Organic Molecules of Life

Living systems are composed of various types of molecules. There are two main types: Organic and Inorganic molecules. All organic molecules contain carbon and those that don't are classified as Inorganic molecules. Organisms maintain reserves of small organic molecules that they can assemble into complex Macromolecules such as carbohydrates, lipids, proteins, and nucleic acids. These are the building blocks of the living organisms.

How are macromolecules formed?

Small molecules common to all organisms are ordered into unique macromolecules.
Many macromolecules consist of polymers. A polymer is a large molecule built up from smaller building block molecules, called monomers. Monomers (subunits) are the building block molecules. The inherent differences between human siblings reflect variations in polymers, particularly DNA and proteins. Macromolecules that make up living organisms are formed via polymerization.
Polymerization is the linking together of monomers to form polymers. Large organic molecules are often built from smaller ones by condensation, a process in which an enzyme covalently bonds two molecules together. A condensation reaction occurs via the loss of a small molecule, usually from two different substances, resulting in the formation of a bond. Polymerization in biological systems typical occurs via dehydration synthesis. Dehydration reaction is synonymous with condensation reaction except that dehydration reaction is limited to those condensations in which the small molecule is water. Dehydration synthesis is synonymous with dehydration reaction.

 

 Figure: Condensation reaction. Three boxes represent molecules attached to each other that have free hydrogen and hydroxyl group. These groups can be utilized to form a bond via dehydration reaction, removing H2O.

Energy is expended to polymerize so all condensation/dehydration reactions require an input of energy in order to move forward!!! Energy is expended to make polymers!

How are macromolecules broken or digested?

Hydrolysis, which is the reverse of condensation, breaks apart large organic molecules into smaller ones. Hydrolysis enzymes break apart polymers into monomers. By breaking the bonds between monomers, Hydrolysis liberates the energy that polymers contained during dehydration synthesis; thus, some of the energy required to polymerize is returned upon hydrolysis. Hydrolysis plays a very important role in the liberation of usable energy (ATP) within cells. Enzymes are employed in biological systems to effect most hydrolysis reactions. Example: Digestion of food involves numerous hydrolysis reactions.

Figure: Hydrolysis reaction requires water to break the bond between two molecules and give back the free hydrogen and hydroxyl groups.

Major Macromolecules Carbohydrates

Carbohydrates are organic compounds that consist of carbon, hydrogen, and oxygen in a 1:2:1 ratio. Cells use different kinds of carbohydrates as structural materials, for fuel, and for storing and transporting energy. The three main types of carbohydrates in living systems are monosaccharides, oligosaccharides, and polysaccharides.

Monosaccharides (one sugar unit) are the simplest type of carbohydrate, but they have extremely important roles as monomers of larger molecules. The molecular formula of monosaccharides is (CH2O)n. The number of carbons (n in the formula above) varies between monosaccharide types, but for every carbon in a monosaccharide, there is also one water-molecule equivalent (H2O in the formula). Glucose is the main “fuel” for bacteria, plants and animal cells.
Monosaccharides are the building blocks of more complex carbohydrates. For example, two monosaccharides can bond to form a disaccharide (two sugar unit).
Examples: Sucrose (glucose+fructose) (Table Sugar)
Lactose (glucose+galactose) (Milk Sugar)
Maltose (glucose+glucose) (figure Right)
Before disaccharides can be used by organisms, they must be broken down into their monosaccharide units. The disaccharides have the molecular formula C12H22O11.
A disaccharide is formed upon the formation of a glycosidic linkage (a type of bond) between monosaccharides. This glycosidic linkage forms via a dehydration synthesis reaction.
The “complex” carbohydrates, or polysaccharides, are straight or branched chains of many sugar monomers, often hundreds or thousands of them. There may be one type or many types of monomers in a polysaccharide (many sugar units). Most macromolecular carbohydrates are polysaccharides. Polysaccharides typically serve as (i) carbon and energy storage molecules (starch, glycogen) or (ii) as structural material (e.g., in plants, insects, and fungi).
Most plants make much more glucose than they can use. The excess is stored as starch inside cells that make up roots, stems, and leaves. Some starches are made of thousands of monosaccharide (glucose) units.
Potatoes, beans, and grains such as rice, corn, and wheat are examples of plants that store large quantities of starch. When sugars (fuel for energy) are in short supply, hydrolysis enzymes break the bonds between starch’s monomers to release glucose subunits. Some common Polysaccharides and their characteristics are given below:

Functions of Carbohydrates

1. Providing energy and regulation of blood glucose
2. Sparing the use of proteins for energy
3. Breakdown of fatty acids and preventing ketosis
4.  Biological recognition processes
5. Flavor and Sweeteners
6. Dietary fiber, which is also a form of carbohydrate, is essential for the elimination of waste materials and toxins from the body

Major Macromolecules Proteins

Of all biological molecules, proteins are the most diverse in both structure and function. A tremendous number of different proteins, including some structural types, actively participate in all processes that sustain life. Amazingly, cells can make all of the thousands of different kinds of proteins they need from only twenty kinds of monomers called amino acids. Proteins are polymers of amino acids.

