Molecular Biology test revision notes

2.1 Molecules to metabolism: page 43 (see page 43 for learning objectives)  Elements in living things (page 43):  Carbon, hydrogen, oxygen and nitrogen are the four most common elements found in living organisms Carbon, hydrogen and oxygen are found in all the key organic molecules (proteins, carbohydrates, nucleic acids and lipids)  Proteins and nucleic acids also contain nitrogen Any compound that does not contain carbon is inorganic. Molecular biology explains the roles of the chemical substances involved in life processes Carbon compounds including carbohydrates, lipids, proteins and nucleic acids form the basis for life.  Carbon atoms (pages 43-44): (see page 43, figure 2.1)  Every organic compound contains two or more atoms of carbon Carbon atoms can also form double and triple bonds with other atoms, so increasing the variety in the molecular structure of organic compounds.  Carbohydrates, proteins, lipids and nucleic acids are the main types of carbon Carbon compounds - the building blocks of life (pages 44-46) : Carbohydrates are compounds that contain only the elements carbon, hydrogen and oxygen (and are the most abundant group of biological molecules) Lipids contain the same three elements, but with much less oxygen Lipids may contain small amounts of other elements such as phosphorus.  Proteins, unlike carbs and lipids, always contain nitrogen (sulfur, phosphorus and other elements are also often present)  Many organic molecules are very large and complex, but they are build of small subunits. Small subunits called monomers are build into complex molecules called polymers in a process known as polymerisation. Carbohydrates (page 45):   The most abundant category of molecule in living things.  In both plants and animals, they are used as a source of energy.  Carbohydrates occur in different forms: Monosaccharides (with the general formula (CH2O)n where n= the number of carbon atoms in the molecule, are monomers- single sugars made up of one subunit) Disaccharides are sugars with two subunits joined together by a condensation reaction (see page 46)  Polysaccharides are long molecules consisting of a chains of monosaccharides linked together (See table 2.4, page 54)  Monosaccharide examples: glucose, galactose, fructoseExample of use in plants: Fructose makes fruits taste sweet, and attracts animals to eat them- thereby dispersing the seeds insideExample of use in animals: Glucose is the source of energy for cell respiration - it is obtained from the digestion of carbohydrate foods.  Disaccharide examples: lactose, maltose, sucrose Example of use in plants: Sucrose is transported from leaves to storage tissues and other parts of the plant to provide an energy Example of use in animals: Lactose is found in milk and provides energy for young mammals  Polysaccharide examples: starch, glycogen, celluloseExample of use in plants: Cellulose is a structural component of plant cell walls + starch is used as a food store Example of use in animals: Glycogen is the storage carbohydrate of animals, found in the liver and muscles. Lipids (page 45):  Insoluble in water, but do dissolve in organic solvents Known as energy storage molecules in plants and animals  One group: triglyceride lipids, includes fats and oilsSolid=fat, liquid=oil.  Animals store energy as fat whereas plants store oils  Lipids contain twice as much energy per gram as carbohydrates Second group of lipids: steroids, which consist of four interlinked rings of carbon (examples of steroids: vitamin D and cholesterol) Protein (page 45): READ UP!!!! Proteins are built up of building blocks called amino acids The simplest amino acid is glycine There are more than 100 naturally occurring amino acids, but only 20 are used in building the bodies of living things.  Proteins are built up of amino acids in condensation reactions.  Nucleic acids (page 46):  Found in all living cells and in viruses Two types of nucleic acid found in cells are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).  DNA is found in the nucleus, mitochondria and chloroplasts of eukaryotes, while RNA maybe occur in the nucleus but is found usually in the cytoplasm. Vital to inheritance and development  Nucleic acids are long molecules consisting of chains of units called nucleotides Each nucleotide consists of a pentose sugar - ribose in RNA and deoxyribose in DNA - linked to phosphoric acid and an organic base.  Nucleic acid chains are longer and more complex than those found in proteins. Condensation (p46-47):  In a condensation reaction, two molecules can be joined to form a larger molecule, held together by strong covalent bonds Condensation is an example of an anabolic reaction (which builds up monomers to form macromolecules)  An enzyme is required to catalyse the process of condensation, and it produces one molecule of water  For example: Glucose(monosaccharide) + Galactose(monosaccharide) -▸ Lactose(disaccharide) + water Two amino acids can be linked to form a dipeptideWhen more than two amino acids are joined in this way, a polypeptide is formed (polypeptide chains form protein molecules) Hydrolysis (p48): Hydrolysis reactions occur every time food is digested. These reactions involve breaking down polysaccharides, polypeptides and triglycerides into smaller subunits.Hydrolysis is a reaction of a catabolic reaction, in which macromolecules are broken down into monomers. Water molecules are used in hydrolysis reactions, which are the reverse of anabolic reactions. Enzymes are used to catalyse the reactions. Hydrolysis of a starch (a polysaccharide) : uses water and produces many molecules of glucoseHydrolysis of a protein (made of polypeptide chains) : uses water and produces many amino acidsHydrolysis of a triglyceride: uses water and produces fatty acids and glycerol molecules 

