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

Learning outcome

Water Carbohydrate Lipid Protein Nucleic acid

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

ºC.

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

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.

Describe the basic

structure and classes of

amino acids

Explain how amino

acids are grouped.

Describe the formation

and breakdown of

dipeptide.

Explain primary (1º),

secondary (2º), tertiary

(3º) and quartenary (4º)

levels of proteins and

the types of bonds

involved)

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 Description Importance

Low viscosity Viscosity: a measure of liquid resistance to flow. Samller the size of molecules, .................................... the viscosity. Water is a ............................... polar molecule, which have ......................... viscosity.

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 Monomer Types of glycosidic bond function Structure + diagram

Starch Amylose Energy storage in ……………………

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

Phospholipids Steroid Fat 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

• 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.

A type of lipids in which one glycerol join to two fatty acids and one of fatty acid groups is replaced by phosphorus & nitrogen.

A type of lipid containing carbon skeleton consisting of 4 fused rings.

Triglyceride

3 Fatty Acid

An alcohol containing 3 carbon atom

A molecule containing a long chain of hydrogen and carbon atom ( hydrocarbon chain), with a ………………group (-COOH) at one end.

Glycerol

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 more …………………………..bond between carbon atoms in the hydrocarbon chain

A ………………………………………..fatty acid contain two or more double bond.

…………………………..double bond in the hydrocarbon chain.

[diagram]

Comparison of saturated fat and unsaturated fat

Aspect Saturated Fat Unsaturated Fat

State of matter ……………….in room

temperature

………………………….in room

temperature

Fatty acid …………………double bond Contain one or more double bond

Source Most ………………… fat Most ………………. fat (oil)

Example Butter 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. Non polar amino acid

ii. Polar amino acid (no charge in R group)

iii. Acidic amino acid (negative charge in R group)

iv. 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 It’s 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

Description Example Types of bond

involve Diagram Importance Explanation

Primary Protein

……………………….. bonds

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.

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.

Secondary protein

………………….……… bonds at regular interval along the polypeptide backbone.

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

α-helix A delicate coil held together by hydrogen bonding between every fourth amino acids. β 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

Conjugated protein Fibrous protein Globular Protein

Description Polypeptide chains which associated with ………………………………………..(non protein)

• Remains as long chain • Often with several polypeptide

chains cross-linked together for additional strength

• Insoluble protein • Important structural molecule

• 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 Glycoprotein- protein +

Lipoprotein

Haemoglobin

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

All enzyme, antibodiees, haemoglobin, myoglobin

Fibrous Protein Globular Protein

Repetitive …………………………. sequences of amino acids …………………………………. amino acid sequence

Actual sequences may vary slightly between two examples of the same

protein

Sequence ……………………………..specific and never varies between two

examples of the same protein

Polypeptide chains form long ……………………………strands Polypeptide chains folded into ……………………………………shape

Length of chain may vary in two examples of the same protein 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. Adenine (A) iii. Thymine (T)

ii. Guanine (G) iv. Cytosine (C)

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.

Antiparellel: 2 strands of the DNA double helix are found to be orientated

in opposite directions.

Ribonucleic acid

Single stranded polymer of nucleotides

Pentose sugar : ribose

Nitrogenous bases :

Guanine Adenine

Cytosine Uracil (replacing thymine)

3 types of RNA :

Types of RNA Function

Ribosomal RNA Combines with proteins to form ribosomes.

Messenger RNA Provides the instructions for assembling amino acids into a polypeptide.

Transfer RNA Delivers amino acids to a ribosome for their addition into a growing polypeptide chain

Comparison between DNA and RNA

DNA RNA

Double stranded & helix Single stranded & linear

Larger molecular mass Smaller molecular mass

Pentose sugar : deoxyribose Pentose sugar : ribose

Organic bases: A,T,C,G Organic bases: A,U,C,G

Manufactured in nucleus Manufactured in nucleus but found throughout the cell

Chemically very stable Chemically unstable

Permanent Temporary existing

Only one basic form 3 basic forms : mRNA, tRNA & rRNA

A:T & G:C = 1 : 1 A&U : G&C = varies