Figure 4-00

Nucleic Acids
Nucleic
and the Acids
RNA World

Chapter 4
 Learning Goals
1. What is the Central Dogma of Molecular Biology?
2. Nucleotides are monomers that consist of a sugar, a phosphate
group, and a nitrogen-containing base. Be able to identify the parts of
a nucleotide.
3. Ribonucleotides polymerize to form RNA. Deoxyribonucleotides
polymerize to form DNA. During polymerization, what
phosphodiester bonds are formed that link 2 nucleotides together
along the S-P backbone? Be able to draw this reaction and a
phosphodiester bond.
3. DNA and RNA’s primary structure consists of a sequence of nitrogen-
containing bases, which contain information in the form of a
molecular code.
4. What are the different types of RNA? Which type is then translated
into protein? What is the function of other RNA types?
5. What is DNA’s secondary structure? What is antiparallel,
complementary base pairing, and twisted into a double helix. How is
RNA’s secondary structure different?
6. What are the differences between DNA and RNA?
 Nucleic Acids
• DNA and RNA
• strands of nucleotide monomers
• storage and transmission of genetic info
• structural & catalytic roles (many types of RNA)

All RNA types

coded for by
genes

mRNA, rRNA, tRNA, snRNA, miRNA:

Genes code for many different types of
RNA. mRNA will become protein.
image reference
 Central Dogma

Genes

Messengers

Work Force
 What Is a Nucleic Acid?
• A nucleic acid is a polymer of nucleotides each composed of:
•1) phosphate group bonded to a
•2) sugar, which in turn is bonded to a
• 3) nitrogenous base.
 Phosphate group
• Phosphate group attached to 5’ Carbon
Triphosphates: high E stored in bonds

Primes indicate carbons on the sugar

 Sugar: H or OH
• The
sugar is ribose in ribonucleotides
deoxyribose in
deoxyribonucleotides.

•How are these sugars different?

• Note 2’ Carbon: deoxyribose  H
ribose  OH
 Nitrogenous Bases
• 2 types nitrogenous bases:
• PURINES- adenine (A) and guanine (G)
•PYRIMIDINES- cytosine (C), uracil (U),
& thymine (T)

• A, G, and C: found in all nucleic acids.

• U is found only in ribonucleic acids (RNA)
• T is found only in deoxyribonucleic acids
(DNA).

Bases are linked to 1’ C

Nucleotides

Nomenclature:
• Ribonucleic acid
(RNA) is made from
ribonucleotides
• Deoxyribonucleic
acid (DNA) is made
from
deoxyribonucleotides.
 Directionality

5’ end 1.In a nucleic acid, each nucleotide

sugar is linked to the phosphate
group of the neighboring nucleotide
via a phosphodiester bond.

2.DNA has “polarity” = the 2 ends

differ
• At the top of the figure, you can see
the free 5’ phosphate group; at the
bottom, notice the free 3’ hydroxyl
group.

3. This strand is read 5’-AGCT-3’ from

top to bottom.
• Note: by convention, if a DNA
sequence is not specified as 5’ or 3’,
3’ end
the end at the left (or top) is the 5’
end.
 How Do Nucleotides Polymerize to Form Nucleic Acids?
Nucleotide polymerization:
• phosphodiester bonds link together 2
nucleotides—

•Where? Bond forms between the PO4

group of one nucleotide and the OH
group of the sugar of another
nucleotide

Note that the incoming nucleotide

is an NTP = nucleotide triphosphate.
After polymerization, the incorporated
nucleotide only has one phosphate group
Note how the bond links together the
(see red arrow to right)
3’ C of one nucleotide to the 5’ C of
the next
 Figure 4-3 Slide 3
The sugar-phosphate
spine of RNA

Nucleotides:
Sugar-phosphate
backbone + nitrogenous Nitrogenous
base bases

3’ and 5’ carbons joined by

3 and 5 carbons

phosphodiester linkage
joined by
phosphodiester
linkage

Unlinked 3’ carbon:
Unlinked 3 carbon:
new nucleotides
new nucleotides
are added are
here

added here
Nucleosides:
Sugar-base ONLY
Which part of the DNA molecules carries the code?

A.Sugar phosphate backbone

B. 2’ Carbon
C. Ribose
D. Nitrogenous base
 DNA Structure and Function
• James Watson (25 year old postdoctoral fellow) and
Francis Crick (37 year old graduate student)

•“They were trying to propose a secondary structure

that could explain several important observations
about the DNA found in cells.”
 Based their modeling on evidence from
several different research groups

1. Chemists had determined that DNA polymerized through

phosphodiester linkages, so they knew that DNA had a sugar-
phosphate backbone.

2. Erwin Chargaff’s rule:

DNA:
1) total # purines = total # pyrimidines
2) # A’s = # T’s, # C’s = # G’s.

