The Chemistry of Biological Molecules

Matter: Elements and Compounds:

Matter is anything that has mass and occupies space, exists as a solid, liquid, or gas. (Common states)

-Elements cannot be broken down into simpler substances. They have only one type of atom present

Carbon, Hydrogen, Oxygen, and Nitrogen all make of 96% of living matter

The other 4% (trace elements) Ca, P, S, Na, Cl, and Mg

-Compounds are molecules with two or more elements such as CO2 or H2O that are in fixed ratios. They have more than one atom present

Matter tree:

MATTER

Pure substances Mixtures

Elements Compounds Heterogeneous Homogenous

Mechanical Suspension Solutions

Structure and Behaviour of Atoms:

An Atom is the smallest possible unit that has all the physical and chemicals properties of an element. It is made up of subatomic particles –> NEUTRON, PROTON, ELECTRON

Name	Symbol	Charge	Mass (g)	Mass (amu)	Location
Proton	P⁺	+1	1.673 x 10^-24	1	Nucleus
Neutron	n⁰	0	1.675 x 10^-24	1	Nucleus
Electron	e^–	–1	9.109 x 10^-28	0.0005	Outside Nucleus

An isotope is an element with the same number of protons and electrons but a different number of neutrons

Ex.) Carbon-12 and Carbon-14

There are also radioactive isotopes , the nucleus will randomly emit subatomic particles or energy. There are uses for isotopes such as radioactive tracers which can be attached to chemicals and the flowed through the body, or a biochemical reaction. Isotopes of P, N, and H are used in finding the structure of DNA, and radioactive cobalt is used to locate cancerous tumors.

The chemical properties of an atom will depend on the number of valence electrons because they react in reactions.

A covalent bond is a STRONG sharing of electrons.

EX.)There is a sharing of electrons within the water molecules, the shells overlap

There are two types of covalent bonds.

1.) NONPOLAR BOND caused by an EQUAL sharing of electrons which most of the time have the same electronegativity, such as the diatomic elements O2, Cl2, H2, Br2

2.) POLAR BOND is formed by an UNEQUAL sharing of electrons, they usually have different electronegativities. When they share electrons, the shared electrons will spend more time on the more negative side, creating separate poles, such as the water molecule

An Ionic bond is created by an electrostatic attraction once there is a transfer from the valence electron of the cation (metal) to the anion (electron acceptor). Such as NaCl, sodium gives up its electron to the chlorine and then the positive and negative attraction occurs

A Hydrogen bond occurs when a hydrogen atom is covalently bonded to one electronegative atom. (weakest bond)(collectively strong)

Weak bonds are important to help stabilize the shape of DNA and help in replication.

The Water Molecule:

It is a polar molecule that is held together by hydrogen bonds. It is cohesive (sticks to itself) and adhesive (it sticks to hydrophilic substances(other polar molecules))

Water also has a high heat capacity, it resists temperature change when it absorbs, the hydrogen bonds have to be broken

It also has a high heat of vaporization, the evaporative cooling prevents overheating, the molecules with the highest kinetic energy will become as gas and the remaining will lower the average kinetic energy

It is also a versatile solvent because if its polarity. Is is a “universal solvent”. Although, fats, oils, and waxes will not dissolve in water. The compounds that do dissolve are charged polar molecules. (hydrophilic)

Aqueous solutions- most biochemical reactions involves solutes dissolved in water, Ph is important in these solutions

Dissociation of the water molecule is reversible reaction

Acids- substances that dissociate they release hydrogen ions, which increases the concentration of H+ and lowers the Ph

EX.) HCl—> H+ + Cl-

Bases- substances that increase hydroxide ions, increases the Ph

Buffer- Are a chemical that keeps the pH within normal limits

Uses H+ and OH- to form weak acids and bases to help minimize any large changes. Tums and carbonic acid are both bases that keep stomach acid at its normal range and blood at its normal range.

The building blocks of organisms:

Organic molecules are made up of carbon with different functional groups attached .

Functional groups give chemical properties to the molecules that contain them:

1.) Hydroxl group- polar molecule that makes water soluble

2.) Carbonyl group- polar group, oxygen can be involved in hydrogen bonding, water soluble, functional group of sugars

3.) Carboxyl group- polar group, water soluble, has acidic properties

4.)Amino group- polar group, water soluble, functional group of proteins, are week bases

5.)Phosphate group- polar group, water soluble, acidic properties, ATP

Chemical reactions:

Most reactions involve the transfer of a functional group from one molecule to another, or just the creation or breaking down of a carbon-carbon bond

Dehydration/condensation synthesis is an anabolic reaction where a bond is formed. The removal of H and OH has to occur (water molecule). We use this to link monomers to form polymers.

Hydrolysis reaction is a catabolic reaction (breaking down) where an H and OH is added (water) which breaks the monomers back in to polymers.

Bond Names:

THERE ARE 4 MACROMOLECULES, each has a specific bond name. Ester bonds form between an acid and an alcohol.