Functions of Proteins

Main functions of Protein

1.  Protein's main function is to build, maintain and repair all our body tissues, such as muscles, organs, skin and hair.
2. Protein can also be used as energy source by body, but this usually only happens when carbohydrate and fat stores are in short supply.

Biological function of Protein
1. Protein acts as storage material of food and energy.
2. Many proteins are enzymes that catalyze biochemical reactions, and are vital to metabolism.
3. Proteins are molecular instrument through which genetic information is expressed.
4. They act as antibodies to prevent disease.
5. The milk proteins help the growth of infant mammals.
6. Like other biological macromolecules such as polysaccharides, lipids and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells.
7. Many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism.
8. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape.
9. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle.
10. Proteins are also necessary in animals’ diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism.

Amino Acids and Important Facts

An amino acid (AA) is a small organic compound with an amine group(NH3), a carboxyl group (COOH) (the acid), and one or more atoms called an “R group.” In most amino acids, all three groups are attached to the same carbon atom. Amine group acts like a base, tends to be positive. Carboxyl group acts like an acid, tends to be negative. Side chain “R” group is variable, from 1 to 20. During protein synthesis, the amine group of one amino acid becomes bonded to the carboxyl group of the next to make a polypeptide chain.

Amino acids contain carbon (C), hydrogen (H), oxygen (O), nitrogen (N) and sulfur (S)
There are 20 different kinds of amino acids (AA)

Amino acids are divided into two groups- 1. Essential AA
                                                                    2. Non-essential AA
1. An essential amino acid or indispensable amino acid is an amino acid that cannot be synthesized by the organism (usually referring to humans), and therefore must be supplied in the diet.
2. A non-essential amino acid is an amino acid that can be synthesized by the organism (usually referring to humans).So there is no deficiency of this AA in the body if they are not supplied in the diet.
Protein synthesis involves covalently bonding amino acids into a chain. The bond that forms between two amino acids is called a peptide bond. Enzymes repeat this bonding process hundreds or thousands of times, so a long chain of amino acids (a polypeptide) forms.

 

 Important Fact

1. Most microorganisms and plants can biosynthesize all 20 standard amino acids, while animals (including humans) must obtain some of the amino acids from the diet. The amino acids that an organism cannot synthesize on its own are referred to as essential amino acids
2. In animals, amino acids are obtained through the consumption of foods containing protein. Ingested proteins are then broken down into amino acids through digestion, which typically involves denaturation of the protein through exposure to acid and hydrolysis by enzymes called proteases. Some ingested amino acids are used for protein biosynthesis, while others are converted to glucose through gluconeogenesis, or fed into the citric acid cycle. This use of protein as a fuel is particularly important under starvation conditions as it allows the body's own proteins to be used to support life, particularly those found in muscle. Amino acids are also an important dietary source of nitrogen.

Lipids and Examples of lipids

Lipids are fatty, oily, or waxy organic compounds. Lipids are a structurally heterogeneous class of biological molecules that are, as their common characteristic, hydrophobic. Which means that they are insoluble in water. The building blocks of lipids are fatty acids and glycerol. Lipids posses numerous C-H bonds (i.e., they are very hydrocarbon-like). Examples of lipids include: (i) Fats, (ii) Oils, (iii) Waxes, (iv) Phospholipids, and (v) Steroids, etc.
Lipids are similar to carbohydrates in that they contain only carbon, hydrogen, and oxygen. They differ from carbohydrates in one important way: no specific ratio (C:H:O). Many also serve as source of energy. In fact, a gram of fat can produce over twice as much energy as a gram of carbohydrate. Lipids are also a storage form of energy. The proportion of hydrogen to oxygen in carbohydrates is two to one. In lipid it is much higher.

