Biochem Student Notes PDF

# MACROMOLECULES These are large organic molecules that are extremely important to living organisms. Keep in mind that most organic molecules are mainly made up of the atoms found in the acronym "CHON"... that is, carbon, hydrogen, oxygen and nitrogen (there are smaller amounts of other elements, to...

# MACROMOLECULES These are large organic molecules that are extremely important to living organisms. Keep in mind that most organic molecules are mainly made up of the atoms found in the acronym "CHON"... that is, carbon, hydrogen, oxygen and nitrogen (there are smaller amounts of other elements, too). Sometimes these large molecules are made up of repeating subunits. ## There are four types of these molecules: 1. carbohydrate (like starch & sugars) 2. lipid (like fats & oils) 3. protein (like enzymes) 4. nucleic acid (like DNA) ## Structure of Monomers and Polymers A monomer is a small molecule.. A polymer is a long-chain molecule made up of a repeated pattern of monomers. ## Three of these types of molecules are called polymers (which are molecules composed of long chains of smaller, repeating subunits). Lipids are the only type of molecule here that isn't a polymer, but they're still made up of a few smaller parts put together. # CONDENSATION REACTION This is the type of chemical reaction that occurs when two smaller subunits are put together, and they release a water molecule. This is because a hydrogen (H) on one subunit interacts with a hydroxyl (OH) on the other subunit, making water (H2O). This process absorbs energy and is called an anabolic reaction because it builds up molecules from smaller ones. The energy is stored in the bonds. Because energy is absorbed in the process, these newly formed molecules can then be considered a good source of energy (like the sugar molecule being formed here). # HYDROLYSIS REACTION This is a type of chemical reaction that occurs when large molecules are broken apart into smaller ones. A water molecule is used up to make this process happen. This involves breaking down molecules, and is an example of a catabolic reaction. This can be thought of as the "reverse" of a condensation reaction, and energy is released (this happens in the process of digestion). For condensation and hydrolysis reactions to happen in living systems, they require the assistance of enzymes. ## ENZYMES: Special protein molecules that speed up chemical reactions with high efficiency (more on this to follow), and don't get consumed in the process (known as "catalysts"). # MAJOR MACROMOLECULES ## 1. CARBOHYDRATES Extremely common molecules found in living things that consist of C, H, and O atoms. ## Glucose CH₂OH Simple carbohydrates are made up of single sugar units (which are small chains or rings of carbon atoms), known as a simple sugar. Glucose is a common example. They are also referred to as monosaccharides. ## Disaccharides are two sugars put together, specifically (shown in this picture below). Oligosaccharides are sugars where a small amount simple sugars are joined together (two or three). They attach to each other using bonds called glycosidic linkages. Joining these molecules together involves a condensation reaction and will absorb energy and release water. These molecules have many hydroxyl (-OH) groups (which you can see in the picture) and can attract to each other using hydrogen bonds. They can also attract water as well, depending on how the -OH groups are arranged. Polysaccharides are composed of hundreds to thousands of monosaccharide sub-units. They are also called complex carbohydrates. Some are straight chain, and some are branched. ## POLYMERS are types of molecules with repeating units. They are important to a cell because they are good for energy storage and structural support. Some examples are starch, glycogen, and cellulose. The process of photosynthesis produces carbohydrates. ## 2. LIPIDS These molecules are also made of C, H and O atoms. (like in this triglyceride molecule shown here) They have fewer O-H bonds which are normally quite polar ("water loving" - hydrophilic). Instead, lipids have more C-H bonds which are non-polar ("water hating" - hydrophobic). Lipids can be classified as either fats, steroids, waxes or phospholipids (these make up cell membranes). Therefore they're insoluble in water but are soluble in other hydrophobic, non-polar/lipid-like molecules. Organisms use lipids to store energy, builds membranes and other cell parts, and to act as chemical signalling molecules. ## Fats are the main energy storing molecule in organisms. They pack together and have many carbon-hydrogen energy-rich bonds. ## The most common type of fat in plants and animals is the triglyceride (above diagram). Here, one molecule of glycerol joins to three fatty acid molecules. A condensation reaction takes place between the hydroxyl groups (-OH) on the glycerol and the carboxyl groups (-COOH) on each fatty acid molecule. This produces three water molecules in the process. These fatty acids can have all single Carbon-Carbon (C-C) bonds, or they can have one or more double bonds in their structure (C=C). If a fatty acid contains only one carbon double bond, it's called a monounsaturated fatty acid. If it has two or more double bonds, it's called a polyunsaturated fatty acid. When double bonds are present, the molecule doesn't look straight, and it gets a bend or "kink" in it. Thus, they can't align (or stack) with other straight-chain (saturated) fatty acids which have no double bonds. Because they can't stack tightly, the unsaturated fatty acids tend to be liquids at room temperature. Normally, tight stacking helps them be solids at room temperature. ## 3. PROTEINS These are the most diverse molecules. The genetic