Chemistry of Life 3 1 Lifes molecular diversity

Chemistry of Life

3. 1 Life’s molecular diversity is based on the properties of carbon • A carbon atom forms four covalent bonds – It can join with other carbon atoms to make chains or rings Structural formula Ball-and-stick model Space-filling model Methane The 4 single bonds of carbon point to the corners of a tetrahedron.

• Carbon skeletons vary in many ways Ethane Propane Carbon skeletons vary in length. Butane Isobutane Skeletons may be unbranched or branched. 1 -Butene 2 -Butene Skeletons may have double bonds, which can vary in location. Cyclohexane Benzene Skeletons may be arranged in rings.

3. 3 Cells make a huge number of large molecules from a small set of small molecules • Most of the large molecules in living things are macromolecules called polymers – Polymers are long chains of smaller molecular units called monomers – A huge number of different polymers can be made from a small number of monomers

• Cells link monomers to form polymers by dehydration synthesis 1 2 3 Short polymer Unlinked monomer Removal of water molecule 1 2 3 Longer polymer 4

• Polymers are broken down to monomers by the reverse process, hydrolysis 1 2 3 4 Addition of water molecule 1 2 3 Coating of capture strand

Macromolecules • • Carbohydrates (simple sugar) Lipids (fatty acids) Proteins (amino acids) Nucleic acids (nucleotides)

Carbohydrates • have the general formula [CH 2 O]n where n is a number between 3 and 6 • function in – short-term energy storage (such as sugar); – as intermediate-term energy storage (starch for plants and glycogen for animals); and – as structural components in cells (cellulose) in the cell walls of plants and many protists), and chitin in the exoskeleton of insects and other arthropods.

• The monosaccharides glucose and fructose are isomers – They contain the same atoms but in different arrangements Glucose Fructose

Carbohydrates • Monosaccharides are single (mono=one)sugars • ribose (C 5 H 10 O 5) • glucose (C 6 H 12 O 6)

Carbohydrates • formed when two Monosaccharides are chemically bonded together • Sucrose, a common plant disaccharide is composed of the monosaccharides glucose and fructose. • Lactose, milk sugar, is a disaccharide composed of glucose and the monosaccharide galactose.

Dehydration reaction

Synthesis and digestion of disaccharides

3. 6 Connection: How sweet is sweet? • Various types of molecules, including nonsugars, taste sweet because they bind to “sweet” receptors on the tongue Table 3. 6 http: //www. cancer. gov/cancertopics/factsheet/Risk/artificial-sweeteners

Sweets

Discovery • Charles Zuker, a neuroscientist at Howard Hughes Medical Institute, made a startling announcement: All the sweet things in life are perceived by two receptors. • More than 30 receptors code for bitter taste but only a single receptor devoted to sweet. • Bitter there are many and many are toxic • Sweet all tasty and good http: //www. discover. com/issues/aug-05/departments/chemistry-of-artificial-sweeteners/

G-coupled Receptor Family

G-coupled proteins • a protein family of transmembrane receptors that transduce an extracellular signal (ligand binding) into an intracellular signal (G protein activation). http: //upload. wikimedia. org/wikipedia/en/3/33/G-protein-coupled_receptor. png http: //en. wikipedia. org/wiki/G-protein_coupled_receptor

Receptor binding • Sucralose, for instance, fits more snugly in the receptor than sucrose, partly because its chlorine atoms carry a stronger charge than the oxygen atoms they replaced.

(Polysaccharide) • are large molecules composed of individual monosaccharide units. • The formation of the ester bond by condensation • (the removal of water from a molecule) allows the linking of monosaccharides into disaccharides and polysaccharides.

Carbohydrates (Polysaccharide)

• Starch and glycogen are polysaccharides that store sugar for later use • Cellulose is a polysaccharide in plant cell walls Starch granules in potato tuber cells Glycogen granules in muscle tissue Cellulose fibrils in a plant cell wall Cellulose molecules Figure 3. 7 Glucose monomer STARCH GLYCOGEN CELLULOSE

Starch • starch is a combination of two polymeric carbohydrates (polysaccharides) called amylose and amylopectin. They differ in the glycosidic bonds they make in between glucose molecules. • Can humans digest starch? • What enzyme is used to digest starch?

Glycogen • Glycogen is a polysaccharide that is the principal storage form of glucose (Glc) in animal and human cells. • Glycogen is found in the form of granules in the cytosol in many cell types.

Glycogen • Hepatocytes (liver cells) have the highest concentration of it - up to 8% • In the muscles, glycogen is found in a much lower concentration (1% of the muscle mass), but the total amount exceeds that in liver. • Glycogen plays an important role in the glucose cycle.

Glucose cycle • When glucose enters a cell it is rapidly converted to glucose 6 -phosphate, by hexokinase. The glucose cycle can occur in liver cells due to a liver specific enzyme glucose-6 -phosphatase, which catalyse the dephosphorylation of glucose 6 -phosphate back to glucose.

Insulin • http: //en. wikipedia. org/wiki/Insulin

Glucagon • http: //en. wikipedia. org/wiki/Glucagon

Cellulose • Plants make it except tunicates (animals) • Cellulose is synthesized in higher plants by enzyme complexes localized at the cell membrane called cellulose synthase http: //en. wikipedia. org/wiki/Cellulose

Lipid • involved mainly with long-term energy storage • They are generally insoluble in polar substances such as water. • Secondary functions of lipids are as structural components (as in the case of phospholipids that are the major building block in cell membranes) and as "messengers" (hormones) that play roles in communications within and between cells.