Fats and oils

Fats are lipids with one, two, or three long chain fatty acids bonded (called an ester linkage) to a small alcohol called glycerol. When three fatty acids attach to a glycerol, the resulting molecule, which is called a triglyceride, is entirely hydrophobic.
Fatty

Fatty acids are long-chain hydrocarbons with a carboxyl group (-COOH) at one end.
Fatty acids can be saturated or unsaturated. Saturated types have only single bonds in their tails. In other words, their carbon chains are fully saturated with hydrogen atoms. Saturated fatty acids have no C=C double bonds. Unsaturated fatty acids have one or more C=C double bonds. The tails of unsaturated fatty acids have one or more double bonds that limit their flexibility. Increasing the unsaturation of a fatty acid results in a decreasing melting point.
Fats and oils possess more energy per molecule and less hydration compared with carbohydrates, resulting in fats or oils possessing much more energy stored per unit mass or volume. During digestion, the fat or oil is broken down into these simple molecules (monomers). Fats and oils function in biological systems as energy storage molecules (e.g., nuts, seeds, and animals).

1.Saturated fatty acids have no C=C double bonds. eg. Octanoic acid

2. Unsaturated fatty acids have one or more C=C double bonds. eg. 3-octanoic acid

3. Increasing the unsaturation of a fatty acid results in a decreasing melting point. eg, 3,6-octanoic
acid

Fats
Fats are solid at ordinary temperatures. Generally, fats are produced by animals. In animals, fats are stored in adipose cells. Fats are also important as cushions for body organs and as an insulating layer beneath skin.

Oils
Oils are liquid at ordinary temperatures. Generally, oils are produced by plants. Some common vegetable oils are peanut, soybean, and corn oil.

Waxes
Both plants and animals produce waxes. The waxy coating on some plants leaves is an example of plant waxes. Beeswax is an example of a wax produced by an animal.

Phospholipids & Steroids

Phospholipids
Phospholipids differ from triacylglycerol in the sense that, one fatty acid (out of three) is replaced with a phosphate group, which in turn is bound to additional functional groups.
Structurally and functionally, the important thing about phospholipids is that these molecules are simultaneously hydrophobic (at one end, thefatty acid end) and hydrophilic (at the other end, the phosphate end). Phospholipids are the most abundant lipids in cell membranes, which have two layers of lipids.

Steroids
Steroids are lipids with a rigid backbone of four carbon rings and no fatty acid tails. All steroids possess a common ring structure. These ring structures vary by attached functional groups. Cholesterol is example of a steroid; cholesterol is a membrane component. The common steroid structure is the basis of sterol hormones including the human sex hormones (the estrogens and the androgens, including testosterone).

Nutrition and Health facts regarding lipid consumption

• Most of the lipid found in food is in the form of triacylglycerols, cholesterol and phospholipids.
•  A minimum amount of dietary fat is necessary to facilitate absorption of fat-soluble vitamins (A, D, E and K) and carotenoids.

• Humans and other mammals have a dietary requirement for certain essential fatty acids, such as linoleic acid (an omega-6 fatty acid) and alpha-linolenic acid (an omega-3 fatty acid) because they cannot be synthesized from simple precursors in the diet. Both of these fatty acids are 18-carbon polyunsaturated fatty acids differing in the number and position of the double bonds.

• Most vegetable oils are rich in linoleic acid (safflower, sunflower, and corn oils). Alpha-linolenic acid is found in the green leaves of plants, and in selected seeds, nuts and legumes (particularly rapeseed, walnut and soy).

•  Fish oils are particularly rich in the longer-chain omega-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA).
• A large number of studies have shown positive health benefits associated with consumption of omega-3 fatty acids on infant development, cancer, cardiovascular diseases, and various mental illnesses, such as depression, attention-deficit hyperactivity disorder, and dementia. In contrast, it is now well-established that consumption of trans fats, such as those present in partially hydrogenated vegetable oils, are a risk factor for cardiovascular disease.

The American Heart Association's Nutrition Committee strongly advises the fat guidelines for healthy Americans over age two.

1. Limit total fat intake to less than 25–35% of your total calories each day;
2. Limit saturated fat intake to less than 7% of total daily calories;
3. Limit trans fat intake to less than 1% of total daily calories;
4. The remaining fat should come from sources of monounsaturated and polyunsaturated fats such as nuts, seeds, fish and vegetable oils; and
5. Limit cholesterol intake to less than 300 mg per day, for most people.
6. For example, a sedentary female who is 31–50 years old needs about 2,000 calories each day. Therefore, she should consume less than 16 g saturated fat, less than 2 g trans fat and between 50 and 70 grams of total fat each day (with most fats coming from sources of polyunsaturated and monounsaturated fats, such as fish, nuts, seeds and vegetable oils).

