The chemical context of life

Chemistry of LifeElement - any substance that is comprised of one

type of atom and cannot be broken down into another substance.

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ExamplesHydrogenOxygenCarbonGoldSilver

Atom - the smallest unit of matter that still retains the properties

of the element.

Atoms contain the same amount of

protons and electrons (net charge = 0)

Nucleus - center of the atom containing protons and neutrons.

• Proton - heavy positively charged particle.• Neutron - heavy neutral particle.Orbitals - area around the nucleus containing electrons.• Electron - light negatively charged particle.

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Isotopes - atoms of the same element with differing numbers of neutrons

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Chemical bonds

• Ionic bonds - formed through the transfer of electrons between two atoms. The bond is due to the attraction of oppositely charged ions (atoms with a negative or positive charge).

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Chemical bonds

• Covalent bonds - formed through the sharing of atoms between atoms.

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Mixture - a substance composed of two or more elements or compounds which are physically mixed together, but not chemically combined.

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Solution - mixture of two or more substances in which the substances are evenly distributed.

• Solute - substance that is dissolved.• Solvent - substance in which the solute is dissolved.

http://intro.chem.okstate.edu/ChemSource/Solutions/image3QT.JPG

Water is the solvent of life

Chemical elements and water

• Elements of life (most common)– Carbon, hydrogen, oxygen

• Other necessary elements & function– Nitrogen (amino acids), – Calcium (bones, teeth), – Phosphorous (ATP, DNA), – Iron (hemoglobin), – Sodium (nerve transmision)

Like no other common substance, water exists in nature in all three physical states:

– as a solid– as a liquid– as a gas

Properties of water

• Transparency:– Light can easily pass through– Reach inside cytoplasm (water) to

• chloroplast, retina

– Reach organisms in water

• Cohesion:– Water molecules stick together (surface)

• Water can be pulled up trees• Small animals can live on water surface (mosquito)

Properties of water

• Solvent Properties (universal solvent)– Allow substance carried in water

• blood, sap

– Thermal properties (large heat capacity)• requires lg. Amounts of energy to heat• remains stable temperature

– fish, blood (carry heat to cold parts)

Properties of water

• Thermal properties (cooling from evaporation)– evaporate at temperatures below boiling

• heat energy required to break hydrogen bonds, taken from liquid water cooling it down

Properties of Water

• Cohesion - attraction between molecules of the same substance.

• Adhesion - attraction between molecules of different substances.

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Oceans and lakes don’t freeze solidbecause ice floats

Cohesion:Water molecules stick together

surface tension

Cohesion:water molecules can move great

distances

Water and Organismsplants and animals

• Coolant: sweat, blood• Transport medium: blood, sap• Habitat

• Polar molecules are also soluble in water because they can also form hydrogen bonds with water.

• Even large molecules, like proteins, can dissolve in water if they have ionic and polar regions.

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 3.8

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 3.7

Significance of water to living organisms

• Coolant: sweat• Transport medium: blood, sap• Habitat:

Biochemistry

• The chemistry of Life• Bio-molecules

– Proteins– Carbohydrates– Lipids (fats, membranes…)– Nucleic Acids (DNA…)

Trace elements

May be needed inonly small amountsbut may causeharm if absent(iodine)

goiter

Organic Compounds

• Contain carbon & found in living organisms– Inorganic Carbon compounds: CO2,

– Many inorganics found in living organisms• Iron in blood

Macromolecules (polymers) are formed from smaller building blocks called monomers.

Polymer (“chain”) Monomer (“links”)

carbohydrate monosaccharides

protein amino acid

nucleic acid nucleotide

Macromolecules - large molecules formed through

the joining of many monomers (small molecular units) into polymers (larger

molecules).

• We will be studying 4 important macromolecules: Carbohydrates, lipids, proteins, nucleic acids.

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Carbohydrates - sugars which contain C, H and O and are the main energy source for all living things (some

organisms also use carbohydrates for structural purposes).

• Monosaccharides - single sugar molecules (glucose, galactose).

• Disaccharides - carbohydrates composed of two sugar molecules (lactose).

• Polysaccharides - large carbohydrates composed of many monosaccharide monomers (starch, cellulose, glycogen).

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Condensation Reaction: monomers form chains– Remove water to form bonds– Protein synthesis– Fatty acid synthesis

1 2 3

Unlinked monomer

Removal ofwater molecule

1 2 3 4

Longer polymerFigure 3.3A

Short polymer

• Hydrolysis - reverse process of condensation polymers are broken down to monomers– Using water

1 2 3

Addition ofwater molecule

1 2 3

4

• Proteins are involved in – cellular structure– movement– defense– transport– communication– hair– Enzymes

PROTEINS

Proteins have levels of organization.

Proteins can be denatured.

• amino acids link– dipeptides– polypeptide chains (Proteins)

• The bonds are called peptide bonds

Protein Synthesis

Dehydrationsynthesis

Figure 3.13

Carbohydrate Polymers

• Monomer: glucose (energy)– Monosacccharide

• Polysaccharides:– Glycogen: energy storage

• Animal muscles

– Starch: plant energy storage– Cellulose: plant structure

The structure of glucose

A disaccharide is made by linking two monosaccharides together.

glucose + fructose = sucroseglucose + galactose = lactose

Examples

• Monosaccharides:– Glucose & Fructose

• Disaccharides:– Sucrose (glucose + fructose)– Maltose (glucose + glucose)

• Polysaccharides– Starch– Gycogen

Functions of Lipids (fats)

Energy storage:

Insulation:

Protection:

Membranes (phospholipids):

Glycerol & fatty acid

Structure of Triglycerides

Enzymes

• Enzyme– Protein– Biological catalyst– Example: amylase

• Active Site– Location where substrate (reactant) binds

Proteins - macromolecules that contain N, H, O and C. Are comprised of amino acid (the order and combination of these

amino acids determines the role of the protein) subunits.

Types of proteins:• Enzymes - carry out the

chemical reactions in the organism (lactase, DNA helicase, catalase).

• Structural Proteins - aid in building muscles, bones and other components of the organism (keratin, collagen).

• Functional Proteins - assist in organism’s daily functioning such as messengers (hemoglobin, insulin), defense or transport.

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Lock and Key Model (enzyme-substrate specificity)

Factors influencing enzyme activity• Optimum pH

• Optimum Temperature

Please diagram

Effects of variables on enzymes

• Temperature• pH

Denaturation

• Structural change in protein– Loss of functionality

I. Why Study DNA Replication?

1) To understand cancer

2) To understand aging

3) To understand diseases related to DNA repair

Werner’s Syndrome

Keith Richards (of the Rolling Stones)

Example of premature agingNOT caused by a hereditary disease

Nucleic Acids - macromolecules that contain H, O, N, C and P. The 2 kinds of nucleic acids are DNA and RNA which store and

transmit genetic information (the “blueprint” to make you).

• Comprised of nucleotide (5-C sugar, phosphate group and nitrogenous base) monomers.

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