SBS3053 : LECTURE 4

BIOLOGICAL MOLECULES; GENE

STRUCTURE & FUNCTION

DR HANINA MOHD NOOR 2-1

 TOPICS
• Macromolecules
• Carbohydrates
• Protein: Structure and Function
• How do Genes Work – the Function of
Genes
• What is Nucleic Acids : Structure and
Function
• Physical Chemistry of Nucleic Acids
2-2
 MACROMOLECULES
• Macromolecules
– Are large molecules composed of smaller
molecules
– Are complex in their structures

• Most macromolecules are polymers, built from

monomers

• Three of the classes of life’s organic

molecules are polymers
– Carbohydrates
– Proteins
– Nucleic acids
 CARBOHYDRATES
• Serve as fuel and building material
• Include both sugars and their polymers

• Polysaccharides – polymers of sugars

 Storage polysaccharides – Starch; Glycogen
 Structural polysaccharides – Cellulose;
Chitin (cellulose derivatives)

2-4
 PROTEIN STRUCTURE
Proteins are chain-like polymers of small
subunits, amino acids

– DNA has 4 different nucleotides

– Proteins have 20 different amino acids with:

• An amino group
• A hydroxyl group
• A hydrogen atom
• A specific side chain 2-5
 POLYPEPTIDES
• Amino acids are joined together via peptide
bonds
• Chains of amino acids are called polypeptides
• Proteins are composed of 1 or more polypeptides
• Polypeptides have polarity as does DNA
– Free amino group at one end is the amino- or N-
terminus
– Free hydroxyl group at the other end is the carboxyl-
or C-terminus

2-6
Four Levels of Protein Structure: Primary
• Primary structure
– Is the unique sequence of amino acids in
Gly Pro Thr Gly

a polypeptide + HN3
Amino end
Amino acid
subunits
Leu Pro
Cys Lys Seu
Thr

Glu
Gly

Met
Val
Lys
Val
Leu
Asp
Ala Val Arg
Gly
Ser
Pro
Ala

Glu Lle
Asp
Thr
Lys
Ser
Lys Trp Tyr
Leu Ala
Gly
lle
Ser
Pro Phe
His Glu
His
Ala
Glu
Val
Ala Thr PheVal
Asn
lle
Thr
Asp Tyr Ala
Arg
Ser Arg Ala
Gly Pro
Leu
Leu
Ser
Pro
SerTyr
Tyr
Thr Ser
Thr
Ala
Val o
Val Glu c
ThrAsnPro Lys
o–
Carboxyl end
 Four Levels of Protein Structure: Secondary
• Secondary structure
– Is the folding or coiling of the polypeptide
into a repeating configuration
– Includes the  helix and the  pleated
sheet
 pleated sheet
O H H O H H O H H O H H
R R R
Amino acid C C N C C N C C N C C N
C N C C N C C N C C N C C
subunits R R R R
H O H H OH H OH H O

R R R R
O C O O C O H
C H H H C
H C N HC H H
C N HC N N C NH C N C N HC N
H H C H O C H
C O C O O C
R R R
R H R H
C C
N H O C N H O C
N H
O C O C
N H
 helix
H C R H C H C R H C R
R
N H O C N H
O C
O C N H O C N H
C C
R H R H

 helix  pleated sheet

Four Levels of Protein Structure: Tertiary
• Tertiary structure
– Is the overall three-dimensional shape of
a polypeptide
– Results from interactions between amino
acids and R groups
Hydrophobic
interactions and
CH van der Waals
CH22
CH
H3C CH3 interactions
O
Hyrdogen H H3C CH3 Polypeptide
bond O CH backbone
HO C
CH2 CH2 S S CH2
Disulfide bridge
O
CH2 NH3+ -O C CH2
Ionic bond
Four Levels of Protein Structure: Quaternary
• Quaternary structure
– Is the overall protein
structure that results
from the aggregation Polypeptide
of two or more chain

polypeptide subunits

Collagen
 Chains

Iron
Heme

 Chains
Hemoglobin
Protein Types and functions

Othman
 SUMMARY
• Proteins are polymers of amino acids
linked through peptide bonds

