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Chapter 5: Biological Molecules

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1 Chapter 5: Biological Molecules
Carbon based compound Consist of C, H, O atoms Sometimes P, N, S atoms Properties depends on : Arrangement of carbon skeleton Functional group

2 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

3 Carbonyl Hydroxyl groups Carboxyl groups FUNCTIONAL GROUPS Amino groups Sulfhydryl groups Phosphate groups

4 a) Hydroxyl groups Hydrogen atoms bonded to oxygen atom
Located at one end of the carbon skeleton Called alcohols Specific names end in – ol Eg : Propanol, Ethanol

5 H H C OH H H H C C OH Methanol Ethanol H H H H C C C H H OH H 2-Propanol

6 Functional properties
Polar Electronegative oxygen atom drawing electrons toward itself Attract water molecules, help to dissolve organic compounds. Eg : Sugar

7 b) Carboxyl group When an oxygen atom is double-bonded to a carbon atom that is also bonded to a hydroxyl group. - COOH Compound with carboxyl groups : Carboxylic acid or Organic acid

8 H O H C C OH H Acetic acid

9 Functional properties
Act as source of Hydrogen ions (H+) Acidic properties The covalent bond between O and H So polar H+ ions tend to dissociate reversibly

10 c) Carbonyl group Consist of carbon atom joined to an oxygen atom by a double bond - CO Known as ketones If the carbonyl group is within a carbon skeleton Known as aldehydes If the carbonyl group is at the end of skeleton

11 H O H H C C C H H H H H O H C C C H H H Acetone (ketone) Propanal (Aldehyde)

12 Functional properties
Ketone and aldehyde is a structural isomer with different properties

13 d) Amino groups Consists of a nitrogen atom bonded to two hydrogen atom and to the carbon skeleton - NH2 Known as amines Eg : Amino acid

14 H H O N C C OH H H Glycine

15 Functional properties
Acts as a base Able to pick up proton from surrounding H H N N H Non-ionized ionized

16 e) Sulfhydryl groups Consists of a sulfur atom bonded to an atom of hydrogen Resemble a hydroxyl group in shape - SH Known as thiols Eg : Ethanethiol

17 H H H C C SH H H Ethanethiol

18 Functional properties
2 sulfhydryl groups can interact to help stabilize protein structure

19 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

20 OH OH H O H C C C O P O- H H H O- Glycerol phosphate

21 Functional properties
Makes the molecule of which it is a part an anion (negatively charge ion) Able to transfer energy between organic molecules


23 Macromolecules Known as large molecules : chain-like molecules
Called polymers Long molecules consisting of many similar or identical building block Linked by covalent bond Form by monomers

24 Biological molecules Carbohydrates Lipid Protein Nucleic acid


26 Carbohydrates Include sugar and polymers of sugar
The simplest carbohydrates : Monosaccharides (simple/single sugar) Disaccharides : double sugars (2 monosaccharides joins by condensation reaction)

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

28 Monosaccharides From the Greek words, Monos : single and Sacchar : sugar Three types; glucose,galactose,fructose Generally have molecular formula that are multiple of unit CH2O Glucose, C6H12O6 – common monosaccharides Contain a carbonyl group and multiple of hydroxyl groups

29 The structure and classification of some monosaccharides :
Location of carbonyl group Length of carbon skeleton Spatial arrangement around asymmetric carbons

30 The size of carbon skeleton (range from 3 to 7)
Sugar is either aldose or ketose, depending on the location of carbonyl group Glucose and Galactose – aldose Fructose – ketose The size of carbon skeleton (range from 3 to 7) 6-carbon sugar : Hexose 5-carbon sugar : Pentose

31 Spatial arrangement of the parts around asymmetric carbon.
Carbon attached to 4 different kinds of partner Eg : Glucose and Galactose

32 Glucose Galactose

33 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)


35 In aqueous solution, glucose molecules form ring structure

36 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

37 Maltose Glucose Glucose


39 Polysaccharides Macromolecules
Consists of few hundred to a few thousand of monosaccharides Link by glycosidic linkage The process known as condensation (eliminates water) Serve as : Storage material Building material

40 Storage material: Starch (plants) Glycogen (animals)

41 Storage material Starch Consists entirely glucose monomers
Storage polysaccharides for plants Consists entirely glucose monomers Mostly joined by α (1-4) linkages The angle – formed polymer helical Type of starch : Amylose Amylopectin

