the nature and importance of biomacromolecules in the chemistry of the cell:

– synthesis of biomacromolecules through the condensation reaction – lipids and their sub-units; the role of lipids in the plasma membrane – examples of polysaccharides and their glucose monomer

– structure and function of DNA and RNA, their monomers, and complementary base pairing

- the nature of the proteome; the functional diversity of proteins; the structure of proteins in terms of primary, secondary, tertiary and quaternary levels of organisation

All of these organic molecules always contain the elements Carbon (C), Hydrogen (H) and Oxygen (O). Proteins also contain Nitrogen (N) and sometimes sulfur (S). Nucleic acids have C, H, O, N and Phosphorus (P).

Condensation Reaction A condensation reaction is a chemical reaction in which two molecules or moieties (functional groups) combine to form a single molecule, together with the loss of a small molecule. When this small molecule is water, it is known as a dehydration reaction; other possible small molecules lost include hydrogen chloride (HCl), methanol (CH3OH)or acetic acid (CH3CO2H).

The condensation of two amino acids to form a peptide bond (red) with the

expulsion of water (blue).

The major classes of organic compounds are: Carbohydrates Proteins Lipids Nucleic acids. What is the basic unit for each of these organic molecules? How do the units combine to form complex molecules? Where is each kind of molecule found in the cell? What are the functions of the molecules? Each of the above compounds are complex macromolecules called polymers which are made up of smaller sub-units called monomers.

Carbohydrates This class of compounds uses only carbon, oxygen, and hydrogen and are called carbohydrates

Below are some examples of carbohydrates ( Sugars, starch, cellulose and glycogen): •Glycogen is a complex polysaccharide created in animals for the purpose of storing chemical energy. The small black granules (dots) are glycogen.

•Starch is the long term energy storage molecule for most plants.

Carbohydrates Monosaccharides (one unit) can be joined together

to form disaccharides (two units) and release H2O in the process (condensation reaction)

Monosaccharides and disaccharides are called simple sugars.

Complex carbohydrates are called polysaccharides.

Simple carbohydrates Have one or two sugar units

Their general formula is (CH2O)n.

Monosaccharides

e.g. glucose (C6H12O6) (also called grape sugar)

Monosaccharides Glucose is the product of photosynthesis

Simple long chain sugars form rings

Other monosaccharides include galactose, mannose and fructose (C6H12O6) (see below)

Disaccharides Sucrose (glucose + fructose sucrose + water)

Sucrose (C12H22O11)

Polysaccharides Complex carbohydrate

Examples

Starch

Cellulose

Glycogen

Polysaccharides Glycogen

form of energy storage in animals

contains a protein as a starting point

circular in shape

Protein

Polysaccharides Starch

Main form of sucrose storage in plants

Polysaccharides Cellulose

structural polysaccharide

formula similar to starch

every plant cell wall contains cellulose

Proteins

very large molecules fold and form complex shapes four different levels of organisation thousands of different proteins in each cell example

casein in milk (C708H1130N180O224S4P4)

Primary shape linear sequence of amino acids (monomers) different proteins have different sequences of amino

acids 20 different naturally occurring amino acids

Primary shape two amino acids join together to form a dipeptide many amino acids join together to form a polypeptide

Condensation Reaction

Primary shape

Primary shape

Secondary shape

Amino acid chain can fold in three different ways

Hydrogen bonds (weak) form between units to stabilize shape

Alpha helix (α-helix)

Beta pleated sheets (β-pleated sheets)

Random coils

Secondary shape

Alpha helix (α-helix)

Secondary shape

Beta pleated sheets (β-pleated sheets)

Secondary shape

Random coils

Tertiary structure

Quaternary structure

Proteins….

Examples of proteins include: hormones acting as messengers; enzymes speeding up reactions; cell receptors acting as ‘antennae’; antibodies fighting foreign invaders; membrane channels allowing specific molecules to enter or leave a cell; they make up the muscles for moving; let you grow hair, ligaments and fingernails; and let you see (the lens of your eye is pure crystallised protein).

If there is a job to be done in the molecular world of our cells, usually that job is done by a protein.

CATALASE

An enzyme which removes Hydrogen peroxide from your body so it does not become toxic

A protein hormone which helps to regulate your blood sugar levels

Proteins…. Proteins are large complex molecules

built of monomers called amino acids. The amino acids are held together by peptide bonds, so proteins are known as polypeptides.

