Chapter 2

Chemical Principles

part B

Structure and Function• The chain of carbon atoms in an organic molecule is the carbon skeleton• Saturated hydrocarbons: Carbon-carbon single bond

– Ethane – C2H6

– Hexane – C6H14 - Cyclohexane

• Unsaturated hydrocarbons: Carbon-carbon double bond, – Ethylene – C2H4 Benzene – C6H6

Structure and Function

• Replacing one of the H atoms in propane molecule with a functional group:– Propane – C3H8

– With OH- will become an alcohol (Propanol) Propanol - C3H7OH - Isopropanol

• Replacing two more H atoms from the same C with Oxygen –will become an acid - Propanoic acid - CH3CH2COOH – C2H5COOH

Radical Functional group – carboxyl group - COOH

Functional group – hydroxyl group

Organic compounds in life organisms

Macromolecule Functional group

Carbohydrates R-OH (alcohol)

Lipids R-COOH (acid)R-OH (alcohol)

R-COOC (ester)

Proteins R-NH2 (amino)R-COOH (acid)R-SH (sulfhydryl)

Nucleic acids R-CH3 (methyl)R-PO4 (phosphate)

• The small molecules are called monomers.

• Monomers join by dehydration synthesis or condensation reactionsinto large molecules -polymers .

• Macromolecules are polymers consisting of many small repeating molecules-monomers.

Organic Compounds

Cellulose (C6H10O5)n

Glucose C6H12O6

n

M

M M

n

M M M

M M M M M M

Organic Compounds

1. Monomers join by dehydration synthesis or condensation reactions.

2. Macromolecules degrade to monomers by hydrolysis or decomposition reactions

Figure 2.8

1

2

R-OH + HO-R R-O-R + H2O

Enzyme 1

Enzyme 2

Organic compounds in life organisms

Macromolecule Functional group Monomer

Carbohydrates R-OH (alcohol) Monosaccharides

Lipids R-COOH (acid)R-OH (alcohol)

R-COOC (ester)

GlycerolFatty acids

Proteins R-NH2 (amino)R-COOH (acid)R-SH (sulfhydryl)

Amino acids

Nucleic acids R-CH3 (methyl)R-PO4 (phosphate)

Nucleotides

• Consist of C, H, and O with the formula (CH2O)n

• Monomers - Monosaccharides are simple sugars with 3 to 7 carbon atoms.– glucose, fructose, galactose, ribose, deoxyribose

• Disaccharides are formed when two monosaccharides are joined in a dehydration synthesis.– Sucrose (glucose-fructose), lactose (glucose-galactose)

• Disaccharides can be broken down by hydrolysis.

Figure 2.8

1. Carbohydrates

Glucose – C6H12O6

• Oligosaccharides consist of 2 to 20 monosaccharides.

• Polysaccharides consist of tens or hundreds of monosaccharides joined through dehydration synthesis.

– Starch, glycogen, dextran, and cellulose are polymers of glucose that are covalently bonded differently.

– Chitin is a polymer of two sugars repeating many times.

Function of Carbohydrates

• Cell structures – Nucleic acids - ribose, deoxyribose

– Cell wall – peptidoglycan, cellulose, chitin

– Bacterial capsule

• Cell energy– Energy sources

– Short term energy storage

• Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), phospholipids, and others.

• Consist of C, H, and O.A. Simple lipids - called fats – contain an alcohol glycerol and a

group of compounds as fatty acids• Fatty acids - long chains of carbon and hydrogen atoms, with a carboxylic acid group at one end

• Saturated

• Unsaturated fats have one or more double bonds between carbons in the fatty acids.

– Are nonpolar and insoluble in water

C C

C C

2. Lipids

• A molecule of fat is formed when a molecule of glycerol combines with one to three fatty acid molecules by dehydration synthesis

– Monoglycerides, diglycerides, triglycerides

– Saturated and Unsaturated fatty acids

Figure 2.9c

B. Complex lipids

– Contain C, H, and O + P, N, or S.

– Membranes are made of phospholipids

• Steroid skeleton consist of four carbon rings

• Steroids vary by the functional groups attached to these rings

• Sterol - modified steroid with an –OH group attached to the ring A.

• Are part of membranes.

C. Steroids

Figure 2.11

Function of Lipids

•Plasma membranes•Cell organelles•Some cell walls •Long term energy storage

3. Proteins• Consist of one or more polypeptide molecules typically folded into

a globular or fibrous form, facilitating a biological function.

• Protein macromolecules monomers - amino acids

– Only 20 amino acids

Amino acids

Table 2.4.1

• A peptide bond is a covalent bond that is formed between two amino acids when the carboxyl group of one molecule reacts with the amino group of the another molecule.– Peptide bonds between amino acids are formed by dehydration synthesis.