information in DNA is there so that it can code for the production of proteins. Proteins are used for structure and function. They are the molecules that make cellular activities take place. ## Proteins are POLYMERS just like polysaccharides (carbohydrate molecules with repeating units). Instead, proteins are polymers of repeating amino acids. These proteins are called polypeptides (smaller chains are called peptides). Proteins can contain thousands of amino acid units. ## Amino Acid Structure Each amino acid has two main functional groups. One is the amino group (-NH2), and the other is the carboxyl group (-COOH) (see the diagram). The "R" group is what makes each amino acid different because this group can vary in its chemistry, and there are 20 different R groups, thus there are 20 different types of amino acids. Of the 20 amino acids that we eat, 9 of them are essential and we must have them in our diet to live. Our body can make the other 11. When two amino acids come together, the amino group reacts with the carboxyl group making a peptide bond. This is a condensation reaction because water is made from the -OH on the carboxyl group and the -H on the amino group when they join. Check out the 20 main types of amino acids that can join together (which have different R groups): Once polypeptides form, certain amino acids further down the chain can attract others, and a protein can fold up in different 3D structures. The specific structure has to do with its function in life. For example, the amino acid cysteine has an R group with a sulfur atom, and it can join up with other amino acids with the same R group, creating a disulfide bond. This is why hair is curly. 1. **Primary structure:** the sequence of amino acids in the chain. 2. **Secondary structure:** coils (called alpha helixes) and folds (called beta-pleated sheets). 3. **Tertiary structure:** supercoiling of the secondary structure. R-groups attracting other R-groups in the same structure causes this. 4. **Quaternary structure:** when two or more separate proteins come together to perform a specific function (like hemoglobin in blood). They hold together using hydrogen bonds, ion/dipole attractions, or disulphide links on certain R groups. ## 4. NUCLEIC ACIDS These are the informational macromolecules, like DNA. They store hereditary information and can produce identical copies of themselves (explained later in the course). DNA is also a polymer, and is a double-stranded molecule (refer to the illustration). DNA is made up of repeating units which each contain a base, sugar, and phosphate group. There are four different types of molecules called "bases" in DNA: adenine (A), guanine (G), cytosine (C), and thymine (T). A different type of nucleic acid, which is single-stranded form (see picture), is called RNA, which uses a uracil (U) base substituted for every thymine (T). You may recall that RNA is made from DNA in the nucleus (transcription), and then this RNA finds a ribosome in the cytoplasm and makes protein from its "codes" (translation). The molecule is held together (along its length at the center) using these bases. The bases A and G are called purines (composed of a double ring), and the bases T and C are called pyrimidines (composed of a single ring). The G/C pair bonding is strongest because it has three hydrogen bonds, and the A/T pair bonding is not as strong because it has only two hydrogen bonds holding them together. The two "backbones" of the molecule (it looks kind of like a "ladder") is made up of alternating phosphate and sugar groups. This sugar is a "deoxyribose" in DNA, and is a "ribose" in RNA. These bonds will only happen if each strand backbone (both strands) run in the opposite direction. Because of this, these two strands are said to run antiparallel to each other. They are said to run 3'-5' and 5'-3' (the carbon atoms get numbered in this molecule). Here you can see how the carbons are numbered in the 5-carbon sugar. Carbon #1 is numbered starting on the top right beginning at the oxygen atom. Carbon #5 is the "last" carbon. (see diagram) The backbone of the DNA strand uses the 3' carbon and the 5' carbon attachment points. ## CELL MEMBRANES The contents of the outside and the inside of the cell are separated by a thin, flexible film called the cell membrane or plasma membrane. It holds the cell contents and controls what goes in and out of the cell. Membranes are also found surrounding cell organelles. They are composed of a bilayer (double layer) of fat (lipid) molecules called phospholipids. Other compounds like proteins and carbohydrates can be seen suspended in the membrane. Because of this, and that the parts of the membrane can move around (the membrane isn't solid): it represents a "fluid mosaic model". Membranes can't be punctured easily (for example, with a needle - the surrounding membrane will move in to fill the gap as the needle is removed). Essentially, membranes are oily. Therefore, substances that are hydrophobic (just like the membrane) can dissolve or "anchor" in the membrane. # PASSIVE TRANSPORT Cell membranes are selectively permeable - only certain substances are able to pass through them. Many small, uncharged molecules such as water, oxygen, carbon dioxide and some fats are able to pass either straight through the bilayer directly (fats can pass through fairly easily because the membrane is also made of fats) OR through channels formed by proteins in the membrane. However, ions, small charged molecules and large molecules such as amino acids, carbs, etc. can't pass through the membrane easily. The ones that can pass through undergo a process called simple diffusion (moving from a high concentration to low concentration). The difference in concentration between two areas