There are usually multiple peptide chains joined together e.g. Haemoglobin has 4 polypeptide chains comprising it.

The polypeptide chains are then folded into a particular shape unique to that type of protein

Proteins can be fibrous or globular; fibrous proteins normally are involved in body structures (structural proteins), globular proteins are normally biochemical.

Globular Proteins

The globular proteins have a number of biologically important roles. They include:

Cell motility – proteins link together to make filaments to make movement possible.

Organic catalysts in biochemical reactions – enzymes that speed up reactions.

Regulatory proteins – hormones transcription factors.

Membrane proteins – MHC markers, protein channels, gap junctions.

Defence against pathogens – poisons/toxins, antibodies.

Transport and storage – haemoglobin, myosin.

Structural Proteins Hair (keratin)

Fingernails (keratin)

Skin (collagen)

Muscles (myosin, etc)

Cartilage (glycoprotein: proteins attached to carbohydrates

Ligaments (collagen plus glycoproteins)

Eye cornea (collagen/keratin)

Conjugated Proteins Some proteins have chains of amino acids conjugate

with other groups.

e.g. nucleoproteins – they comprise a molecule containing both protein and nucleic acid

haemoglobin – four molecules of protein, each conjugated with an iron molecule

Inactive to active molecules Insulin (a hormone) when initially produced is

inactive.

It is produced as a single chain of amino acids with the folds held together by three disulfide bonds.

It is activated by the removal of a length of the amino acid chain to leave two chains of amino acids held together by three disulfide bonds.

Inactive to active molecules

Proteome The complete array of proteins produced by a single

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

The study of the proteome is called proteomics.

No protein acts in isolation; therefore scientists are moving away from studying single proteins

Lipids Lipids (oils and fats) are another class of organic

compounds built from oxygen, hydrogen, and carbon.

Lipids have little affinity for water.

Lipids have a structural role, for example the plasma membrane is composed to a large part by phospholipids.

Lipids also have biochemical role, for example some hormones are made of lipids (e.g. steroids).

Lipids are the long term energy storage molecule for all animals.

Lipids carry more energy per molecule than either carbohydrates or proteins.

Lipids Fats are composed of the subunits fatty acids and

glycerol.

Triglycerides are a common form of fat.

Triglycerides have a single glycerol with three fatty acid chains attached

This diagram represents a triglyceride, a simple and common form of fat

Triglycerides The fatty acid chains have no affinity for water and are

insoluble in water

They are called hydrophobic (hate water)

Some common formulae for fats are:

stearin (C57H110O6)

palmitin (C51H98O6)

linolein (C57H98O6)

Lipids with straight fatty acid chains pack closely together and are solid at room temperature.

Lipids with bent fatty acid chains are further apart and are liquid at room temperature.

Phospholipids Consists of two fatty acid chains attached to a glycerol

molecule with a a phosphate molecule also attached.

Other small molecules may also attached to the phosphate

Phospholipids are a major component of cell membranes.

Hydrophilic

Hydrophobic

Nucleic acids Very large macromolecules concerned with the storage

and transmission of inherited information and protein synthesis.

Made up of repeating units called nucleotides.

Two types:

deoxyribonucleic acid (DNA)

located in the nucleus of eukaryotes

ribonucleic acid (RNA).

formed using a DNA template (transcription) in the nucleus and used to make, in conjunction with ribosomes, proteins in the cytosol (translation).

Nucleic acids Each nucleotide unit, or monomer, is made up of

a sugar (deoxyribose or ribose) part

‘deoxy’ means ‘missing an oxygen molecule’

a phosphate part

a Nitrogenous (N) base

Deoxyribonucleic acid made of two sugar – phosphate backbones

has four different N-bases

Adenine (A)

Thymine (T)

Cytosine (C)

Guanine (G)

A binds with T and G binds with C

Complementary base pairs

Forms a double helix

DNA double helix is 2 nm wide and one complete turn of the helix is 3.4 nm

The four DNA nucleotide Nitrogenous bases

Ribonucleic acid Three different types of RNA

messenger RNA (mRNA) – carries genetic message from nucleus in eukaryotic cells to ribosomes in the cytosol

ribosomal RNA (rRNA) – with particular proteins makes up part of the ribosome

transfer RNA (tRNA) – carry amino acids to ribosomes where they construct proteins

The strands of nucleotides in each of the RNAs fold differently