3. Rosalind Franklin’s X-ray scattering data gave the dimensions of

the DNA molecule:
• regular repeating pattern of .34 nm, 2.0 nm and 3.4 nm
• suggested molecule was helical or spiral in nature.
Chargaff’s Rule Purine = Pyrimidines

G=C
A=T
 X-Ray Crystallography

Diffracted
rays
X-ray beam

Crystallized
molecules
Film “Photo 51”
May, 1952
The patterns are determined by the
crystal's symmetry.
Electron density maps give info
about the 3D structure of the
molecule
KEY DISOCOVERY:
Important X-ray diffraction studies
by Rosalind Franklin that implied
DNA molecules form a helix with a
repeating structure.
 Physical Model of DNA Molecule

1. Antiparallel strands.

2. When coiled into a

helix, the sugar-
phosphate backbone
was on the outside.

3. To fit, the nitrogenous

bases had to form
Purine-Pyrimidine
pairs

James Watson Francis Crick

Watson and Crick’s DNA Structure

*regular repeating
pattern of .34 nm,
2.0 nm and 3.4 nm
DNA Exterior
Sugar Phosphate
Backbone:
Negative charges on
exterior of S-P backbone
render DNA water soluble.

“like dissolves like”

Polar and charged
 DNA Interior
H bonds and hydrophobic
interactions contribute to
DNA Stability

1. Hydrogen bonds are weak bonds;

however, in total, they contribute
to the stability of the DNA double
helix.

2. This base stacking also

contributes to the stability of
DNA.
• The nonpolar, flat surfaces of
the bases stacking as tightly
as possible with one another
cause them to group together
away from water molecules.

The nitrogenous bases form a hydrophobic interior

 Base Pairing
• Thetwo DNA strands
form complementary
base pairs A-T and G-C
through hydrogen
bonding.

2 nm
 A-T and C-G =
Watson-Crick Base Pairing or Complementary Base Pairing
T pairs
%A = %T
%G = %C

G-C pair stronger Antiparallel

strands:
one strand runs
5’  3’

Its complementary
strand runs 3’ 5’
A-T pair weaker

Affects melting T
If the one strand of a double helix has the following
sequence:

5’-GGATCCTTAA-3’

How many hydrogen bonds hold the helix together?

A.23
B.24
C.25
D.26
E.None, hydrogen bonds aren’t involved
 The Double Helix

The double-helix structure explains Minor

–Hydrophilic, negatively charged sugar groove

phosphate backbone exposed.

–Hydrophobic base interactions
toward interior Major
Length of one
complete groove
turn of helix
(10 rungs per
turn) 3.4 nm

–EXPLAINS Franklin and Wilkins’ x-ray

diffraction data Distance
between

–EXPLAINS Chargaff’s rule bases 0.34

nm

Width of the
helix 2.0 nm
 DNA Is an Information-Containing Molecule
• The nitrogenous base sequence
of DNA stores information
required for all living cells.

• Complementary base pairing

provides a simple mechanism
for DNA replication, since each
strand can serve as a template
for formation of a new
complementary strand.
 Making a copy of DNA .

DNA forms a template for its own synthesis

1. Strand separation: DNA strands separate when

hydrogen bonds between complementary base pairs
are broken.

.
2. Polymerization: Each separated strand
of DNA can serve as a template for the
formation of a new strand.

Free nucleotides attach according to

complementary base pairing.

3. With new S-P backbone formed,

strands rewind into a double helix.
Result: 2 identical DNA double helices,
each with one old and one new strand.
Semi-conservative replication
New Old Old New
 Franklin and Wilkins analyzed DNA by bombarding DNA
crystals with X-rays. Their analysis yielded two
numbers that sparked interest—3.4 nm and 0.34 nm.
What is the significance of these numbers in DNA
structure?

A. It turned out to be just a coincidence.

B. DNA molecules are 3.4 nm long and 0.34 nm wide.

C. The width of a DNA molecule is 3.4 nm, whereas the width of a nucleotide
monomer is 0.34 m.

D. These numbers tell us there are 10 rungs, or steps, on the DNA “ladder” for
every turn of the helix.

E. The 10-to-1 ratio signifies that DNA molecules are ten times longer than they
are wide.
https://www.thoughtco.com/dna-versus-rna-608191
 There are many types of RNA:

The Central Dogma states: DNAmRNAprotein

However, the genes located on the DNA code for other types of
RNA, not just mRNA. The other RNA types DO NOT code for
proteins, but are functional units that carry out or participate in other
processes.

EX: rRNA, tRNA, miRNA, snRNA

 Genes along the DNA code for many types of RNA. Genes that code for
mRNA will be translated into protein.

KhanAcademy Image
 RNA 20 Structure
• RNA’s secondary structure, like
DNA’s, results from complementary A-
U and G-C base pairing.

•The bases of RNA typically form

hydrogen bonds with complementary
bases on the same strand.

•The RNA strand folds over, forming a Still Anti-parallel

hairpin structure where the bases on
one side of the fold align with an
antiparallel RNA segment on the other
side of the fold (Figure 4.13).
 RNA can fold into tertiary and quaternary structures:
• Hairpins and other RNA secondary structures may have additional folds
or are attached to other RNA strands
• This structural complexity produces RNA molecules that vary greatly in
their shapes and chemical properties.

rRNA

Note how the ribosomal RNA is

intertwined and associated with
the ribosome protein unit.
RNA is more unstable than DNA due
to which of the following?

A.Uracil
B. 3’ OH
C. 2’ OH
D. 5’ Phosphate
© 2017 Pearson Education, Inc.