• A single linear chain of amino acids bonded together by peptide bonds is called polypeptide

• For chains under 40 residues the term peptide is frequently used instead of protein.

Peptide Bonds

Figure 2.14

Proteins structure - Primary structure

• The primary structure of a protein is the amino acid sequence of the peptide chains. – It is reported starting from the amino-terminal (NH2) end to the carboxyl-

terminal (COOH)

Met - Cys - Val - Ala - Tyr - Arg

Peptide bonds

R

R R

R

R

R

Proteins structure - Primary structure

Insert Fig 2.15Insert Fig 2.15a

Peptide bonds

(a) Primary structure: polypeptide strand

Hydrogen bond

(b) Secondary structure: helix and pleated sheets (with three polypeptide strands)

Helix

Pleated sheet

Disulfidebridge

(c) Tertiary structure: folded helix and pleated sheet

(d) Quaternary structure: two or more polypeptides in their folded states

Hydrogenbond

Disulfide bridge(between cysteine molecules)

Ionic bond

Details of bonds associatedwith tertiary structure

Hydrophobic interaction

Polypeptidestrand

Figure 2.15 Protein structure.

Functionally active

Functionally active

• Conjugated proteins consist of polypeptide chain bound to other organic molecules:• Glycoproteins• Nucleoproteins• Lipoproteins

Function of Proteins

• Are essential in cell structure and function.

– Enzymes are proteins that speed chemical reactions.

– Transporter proteins move chemicals across membranes.

– Structural or mechanical functions, that maintain cell shape ( actin, cell wall).

– Cell signaling - complex system of communication that coordinates cell actions.

– Flagella are made of proteins.

– Some bacterial toxins are proteins.

– Immune responses – antibodies, cytokines are proteins.

4. Nucleic Acids• Macromolecules - DNA and RNA

• Monomers are nucleotides.

• Nucleotides consist of a:• Sugar pentose (with 5 carbons)

• ribose• deoxyribose

• Nitrogen-containing base (purine or pyrimidine)

• Phosphate group

Purines – Adenine and GuaninePyrimidines – Cytosine, Thymine and Uracil

• Monomers are deoxyribonucleotides – sugar-deoxyribose– Purines - Adenine and Guanine; Pyrimidines - Cytosine and Thymine

• Primary structure – nucleotide sequence• The primary structure of DNA or RNA molecule is reported

from the 5' end to the 3' end – 5’ end – PO4 (phosphate group)– 3’ end – OH (hydroxyl group)

• The sugar-phosphate backbone of one strand is upside down, or antiparallel, relative to the backbone of the other strand.

DNA

Figure 2.16

PO4

PO4OH

OH

Insert Fig 2.16

Phosphate Sugar Adenine (A) -

Thymine (T) Sugar Phosphate

Adenine nucleotide Hydrogen bonds

Individual DNA nucleotides are composed of a deoxyribose sugar molecule covalently bonded to a phosphate group at the 5’ carbon, and to a nitrogen-containing base at the 3’ carbon. The two nucleotides shown here are held together by hydrogen bonds.

Sugars

PhosphatesSugar-phosphate backbone

Thymine nucleotide

DNA – secondary structure – double helix

• Two molecules form

the double helix

• A hydrogen bonds with T (2 hydrogen bonds)

• C hydrogen bonds with G (3 hydrogen bonds)

RNA

• Monomers are ribonucleotides – sugar ribose

• Primary structure – nucleotide sequence

• Single-stranded

• Can form secondary structure – A hydrogen bonds with U (2 hydrogen bonds)

– C hydrogen bonds with G (3 hydrogen bonds)

Figure 2.17

tRNA

siRNA

Function of Nucleic acids

• DNA contains all the information - coding which is used to control functions, behavior and development of an organism. – Long term storage device to store the genetic instructions. – The code from which all proteins in the cell are synthesized– Code for the way proteins turn genes on or off.

• RNA carries out the instructions encoded in DNA– Protein synthesis– In some organisms it is also responsible for carrying the genetic code. – Some RNA are involved in the regulation of the gene expression

• Is made by dehydration synthesis.

• Is broken by hydrolysis to liberate useful energy for the cell.

ATP

ADP

ATP – Adenosine triphosphate

Function of ATP

• ATP is the main energy source for the majority of cellular functions.

• Important player in cell respiration. • Synthesis of macromolecules in the cell - DNA and RNA,

proteins, lipids and carbohydrates. • Supply energy for the transport of macromolecules across

cell membranes.• ATP is critically involved in maintaining the locomotion

of the cell .

Learning objectives

• Identify the structure and function of carbohydrates. • Identify the structure and function of lipids. • Identify the structure and function of proteins. • Identify the structure and function of nucleic acids• Describe the role of ATP in cellular activities.