Organic Chemistry

Carbon: The Backbone of Life

• Living organisms consist mostly of carbon-based compounds due to its ability to form large, complex, and diverse molecules

• Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds

2

Carbon: Organic Chemistry

• The study of carbon compounds is called Organic chemistry (main elements = CHONPS)

• Organic compounds range from simple molecules to colossal ones

• Most organic compounds contain hydrogen atoms in addition to carbon atoms with O, N and P among others thrown in from time to time.

3

Carbon has 4 valence electrons, thus makes 4 bonds

• With four valence electrons, carbon can form four covalent bonds with a variety of atoms

• This ability makes large, complex molecules possible

• In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape

4

Those four bonds can vary…

5

Carbon Skeletons Vary

• Carbon chains form the skeletons of most organic molecules and can vary in length and shape

Functional Groups

A few chemical groups are key to the function of biomolecules

• Distinctive properties of organic molecules depend on the carbon skeleton and on the molecular components attached to it

• A number of characteristic groups can replace the hydrogens attached to skeletons of organic molecules

7

• FGs are the pieces that

are most commonly

involved in chemical

reactions

• The number and

arrangement of

functional groups give

each molecule its

unique properties

• Let’s meet the FGs

8

Functional Groups

STRUCTURE

EXAMPLE

Alcohols

(Their specific

names usually

end in -ol.)

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

(may be written

HO—)

Ethanol

• Is polar as a result

of the electrons

spending more

time near the

electronegative

oxygen atom.

• Can form hydrogen

bonds with water

molecules, helping

dissolve organic

compounds such

as sugars.

Hydroxyl

Carbonyl

STRUCTURE

EXAMPLE

Ketones if the carbonyl

group is within a

carbon skeleton

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Aldehydes if the carbonyl

group is at the end of the

carbon skeleton

• A ketone and an

aldehyde may be

structural isomers

with different properties,

as is the case for

acetone and propanal.

Acetone

Propanal

• Ketone and aldehyde

groups are also found

in sugars, giving rise

to two major groups

of sugars: ketoses

(containing ketone

groups) and aldoses

(containing aldehyde

groups).

Carboxyl

STRUCTURE

EXAMPLE

Carboxylic acids, or organic

acids

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Acetic acid

• Acts as an acid; can

donate an H+ because the

covalent bond between

oxygen and hydrogen is so

polar:

• Found in cells in the ionized

form with a charge of 1– and

called a carboxylate ion.

Nonionized Ionized

Amino

Amines

Glycine

STRUCTURE

EXAMPLE • Acts as a base; can

pick up an H+ from the

surrounding solution

(water, in living

organisms):

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

• Found in cells in the

ionized form with a

charge of 1.

Nonionized Ionized

Sulfhydryl

Thiols

(may be

written HS—)

STRUCTURE

EXAMPLE • Two sulfhydryl groups can

react, forming a covalent

bond. This “cross-linking”

helps stabilize protein

structure.

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

• Cross-linking of cysteines

in hair proteins maintains

the curliness or straightness

of hair. Straight hair can be

“permanently” curled by

shaping it around curlers

and then breaking and

re-forming the cross-linking

bonds.

Cysteine

Phosphate

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Organic phosphates

Glycerol phosphate

• Contributes negativecharge to the moleculeof which it is a part(2– when at the end ofa molecule, as at left;1– when locatedinternally in a chain ofphosphates).

• Molecules containingphosphate groups havethe potential to reactwith water, releasingenergy.

Methyl

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Methylated compounds

5-Methyl cytidine

• Addition of a methyl groupto DNA, or to moleculesbound to DNA, affects theexpression of genes.

• Arrangement of methylgroups in male and femalesex hormones affects theirshape and function.

• Adenosine triphosphate (ATP), is made of adenosine bonded to three phosphate groups. Adding or removing phosphate groups stores and releases energy.

• Draw

16

Example of FG in action-ATP: Chemical Energy for Cells

Organic Macromolecules: Carbohydrates, Lipids, Proteins, and Nucleic Acids

The FOUR Classes of Large Biomolecules

• All living things are made of four classes of biomolecules:

• Carbohydrates

• Lipids

• Protein

• Nucleic Acids

• Macromolecules are large molecules composed of thousands of covalently bonded atoms

• Their structure determines their function!!!

