Unit 1 - IntroductionUnit 1 - Introduction

I. Biology - the study of life.

A.Enormous in scope.

B. Size scale from submicroscopic molecules to global distribution of biological communities.

C. Encompasses life over huge spans of time from contemporary organisms to ancestral life.

• Biology is an ongoing process.•During the last few decades we have had an information explosion.

II. 10 Major ThemesII. 10 Major Themes

A. Emergent Properties - properties that emerge as a result of interactions between components.

The cell – basic unit of structure and function.

C. Heritable Information.C. Heritable Information.

DNA and genes

D. Correlation between Structure & Function

E. Interaction with the Environment

F. Regulation

G. Unity & Diversity • 1.5 million species• 6 kingdoms

8. Evolution. 8. Evolution.

Core theme of biology. Life evolves, similar species share common

ancestry, less closely related species share more ancient common ancestors.

9. Scientific Inquiry

10. Science, Technology & Society

III. WaterIII. Water

The cradle of life.

A. Unique properties of water:A. Unique properties of water:

1. Liquid at normal temp.

2. Provides a medium in which other molecules can interact.

3. Composes 2/3 of most organisms.

4. Forms weak chemical associations.

5. Simple atomic structure.

B. Water acts like a magnet.B. Water acts like a magnet.

1. Electronegativity attracts electrons of hydrogen and oxygen in a water molecule. A polar molecule.

2. Water clings to polar molecules.

2. Water clings to polar molecules.

Cohesion – Attraction of like molecules. (Attraction of water to water.)

Adhesion – Attraction of unlike molecules. (Attraction of water to another molecule.)

Water con’t.Water con’t.

3. Water stores heat, and has a high specific heat, because of polarity.

Water con’t.Water con’t.

4. Water is a powerful solvent. Water molecules gather around charged molecules.

Water con’t.Water con’t.

5. Water organizes nonpolar molecules. Water excludes nonpolar molecules.

a. Hydrophobic – not soluble in water, nonpolar.

b. Hydrophilic – soluble in water, polar.

Water con’t.Water con’t.

6. Water ionizes.

Water con’t.Water con’t.

7. Buffers – minimize changes in H+ and OH – concentrations.

III. CarbonIII. Carbon

A. Four bond sites.

III. Carbon, con’t.III. Carbon, con’t.B. Bonds with itself

to form chains or polymers.Subunits are joined

by covalent bonds. -OH is removed from one subunit and H+ is removed from the other subunit.

Dehydration synthesisDehydration synthesis

A condensation reaction. A molecule of water is removed as subunits are linked. Requires the input of energy to assemble.

Anabolic pathways build macromolecules from subunits.

This process is carried out by enzymes.

Hydrolysis ReactionHydrolysis Reaction

A molecule of water is added as subunits are broken apart. This process is also carried out by enzymes.

Catabolic pathways disassemble molecules into subunits.

C. Can form single, double, or triple bonds.

D. Can form isomers (molecules with the same molecular formula but a different structural formula.)

3 types of isomers:3 types of isomers:

1. Structural isomers – differ in the covalent arrangement of their atoms.

2. Geometric isomers – molecules that have the same covalent partnerships, but differ in their spatial arrangements.

3. Enantiomers – isomers that are mirror images of each other.

E. Functional Groups:E. Functional Groups:

1. Hydroxyl Group - -OH polar molecule, the alcohols, names end in –ol.

2. Carbonyl Group - -CO or C=O at the end of a molecule an aldehyde and their names end in –al. If the C=O is not at the end the molecule it is a ketone and their names end in –one.

E. Functional Groups:con’t.E. Functional Groups:con’t.

3. Carboxyl Group - -COOH or carboxylic acids or organic acids. The hydrogen on the end tends to dissociate creating the hydronium ion.

