Introduction

According to the hierarchy of organization in biology, the unit of life (the cell), consists of a variety of organelles. The

of chemicals. These chemicals, or biomolecules, are the foundat

it is important that we have an understanding of the substances that are the primary constituent of cellular elements (organe

group the major biomolecules into four categories: carbohydrates, phospholipids, proteins, and nucleic acids.

The Principle of Polymerization

The Diversity of Polymers

As mentioned above, polymers (biomolecules) can be classified into four major categories: carboh

Carbohydrates

The carbohydrates, or sugars, are biomolecules that always contain carbon, hydrogen, and oxygen, Typically the ratio of thes

1:2:1 (C:H:O). This ratio, however, is modified for larger carbohydrates due to the elimination of the water molecule(s) during dehydration. We

can group the carbohydrates into three major groups: the

Monosaccharides

-Always have the C:H:O ratio of 1:2:1

-Simplest sugars

-The basis of cellular metabolism (Chapter 9)

-Naturally occur in ringed structures

Major examples:

-Glucose C6H12O6

-Fructose C6H12O6

-Galactose C6H12O6

-Always have the form

-This formula is different from the expected 1:2:1

ratio because of the removal of the water molecule

-Made up of TWO monosaccharides that have been

bound together because of dehydration

-Name of the bond is

Major Examples

-Sucrose

-Lactose

-Maltose

Biomolecules typically exist in large and complex structures

structures polymers. Much like constructing a brick wall, these polymers are

made from simpler pieces - we call these s simpler pieces

many monomers combine to form polymers. It is important to note that

polymers can sometimes be extremely large, millions of atoms, while some

polymers are relatively small. Also, in some cases, biomolecules exist in their

monomer form naturally (i.e. glucose).

The principle of polymerization is fairly simple. To make a polymer from a g

of monomers, water must be removed in order to connect the monomers

together - this process is known as dehydration or condensation

reaction, the breaking down of polymers into monomers would, in turn, require

the addition of water - this process is known as hydrolysis

dehydration and condensation make sense as they both refer to the production

of water; the term hydrolysis is also logical as hydro-

refers to splitting.

Biomolecules Chapter 5

According to the hierarchy of organization in biology, the unit of life (the cell), consists of a variety of organelles. The

of chemicals. These chemicals, or biomolecules, are the foundation of biological systems. Understandably, before we discuss the structure of cells,

it is important that we have an understanding of the substances that are the primary constituent of cellular elements (organe

les into four categories: carbohydrates, phospholipids, proteins, and nucleic acids.

As mentioned above, polymers (biomolecules) can be classified into four major categories: carbohydrates, lipids, proteins, and nucleic acids.

The carbohydrates, or sugars, are biomolecules that always contain carbon, hydrogen, and oxygen, Typically the ratio of thes

or larger carbohydrates due to the elimination of the water molecule(s) during dehydration. We

can group the carbohydrates into three major groups: the monosaccharides, the disaccharides, and the polysaccharides

Disaccharides

Always have the formula C12H22O11

This formula is different from the expected 1:2:1

ratio because of the removal of the water molecule

Made up of TWO monosaccharides that have been

bound together because of dehydration

Name of the bond is glycosidic linkage

Major Examples:

Sucrose (aka table sugar) --> glucose+fructose

Lactose (aka milk sugar) --> glucose+galactose

Maltose --> glucose+glucose

-Complex and huge formulas

-Usually, the monomer is glucose

-Bonds that link a

are still called glycosidic linkages that are formed

via dehydration reactions

Major Examples:

-Chitin-

* found on outside of fungi and arthropods

*humans cannot break down this polysaccharide

-Cellulose-

*makes up plant

*humans cannot breakdown this polysaccharide

*cellulose is dietary fiber

-Glycogen-

*animal storage of carbohydrates

*we store glucose as this polymer

*we build up glycogen in brain and muscles

-Starch-

*plant storage of carbohydra

*plants and animals use starch as a food source

*a classic example is a potato

Biomolecules typically exist in large and complex structures - we call these large

. Much like constructing a brick wall, these polymers are

we call these s simpler pieces monomers. In short,

many monomers combine to form polymers. It is important to note that

metimes be extremely large, millions of atoms, while some

polymers are relatively small. Also, in some cases, biomolecules exist in their

The principle of polymerization is fairly simple. To make a polymer from a group

of monomers, water must be removed in order to connect the monomers

condensation. The reverse

reaction, the breaking down of polymers into monomers would, in turn, require

hydrolysis. The terms

dehydration and condensation make sense as they both refer to the production

refers to water and -lysis

According to the hierarchy of organization in biology, the unit of life (the cell), consists of a variety of organelles. The organelles, in turn, are made

ion of biological systems. Understandably, before we discuss the structure of cells,

it is important that we have an understanding of the substances that are the primary constituent of cellular elements (organelles). Biochemists

ydrates, lipids, proteins, and nucleic acids.

