Lesson 2.

DNA, RNA, and

Proteins

General Biology 2
Science, Technology, Engineering, and Mathematics
Illustrate the molecular structure of DNA,
RNA, and proteins (STEM_BIO11/12-IIIa-
b-4).

2
● Describe the structure of DNA and its
organization in prokaryotic and eukaryotic
cells.

● Describe the structure of RNA and relate to

the molecule’s enzymatic property.

● Describe the levels of protein structure and

the determination of their resolution.
3
 The Structure of DNA

The Discovery of DNA

Friedrich Miescher (1844–
1895) isolated the material
“nuclein” when studying pus
cells from surgical bandages.

● Deoxyribonucleic acid
(DNA)
● Ribonucleic acid (RNA) Friedrich Miescher (1844–
1895) 4
 The Structure of DNA
primary genetic
storage of
material in almost
all living
genetic
organisms information
The Role of
DNA
Molecules
capacity to be
provide avenues
replicated and
for mutation to
inherited during
enhance genetic
reproduction of
diversity
cell 5
 The Structure of DNA

nitrogenou The
s base subunits of
nucleic
acids are
called
nucleotide
s.

6
The Structure of DNA

The
subunits of
nucleic
acids are
called
nucleotide
s.
pentose
sugar 7
 The Structure of DNA

The
subunits of
nucleic
acids are
called
nucleotide
s.
phosphate
group 8
The Structure of DNA

The
components
of
nucleotides
are bound
by two
types of
chemical
glycosidi bonds.
c bond
9
 The Structure of DNA

The
components
of
nucleotides
are bound
by two
types of
chemical
phosphoest bonds.
er bond
10
The Structure of DNA

nitrogenous A
base
nucleoside
is the
complex of
a sugar and
a base.
Four types
pentose are present
sugar
in DNA.
11
 The Structure of DNA

Monomers of DNA
The sugar in DNA is a deoxyribose. The nucleotides
in DNA are named after the nitrogenous base they
have.

Thymine Cytosine Adenine Guanine

12
 The Structure of DNA

ester
bond

Phosphodiest
er bond

ester
bond

13
 The Structure of DNA

The Polynucleotide Chain

The uniqueness of a polynucleotide chain of DNA is
found on the sequence of the nitrogenous bases.
By convention, it is written in the 5’ to 3’ direction.

● For example, 5’-ATGGCCTTAATGAG-3’ or

simply, ATGGCCTTAATGAG

14
 The Structure of DNA

Tautomers of Nitrogenous Bases

The cyclic bases are classified to purines and
pyrimidines.

Single-ringed bases Double-ringed bases

15
 The Structure of DNA

Tautomers of Nitrogenous
Bases
The bases exists in alternative
forms called tautomeric
states.

● Pyrimidines: amino and

imino Amino and keto tautomers are
● Purines: keto and enol the physiologically important
forms. 16
 The Structure of DNA

The DNA Helix

Two strands of DNA

polynucleotide chains are bound
together vía complementary
base pairing.

DNA is a double-stranded
nucleic acid. 17
 The Structure of DNA

The DNA Helix

The two strands of DNA are said
to be antiparallel.

● One strand runs in 5′→3′

direction, while the other
runs in 3′→5′ direction.

DNA is a double-stranded
nucleic acid. 18
 The Structure of DNA

The DNA Helix

The two strands of DNA are said
to be antiparallel.

● For example, if a given strand

is
○ 5’-AGTGTGGCA-3’
● The complementary strand is
DNA is a double-stranded
○ 3’-TCACACCGT-5’
nucleic acid. 19
 The Structure of DNA

The DNA Helix

Rosalind Franklin (1920–

1958) and her colleague
Maurice Wilkins (1916–
2004) performed x-ray
crystallography technique to
analyze the structure of DNA. The Photo 51 shows DNA
to be regular and
repetitive. 20
 The Structure of DNA

The purine content is

roughly equal to the
pyrimidine content.

Adenine and thymine

Chargaff’s
have equal quantities in
Rules
DNA.
Guanine and cytosine
have equal quantities in
DNA.
21
 The Structure of DNA
The uniformity in size of
Watson and DNA is due to the
Crick, with complementary base
the aid of pairing.
the works of The pairings involve
Franklin, specificity in H bond
Wilkins, and formation.
Chargaff, The DNA structure is
postulated helical, similar to a
that: twisted ladder.
22
 The Structure of DNA

The DNA Helix

The H bonds of DNA molecule

23
Remember the acronyms PuAG
(read as poo-wag) and PyCT (read
as pee-sit) to remember the
classification of bases. PuAG stands
for Purine, Adenine, and Guanine,
while PyCT stands for Pyrimidine,
Cytosine, and Thymine.

