ability of different animals to use them as an energy source. 6. Describe the diverse range of functions of carbohydrates in living systems, often as part of a covalent complex with proteins. FATS, LIPIDS, AND MACROMOLECULES Fats and lipids are not classed as macromolecules as they are not synthesised in the same way as they are, but they are still important molecules in the cell. There are two types of fats; Saturated fats: It is “saturated” in Hydrogens as it has the maximum possible hydrogen links. At room temperature, the molecules of a saturated fat such as the fat in butter, are packed closely together forming a solid. Unsaturated fats: It is not “saturated” in Hydrogens as it does not have the maximum possible Hydrogen links, and instead has some double carbon links. At room temperature, the molecules of an unsaturated fat such as olive oil cannot pack together closely enough to solidify because of the kinks in some of their fatty acid hydrocarbon chain. Fats are important to the human body and animals etc; however, if it is in the wrong place or the wrong form, it can be quite harmful. Lipids are also rather important molecules. Lipids are fatty acid tails which allow for the formation of membranes. Lipids contain two hydrophobic tails (two fatty acid tails), one is often saturated and the other is unsaturated. These are linked through glycerol to a phosphate functional group. At the top is one of five head groups which are hydrophilic. This hydrophilic-hydrophobic relationship allows for the phospholipid layer to form.  Using simple repeating molecules, you can build up more complex molecules called macromolecules. This process is essentially taking individual monomers and joining them in a linear fashion, making them into polymers. Simple changes of the macromolecules can give a large diversity, this can range from the length of the polymer, the overall composition of units, and the changing order of units. In general, these units are joined by a dehydration reaction (or Condensation Reaction). Each unit is added onto one end only, giving the molecule a “direction”. CARBOHYDRATES Stereochemistry is the branch of chemistry concerned with the three-dimensional arrangement of atoms and molecules and the effect of this on chemical reactions. In the image to the right, we can see two identical molecules, yet are mirrored of each other. These are called enantiomers. L-alanine is found within living systems while D-alanine is not (can be found sometimes). Carbohydrates are also known as sugars. They can be summarised as: Often attached to proteins. Protects proteins in cells. Provides recognition for cells. Provides volume for long proteins. Provides strong flexible extra-cellular structures; plant cell walls, bacterial cell walls, cartilage, connective tissues. Monosaccharides are simple sugars that consist of carbon atoms, a carbonyl group, and hydroxyl group. If the carbonyl group is positioned at the end of the molecule, an aldehyde sugar (aldoses) forms, and if it is positioned within the carbon chain, a ketose sugar (ketoses) will form. An example includes Glucose and Galactose being aldoses, while Fructose is a ketoses. Note that the Glucose and Galactose are enantiomers. Monosaccharides can form into a ring structure when dissolved in water. There is an equilibrium between the two forms. The circular ring forms a stereocentre whereas the linear form has one less stereocentre (stereocentres leads to stereoisomers). Consequently, this interchange allows for differences between monosaccharides, such as glucose. The linear formation of Glucose allows for the linked form to swap between two enantiomers; alpha-glucose and beta-glucose. Disaccharides happen when two ring monosaccharides are joined together with the dehydration reaction. You can degrade these through hydrolysing the glycosidic bond with specific enzymes. When alpha-glucose polymerises, it creates a polysaccharide called starch. Humans can digest starch as an energy source. When beta-glucose polymerises, it forms cellulose, which is a major component of plant cell walls. Humans lack the digestive enzymes to hydrolyse the glycosidic bonds. Cellulose can form long fibres with hydrogen bonding between the hydroxyl groups that are on the side. This allows the fibres to get close to each other and become strong, making it harder to break a part. Mammals lack the digestive enzymes to break cellulose a part, but ruminants evolved to do so. Ruminants are mammals that can acquire nutrients from plant-based food through using bacteria that contain enzymes able to hydrolyse glucose polymers. The bacteria essentially trans convert the cellulose into alpha-glucose. Starch, on the other hand, is a very useful energy source within humans. Glycogen is a storage macromolecule for alpha- glucose in many animals. Glycogen is a polymer that can form many branched strings as well as a linear string. Glycogen is stored in liver and muscles. In addition to polymers of glucose units, which gives us maltose, you can also have disaccharides of a galactose unit. A galactose unit plus an alpha-glucose unit produces lactose. Lactose intolerance is when a person does not contain the enzyme lactase to hydrolyse it. WEEK TWO IDEAS AND UNDERSTANDING: 1. Recognise the different chemical structures for ribose, deoxyribose, a nucleoside and a nucleotide. 