Chapter 1: the Chemical Nature of the Cell

Chapter 1: The Chemical nature of the Cell

The Cell theory states that:

·  all living things are composed of cells and the products of cells

·  cells are the basic functional unit of living things

·  all cells arise from pre-existing cells

Each cell is a highly organised assembly of atoms and molecules, which interact in thousands of chemical reactions. Cells can be likened to chemical factory.

The cell – a chemical factory

Matter has mass and takes up space; it consists of particles called atoms. Each atom has a nucleus containing protons (+) and neutrons (0). Negatively charged electrons (-) spin around the nucleus in regions of space known as orbitals.

All living things are composed of chemicals. These chemicals fall into two categories:

1.  Organic chemicals are complex carbon containing molecules

§  Proteins

§  Carbohydrates

§  Lipids

§  Nucleic acids

2.  Inorganic chemicals do not contain carbon in a complex form

§  Water H2O

§  Carbon dioxide CO2

§  Oxygen O2

§  Mineral ions such as: K+,Cl-,Mg2+,NO3- etc

Water is a polar molecule, with negatively and positively charged ends.

This property means that water can interact with other charged particles, such as polar molecules or ions (e.g. Na+, NO3- etc).

Polar substances can form H bonds with polar molecules of water and so dissolve – they are called hydrophilic (water loving)

Non-polar substances will not dissolve in water because they cannot form H bonds with water – they are hydrophobic.

Rule for substances to form a solution: ‘like dissolves like’

Biological macromolecules

Biological macromolecules (or biomacromolecules) are large molecules that have important functional and structural roles in cells.

There are 4 classes of biomacromolecules:

1.  Proteins

2.  Nucleic Acids

3.  Carbohydrates

4.  Lipids

Each kind of biomacromolecule has characteristics or properties that make it effective for carrying out its particular function: that is the structure and properties suit the purpose.

The synthesis of biomacromolecules

Autotrophs: organisms that are able to synthesise their own biomacromolecules from inorganic compounds.

§  Plants and algae à photosynthesis

§  Certain species of bacteria use the energy released from areas of geothermal activity à chemosynthetic bacteria

Heterotrophs: synthesise their own biomacromolecules from organic molecules they have ingested.

§  animals

§  fungi

§  majority of bacteria

§  many protists

Making a polymer (polymerisation)

Biomacromolecules are synthesised inside cells. This involves linking smaller repeating units; each called a monomer, to form large chains called polymers.

This process is known as polymerisation.

Carbohydrates, proteins and nucleic acids are made up of interlinked subunits, and therefore are called polymers.

Monomers link together when the hydroxyl (-OH) group of one monomer reacts with the hydrogen of another monomer, forming a water molecule. This reaction is called condensation polymerisation.

Carbohydrates

·  Most common compounds in living things

·  Composed of C, H and O in ratio: nCH2O

·  Classified as:

·  Monosaccharides (simple sugars)

·  Disaccharides

·  Polysaccharides

·  Important source of energy

·  Important structural component (cellulose) in plants

·  Can combine with other substances to form important compounds e.g. Glycoproteins (= carbohydrate + protein)

The main polysaccharides:

Starch: branched chains of glucose molecules used as a storage molecule in plants

Glycogen: branched chains of glucose used as storage molecule in animals

Cellulose: composed of glucose molecules, forms part of cell wall of plants

Chitin: forms the basis of the insect exoskeleton and cell walls of fungi. Made up of chains of modified glucose molecules

Lipids

·  diverse group of molecules that include fats and oils, phospholipids, terpenes, waxes, glycolipids and steroids

·  They are usually hydrophobic in water

·  Structural component of membranes – phospholipid bi-layer

·  contain C,H and O (less O than carbohydrates), and may also contain P and N

Functions of lipids

o  Energy source (X 2 [CH2O])

o  Specific biological functions, such as transmission of chemical signals within and outside cell

o  Oils (such as found in sunflower and canola seeds) store energy and matter for new growth

o  Fats in animals promote insulation, and acts as food reserve (e.g. polar bears); and protect vital organs such as the kidneys (perirenal fat) and heart (pericardial fat)

o  Terpenes in plant essential oils: give characteristic odours and flavours

o  Waxes and cutins

o  Steroids: includes steroid hormones, bile salts and cholesterol

Structure of Lipids

Lipids are classified according to their solubility, which inturn depends on their shape and intermolecular bonding. Lipid molecules have large non-polar regions so are hydrophobic and insoluble in water.

1.  Triglycerides: fats and oils of plants and animals are composed of triglyceride molecules. These molecules consist of three fatty acids attached to a glycerol backbone.

a.  Saturated fatty acids (animal fat):

·  Single bond between carbon atoms and maximum number of H atoms attached to each C.

