CHAPTER 1

The Chemical Nature of Cells

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

Study Design

Internal Environment

• Inside a cell is a chemical world.

• Energy is constantly being used or produced in chemical reactions

• Molecules are constantly being created or broken down.

Biochemical Processes

Anabolic Reactions

• Building materials

• Requires energy

• Eg. Photosynthesis

Catabolic Reactions

• Breaking down materials

• Releases energy

• Eg. Cellular respiration

Metabolism

The sum total of all chemical reactions occurring in the body.

• Takes into account all catabolic and anabolic reactions

Chemicals in a Cell

Who are the key players in the chemistry of a cell ?

• Water

• Carbohydrates

• Proteins

• Lipids

• Nucleic Acids

Water H2O• Oxygen and Hydrogen joined by a strong

covalent bond

• Oxygen has a slightly

negative charge while

hydrogen has a slightly

positive charge. • Water molecules are

attracted to each other –

highly cohesive (Remember transpiration)

Definition

Hydrogen bond

A weak bond between two molecules or parts of the same molecule; the hydrogen atom is slightly positive and is attracted weakly towards an atom of N, O or F

Hydrogen Bonds

Water H2O

• Water molecules tend to stick together by H bonds

• Exists in 3 states

• Solid - as temperature drops, molecular movement drops. Below 4°C movement not sufficient to break H bonds, making a lattice structure which is less dense than water as molecules are further apart than when a liquid

• Liquid – H bonds between water molecules constantly breaking and reforming, but the time apart is so brief, it maintains it cohesive nature

• Gas – movement of molecules increases to a point that H bonds no longer hold them together

http://mrtremblaycambridge.weebly.com/p4-simple-kinetic-molecular-model-

of-matter.html

5/11/14

Water H2O - Universal Solvent

• Hydrophilic or Polar substances

• dissolve easily in water

• eg salt

• Hydrophobic or Non-Polar substances

• will not dissolve easily in water

• eg fats

Water H2O - Universal Solvent

Dissolving

• H2O + NaCl H2O + Na+ + Cl-

• Attraction between Na+ and oxygen and Cl- and hydrogen splits the NaCl molecule

pHA measure of hydrogen H+ ions in a solution.

Below 7 – increasing H+ ions

Above 7 – increasing OH- ions

pH 7 Equal H+ & OH- ions

Cells must regulate their pH

pH• pH of body fluids is kept relatively constant because H+ ions are

continually being used and produced in cells

• Cells contain buffer substances that combine with or release H+ ions in a cell to prevent severe shifts in pH of a cell or fluid

Some fluids – eg urine, blood – have a

range for their pH, as the kidneys assist in

maintaining the pH of the blood and body tissues by excreting more or less of

a particular ion

Terms

• Monomer – a molecule or compound that can join together to form a dimer(2), trimer(3) or polymer (many)

• Polymer – a large molecule made of manyrepeated units (monomers)

Monomer Polymer

Glucose Polysaccharide

Amino Acid Protein

Fatty Acid Lipids

Nucleotides Nucleic acids

Condensation Reaction

• the joining of monomers involves the release of water molecules

2 Hydrogen molecules and 1 Oxygen

molecule are released, joining together to

make H2O

• Occurs when a polymer is broken down and a water molecule is used

• The opposite of a condensation reaction.

Hydrolysis Reaction

Definition

Biomacromolecule

• A naturally occurring substance of large molecular weight

http://maxeybio.blogspot.com.au/2013/10/the-building-blocks-of-life.html 5/11/14

Carbohydrates

• Energy rich molecules

• Consist of C (5 or 6 C ring), H and O in a 1:2:1 ratio (C:H:O).

