Unit 2

Molecular Biology

Essential Ideas

2.1 - Living organisms control their composition by a complex web of chemical reactions

Basic Background

• Organic chemistry = carbon• Biochemistry – attempts to explain the

chemical characteristics of living organism

• 4 categories of organic compounds– Carbohydrates– Lipids– Proteins– Nucleic acids

Basic Background

• Water is the medium of life• Proteins act as enzymes• Genetic information stored in DNA• Compounds of carbon, hydrogen and

oxygen are used to supply and store energy

Section 2.1 Molecules to MetabolismUnderstandings:• Molecular biology explains living processes in terms

of the chemical substances involved.• Carbon atoms can form four covalent bonds, allowing

a diversity of stable compounds to exist.• Life is based on carbon compounds, including

carbohydrates, lipids, proteins, and nucleic acids. • Metabolism is the web of all the enzymes-catalysed

reactions in a cell or organism.

Understandings continued:• Anabolism is the synthesis of complex molecules

from simpler molecules, including the formaion of macromolecules from monomers by condensation reactions.

• Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

Molecular biology – the chemistry of living organisms

Interactions between organic moleculesExample of Metabolism Insulin (protein hormone)

Facilitates the movement of glucose from the bloodstream into the cell’s interior

Interacts with protein channels to open them Glucose moves high to low

Molecular biology – the chemistry of living organisms

Insulin cont. Why can’t glucose go through the phospholipid

bilayer? Polarity

Insulin and channels are both proteinsCoded by DNA

What category of organic molecule is glucose

Each organic molecule is

represented

Carbon-based life

Are all compounds that contain carbon organic?

Atomic # of carbon is ______Carbon has ___ valence electronsCarbon always forms 4 __________ bonds (share)Covalent bonds are strong bonds.

Carbon dioxide

Challenge yourself

Read through the following example of molecular interactions leading to a physiological response. Try to classify each of the named molecular components as a carbohydrate, lipid, protein or nucleic acid.

Reading

When a predator, such as a snake, catchers and eats a small rodent, one of the main sources of nutrition that the snake is consuming is the muscle of the prey animal. That muscle is primarily composed of two molecules: actin and myosin. When the ingested muscle reaches the intestines of the snake, enzymes (such as trypsin) help the snake digest the actin and myosin into amino acids. Other enzymes (such as lipase) help the snake digest the triglyceride fats within the adipose tissue of the rodent.

Biochemical compounds important to living organisms

• nucleotides• Amino acids

• Glycerol • Fatty acids

• monosaccharides

Carbohydrates(C, H, O)

1:2:1

Lipids(C, H, O)

Nucleic Acids

(C, H, O, N, P)

Proteins(C, H, O, N &Sometimes S)

Common categoriesCategory Subcategory Example molecules

Carbohydrates Monosaccharides Glucose, galactose, fructose, ribose

Disaccharides Maltose, lactose, sucrose

Polysaccharides Starch, cellulose, chitin

Proteins Enzymes, antibodies, peptide hormones

Lipids Triglycerides Fat stored in adipose cells

Phospholipids Bilayer in cell membranes

Steroids Some hormones

Nucleic acids DNA, RNA, ATP

Skill: Drawing Molecules

Glucose:

Skill: Drawing Molecules

• Ribose:

Skill: Drawing Molecules

• Saturated Fatty Acid

Skill: Drawing Molecules• Generalized amino acid:

Skill: Identification of biochemicals as carbohydrates, lipids, proteins and nucleic acids.

Metabolism: reactions controlled by enzymes

• all the reactions within all of the cells (and fluids such as blood or digestion in the small intestines) comprise the metabolism of the organism.

• Catalyzed by enzymes

Factors determining if reactions occur

• Identity of the colliding molecules• Orientation of the colliding molecules

(where they hit each other)• The speed of the molecules when they

collide

Examples of a reaction

• Creating ATP – cellular respiration• Replication of DNA• Synthesis of RNA• Synthesis of proteins• Photosynthesis

Metabolism

Anabolism• Synthesis of complex

molecules• Require energy (ATP)• Condensation/dehydration

synthesis• Examples:

– Protein synthesis– DNA synthesis– Photosynthesis

Catabolism• Breakdown of complex

molecules• Release energy• Hydrolysis• Examples

– Digestion of food– Digestion of dead organic

matter by decomposers

Application:Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.