is called a concentration gradient, and diffusion always occurs down a concentration gradient (from high to low conc.) until it is all balanced out - a state called dynamic equilibrium. The rate of diffusion depends on the temperature and the concentration of solute molecules (what's dissolved) in solution. Diffusion occurs faster at high temperatures because the molecules are moving faster when it's warmer. # FACILITATED DIFFUSION (still passive) Small molecules can diffuse easily across a membrane. Sometimes, they are bigger and need some help getting across. There are special proteins imbedded in the membrane that assist with the movement of these molecules. These transmembrane carrier proteins can be like tubes for these substances to pass through. Facilitated diffusion still uses no energy, but it needs helper proteins, compared to simple diffusion (doesn't get any help). # ACTIVE TRANSPORT Recall, simple diffusion and facilitated diffusion are used by cells to move substances through membranes from areas of high concentration to areas of low concentration until concentrations are equal (dynamic equilibrium). This process doesn't use any energy, as it happens automatically. However... When various molecules need to be concentrated and forced against the concentration gradient (ex. moving nutrients into concentrated places), the cell may need to use its own energy to pump these things across the membranes forcefully. Recall that there is a molecule called ATP which provides the energy needed in many processes. This is one of those processes where it's required. ## Adenosine Triphosphate Recall: When ATP (adenosine triphosphate) breaks down into ADP (adenosine diphosphate), it gives off energy: ACTIVE transport requires energy supplied by ATP. For example, nutrients in your intestines are actively pumped into your bloodstream where nutrients are lower (using ATP energy). Even though these nutrients would be able to diffuse into your bloodstream using simple diffusion, your body uses active transport to ensure that almost all of the nutrients are removed, and eliminate the risk of wasting any nutrients that pass by undigested. There's other types of pumps like the sodium-potassium pump which pump sodium and potassium against their concentration gradients for use in nerve and muscle cells (requires ATP to do this). More on this later in the course. # BULK TRANSPORT Sometimes, cells need to transport large quantities of substances, or large substances into or out of cells. There are two methods, and both use ATP in the process: ## 1. ENDOCYTOSIS This method is used to bring large amounts of material (or large substances) into the cell from extracellular fluid. There are two forms of this type: 1. Phagocytosis: bulk transport of solids into the cell 2. Pinocytosis: bulk transport of liquid (extracellular fluid) into the cell. ## 2. EXOCYTOSIS This method moves large amounts of material (or large molecules) out of the cytoplasm (this is the reverse of endocytosis). The material to be moved out is enclosed in a membrane sac called a secretory vesicle. This vesicle fuses with the cell membrane and spills its contents into the extracellular fluid. # ATP Adenosine triphosphate (ATP) is the main source of free energy in living things. ## An ATP Molecule When energy is needed, an enzyme makes the third phosphate on the molecule break off, resulting in a molecule of ADP (adenosine diphosphate) + energy. This is an example of the hydrolysis reaction. When this free phosphate (written "Pi") attaches itself to other molecules that have work to do, it provides extra energy and makes the molecule more reactive. This attachment is called phosphorylation. ATP plays a VERY important role in metabolism and it's a molecule produced in large amounts in the processes of photosynthesis and cellular respiration (we will discuss this in the next unit). So overall: ADP can then be "recharged" back to ATP. This happens in cellular respiration (next unit). # REDOX REACTIONS Many chemical reactions involve transferring electrons from one molecule to another. When a molecule loses electrons, this process is called oxidation. When a molecule gains these electrons that are lost, this process is called reduction. Because oxidation (losing) is always accompanied by a reduction (gaining), it is called a "redox" reaction (think about it!) The substance that provides the electron is called the reducing agent (because it causes something to be reduced). The substance that takes the electron is called the oxidizing agent (because it causes something to be oxidized). Therefore, a substance that gets oxidized is a reducing agent, and a substance that gets reduced is an oxidizing agent. An easy way to remember this is the phrase "LEO goes GER" (like Leo the lion goes "grrrrr") LEO means that LOSING ELECTRONS is OXIDATION GER means that GAINING ELECTRONS is REDUCTION Sometimes the movement of electrons happen in a longer sequence, kind of like a "chain". The electron is moved along from molecule to molecule, as long as each molecule it goes to has a stronger and stronger attraction for an electron along the way. This is kind of like a "hot potato" passed along. Being oxidized can also mean gaining an oxygen atom, or losing a hydrogen atom. Being reduced can also mean gaining a hydrogen atom, or losing an oxygen atom. # METABOLISM Metabolism can be viewed as being the sum of all the anabolic chemical reactions ("building up" - molecules joining together) and catabolic chemical reactions ("breaking down" - molecules coming apart) in living things. ## Kinetic energy: the energy possessed by moving objects. ## Potential energy: stored energy, like chemical potential energy. In biology this is relevant (later in the