The carbohydrates, or sugars, are biomolecules that always contain carbon, hydrogen, and oxygen, Typically the ratio of these three elements is

or larger carbohydrates due to the elimination of the water molecule(s) during dehydration. We

polysaccharides.

Polysaccharides

Complex and huge formulas

Usually, the monomer is glucose

Bonds that link all the monosaccharides together

are still called glycosidic linkages that are formed

via dehydration reactions

outside of fungi and arthropods

*humans cannot break down this polysaccharide

*makes up plant structure/body

*humans cannot breakdown this polysaccharide

*cellulose is dietary fiber

*animal storage of carbohydrates

*we store glucose as this polymer

*we build up glycogen in brain and muscles

*plant storage of carbohydrates

*plants and animals use starch as a food source

*a classic example is a potato

Lipids

The lipids are the only group of biomolecules that do not form tradition polymers. It is important to systematically break down this group of

biomolecules into three major categories: the fats, the phospholipids, and the steroids. The lipids are considered to be highly nonpolar when

compared with other biomolecules - remember that nonpolar means that these substances will not mix well with water.

Fats

-Two pieces to every fat: glycerol head and fatty

acid tail.

-Typically, there are three fatty acid tails attached

to a single glycerol.

-Fatty acid tails consist of long hydrocarbons.

-Ester linkages bond the glycerol head and fatty

acid tails.

-Saturated means that all the bonds are single.

-Unsaturated means that some bonds are double

bonds.

-Saturated fats are animal fats and are solid at

room temperature.

-Unsaturated fats are plant fats and are liquid at

room temperature.

-The major function of fats is energy storage - fat is

the preferred mechanism of storing energy. Fig. 5-11b

(b) Fat molecule (triacylglycerol)

Ester linkage

Phospholipids

-Three pieces to every phospholipid: glycerol head,

two fatty acid tails, and a phosphate head.

-The phosphate head is very polar while the rest of

the phospholipid is highly nonpolar. Fig. 5-13

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

Fatty acids

Hydrophilichead

Hydrophobictails

Choline

Phosphate

Glycerol

Hyd

rop

ho

bic

tails

Hyd

rop

hil

ic h

ead

-Therefore, we can consider the molecule to be

amphipathic because it has regions that are

nonpolar and other regions that are polar.

-Phospholipids are the major component of the cell

membrane that surrounds cells. Fig. 5-14

Hydrophilichead

Hydrophobictail

WATER

WATER

Steroids

-Always contain at least four carbon rings that

are fused (connected) together. Fig. 5-15

-The classic example of a steroid is cholesterol.

-Cholesterol can be found in the cell membrane

between phospholipids - the cholesterol

molecules help to maintain membrane fluidity.

-As expected, steroids are almost exclusively

nonpolar - therefore, they are not attracted to

water.

Proteins

Proteins (aka polypeptides) represent the most diverse group of biomolecules. The monomers of proteins are the amino acids. Proteins have

diverse shapes (conformations) based on sequences of amino acids. Amino acids are the monomers of proteins. The sequence of the amino acids

is predicated by the order of nucleic acids in DNA and RNA. In other words, different proteins have different amino acid compositions in a specific

order that is based on the genetic code. This principle is known as the Central Dogma of Molecular Biology and will be explored in Chapters 16

and 17. The amazing variety of these biomolecules, understandably, gives rise to a plethora of different functions that proteins may have. Table 5-1

As mentioned before, the monomers of

proteins are amino acids. There are 20 amino

acids that can be found naturally. Though we

are not concerned with knowing the names and

structures of the specific amino acids (you do

have to know the basic structure), we are

interested in understanding how amino acids

come together to form the elaborate

conformation of the protein. The following

table will illustrate a hierarchy of design - this

helps us to understand how simple amino acids

can combine to form elaborate proteins. Fig. 5-UN1

Aminogroup

Carboxylgroup

Alpha-carbon

The difference between each amino acid is the

'R' group. Different amino acids have different

atoms that compose the 'R' group.

The function that we most commonly make reference to is the action of proteins as enzymes. An enzyme is a biological catalyst that must be

present for biochemical reactions to proceed in a timely manner. Without enzymes, most biochemical reactions would not take place within our

lifetime! Since living organisms complete thousands of chemical reactions, it must be important for there to be a different enzyme for each

reaction. In other words, enzymes are all different - each enzyme has a specific shape and an ability to catalyze only one certain chemical reaction.

Primary Level

-The primary level refers to the

sequence of amino acids.

-The sequence of amino acids is

determined by the genetic code

(DNA).

-Peptide bonds are formed by

dehydrogenation reactions between

the two amino acids.

