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Overview: The Molecules of Life

All living things are made up of four classes of large biological molecules: carbohydrates,

lipids, proteins, and nucleic acids.

Macromolecules are large molecules composed of thousands of covalently connected

atoms, carbohydrates, , proteins, and nucleic acids …. lipids are not large enough to be

considered as macromolecule.

Concept 5.1: Macromolecules are polymers, built from monomers

A polymeris a long molecule consisting of many similar building or identical blocks linked

by covalent bond.

These small building-block molecules are called monomers. In addition to forming

polymers, some monomers have functions of their own.

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

Carbohydrates

Proteins

Nucleic acids

The Synthesis and Breakdown of Polymers

In cells, these processes are facilitated by enzymes.

A dehydration reaction occurs when two monomers bond together through the loss of a

water molecule

Polymers are disassembled to monomers by

hydrolysis, a reaction that is essentially the

reverse of the dehydration reaction.

When a bond forms between two monomers,

each monomer contributes part of the water

molecule that is released during the reaction: One

Biological Macromolecules and Lipids

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monomer provides a hydroxyl group ( - OH), while the other provides a hydrogen ( - H).

This reaction is repeated as monomers are added to the chain one by one, making a polymer

(also called polymerization or Condensation reaction)

Hydrolysis means water breakage.

The bond between monomers is broken by the

addition of a water molecule, with a hydrogen

from water attaching to one monomer and the

hydroxyl group attaching to the other.

Note:

The number of covalent bond in the compound

that consist of several monomers = number of monomer - 1

(also equal the number of H2O molecules release when synthesis or require to breakdown this molecule)

Concept 5.2: Carbohydrates serve as fuel and building material

Carbohydrates include sugars and the polymers of sugars.

The general formula for any carbohydrate is (CH2O)x.

The name of any carbohydrate compound ends with OSE , with the exception of some old

names like glycogen , starch ...

The simplest carbohydrates are monosaccharides, or single sugars.

polysaccharides, composed of many sugar building blocks.

2 ) How many H2O molecules release

when synthesis this compound? 99

1 ) How many covalent bonds are in a compound made of 100

monomers? Number of monomers -1 …= 100 -1 = 99

3 ) How many H2O molecules require to breakdown this

compound? 99

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Sugars

Monosaccharides have molecular formulas

that are usually multiples of (CH2O)X. where

X is any number between three and seven.

Glucose (C6H12O6 ) is the most common

monosaccharide.

Monosaccharides are classified by:

The location of the carbonyl group (as

aldose or ketose)

The number of carbons in the carbon

skeleton.

If the carbonyl group in C1 its Aldose , if the

carbonyl group in C2 its Ketose.

Monosaccharides are highly divers:

1) They are different in number of C.

2) They are different in location of carbonyl

group.

3) They are different in the form , there is

open chain and ring structure, also the

ring structure (Cyclic) could be: β or α.

Though often drawn as linear skeletons, in aqueous

solutions many sugars form rings (ring structure more

stable).

Monosaccharides serve as a major fuel for cells and as

raw material for building molecules

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The carbonyl group of C1 react with the hydroxyl group of C5. This is the most stable ring

form.

The oxygen of the hydroxyl group of C5 joined the ring.

All OH groups on the right side of liner structure are written downwards.

All OH groups on the left side of liner structure are written upwards.

C6 is outside the ring.

approximately 80% of glucose present in the ring structure.

If the OH group where the ring is formed (C1 in glucose & C2 in fructose) in the right side it is α sugar

while If the OH group in the left side it is β sugar.

Monosaccharides functions:

1. particularly glucose, are major nutrients for cells. In the process known as cellular

respiration, cells extract energy from glucose molecules.

2. as raw material for the synthesis of other types of small organic molecules, such as amino

acids and fatty acids.

3. monomers for disaccharides or polysaccharides.

Disaccharide

A disaccharide is formed when a dehydration reaction joins two monosaccharides

This covalent bond is called a glycosidic linkage.

The molecular formula of disaccharide : (C6H12O6)*2 – H2O……(C12H22O11)

There are 3 examples of disaccharides:

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1. Maltose is a disaccharide formed by the linking of two molecules of α glucose. Also

known as malt sugar

The type of bond in maltose is α-1,4-glycosidic linkage

2. The most prevalent disaccharide is sucrose, or table sugar. Its two monomers are glucose

and fructose.

The type of bond in sucrose is α-1,2-glycosidic linkage

3. Lactose, the sugar present in milk, is another disaccharide, in this case a glucose

molecule joined to a galactose molecule.

The type of bond in Lactose is α-1,4-glycosidic linkage.

Polysaccharides

Polysaccharides, the polymers of sugars, have storage and structural roles.

