Comparison of Abilities

Human eye

Light microscope

Transmission Electron Microscope

Levels of OrganisationLiving Organisms

systems

organs

tissues

cells

Biomolecules

Organic

carbohydrates proteins lipids nucleic acids

Inorganic IonsWater

(inorganic)

Levels of OrganisationBiomolecules

Organic

carbohydrates proteins lipids nucleic acids

Inorganic IonsWater

(inorganic)

simple sugars amino acids fatty acids nucleotides

glycerol

The nature of the cell

Intracellular aqueous environment

Extracellular aqueous environment

Cell boundary or plasma membrane

• Insoluble• Semi-permeable

What all cells need to do

Make specific Biomacromolecules

Control and regulate chemicalReactions

Produce energy to drive Chemical reactions

Take in small moleculesProduce useful products for export from the cell

Receive and respond to

chemical signalsRemove waste

products

Grow, reproduce and pass on genetic information to the next generation of cells

Cell structure needs to meet the needs of molecules

• The processes within a cell are due to molecules interacting with each other

• Molecules need to move into and around the cell at a certain rate to reach sites of specific activity

• Molecules need to be in adequate concentrations if chemical reactions are going to occur at the right rate

• Cell structure needs to facillitate the movement of molecules and maintain them in adequate concentrations so reactions can occur to maintain cell functioning

Why size and shape matters• Cells need to maximise their surface area to ensure the rapid

movement of of molecules. This becomes a problem as the volume of the cell increases. Size does matter!

Shape A B C

L x W x H 1x1x1 10x10x

10

10x100x1

Surface Area (6a2)

6 600 2200

Volume (a3)

1 1000 1000

SA:V

(SA/V)

6 0.6 2.2

A

B

C

So how do organisms deal with having cells with an insufficient

SA:V to facilitate the transport of molecules?

• ORGANELLES!• Each of the intracellular organelles will be

studied this semester, but the emphasis will be on their various functions, and how they compensate for the relatively large volumes of eukaryotic cells

• Prokaryotic cells being smaller, do not have this necessity

Animal Cells

Plant Cells

The functions of organelles:

• Movement of substances across the plasma membrane

• The protein secretory pathway

• Photosynthesis

• Cellular respiration

• The signal transduction pathway

• Aspects of the immune response

• Packaging and export of cellular products

A little chemistry …

Covalent bonding

involves atoms joining to form

molecules

In order to form a stable molecule, each atom must share sufficient

electrons in order to result in a full outer

shell

If an atom only has one shell of electrons, 2 is sufficient to fill it

The second shell and onwards all require a minimum of 8

electrons in order to achieve stability

Oxygen has an atomic

number of 8

Hydrogen has an atomic

number of 1

A little chemistry …… and a hydrogen

atom contains 1 proton and 1 electron

So an oxygen atom contains 8 protons

and 8 electrons

A little chemistry …

When oxygen and hydrogen bond, the

hydrogen is stable, it has a full outer shell

… but the oxygen is still left short one

electron

A little chemistry …

This allows an additional hydrogen

atom to bond with the oxygen

… thus creating a stable molecule

A little chemistry …

Thus we achieve the structure of a water

molecule: One oxygen atom bonded

to two hydrogen atoms

How water interacts with other substances

• If a substance is composed of charged atoms, these will be attracted to the negatively charged oxygen atom or the positively charged hydrogen atoms. These are known as polar or hydrophyllic.

• If a substance has no charge, then it will not be able to interact with the water molecules. These are known as non-polar or hydrophobic.

pH

• pH is simply a measure of the number of hydrogen ions vs the number of hydrogen ions in a solution.

• More H+ = lower pH (0-6) = acidic• More OH- = higher pH (8-14) = basic• Equal H+ and OH- = pH 7 = neutral

Water molecules are cohesive -> they form hydrogen bonds

Substances that dissolve in water are called hydrophilic or polar

Substances that are insoluble in water are called hydrophobic or non-polar

Monomers: Polymers:

Sugars Carbohydrates (Polysaccharides)

Amino Acids Proteins

Fatty acids & glycerol Lipids

Nucleotides Nucleic Acids

From molecules to biomacromolecules• Biomacromolecules are giant molecules.

They play essential roles in both the structure and function of cells

• Cells import water, mineral ions and a host of small organic molecules like simple sugars, fatty acids and amino acids.