18

The FOUR Classes of Large Biomolecules

• Macromolecules are polymers, built from monomers• A polymer is a long molecule made of many similar building

blocks called monomers

• Three of the four classes of life’s organic molecules are polymers

– Carbohydrates

– Proteins

– Nucleic acids

19

Building polymers

• A dehydration reaction links monomers together by removing a water molecule

(leave space for a drawing!)

• Hydrolysis is the reverse, and disassembles polymers by adding water

• Why is water important for food digestion?

20

(Draw this!) Dehydration Synthesis

21

(Draw this!) Hydrolysis

22

Biomolecule 1: Carbohydrates

• Include sugars and sugar polymers called

starches. They provide chemical energy and

building material.

• The simplest carbohydrates are monosaccharides, or

single sugars with formula ratios of 1C:2H:1O used for

quick energy (draw one)

• Carbohydrate macromolecules are polysaccharides,

or chains of sugars; often used to build cell parts or for

energy storage (draw one)

23

Sugars: Monosaccharides

• Glucose (C6H12O6) is the most

common monosaccharide

• Monosaccharides are classified by

– The location of the carbonyl group

– The number of carbons in the

carbon skeleton24

Sugars: Disaccharides

• A disaccharide is formed when dehydration

reaction joins two monosaccharides

25

Synthesizing Maltose & Sucrose

26

Types of Polysaccharides

• Starch is a storage polysaccharide of plants that consists entirely of glucose monomers

• Plants store surplus starch as granules within chloroplasts and other plastids

• The simplest form of starch is amylose

27

Types of Polysaccharides

• Glycogen is a

storage

polysaccharide in

animals (“animal

starch”)

• Humans and other

vertebrates store

glycogen mainly in

liver and muscle cells

28

Types of Polysaccharides

• Cellulose is a polysaccharide used to build

plant cell walls

• Like starch, cellulose is a polymer of glucose,

but the glycosidic linkages differ

29

Such Elegance!

30

Polysaccharide Random Acts of Biology

• Cellulose in human food passes through the

digestive tract as insoluble fiber

• Some microbes use enzymes to digest cellulose

• Many herbivores, from cows to termites, have

symbiotic relationships with these microbes

• Chitin is the structural polysaccharide in animal

exoskeletons (crunch!) and fungi cell walls

(surprise!)

31

Biomolecule 2: Lipids

Lipids are a diverse group of hydrophobic

molecules

• Lipids are the one class of large biological

molecules that do not form polymers

• The unifying feature of lipids is having little or no

affinity for water (water fearing)

• Lipids are hydrophobic because they are non-

polar

• The most biologically important lipids are fats,

phospholipids, and steroids

32

Fats: Start with a Simple Little Glycerol Molecule

• Fats are constructed from two

types of smaller molecules:

glycerol and fatty acids

• Glycerol is a three-carbon alcohol

with a hydroxyl group attached to

each carbon

• A fatty acid consists of a carboxyl

group attached to a long carbon

skeleton

33

Dehydration Rxn 1: Add a Fatty Acid

• Next, add a “fatty acid” through a dehydration

synthesis reaction

• What makes it an acid? The C double bond O,

single bond OH!

34

Dehydration Rxn 2!!

• Next, add a SECOND “fatty acid” through a

dehydration synthesis reaction

Dehydration Reaction THREE!!!

• How many

water

molecules

will it take to

disassemble

this

molecule?

36

Saturated or Unsaturated?

• Fats made from

saturated fatty acids

are called saturated

fats, and are solid at

room temperature

• Most animal fats are

saturated (lard)

• Saturated fatty acids havethe maximum number of hydrogen atoms possible and no double bonds, so they are straight

37

Saturated or Unsaturated?

38

• Fats made from

unsaturated fatty acids

are called unsaturated

fats or oils, and are

liquid at room

temperature

• Plant fats and fish fats

are usually unsaturated

• Unsaturated fatty acids have one or more double bonds, so they bend

Fats: Major function is storage!

• The major function of

fats is long-term

energy storage!

• Humans and other

mammals store their

fat in adipose cells

• Adipose tissue also

cushions and

insulates the body

39

Phospholipids

• Phospholipids are the

major component of all cell

membranes; b/c the

phosphate head is

hydrophilic and the lipid

tail is hydrophobic, they

self assemble into a bi-

layer in water (draw)

40

Choline

Phosphate

Glycerol

Fatty acids

Hydrophilichead

Hydrophobictails

(c) Phospholipid symbol(b) Space-filling model(a) Structural formula

Hyd

rop

hil

ic h

ea

dH

yd

rop

ho

bic

tail

sA Single Phospholipid Molecule

Steroids

• Steroids are lipids with a carbon skeleton

consisting of four fused rings

• The steroid Cholesterol is a component in animal

cell membranes

• Although cholesterol is essential in animals, high

levels in the blood may contribute to

cardiovascular disease

42

Biomolecule 3: Proteins

• Proteins are very diverse.

