The Molecules of Cells. Organic Chemistry: Carbon Based Compounds A. Inorganic Compounds: Compounds without carbon. B. Organic Compounds: Compounds synthesized.

The Molecules of Cells

Organic Chemistry: Carbon Based Compounds

A. Inorganic Compounds: Compounds without carbon.

B. Organic Compounds: Compounds synthesized by cells and containing carbon (except for CO and CO2). Diverse group: Several million organic compounds

are known and more are identified every day.

Common: After water, organic compounds are the most common substances in cells. Over 98% of the dry weight of living cells is made up of

organic compounds. Less than 2% of the dry weight of living cells is made up of

inorganic compounds.

Carbon: unique element for basic building block of molecules of life

Carbon has 4 valence electrons: Can form four covalent bonds Can form single , double, triple bonds. Can form large, complex, branching molecules and

rings. Carbon atoms easily bond to C, N, O, H, P, S.

Huge variety of molecules can be formed based on simple bonding rules of basic chemistry

Organic Compounds are Carbon Based

Carbon Can Form 4 Covalent Bonds

Different Carbon Skeletons of Organic Compounds

Diversity of Organic Compounds

Hydrocarbons: Organic molecules that contain C and H only. Good fuels, but not biologically important. Undergo combustion (burn in presence of oxygen). In general they are chemically stable. Nonpolar: Do not dissolve in water (Hydrophobic).

Examples: (1C) Methane: CH4 (Natural gas). (2C) Ethane: CH3CH3 (3C) Propane: CH3CH2CH3 (Gas grills). (4C) Butane: CH3CH2CH2CH3 (Lighters). (5C) Pentane: CH3CH2CH2CH2CH3 (6C) Hexane: CH3CH2CH2CH2CH2CH3 (7C) Heptane: CH3CH2CH2CH2CH2CH2CH3 (8C) Octane: CH3CH2CH2CH2CH2CH2CH2CH3

Hydrocarbons have C and H only

Isomers: Compounds with same chemical formula but different structure (arrangement of atoms)

Isomers have different physical and chemical properties

Structural Isomers: Differ in bonding arrangements

Butane (C4H10) Isobutane (C4H10)

CH3

|CH3--CH2--CH2--CH3 CH3---CH---CH3

Number of possible isomers increases with increasing number of carbon atoms.

Functional groups play pivotal role in chemical & physical properties of organic molecules

Compounds that are made up solely of carbon and hydrogen are not very reactive. Functional groups: One or more H atoms of the carbon skeleton may be

replaced by a functional group. Groups of atoms that have unique chemical and

physical properties.

Usually a part of molecule that is chemically active. Similar activity from one molecule to another.

Together with size and shape, determine unique bonding and

chemical activity of organic molecules.

Functional Groups Determine Chemical & Physical Properties of Organic Molecules

Six Important Functional Groups:Hydroxyl (-OH-) Carbonyl (>C=O)Carboxyl (-COOH)Amino (-NH2)

Sulfhydryl (-SH)Phosphate (-OPO3

2-)

Notice that all six functional groups are polar.

A. Hydroxyl Group (-OH) Is a polar group: Polar covalent bond between O and H.

Can form hydrogen bonds with other polar groups.

Generally makes molecule water soluble.

Example:

Alcohols: Organic molecules with a simple hydroxyl

group:

Methanol (wood alcohol, toxic)

Ethanol (drinking alcohol)

Propanol (rubbing alcohol)

B. Carbonyl Group (>CO)

Is a polar group: O can be involved in H-bonding. Generally makes molecule water soluble.

Examples: Aldehydes: Carbonyl is located at end of molecule Ketone: Carbonyl is located in middle of molecule

Examples: Sugars (Aldehydes or ketones) Formaldehyde (Aldehyde) Acetone (Ketone)

Sugars Have Both -OH and =CO Functional Groups

C. Carboxyl Group (-COOH) Is a polar group

Generally makes molecule water soluble

Acidic because it can donate H+ in solution

Example:

Carboxylic acids: Organic acids, can increase acidity

of a solution: Acetic acid: Sour taste of vinegar. Ascorbic acid (Vitamin C): Found in fruits and vegetables. Amino acids: Building blocks of proteins.

D. Amino Group (-NH2) Is a polar group

Generally makes molecule water soluble

Weak base because N can accept a H+

Amine -general term given to compound with (-NH2)

Example:

Amino acids: Building blocks of proteins.