Nucleic acids and classification

Nucleic acids are complex organic polymers that store and transfer genetic information within a cell. Inside a cell, they are the source of genetic information stored as chromosomes. Nucleic acids are composed of long chains of nucleotides linked by dehydration synthesis.

Two types:
a. Deoxyribonucleic acid (DNA-double helix)
b. Ribonucleic acid (RNA-single strand)
DNA serves as genetic material, whereas RNA plays a vital role in using genetic information to dictate the amino acid sequence to manufacture proteins.

Each Nucleotides are composed of 3 parts:
1- phosphate group (P)
2- pentose sugar (5-carbon)
3- nitrogenous bases: These can be any one of five types given below-
• adenine (A)
• thymine (T) (DNA only)
• uracil (U) (RNA only)
• cytosine (C)
• guanine (G)

DNA, Gene and Genome

DNA: Deoxyribonucleic acid, one of the two forms of nucleic acid in living cells. Polymers of nucleic acids. The genetic material of life. Each strand of DNA consists of a chain of four kinds of nucleotides (because of four different Nitrogenous bases). The order of nucleotide bases in a strand of DNA—the DNA sequence—is genetic information.

Gene: A DNA segment containing biological information which encode for an RNA and/or polypeptide molecule.

Genome: A genome is the full set of genes in each cell of an organism.

The hereditary nature of every living organism is defined by its genome, which consists of a long sequence of nucleic acid that provides the information needed to construct the organism. Genes are the basic unit of genetic information. They determine the nature and the function of the cell. The human genes (about ~ 30- 40,000) are referred to as the human genome. A genome is the full set of genes in each cell of an organism. It is the sequence of the individual subunits (bases) of the nucleic acid that determines hereditary features. By a complex series of interactions, this nucleotide sequence is used to produce all the proteins of the organism in the appropriate time and place. The proteins either form part of the structure of the organism, or have the capacity to build the structures or to perform the metabolic reactions necessary for life.

The human genome consists of two distinct parts:
1. Nuclear genome:
3.2 X 109 bp of DNA
30,000 – 40,000 genes
2. Mitochondrial genome:
circular DNA molecule of 16,569 nucleotides & consisting of 37 genes
Adult human body contains approximately 1013 cells.
Each cell has its own copy or copies of the genome.

Human chromosomes

Chromosome: Discrete unit of genome carrying many genes. Each chromosome consists of very long molecule of duplex DNA and approximately equal mass of proteins.
Each species have their unique number of chromosomes. All Human cells contain 23 pairs of chromosome, which is a total of 46 chromosomes in each cell. Human body cells have two of each type of chromosome, which means that their chromosome number is diploid (2n). 22 of the pairs are called autosomes and are numbered from largest to smallest. The autosomes are not involved in determining sex. The two members of each pair have the same length and shape, and they hold information about the same traits, Except for a pairing of sex chromosomes (XY) in males,
The 23rd pair are the sex chromosomes:

•  XX in females
•  XY in males

The Central Dogma of Molecular Biology

The idea that genetic information is stored as DNA, copied into RNA, and then used to build proteins is considered the central dogma of molecular biology.

The instructions in DNA determine the structure and function of all living
things. Every time a cell reproduces, it must make a copy of these instructions for the new cell. When cells need to build a functional molecule (usually a protein), they copy the information in the genes into an RNA molecule instead of using the DNA blueprint directly.




Here’s an outline of the process:

1. Cells use transcription to copy the information in DNA into newly synthesized RNA molecules.
2. The information to build proteins is copied into a special type of RNA called messenger RNA (mRNA), which carries the blueprint for the protein from the nucleus to the cytoplasm where it can be used to build the protein.
3.  In a process called translation, proteins are build from the information carried in mRNA molecules.

Transcription
Transcription is the process by which the information contained in a section of DNA is transferred to a newly assembled piece of messenger RNA (mRNA). An essential enzyme called RNA polymerase finds the genes within the DNA it needs to copy with the help of proteins called transcription factors. Transcription occurs in the nucleus.

Translation
Messenger RNA is the only kind of RNA that carries a protein-building message. By the process of translation, the protein-building information in an mRNA is decoded (translated) into a sequence of amino acids. The result is a polypeptide chain that twists and folds into a protein. Simply, Translation is the process where ribosomes (a type of cellular machinery needed for holding the mRNA when translating) synthesize proteins using the mature mRNA transcript produced during transcription. Translation occurs in the cytoplasm.