Biology of Molecules: Proteins and Water - PDF

CENTRE FOR PRE-UNIVERSITY STUDIES BIO3114 (BIOLOGY 1) Topic 1: The biology of molecules Part II NORLAILA NAJWA BINTI RAHMAN [email protected] Topic 1: The biology of molecules Part II Learning outcomes Define and explain the terms...

CENTRE FOR PRE-UNIVERSITY STUDIES BIO3114 (BIOLOGY 1) Topic 1: The biology of molecules Part II NORLAILA NAJWA BINTI RAHMAN [email protected] Topic 1: The biology of molecules Part II Learning outcomes Define and explain the terms of monomer, polymers and macromolecule Describe and explain the function and roles of carbohydrates, protein, lipids and nucleic acids Describe and draw molecular structure of monomers and polymers of carbohydrates, protein, lipids and nucleic acids. Describe and explain the synthesis and breakdown of polymers i.e condensation and hydrolysis with reference to the terminologies glycosidic bonds, ester bonds, peptide bonds, and phosphodiester bonds. Learning outcomes Describe and draw the arrangement and formations of the polymer (carborhydrates, protein, lipids) based on the structure of the molecules with reference to the hydrogen bonding, van der waals, ionic bonding and covalent bondings. Explain effects of the arrangement of the polymer on the organisms. Explain how hydrogen bonding occurs between water molecules Explain the properties of water to its roles in living organism. Proteins Role and function of proteins Proteins are large, complex molecules composed of amino acids The amino acids are linked together into long chains called polypeptides. A protein consists of one or more polypeptide chains. The polypeptide chains fold into complex three-dimensional shapes. Proteins are one of the three main classes of food that provide energy to the body. Proteins have various functions as enzymes, in cell movement, hormones, antibodies and structural material. Protein | Basic Structure of Amino acids An amino acid has both an amino group & a carboxyl group a central carbon atom which is bonded to an amine group, –NH2, and a carboxylic acid group, –COOH. All parts of an amino acid molecule are covalently bonded to a central carbon atom. The R group or the side chain will determine the classes of each amino acid. Twenty common amino acids are assembled into the thousands of different proteins in the human body. These amino acids are divided into various groups such as polar, non-polar, acidic and basic. Protein | Group of Amino acids 4 chemical groups of amino acids based on their side chains (R group). Protein | Peptide bond two amino acids can join together. One loses a hydroxyl (–OH) group from its carboxylic acid group, while the other loses a hydrogen atom from its amine group. The link is called a peptide bond. Protein | Peptide bond ❖ Polymer/polypeptide chain is formed from condensation of amino acids which are joined by peptide linkages/bonds. peptide bond The level of proteins structure 1. Primary structure 2. Secondary structure ❖ Result from hydrogen bonds at regular ❖ The amino acid sequence of a protein. intervals along the polypeptide backbone. ❖ Peptide bond only. ❖ A slight change in primary structure can ❖ Typical shapes: affect a protein’s conformation and ability to 1.coiled (an alpha helix) function. 2.folded (beta-pleated sheets). The level of proteins structure 3. Tertiary structure ❖ Determined by a variety of interactions among R groups and between R groups and the polypeptide backbone. ❖ These interactions include: 1. hydrogen bonds among polar and/or charged areas 2. ionic bonds between charged R groups 3. hydrophobic interactions among hydrophobic R groups. 4. van der Waals interactions among hydrophobic R groups to function. 5. disulfide bridges (strong covalent bonds) between the sulfhydryl groups (SH) of cysteine monomers which stabilize the structure. Interactions are relatively weak. The level of proteins structure 4. Quaternary structure ❖ Result from the aggregation of two or more polypeptide subunits. (a) Collagen: a fibrous protein of three polypeptides that are super coiled like a rope. This provides the structural strength for their role in connective tissue. (b)Haemoglobin: a globular protein with two copies of two kinds of polypeptides. (Total= 4 polypeptide chains) The level of proteins structure  Protein | Globular & Fibrous Globular protein.Fibrous protein - Folded into spherical (globular) shapes. - Long parallel polypeptide chains. - Usually soluble as hydrophobic side chains in centre - Usually insoluble. of structure. - Many have structural roles. - Roles in metabolic reactions. - E.g. keratin in hair and the outer layer of - E.g. enzymes, haemoglobin in blood. skin, collagen (a connective tissue) Protein | Globular proteins A protein whose molecules curl up into a ‘ball’ shape, such as myoglobin or haemoglobin, is known as a globular protein. Globular proteins usually curl up so that their non-polar, hydrophobic R groups point into the centre of the molecule, away from their watery surroundings. Water molecules are excluded from the centre of the folded protein molecule. The polar, hydrophilic R groups remain on the outside of the molecule. Hence, globular proteins are soluble. Protein | Fibrous protein (Collagen) Insoluble fibrous protein found in skin The polypeptides which make up a collagen molecule are in the shape of a stretched-out helix. Every third amino acid is glycine. Glycine is found on