1.) Carbohydrates – form an ESTER BOND which is called the GLYCOSIDIC BOND (glycol=sugar)

2.)Nucleic Acids-Form an ester bond between the sugar and phosphate groups called a PHOSHODIESTER bond

Ex.) sugar phosphate backbone of DNA

3.)Lipids- Form an ester bond between the glycerol and fatty acids

4.) Proteins form peptide bonds between the carboxyl and amino group

The first macromolecule: Carbohydrates

Take the form of (CH2O) in different ratios, for example C5H10O5 is the ratio for ribose.

1.)The most simplest form of a carbohydrate is MONOSACCHARIDES which is one sugar unit. They are small and water soluble, they are the building blocks for polymers.

Three types of monosaccharides:

6 carbons:

1.)Glucose-plants

2.)Fructose-corn sugar

3.)Galactose-milk sugar

5 carbons:

1.)Ribose

2.)Deoxyribose

They all have a short lifespan because they are used quicker for energy, they form disaccharides when linked together

2.)Disaccharides (two sugar units)

They are for short term energy but still longer than monosaccharides

Three types made from a dehydration reaction where H2O is removed when two monosaccharides are added together

1.) glucose+fructose–>sucrose +h2o

2.)glucose+galactose–>lactose+h2o

3.)glucose+glucose–>maltose+h2o

They become the disaccharides through a dehydration/condensation reaction

This is a hydrolysis reaction, but the opposite going (<—) creates the disaccharide

3.)Polysaccharides

They are a long term storage. In plants the polysaccharide is starch, in animals it is glycogen. Cellulose is also found in plants for structure and rigidity.

Functions:

Glycogen is also for structure in animals

Plants–> have cellulose for structure

Insects–>chitin(exoskeleton)

The next macromolecule is lipids:

They are insoluble in H2O because they are non polar.

Neutral fats are also called triglycerides such as lard, butter, and plant oils

Glycerol and three fatty acids join in a dehydration reaction to make a triglyceride

X=glycerol Y=3 fatty acids

—> dehydration

<— condensation

There are two types of fatty acids:

Saturated fats (with hydrogen)	Unsaturated fats
no double bonds because the carbons are fully utilized maximum amount of H’s not chemically reactive most are animal fats hard at room temperature they can lead to heart disease	can have double bonds less than the maximum amount of carbons more reactive mostly plant oils such as vegetable liquid at room temperature

The saturated has no double bonds and the unsaturated has a double bond

Lipids are important because they provide a long term storage, in animals they give 2x as much as energy than carbohydrates. They also insulate and provide padding in the body.

There are also phospholipids which is made up of glycerol and instead of three fatty acids the third is replaced with a phosphate group. It contains polar and nonpolar areas which is partially water soluble. Ex.) It is found in the plasma membrane of cells, mitochondria, chloroplasts, and vesicles

There are waxes which are made out of a long chain of fatty acids joined to a long chain of alcohol, they are nonpolar and waterproof

There are soaps which is a fatty acid joined to an inorganic base. EX.) bile which is a natural soap produced by the liver and stored in the gallbladder for the emulsification of fats

Steroids are also fats, with a different structure, they consist of 4 fused carbon rings with different groups attached. It is a fat because it is insoluble in water. Cholesterol is a fat that makes steroids such as testosterone and estrogen.

The third macromolecule is proteins:

They’re used for hormones, enzymes, keratin plays a role in hair and nails, myosin and actin play a role in cell movement and muscle contraction

There’s about 20 different amino acids:

A peptide bond makes a protein, a chain of amino acids (peptide bonds) is called a polypeptide

Structure:

Proteins	Shape	Bondsà
Primary	Line	Peptide bonds
Secondary	Alpha helix, beta pleated sheet	Peptide bonds	Hydrogen bonds
Tertiary	Folded 3D shape	Peptide bonds	Hydrogen bonds	Covalent or ionic
Quaternary	2 or more linked polypeptides	Peptide bonds	Hydrogen bonds	R groups (also in 3) disulfide bridges

The shape is important in proteins, it determines the function , a change in shape of denaturing in other words by applying heat or changing pH, it causes the protein to no longer function

EX.) cooking eggs turns the protein opaque,

Trypsin and pepsin are both fully functional at the height, once the pH is increased or decreased the enzymes lose their function

Nucleic acids are the last macromolecules:

They are important in the growth, reproduction of cells in organisms

There are three examples:

1.)DNA (deoxyribonucleic acid)

2.)RNA (ribonucleic acid)

3.)ATP (adenosine triphosphate)

These nucleic acids are made up of nucleotides, which is made up of 3 parts:

1.)Pentose sugar

2.)Phosphate group

3.)Nitrogenous base

In DNA and RNA there is the phosphate group, in DNA deoxyribose is the sugar, and in RNA the sugar is ribose. The bases are also a little different, in DNA adenine, cytosine, guanine, thymine, then in RNA the bases are adenine, cytosine, guanine, and uracil.

The bases can be single or should ringed, pyrimidine is single, purine is double ringed

Adenine and guanine=purines

Cytosine and thymine=pyrimidines

When cytosine and guanine bond together they are attached by 3 hydrogen bonds, but adenine and thymine are held together by 2 hydrogen bonds

The structure of DNA is held together by two strands made of nucleotides running in opposite direction.

ATP is a nucleic acid that acts like an energy carrier in cells, it base is adenine and sugar is ribose. It has three phosphate groups, one is removed under a hydrolysis reaction.