course). For reactions to occur, a certain amount of energy is needed to get it going, usually called the "activation energy". This allows the "activated complex" (see the diagrams below), to form. In a chemical reaction, energy can be released or absorbed in the process. Before the reactant molecules change chemically, they have to go through a transition state which happens when bonds are breaking and forming at the same time (this is a state of higher energy). Chemicals store a certain amount of energy in their bonds. If the reactants store more energy than the products that are made, this stored energy is given off, and this is an exergonic process. Exothermic means the same thing except it only deals with heat energy given off (feeling warm), hence "therm" in the name. If the reactants store less energy in their bonds as the products do, energy is absorbed, and is an endergonic process. Endothermic means absorbing energy as well but in this case it only deals with heat (absorbing heat feeling cold). Notice ∆H in the diagrams. It stands for the enthalpy for the reaction, which refers to the amount of energy available in chemical substances. It's negative when the reaction gives off energy, and has a positive value when it absorbs energy, because ∆H = (Hfinal - Hinitial). ## METABOLIC REACTIONS ARE REVERSIBLE. You may have been taught that chemical reactions aren't reversible, but in living systems, many chemical reactions can go forward and backwards, with the help of enzymes (specialized protein molecules). Metabolic pathways can be very complicated. We will study a few small ones. # ENZYMES Enzymes are catalysts made out of protein. A catalyst is a substance that speeds up a chemical reaction without taking part in the reaction itself, so it stays intact and can be re-used over and over again. Normally, molecules need some extra energy to start reacting together. Heat is this energy needed in many cases. In biological systems, this is not an option because heat can destroy (denature) proteins by changing their shape, and then life would cease to exist. Enzymes allow the molecules that need reacting to come closer together, and assist in the reaction without the heat. It basically lowers the activation energy needed and makes the transition state (activation complex) easier to attain (see diagram). The substrate is the reactant that the enzyme reacts with (the molecule that will ultimately be changed). The substrate (or substrates) will then bind to the enzyme's active site (a pocket or groove in the enzyme). This overall attachment is then called the enzyme-substrate complex. When the chemical reaction takes place at this point, the shapes of the molecules change slightly, allowing them to then break free of the enzyme. Only the proper substrate is able to bind to a specific active site, and this is called the induced-fit model. The enzyme can then be used over and over again. Some enzymes require cofactors (inorganic substances like minerals), or coenzymes (organic substances such as vitamins) before they can work properly. # ENZYME INHIBITION Competitive inhibitors are very similar (in shape) to the substrate for the enzyme. If there's a lot of it, it can flood the active site, and block proper enzyme function. If the "regular" substrate is plentiful, it can out-compete the inhibitor, and the enzyme can start to resume normal function. Noncompetitive inhibitors attach to a different site other than the active site. This binding ends up changing the enzyme's shape, and causes the shape of the active site to change slightly, therefore enzyme function is affected (less active). # ALLOSTERIC REGULATION Cells can control enzyme activity in two ways: 1. **By inhibiting the enzyme's action.** Enzymes can possess reactive sites other than the active site, called allosteric sites. An allosteric activator is a molecule that binds here which then stabilizes the active form of the enzyme. An allosteric inhibitor is a molecule that binds here which stabilizes the inactive form (noncompetitive inhibitors attach to these allosteric sites). 2. **By restricting the production of the enzyme itself.** Feedback inhibition is a method used to keep enzyme levels in check. Often, there is a long series of sequential reactions, each controlled by a specific enzyme. Along the chain somewhere (perhaps the end), the molecule produced there can act as an allosteric inhibitor to one of the enzymes at the beginning of the sequence, slowing down all the sequence of events. Overall, it controls the production of the end product. Or, in other words, the end product can slow its own production down, so it doesn't get out of control, and keep an appropriate level. This is an example of negative feedback. # EXAMPLES OF ENZYMES: The names of enzymes usually have the ending "-ase" in their name. Recall from your previous biology course these examples of enzyme types: Proteases, Carbohydrases, Lipases (digestive enzymes). Here are some more examples (from a nearly countless amount that exist): - Lactase - digests lactose sugar... some people don't have much of this: "lactose intolerant") - Helicase - unravels DNA - DNA polymerase – makes DNA from its building blocks - Amylase - breaks down sugars, found in saliva - Alcohol dehydrogenase - breaks down alcohol in the liver There are many, many other enzymes that join and dismantle other molecules. # INDUSTRIAL USES In brewing, baking and winemaking, yeast cells catalyze the conversion of glucose into ethanol (alcohol) and carbon dioxide gas. This gas creates the air pockets in baked goods. Glucose is made from enzymes that digest corn, wheat and barley. Enzymes can be also used for cleaning, making dairy products, making leather and paper as well as many other uses.