·  Solid: examples include lard, butter, fats and blubber

b.  Unsaturated fatty acids (plant):

·  Double bonds between some C atoms. Do not have maximum number of H atoms with C atoms

·  Oils: example include canola, sunflower, olive and aromatic oils of plants

Lipids in the membranes of cells

1.  Phospholipids: form when a phosphate group is added to the glycerol rather than a third fatty acid. The phosphate region is hydrophilic, whereas the fatty acid tails are hydrophobic so these molecules form lipid bi-layers that make up the cell membranes.

2.  Glycolipids: form when a carbohydrate attaches to the glycerol backbone rather than a third fatty acid. Important in communication as found projecting from cells. Detect and bind with signalling molecules.

3.  Cholesterol: component of cell membranes (except inner membrane of mitochondria and chloroplasts) and of myelin around nerves. Belong to a group of lipids known as steroids.

Important for/as:

§ maintaining level of firmness in cell membrane

§ starting point for synthesis of steroid hormones: vitamin D, testosterone and oestrogen

§ bile synthesis

Proteins

Consist of:

·  structural proteins: a vital structural component of all cells, and hence body tissues, organs and systems

·  functional proteins: the intracellular and extracellular enzymes, hormones and many other substances.

The basic building blocks of proteins are amino acids.

Amino Acids

·  There are 20 amino acids

·  All amino contain:

o  An amino (amine) group (NH2)

o  A carboxylic acid group (COOH)

o  R group

·  The difference in the R group distinguishes one amino acid from another and determines its properties

·  Some R groups give the protein molecule polar regions, and other groups make regions non-polar.

·  Non-polar hydrophobic regions are tucked away within the protein, away from water molecules; whereas polar hydrophilic regions tend to be on the surface of the protein exposed to water molecules

From amino acids to proteins

The process of synthesising protein molecules can be explained by the 4 levels that give rise to the final structure:

1.  Primary structure:

·  the amino acid sequence in the polypeptide

·  amino acids bond together in the process of condensation polymerisation and each bond between 2 amino acids is termed a peptide bond

2.  Secondary structure:

·  refers to the coiling and folding the polypeptide chain undergoes once it is formed

·  occurs due to H bonding occurring between particular AA

o  α – helices: tight coils

o  β – sheets: folding forms

o  random loops: unchanged

·  β – sheets and random loops form the basis of the active site in enzymes

3.  Tertiary structure

·  Hydrophilic R groups attract other hydrophilic R groups according to the ‘like attracts like’ rule

·  This interaction causes the polypeptide chain to fold, coil or twist into the proteins functional shape or conformation.

·  The interaction between the R groups of amino acids result in H bonds, ionic bonds or disulfide bridges between adjacent cysteine acids.

·  It is the tertiary structure of the protein which determines its function

4.  Quaternary structure

·  Refers to biologically active proteins that consist of more than on polypeptide chain; held together by the interactions between atoms in the separate polypeptide chains. Antibodies consist of 4 PP chains held together by disulphide bonds

Nucleic Acids

·  large polymers made up of nucleotides

·  carry genetic or heredity information in cells (DNA and RNA) and involved in protein synthesis (RNA)

·  Deoxyribosenucleic acid (DNA) and Ribonucleic acid (RNA) are the two nucleic acids

·  DNA is double stranded, RNA is single stranded

Nucleotides

·  monomers of nucleotides

·  Each nucleotide has:

o  5 carbon sugar (ribose in RNA; deoxyribose in DNA)

o  Negatively charged phosphate group

o  An inorganic N containing base

o  There are 4 bases in DNA:

§  Adenine (A)

§  Thymine (T)

§  Guanine (G)

§  Cytosine (C)

·  In each nucleotide strand the sugar molecule of one nucleotide binds with the phosphate group of the next nucleotide, leaving the base sticking out from the sugar

·  Each nucleotide links together in 5' to 3' to form long polymers; that is the phosphate group attached to the 5' carbon of one ribose monomer bonds to the hydroxyl group attached to the 3' of another ribose monomer forming a phosphodiester bond

·  In this reaction the H from the sugar and hydroxyl from the phosphate ‘condense’ out as a water molecule

DNA

·  H bonds between complementary bases in each strand, create the rungs in the ladder, which link the two nucleotide strands together

o  A:T

o  G:C

·  This forms a twisted ladder or spiral staircase; the double helix

RNA

·  single stranded

·  ribose sugar has one less oxygen than deoxyribose in DNA

·  T (in DNA) replaced with Uracil (U)

·  mRNA carries gene information to ribosomes in cytoplasm (either free floating or attached to ER (Rough ER); coding for protein synthesis

The function of DNA

·  Segment of DNA on a chromosome that codes for a particular protein = GENE

·  Each sequence of three bases forms a triplet code; which in turn codes for a particular amino acid

·  mRNA takes the genetic information contained in the base sequence of a gene, from the nucleus to a ribosome

·  Here the base sequences are ‘read’ three bases at a time; that is in codons

·  The ribosomes are composed of proteins + rRNA

·  The incoming amino acids are attached to tRNA

·  Each tRNA has an anticodon that is complementary to a specific codon on mRNA

·  The amino acids then interlink in precise sequence determined by the triplet code on the mRNA