SBU1053 Chapter 2 Biomolecules PDF

Chapter 2 : Biomolecules Dr. Azi Azeyanty Bt Jamaludin  2.1 Basic Chemistry Matter is anything that takes up space and has mass. The three states of matter are solid, liquid, and gas. All matter, living or nonliving, is made up of elements. Elements...

Chapter 2 : Biomolecules Dr. Azi Azeyanty Bt Jamaludin  2.1 Basic Chemistry Matter is anything that takes up space and has mass. The three states of matter are solid, liquid, and gas. All matter, living or nonliving, is made up of elements. Elements are substances that cannot be broken down into simpler substances by ordinary chemical means. Elements That Make up 95% of Organisms (by weight) C Carbon H Hydrogen N Nitrogen O Oxygen P Phosphorus S Sulfur  Atomic Structure An atom is the smallest part of an element that displays the properties of the element. Atoms are made up of subatomic particles. Protons-positively charged, found in nucleus Neutrons-uncharged, found in nucleus Electrons-negatively charged, move around nucleus Ex: Helium (He)  Electrons In an electrically neutral atom, the positive charges of protons in the nucleus are balanced by negative charges of electrons. Electrons move around the nucleus in orbitals. Electrons move in energy levels (electron orbitals). First contains two electrons. Every one after that can hold eight electrons. Octet rule 2.2 Molecules and Compounds Molecules form when two or more of the same elements bond together (example: O2). Compounds form when two or more different elements bond together (H2O). When a chemical reaction occurs, energy may be given off or absorbed because of the energy present in bonds.  Ionic Bonding Ions form when electrons are transferred from one atom to another. For example: Na, with one electron in its 3rd orbital, tends to be an electron donor. Becomes positive after giving up one electron. Cl, with seven electrons in its 3rd orbital, tends to be an electron acceptor. Becomes negative after gaining one electron. After the transfer of electrons between Na and Cl: Both the Na and Cl ions have eight electrons in their outer orbitals. Ions now have opposite electrical charges. Ionic compounds are held together by an attraction between oppositely charged ions called an ionic bond.  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Na Cl Each atom now has 8 sodium atom (Na) chlorine atom (Cl) electrons in its outermost orbital. Electron transfer creates – charge imbalance. + Charge imbalance creates Na Cl ionic bond. Sodium ion (Na+) Chloride ion (Cl+) sodium chloride (NaCl) Figure 2.7a Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.  Covalent Bonding A covalent bond results when atoms share electrons in such a way that each atom has an octet of electrons in the outer orbital. An atom may share electrons with one or more atoms. After sharing electrons, each atom has a completed outer orbital. For example, two hydrogen atoms can share their single electron. If the sharing of electrons between two atoms is fairly equal, a nonpolar covalent bond results. A single covalent bond results from sharing one A double covalent bond results from sharing two pair of electrons pairs of electrons  If the sharing between two atoms is unequal, it is described as polar covalent bond. As in water, the sharing of electrons between oxygen and each hydrogen is unequal. Oxygen is more electronegative than hydrogen Electronegativity is the attraction of an atom for electrons in a covalent bond.  Hydrogen Bonding Polarity within a water molecule causes the hydrogen atoms in one molecule to be attracted to the oxygen atoms in other water molecules. The attraction between partially (-) oxygen and partially (+) hydrogen results in a hydrogen bond. Bond is weak individually but strong collectively. Hydrogen bonding between water molecules  2.3 Water The first cell(s) evolved in water. Organisms are composed of 70–90% water. Water is a polar molecule. Water molecules form hydrogen bonds which cause them to cling to one another. Water is liquid at temperatures typical of the Earth’s surface due to hydrogen bonding.  Properties of Water Water has a high heat capacity A calorie is the amount of heat energy needed to raise the temperature of 1 g of water 1°C. The hydrogen bonds that link water molecules help water absorb heat without a great change in temperature. Because the temperature of water rises and falls slowly, organisms are better able to maintain their normal internal temperatures.  