Organic Molecules

Six Functional Groups

Six Functional Groups

Early Origin-of-Life Experiments Could the first steps of chemical evolution have

occurred on ancient Earth? To find out, Stanley Miller combined methane (CH4),

ammonia (NH3), and hydrogen (H2) in a closed system with water, and applied heat and electricity as an energy source.

The products included hydrogen cyanide (HCN) and formaldehyde (H2CO), important precursors for more-complex organic molecules and amino acids.

In more recent experiments, amino acids and other organic molecules have been found to form easily under these conditions.

Figure 3-3Nonpolar side chains

Polar side chains

Electrically chargedside chains

Glycine (G) Gly

Alanine (A) Ala

Valine (V) Val Leucine (L) Leu

Isoleucine (I) Ile

Methionine (M)Met

Phenylalanine (F)Phe

Tryptophan (W)Trp

Proline (P)Pro

Serine (S)Ser

Threonine (T)Thr

Cysteine (C)Cys

Tyrosine (Y)Tyr

Asparagine (N) Asn

Glutamine (Q)Gln

Acidic Basic

Aspartate (D)Asp

Glutamate (E)Glu

Lysine (K)Lys

Arginine (R)Arg

Histidine (H)His

No charged or electronegative atoms to form hydrogen bonds; not soluble in water

Charged side chains form hydrogen bonds; highly soluble in water

Partial charges can form hydrogen bonds; soluble in water

The Nature of Side Chains The 21 amino acids differ only in the variable side chain

or R-group attached to the central carbon

R-groups differ in their size, shape, reactivity, and interactions with water. (1) Nonpolar R-groups: Do not form hydrogen bonds; coalesce in water(2) Polar R-groups: Form hydrogen bonds; readily dissolve in water

Amino acids with hydroxyl, amino, carboxyl, or sulfhydryl functional groups in their side chains are more chemically reactive than those with side chains composed of only carbon and hydrogen atoms.

Primary Structure

A protein’s primary structure is its unique sequence of amino acids.

Because the amino acid R-groups affect a polypeptide’s properties and function, just a single amino acid change can radically alter protein function.

Figure 3-11

Normal amino acid sequence Single change in amino acid sequence

4 5 6 7 4 5 6 7

Normal red blood

cells

Sickled red blood

cells

Secondary Structure

Secondary structure results in part from hydrogen bonding between the carboxyl oxygen of one amino acid residue and the amino hydrogen of another. A polypeptide must bend to allow this hydrogen bonding—thus, -helices or -pleated sheets are formed.

Secondary structure depends on the primary structure—some amino acids are more likely to be involved in α-helices; while others, in β-pleated sheets.

Secondary Structure increases stability by way of the large number of hydrogen bonds.

Hydrogen bonds form between peptide chains.

Secondary structures of proteins result.

-helix -pleated sheet

-helix -pleated sheet

Ribbon diagrams of secondary structure.

Hydrogen bonds

Arrowheads are at the carboxyl end of the arrows

Tertiary Structure

The tertiary structure of a polypeptide results from interactions between R-groups or between R-groups and the peptide backbone. These contacts cause the backbone to bend and fold, and contribute to the 3D shape of the polypeptide.

R-group interactions include hydrogen bonds, van der Waals interactions, covalent disulfide bonds, and ionic bonds.

Hydrogen bonds can form between hydrogen atoms and the carboxyl group in the peptide-bonded backbone, and between hydrogen atoms and atoms with partial negative charges in side chains.

Tertiary Structures of Proteins

Interactions that determine the tertiary structure of proteins

Hydrogen bond between side chain and carboxyl oxygen

Hydrogen bond between two side chains

Hydrophobic interactions (van der Waals interactions)

Ionic bond

Disulfide bond

Tertiary Structures of Proteins

Tertiary structures are diverse.

A tertiary structure composed mostly of -helices

A tertiary structure composed mostly of -pleated sheets

A tertiary structure rich in disulfide bonds

Van der Waals Interactions van der Waals interactions are electrical

interactions between hydrophobic side chains. Although these interactions are weak, the large number of van der Waals interactions in a polypeptide significantly increases stability.

Covalent disulfide bonds form between sulfur-containing R-groups.

