Chapter 1: Molecules of life [ 5 major classes molecules which make up the bodies of living organism] Learning outcome Water

Explain the structure of water molecule Describe the properties of water and its importance: universal solvent, low viscosity, high specific heat capacity, high latent heat of vaporization, high surface tension, maximum density at 4 C. Carbohydrate Describe various forms and classes of carbohydrates such as monosaccharide, disaccharides and polysaccharides Describe the formation and breakdown of maltose Describe the structures and function of starch, glycogen and cellulose Lipid State the types of lipid: fat, oil, phospholipids and steroids Describe the structure of fatty acid and glycerol Describe the formation and breakdown of triglycerides. Protein Describe the basic structure and classes of amino acids Explain how amino acids are grouped. Describe the formation and breakdown of dipeptide. Explain primary (1), secondary (2), tertiary (3) and quartenary (4) levels of proteins and the types of bonds involved) Nucleic acid Describe the structure of nucleotide as the basic composition of nucleic acid (DNA and RNA) Describe the structure of DNA based on Watson and Crick Model State the types and function of RNA State the differences of DNA and RNA

1.1: Water
Structure of Water molecule Water molecule is consists of one atom and two . Atoms. The 2 hydrogen atoms are combined with the oxygen atom by .. of electron which form the bond. The water molecule is a . Molecule. The bond angle of water is . Water molecule is a .. molecule, due to the . Distribution of shared electrons. The uneven distribution of electrons is course by the different . Between oxygen and hydrogen. Oxygen are . Electronegative than hydrogen, Shared electrons are more .. to oxygen than to hydrogen. Therefore, . Is partial negative (.) and hydrogen is partial . (+).

Hydrogen bond Polarity of water causes water molecules to be .to each other. A partial positive of one molecule attracted to the partial negative from another water molecule forming a .. bond. Hydrogen bond is a type of weak attraction that able to holds water molecules together.

Table of properties n importance Water properties Low viscosity Description Viscosity: a measure of liquid resistance to flow. Samller the size of molecules, .................................... the viscosity. Water is a ............................... polar molecule, which have ......................... viscosity. Importance Suitable medium for transportation in living organism. Example: blood flow easily through vessels; flow of water in xylem and phloem vessels to transport nutrient around their bodies. Less energy used by aquatic organism when swimming in water.

High latent heat of vaporization

Most liquid contract on cooling, reaching its .. density at freezing point, but water reach it maximum density at.., not at freezing point. Explanation: 1. 2.

High specific heat capacity

Water have a high specific heat capacity due to the present of . Bond. . Energy needed to break the .. bonding between the water molecules. Hence, temperature of water always remain constant.

Make water as good heat absorber because large amount of heat need to raise water temperature Enable water temperature remain constant against sudden temperature change Allow aquatic environments maintain constant temperature give strong support for hydrogen-bonded network of liquid water.

High surface tension

Maximum density at 40C

Universal solvent

..of water makes it a universal solvent for ionic substances *example:+and many covalent compound.*example:.+ Ionic compound dissolve in water: - Ionic compound consists of ..............................(cation) and .............................. (anion) - The partial positive hydrogen atoms in the water molecule attract negatively charged ions, while - The partially negative oxygen atom in the water molecules attracts positively charged ions. Organic compound dissolve in water: - Only ........................ organic molecule dissolve in water. - Example: - Becauce water molecule able to form ....................... bond between water molecules and ................................... groups in these organic molecule.

Most cell component (including some protein, and polysaccharides) dissolve in water Metabolic reactions normally takes place in solution Able to dissolve salts, acids, sugar, as well as nutrients and gases which make it able to transport within and between the cell.

Carbohydrate Describe various forms and classes of carbohydrate Describe the formation and breakdown of maltose Describe the structures and functions of starch, glycogen and cellulose

Monosaccharide:

Ring form form

Disaccharide: Characteristic of disaccharide : 1. 2. 3.

Formation of maltose: involve the reaction.