Lipid • Lipids are composed of three fatty acids (usually) covalently bonded to a 3 -carbon glycerol. The fatty acids are composed of CH 2 units, and are hydrophobic/not water soluble.

• Fats are lipids whose main function is energy storage – They are also called triglycerides • A triglyceride molecule consists of one glycerol molecule linked to three fatty acids Fatty acid Figure 3. 8 B

Structure of Fatty Acids

Saturated and unsaturated fatty acids

• The fatty acids of unsaturated fats (plant oils) contain double bonds – These prevent them from solidifying at room temperature • Saturated fats (lard) lack double bonds – They are solid at room temperature Figure 3. 8 C

Structure of Triacylglycerols (Fats)

Synthesis of fat

Phospholipids

Structure of Phospholipids

Phosphatidylcholine • Major component of lecithin, protective sheats of the brain

Phosphatidylethanolamine • Major component of cephalin; it is found particularly in nervous tissue such as the white matter of brain, nerves, neural tissue, and in spinal cord. • Major phospholipid of bacteria

Structure of Phospholipids

Sphingomyelin • sphingomyelin is a major component of myelin, the fatty insulation wrapped around nerve cells by Schwann cells or oligodendrocytes. • Multiple Sclerosis is a disease characterized by deterioration of the myelin sheath, leading to impairment of nervous conduction.

Structure of Glycolipids

Glycolipids • Glycolipids are carbohydrate-attached lipids. Their role is to provide energy and also serve as markers for cellular recognition. • Ganglioside is a compound composed of a glycosphingolipid (ceramide and oligosaccharide) with one or more sialic acids (AKA n-acetylneuraminic acid) linked on the sugar chain. It is a component the cell plasma membrane which modulates cell signal transduction events. They have recently been found to be highly important in immunology. Natural and semisynthetic gangliosides are considered possible therapeutics for neurodegenerative disorders.

3. 9 Phospholipids, waxes, and steroids are lipids with a variety of functions • Phospholipids are a major component of cell membranes • Waxes form waterproof coatings • Steroids are often hormones Figure 3. 9

Cholesterol in the membrane

Cholesterol • Cholesterol is a sterol (a combination steroid and alcohol) and a lipid found in the cell membranes of all body tissues, and transported in the blood plasma of all animals.

LDL and HDL • When doctors talk to their patients about the health concerns of cholesterol, they are often referring to "bad cholesterol", or lowdensity lipoprotein (LDL). "Good cholesterol" is high-density lipoprotein (HDL); this denotes the way cholesterol is bound in lipoproteins, the natural carrier molecules of the body. http: //en. wikipedia. org/wiki/Low-density_lipoprotein

HDL and LDL • High-density lipoproteins (HDL) form a class of lipoproteins, varying somewhat in their size (8 -11 nm in diameter) and contents, that carry cholesterol from the body's tissues to the liver. • Generally, LDL transports cholesterol and triglycerides away from cells and tissues that produce more than they use, towards cells and tissues which are taking up cholesterol and triglycerides.

Nucleic Acids • composed of monomer units known as nucleotides. • The main functions of nucleotides are information storage (DNA), protein synthesis (RNA), energy transfers (ATP and NAD), and signaling molecules (c. AMP) • Nucleotides consist of a sugar, a nitrogenous base, and a phosphate.

A nucleotide

• The monomers of nucleic acids are nucleotides – Each nucleotide is composed of a sugar, phosphate, and nitrogenous base Nitrogenous base (A) Phosphate group Figure 3. 20 A Sugar

DNA

Polymerization of Nucleotides (Phosphodiester bond)

RNA

Proteins • They are very important in biological systems as control and structural elements. • The building block of any protein is the amino acid, which has an amino end (NH 2) and a carboxyl end (COOH). • The R indicates the variable component (R-group) of each amino acid.

• Each amino acid contains: – an amino group – a carboxyl group – an R group, which distinguishes each of the 20 different amino acids Figure 3. 12 A Amino group Carboxyl (acid) group

• Each amino acid has specific properties Leucine (Leu) HYDROPHOBIC Figure 3. 12 B Serine (Ser) Cysteine (Cys) HYDROPHILIC

3. 13 Amino acids can be linked by peptide bonds • Cells link amino acids together by dehydration synthesis • The bonds between amino acid monomers are called peptide bonds Carboxyl group Amino group PEPTIDE BOND Dehydration synthesis Amino acid Figure 3. 13 Amino acid Dipeptide

Amino acids are linked together by joining the amino end of one molecule to the carboxyl end of another. Removal of water allows formation of a type of covalent bond known as a peptide bond. Formation of a peptide bond between two amino acids by the condensation (dehydration) of the amino end of one amino acid and the acid end of the other amino acid.

Protein Structure • • Primary Secondary Tertiary Quaternary

Primary structure • The primary structure of a protein is the sequence of amino acids, which is directly related to the sequence of information in the RNA molecule. • The primary structure is the sequence of amino acids in a polypeptide.

Secondary Structure • It is the tendency of the polypeptide to coil or due to Hbonding between R-groups

Tertiary Structure • It occurs due to bonding (or in some cases repulsion) between R-groups.

Quaternary structure • formed from one or more polypeptides.

3. 15 A protein’s primary structure is its amino acid sequence Primary structure Amino acid Secondary structure Hydrogen bond Pleated sheet Alpha helix Figure 3. 15, 16

3. 17 Tertiary structure is the overall shape of a polypeptide Tertiary structure Polypeptide (single subunit of transthyretin) Quaternary structure Transthyretin, with four identical polypeptide subunits Figure 3. 17, 18