Amino acid Structure:

Central carbon with: H atom Carboxyl group Amino group Variable R-group

Amino Acid Structure:

H

|

(Amino Group) NH2---C---COOH (Carboxyl group) | R

(Varies for each amino acid)

Amino Acids Have Both -NH2 and -COOH Groups

E. Sulfhydryl Group (-SH) Is a polar group

Generally resembles a hydroxyl group

Two sulfhydryl groups may interact to form disulfide

bridges which stabilize protein structure (Tertiary

structure).

Thiols -general term given to compound with (-SH)

Example:

Cysteine: an amino acid.

F. Phosphate Group (-OPO32-)

Is a polar group

A phosphorus atom is bonded to four oxygen atoms, one of

which is bonded to the carbon skeleton.

Phosphates make the molecules of which it is a part an anion

(negatively charged).

The bonds holding phosphate groups is one way energy is stored

and transferred between organic molecules.

Organic Phosphates -general term given to a compound with (-

OPO32-)

Example:

Phosphatidylcholine: a type of phospholipid found in plasma

membranes.

The Macromolecules of Life:Carbohydrates, Proteins, Lipids, and Nucleic Acids

I. Most Biological Macromolecules are Polymers

Polymer: Large molecule consisting of many identical or similar “subunits” linked through covalent bonds.

Monomer: “Subunit” or building block of a polymer.

Macromolecule: Large organic polymer. Most macromolecules are constructed from about 70 simple monomers.

Relatively few monomers are used by cells to

make a huge variety of macromolecules

Macromolecule Monomers or Subunits

1. Carbohydrates 20-30 monosaccharidesor simple sugars

2. Proteins 20 amino acids

3. Nucleic acids (DNA/RNA) 4 nucleotides

(A,G,C,T/U)

4. Lipids (fats and oils) ~ 20 different fatty acids

and glycerol.

Making and Breaking Polymers There are two main chemical mechanisms in

the production and break down of macromolecules. Condensation or Dehydration Synthesis Hydrolysis

In the cell these mechanisms are regulated by enzymes.

Making PolymersA. Condensation or Dehydration Synthesis reactions: Synthetic process in which a monomer is covalently

linked to another monomer. The equivalent of a water molecule is removed.

Breaking PolymersB. Hydrolysis Reactions: “Break with water”. Degradation of polymers into component monomers. Involves breaking covalent bonds between subunits. Covalent bonds are broken by adding water.

Synthesis and Hydrolysis of Sucrose

III. Carbohydrates: Molecules that store energy and are used as building materials

General Formula: (CH2O)n

Simple sugars and their polymers. Diverse group includes sugars, starches, cellulose. Biological Functions:

• Fuels, energy storage • Structural component (cell walls)• DNA/RNA component

Three types of carbohydrates:A. MonosaccharidesB. Disaccharides C. Polysaccharides

A. Monosaccharides: “Mono” single & “sacchar” sugar

Preferred source of chemical energy for cells (glucose) Can be synthesized by plants from light, H2O and CO2.

Store energy in chemical bonds. Carbon skeletons used to synthesize other molecules.

Characteristics:1. May have 3-8 carbons. 2. Names end in -ose. Based on number of carbons: Glucose (“fuel of life”) Fructose (fruit sugar) Galactose (milk sugar)3. Can exist in linear or ring forms4. Isomers: Many molecules with the same molecular

formula, but different atomic arrangement. Example: Glucose and fructose are both C6H12O6.

Linear and Ring Forms of Glucose

B. Disaccharides: “Di” double & “sacchar” sugar

Covalent bond formed by condensation reaction between 2 monosaccharides.

Examples:

1. Maltose: Glucose + Glucose. • Energy storage in seeds. • Used to make beer.

2. Lactose: Glucose + Galactose. • Found in milk.• Lactose intolerance is common among adults.

• May cause gas, cramping, bloating, diarrhea, etc.

3. Sucrose: Glucose + Fructose. • Most common disaccharide (table sugar). • Found in plant sap.

Maltose and Sucrose are Disaccharides

C. Polysaccharides: “Poly” many (8 to 1000)

Functions: Storage of chemical energy and structure.

Storage polysaccharides: Cells can store simple sugars in polysacharides and hydrolyze them when needed.

1. Starch: Glucose polymer (Helical)

Form of glucose storage in plants (amylose) Stored in plant cell organelles called plastids

2. Glycogen: Glucose polymer (Branched)

Form of glucose storage in animals (muscle and liver

cells)

Three Different Polysaccharides of Glucose

Structural Polysaccharides: Used as structural components of cells and tissues.

1. Cellulose:

The major component of plant

cell walls. CANNOT be digested by

animal enzymes.