2.2 Water (page 49) Hydrogen bonds (p49)  Water has a small positive charge on the two hydrogen atoms and a small negative charge on the oxygen atom. Water is a polar molecule  Hydrogen bonds form between water molecules, because they are polar.  A weak bond (a hydrogen bond) can form between the hydrogen negative charge of one water molecule and the positive charge of another  Cohesion and adhesion (p49-50) Hydrogen bonds between water molecules hold them together in a network, resulting in cohesion.  Cohesive forces give water many biologically important properties: "They enable water to be drawn up inside the xylem of a plant stem in a continuous column. Strong pulling forces, produced by as water evaporates from the leaves at the top of tall trees, draw water and dissolved minerals up great distances to the tip of branches high above the ground."  Cohesion is also responsible for surface tension, which enables some small organisms to 'walk on water'  Contributes to the thermal properties of water as well.  Adhesion:  Water tends to be attracted and adhere to the walls of its container  Adhesive forces occur between water molecules and different molecules in vessels that contain the water.  Adhesion attracts water molecules to the sides of the xylem and is important as water is drawn up the stem of the plant  Adhesive forces are greater in a more narrow tube, where relatively more water molecules are in contact with the sides  Thermal properties (p50): A large amount of energy is needed to break the many weak hydrogen bonds between water molecules. For water to evaporate, many hydrogen bonds must be broken, so evaporation requires a lot of energy. Therefore, water is a liquid at most temperatures found on earth.  A stable temperature is important to living things, because the range of temperatures in which biological reactions can occur is quite narrow. The thermal properties of water allow it to keep an organism's temperature fairly constant.  Water can act as a temperature regulator ( see example on page 50 )  SEE TABLE 2.3 Solvent properties:  Water is known as the 'universal solvent'  Water is the medium in which most biochemical reactions take place since almost all substances dissolve well in it. Substances are classified into two groups according to their solubility (Hydrophobic (usually uncharged, for example: fats and oils + large proteins that do not carry any polar groups)  and hydrophilic (sugars and salts + amino acids with polar side groups) Uncharged and non-polar substances are not very soluble in water (because water molecules would rather remain hydrogen-bonded to each other than allow such molecules to come between them.) OXYGEN CAN DISSOLVE IN WATER, BUT ITS SOLUBILITY IS VERY LOW (almost all oxygen carried in the blood is bound to hemoglobin, and not in solution). CHOLESTEROL IS ONLY SLIGHTLY SOLUBLE IN WATER AND DISSOLVES IN THE BLOOD IN VERY SMALL AMOUNTS (Cholesterol is transported in the circulatory system with lipoproteins, which have an outer surface made up of amphipathic proteins and lipid. The outward-facing surfaces of these molecules are hydrophilic and the inward-facing surfaces are lipophilic. Triglycerides are carried inside such molecules, while phospholipids and cholesterol, being amphipathic themselves, are transported in the surface layer of lipoprotein particles.)Two types of lipoproteins in blood: The more lipid and less protein a lipoprotein has, the lower the density.  low-density lipoprotein (LDL) high-density lipoprotein (HDL) 