Maltose (malt sugar) Glucose + Glucose α-1,4-glycosidic linkage

Sucrose (table sugar) Glucose + Fructose

α-1,2-glycosidic linkage

Lactose (milk sugar) Glucose + Galactose α-1,4-glycosidic linkage

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The structure and function of a polysaccharide are determined by its sugar monomers and

the positions of glycosidic linkages.

Storage Polysaccharides

Starch, a storage polysaccharide of plants, consists entirely of glucose monomers.

Starch is energy storage polysaccharide in plants.

There are two kinds of starch:

Amylose : helical and unbranched , composed of α glucose linked by α-1,4-glycosidic

linkage

Amylopectin: helical and branched , composed of α glucose linked by α-1,4-

glycosidic linkage , but at the branches points the type of bond is α-1,6-glycosidic

linkage. (more complex)

Most animals, including humans, have enzymes that can hydrolyze plant starch which called

Salivary α-amylase, making glucose available as a nutrient for cells.

The simplest form of starch is amylase.

Glycogen is a energy storage polysaccharide in animals.

Glycogen similar to amylopectin in structure (helical and branched) but more branched than

amylopectin.

Composed of α glucose linked by α-1,4-glycosidic linkage , but at the branches points the

type of bond is α-1,6-glycosidic linkage.

Humans store glycogen mainly in liver and muscle cells.

Structural Polysaccharides

The polysaccharide cellulose is a major component of the tough wall of plant cells.

Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ.

Starch: 1-4 linkage of α glucose monomers.

Cellulose: 1–4 linkage of β glucose monomers.

Cellulose is linear and unbranched.

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Enzymes that digest starch by hydrolyzing its α linkages are unable to hydrolyze the β

linkages of cellulose due to the different shapes of these two molecules.

Some microorganisms (bacteria and fungi) can digest cellulose, breaking it down into

glucose monomers.

few organisms possess enzymes that can digest cellulose. Almost all animals, including

humans, do not; the cellulose in our food passes through the digestive tract and is eliminated

with the feces.

Along the way, the cellulose abrades the wall of the digestive tract and stimulates the lining

to secrete mucus, which aids in the smooth passage of food through the tract.

Thus, although cellulose is not a nutrient for humans, it is an important part of a healthful

diet.

Most fruits, vegetables, are rich in cellulose.

Some microorganisms can digest cellulose, breaking it down into glucose monomers. A cow

harbors cellulose digesting prokaryotes in its gut.

Another important structural polysaccharide is chitin, the

carbohydrate used by arthropods (insects, spiders) to build their

exoskeletons.

Chitin is similar to cellulose (linear and unbranched), with β

linkages, except that the glucose monomer of chitin has a

nitrogen-containing attachment.

Chitin is indigestible by humans.

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Concept 5.3: 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

Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar

covalent bonds

The most biologically important lipids are fats, phospholipids, and steroids

Fats

fats are not polymers, they are large molecules assembled

from smaller molecules by dehydration reactions.

A fat is constructed from two kinds of smaller molecules:

glycerol and fatty acids.

Glycerol is an alcohol; each of its three carbons bears a

hydroxyl group.

A fatty acid has a long carbon skeleton, usually 16 or 18

carbon atoms in length.

The carbon at one end of the skeleton is part of a carboxyl

group, the functional group that gives these molecules the

name fatty acid.

The rest of the skeleton consists of a hydrocarbon chain.

The relatively nonpolar C-H bonds in the hydrocarbon chains of fatty acids are the reason

fats are hydrophobic.

In making a fat, three fatty acid molecules are each joined to glycerol by an covalent bond

called ester linkage, a bond formed by a dehydration reaction between a hydroxyl group and

a carboxyl group.

The resulting fat, also called a triacylglycerol, thus consists of three fatty acids linked to one

glycerol molecule. (Still another name for a fat is triglyceride).

Storage Polysaccharides

Structural Polysaccharides

Starch(Amylopectin & Amylopectin) Starch cellulose

Glycogen chitin

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There is 2 types of fatty acid:

Saturated

Unsaturated

These terms refer to the structure of the

hydrocarbon chains of the fatty acids.

If there are no double bonds between carbon

atoms composing a chain, then as many

hydrogen atoms as possible are bonded to the

carbon skeleton. Such a structure is said to be

saturated with hydrogen, and the resulting fatty acid is therefore called a saturated fatty acid.

An unsaturated fatty acid has one or more double

bonds, with one fewer hydrogen atom on each

double-bonded carbon.

Nearly every double bond in naturally occurring

fatty acids is a cis double bond, which creates a

kink in the hydrocarbon chain wherever it occurs.

A fat made from saturated fatty acids is called a

saturated fat. Most animal fats are saturated.

Saturated animal fats—such as lard and butter—

are solid at room temperature.

