Chapter 5: Biological Molecules

Carbon based compoundConsist of C, H, O atomsSometimes P, N, S atoms

Properties depends on :Arrangement of carbon skeletonFunctional group

Functional groups

Def : the component of the organic molecules that commonly involved in chemical reactions.

Usually located at the terminal of molecules structure

Provide a unique properties to molecules

FUNCTIONAL GROUPS

Hydroxyl groups Carboxyl groups

Amino groups Sulfhydryl groups

Phosphate groups

Carbonyl

a) Hydroxyl groups

Hydrogen atoms bonded to oxygen atomLocated at one end of the carbon skeletonCalled alcoholsSpecific names end in – olEg : Propanol, Ethanol

H

H C OH

H

Methanol

H H

H C C OH

H H

Ethanol

H H H

H C C C H

H OH H

2-Propanol

Functional properties

PolarElectronegative oxygen atom drawing electrons

toward itself

Attract water molecules, help to dissolve organic compounds.Eg : Sugar

b) Carboxyl group

When an oxygen atom is double-bonded to a carbon atom that is also bonded to a hydroxyl group.

- COOHCompound with carboxyl groups :

Carboxylic acid or Organic acid

H O

H C C OH

H

Acetic acid

Functional properties

Act as source of Hydrogen ions (H+)Acidic properties

The covalent bond between O and H So polarH+ ions tend to dissociate reversibly

c) Carbonyl group

Consist of carbon atom joined to an oxygen atom by a double bond

- COKnown as ketones

If the carbonyl group is within a carbon skeleton

Known as aldehydesIf the carbonyl group is at the end of skeleton

H O H

H C C C H

H H

H H O

H C C C H

H H

Acetone (ketone) Propanal (Aldehyde)

Functional properties

Ketone and aldehyde is a structural isomer with different properties

d) Amino groups

Consists of a nitrogen atom bonded to two hydrogen atom and to the carbon skeleton

- NH2

Known as aminesEg : Amino acid

H H O

N C C OH

H H

Glycine

Functional properties

Acts as a baseAble to pick up proton from surrounding

H H

N N H

H H

Non-ionized ionized

e) Sulfhydryl groups

Consists of a sulfur atom bonded to an atom of hydrogen

Resemble a hydroxyl group in shape- SHKnown as thiolsEg : Ethanethiol

H H

H C C SH

H H

Ethanethiol

Functional properties

2 sulfhydryl groups can interact to help stabilize protein structure

f) Phosphate group

Phosphorus atom is bonded to four oxygen atoms

- OPO32-

It is an ionized form of a phosphoric acid group ( - OPO3H2)

Known as organic phosphate

OH OH H O

H C C C O P O-

H H H O-

Glycerol phosphate

Functional properties

Makes the molecule of which it is a part an anion (negatively charge ion)

Able to transfer energy between organic molecules

MACROMOLECULE

Macromolecules

Known as large molecules : chain-like molecules

Called polymersLong molecules consisting of many similar or

identical building blockLinked by covalent bondForm by monomers

Biological molecules

CarbohydratesLipid Protein Nucleic acid

CARBOHYDRATES

Carbohydrates

Include sugar and polymers of sugarThe simplest carbohydrates :

Monosaccharides (simple/single sugar)

Disaccharides : double sugars

(2 monosaccharides joins by condensation reaction)

Polysaccharides (polymers composed of many sugar building blocks)Eg : Carbohydrates

Monosaccharides

From the Greek words, Monos : single and Sacchar : sugar

Three types; glucose,galactose,fructoseGenerally have molecular formula that are

multiple of unit CH2O

Glucose, C6H12O6 – common monosaccharides

Contain a carbonyl group and multiple of hydroxyl groups

The structure and classification of some monosaccharides :

Location of carbonyl group

Length of carbon skeleton

Spatial arrangement around asymmetric carbons

Sugar is either aldose or ketose, depending on the location of carbonyl groupGlucose and Galactose – aldoseFructose – ketose

The size of carbon skeleton

(range from 3 to 7)6-carbon sugar : Hexose5-carbon sugar : Pentose

Spatial arrangement of the parts around asymmetric carbon.