• The basic unit is a sugar molecule

• Can be simple or complex carbohydrates

http://jennifer.nutritiontransition.co.uk/carbohydrates.htm

5/11/14

• Monosaccharides• one subunit (saccharide)

• Examples

• Glucose C6H12O6

• Fructose C6H12O6

Simple Carbohydrates

Glucose and

Fructose are

structural

isomers

http://www.nutriology.com/carbfunctions.php 5/11/14

Simple Carbohydrates

Glucose C6H12O6 Galactose C6H12O6

Fructose C6H12O6

Simple CarbohydratesDisaccharides

• two subunits (saccharides)

• Examples

• Sucrose, Lactose, Maltose …… all C12H22O11

Glucose + Fructose Sucrose + water

C6H12O6 + C6H12O6 C12H22O11 + H2O

Condensation reaction –

water released

Simple Carbohydrates

• Lactose (C12H22O11)

Glucose + Galactose

• Maltose (C12H22O11)

Glucose + Glucose

• Cellobiose (C12H22O11)

Glucose + Glucose

Trivia

Glucose Glucosamine

Galactose Galactosamine

(Building block for

chitin)

(Building block

for cartilage)

Complex Carbohydrates

Polysaccharides

• Eg. Starch, cellulose, glycogen

• All made with glucose monomers (saccharides)

• Glycogen

• Used for energy in animals

• Stored in liver and muscles

• Starch

• Storage of excess glucose in plants

• Insoluble, no effect on diffusion

• Cellulose (C6H10O5) n• Structural polysaccharide in plants

Proteins

• All have C,H,O,N

• Some have S and P

• Makes up 18% of cell contents

• Monomer

• Amino acids (RCH(NH2)COOH)

• R group varies - different A/A

• 20 naturally occurring A/A

• We can make 11 A/A,

• Other 9 from our food

Amino Acids

http://en.wikipedia.org/wiki/Prot

ein_structure 5/11/14

Bonding together• peptide bond forms between the amino group of

one amino acid and the carboxyl group of another

• Water molecule is released – condensation reaction

• A number of amino acids joined together –polypeptide

• Polypeptide chains fold different ways depending on their function

http://www.ib.bioninja.com.au/higher-level/topic-

7-nucleic-acids-and/75-proteins.html 5/11/14

Proteins - Structure

Four steps to structure

Primary Structure

• Linear sequence of amino acids

Secondary Structure

• Folding of chain into

• Alpha Helix (coil)

• Beta Sheet (Pleated)

• Random coil (not alpha or beta)

• Held by hydrogen bonds

Secondary StructureSome examples:

• The major protein of wool is alpha-keratin, a spiral molecule. If the fibre is stretched and the H bonds are broken the fibre becomes extended. If the fibre is then ‘let go’, the H bonds reform and the fibre returns to its original length.

• The major protein of silk is fibroin that is fully extended and lacks the coiling found in the structure of wool. The silk molecules from a beta-pleated sheet. The polypeptide chains of silk are already extended and cannot be extended further.

• Any major protein or portion is called random coiling if it does not fit into alpha- or beta-coiling. The O2 binding protein of muscle, myoglobin, has random sharp turns in its coil. The place of the random coil is often the most active site of a molecule.

Alpha Helix

Beta pleated

Random Coil

http://en.wikipedia.org/wiki/Pancreatic_lip

ase 5/11/14

Proteins - Structure

Tertiary Structure

• Complex shape

• Irregular folding held in place by ionic or hydrogen bonds

• The 3-D shape of a protein is critical for its function – if changed, esp. at its active site, the protein can no longer function

Quaternary Structure

• Two or more tertiary structures join to form a protein

http://biology.tutorvista.com

/biomolecules/proteins.html

5/11/14

Proteins – Quaternary structure

Fibrous Proteins

• Stringy and physically tough

• Actin, Collagen, Elastin, Fibronectin, Keratin, Myosin, Tropomyosin, Tubulin,

Globular Proteins

• Generally spherical or globular

• most hormones, enzymes, antibodies

• Albumins, Alpha globulin, Beta globulin, Cadherin, Fibrin, Gamma globulin, Haemoglobin, Immunoglobins, Myoglobin, Selectin, Serum albumin, Thrombin

http://www.differencebetween.net/scienc

e/health/difference-between-globular-

protein-and-fibrous-proteins/ 5/11/14

Conjugated Proteins

These are proteins which are joined to other molecules

Examples

• Glycoproteins Protein + sugar

• Nucleoproteins protein + nucleic acid

• Haemoglobin Tertiary structure + heme group

http://www.rottentomatoes.com/q

uiz/higher-biology-quiz 5/11/14

Types of Proteins

• Structural – Collagen, Keratin

• Enzyme – Amylase, ATP synthase

• Contractile – Actin, Myosin

• Immunoglobulin – Antibodies

• Hormone – Insulin

• Receptor – Insulin receptors

• Transport - Haemoglobin

Activating Proteins

• Not all enzymes are made ready to work

• They must be activated. Why?