The hydrocarbon chains of their fatty acids—the “tails” of the fat molecules—lack double

bonds, and their flexibility allows the fat molecules to pack together tightly.

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In contrast, the fats of plants and fishes are generally unsaturated, meaning that they are built

of one or more types of unsaturated fatty acids.

Usually liquid at room temperature, plant and fish fats are referred to as oils

The kinks where the cis double bonds are located prevent the molecules from packing

together closely enough to solidify at room temperature.

A diet rich in saturated fats is one of several factors that may contribute to the cardiovascular

disease known as atherosclerosis.

The major function of fats is:

1. Energy storage (the hydrocarbon chains of fats are similar to gasoline molecules and just

as rich in energy).

2. Shocks absorption (adipose tissue cushions such vital organs as the kidneys).

3. Insulation (a layer of fat beneath the skin insulates the body).

Phospholipids

Cells as we know them could not exist without another

type of lipid—phospholipids. Phospholipids are

essential for cells because they are major constituents of

cell membranes.

a phospholipid is similar to a fat molecule but has only

two fatty acids attached to glycerol rather than three.

1 glycerol + 2 F.A

Saturated Fats Unsaturated Fats All F.A are saturated One or more F.A are unsaturated

High C to H ratio low C to H ratio

High melting point Presence of kinks

Solid at room temperature Liquid at room temperature

In animals (Fat) In plants (vegetable oil)

Less healthy More healthy

Ex, butter Ex, olive oil , corn oil, soya oil

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The third hydroxyl group of glycerol is joined to a phosphate group, which has a negative

electrical charge in the cell.

Typically, an additional small charged or polar molecule is also linked to the phosphate

group. Choline is one such molecule , but there are many others as well, allowing formation

of a variety of phospholipids that differ from each other.

The two ends of phospholipids show different behaviors with respect to water. The

hydrocarbon tails are hydrophobic and are excluded from water. However, the phosphate

group and its attachments form a hydrophilic head that has

an affinity for water.

When phospholipids are added to water, they self-

assemble into a double-layered sheet called a “bilayer”

that shields their hydrophobic fatty acid tails from water

At the surface of a cell, phospholipids are arranged in a similar bilayer.

The hydrophilic heads of the molecules are on the outside of the bilayer, in contact with the

aqueous solutions inside and outside of the cell.

The hydrophobic tails point toward the interior of the bilayer, away from the water.

Phospholipids Function

Major structural component of plasma membrane of all cells.

Saturated Phospholipids Unsaturated Phospholipids Solid Liquid

All F.A are saturated One or more F.A are unsaturated

High C to H ratio low C to H ratio

NO kinks Presence of kinks

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Steroids

Steroids are lipids characterized by a carbon

skeleton consisting of four fused rings. Different

steroids are distinguished by the particular

chemical groups attached to this ensemble of

rings.

Cholesterol, a type of steroid, is a crucial

molecule in animals.

It is a common component of animal cell membranes and is also the precursor from which

other steroids, such as the vertebrate sex hormones, are synthesized.

A high level of cholesterol in the blood may contribute to atherosclerosis.

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Concept 5.4: Proteins include a diversity of structures, resulting in a

wide range of functions

Proteins are all constructed from the same set of 20 amino acids, linked in unbranched

polymers.

The bond between amino acids is called a

peptide bond, so a polymer of amino acids is

called a polypeptide.

A protein is a biologically functional

molecule made up of one or more

polypeptides, each folded and coiled into a

specific three-dimensional structure.

When two amino acids are positioned so that

the carboxyl group of one is adjacent to the

amino group of the other, they can become

joined by a dehydration reaction, with the

removal of a water molecule.

The resulting covalent bond is called a

peptide bond. Repeated over and over, this

process yields a polypeptide, a polymer of many amino acids linked by peptide bonds.

Note that one end of the polypeptide chain has a free amino group (the N-terminus of the

polypeptide), while the opposite end has a free carboxyl group (the C-terminus).

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Amino Acid Monomers

All amino acids share a common structure.

A.A consider as monomers of proteins.

An amino acid is an organic molecule with both an amino group and a carboxyl group .

At the center of the amino acid is an asymmetric carbon atom called the alpha (α) carbon.

Its four different partners are an amino group, a carboxyl group, a hydrogen atom, and a

variable group R.

The R group, also called the side chain, differs with each amino acid.

The amino acids are grouped according to the properties of their side chains.

One group consists of amino acids with nonpolar side chains, which are hydrophobic

Another group consists of amino acids with polar side chains, which are hydrophilic.

Acidic amino acids have side chains that are generally negative in charge due to the presence

of a carboxyl group.

Basic amino acids have amino groups in their side chains that are generally positive in

charge.