42 Amylose Amylopectin The simplest form of starch Unbranched
More complex form Branched polymer 1-6 linkages at the branch point

43 Amylose

44 amylopectin

45 Animal stored polysaccharides – Glycogen
Polymer resemble amylopectin but more extensively branched Branch linkages every 8 – 10 residues Human and vertebrates stored glycogen in liver and muscle cells


47 Building materials; Cellulose Chitin

48 Building material- cellulose
Known as structural polysaccharides Eg : Cellulose Major component of the tough walls that enclose plant cells Polymer of glucose but the glycosidic linkages is different from starch

49 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

50 Cellulose molecule is straight
Unbranched The 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

51 Cellulose


53 Chitin – structural polysaccharides used by arthropods
To build up exoskeleton Is hardened with the aid of calcium carbonate (salt) Same like cellulose but the glucose monomer has a nitrogen-containing appendage

54 Chitin


56 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 molecules Examples; fatty and oils, waxes, phospholipids steroid and cholesterol

57 Importances of lipid: Stored energy in adipose tissues
Components of the cell membranes Part of hormones, pigment and cholesterol

58 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)



61 Simple Lipids: A) fats (triglycerol)
Constructed from glycerol (C3H8O3) and fatty acids Triglycerol consist of : 3 fatty acid (tail) and 1 glycerol molecules (head) By condensastion proces by ester linkage


63 B) Phospholipid Consist 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


65 Sphingolipid Consist of three-carbon backbone known as sphingosine
Sphingosine : nitrogen-containing alcohol Play an important role in signal transmission and cell recognition

66 Amphiphatic molecules
Polar head and two non-polar fatty acid tail Structure : Sphingosine backbone Amide link to fatty acid Polar molecule



69 Types of sphingolipids
Divided into two sub categories : Sphingomyelins Glycosphingolipids Found in animal cell membranes Especially in myelin sheath, surround nerve cells axon

70 Consist of phosphorylcoline and ceramide (sphingosine bonded to fatty acid via amide linkage)
Glycosphingolipids Distributed mainly on the surface of the cell Help cell to interact with its surrounding Acts as a distinguishing markers

71 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

72 Generally solid at room temperature
Found naturally as coating on fruits, insect exoskeleton, leaves Birds have glands producing wax for feathers

73 Simple lipids Divided into : Prostalglandins (hormone-like molecules)

74 Prostalglandins A group of lipids derived enzymatically from fatty acid Unsaturated fatty acids Contain 20 carbon atom, including 5-carbon ring

75 Prostalglandins…functions
Cause constriction in vascular smooth muscle cells Cause aggregation or dissaggregation of platelet Control human regulation Control cell growth

76 Terpene Derived biosynthetically from isoprene
Molecular formula, (C5H8)n n : represents isoprene units Types of terpene : Steroid Bile salt

77 Steroids Carbon skeleton consists of four fused ring
Different steroid will have different functional group attach to the rings The most abundant steroids : Cholesterol

78 Cholesterol Common component in animal cell membranes
Amphiphatic molecules

79 Draw a structure of this compenents: A) unsaturated fatty acid
Assignment Draw a structure of this compenents: A) unsaturated fatty acid B) saturated fatty acid C) phospholipid D) triglycerol E) sphingosine F) sphingomyelin buses of steroid 1 page essays Times new roman font 12, spacing 1.5

80 G) prostoglandine H) terpene i) steroid J) cholesterol


82 PROTEIN Large molecules
Composed of carbon, hydrogen, oxygen and nitrogen Sulphur – rarely Composed of simple sub-unit : amino acids Polymer of protein : polypeptide

83 Polypeptides Constructed from the same 20 amino acid
Protein consists of one or more polypeptides folded and coiled Forming specific conformation

84 Amino acid Monomer Organic molecules possessing both carboxyl and amino groups

85 At the center of amino acid – asymmetric carbon atom called alpha (α) carbon
Partner of carbon : Amino group Carboxyl group A hydrogen atom Variable group, R

86 R group : also known as the side chain
Differs with each amino acid Have 20 amino acids Divided into 3 groups : Non-polar Polar Electrically charged

87 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)