Water has a high heat of vaporization Converting 1 g of the hottest water to a gas requires an input of 540 calories of heat energy. Gives animals in a hot environment an efficient way to release excess body heat. Also helps moderate temperatures along coasts. Water is a solvent Due to its polarity, water facilitates chemical reactions, both outside and within living systems. It dissolves many chemical substances. A solution contains dissolved substances, which are then called solutes. Hydrophilic molecules attract water. Hydrophobic molecules do not attract water.  Water molecules are cohesive and adhesive Water molecules cling together because of hydrogen bonding (cohesion). Water’s positive and negative poles allow it to adhere to polar surfaces (adhesion). Water is an excellent transport system, both outside and within living organisms. For example, blood transports dissolved and suspended substances throughout the body. Water has a high surface tension The stronger the force between molecules in a liquid, the greater the surface tension. This allows some insects to walk on the surface of a pond or lake.  Frozen water (ice) is less dense than liquid water As liquid water cools, the molecules come closer together (densest at 4°C). Water expands as it freezes because a crystal lattice forms with hydrogen bonds farther apart. Ice floats on liquid water because it is less dense. Bodies of water freeze from the top down.  2.4 Acids and Bases Acidic Solutions (High H+ Concentrations) Acids are substances that release hydrogen ions (H+) when dissociated in water. An example: HCl H+ + Cl- Basic Solutions (Low H+ Concentrations) Bases are substances that dissociate in water, release hydroxide ions (OH-) or take up hydrogen ions (H+) An example: NaOH Na+ + OH- When water ionizes, it releases an equal number of hydrogen ions (H+) and hydroxide ions (OH-) = Neutral  The pH scale indicates the acidity or alkalinity of a solution. Scale ranges from 0 – 14. A pH below 7 is acidic. [H+] > [OH-] A pH above 7 is alkaline. [OH-] > [H+] A pH of 7 is neutral. [H+] = [OH-]  Buffer and pH A buffer is a chemical or combination of chemicals that keep pH within normal limits. Bicarbonate ions (HCO3-) and carbonic acid (H2CO3) found in human blood buffers the pH to 7.4. If hydrogen ions (H+) are added to blood, this reaction occurs: H+ + HCO3- H2CO3 If hydroxide ions (OH-) are added to blood, this reaction occurs: OH- + H2CO3 HCO3- + H2O These reactions prevent any significant change in blood pH.  2.5 Organic Molecules Organic molecules always include: Carbon (C) and hydrogen (H) Those with only (H) and (C) are called hydrocarbons. The chemistry of carbon accounts for the formation of great variety of organic molecules. Carbon atoms contain four valence electrons. A carbon atom may share electrons with another carbon atom or other atoms in order to achieve eight electrons. Satisfying the octet rule  Functional groups are a specific combination of bonded atoms that always react in the same way. The more common functional groups are listed in the Table:  Macromolecules contain many molecules joined together. Monomers: Simple organic molecules that exist individually. Polymers: Large organic molecules form by combining monomers Polymers in cells and their monomers  Cells use common reactions to join monomers. In a dehydration reaction an -OH and -H are removed as a water molecule. In a hydrolysis reaction, components of water are added.  2.6 Carbohydrates Carbohydrates function for quick fuel and short-term energy storage in organisms. Play a structural role in woody plants, bacteria and insects. On cell surfaces, involved in cell-to-cell recognition.  