THE CHEMISTRY OF LIFE. REVIEW

We usually say atom is the smallest part of matter but scientists have found out that
there are small particles inside atoms. Do you remember their names? Proton, neutron
and electron.

Where are protons?
- Protons are in the nucleus.
Which particles are in the nucleus?
- Protons and neutrons are in the nucleus
Where are electrons?
- They move around, in the orbit.
Do neutrons have charge?
- No, they don’t.
Do protons have charge?
- Yes, they have positive charge.
Do electrons have mass?
- We say they don’t have mass (because their mass is very very small, much
smaller than proton and neutron mass).
Where is the mass of an atom?
- It’s in the nucleus

A chemical reaction is a process that leads to the transformation of one set of chemical substances to another.[1] Chemical reactions are studied by chemists under a field of science called chemistry. Chemical reactions can be either spontaneous, requiring no input of energy, or non-spontaneous, often coming about only after the input of some type of energy, viz. heat, light or electricity. Classically, chemical reactions encompass changes that strictly involve the motion of electrons in the forming and breaking of chemical bonds, although the general concept of a chemical reaction, in particular the notion of a chemical equation, is applicable to transformations of elementary particles, as well as nuclear reactions.

The substance/substances initially involved in a chemical reaction are called reactants. Chemical reactions are usually characterized by a chemical change, and they yield one or more products, which usually have properties different from the reactants.

Reaction EnergyAll chemical reactions are accompanied by a change in energy. Some reactions release energy to their surroundings (usually in the form of heat) and are called exothermic. For example, sodium and chlorine react so violently that flames can be seen as the exothermic reaction gives off heat. On the other hand, some reactions need to absorb heat from their surroundings to proceed. These reactions are called endothermic.

Reactions that proceed immediately when two substances are mixed together (such as the reaction of sodium with chlorine or urea with ammonium chloride) are called spontaneous reactions. Not all reactions proceed spontaneously. For example, think of a match. When you strike a match you are causing a reaction between the chemicals in the match head and oxygen in the air. The match won't light spontaneously, though. You first need to input energy, which is called the activation energy of the reaction. In the case of the match, you supply activation energy in the form of heat by striking the match on the matchbook; after the activation energy is absorbed and the reaction begins, the reaction continues until you either extinguish the flame or you run out of material to react.

There are several differences between a physical and chemical change in matter or substances.

A physical change in a substance doesn't change what the substance is. In a chemical change where there is a chemical reaction, a new substance is formed and energy is either given off or absorbed.
For example, if a piece of paper is cut up into small pieces it still is paper. This would be a physical change in the shape and size of the paper. If the same piece of paper is burned, it is broken up into different substances that are not paper.
Physical changes can be reversed, chemical changes cannot be reversed with the substance changed back without extraordinary means, if at all. For example, a cup of water can be frozen when cooled and then can be returned to a liquid form when heated.

If one decided to mix sugar into water to make sugar water, this would be a physical change as the water could be left out to evaporate and the sugar crystals would remain. However, if one made a recipe for a cake with flour, water, sugar and other ingredients and baked them together, it would take extraordinary means to separate the various ingredients out to their original form.

Diffusion is a time-dependent process, constituted by random motion of given entities and causing the statistical distribution of these entities to spread in space. The concept of diffusion is tied to notion of mass transfer, driven by a concentration gradient.

The concept of diffusion emerged in the physical sciences. The paradigmatic examples were heat diffusion, molecular diffusion and Brownian motion.

Diffusion - the process by which molecules spread from areas of high concentratiion, to areas of low concentration. When the molecules are even throughout a space - it is called EQUILIBRIUM

Concentration gradient - a difference between concentrations in a space.

OSMOSIS

Watch this animation of water molecules moving across a selectively permeable membrane. Water molecules are the small blue shapes, and the solute is the green.

The solute is more concentrated on the right side to start with, which causes molecules to move across the membrane toward the left until equilibrium is reached.

Mixture refers to the physical combination of two or more substances the identities of which are retained. Mixtures are either homogeneous or heterogeneous. A homogeneous mixture is a type of mixture which the composition is uniform. A heterogeneous mixture is a type of mixture the composition of which can easily be identified since there are two or more phases present. Air is a homogeneous mixture of the gaseous substances nitrogen,oxygen,and smaller amounts of other substances.Salt,sugar,and many other substances dissolve in water to form homogeneous mixture. Homogeneous mixture are also called solution.

An organic compound is any member of a large class of chemical compounds whose molecules contain carbon.

Carbohydrates: Mainly sugars and starches, together constituting one of the three principal types of nutrients used as energy sources (calories) by the body. Carbohydrates can also be defined chemically as neutral compounds of carbon, hydrogen and oxygen.

Carbohydrates come in simple forms such as sugars and in complex forms such as starches and fiber. The body breaks down most sugars and starches into glucose, a simple sugar that the body can use to feed its cells. Complex carbohydrates are derived from plants. Dietary intake of complex carbohydrates can lower blood cholesterol when they are substituted for saturated fat.

Carbohydrates are classified into mono, di, tri, poly and heterosaccharides. The smallest carbohydrates are monosaccharides such as glucose whereas polysaccharides such as starch, cellulose and glycogen can be large and even indeterminate in length.

Monosaccharides

These are the basic compounds with a cyclic structure consisting of carbon, hydrogen and oxygen in the ratio 1:2:1. 'Mono' refers to single and saccharides means sugar. Glucose, fructose and galactose are types of monosaccharides.

Disaccharides

These carbohydrates mean 'two sugars', which refer to the commonly available types such as sucrose, maltose and lactose. When two monosaccharides bond together by a condensation reaction, they release one molecule of water and a disaccharide is formed. This bond is called a glycosidic bond.