Peptide

bond

Fig. 5-18

Amino end(N-terminus)

Peptide

bond

Side chains

Backbone

Carboxyl end(C-terminus)

(a)

(b)

Secondary Level

-The secondary level of structure

refers to the formation of alpha

helixes and beta sheets.

-These two types of structures are

formed by Hydrogen-Bond

interactions between the amino

groups and carboxyl groups of

different amino acids.

Fig. 5-21c

Secondary Structure

pleated sheet

Examples of

amino acid

subunits

helix

Tertiary Level

-The tertiary level involves interactions

between the different 'R' groups.

-It is with this level that the polypeptide

begins to take a true shape.

-Many proteins exist as functional at this

level - while some do have quaternary

levels of structure.

-Ionic interactions, hydrophilic (polar)

interactions , hydrophobic (nonpolar)

interactions, sulfur bonds, and hydrogen

bonds are all involved in forming the

elaborate 3-dimensional structure of the

polypeptide/protein.

Fig. 5-21f

Polypeptidebackbone

Hydrophobicinteractions andvan der Waalsinteractions

Disulfide bridge

Ionic bond

Hydrogenbond

Quaternary Level

-The quaternary level can be seen

with some proteins, but many

proteins do not have this level of

organization.

-Quaternary level of protein

structure occurs when several

polypeptide chains (several large

pieces) combine to form an

immensely elaborate protein.

-Two examples are hemoglobin and

collagen.

Fig. 5-21g

Polypeptidechain

Chains

Heme

Iron

Chains

Collagen

Hemoglobin

As has been described in the table above, the ability of a protein to operate correctly is dependent from the very beginning. In other words, a

problem at the primary level will have affects that will ultimately lead to a bad and nonfunctioning protein. This idea is the focal point of the

following illustration.

Fig. 5-22

Primarystructure

Secondaryand tertiarystructures

Quaternarystructure

Normalhemoglobin(top view)

Primarystructure

Secondaryand tertiarystructures

Quaternarystructure

Function Function

subunit

Molecules donot associatewith oneanother; eachcarries oxygen.

Red bloodcell shape

Normal red bloodcells are full ofindividualhemoglobin

moledules, eachcarrying oxygen.

10 µm

Normal hemoglobin

1 2 3 4 5 6 7

Val His Leu Thr Pro Glu Glu

Red bloodcell shape

subunit

Exposedhydrophobicregion

Sickle-cellhemoglobin

Moleculesinteract withone another andcrystallize intoa fiber; capacity

to carry oxygen

is greatly reduced.

Fibers of abnormalhemoglobin deformred blood cell intosickle shape.

10 µm

Sickle-cell hemoglobin

GluProThrLeuHisVal Val

1 2 3 4 5 6 7

Sickle-cell anemia affects individuals with certain

abnormalities in the genetic code. As shown to the

left, the functioning genetic code will code for the

amino acid GLU at position 6; however, the amino

acid VAL is in position 6 in the sickle-cell genetic

code. Following down the improper primary

structure, we can see that the secondary, tertiary,

and quaternary levels are all affected. The result is

an abnormal hemoglobin molecule that is unable

to efficiently carry oxygen. This example not only

illustrates the hierarchy of protein structure, it also

illustrates genetics (the inheritance of DNA from

parents) as well as how molecular biology can

affect the organism globally.

Now would also be a good time to simply introduce

the Central Dogma of Molecular Biology since the

sickle cell example provides such an excellent

example:

DNA --> mRNA --> protein

In summation, the biochemical abilities of an

organism is entirely dependent on the genetic code

provided from parents.

Nucleic Acids

The importance of nucleic acids should now be understood. Nucleic acids, DNA and RNA, serve as a resource of genetic information that is

ultimately responsible for the ability to produce different proteins. In truth, it is the differences in proteins between us that separates us in

physical appearance. The following picture illustrates the central dogma even further.

Fig. 5-26-3

mRNA

Synthesis ofmRNA in thenucleus

DNA

NUCLEUS

mRNA

CYTOPLASM

Movement ofmRNA into cytoplasmvia nuclear pore

Ribosome

AminoacidsPolypeptide

Synthesisof protein

1

2

3

DNA and RNA are both polymers of nucleotide monomers. Each

nucleotide contains three pieces: a 5-carbon sugar (ribose for RNA

or deoxyribose for DNA), a nitrogenous base, and a phosphate

group. The differences between the different nucleotides is the

nitrogenous base - this gives us A, T, G, and C for DNA and A, U, G,

and C for RNA. Fig. 5-27ab

5' end

5'C

3'C

5'C

3'C

3' end

(b) Nucleotide

Nucleoside

Nitrogenousbase

3'C

5'C

Phosphategroup Sugar

(pentose)