Simple Carbohydrates Monosaccharides are sugars with 3 - 7 carbon atoms. Pentose refers to a 5-carbon sugar Hexose refers to a 6-carbon sugar Figure 2.14 C6H12O6  Disaccharides contain two monosaccharides joined by the dehydration reaction. Examples – maltose, sucrose, lactose Polysaccharides such as starch, glycogen, and cellulose are long polymers that contain many glucose subunits. Figure 2.15  Starch and Glycogen Starch is the storage form of glucose in plants. May contain up to 4,000 glucose units. Fewer side branches than glycogen. Glycogen is the storage form of glucose in animals. Liver stores glucose as glycogen. In between meals, the liver releases glucose stored in glycogen  Cellulose Some polysaccharides function as structural components of cells. Cellulose is found in the cell walls of plants. Accounts for the strong nature of the cell walls. Has different chemical linkage than starch or glycogen. Prevents us from digesting foods with cellulose. Chiton, found in the exoskeleton of crabs, is another structural polysaccharide.  2.7 Lipids Lipids contain more energy per gram than other biological molecules. Types Fats and oils used for energy storage. Phospholipids from membranes. Steroids include sex hormones. Lipids are diverse in structure and function. Lipids have one common characteristic – they do not dissolve in water (hydrophobic).  Fats and Oils Fats Usually of animal origin Solid at room temperature Store energy, insulate against heat loss, form protective cushion Oils Usually of plant origin Liquid at room temperature A fat molecule is also known as a triglyceride or neutral fat. A triglyceride consists of : One glycerol backbone + Three fatty acids. A fatty acid is a hydrocarbon chain that ends with the acidic group — COOH. Saturated fatty acids have no double bonds between carbon atoms. Unsaturated fatty acids have one or more double bonds between carbon atoms.  Phospholipids Phospholipids are comprised of two fatty acids and a phosphate group. The phosphate group is polar so the molecules are not electrically neutral. The phosphate group forms a polar head (hydrophilic) while the rest of the molecule is a nonpolar (hydrophobic) tail. Spontaneously form a bilayer in which the hydrophilic heads face outward toward watery solutions and the tails form the hydrophobic interior.  Steroids Steroids have a backbone of four fused carbon rings. Examples: Cholesterol, Testosterone, Estrogen Figure 2.22 a. Testosterone b. Estrogen  2.8 Proteins Proteins are polymers composed of amino acid monomers Amino acids Amino group (-NH2) Acidic group (-COOH) R group varies Proteins perform many functions. Structural proteins give support (keratin, collagen) Enzymes speed up chemical reactions Hormones are chemical messengers Actin and myosin move cells and muscles. Some proteins transport molecules in blood. Antibodies protect cells. Channels allow substances to cross membranes Figure 2.24  Peptides Peptides A polypeptide is a single chain of amino acids. A peptide bond joins two amino acids. Figure 2.24 Levels of Protein Organization Proteins have up to 4 levels of structural organization. Primary structure is the linear sequence of the amino acids. Secondary structure occurs when the protein takes on a certain orientation in space Two types include: Alpha helix & Beta sheet  The tertiary structure is the final three-dimensional shape. Maintained by various types of bonding between R groups. Covalent, Ionic, Hydrogen bonding, Disulfide bonding. Quaternary structure is found in proteins with multiple polypeptide chains. Separate polypeptide chains are arranged to give this highest structure The final shape of a protein is very important to its function. A protein is denatured when it loses structure and function. Occurs when proteins are exposed to extreme heat or pH.  2.9 Nucleic Acids The two types of nucleic acids are: DNA (deoxyribonucleic acid) Stores genetic information in the cell and in the organism DNA replicates to transmit its information when a cell divides or organism reproduces RNA (ribonucleic acid) Both DNA and RNA are polymers of nucleotides Every nucleotide is a molecular complex of Phosphate, Pentose sugar (ribose or deoxyribose), Nitrogen-containing base. DNA contains: Adenine (A), Thymine (T), Guanine (G) and Cytosine (C) In RNA, uracil (U) replaces thymine  Structure of DNA The nucleotides form a linear molecule called a strand. DNA is a double helix of two strands. The two strands are held together by hydrogen bonds. Rings of the ladder are formed by complementary paired bases. Adenine (A) always pairs with thymine (T) Cytosine (C) always pairs with guanine (G)  Structure of RNA RNA is single-stranded. Several types are involved in carrying information from DNA to make proteins.