88 Polar Amino acid with polar side chain Hydrophilic Example :
Serine (Ser), Threonine (Thr), Cysteine (Cys), Tyrosine (Tyr), Asparagine (Asn), Glutamine (Gln)

89 Electrically charged Amino acid with side chains that are electrically charged If +ve : basic amino acid If –ve : acidic amino acid

90 Hydrophilic Example : Aspartic acid (Asp), Glutamic acid (Glu), Lysine (Lys), Arginine (Arg), Histidine (His)

91 Aspartic acid Lysine

92 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

93 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)


95 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

96 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


98 Four level of protein structure
Primary structure Secondary structure Tertiary structure Quaternary structure

99 Primary structure Linear polymer Linked by peptide bond
Example : Transthyretin Globular protein found in the blood that transport vitamin A


101 Secondary structure Consists of polypeptide chain repeatedly coiled or folded Due to hydrogen bonds between the repeating constituents of polypeptide backbone


103 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

104 The division of protein secondary struc…
α-helix Polypeptide coil held together by hydrogen bonding Occur between 4th amino acid Hydrogen bond occur between –CO and –NH of the backbone The bond maintain the structure of α-helix Example : keratin in hair


106 β-pleated sheet 2 or more regions of polypeptide chain lying side by side Connected by Hydrogen bond Present either as parallel or anti-parallel Example : Silk


108 Tertiary structure Conformation of secondary structure
Interaction between side chains (R group) Types of interactions : Hydrophobic interaction Hydrogen bond Ionic bond Disulphide bridge

109 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

110 Hydrogen bond Ionic bond Disulfide bridge
Occur between polar amino acid side chain Ionic bond Linkage between positively and negatively charged side chain Disulfide bridge Formed between 2 cystein monomers


112 Quartenary structure Consist of the overall protein structure that result from the aggregation of the polypeptide subunit Complex molecule Example : Collagen and hemoglobin

113 Collagen Fibrous protein
3 helical polypeptides, supercoiled forming rope-like structure Found in connective tissues

114 Hemoglobin Globular protein 4 polypeptide chain
2 are α-chains and 2 are β-chains Present of non-polypeptide component eg: heme group and iron atom


116 Conjugated protein Proteins incorporated with non-protein components
Exist within the structure and perform specific function Non-protein component : prosthetic group Example : Hemoglobin and Heme Mucin and Carbohydrate

117 Denaturation and Renaturation
Physical or chemical aspect which cause the protein to lose their native conformation Interrupt the function of protein (Inactive) Interrupt the chemical bonding Factors affecting : pH, [salt], temperature and chemical substance

118 Renaturation The process of returning back the protein conformation into its normal state Happen when the denaturing agent been removed

119 Functions Formation of cell membrane
Synthesize of new cells and tissues Formation of enzyme Antibodies Hormones Contractile proteins – cell motility

120 NUCLEIC ACID Compound consist of polymers or unit of inheritance known as gene 2 types : Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)

121 Functions Enable living organisms to reproduce their complex components DNA directs RNA synthesis RNA controls protein synthesis DNA inherits from parents

122 The structure of nucleic acid
Nucleic acid : Macromolecules Exists as polymers called polynucleotide The basic unit : Nucleotide Composed of three parts Pentose sugar Nitrogenous base Phosphate group


124 Nucleotide monomers Nucleotide without phosphate group : Nucleoside
Nitrogenous base consist of 2 families : Pyrimidines Purines

125 Pyrimidines Six-membered ring of carbon and a nitrogen atoms
The members : Cytosine (C) Thymine (T) – found in DNA Uracil (U) – found in RNA


127 Purines Larger than pyrimidines
Six-membered ring fused to five-membered ring The members : Adenine (A) Guanine (G)


129 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


131 To complete the nucleotide, require a phosphate group

132 Phosphate group attached to carbon-5 in the pentose sugar
Nitrogenous base attached to carbon-1 in the pentose sugar

133 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


135 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

136 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)


138 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



141 Only certain bases are compatible with each other
Adenine (A) always paired to Thymine (T) Guanine (G) always paired to Cytosine (C)

142 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

143 This pairing enable the researcher to predict the other strand sequences

144 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

145 In RNA, Thymine (T) is paired to Uracil (U) rather than Adenine (A)
RNA also have polarity Single-stranded

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