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Proteins Function

1. Enzymatic proteins (catalyst)

2. Storage proteins (ovalbumin)

3. Transport proteins (Hemoglobin which transport

O2)

4. Structural proteins (collagen)

5. Defensive proteins (Antibodies)

6. Hormonal proteins (insulin)

7. Receptor proteins

8. Contractile proteins “ motors” (actin & myosin)

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Four Levels of Protein Structure

Proteins share three superimposed levels of structure, known as

primary, secondary, and tertiary structure. (composed of one

polypeptide)

A fourth level, quaternary structure, arises when a protein

consists of two or more polypeptide chains.

1. Primary Structure: Linear chain of amino acids

Primary structure of a protein is its sequence of amino acids.

The precise primary structure of a protein is determined by

inherited genetic information.

Primary structure in turn dictates secondary and tertiary structure

2. Secondary Structure: Regions stabilized by hydrogen bonds between atoms of the

polypeptide backbone

Most proteins have segments of their polypeptide chains repeatedly coiled or folded in

patterns that contribute to the protein’s overall shape.

These coils and folds, collectively referred to as

secondary structure, are the result of hydrogen

bonds between backbone constituents (not the R

group).

One such secondary structure is the helix, a

delicate coil held together by hydrogen bonding

between every fourth amino acid.

The other main type of secondary structure is the

pleated sheet. two or more segments of the

polypeptide chain lying side by side (called

strands) are connected by hydrogen bonds

between parts of the two parallel segments of

polypeptide backbone.

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3. Tertiary Structure : Three-dimensional shape stabilized by interactions between side

chains

tertiary structure is the overall shape of a polypeptide resulting from interactions between

the side chains (R groups) of the various amino acids.

interaction that contributes to tertiary structure:

Hydrophobic interaction. As a polypeptide folds into its functional shape, amino acids

with hydrophobic (nonpolar) side chains usually

end up in clusters at the core of the protein, out of

contact with water. van der Waals interactions help

hold them together.

Hydrogen bonds between polar side chains and

ionic bonds between positively and negatively

charged side chains also help stabilize tertiary

structure.

Covalent bonds called disulfide bridges may further reinforce the shape of a protein.

Disulfide bridges form where two cysteine monomers, which have sulfhydryl groups (—

SH) on their side chains, are brought close together by the folding of the protein.

4. Quaternary Structure: Association of two or

more polypeptides (some proteins only)

Quaternary structure is the overall protein structure

that results from the aggregation of two or more

polypeptide chain.

For example, Hemoglobin, the oxygen-binding

protein of red blood cells, is an example of a globular protein with quaternary structure. It

consists of four polypeptide subunits.

Another example is collagen, which is a fibrous protein that has three identical helical

polypeptides intertwined into a larger triple helix, giving the long fibers great strength.

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Denaturation of protein

• Is the disruption in protein bond resulting in loss of protein structure and function

• The denatured protein is biologically inactive.

• Factors that cause protein to denature:

Temperature (heating)

pH

When a protein denatured by heat or chemicals, it can sometimes return to its functional

shape (renaturation)when the denaturing agent is removed. (Sometimes this is not possible)

Concept 5.5. Nucleic acids

Nucleic acids (polynucleotides): many nucleotides linked by many covalent bond called

phosphodiester bond.

Nucleic acids are polymers made of monomers called nucleotides.

The two types of nucleic acids:

1. deoxyribonucleic acid (DNA)

2. ribonucleic acid (RNA)

A nucleotide, in general, is composed of three parts:

1. five-carbon sugar (a pentose)

2. nitrogen-containing (nitrogenous) base

3. one to three phosphate groups. The beginning

monomer used to build a polynucleotide has three

phosphate groups, but two are lost during the

polymerization process

The portion of a nucleotide without any

phosphate groups is called a nucleoside.

The nitrogenous bases

Each nitrogenous base has one or two rings

that include nitrogen atoms.

There are two families of nitrogenous bases: pyrimidines and purines.

A pyrimidine has one six-membered ring of carbon and nitrogen atoms. The members of the

pyrimidine family are cytosine (C), thymine (T), and uracil (U).

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Purines are larger, with a six-membered ring fused to a five-membered ring. The purines are

adenine (A) and guanine (G).

Adenine, guanine, and cytosine are found in both DNA and RNA; thymine is found only in

DNA and uracil only in RNA.

In DNA the sugar is deoxyribose; in RNA it is ribose

The only difference between these two sugars is that deoxyribose lacks an oxygen atom on

the second carbon in the ring, hence the name

deoxyribose

The two free ends of the polymer are distinctly

different from each other. One end has a phosphate

attached to a 5′ carbon, and the other end has a

hydroxyl group on a 3′ carbon; we refer to these as

the 5′ end and the 3′ end, respectively.

We can say that a polynucleotide has a built-in

directionality along its sugar-phosphate backbone, from 5′ to 3′.