Example

• Pepsinogen Pepsin

• Pepsinogen is inactive

• Pepsinogen + HCl Pepsin

• Pepsin breaks down polypeptides

What is the Proteome ?

Proteome

• The complete array of proteins produced by a cell or organism in a particular environment

Proteomics

• The study of the proteome

http://pharmaceuticalintelligence.com/tag/clinical-omics/

5/11/14

Lipids

• These are : Fats, Oils, Waxes

• All contain Carbon, Hydrogen, Oxygen

• They have little H2O so they carry more energy per molecule than other compounds

• Animals store excess glucose as fat

Lipids - Fats

Insoluble in water (hydrophobic)

• Each molecule comprises

• Fatty acid(s) and

• Glycerol C3H5(OH)3

• Minimum of one fatty acid

and one glycerol (mono, di & tri)

Eg Triglycerides

- Solid Vs Liquid Fats

Triglyceride

Note the lack of oxygen in the triglyceride molecule

Saturated Vs Unsaturated Fats• Saturated Fats:

• All single bonds between C, so it is saturated with H.

• Can be packed close

together – solid at room

temperature.

• Unsaturated Fats:

• Not all C have a H attached due to double bond, so are unsaturated (more than one C double bond = polyunsaturated), creating kinks in the tail.

• Due to the kinks they are not so tightly packed –liquid at room temperature.

Lipids - Phospholipids

Phospholipid molecules have:

• Two fatty acids

• Glycerol molecule and

• Phosphate group

• Includes a variable

group which makes

each molecule different

- Phospholipids are

a major component

of cell membranes

Cholesterol

• A steroid / lipid molecule

• Maintains the fluidity of a membrane

Fats and Energy

• Fats are energy rich molecules

• Per gram, fats store twice the energy as polysaccharides

• Animals store energy as fat

• Plants store energy as polysaccharides

Why the difference?

Hint:

Nucleotides

There are two types

1. Deoxyribonucleic Acid – DNA

2. Ribonucleic Acid – RNA

DNA

• A molecule made of nucleotides

• Each nucleotide is made of three things

• Sugar

• Phosphate group

• Nitrogen base

These are the same

for all nucleotides

http://scienceaid.co.uk/biology/gene

tics/images/nucleotide.jpg

5/11/14

DNA

There are four different nitrogen bases which create four nucleotides

• Adenine

• Thymine

• Cytosine

• Guanine

DNA• Nucleotides are joined into chains

Complementary Bases

• Adenine bonds with Thymine

• Guanine bonds with Cytosine

• This creates a double stranded molecule

To summarise…

How much DNA ?

• The average length of a chromosome is around 5cm.

• That is about 2m of DNA per cell.

• How do you fit it all into such a small space?

Histone Proteins

The DNA strand is wrapped around special proteins called histones to makechromosomes

Why have DNA ?

• DNA controls the functioning of cells by controlling the proteins a cell makes.

• DNA carries the information required to create polypeptide chains.

• Sets of three nucleotides act as a code for one amino acids

http://www.chemicalconnection.org.uk/chemistry

/topics/view.php?topic=5&headingno=13 5/11/14

RNA – Ribonucleic Acid

Like DNA it:

• Is a polymer of nucleotides

• Has the nucleotides G, C, A ,U (Uracil)

Unlike DNA

• RNA is a single strand of nucleotides

• Ribose replaces deoxyribose as the sugar in the nucleotide

• Thymine is replaced with Uracil

• Uracil bonds with Adenine

RNA

Three main types of RNA

• Messenger RNA (mRNA)

• Carries genetic messages to the ribosome for protein synthesis

• Ribosomal RNA (rRNA)

• A structural unit of the ribosome

• Transfer RNA (tRNA)

• Carries amino acids to the ribosome for assembly into a polypeptide