4. Amino Group - NH2 or Amines, can act as a base.

E. Functional Groups:con’t.E. Functional Groups:con’t.

5. Sulfhydryl Group - -SH Thiols that help to stabilize the intricate structure of proteins.

6. Phosphate Group - -PO4 Transfer energy between organic molecules.

4 Major Classes of Organic Molecules

4 Major Classes of Organic Molecules

Energy:Energy:

Carbohydrates and Lipids• Similar in all organisms• Unit sequence is not coded by DNA (based on

particular enzymes only.

Information:Information:

Proteins and Nucleic Acids.• Distinctive in each organism.• Unit sequence is coded by DNA.

CarbohydratesCarbohydrates

Sugars and their polymers

1. Monosaccharides – 1. Monosaccharides –

Simple sugars CH2O

Names end in –ose Hexoses, trioses,and pentoses. Sugars form rings in water solutions.

2. Disaccharides2. Disaccharides

Double sugars In this form the sugar is protected from

being metabolized during transport.

3. Polysaccharides3. Polysaccharides

Few hundred to thousands of monomers long

General formula (C6H10O5)n

Storage polysaccharidesStorage polysaccharides

Starch – polymer of glucose.• Amylose – helical chain (simplest form) found

in plants.• Amylopectin – helical chain with branches, also

found in plants.• Glycogen – animal starch, stored in the liver

and muscle (in humans stores about 1 days worth)

Structural polysaccharidesStructural polysaccharides

Cellulose – composed of chains of the form of glucose.• Cellulose chains – hydrogen bonds hold the

chain together into units called. Microfibrils.• Several intertwined microfibrils make a

cellulose fibril.• Several cellulose fibrils can supercoil making a

very strong cable.

Enzymes can digest glucose but few organisms can digest glucose.

ChitinChitin

Exoskeleton of insects and some fungi. Contains the amino group. Sometimes called an amino sugar.

LipidsLipids

1. Have little or no affinity for water.

2. 3 main groups:a. Fats

b. Phospholipids

c. Steroids

3. Fats3. Fats

Made of glycerol and 3 fatty acids (triglycerides).

Saturated fats – all single bonds between the carbons in the fatty acids. Animal fats, solidify at room temperature.

Unsaturated fats – have some double and/or triple bonds between carbons. Plant fats, liquid at room temp.

3. Fats con’t.3. Fats con’t.

Hydrogenated fats are unsaturated fats with hydrogens added such as peanut butter and margarine.

In animals, fat is used for energy storage because it takes up less space than carbohydrates.

4. Phospholipids4. Phospholipids

Composed of 2 fatty acids and 1 phosphate group attached to the glycerol molecule.

Major component of the cells membranes.

5. Steroids5. Steroids

Have a carbon skeleton of 4 interconnected rings.

Cholesterol – part of the animal cell membrane and is a precursor for many other steroids.

ProteinsProteins

Many structures

Many functions

1. Used for:1. Used for:

a. Structural support

b. Storage

c. Transport of other substances

d. Signaling from one part of the organism to another.

e. Movement

f. Defense against foreign substances

g. Enzymes used for chemical reactions

2. Protein facts:2. Protein facts:

a. Proteins are the most structurally complex molecules known. Each type of protein has a complex three-dimensional shape or conformation.

b. All protein polymers are constructed from the same set of 20 monomers, called amino acids.

c. Polymers of proteins are called polypeptides.d. A protein consists of one or more polypeptides

folded and coiled into a specific conformation.

3. A polypeptide is a polymer of amino acids connected in a specific sequence.

3. A polypeptide is a polymer of amino acids connected in a specific sequence.

a. Amino acids consist of four components attached to a central carbon atom.

b. These components include a hydrogen atom, a carboxyl group, an amino group, and a variable R group (or side chain).

• Differences in R groups produce the 20 different amino acids.

c. One group of amino acids has hydrophobic R groups.

c. One group of amino acids has hydrophobic R groups.

d. Another group of amino acids has polar R groups, making them hydrophilic.

d. Another group of amino acids has polar R groups, making them hydrophilic.

e. The last group of amino acids includes those with functional groups that are charged (ionized) at cellular pH.Some R groups are bases, others are acids.

e. The last group of amino acids includes those with functional groups that are charged (ionized) at cellular pH.Some R groups are bases, others are acids.