Breakdown of bond in maltose

Polysaccharide Polysaccharide Starch Amylose Monomer Types of glycosidic bond function Energy storage in Structure + diagram

Amylopectin

Glycogen

Energy storage in .. Usually found in and . tissues

Cellulose

Building component of cell

Long, parallel , .. chain hold together by . Bond.

Lipid: Characteristic: Insoluble in water [.] Soluble in .. solvent, example:. Non polymer

Type of lipid: *base on the..+ Lipid Triglyceride Fat One type of lipid molecule made of 3 molecules of fatty acids join to 1 molecule of glycerol by an ester linkage/bond Oil [Unsaturated fat] One type of lipid molecule made of 3 molecules of fatty acids join to 1 molecule of glycerol by an ester linkage/bond At least unsaturated fatty acid must present. Phospholipids A type of lipids in which one glycerol join to two fatty acids and one of fatty acid groups is replaced by phosphorus & nitrogen. Steroid A type of lipid containing carbon skeleton consisting of 4 fused rings.

Triglyceride
3 Fatty Acid
A molecule containing a long chain of hydrogen and carbon atom ( hydrocarbon chain), with a group (-COOH) at one end.
An alcohol containing 3 carbon atom

Fatty Acid: A molecule containing a long chain of hydrogen and carbon atom (chain), with a group (-COOH) at one end. Unsaturated fatty acid Saturated fatty acid Contain one or ..double more ..bond bond in the hydrocarbon between carbon atoms in the chain. hydrocarbon chain A ..fatty acid contain two or more double bond.

[diagram]

Glycerol

Comparison of saturated fat and unsaturated fat

Aspect State of matter Fatty acid Source Example

Saturated Fat .in room temperature double bond Most fat Butter

Unsaturated Fat .in room temperature Contain one or more double bond Most . fat (oil) Olive oil, all vegetative oil

Protein : Large, complex molecule composed of .which linked together by . bond. Structure of amino acid All amino acids have an group, NH2, and a .. group, -COOH R: also called .. chain / side group Different amino acid have different . group, it is used in the grouping of amino acid.

Classification of amino acid On the basis of polarity of R group, 20 amino acids can be classified into 4 groups: i. ii. iii. iv. Non polar amino acid Polar amino acid (no charge in R group) Acidic amino acid (negative charge in R group) Basic amino acid (positive charge in R group)

Non polar amino acid

Consist amino acids with non polar side group Hydrophobic molecules (except proline) have no electrical charge Its hard to create ions from side groups - electrical charge of R is symmetrically distributed

Polar amino acid

Consist amino acids with polar side group Hydrophilic molecules Produce partially charge but do not receive/donate electron Electrical charge in the polar groups is asymmetrical

Acidic amino acid

Side chain : negative in charge Due to presence of additional carboxyl group in side chains often exist in anionic (COO) form Hydrophilic molecules

Basic amino acid

Side chain: positive in charge Hydrophilic molecules addition of hydrogen ion can be neutralised by amino groups of the side chains - which then become cations (NH3+)

Exlain the Formation and breakdown of peptide bond , state the reaction take place

Level of the protein Level of Protein Primary Protein Description Importance 1. determines the protein overall & . 2. The sequence of amino acids is determined by in the cell nucleus. 3. The change in the sequence of amino acids will influence the biological function of particular protein. Example Explanation 1. describes the linear sequence of amino acids in the protein chain 2. Each amino acids joints together by the peptide bond in specific sequence.

Types of bond involve

Diagram

.. bonds

Secondary protein

. bonds at regular interval along the polypeptide backbone.

A repeating coiled or folded pattern that contribute to the proteins overall conformation. (3D structure of polypeptide backbone)

-helix A delicate coil held together by hydrogen bonding between every fourth amino acids. pleated sheet 2 or more regions of the polypeptide chain lie parallel to each other. Hydrogen bonds between the parts of the backbone in the parallel regions hold the structure together.

These interaction (bonds) include: Hydrogen bond Ionic bond Disulphide bridge Van der Waals forces and hydrophobic interaction

The three-dimensional structure of a polypeptide Group the protein into the globular protein and fibrous protein.

