Chapter 5: Biological Molecules Carbon based compound Consist of C, H, O atoms Sometimes P, N, S atoms Properties depends on : Arrangement of carbon.
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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
- OPO32It 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