BIOCHEMISTRY OF LIFEORGANIC COMPOUNDS

Water

• Water is the main solvent in our bodies and many of the chemical reactions of the body take place in water.

• The total of the reactions that take place in our bodies is called metabolism

• Water (H2O) consists of 2 hydrogen atoms and 1 oxygen atom linked by a covalent bond

• Water is a polar molecule meaning that due to uneven distribution of electrons, one end of the molecule has a positive electrical charge and the other end has a negative electrical charge – it has electrical poles

• In water, the oxygen end has a slightly negative charge and the hydrogen ends have a slightly positive charge.

Water is a very unusual substance and has some very important properties; it has a very high melting and boiling point (0oC and 100oC), it has a high viscosity, it’s solid form is less dense than the liquid form and has high surface tension.

Water• An electrostatic attraction between the positive charge at the hydrogen

end and the negative charge at the oxygen end result in the formation of a hydrogen bond.

• Many of the unique properties of water are caused by the hydrogen bonding of the molecules.

• The ability of ions and other molecules to dissolve in water is due to it’s polarity.

• Substances that readily dissolve in water are called hydrophillic or polar• Substances that do not tend to dissolve in water are called

hydrophobic or non-polar

• For Example Sodium chloride (NaCl) will dissociate into its two parts Na+ and Cl- when it comes into contact with water. The positive sodium (Na) ions are attracted to the negative oxygen and the negative chloride (Cl-) is attracted to the positive hydrogen of water. A ring of water molecules surround each sodium and chloride atom and they remain in solution.

Water• Water exists in three states; solid, liquid & gas• The hydrogen bonds that hold water molecules

together are relatively weak and continually break and reform when in liquid state.

• When water is heated to temperatures of 100oC or greater the movement of the molecules is so great that the hydrogen bonds can no longer hold them together and the water is converted into a gas (steam)

• At temperatures below 4oC the movement of molecules is such that the hydrogen bonds do not break and reform They form a lattice structure which holds each water molecule further away from each other than would normally occur in the liquid form and causes water to become solid (ice).

• Ice is less dense than liquid water, and therefore floats on the liquid water – an very important property.

In ice every water molecule is bonded to 4 others.

Organic Molecules•Organic molecules are the chemicals of

life. They are compounds composed of more than one type of element, that are found in and produced by living organisms.

•Organic molecules contain carbon-hydrogen bonds, whereas inorganic molecules do not.

•The four major groups of organic molecules are carbohydrates, proteins, lipids and nucleic acids

ORGANIC COMPOUNDS•Organic compounds are immensely

important in living things, they:

▫Make up the structures of the body

▫Regulate chemical processes going on in the body

Organic Molecules•Organic molecules are often very large

and made up of smaller sub-units bonded together in various ways.

•Compounds formed in this way are called polymers

•The sub-units that make up the polymers are called monomers

What is an organic compound?• Organic compounds are all complex compounds

of carbon (excluding oxides, carbonates & bicarbonates)

• This means that they are chemicals that contain the element carbon

▫ Organic compounds were originally thought to only be found in living things. It is now known that it is not the case.

▫ However, organic compounds make up about 30% of what makes up a cell (a substantial amount)

What are some organic compounds?•The main organic compounds found in

living organisms are:

▫Carbohydrates▫Lipids▫Proteins▫Nucleic acids

Carbohydrates•Carbohydrates include sugars and

starches•When combusted carbohydrates release

energy•The main function of carbohydrates in

organisms is to produce and store energy

Carbohydrates• Carbohydrates are organic compounds

composed of carbon (C), hydrogen (H) and oxygen (O).

• The basic unit of a carbohydrate is a sugar molecule (monosaccharide)

• When two sugar molecules are joined a water molecule is released

• Carbohydrates that contain one or two sugar units are called simple carbohydrates

• Those that contain many sugar molecules are called complex carbohydrates

Types of carbohydrates•Monosaccharides

▫(means single sugars)▫All monosaccharides are sweet, soluble in

water and will crystallize (form crystals)▫Glucose and fructose are monosaccharides▫Glucose and fructose are found in…

C6H12O6

Types of Carbohydrates•Disaccharides

▫(means double sugar)▫Dissarcharides are made up of two

monosaccharides▫Maltose, sucrose & lactose are types of

disaccharides

C12H22O11

Types of Carbohydrates•Polysaccharides (means multi-sugar)

▫Polysaccharides are not soluble in water, do not taste sweet and do not form crystals

▫They form long chains of many units of sugars

▫This makes them ideal storage unitsStarch (plants) & glycogen (animals) are

how energy is stored in organismsCellulose is another form of polysaccharide.

It is used in plants cell walls.