2. Understand that the basis of the DNA genetic code is the linear sequence of nucleotides adenosine (A), guanine (G), cytosine (C) and thymine (T) in the DNA polymer (or strand). In RNA uracil (U) is substituted in place of thymine. 3. Describe the overall structure of the DNA double helix including the stacking of base pairs within the core of the structure, the base pair rules (A-T and G-C), the phosphodiester backbone and the anti-parallel nature of the two strands in the double helix. 4. Draw out the chemical structure of two nucleotides joined by a 3´-5´ phosphodiester bond. You do not need to be able to draw the chemical structures of the nitrogenous bases. 5. Predict the sequence of a DNA strand that would be the "reverse complement" of a given DNA sequence. This highlights the principles of base pairing and the anti-parallel nature of the double helix. 6. Describe the very elegant experiment by Alfred Hershey and Martha Chase that first proved DNA is the genetic molecule and not protein. This highlights the principles of bacterial viruses as valuable experimental tools and being able to incorporate isotopes of atoms into biological molecules to enable them to be detected in the laboratory. In this case, they were radioactive isotopes, but modern methods of ultra-accurate mass detection mean that stable (i.e. non radioactive) isotopes can also be used. 7. Explain how gel electrophoresis allows DNA molecules to be separated based on their size and how chemical stains can be used to visualise DNA within the agarose gel. This is reinforced within the laboratory component of the course. NUCLEIC ACIDS Nucleic acids are polymers, which are made up of nucleotides. There are two primary types of nucleotides; ribonucleotides and deoxyribonucleotides. Nucleotides are made up of a phosphate group, a sugar, and a nitrogenous base (Guanine, Adenine, Cytosine, Uracil, or Thymine). The phosphate is bonded to the sugar molecule, which is then bonded to the nitrogenous base. So, how does this DNA synthesis occur? It uses a dehydration reaction. (You should be able to draw these diagrams) Note that there is a direction to the DNA molecule. There is a 5’ end and a 3’ end, you always add to the 3’ end. However, when it comes to degradation (hydrolysis) it can be linear or random. The enzymes nuclease is called endonucleases if they chop the molecule in the middle, or exonuclease if they are chopped from one end (often the 3’ end).  The DNA structure has anti-parallel strands that are twisted together to form a double helix with the sugarphosphate on the outside of the spiral, and the nitrogenous bases on the inside. Each base is paired; Adenine with Thymine, and Guanine with Cytosine. Two hydrogen bonds form when A and T pair, but three hydrogen bonds form when G and C pair, as a result of this G-C bonding is slightly stronger. DNA – THE GENETIC MATERIAL Before the Hershey and Chase blender experiment, there was no clear evidence that DNA was the genetic material. Scientists assumed proteins, and their many amino acids, were the genetic material. This is because it had more information than DNA, which was “too simple” with its 4 bases.This experiment came about when Alfred Hershey was studying bacteriophage genetics. Bacteriophage, or phage for short, are viruses that specifically attack and infect bacteria. It was known to them that phage have an outer protein coat and an inner core of DNA. Phage rely on bacteria to reproduce. Hershey knew from electron micrographs that during infection, phage attach to bacteria by their tails. He assumed that after attaching, genes are pumped into the bacterial host, which then direct the bacterium’s enzymes to replicate new phage particles. Hershey and Chase set out to determine exactly what caused the transformation of bacteria into a phage-producing factory. In 1952, Hershey and Chase set out to test this. According to previous chemical analyses, it was known that DNA was high in phosphorus (P) atoms but had no sulphur (S). Conversely, proteins contained sulphur atoms, but no phosphorus. So, knowing this, radioactive Phosphorus (32P) or sulphur (35S) to selectively label phage DNA and protein. They then designed anexperiment to test which component entered the bacteria for infection. In two parallel experiments, they combined the radiolabelled phage with bacteria that were not labelled. Once the phages attached, the attachments were disrupted by mixing the culture in a Waring blender. Next, the samples were spun in a centrifuge to separate the phage from the bacteria. Since the bacteria are larger, they collected at the bottom while the phage stayed above. After examination, the phosphorus pelleted with the bacteria. Thus, DNA was used inside the bacteria to make new phage particles. WEEK THREE IDEAS AND UNDERSTANDING: 1. Known the structure of amino acids including "backbone" and "side chain". 2. Name the 20 amino acids, their 3-letter codes and the chemical class they belong to. 3. Explain how the four chemical classes of amino acids differ and predict how the chemical properties of each class will influence the function of the amino acid within a protein. 4. Predict the Zwitter-ionic structure of a given amino acid and calculate the predicted charge of a given amino acid sequence (at pH 7). 