2.3 Carbohydrates and lipids (pages 54 - 58)Carbohydrates (page 54) READ UP!!  Carbs are the most abundant category of molecule in living things.  Monosaccharides are linked together by condensation reactions to form polymers such as disaccharides and polysaccharides.  The covalent bond between two monomers in a carbohydrate is known as a gylcosidic link, and a water molecule is released in the condensation reaction.  GLUCOSE (C6H12O6)  is the most common monosaccharide (SEE FIGURE 2.2 ON PAGE 44 TO SEE THE STRUCTURES OF ALPHA-D-GLUCOSE AND BETA-D-GLUCOSE) These two forms of the molecule (known as isomers) have different arrangements, which gives them different properties.  When a bond is formed between two glucose monomers, a disaccharide called maltose is produced.  Polysaccharides may contain 40 to 1000 monomers (starch, glycogen and cellulose are all polymers of glucose monomers) Lipids: Fats and oils are the two main groups of lipids  SEE "KEY PROPERTIES OF LIPIDS ON PAGE 55" (TABLE 2.5) Fatty acids (page 56):Fatty acids consist of a long chain of carbon atoms that are joined to hydrogen atoms (hydrocarbon chains) The number of carbon atoms in fatty acid is usually an even number most commonly between 14 and 22. At one end of the chain is a carboxyl group (COOH) and at the other a methyl (CH3) group. If the carbon chain is linked to the max number of H atoms w/ no double bonds it is said to be saturated.  If a chain contains a double bond between two of the carbon atoms it is said to be unsaturated.  A chain w/ just one double bond is monounsaturated  A chain with two or more double bonds is polyunsaturated. Cis vs. Trans fatty acids (page 56-57) Unsaturated fatty acids may be either cis or trans configuration. If the 'spaces' where additional hydrogen atoms could bond are both on the same side of the hydrocarbon chain and the carbon chain is slightly bent, the fatty acid is a cis fatty acid.  Cis fatty acid examples: the omega-3 group, omega-3 fatty acids come from acids in our diet such as fish (salmon) + walnut and flax seeds.the omega-6 group, comes from vegetable oils  If the spaces are on opposite sides and it is a straight chain, it is a trans fatty acid A diet high in saturated fatty acids can be correlated with health issues & can increase risk of coronary heart disease (CHD). Saturated fatty acids can be deposited inside the arteriesIf the deposits combine with cholesterol they may lead to atherosclerosis, a condition that reduces the diameter of the arteries and leads to high blood pressure. People with a diet high in unsaturated fatty acids tend to have a lower risk of CHD. These fats do not combine with cholesterol, so arteries remain unblocked and healthy. Triglycerides (page 58): Triglycerides are formed by condensation reactions between three fatty acids and one glycerol molecule (figure 2.6) Three molecules of water are released and the bonds between the fatty acids and the glycerol are known as ester bonds. Triglycerides play a major role in the structure of membranes

2.4 Proteins (pages 59 - 61)Polypeptides:Polypeptides are built up from amino acid monomers during condensation reactions (figure 2.5) "Two different amino acids are joined with a reaction between the amino (NH2) group of one amino acid and the carboxyl (COOH) group of the other forming peptide bond and producing a dipeptide. If further condensation reactions occur, a series of amino acids can be joined to form a polypeptide."  The covalent bonds linking amino acids produce what is known as the primary structure structure of any protein that is formed from the polypeptide.  In living cells, polypeptides can consist of up to 400 amino acids  These can be linked together in any sequence, so there is a huge range of possible polypeptides. The sequence of amino acids is coded for by an organism's genes. Building a protein: Proteins consist of one or more polypeptides linked together. The complex three-dimensional structure known as the tertiary structure is held together by ionic bonds and disulphide bridges  The sequence of amino acids in a polypeptide determines the three-dimensional shape of a protein Denaturation: "irreversible changes to the structure of an enzyme or other protein so that it can no longer function." Denaturation destroys the complex structure of a protein.  Heat or the presence of strong acids or alkalis can disturb the bonds between the different parts of a protein molecule and disrupt its structure.  The primary structure of the protein will remain but the secondary, tertiary and quaternary structures are usually lost Enzymes are easily denatured by extremes of pH or temperature & lose the ability to function as catalysts. Example of denaturation: the heat used to cook meat denatures the proteins found in it so that its texture is changed, and eggs become hardened as they cook and their proteins are denatured. Functions of proteins:  The function is determined by the shape of the molecule.  Two types of proteins: globular and fibrous proteins  Fibrous proteins are long, insoluble molecules made up of parallel polypeptide chains. The chains are cross-linked along their lengths. Example: Keratin, found in hairGlobular proteins have polypeptide chains that are folded into compact, spherical shapes. The hormone insulin is a globular protein and so are enzymes (each enzyme has its own 3d shape, which allows it to work as a catalyst) The proteins found in an organism are known as its proteome. (the term derived from a combination of the words 'protein' and 'genome') 

2.5 Enzymes (pages 62 - 67) Enzymes and active sites: An enzyme is a biological catalyst. They speed up biochemical reactions, such as digestion and respiration, but they remain unchanged at the end of the process. All enzymes are proteins with long polypeptide chains that are folded into 3D shapes. If the 3D shape is destroyed or damaged (denatured), it can no longer carry out its job. In the structure of every enzyme, there is a specially shaped region known as the active site*.  *it is here the substrate and enzyme bind together The substrates are the chemicals involved in the reaction catalysed by the enzyme.  The 'lock and key hypothesis': to catalyse a reaction requires one special enzyme (see figure 2.15, page 62)  When a substrate molecule collides with the active site of an enzyme, it binds to form an enzyme-substrate complex Once in the active site, substrates may be bonded together to form a new substance or they may be broken apart in processes such a digestion or respiration. Factors affecting enzyme reaction: TemperaturepHConcentration of substrate Enzymes in industry: Immobilised enzymes: 

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