4. Amino acids are joined together when a dehydration reaction removes a hydroxyl group from the carboxyl end of one amino acid and a hydrogen from the amino group of another. The resulting covalent bond is called a peptide bond.

4. Amino acids are joined together when a dehydration reaction removes a hydroxyl group from the carboxyl end of one amino acid and a hydrogen from the amino group of another. The resulting covalent bond is called a peptide bond.

5. A protein’s function depends on its specific conformation

5. A protein’s function depends on its specific conformation

a. A functional protein consists of one or more polypeptides that have been precisely twisted, folded, and coiled into a unique shape.

b. It is the order of amino acids that determines what the three-dimensional conformation will be.

c. A protein’s specific conformation determines its function.

d. In almost every case, the function depends on its ability to recognize and bind to some other molecule.

1) For example, antibodies bind to particular foreign substances that fit their binding sites.

2) Enzymes recognize and bind to specific substrates, facilitating a chemical reaction.

e. Protein Structuree. Protein Structure

1) Three levels of structure: primary, secondary, and tertiary structure, are used to organize the folding within a single polypeptide.

2) Quarternary structure arises when two or more polypeptides join to form a protein.

3) The primary structure of a protein is its unique sequence of amino acids.

• The precise primary structure of a protein is determined by inherited genetic information.

Even a slight change in primary structure can affect a protein’s conformation and ability to

function.

Even a slight change in primary structure can affect a protein’s conformation and ability to

function.

4) The secondary structure of a protein results from hydrogen bonds at regular intervals along the polypeptide backbone.

Typical shapes

that develop from

secondary structure

are coils (an alpha

helix) or folds

(beta pleated sheets).

5) Tertiary structure is determined by a variety of interactions among R groups and between R groups and the polypeptide backbone.

These interactions include hydrogen bonds among polar and/or charged areas, ionic bonds between charged R groups, and hydrophobic interactions and van der Waals interactions among hydrophobic R groups.

While these three interactions are relatively weak, disulfide bridges, strong covalent bonds that form between the sulfhydryl groups (SH) of cysteine monomers, stabilize the structure.

Quarternary structure results from the aggregation of two or more polypeptide subunits. Examples:• Collagen is a fibrous protein of three polypeptides that are

supercoiled like a rope.– This provides the structural strength for their role in connective tissue.

• Hemoglobin is a globular protein with two copies of two kinds of polypeptides.

f. A protein’s conformation can change in response to physical and chemical conditions.

Alterations in pH, salt concentration, temperature, or other factors can unravel or denature a protein.

• These forces disrupt the hydrogen bonds, ionic bonds, and disulfide bridges that maintain the protein’s shape.

Some proteins can return to their functional shape after denaturation, but others cannot, especially in the crowded environment of the cell.

In spite of the knowledge of the three-dimensional shapes of over 10,000 proteins, it is still difficult to predict the conformation of a protein from its primary structure alone.

• Most proteins appear to undergo several intermediate stages before reaching their “mature” configuration.

• The folding of many proteins is protected by chaperonin proteins that shield out bad influences.

h. Enzymesh. Enzymes

Protein molecules, Names end in –ase,These are organic catalysts.Used by a cell to lower the activation energy

needed to start a chemical reaction. Induced-fit model is used to describe how an

enzyme works.Speed – 1,000 or more reactions/second.

Enzyme helpers:Enzyme helpers:

1. Cofactors – small nonprotein molecules that are required for proper enzyme catalysis (ex. Zn, Fe, Cu)

2. Coenzymes – organic compounds (ex. Vitamins)

i. Some factors that affect enzyme action:

i. Some factors that affect enzyme action:

1. Temperature

2. pH

3. Salinity

The End of Unit 1The End of Unit 1