lecture 4 organic molecules and inorganic molecules 1. inorganic molecules. 2. water 3. organic...

Lecture 4 Organic

molecules and Inorganic molecules

1. Inorganic molecules.2. Water3. Organic molecules

Prepared by Mayssa Ghannoum

Overview

In this lecture we will examine the major group of molecules that make up living organisms along with some of the properties and functions of these molecules.

Living organisms are composed of both inorganic and organic molecules.

Inorganic molecules

Inorganic molecules: are relatively small, simple molecules that

do not contain carbon atom C. There are a few carbon-containing

molecules, such as carbon monoxide and carbon dioxide, that are

also classified as inorganic molecules. Inorganic compounds,

such as water, are made up of inorganic molecules

Minerals are mainly oxides and sulfides, which are strictly

inorganic. In fact, most of the earth and the universe is inorganic

Water molecule

Water is the only common substance to exist

in the natural environment in all three physical

states of matter: solid, liquid, and gas.

All living organisms require water more than

any other substance

The polarity of water molecules results in hydrogen bonding

Water is a small polar molecule made of

one oxygen atom joined to 2 hydrogen

atoms.

The oxygen atom has slight negative charge

and the 2 hydrogen atoms have slight

positive charges.

Polarity allows water molecules to form

hydrogen bonds with each other

Properties of water

CohesionAdhesionHigh Specific HeatHigh Heat of VaporizationLess Dense as a SolidSolvent of Life

Cohesion

Attraction between particles of the same substance ( this is why water is attracted to itself).

Results in Surface tension (a measure of the strength of water’s surface).

Produces a surface film on water that allows insects to walk on the surface of water.

Cohesion due to hydrogen bonding contributes to the transport of water and dissolved nutrients against gravity in plants.

Adhesion

Is an Attraction between different substances, for example, between water and plant cell walls.

Adhesion also causes water to:

Form spheres & hold onto

plant leaves

Attach to a silken spider

web

High Specific Heat

Water is effective as a heat bank because it can absorb or release a relatively large amount of heat with only a slight change in its own temperature.

Heat and temperature

Kinetic energy: is the energy of motion.

Heat: is a form of energy

Temperature measures the intensity of heat due to the average kinetic energy of molecules.

Celsius Scale is used as temperature indicator .

The unit of heat is calorie (cal).

High Specific Heat

The specific heat is the amount of heat that must be

absorbed or lost for one gram of the substance to change its

temperature by one Celsius.

The specific heat of water is 1 cal/g/ºC

Water resists changing its temperature because of its high

specific heat which can be traced to: hydrogen bonding

Heat is absorbed when hydrogen bonds break. Heat is released when hydrogen bonds form.

High Heat of Vaporization

Evaporation: is transformation of a substance from liquid to gas.

Heat of vaporization is the heat a liquid must absorb for 1 g to be converted to gas.

As a liquid evaporates, its remaining surface cools, a process called evaporative cooling.

Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water.

Water is less Dense as a Solid

Ice is less dense as a solid

than as a liquid (ice floats)

Liquid water has hydrogen

bonds that are constantly

being broken and

reformed.

Frozen water forms a

crystal-like lattice whereby

molecules are set at fixed

distances.

Acids, Bases and PH

A water molecule can transfer an H+ to another water molecule to form H3O+ (Hydronium ion ) and OH– (Hydroxide).

Hydrogen Ions Hydroxide ions Acid Base

The pH of a solution is defined by the negative

logarithm of H+ concentration, written as pH = –

log [H+]

H2O H+ + OH-

The PH Scale Biologists use something called the pH scale.

Most Biological fluids pH value is within the range 6-8.

Adding certain solutes, called acids and bases, modifies the concentrations of H+ and OH–.(Fig3.9).

An acid is any substance that increases the [H+] .

Acidic solutions have pH values less than 7.

A base is any substance that reduces the [H+].

Basic solutions have pH values greater than 7.

The PH Scale

Buffers

Weak acids or bases that react with strong acids or bases to prevent sharp, sudden changes in pH (neutralization).

Produced naturally by the body to maintain homeostasis

Weak Acid Weak Base

Organic molecules

Are molecules that contain two or more carbon atoms.

All living things are made up of four classes of large biological

molecules:

1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic acids

Macromolecules are polymers, built from monomers

A polymer (poly- means many) :is a long molecule consisting of

many similar or identical building blocks linked by covalent bonds.

A monomer (mono- means one): is the repeating unit that serves as

the building block of a polymer.

