Download Week 12 – Basic Chemical Structures of Important Organic

Week 12 – Basic Chemical Structures of Important Organic Molecules
An organic compound always contains at least two, and often many more, atoms of carbon.
The other principal elements found in organic molecules are oxygen and hydrogen. Nitrogen
if found in many organic compounds – proteins and nucleic acids, and phosphorous is a key
element in the nucleic acids.
1) Carbohydrates
Carbohydrates contain only the elements carbon, hydrogen and oxygen. They are the
most abundant class of biomolecules. In animals their main function is to act as an
easily accessible source of energy. They carry out this important function in plants as
well but also serve an important structural function (remember cellulose).
Carbohydrates include sugars, starch, cellulose, chitin and glycogen. As a group,
carbohydrates are most conveniently classified on the basis of size. The simplest and
smallest carbohydrates are the monosaccharides (single sugar). All monosaccharides
have the general formula (CH2O)n. The letter n equals the number of carbon atoms in
the molecule with the most common number being 6 giving us the 6-carbon sugars or
hexoses. The five carbon sugars found within nucleic acids are pentoses.
The best known hexose sugar, and the most abundant, is the monosaccharide glucose
(C6H12O6). Notice that the ratio of carbon atoms to hydrogen atoms is always 1:2.
Other monosaccharides are: fructose, galactose and ribose.
All monosaccharides are soluble, taste sweet and form crystals.
Monosaccharides are also known as carbohydrate monomers because the same
molecule (e.g. glucose) can bond with itself many times to form more complex
sugars.
The basic molecular structures of glucose and ribose are:
Glucose (6C = hexose)
Ribose (5C = pentose)
Disaccharides are formed when two monosaccharides join. Three common examples
are sucrose, maltose and lactose. Lactose is formed from glucose bonding with
galactose and sucrose is formed by a glucose molecule bonding with a fructose
molecule. See sucrose below.
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Oligosaccharides are sugars that typically have between three and ten monosaccharide
units joined together e.g. the carbohydrate units bonded to a glycoprotein embedded
in a cell membrane of a red blood cell are typically oligosaccharides and help
determine whether the blood type is A, B or O. Some of the important processes
involving oligosaccharides in animals are shown below.
Polysaccharides are complex carbohydrates comprise of more than ten
monosaccharide units joined together. Important examples in biology are cellulose in
plants, chitin in fungi & exoskeletons of arthropods (e.g. insects), and glycogen in
animals.
Schematic 2-D cross-sectional view of glycogen.
A core protein of glycogenin is surrounded by
branches of glucose units. The entire globular
granule may contain approximately 30,000 glucose units
Starch in plants e.g. in potatoes
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Tony Molyneux
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2011
2) Proteins
Proteins always contain carbon, hydrogen, oxygen and nitrogen. The monomer unit is
known as an amino acid. Every amino acid is comprised of an amino group (- NH2)
and a carboxyl group (-COOH). The central carbon is linked to a hydrogen atom and
another group of atoms, which varies, but is given the general letter ‘R’. The amino
acid varies according to what ‘R’ is and there are about 20 different amino acids. The
basic monomer unit is shown below:
A dipeptide is formed when two amino acids bond together. Polypeptides are formed
by the bonding of many amino acids to form large single chains or more complex
compounds formed from the bonding of several polypeptide chains and with or
without varying degrees of folding within a chain. Proteins can be classed as primary,
secondary, tertiary or quaternary depending on the complexity of the folding and
number of chains bonded together. A typical human cell can contain 10 million
protein molecules of about 10 000 different types.
Typical examples of these proteins are:
Primary – e.g. the order of amino acids joined together in a single chain;
Secondary – e.g. keratin found in skin, hair and nails; silk fibres of a spider web;
Tertiary – e.g. some enzymes such as lipase and sucrase; collagen (collagen fibres
have a high tensile strength than steel);
Quaternary – e.g. insulin – a hormone produced in the pancreas; haemoglobin, many
enzymes
Proteins are important biomolecules because they are involved in the structure and
function of organisms e.g. enzymes, hormones are proteins as are large components of
our muscle, skeletal and organ systems.