Proteins• Proteins are vital in the formation of structures in organisms.• Proteins are made from amino acids (there are 20 occurring

naturally)• Humans need all 20 but cannot make all 20 so must rely on

their food in order to get them.• Proteins form enzymes which are extremely important in

speeding up chemical reactions in organisms.• Proteins such as keratin is found in hair, nails, hooves, horns

& feathers.• Elastin and collagen are important connective tissue

proteins.• Protein is also important in muscles.• Haemaglobin is a protein present in blood (it is the pigment

that carries oxygen in our blood)

Proteins

• Each amino acid has one part of its molecule different from other amino acids. The R group in the general formula is the part that varies.

• Two amino acids join together as a dipeptides when a peptide bond forms between the amino group of one amino acid and the carboxyl group of another.

• When a number of amino acids join this way a polypeptide is formed.

• Each type of protein has its own particular sequence of amino acids.

• Polypeptide chains become folded in different ways depending on their function.

Structure and Shape of Proteins• Primary Structure

▫ The specific linear sequence of amino acids in the protein.• Secondary Structure

▫ The folding of amino acid chains. Hydrogen bonds form between segments of folded chain that have come close together & help stabilise the 3D shape. Alpha helix– spiral molecule Beta-pleated sheet Random coiling – doesn’t fit into either the alpha or beta coiling

• Tertiary Structure▫ Total irregular folding held together by ionic or hydrogen bonds

forming a complex shape • Quaternary Structure

▫ Two or more polypeptide chains interact to form a protein (eg. Haemaglobin, collagen)

ProteinsType of Protein Function ExampleStructural Fibrous support tissue in skin,

bone, tendons, cartilage, blood vessels, heart valves and cornea of the eye

Collagen, keratin

Enzyme Catalyse reactions ATP SynthaseContractile Muscle movement Myosin, actinImmunoglobulin Defence against disease AntibodiesHormone Regulate body acitivty InsulinReceptor Respond to stimuli Insulin

receptorstransport Carry other molecules haemoglobin

Proteins• In every living organism proteins are involved in one way

or another in almost every chemical reaction.• They may be the enzymes involved, the reactants or the

products, or all three• The complete array of proteins produced by a single

organism in a particular environment is called the proteome of the cell or organism

• The study of the proteome is called proteomics

Lipids• Lipids include natural fats, oils and waxes• At room temperature fats are solid and at room

temperature oils are liquid• Lipids supply energy, in fact more energy than

carbohydrates as they contain very little water.• Lipids are essential in the plasma membrane

(cell membranes) and in sub-cutaneous fat (essential for preventing heat loss in animals)

• Fats have little or no attractions for water and are insoluble in it (hydrophobic)

Lipids•A fat molecule is made of two kinds of

molecules; fatty acids and glycerol•Triglycerides are a common form of fats they

have a single glycerol and three fatty acid molecules attached

•Phospholipids are another kind of fat and have TWO fatty acids attached to a glycerol, and, a phosphate group attached to the glycerol.

•Phospholipids are a major component of cell membranes

Nucleic Acids• Nucleic acids are found in cells• There are two types of nucleic acid

▫ DNA – deoxyribonucleic cid▫ RNA – ribonucleic acid

• Nucleic acids are the genetic material of all organisms

• They are responsible for the features of an organism

• Both DNA & RNA are made up of long chains of subunits called nucleotides

• (DNA/RNA = polymer, nucleotides = monomer)

Nucleic Acids• Each nucleotide has a sugar (deoxyribose), phosphate

and a nitrogen containing base.• The sugar and phosphate are the same in each unit,

but there are four different nitrogen containing bases: adenine (A), thymine (T), cytosine (C) & guanine (G)

• Nucleotide sub-units are assembled to make a chain in which the sugar of one nucleotide is bonded with the phosphate of the next nucleotide in the chain.

• Each DNA molecule contains two chains that bond with each other because the bases in one chain pair with the bases in another (A & T, and C & G)

• The two chains form the double helix of DNA

Nucleic Acids•DNA controls all of the functions of a cell

through the production of proteins.•The DNA sequence codes for amino acids

to be produced, which produce chains of polypeptides (proteins) which control all metabolic processes in the cell.

• (How does DNA code for proteins?)

Nucleic AcidRibonucleic Acid (RNA)• Is also a polymer of nucleotides• It is an unpaired chain of nucleotides (single strand)

and exists in three forms▫messengerRNA (mRNA)

Carries the message to the ribosomes where the message is translated into a particular protein

▫ribosomalRNA (rRNA) Together with proteins makes the ribosomes found in the

cytosol▫transferRNA (tRNA)

Carry amino acids to ribosomes where they are used to construct proteins