Carbohydrates serve as fuel and building material

Carbohydrates include both sugars and polymers of sugars

1) Sugars

a- Monosaccharide ≡ single sugar e.g., glucose (The major nutrient in the cell) and fructose

b- Disaccharide ≡ consists of two monosaccharides joined by a glycosidic linkage e.g Maltose also called malt sugar (glucose +glucose)

Sucrose also called table sugar (glucose + fructose)

Carbohydrates serve as fuel and building material

2) Polysaccharides

a) Storage polysaccharide e.g., starch (represents stored energy)

b) Structural polysaccharide e.g. cellulose ( is a major component of the tough walls that enclose plant cells).

Glycosidic linkage is a covalent bond formed between two monosaccharides.

Lipids are a diverse group of hydrophobic molecules

Lipids are grouped together because they share one

important trait: They mix poorly, if at all, with water.

Composition of Lipids:

C, H, and small amounts of O.

Types of lipids:

1) Fats: are constructed from 2 kinds of smaller

molecules glycerol and fatty acids. Fats have 3 fatty

acids attached to a glycerol.

There are 2 types of fats:

1- Saturated fat: a molecule without any

double bonds between carbon atoms

composing the chain (e.g., butter).

2- Unsaturated fat: a molecule that has

one or more double bonds, formed by the

removal of hydrogen atoms from the

carbon skeleton (e.g., fats of plants and

fishes).

2) Phospholipids

Phospholipids have 2 fatty acids and a phosphate

group attached to glycerol

Phospholipids are essential for cells because they

make up cell membranes.

The two ends of phospholipids show different

behavior toward water.

a- Hydrocarbon tails are hydrophobic and are

excluded from water.

b- The hydrophilic head that has an affinity for water

3) Steroids

Many hormones, as well as cholesterol, are steroids

Cholesterol is a common component of animal cell

membranes and is also the precursor from which other

steroids are synthesized.

Cholesterol is synthesized in the liver

A high level of cholesterol in the blood may contribute to

atherosclerosis (Hardening of the arteries)

Proteins Proteins are built from 20 kinds of amino acids.

Amino acids: are organic molecules possessing both carboxyl and

amino groups.

Examples of amino acids: serine, threonine, lysine, tryptophan,

proline…etc

Polypeptides: are polymers of amino acids linked by peptide bonds.

- A protein is consists of 1 or more polypeptides.

- At one end of the polypeptide chain is a free amino group

(N-terminus);

at the opposite end is free carboxyl group (C-terminus).

Proteins have important and Various functions

1. Enzymes: Catalysis of cellular reactions

2. Structural Proteins: Maintain cell shape

3. Transport: Transport in cells/bodies (e.g. hemoglobin).

Channels and carriers across cell membrane.

4. Communication: Chemical messengers, hormones, and

receptors.

5. Defensive: Antibodies and other molecules that bind to foreign

molecules and help destroy them.

6. Contractile: Muscular movement.

7. Storage: Store amino acids for later use (e.g. egg white).

Levels of Proteins structure

1. Primary structure: is a unique sequence of amino acid.

2. Secondary structure: is a coiled and folded chain with repeated segments polypeptide.

3. Tertiary structure: is a superimposed on the patterns of secondary structure.

4. Quaternary structure: is a protein that consists of two or more polypeptide chains. e.g. hemoglobin.

Nucleic Acids store and transmit hereditary information for all living things

There are two types of nucleic acids in living things:

A. Deoxyribonucleic Acid (DNA)

Contains genetic information of all living organisms. Has segments called genes which provide information to make each

and every protein in a cell Double-stranded molecule which replicates each time a cell divides.

B. Ribonucleic Acid (RNA)

Three main types called mRNA, tRNA, rRNA RNA molecules are copied from DNA and used to make gene

products (proteins). Usually exists in single-stranded form.

DNA and RNA are polymers of nucleotides that determine the primary structure of proteins

Nucleotide: Subunits of DNA or RNA.

Nucleotides have three components:

1. Pentose sugar (ribose or deoxyribose)

2. Phosphate group to link nucleotides (-PO4)

3. Nitrogenous base (A,G,C,T or U)

Purines: Have 2 rings.

Adenine (A) and guanine (G)

Pyrimidines: Have one ring.

Cytosine (C), thymine (T) in DNA or uracil (U) in RNA.

James Watson and Francis Crick Determined the 3-D Shape of DNA in 1953

Double helix: The DNA molecule is a double helix.Antiparallel: The two DNA strands run in opposite

directions.

Strand 1: 5’ to 3’ direction (------------>)

Strand 2: 3’ to 5’ direction (<------------)Complementary Base Pairing: A & T (U) and G & C.

A on one strand hydrogen bonds to T (or U in RNA).

G on one strand hydrogen bonds to C.

Replication: The double-stranded DNA molecule can easily replicate based on A=T and G=C pairing.