5. Recognise the planar nature of the peptide bond as the structure that joins amino acids in the protein polymer. 6. Describe the four levels of protein structure (1°, 2°, 3° and 4°) and how they interrelate in a hierarchical way to describe the overall structure of a protein. 7. Describe the differences between a folded (native) and an unfolded (non-native) protein and the experiment of Christian Anfinsen that showed that the 1° sequence of amino acids dictates the 3-dimensional structure and hence function of a protein.  8. Explain the chemical interactions that drive proteins to fold into stable 3-dimensional structures. This includes the preference for polar side chains to interact with water molecules and non polar side chains to avoid interactions with water. The backbone polar atoms need to engage in hydrogen bonding, and this is achieved through the 2° structures a-helix and b-strand. 9. Recognise that in water soluble proteins the non-polar amino acids form the hydrophobic core of the protein with the hydrophilic polar amino acids on the surface. For proteins embedded in the lipid membrane, the opposite is true, the non-polar amino acids are on the surface to interact with lipids and the polar amino acids are in a water- filled pore or at the outer edges beyond the membrane bilayer. 10. Explain the importance of covalent disulphide bonds and non-covalent bonds in the formation and stability of the 3-dimensional structures of proteins. 11. The concept of a "domain" as a continuous section of a protein sequence that can fold up in 3- dimensions independently of the rest of the protein. Assembling, replicating and shuffling "domains" has facilitated the efficient evolution of complex multi-domain proteins. AMINO ACIDS AND THEIR STRUCTURES An amino acid contains a central carbon surrounded by four groups; an amino group, a carboxyl group, a hydrogen, and a side chain. The side chain (R) changes per amino acid. There are 20 amino acids grouped into four groups; polar non-charged, non-polar, charged positive, and charged negative. Note that cysteine can sometimes be grouped with the non-polar group. You must memorise all 20 amino acids, their groups, and their three-letter code. Just like other macromolecules, the amino acids link up to make a polypeptide chain through the dehydration reaction. The bonds that are created are called peptide bonds. These link the carboxyl group of one amino acid to the amino acid of the next. The peptide bonds are formed one at a time, starting with the amino acid at the amino end (N-terminus) to the carboxyl end (Cterminus). The polypeptide has a repetitive backbone (purple) to which the amino acid side chains (yellow and green) are attached. The peptide bond is a partial double bond – it is rigid and directional. However, the bonds around it are flexible and can rotate. This peptide bond limits the amount of possible three-dimensional structures the polypeptide can take on. When polypeptides form to become proteins, there are four structures it goes through: Primary structure: A unique sequence of amino acids in a protein. Secondary structure: A pleated or coiled strand; α-helix: Polypeptide’s backbone is coiled. β-strand: Segments bend 180 and fold in the same place. Strands discovered by Linus Pauling in 1951. Tertiary structure: Three dimensional fold that results from interactions between R-groups or between the backbone and R groups. Quaternary structure: Arrangement of multiple subunits. The folding occurs due to the drive to minimise interactions between non polar side chains and water, while maximising interactions of polar side chains with water.  Allow for the limited combinations of Φ and Ψ dictated by steric hindrance. ANFINSEN’S RENATURATION EXPERIMENT Christian Anfinsen proved that the primary structure of the amino acid is enough to determine the protein’s shape and structure. This structure (primary) can consist of non-covalent forces; hydrogen bonds, ionic bonds, hydrophobic interactions, and disulphide bonds. Anfinsen used Ribonuclease A in his experiment as it is a protein that can hydrolyse phosphodiester bonds in RNA (gives him something to measure) and is readily available in large quantities. Furthermore, the 8 cysteines in the structure allow for 4 disulphide bonds to form. The experiment started with the ribonuclease A in a test tube. It is then treated with harsh chemicals; Urea (to break up the hydrogen bonds), and β-mercapto ethanol (to break up the disulphide bonds). This caused the three-dimensional structure to unravel and go into a denatured state. In the denatured state, it could not hydrolyse the phosphodiester bonds in RNA. Using gel filtration chromatography, Anfinsen removed the denatured protein from the harsh chemicals. This allowed hydrogen bonds and disulphide bonds to reform. This allowed it to once again gain the activity of hydrolysing phosphodiester bonds. This was enough proof to show that the primary sequence dictates the protein structure and function. 