• In contrast, cells can only acquire biomacromolecules by making them. They are made in a condensation reaction.

Glucose, Fructose Sucrose, LactoseStarch, Glycogen & Cellulose

hexose shape pentose shape

Mostly ends in –ose

C, H, O => organic

Condensation reaction

• Monomers are flanked by a hydroxide and a hydroxyl group• When the reaction is facilitated by an enzyme, they will

come together in the correct alignment

The Condensation Reaction

MonomerH - O O - H MonomerH - O O - H

• The correctly aligned interaction of the hydroxide group of one monomer with the hydroxyl group of another will cause the molecules to join, with water as a by-product

The Condensation Reaction

MonomerH - O O - H MonomerH - O O - HH2O

• The end result is a larger molecule, with its two monomers joined by an oxygen bridge

The Condensation Reaction

MonomerH - O MonomerO O - H

• This is simply the opposite to a condensation reaction• When an enzyme exerts pressure on the large molecule, the oxygen

bridge is put under stress• This allows water to enter the bond

Hydrolysis

MonomerH - O MonomerO O - HH2O

• One of the hydrogen atoms attaches to the oxygen, whilst the other oxygen and hydrogen attach to the other monomer in the form of a hydroxyl group.

• The larger molecule has been divided in to two smaller subunits

Hydrolysis

MonomerH - O O - H MonomerH - O O - HH2O

Energy storage• In Animals

• Food broken down to glucose• Excess glucose stored as glycogen• Excess glycogen stored as fat

• In Plants• Glucose produced via photosynthesis• Glucose combined with fructose to form sucrose• Sucrose transported to other parts of plant• Excess sucrose stored as starch

Lipids• Comprised of two types of subunits:

• Fatty acids• Glycerol

• Molecules contain less water than carbohydrates, so can contain more energy

• Thus lipids are a very important energy store for animals

Triglycerides

Phospholipids

How the monomers interact• The reason that lipids are not polymers is that

there is only one gycerol subunit with three carbon atoms on to which the fatty acid chains can attach.

• In triglycerides, one chain attaches to each of the three carbon atoms

• In phospholipids, one of the carbons is taken up by a phosphate group, therefore there is only space for two fatty acid chains

Other than phospholipids, which contain P, most others will only contain C, H & O

DNA: deoxyribonucleic acidRNA: ribonucleic acid

SUGAR

PHOSPHATE

Nucleic acids contain C, H & O in addition to N & P

DNA:Adenine (A)Thymine (T)Cytosine (C)Guanine (G)

RNA:Adenine (A)Uracil (U)Cytosine (C)Guanine (G)

Differences between DNA & RNA

DNA RNA

A, C, G, T A, C, G, U

Paired strands Single strand

H+ at 2’ OH- at 2’

Summary of animation• mRNA copy of gene on DNA made in nucleus

• mRNA swims out to ribosome (made from rRNA) in cytoplasm

• Ribosome reads code, for every 3 base pairs, 1 amino acid is added to the chain

• Amino acids are brought to the ribosome by tRNA transfer molecules

• Once process is complete, protein is released from the ribosome.

3 groups: Amino group, Carboxyl group & R-group

When joined together they form peptide bonds

Aside from the C, H, O & N in the base molecule, the R group may also contain S & P

Protein structure• Primary structure

• The linear sequence of amino acids

• Secondary structure• The type of peptide bond determines how sections of the

protein fold – spiral helix / pleated sheet / random coils• Shape reinforced by additional H bonds

• Tertiary structure• Eventual 3D shape formed by folding• Shape reinforced by additional H bonds

• Quanternary structure• When a protein is formed by the interaction of 2 or more

polypeptide chains

Primary structure: Secondary structure:

Tertiary structure:

Quaternary structure:

Active vs inactive proteins• Not all proteins are produced in an active form• Often they will need to be activated by a specific

enzyme (also a protein)• In the case of the hormone insulin, it will only be

activated when a disulphide bond is broken in the active site of the activating enzyme, thereby releasing one of its 3 polypeptide chains

• So in our study of proteins, knowing the action of one is often not helpful, we need to know the make-up of the organism’s entire proteome.

Biomacromolecule

Type of bonding

Carbohydrates Glycosidic bond

Lipids Ester bond

Nucleic acids Phosphodiester bond

Proteins Peptide bond