Polysaccharides

These are also called monomers and are composed of thousands of molecules of the basic units of glucose. Carbohydrates stored in the form of starch contain these type of compounds. Amylose, which is a straight chain compound and amylopectin, which is a branched compound, are the most common types of polysaccharides.

Nucleotides

It is another complex carbohydrate which contains many molecules of cyclic sugar. Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are complex five sided sugars classified under this category. The difference between RNA and DNA is that the former has one extra hydroxyl group.

All Lipids are hydrophobic: that’s the one property they have in common. This group of molecules includes fats and oils, waxes, phospholipids, steroids (like cholesterol), and some other related compounds.

Fats and oils are made from two kinds of molecules: glycerol (a type of alcohol with a hydroxyl group on each of its three carbons) and three fatty acids joined by dehydration synthesis. Since there are three fatty acids attached, these are known as triglycerides.

The terms saturated, mono-unsaturated, and poly-unsaturated refer to the number of hydrogens attached to the hydrocarbon tails of the fatty acids as compared to the number of double bonds between carbon atoms in the tail. Fats, which are mostly from animal sources, have all single bonds between the carbons in their fatty acid tails, thus all the carbons are also bonded to the maximum number of hydrogens possible. Since the fatty acids in these triglycerides contain the maximum possible amouunt of hydrogens, these would be called saturated fats. The hydrocarbon chains in these fatty acids are, thus, fairly straight and can pack closely together, making these fats solid at room temperature. Oils, mostly from plant sources, have some double bonds between some of the carbons in the hydrocarbon tail, causing bends or “kinks” in the shape of the molecules. Because some of the carbons share double bonds, they’re not bonded to as many hydrogens as they could if they weren’t double bonded to each other. Therefore these oils are called unsaturated fats. Because of the kinks in the hydrocarbon tails, unsaturated fats can’t pack as closely together, making them liquid at room temperature. Many people have heard that the unsaturated fats are “healthier” than the saturated ones. Hydrogenated vegetable oil (as in shortening and commercial peanut butters where a solid consistency is sought) started out as “good” unsaturated oil. However, this commercial product has had all the double bonds artificially broken and hydrogens artificially added (in a chemistry lab-type setting) to turn it into saturated fat that bears no resemblance to the original oil from which it came (so it will be solid at room temperature).

Proteins (also known as polypeptides) are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code.

Biochemistry refers to four distinct aspects of a protein's structure:

Primary structure
the amino acid sequence of the peptide chains.

Secondary structure
highly regular sub-structures , which are locally defined, meaning that there can be many different secondary motifs present in one single protein molecule.

Tertiary structure
three-dimensional structure of a single protein molecule; a spatial arrangement of the secondary structures. It also describes the completely folded and compacted polypeptide chain.

Quaternary structure
complex of several protein molecules or polypeptide chains, usually called protein subunits in this context, which function as part of the larger assembly or protein complex.

Nucleic Acids
DNA and RNA

Living organisms are complex systems. Hundreds of thousands of proteins exist inside each one of us to help carry out our daily functions. These proteins are produced locally, assembled piece-by-piece to exact specifications. An enormous amount of information is required to manage this complex system correctly. This information, detailing the specific structure of the proteins inside of our bodies, is stored in a set of molecules called nucleic acids.

The nucleic acids are very large molecules that have two main parts. The backbone of a nucleic acid is made of alternating sugar and phosphate molecules bonded together in a long chain.

Though only four different nucleotide bases can occur in a nucleic acid, each nucleic acid contains millions of bases bonded to it. The order in which these nucleotide bases appear in the nucleic acid is the coding for the information carried in the molecule. In other words, the nucleotide bases serve as a sort of genetic alphabet on which the structure of each protein in our bodies is encoded.

DNA
In most living organisms (except for viruses), genetic information is stored in the molecule deoxyribonucleic acid, or DNA. DNA is made and resides in the nucleus of living cells. DNA gets its name from the sugar molecule contained in its backbone(deoxyribose); however, it gets its significance from its unique structure. Four different nucleotide bases occur in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T).

The versatility of DNA comes from the fact that the molecule is actually double-stranded. The nucleotide bases of the DNA molecule form complementary pairs: The nucleotides hydrogen bond to another nucleotide base in a strand of DNA opposite to the original. This bonding is specific, and adenine always bonds to thymine (and vice versa) and guanine always bonds to cytosine (and vice versa).

The double-stranded DNA molecule has the unique ability that it can make exact copies of itself, or self-replicate. When more DNA is required by an organism (such as during reproduction or cell growth) the hydrogen bonds between the nucleotide bases break and the two single strands of DNA separate. New complementary bases are brought in by the cell and paired up with each of the two separate strands, thus forming two new, identical, double-stranded DNA molecules.

RNA

Ribonucleic acid, or RNA, gets its name from the sugar group in the molecule's backbone - ribose. Several important similarities and differences exist between RNA and DNA. Like DNA, RNA has a sugar-phosphate backbone with nucleotide bases attached to it. Like DNA, RNA contains the bases adenine (A), cytosine (C), and guanine (G); however, RNA does not contain thymine, instead, RNA's fourth nucleotide is the base uracil (U). Unlike the double-stranded DNA molecule, RNA is a single-stranded molecule. RNA is the main genetic material used in the organisms called viruses, and RNA is also important in the production of proteins in other living organisms. RNA can move around the cells of living organisms and thus serves as a sort of genetic messenger, relaying the information stored in the cell's DNA out from the nucleus to other parts of the cell where it is used to help make proteins.