• Urea (organic) was discovered in urine – 1720’s

• It was widely believed that organic compound could only be made with help of a “vital principle” (vitalism)

• Vitalism = living organism and inanimate things differed fundamentally because living organisms contained a non-physical element.

Application

• Urea is in nitrogenous waste• In humans– Produced in the liver– Enters the bloodstream– Filtered out by the kidneys– A component of urine

Application

• Wohler – German physician & chemist– 1828

• Mixed cyanic acid and ammonium– Crystalline substance formed

• Crystals were urea• Organic molecule synthesized from

inorganic substances

Work is published

Vitalism is questioned as

scientific theory

Click here

Importance

• Scientific theories undergo modifications• Important discoveries are made

accidentally• Scientific discovery is not always

appreciated immediately for its importance

2.2. Water

• Understanding:– Water molecules are polar and

hydrogen bonds form between them.– Hydrogen bonding and dipolarity

explain the cohesive, adhesive, thermal and solvent properties of water.

– Substances can be hydrophilic or hydrophobic

Structure of Water

• Water is the solvent = aqueous• What type of bond is between the oxygen

and the hydrogen atoms of water? – Polar covalent bond

• Because of that bonding, it has – Dipolarity

• And thus short-lived hydrogen bonds

Cohesion

• Same type of molecules• Why– Water forms into droplets when it splits– Water has a surface tension– Water is able to move a water ‘column’ in

the vascular tissues of plants

Adhesion

• Attraction between two unlike molecules• Water is attracted to cellulose• Leads to capillary action

Application • Use of water as a coolant in sweat.

Thermal properties• High specific heat– Water can absorb or give off a lot of

heat without changing temp much– Ocean/beach day vs night

• High heat of vaporization– Water absorbs a lot of heat when it

evaporates

Water evaporates

through stomata – cools plant

Examples

• Basilisk lizards can run on water

Application

• Modes of transport of glucose, amino acids, cholesterol, fats, oxygen, and sodium chloride in blood in relation to their solubility in water.

Solvent properties

• Water is solvent to other polar molecules– Proteins, carbs, nucleic acids

• Excellent medium for transport– Xylem carries water & dissolved minerals– Phloem moves dissolved sugar

• Blood most common transport in animals– Blood plasma– Glucose, amino acids, fibrinogen, hydrogen

carbonate ions

SubstanceHigh or low relative solubility in water

Mode of transport in an aqueous environment

Glucose Polar molecule/high solubility

No special mode of transport needed/dissolves directly in aqueous plasma

Amino acids Varying polarity but all are reasonably soluble

No special mode of transport needed/ dissolves directly in aqueous plasma

Cholesterol Largely non-polar/very low solubility

Transported by blood proteins that have polar amino acids on the outer portion to give water solubility, & non-polar amino acids internally to bind the non-polar cholesterol

Fats Non-polar fatty acid components/very low solubility

Transported by blood proteins that have polar amino acids on the outer portion to give water solubility, & non-polar amino acids internally to bind the non-polar cholesterol

Substance High or low relative solubility in waterMode of transport in an aqueous environment

Oxygen Travels as diatomic O2/low solubility Relatively low solubility in water is exacerbated by the relatively high temperature of warm-blooded animals (oxygen is less soluble in warm aqueous solutions)/haemoglobin is used to bind & transport oxygen molecules reversibly

Sodium chloride Ionizes/high solubility No special mode of transport needed/sodium chloride is an ionic compound, it ionizes into separately charged Na+ and Cl- ions in aqueous plasma

Hydrophobic & hydrophilic• Polar substances = hydrophilic• Non-polar substances = hydrophobic– Organic non-polar = carbon & hydrogen OR large

areas of only hydrogen & carbon (methane)• fatty acids, some proteins depending on the

arrangement of the amino acids• (think integral proteins)

Application

• Comparison of the thermal properties of water with those of methane.

Methane vs WaterFreezing point -183o C 0o C

Boiling point -163o C 100o C

Structure

Phase change No hydrogen bonds influencing phase changes so they escape from each other

Water molecules constantly forming, breaking, and almost instantly reform hydrogen bonds with other water molecules

Liquid to solid No longer has enough molecular motion

Motion low enough, hydrogen bonds lock water molecules into ice crystals

Polar covalent

Non-polar

covalent