Asymmetric carbon :Carbon attached to 4 different kinds of partner

Eg : Glucose and Galactose

Glucose Galactose

Glucose can be divide into 2 part :Depends on the location of the Hydroxyl group

at carbon 1

Known as :Hydroxyl up – β (Beta)Hydroxyl down – α (Alpha)

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In aqueous solution, glucose molecules form ring structure

Dissacharides

Consists of 2 monosaccharides joined by a glycosidic linkage

Glycosidic linkage – covalent bond formed by dehydration reaction

Eg :

Maltose Glucose + Glucose

Sucrose Glucose + Fructose

Glucose Glucose

Maltose

Polysaccharides

MacromoleculesConsists of few hundred to a few

thousand of monosaccharidesLink by glycosidic linkageThe process known as condensation

(eliminates water)Serve as :

Storage materialBuilding material

Storage material:

Starch (plants)Glycogen (animals)

Storage materialStarch

Storage polysaccharides for plants

Consists entirely glucose monomersMostly joined by α (1-4) linkagesThe angle – formed polymer helicalType of starch :

AmyloseAmylopectin

AmyloseThe simplest form of starchUnbranched

AmylopectinMore complex formBranched polymer1-6 linkages at the branch point

Amylose

amylopectin

Animal stored polysaccharides – GlycogenPolymer resemble amylopectin but more

extensively branched

Branch linkages every 8 – 10 residuesHuman and vertebrates stored glycogen

in liver and muscle cells

Building materials;

CelluloseChitin

Building material- cellulose

Known as structural polysaccharidesEg : Cellulose

Major component of the tough walls that enclose plant cells

Polymer of glucose but the glycosidic linkages is different from starch

When glucose form a ring, the hydroxyl group attached to num 1 carbon is positioned either below or above the plane

Glucose monomer in cellulose are all in β configuration

Cellulose molecule is straightUnbranchedThe hydroxyl group free to hydrogen

bonded with the hydroxyl group of other cellulose

In plant cell walls, parallel cellulose held together forming microfibrils

Can be digested by cellulase enzyme

Cellulose

Chitin – structural polysaccharides used by arthropods

To build up exoskeletonIs hardened with the aid of calcium

carbonate (salt)Same like cellulose but the glucose

monomer has a nitrogen-containing appendage

Chitin

LIPIDS

LIPIDS

Characterized:-soluble in nonpolar solvents (chloroform

and ether)-insoluble to water solvent-hydrophobic – no or little affinity to water-not polymer but a large moleculesExamples; fatty and oils, waxes,

phospholipids steroid and cholesterol

Importances of lipid:

Stored energy in adipose tissuesComponents of the cell membranesPart of hormones, pigment and

cholesterol

Types of lipid:

Saturated fatty acid- no double bonds-Exm: animals fat (solid at room

temperature)

Unsaturated fatty acid- one or more double bonds- Exm : fats of plants and fishes (liquid at

room temperature)

SATURATED UNSATURATED

CLASSIFIACTION OF LIPIDS

Simple Lipids:

A) fats (triglycerol)Constructed from glycerol (C3H8O3) and

fatty acidsTriglycerol consist of : 3 fatty acid (tail)

and 1 glycerol molecules (head)By condensastion proces by ester linkage

B) PhospholipidConsist of one moelcule glycerol with two

fatty acid and one phosphate group (- charge)

Amphiphatic moelcule (hydophlilic- head and hydrophobic – tail

It will self essembled or arranged bilayer.Form of micelle

Sphingolipid

Consist of three-carbon backbone known as sphingosine

Sphingosine : nitrogen-containing alcohol

Play an important role in signal transmission and cell recognition

Amphiphatic moleculesPolar head and two non-polar fatty acid tail

Structure :Sphingosine backboneAmide link to fatty acidPolar molecule

Types of sphingolipids

Divided into two sub categories :SphingomyelinsGlycosphingolipids

SphingomyelinsFound in animal cell membranesEspecially in myelin sheath, surround nerve

cells axon

Consist of phosphorylcoline and ceramide (sphingosine bonded to fatty acid via amide linkage)

GlycosphingolipidsDistributed mainly on the surface of the cellHelp cell to interact with its surroundingActs as a distinguishing markers

Waxes

Mixture of monohydroxy alcohols and a long chain of fatty acids

Harder and less greasy than fats

Less dense than water and soluble in alcohol and ether but not in water

Generally solid at room temperature

Found naturally as coating on fruits, insect exoskeleton, leaves

Birds have glands producing wax for feathers

Simple lipids

Divided into :

Prostalglandins (hormone-like molecules)