2. Chitin:

Forms exoskeleton of

arthropods (insects) Found in cell walls of some

fungi

Cellulose: Polysaccharide Found in Plant and Algae Cell Walls

Proteins: Large three-dimensional macromolecules responsible for most cellular functions

Polypeptide chains: Polymers of amino acids linked by peptide bonds in a SPECIFIC linear sequence

Protein: Macromolecule composed of one or more polypeptide chains folded into SPECIFIC 3-D conformations

Proteins have important and varied functions:

1. Enzymes: Catalysis of cellular reactions

2. Structural Proteins: Maintain cell shape

3. Transport: Transport in cells/bodies (e.g. hemoglobin).

Channels and carriers across cell membrane.

4. Communication: Chemical messengers, hormones, and

receptors. (Sometimes divided into hormonal and receptor)

5. Defensive: Antibodies and other molecules that bind to

foreign molecules and help destroy them.

6. Contractile (and Motor Proteins): Muscular movement.

7. Storage: Store amino acids for later use (e.g. egg white).

Protein function is dependent upon its 3-D shape.

Polypeptide: Polymer of amino acids connected in a specific sequence

A. Amino acid: The monomer of polypeptides

Central carbon• H atom• Carboxyl group • Amino group• Variable R-group

Peptide Bonds

Protein Function is dependent upon Protein Structure (Conformation)

CONFORMATION: The 3-D shape of a protein is determined by its amino acid sequence.

Four Levels of Protein Structure

1. Primary structure: Linear amino acid sequence, determined by gene for that protein.

2. Secondary structure: Regular coiling/folding of polypeptide.

3. Tertiary structure: Overall 3-D shape of a

polypeptide chain. 4. Quaternary

structure: Only in proteins with 2 or more

polypeptides. Overall 3-D shape of all chains.

Secondary Structure of Protein: Regular Folding Patterns

Tertiary Structure: Overall 3-D Shape of Protein

Tertiary Structure of Lysozyme

Quaternary Structure: Overall 3-D Shape of Protein with 2 or More Subunits

Chemical & Physical Environment: Presence

of other compounds, pH, temperature,

salts.

Denaturation: Process which alters native

conformation and therefore biological

activity of a protein. Several factors can

denature proteins: pH and salts: Disrupt hydrogen, ionic bonds.

Temperature: Can disrupt weak interactions.

• Example: Function of an enzyme depends

on pH, temperature, and salt concentration.

Nucleic acids store and transmit hereditary information for all living things

There are two types of nucleic acids in living things:

A. Deoxyribonucleic Acid (DNA)

Contains genetic information of all living organisms. Has segments called genes which provide information to

make each and every protein in a cell

B. Ribonucleic Acid (RNA)

Three main types called mRNA, tRNA, rRNA

DNA and RNA are polymers of nucleotides that determine the primary structure of proteins

Nucleotide: Subunits of DNA or RNA.

Nucleotides have three components:

1. Pentose(5-C) sugar (ribose or deoxyribose)

2. Phosphate group to link nucleotides (-PO4)

3. Nitrogenous base (A,G,C,T or U) Purines: Have 2 rings.

Adenine (A) and guanine (G)

Pyrimidines: Have one ring.

Cytosine (C), thymine (T) in DNA or uracil (U) in RNA.

Lipids: Fats, phospholipids, and steroids

Diverse groups of compounds.

Composition of Lipids: C, H, and small amounts of O.

Functions of Lipids: Biological fuels Energy storage Insulation Structural components of cell membranes Hormones

Lipids: Fats, phospholipids, and steroids

Simple Lipids: Contain C, H, and O only.

A. Fats (Triglycerides). Glycerol : Three carbon molecule with three hydroxyls. Fatty Acids: Carboxyl group and long hydrocarbon

chains. Characteristics of fats:

Most abundant lipids in living organisms. Hydrophobic (insoluble in water) because nonpolar. Economical form of energy storage (provide 2X the

energy/weight than carbohydrates). Greasy or oily appearance.

Fats (Triglycerides): Glycerol + 3 Fatty Acids

Lipids: Fats, phospholipids, and steroids

Types of Fats

Saturated fats: Hydrocarbons saturated with H. Lack -

C=C- double bonds. Solid at room temp (butter, animal fat, lard)

Unsaturated fats: Contain -C=C- double bonds. Usually liquid at room temp (corn, peanut, olive oils)

Saturated Fats Contain Saturated Fatty Acids

B. Steroids: Lipids with four fused carbon ringsIncludes cholesterol, bile salts, reproductive, and adrenal

hormones. Cholesterol: The basic steroid found in animals

• Common component of animal cell membranes.

C. Waxes: One fatty acid linked to an alcohol. Very hydrophobic. Found in cell walls of certain bacteria, plant and insect

coats. Help prevent water loss.

Cholesterol: The Basic Steroid in Animals