• Cells are mostly made of Proteins, as they

account for more than 50% of the dry mass of

most cells

• Protein functions include structural support,

storage, transport, cellular communication,

movement, and defense (basically everything

that keeps you alive…)

• Let’s take a look at a few we’ll learn this year!

43

Enzymatic

44

Enzymatic proteins

Enzyme

Example: Digestive enzymes catalyze the hydrolysis

of bonds in food molecules.

Function: Selective acceleration of chemical reactions

Storage

45

Storage proteins

OvalbuminAmino acidsfor embryo

Function: Storage of amino acids

Examples: Casein, the protein of milk, is the major

source of amino acids for baby mammals. Plants have

storage proteins in their seeds. Ovalbumin is the

protein of egg white, used as an amino acid source

for the developing embryo.

Hormonal

46

Hormonal proteins

Function: Coordination of an organism’s activities

Example: Insulin, a hormone secreted by the

pancreas, causes other tissues to take up glucose,

thus regulating blood sugar concentration

Highblood sugar

Normalblood sugar

Insulinsecreted

Defensive

47

Defensive proteins

Virus

Antibodies

Bacterium

Function: Protection against disease

Example: Antibodies inactivate and help destroy

viruses and bacteria.

Transport

48

Transport proteins

Transportprotein

Cell membrane

Function: Transport of substances

Examples: Hemoglobin, the iron-containing protein of

vertebrate blood, transports oxygen from the lungs to

other parts of the body. Other proteins transport

molecules across cell membranes.

Receptor

49

Signalingmolecules

Receptorprotein

Receptor proteins

Function: Response of cell to chemical stimuli

Example: Receptors built into the membrane of a

nerve cell detect signaling molecules released by

other nerve cells.

Structural

60 m

Collagen

Connectivetissue

Structural proteins

Function: Support

Examples: Keratin is the protein of hair, horns,

feathers, and other skin appendages. Insects and

spiders use silk fibers to make their cocoons and webs,

respectively. Collagen and elastin proteins provide a

fibrous framework in animal connective tissues.

Enzymes

51

• SPECIAL PROTEIN: Enzymes are protein

catalysts that speed up reactions; they are

reusable and specific to one function (based

on their shape)

Protein Monomer

• Amino acids are the

monomers of all

proteins.

• Amino acids differ in

their properties due to

differing side chains,

called R groups

52

Side chain (R group)

Aminogroup

Carboxylgroup

carbon

Polypeptides

• Polypeptide chains are made chained

arrangements of the 20 available amino acids

and then folded into proteins.

• A protein consists of one or more polypeptides

53

Nonpolar side chains; hydrophobic

Side chain

Glycine(Gly or G)

Alanine(Ala or A)

Valine(Val or V)

Leucine(Leu or L)

Isoleucine(Ile or I)

Methionine(Met or M)

Phenylalanine(Phe or F)

Tryptophan(Trp or W)

Proline(Pro or P)

Hydrophobic Amino Acids

55

Hydrophilic Amino Acids

56

Electrically charged Amino Acids

Peptide Bonds

• Amino acids are linked by peptide bonds

(through dehydration synthesis)

• A polypeptide is a polymer of amino acids

• Polypeptides range in length from a few to more

than a thousand monomers (Yikes!)

• Each polypeptide has a unique linear sequence

of amino acids, with a carboxyl end (C-terminus)

and an amino end (N-terminus)

57

Peptide Bonds

58

Peptide Bonds

59

Protein Structure & Function

• At first, all we have is a string of AA’s bound with peptide bonds.