Terpene

Prostalglandins

A group of lipids derived enzymatically from fatty acid

Unsaturated fatty acids

Contain 20 carbon atom, including 5-carbon ring

Prostalglandins…functions

Cause constriction in vascular smooth muscle cells

Cause aggregation or dissaggregation of platelet

Control human regulationControl cell growth

Terpene

Derived biosynthetically from isoprene

Molecular formula, (C5H8)n

n : represents isoprene units

Types of terpene :SteroidBile salt

Steroids

Carbon skeleton consists of four fused ring

Different steroid will have different functional group attach to the rings

The most abundant steroids : Cholesterol

Cholesterol

Common component in animal cell membranes

Amphiphatic molecules

AssignmentDraw a structure of this compenents:A) unsaturated fatty acidB) saturated fatty acidC) phospholipidD) triglycerolE) sphingosineF) sphingomyelin

buses of steroid

1 page essays

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G) prostoglandineH) terpenei) steroidJ) cholesterol

PROTEIN

PROTEIN

Large moleculesComposed of carbon, hydrogen, oxygen

and nitrogenSulphur – rarelyComposed of simple sub-unit : amino

acidsPolymer of protein : polypeptide

Polypeptides

Constructed from the same 20 amino acid

Protein consists of one or more polypeptides folded and coiled

Forming specific conformation

Amino acid

MonomerOrganic molecules possessing both

carboxyl and amino groups

At the center of amino acid – asymmetric carbon atom called alpha (α) carbon

Partner of carbon :Amino groupCarboxyl groupA hydrogen atomVariable group, R

R group : also known as the side chainDiffers with each amino acidHave 20 amino acids

Divided into 3 groups :Non-polarPolarElectrically charged

Non-polar amino acids

Amino acid with non-polar side chain

Hydrophobic

Example :Glycine (Gly), Alanine (Ala), Valine (Val), Leucine

(Leu), Isoleucine (Ile), Methionine (Met)

Phenylalanine (Phe), Tryptophan (Trp), Proline (Pro)

Polar

Amino acid with polar side chain

Hydrophilic

Example :Serine (Ser), Threonine (Thr), Cysteine (Cys),

Tyrosine (Tyr), Asparagine (Asn), Glutamine (Gln)

Electrically charged

Amino acid with side chains that are electrically charged

If +ve : basic amino acid

If –ve : acidic amino acid

Hydrophilic

Example :Aspartic acid (Asp), Glutamic acid (Glu), Lysine

(Lys), Arginine (Arg), Histidine (His)

Aspartic acid Lysine

Amino acid polymer

When 2 amino acid with carboxyl group adjacent with the amino group of the other

Enzyme cause catalyzing a dehydration reaction

Resulting in a covalent bond : Peptide bond

This process repeated continuously forming a polypeptides

At one end of polypeptide chain is a free amino group and the opposite end is a free carboxyl group

Chain with amino end (N-terminus) and carboxyl end (C-terminus)

Protein conformation and Function

Functional protein consists of not just a polypeptide chain but one or more polypeptides twisted, coiled and folded

To form a unique molecular, three- dimensional shape

Determining based on the amino acid sequence

Occur or fold spontaneously

The folding is driven by the formation of variety of bonds between parts of the chain

Many protein : Globular (roughly spherical)

Others : Fibrous

Four level of protein structure

Primary structure

Secondary structure

Tertiary structure

Quaternary structure

Primary structure

Linear polymer

Linked by peptide bond

Example : Transthyretin

Globular protein found in the blood that transport vitamin A

Secondary structure

Consists of polypeptide chain repeatedly coiled or folded

Due to hydrogen bonds between the repeating constituents of polypeptide backbone

Both oxygen and nitrogen atoms of the backbone are electronegative

Creates a partial negative charges

The weakly positive H atom attached to N atom has affinity for the O atom of the nearby peptide bond : Hydrogen bond

The division of protein secondary struc…

α-helixPolypeptide coil held together by hydrogen

bondingOccur between 4th amino acidHydrogen bond occur between –CO and –NH

of the backboneThe bond maintain the structure of α-helixExample : keratin in hair

β-pleated sheet2 or more regions of polypeptide chain lying

side by sideConnected by Hydrogen bondPresent either as parallel or anti-parallelExample : Silk

Tertiary structure

Conformation of secondary structure

Interaction between side chains (R group)

