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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)
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
Times new roman font 12, spacing 1.5
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