The shape is held firmly in position by the interaction between side chains of the various amino acids.

Quaternary protein

proteins consists more than one polypeptide chain

Classification of protein: *base on the of protein+ Type of protein Description Conjugated protein Polypeptide chains which associated with ..(non protein) Fibrous protein Remains as long chain Often with several polypeptide chains cross-linked together for additional strength Insoluble protein Important structural molecule Globular Protein Polypeptide chains folded into a compact spherical shape Soluble in water: due to hydrophobic side chain projected from outside of the molecules Important in metabolic reactions

Example

Glycoproteinprotein + Lipoprotein Haemoglobin

Keratin (in hair and skin), collagen (in skin, tendon, bones, cartilage and blood vessel walls)

All enzyme, antibodiees, haemoglobin, myoglobin

Fibrous Protein Repetitive . sequences of amino acids Actual sequences may vary slightly between two examples of the same protein

Globular Protein . amino acid sequence Sequence ..specific and never varies between two examples of the same protein

Polypeptide chains form long strands Length of chain may vary in two examples of the same protein

Polypeptide chains folded into shape Length always identical in two examples of the same protein (specific conformation) Relatively structure (able to denature by heat and pH) Soluble- forms suspension

and structural function Example: collagen, keratin Example: all enzymes, some hormone and haemoglobin

Factors affecting protein. i. pH Extreme pH condition can caused protein to lose its conformation. It will breaks the bonds that cause the 3D shape to be changed. In many cases the globular proteins go back (revert) to a more fibrous form. Any sudden change in pH could adversely affect in performance of enzymes. ii. Temperature High temperatures cause protein to lose its conformation. This process breaks all non-covalent bonds (especially hydrogen bonds) in the molecule, but leaves the linear sequence unaltered. So the primary structure is saved while the secondary and higher structures are disrupted. This transformation is called denaturation. Denaturation under physiological conditions can be reversed this is called renaturation. However, non-physiological conditions usually cause an irreversible change of conformation.

Nucleic Acid: A polymer () consisting of many monomer Structure of Nucleotide

Pentose sugar: 2 types of pentose sugar ..*for DNA+ and .. *for RNA+

Nitrogenous bases: 2 types ..*2 ring+, and . *1 ring+ Formation of phosphodiester bond. - Phosphodiester bond covalent bond that join OH group on carbon 3 of 1 nucleotide & phosphate group on carbon 5 carbon another nucleotide

Deoxyribonucleic acid Double stranded polymer of nucleotides (polynucleotide) Pentose sugar: Deoxyribose Contains 4 types of bases (not include uracil (U) ): i. ii. Adenine (A) Guanine (G) iii. Thymine (T) iv. Cytosine (C) Antiparellel: 2 strands of the DNA double helix are found to be orientated in opposite directions.

Very long & thin molecule Amount A = T and G = C because: A pair with T G pair with C. Helix shape is maintained by hydrogen bonds A only pairs with T and G only pairs to C. This is called complementary base pairing. The purine always pair to the pyrimedine. Ribonucleic acid Single stranded polymer of nucleotides Pentose sugar : ribose Nitrogenous bases : Guanine Cytosine Adenine Uracil (replacing thymine) Transfer RNA Messenger RNA 3 types of RNA : Types of RNA Ribosomal RNA Function Combines with proteins to form ribosomes. Provides the instructions for assembling amino acids into a polypeptide. Delivers amino acids to a ribosome for their addition into a growing polypeptide chain

Comparison between DNA and RNA DNA Double stranded & helix Larger molecular mass Pentose sugar : deoxyribose Organic bases: A,T,C,G Manufactured in nucleus Chemically very stable Permanent Only one basic form A:T & G:C = 1 : 1 RNA Single stranded & linear Smaller molecular mass Pentose sugar : ribose Organic bases: A,U,C,G Manufactured in nucleus but found throughout the cell Chemically unstable Temporary existing 3 basic forms : mRNA, tRNA & rRNA A&U : G&C = varies