Molecular Biology

of the Gene
(一)Definition of a Gene
Mendel's Particles... unit of heredity responsible for phenotype
Morgan's Loci... he placed genes on a chromosome, i.e.,
it's a cellular entity, that is part of chromosome & is mapable
Watson & Crick... it's a sequence of specific nucleotides along
the length of a double helical DNA molecule
Molecular Definition...
length: 1 nucleotide = 0.34nm thus tRNA = 81n x 0.34 = 27.5nm
mass: 1 nucleotide = 340amu thus tRNA = 81n x 340 = 27,540amu
Modern functional definition...
a DNA sequence coding for a specific polypeptide: but, also
must include...
Split Genes... presence of Introns & Exons :
eukaryotic genes contain non-coding segments (introns)
and coding segments (exons - that make proteins)
Others DNA pieces... any definition must also include:
promoters, enhancers, regulator genes, operators,
also segments that code for rRNA, tRNA, & snRNP's

BEST = "A GENE is a region of DNA that CODES for an RNA" end.
(二)Structure of DNA

A. General structure features

1. Repeating polymer of nucleotide units

Each unit composed of 3 components
Pentose(sugar), Base, and Phosphate

Sugars
HOH2C o OH

1' 1' 5' in nucleotides

2'
HO

2′= H Deoxyribose DNA

2′= OH Ribose RNA

The most important difference between DNA

and RNA is the sugar component.

2. Five common bases

2 purine A and G
RNA

3 purimidine C, T and U (T is rare in RNA)

DNA

**Tautomeric forms cause spontaneous mutation**

 (T&U)

Lactam Lactim
O OH

N N
10 -5
O N ketoiminoform O N

R R

3. a) Base attached to sugar = Nucleoside

HOH2C o Base

1' Ribonucleoside
2'
HO OH

HOH2C o Base

1' Deoxyribonucleoside
2'
HO

b) If add phosphate = Nucleotide

The phosphate can go only if any of the available

-OH functional groups.

DNA 3′, 5′ (Can get > 1 phosphate attached)

RNA 2′, 3′ or 5′

α, β, and γ position of phosphate attachment sites

p p p -OH C5 ' o Adenine

2

γ β α Adenosine triphosphate
4' 1'
(ATP)
3' 2'
HO

4. a) In DNA or RNA nucleotide units linked

together from 3′ of one sugar to 5′ of the next
phosphodiester bond.

Backbone = sugar phosphate section

b) Note polarity to the structure

in the way of structure organized

At one end the 5′ gp is not attached to another

unit = 5′ end
At the other hand 3′ group is not attached to
another unit = 3′ end

General rule:
Always write structure 5′→ 3′
If use 3′→ 5′, specify the polarity on structure
c) Shorthands
Base
B1 B2 B3

( p or OH)5' 3'
OH or p
p p

p B1 p B2 p B3 ( OH or p )

p B1B2 B3 p or OH

5. Properties of the base

a) Contain titratable groups
pKa
A 3.3
G 1.6
G 9.6
U 9.3
T 9.8
C 4.4

pKa′s of phosphate
~ 1.8 (α) No charge
~ 6.2-7.2 (β) Minus 1 or 2 charge depend
on the environments
b) Abs UV
 Quantization and differentiation of nucleotides

c) Sugar / Base conformations

Anti- preferred (less steric constrain)

d) Sugar puckers

3′ Exo in DNA 3′ Endo in RNA

(三) Double helix structure of DNA

1953 Watson and Crick

1. a) 2 strands of backbone wound around each

other
b) Form Rt handed helices, Diameter 20Å

2. β-form of DNA
Most common physiological form

a) Surfaces of bases = interior and

(perpendicular) to the helix axis
Backbone outside
b) On inside bases H-bonded
A = T (2 H-bonds)
G = C (3 H-bonds)
c) Bases are flat (aromatic) and stacked
~ 3.4 Å apart
Each turn of helix ~ 10 bp
 ~ 34 Å / turn of helix

d) Backbone runs antiparallel

5′ 3′
3′ 5′

3. Stabilization of structure
a) Ionic forces
Each internal p = 1
−
Backbone repell each other

Need cation to bind the negative charges and

reduce electrostatic repulsion between backbone
(+2 to +4)
+ + +

K , Mg , polyamine -CH2-, basic proteins

2

⊕ 3

N H3

b) H-bonds Important but not the major factor

(1) 2-4 Kcal / mole for H-bonds

But this is not enough to fully stabilize the
DNA structure

(2) Nucleotides in solu ( A and T or G and C)

not hydrogen bond to each other
H-bonding can be fully stabilized by H2O
 c) Stacking interaction

(1) Most important

(2) π e- clouds of the aromatic groups overlap

Inside helix-- H2O excluded by close

proximity of bases (Hydrophobic inside)
Excluding H2O ⇒ H bonding between bases

4. Other helical forms

a) A-form
Found in DNA fibers that are dehydrateted
Found in dsRNA and RNA:DNA
ssRNA can not form β-helix

b) 11 residues / turn
Bases tilted with respect to helix axis (wrt)
Protein can differentiate α & β from DNA
⇒ some regulation

c) Z-form
Observed originally in crystals d(GpC)3 occurs
primary in alternative pu-py (R-Y) sequences.