Diagram above shows the combination of complex folding and bonding together of several peptide chains .
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2011
3) Lipids
Lipids are fats, oils and waxes. Fats and waxes are solid whereas oils are liquid at
room temperature. Lipids contain carbon, hydrogen and oxygen but unlike
carbohydrates, in no set ratio.
They are composed of two basic units; fatty acids and glycerol. Fatty acids have the
general formula RCOOH, where R is a variable group consisting of a hydrocarbon
chain. The most common lipids are triglycerides, formed when three fatty acids bond
with a glycerol molecule (e.g. phospholipids).
The physical nature of the lipid is determined by the length of the carbon chains in the
fatty acids and whether or not these chains are saturated. Lipids formed from saturated
fatty acids are more compact and solid e.g. butter and lard. Lipids with one or more
unsaturated fatty acid chain are liquid e.g. oils such as peanut and olive oils.
Unsaturated fatty acids have one (monounsaturated) or more (polyunsaturated) double
bonds between the carbon atoms and their less packed structure helps lower
cholesterol levels in the blood and is less likely to clog blood vessels.
Lipids are relatively insoluble in water and so play important roles in the control of
water balance in organisms e.g. structure of the cell membrane. Waxes provide a
protective waterproofing on external surfaces reducing evaporative loss of water of
keeping structures such as feathers waterproof.
Lipids store twice as much energy as an equivalent mass of carbohydrate and so are
important energy reserves in living organisms. Water is a by-product of the
breakdown of fat so many desert animals (e.g. camel) uses the fat store in its ‘hump’
to produce water metabolically.
Steroids are classified with lipids, although their structure is quite different, because
they are insoluble in water and soluble in fat solvents. Cholesterol is a steroid and is
an important component of cell membranes and bile. Gall stones are solid cholesterol.
Lipids are NOT made up of monomers because they are not composed of the same
repeating unit or molecule, but two different molecules.
An example of the two types of molecules (glycerol is equivalent to glycerine.
Tony Molyneux
4
2011
4) Nucleic Acids
Nucleic acids are the macromolecules that make up the genetic material of all
organisms. There are two main types deoxyribose nucleic acid (DNA) and ribose
nucleic acid (RNA).
The building blocks of nucleic acids are nucleotides each consisting of a pentose
sugar arranged in a ring – either deoxyribose or ribose; an organic nitrogen base
and a phosphate group.
(ribose)
The four bases found in DNA are cytosine (C), guanine (G), thymine (T) and
adenine (A). DNA is made up of two strands of nucleotides joined together by
pairing between the bases with A always bonding with T and C with G. In each
strand the nucleotides are joined together by bonding between the phosphate
groups.
RNA is only a single strand of nucleotides joined together by the phosphate
groups. The nitrogen bases are similar to those found in DNA except that thymine
is replaced by uracil (U). The significance of this and of the three types of RNA
(ribosomal RNA, messenger RNA and transfer RNA) will become clear when (if)
you study genetics and protein synthesis.
Tony Molyneux
5
2011
5) Vitamins
Vitamins are a mixed assortment of organic compounds grouped together not because
of any chemical similarity between them but because they are all needed in the diet in
small amounts.
There are fat soluble vitamins (e.g. vitamins A, D, E and K), and water soluble
vitamins (e.g. the B-vitamins B1-thiamine, B2-riboflavine, B5, folic acid, vitamin C).
Some vitamins are important coenzymes i.e. they are essential for ensuring the
enzyme functions properly. For example thiamine is a coenzyme for several enzymes
important in the metabolism of carbohydrates.
Some examples of the differing structures of vitamins
Vitamin B12
riboflavin B2
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Tony Molyneux
6
2011