Ionic bonds form between groups that have full and opposing charges.

Quaternary Structure

Some proteins contain several distinct polypeptide subunits that interact to form a single structure; the bonding of two or more subunits produces quaternary structure.

The combined effects of primary, secondary, tertiary, and sometimes quaternary structure allow for amazing diversity in protein form and function.

Quaternary Structures of Proteins

Cro protein, a dimer Hemoglobin, a tetramer

Figure 3-14-Table 3-3

Carbohydrates

Simple Sugars

Monosaccharide Single sugar Ex. Glucose (blood

sugar)

Disaccharide Two sugars Ex. Sucrose, Lactose, Fructose

Linear and Ring Forms

Linear form of glucose Ring forms of glucose

-Glucose

-Glucose

Oxygen from the5-carbon bonds to the1-carbon, resulting in a ring structure

Figure 5-4

Monosaccharides polymerize when hydroxyl groups react to form glycosidic linkages…

-Glucose -Glucose

…between various carbons and with various geometries.

-Galactose -Glucose Lactose (a disaccharide)

Maltose (a disaccharide)

In this case, the hydroxyl groups fromthe 1-carbon and 4-carbon react toproduct a -1,4-glycosidic linkageand water

The hydroxyl groups from the1-carbon and 4-carbon reactto produce an -1,4-glycosidiclinkage and water

Figure 5-4a

Monosaccharides polymerize when hydroxyl groups react to form glycosidic linkages…

-Glucose -Glucose Maltose (a disaccharide)

The hydroxyl groups from the1-carbon and 4-carbon reactto produce an -1,4-glycosidiclinkage and water

Figure 5-4b

…between various carbons and with various geometries.

-Galactose -Glucose Lactose (a disaccharide)

In this case, the hydroxyl groups fromthe 1-carbon and 4-carbon react toproduct a -1,4-glycosidic linkageand water

Polysaccharide

Complex Carbohydrate ( Starch) Ex. Starch, Cellulose, Chitin More than one ring structure

Cellulose, Chitin, Peptidoglycan

Cellulose in plant cell wall Chitin in insect exoskeleton

Peptidoglycan in bacterial cell wall

Figure 5-5a-Table 5-1

Figure 5-5b-Table 5-1

Figure 5-5c-Table 5-1

Glycoproteins: Identification Badge for Cells

Outsideof cell

Insideof cell

Glycoprotein

Lipids

Lipids –Fats, Oils, Waxes, Steroids (cholesterol)

Unsaturated Comes from plants and is liquid at room

temperature Ex. Corn oil, Olive oil, Sunflower oil Better for you

Saturated Comes from animals and is solid at room

temperature Ex. Bacon, animal fat Bad for you

Nucleic Acids

Nucleic Acids

DNA Deoxyribonucleic

Acid Phosphate,

Deoxyribose sugar, Nitrogen Base

Double sided Helical Structure Found in nucleus

RNA Ribonucleic Acid

Phosphate, Ribose sugar, Nitrogen Base

Single sided Can be various

places in the cell depending on type

Figure 4-1

Nucleotide

Sugars

Nitrogen-containing bases

Phosphate group

5-carbon sugar

Nitrogenous base

Ribose Deoxyribose

Cytosine (C) Uracil (U)Pyrimidines

Thymine (T)

Guanine (G) Adenine (A)Purines

Only in RNA Only in DNA

Figure 4-2

Phosphodiester linkage

Condensation reaction

Figure 4-3 The sugar-phosphatespine of RNA

The sequence of bases found in an RNA strandis written in the 5´ 3´direction

Nitrogenousbases

3´ and 5´ carbonsjoined byphosphodiesterlinkage

Unlinked 3´ carbon:New nucleotidesare added here

Figure 4-6bHydrogen bonds form between G-C pairs and A-T pairs.

Guanine Cytosine

ThymineAdenine

Su

gar

-ph

osp

hat

e b

ackb

on

e

Hydrogen bonds

DNA contains thymine,whereas RNA contains uracil

5

53

3

Majorgroove

Minorgroove

Length of onecompleteturn of helix(10 rungs perturn) 3.4 nm

Distancebetweenbases 0.34nm

Width of thehelix 2.0 nm