the insides of the strands and its small size allows the three strands to lie close together and so form a tight coil. Three helices wind together to form a collagen molecule. Many of these triple helices lie side by side, linked to each other by covalent cross-links between the side chains of amino acids near the ends of the polypeptides. Protein | Fibrous protein Many fibrils lie alongside each other, forming strong bundles called fibres. Advantages of collagen: Flexible High tensile strength Water All forms of life need water to exist. As for human being, about 50-75% of a human body is water. Pure water is a transparent liquid that is colourless, odourless and tasteless So, importance of water to living organisms includes: Act as medium for many chemical reactions Regulation of body temperature Transporting molecules such as oxygen & nutrients Provides an environment for those marine organisms Aid in digestion & lubrication Structure of Water Molecule ❖ Consist of an oxygen atom and two hydrogen atoms ❖ The two hydrogen atoms are joined to the oxygen atom by sharing of electrons forming covalent bond. ❖ The three atoms form a triangle, not a straight line due to the angle between the covalent bond is 104.5° ❖ The water molecule is electrically neutral, but there is a net negative charge on the oxygen atom and a net positive charge on both hydrogen atoms. ❖ A molecule carrying such an unequal distribution of electrical charge is called a polar molecule. ❖ Positively charged hydrogen atoms is attracted to the negatively charged oxygen atoms of nearby water molecules by forces called hydrogen bonds. Water | Properties 1) Water as a solvent Water is a polar molecule; it acts as a universal solvent that is able to dissolve various types of substances. Substances that can mix well and dissolve in water are known as hydrophilic substances (Salts, sugars, acids, alkalis; some gases especially oxygen, carbon dioxide). Substances that do not mix well with water are known as hydrophobic substances (Fats and oils). Any substances that carry a net electrical charge, including both ionic compounds and polar molecules, can dissolve in water. Water is the transport medium in the blood. essential part of many metabolic processes within the body. Water | Properties 2) High specific heat capacity Hydrogen bond Specific heat capacity is the amount of energy required to change the temperature for 1g of a substance by 1ºC. Water has a high specific heat capacity as a result of the extensive hydrogen bonding between its molecules. Since water has a high specific heat capacity, it can absorb large amount of heat energy without drastically rising its temperature. It makes water more resistant to changes in temperature. Importance of water's high specific heat capacity: Enable organisms to regulate their body temperature more effectively. Provide constant environment for aquatic organisms, Water | Properties 3) High latent heat of vaporisation Latent heat of vaporization is energy needed to turn liquid water into water vapor. The hydrogen bonds between water molecules make it difficult for them to be separated and vaporized. This means that high energy is needed to turn liquid water into water vapor. The importance of water’s high latent heat of vaporization: The evaporation of water in form of sweat from the skin, or transpiration in green leaves; allowing the organisms to cool down because the escaping water molecules will carry heat energy with them. Water | Properties 4) Density and freezing properties Water is an unusual chemical because the solid form, ice, is less dense than its liquid form. At 0°C , water is solid (ice). Ice is less dense therefore floats on liquid water Water is densest at 4 °C whilst it is still in liquid form. Importance of this property: At freezing temperature, water will freeze on the top first creating a layer that insulates water below it and preventing it from freezing. Aquatic organisms can survive and live inside a partly frozen pond during winter because the water at the bottom has a temperature of around 4 °C. Water | Properties 5) High surface tension and cohesion Surface tension is a measure of the strength of the water's surface film. Water has a very high surface tension. Water has a high surface tension caused by the strong cohesion and high adhesion properties because of its polar nature. Surface tension permits water to hold up substances heavier and denser than itself. Example: Some aquatic insects such as the water strider rely on surface tension to walk on water. In other words, water is sticky and elastic, and tends to clump water strider relies on the together in drops rather than spread out in a thin film. surface tension of water to skate on the surface of stream without sinking  Surface tension is responsible for capillary action, which allows water (and its dissolved substances) to move through the roots of plants and through the tiny blood vessels in our bodies. Water able to move as continuous column along xylem from roots to the leaves Hydrogen bond between water Hydrogen bond between molecules water molecules & other surface or object Water | Properties 6) Water as a reagent Water takes part as a reagent in some chemical reactions inside cells. In photosysthesis, Separation of H from H2O In hydrolysis mechanism, Use water to breakdown large molecules. Eg. Protein, lipids, carbohydrates Thank you and all the best!