Transcript Chapter 5: Biological Molecules Carbon based compound Consist of C, H, O atoms Sometimes P, N, S atoms Properties depends on : Arrangement of carbon.

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
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
Carbonyl
Hydroxyl groups
Carboxyl groups
FUNCTIONAL
GROUPS
Amino groups
Sulfhydryl groups
Phosphate groups
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
H
H
C
OH
H
H
Methanol
H
H
H
C
C
H
H
Ethanol
H
H
H
C
C
C
H
OH
H
2-Propanol
H
OH
Functional properties
Polar
Electronegative 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.
- COOH
Compound with carboxyl groups :
Carboxylic acid or Organic acid
H
H
O
C
C
H
Acetic acid
OH
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
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
H
H
O
H
C
C
C
H
H
Acetone (ketone)
H
H
H
H
O
C
C
C
H
H
H
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 amines
Eg : Amino acid
H
N
H
H
O
C
C
H
Glycine
OH
Functional properties
Acts as a base
Able to pick up proton from surrounding
H
N
H
Non-ionized
H
N
H
ionized
H
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
H
H
H
C
C
H
H
Ethanethiol
SH
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
H
OH
OH
H
C
C
C
H
H
H
O
O
Glycerol phosphate
P
O-
O-
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 polymers
Long molecules consisting of many similar or
identical building block
Linked by covalent bond
Form by monomers
Biological molecules
Carbohydrates
Lipid
Protein
Nucleic acid
CARBOHYDRATES
Carbohydrates
Include sugar and polymers of sugar
The 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,fructose
Generally 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
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
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
Maltose
Glucose
Glucose
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
Storage material:
Starch (plants)
Glycogen (animals)
Storage material
Starch
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
Amylose
The simplest form of starch
Unbranched
Amylopectin
More complex form
Branched polymer
1-6 linkages at the branch point
Amylose
amylopectin
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
Building materials;
Cellulose
Chitin
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
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 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
Cellulose
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
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 molecules
Examples; fatty and oils, waxes,
phospholipids steroid and cholesterol
Importances of lipid:
Stored energy in adipose tissues
Components of the cell membranes
Part 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 acids
Triglycerol consist of : 3 fatty acid (tail) and
1 glycerol molecules (head)
By condensastion proces by ester linkage
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
Sphingolipid
Consist of three-carbon backbone known
as sphingosine
Sphingosine : nitrogen-containing alcohol
Play an important role in signal
transmission and cell recognition
Amphiphatic molecules
Polar head and two non-polar fatty acid tail
Structure :
Sphingosine backbone
Amide link to fatty acid
Polar molecule
Types of sphingolipids
Divided into two sub categories :
Sphingomyelins
Glycosphingolipids
Sphingomyelins
Found in animal cell membranes
Especially in myelin sheath, surround nerve
cells axon
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
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 5carbon ring
Prostalglandins…functions
Cause constriction in vascular smooth
muscle cells
Cause aggregation or dissaggregation of
platelet
Control human regulation
Control cell growth
Terpene
Derived biosynthetically from isoprene
Molecular formula, (C5H8)n
n : represents isoprene units
Types of terpene :
Steroid
Bile 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
Assignment
Draw a structure of this compenents:
A) unsaturated fatty acid
B) saturated fatty acid
C) phospholipid
D) triglycerol
E) sphingosine
F) sphingomyelin
G) prostoglandine
H) terpene
i) steroid
J) cholesterol
PROTEIN
PROTEIN
Large molecules
Composed of carbon, hydrogen, oxygen
and nitrogen
Sulphur – rarely
Composed of simple sub-unit : amino
acids
Polymer 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
Monomer
Organic molecules possessing both
carboxyl and amino groups
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
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
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, threedimensional 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-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
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
Tertiary structure
Conformation of secondary structure
Interaction between side chains (R group)
Types of interactions :
Hydrophobic interaction
Hydrogen bond
Ionic bond
Disulphide 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 bond
Occur between polar amino acid side chain
Ionic bond
Linkage between positively and negatively
charged side chain
Disulfide bridge
Formed 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
Collagen
Fibrous protein
3 helical polypeptides, supercoiled forming
rope-like structure
Found in connective tissues
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
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
Denaturation and Renaturation
Denaturation
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
Renaturation
The process of returning back the protein
conformation into its normal state
Happen when the denaturing agent been
removed
Functions
Formation of cell membrane
Synthesize of new cells and tissues
Formation of enzyme
Antibodies
Hormones
Contractile 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 parts
Pentose sugar
Nitrogenous base
Phosphate group
Nucleotide monomers
Nucleotide without phosphate group :
Nucleoside
Nitrogenous base consist of 2 families :
Pyrimidines
Purines
Pyrimidines
Six-membered ring of carbon and a
nitrogen atoms
The members :
Cytosine (C)
Thymine (T) – found in DNA
Uracil (U) – found in RNA
Purines
Larger than pyrimidines
Six-membered ring fused to fivemembered 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