3-DIMENSIONAL STRUCTURE & FUNCTION, AND DOMAINS WH Bragg and WL Bragg were trying to understand protein structure using X-ray diffraction and won a Nobel prize in physics for it in 1915. This allowed for us to have 3D images of proteins. It is important to note that proteins are not static like they are in pictures. Here are examples ofan all alpha-helix structure (growth ormone) and an all beta-stranded structure (porin). Remember, these are secondary structures; The driving force for the folding of these forces is their hydrophilic and hydrophobic relationships. When a protein that will be placed in a soluble, such as the growth hormone, the sidechains on the outside are likely to be hydrophilic. When a protein that will be placed in a non-soluble environment, such as the porin, it is most likely to have non-polar sidechains on the outside and thus be hydrophobic. Note that porin has hydrophobic sidechains at the top and bottom – this is important when you consider the cell membrane structure (porin is a pore in the membrane). Domains are a part of a protein that can fold up in three dimensions independently of the rest of the protein. For example, SH3 can be taken from the protein and be expressed in the same way as if it was a part of the protein – note the two images are the same in terms of folding. IDEAS AND UNDERSTANDING: 1. Understand the difference between potential energy and kinetics energy. 2. Understand the implications of the 1st law of Thermodynamics.  3. Describe the energy exchange within chemical reactions including the meaning of endergonic, exergonic and Gibbs free energy. 4. Explain how ATP is used in a coupled reaction to facilitate an otherwise endergonic reaction. 5. Explain how enzymes have all the properties expected of catalysts and how they can lower the activation energy barrier of reactions. 6. Explain the difference between competitive and non-competitive inhibitors. 7. Predict the effect of allosteric activators or inhibitors on the regulation of multi-step biochemical pathways. THERMODYNAMICS AND COUPLED REACTIONS Thermodynamics is the study of how to understand the energetics of chemical reactions. The laws are; 1. Energy can be transferred from one form to another, but it cannot be created or destroyed (or – the total energy of the system is conserved) 2. Total disorder (entropy) in the universe increases: Organisation requires energy Total disorder can happen spontaneously J. Willard Gibbs tried to measure how much energy is available in a reaction that does useful work. Gibbs came up with the Free Energy Equation: ΔG = ΔH -TΔS ΔH = Enthalpy, T = Kelvin, S = Entropy A reaction will only proceed spontaneously if ΔG is negative. Energy can take many different forms; Kinetic Energy: Energy associated with motion. Potential Energy: Energy storied in the location of matter. It also includes the chemical energy stored within the molecular structure. There are two main types of chemical reactions to think of: The first being Exergonic Reactions where ΔG < 0. Energy of reactants is higher than products, thus energy is released in this reaction. The hump is the Activation Energy Barrier, it stops the reaction from occurring. Energy needs to be added for the reaction to progress. Gibbs free energy change is the energy between products and reactants. The second being Endergonic Reactions where ΔG > 0. Energy of reactants is lower than the products What if the reaction is nonspontaneous (endergonic) but also essential? How do you make it happen? You must provide additional energy by using a coupled reaction. ATP (Adenosine triphosphate) has many roles in the body. It is the universal currency of the cell as it can be utilised to release energy. It has high energy in its phosphate bonds which can be released when the phosphate bonds are broken due to hydrolysation. Once the ATP hydrolyses, ADP (adenosine diphosphate) is produced as well as one singular inorganic phosphate and energy. The change in energy in this chemical reaction is -30.7kJ/mol (because the value is a negative, this means that energy is being released, and therefore an exergonic reaction). An example of a coupled reaction is Glutamic Acid + ATP: Glutamic acid + Ammonia causes a chemical reaction that results in an energy change of +14.3kJ/mol. The problem with this is that as it is a positive value, the reaction will not proceed spontaneously. To rectify this, we must introduce an ATP molecule. By introducing a molecule of ATP, one of the phosphate bonds has broken off and has coupled with the glutamic acid. This produces a phosphorylated intermediate. The ammonia (NH3) is then added to form the product glutamine + ADP + the lone inorganic phosphate. By doing this, the reaction is now releasing -30.7kJ/mol, resulting in a spontaneous reaction Next is calculating the Net ΔG To calculate this, the ΔGGlu and the Δ GATP must be added together as seen in the diagram above. There are three types of cellular work that may require ATP: Chemical work. Transport work. Mechanical work. UNDERSTANDING ENZYMES Enzymes provide an alternative pathway for a reaction to proceed, lowering the activation energy barrier. Enzymes do not affect ΔG but do affect the rate of reaction. Enzymes are catalysts which: Alter the rate of a reaction by lowering the activation energy barrier. Work by stabilizing the reaction intermediate. Participate in the reaction but are not consumed by the reaction. Enzymes have active sites: Reactants are called substrates. Substrates bind at the active site. Much of the protein is a scaffold used to arrange specific amino acid side chains within the active site.