• Sequence of amino acids in a polypeptide

(primary structure) gives rise to that
molecule’s:
– Local shape (secondary structure)
– Overall shape (tertiary structure)
– Interaction with other polypeptides (quaternary
structure) 2-12
 SUMMARY
Protein Functions:
– Provide the structure that helps give cells
integrity and shape

– Serve as hormones carrying signals from one

cell to another

– Bind and carry substances

– Control the activities of genes

– Serve as enzymes that catalyze hundreds of

2-13
chemical reactions
NUCLEIC ACIDS: HEREDITARY
INFORMATION
• Concept : Nucleic acids store and
transmit hereditary information
• Genes
– Are the units of inheritance
– Program the amino acid sequence of
polypeptides
– Are made of nucleic acids
 ACTIVITIES OF GENES : HOW DO
GENES WORK?
Genes perform three major roles :

• Replicate faithfully (replication)

• Direct the production of RNAs and

proteins (carrying information) –
transcription & translation

• Accumulate mutations – allow

evolution (collecting mutations)
2-15
 HOW GENES ARE REPLICATE?

• Semiconservative replication keeps one

strand of the parental double helix conserved
in each of the daughter double helices
2-16
 HOW GENES DIRECT THE
PRODUCTION OF POLYPEPTIDES?
• Gene expression is the process by which
a gene product is made

• Two steps are required

– Transcription: copy of DNA is transcribed into
RNA
– Translation: the RNA copy is read or
translated to assemble a protein

• Codon: a sequence of 3 nucleic acid

bases that stand for one amino acid 2-17
 OVERVIEW OF GENE EXPRESSION
Producing a protein from
DNA information involves
both transcription and
translation
– A codon is the 3 base
sequence that
determines what amino
acid is used
– Template strand is the
complementary DNA
strand that is used to
generate the mRNA
– Nontemplate strand is
not used in RNA
2-18
transcription
 HOW GENES ACCUMULATE
MUTATIONS?
Genes change in several ways
• Change one base to another
• Deletions of one base up to a large
segment
• Insertions of one base up to a large
segment
• As the change is more drastic - the
gene or genes involved will be totally
inactivated
2-19
 WHAT IS NUCLEIC ACID
• DNA – Deoxyribonucleic acid

• RNA – ribonucleic acid

• Made up of nucleotides containing 3 basic

component :
- Base (purine @ pyrimidine)
- Phosphate
- Sugar : Ribose (RNA) or Deoxyribose (DNA)

2-20
Fig. 2.6

SUGAR

H
 PURINES AND PYRIMIDINES
• Adenine and guanine - purine
• Cytosine, thymine and uracil - pyrimidine

2-22
Page 16

BASIC STRUCTURE
• Nucleoside = Base + Sugar
• Nucleotide = Base + Sugar + Phosphate

2-23
 THE CHEMICAL NATURE OF
POLYNUCLEOTIDES
• The component parts of DNA

– Nitrogenous bases:
• Adenine (A)
• Cytosine (C)
• Guanine (G)
• Thymine (T)

– Phosphoric acid

– Deoxyribose sugar
2-24
 NUCLEOTIDES AND NUCLEOSIDES
• RNA component parts
– Nitrogenous bases
• Like DNA except
Uracil (U) replaces
Thymine
– Phosphoric acid
– Ribose sugar

• Nucleotides contain
phosphoric acid

• Nucleosides lack the

phosphoric acid
2-25
 DNA LINKAGE
• Nucleotides are nucleosides with a phosphate
group attached through a phosphodiester
bond
• Nucleotides may contain one, two, or even
three phosphate groups linked in a chain