• Once the string of AA’s interacts with itself and its environment (often aqueous), then we have a functional protein that consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape

• The sequence of amino acids determines a protein’s three-dimensional structure

• A protein’s structure determines its function

60

Protein Structure: 4 Levels

• Primary structure is the amino acid chain pipe

cleaner

• Secondary structure consists of alpha helices

(coils) or beta pleats (folds) coiled/folded pipe

cleaner

• Tertiary structure is determined by interactions

among side chains (IMFs and bonds) within the

helix/pleat pipe cleaner connected to itself with

paper clip

• Quaternary structure consists of multiple

polypeptide chains multiple pipe cleaners61

Primary Structure

• Primary structure,

the sequence of

amino acids in a

protein, is like the

order of letters in a

long word

• Primary structure is

determined by

inherited genetic

information

Secondary Structure

• The coils and folds of

secondary structure

result from hydrogen

bonds between repeating

constituents of the

polypeptide backbone

• Typical secondary structures are a coil called an helix and a folded structure called a pleated sheet

63

Tertiary Structure

• Tertiary structure is determined by interactions

between R groups, rather than interactions

between backbone constituents

• These interactions between R groups include

actual ionic bonds and strong covalent bonds

called disulfide bridges which may reinforce the

protein’s structure.

• IMFs such as London dispersion forces (LDFs

a.k.a. and van der Waals interactions), hydrogen

bonds (IMFs), and hydrophobic interactions

(IMFs) may affect the protein’s structure

64

Tertiary Structure

65

Quaternary Structure

• Quaternary structure results when two or

more polypeptide chains form one

macromolecule

• Collagen is a fibrous protein consisting of

three polypeptides coiled like a rope

66

Four Levels of Protein Structure Revisited

67

Sickle-Cell Disease: A change in Primary Structure

• A slight change in primary structure can affect a

protein’s structure and ability to function

• Sickle-cell disease, an inherited blood disorder,

results from a single amino acid substitution in

the protein hemoglobin

68

Sickle-Cell Disease: A change in Primary Structure

69

Changing Protein Structure

• Proteins are fragile. The environment can affect

protein structure and therefore function.

• Alterations in pH, salt, temperature, etc can

cause a protein to unravel; this is denaturing

and the protein doesn’t function anymore

• A denatured protein is biologically inactive

70

Biomolecule 4: Nucleic Acids

• Nucleic acids store, transmit, and help

express hereditary information

• The amino acid sequence of a polypeptide is

programmed by a unit of inheritance called a

gene

• Genes are made of DNA, a nucleic acid

made of monomers called nucleotides

71

Two Types of Nucleic Acids

• There are two types of nucleic

acids

– Deoxyribonucleic acid

(DNA)

– Ribonucleic acid (RNA)

• DNA provides directions for its

own replication

• DNA directs synthesis of

messenger RNA (mRNA) and,

through mRNA, controls protein

synthesis

• Protein synthesis occurs on

ribosomes

72

Figure 5.25-1

Synthesis ofmRNA

mRNA

DNA

NUCLEUS

CYTOPLASM

1

Figure 5.25-2

Synthesis ofmRNA

mRNA

DNA

NUCLEUS

CYTOPLASM

mRNA

Movement ofmRNA intocytoplasm

1

2

Figure 5.25-3

Synthesis ofmRNA

mRNA

DNA

NUCLEUS

CYTOPLASM

mRNA

Ribosome

AminoacidsPolypeptide

Movement ofmRNA intocytoplasm

Synthesisof protein

1

2

3

The Components of Nucleic Acids

• Nucleic Acids are made of monomers called

nucleotides, which consist of a nitrogenous

base, a pentose sugar, and a phosphate group

(draw)

76

Figure 5.26ab

Sugar-phosphate backbone5 end

5C

3C

5C

3C

3 end

(a) Polynucleotide, or nucleic acid

(b) Nucleotide

Phosphategroup Sugar

(pentose)

Nucleoside

Nitrogenousbase

5C

3C

1C

The Devil is in the Details

• Types of nitrogenous bases

– Pyrimidines (cytosine, thymine, and uracil)

have a single ring, that has six-members

– Purines (adenine and guanine) have two rings;

a six-membered ring fused to a five-membered

ring

• DNA vs. RNA nucleotides:

• In DNA, “T” is used and the sugar is deoxyribose; in

RNA, “U” is used and the sugar is ribose

78

The Devil is in the Details

• The backbone of both NAs are made

of phosphate-sugar covalent bonds.

VERY STRONG!

79

The Devil is in the Details

• When NAs link sides it is with hydrogen bonds

between complementary base pairs (A w/ T, C

w/ G). WEAK BOND!

• Complementary pairing can also occur between

two RNA molecules or DNA to RNA

• Note: In RNA, thymine is replaced by uracil (U)

so A and U pair

80

Sugar-phosphatebackbones

Hydrogen bonds

Base pair joinedby hydrogen bonding

Base pair joinedby hydrogen

bonding

(b) Transfer RNA(a) DNA

5 3

53