24
 The Structure of DNA

Stability of the DNA Helix

The base pairs are organized

inside the helix through base
stacking, which contributes
to the DNA molecule’s
overall thermodynamic
stability.
The bases are stacked
in the center of DNA. 25
 The Structure of DNA

Dexterity of the DNA Helix

The DNA is a right-handed
double helical nucleic acid.

● Try to orient your right

thumb up with your fist
partially closed.

The bases are stacked

in the center of DNA. 26
 The Structure of DNA

The Grooves of DNA

The DNA helix has two
different grooves due to the
angle of protrusion of the
deoxyribose.

● Major Groove
● Minor Groove
The DNA has different
grooves. 27
 The Structure of DNA

DNA Conformations

Three conformations of
DNA exist, which differ in
formation, number of
base pairs (bp) per turn,
and shape of helix.
A- B-, and Z-DNA

28
 The Structure of DNA

Comparison of the Three DNA Conformations.

Properties B DNA A DNA Z DNA

low and high
92% 70%
salt
Formation relative relative
concentratio
humidity humidity
n
Base pairs
10 bp/turn 11 bp/turn 12 bp/turn
per turn
29
 The Structure of DNA

Comparison of the Three DNA Conformations.

Properties B DNA A DNA Z DNA

right- right-
Dexterity left-handed
handed handed
Helical
20 Å 23 Å 18 Å
diameter
Complete
33.2 Å 24.6 Å 45.6 Å
turn 30
The Structure of DNA

The
domains of
E. coli
genome

31
 The Structure of DNA

Eukaryotic DNA
Eukaryotic DNA is known to be:
1. linear or with distinct ends called telomeres
2. organized as chromatin (DNA + proteins)
3. packed through proteins called histones into the
following levels:
a. nucleosomes (beads-on-a-string model)
b. 30-nm fibers of folded nucleosomes
c. metaphase chromosomes (max
32
 The Structure of DNA

Different levels of organization of eukaryotic

DNA 33
 The Structure of RNA

The RNA Molecule

RNA, a nucleic acid, is known to
1. be single-stranded,
2. have the base uracil
instead of thymine in DNA,
3. have ribose instead of
deoxyribose in DNA, and
4. a product of transcription
of DNA The 3-D structure of RNA
34
 The Structure of RNA

The RNA Molecule

RNA molecules may also assume enzymatic

functions:

● Ribozymes are a group of catalytic RNA

molecules.

● RNase P is a ribozyme that catalyzes tRNA

35
 The Structure of Proteins

The Amino Acids

Amino acids are the
subunits or monomers of
proteins. Each amino acid
consists of

● a carboxyl group
(COOH)
● an amino group (NH2) The groups of 20 essential amino
acids
● a proton 36
 The Structure of Proteins

Levels of Protein Structure

Amino acids are organized into
polypeptides and proteins via
different levels.

● Primary structure
● Secondary structure
● Tertiary structure
● Quaternary structure Levels of protein
structure 37
 The Structure of Proteins

Primary Structure
This level is attained by the formation of a peptide
bond between each of the amino acids.

Peptide bond is a covalent linkage between

amino acids. 38
 The Structure of DNA

Secondary Structure
Secondary
protein
helix structures
may be in
the form of
pleate a helix or a
d pleated
sheet sheet.

39
 The Structure of Proteins

A more detailed molecular view of secondary

structure 40
 The Structure of DNA

Tertiary Structure
Tertiary
structure
consists of
polypeptide
s and both
helices and
sheets

41
 The Structure of DNA

Quaternary Structure This level is

attained
whenever
multiple
folded protein
subunits form
a single
complex to
confer greater
functionality.
42
 The Structure of Proteins

Protein Data Bank (PDB)

PDB is an enormous
collection of published
experiments on the
structure of DNA, RNA and
proteins.

Hexosaminidase, an
● It enables us to view the
important protein for lipid 3D structure of proteins.
breakdown 43
 The Structure of Proteins

Resolution
Data on protein structures
are usually quantified via
protein resolution, which
is
● smallest distance (in Å
or Angstrom) between
Hexosaminidase, an two distinguishable
important protein for lipid
breakdown
features 44
 The Structure of Proteins

Resolution
● For example, if a protein
has a resolution of 0.2
Å,
○ Two atoms that are
0.2 Å apart (or 2 nm)
are observable.
Hexosaminidase, an
important protein for lipid
breakdown 45
The levels of structures of proteins can easily be
distinguished by the prevailing bonds that
hold and maintain them.
● Peptide bonds hold the substituent amino
acids together.
● Hydrogen bonds form helices and sheets.
● Tertiary structures are stabilized by covalent
and weak non-covalent interactions.
● Quaternary structures require more complex
molecular interactions between large
protein subunits.
46