2-26
 A TRINUCLEOTIDE
The example
trinucleotide has
polarity

– Top of molecule has a

free 5’-phosphate
group = 5’ end

– Bottom has a free 3’-

hydroxyl group = 3’
end

2-27
 DNA CHAIN VS RNA CHAIN
DNA Chain RNA Chain

Sugar Deoxyribose Ribose

Base A,G,C,T A,G,C,U

1) 5’ AGCTTGCTT 3’
2) 5’ UCCGAUCGU 3’
2-28
 SUMMARY
• Nucleic acids are DNA and RNA

• Nucleic acids are built up of nucleotide

• Nucleotides contain a base linked to the 1’-

position of a sugar and a phosphate group

• Phosphate joins the sugars in a DNA or

RNA chain through their 5’- and 3’-hydroxyl
groups by phosphodiester bonds
2-29
 DNA STRUCTURE : DNA HELIX
• The DNA molecule is a
double helix, with sugar-
phosphate backbones
on the outside and base
pairs on the inside

• Arrows indicate that the

two strands are
antiparallel

2-30
 DNA STRUCTURE
•The bases pair in a specific way:
- Adenine (A) with thymine (T) – 2 hydrogen bond
- Guanine (G) with cytosine (C) – 3 hydrogen bond

2-31
PHYSICAL CHEMISTRY OF NUCLEIC
ACIDS : A VARIETY OF DNA
STRUCTURES

(a) A-form; (b) B-form; (c) Z-DNA 2-32

 VARIATION IN DNA
BETWEEN ORGANISMS
• The total percentage
of G + C varies over
a range to 22 to 73%

• Such differences are

reflected in
differences in
physical properties

2-33
PHYSICAL PROPERTIES : DNA MELTING

• With heating, noncovalent forces holding DNA

strands together weaken and break
• When the forces break, the two strands come apart
in denaturation or melting
• Temperature at which DNA strands are ½ denatured
is the melting temperature or Tm
• GC content of DNA has a significant effect on Tm with
2-34
higher GC content meaning higher Tm
 PHYSICAL PROPERTIES : DNA
DENATURATION

• In addition to heat, DNA

can be denatured by:
– Organic solvents
– High pH
– Low salt concentration

• GC content also affects

DNA density

2-35
 SUMMARY
• GC content of a natural DNA can vary from
less than 25% to almost 75%

• GC content has a strong effect on physical

properties that increase linearly with GC
content
– Melting temperature, the temperature at which
the two strands are half-dissociated or
denatured
– Density
– Low ionic strength, high pH and organic
solvents also promote DNA denaturation 2-36
 DNA RENATURATION
• After two DNA strands separate, under proper
conditions the strands can come back together

• Process is called annealing or renaturation

• Three most important factors:

– Temperature – best at about 25º C below Tm
– DNA Concentration – within limits higher
concentration better so that 2 complementary will
find each other
– Renaturation Time – as increase time, more
annealing will occur 2-37
 POLYNUCLEOTIDE CHAIN
HYBRIDIZATION
•Hybridization is a process
of putting together a
combination of two
different nucleic acids

– Strands could be 1 DNA

and 1 RNA
– Also could be 2 DNA with
complementary or nearly
complementary
sequences 2-38
 DNA SIZES
•DNA size is expressed in 3 different ways:

– Number of base pairs

– Molecular weight – 660 is molecular weight of 1
base pair
– Length – 33.2 Å per helical turn of 10.4 base
pairs

•Measure DNA size either using electron

microscopy or gel electrophoresis
2-39
 DNA’S OF VARIOUS SIZES
AND SHAPES

• Phage DNA is typically circular

• Some DNA will be linear
• Supercoiled DNA coils or wraps around itself
like a twisted rubber band 2-40
 SUMMARY
• Natural DNAs come in sizes ranging from
several kilobases to thousands of
megabases

• The size of a small DNA can be estimated

by electron microscopy

• This technique can also reveal whether a

DNA is circular or linear and whether it is
supercoiled 2-41