Types of interactions :Hydrophobic interactionHydrogen bondIonic bondDisulphide bridge

Hydrophobic interaction

Involve amino acid with a non-polar side chain

Formation of cluster at the core of protein – away from water

Once the non-polar amino acid side chain close together, Van der walls interactions hold them together

Hydrogen bondOccur between polar amino acid side chain

Ionic bondLinkage between positively and negatively

charged side chain

Disulfide bridgeFormed between 2 cystein monomers

Quartenary structure

Consist of the overall protein structure that result from the aggregation of the polypeptide subunit

Complex molecule

Example : Collagen and hemoglobin

CollagenFibrous protein3 helical polypeptides, supercoiled forming

rope-like structureFound in connective tissues

HemoglobinGlobular protein4 polypeptide chain2 are α-chains and 2 are β-chainsPresent of non-polypeptide component eg:

heme group and iron atom

Conjugated protein

Proteins incorporated with non-protein components

Exist within the structure and perform specific function

Non-protein component : prosthetic groupExample :

Hemoglobin and HemeMucin and Carbohydrate

Denaturation and Renaturation

DenaturationPhysical or chemical aspect which cause the

protein to lose their native conformationInterrupt the function of protein (Inactive)Interrupt the chemical bonding

Factors affecting : pH, [salt], temperature and chemical substance

RenaturationThe process of returning back the protein

conformation into its normal stateHappen when the denaturing agent been

removed

Functions

Formation of cell membraneSynthesize of new cells and tissuesFormation of enzymeAntibodiesHormonesContractile proteins – cell motility

NUCLEIC ACID

Compound consist of polymers or unit of inheritance known as gene

2 types :Deoxyribonucleic acid (DNA)Ribonucleic acid (RNA)

Functions

Enable living organisms to reproduce their complex components

DNA directs RNA synthesis

RNA controls protein synthesis

DNA inherits from parents

The structure of nucleic acid

Nucleic acid : Macromolecules

Exists as polymers called polynucleotide

The basic unit : Nucleotide

Composed of three partsPentose sugarNitrogenous basePhosphate group

Nucleotide monomers

Nucleotide without phosphate group : Nucleoside

Nitrogenous base consist of 2 families :PyrimidinesPurines

Pyrimidines

Six-membered ring of carbon and a nitrogen atoms

The members :Cytosine (C)Thymine (T) – found in DNAUracil (U) – found in RNA

Purines

Larger than pyrimidines

Six-membered ring fused to five-membered ring

The members :Adenine (A)Guanine (G)

Connected to nitrogenous base is Pentose sugar

In RNA, the sugar is ribose and in DNA, the sugar is deoxyribose

Deoxyribose lack oxygen atom on the 2nd carbon

To complete the nucleotide, require a phosphate group

Phosphate group attached to carbon-5 in the pentose sugar

Nitrogenous base attached to carbon-1 in the pentose sugar

Nucleotide polymers

The nucleotides are joined by a covalent bond : phosphodiester linkages

The linkages between –OH group on 3’ carbon of a nucleotide and the phosphate on the 5’ carbon of the next

The sequence of nitrogenous bases in polymer is unique for each gene

DNA consist of hundred to thousand nucleotides

Arranged in four bases sequence

Example : AGTC

DNA double helix

DNA have 2 polynucleotides that spiral around an axis – form double helix

Proposed by James Watson and Francis Crick in 1953

The sugar-phosphate backbone run in opposite 5’ 3’ direction (antiparallel)

The two sugar-phosphate backbone are on the outside of the helix and the nitrogenous bases are paired inside the helix

Held together by hydrogen bond

Van der Walls interaction form between the stacked bases

Only certain bases are compatible with each other

Adenine (A) always paired to Thymine (T)

Guanine (G) always paired to Cytosine (C)

Adenine will form 2 hydrogen bonds with Thymine

Guanine will form 3 hydrogen bonds with Cytosine

GC formation indicates the strength of the DNA sequences

This pairing enable the researcher to predict the other strand sequences

5’- AGTTACGGTA-3’

3’- TCAATGCCAT-5’

The two strand always complimentary to each other

In cell division, the strand of DNA serve as a template to form a new complimentary strand

The identical copies is distributed to two daughter cells

In RNA, Thymine (T) is paired to Uracil (U) rather than Adenine (A)

RNA also have polarity

Single-stranded