BIO 107 INTRODUCTION: CELL AND DEFINITION OF MOLECULAR

MOLECULAR BIOLOGY BIOLOGY

Early Schools of Thought:
Vitalism vs Mechanism
Holism vs Reductionism
Vitalism
 Intact cells possess a “vital force”.
 To study life, one must study an
intact cell
Mechanism
 To study life, a cell should be
dissected like a machine.
Holism
 The whole is greater than the
sum of its parts.
Reductionism
 All biological phenomena can be
reduced into molecules and
atoms - the laws of physics and
chemistry
Cell Biology - The study of cells and
their structure, function, and behavior.
Biochemistry
 physical and chemical structure
of biomolecules
 nucleic acids, proteins, lipids,
carbohydrates
Microbial Genetics
 information on the genetic
material, its transmission and
expression
 simple systems, i.e. phages,
bacteria
“the study of the chemical and physical
structure of biological macromolecules”
-William Astbury, 1945
“the study of genes and their products
and how these products function and
interact in the organization and
perpetuation of living things”
Problems/Common Question
 What is the genetic material?
 How are macromolecules
(especially proteins) synthesized?
 How does DNA replicate?
 How is information obtained from
DNA?
 How is gene expression
regulated?
 How are cellular substances
transported in and out of the cell?
 How do specialized cells work?
 muscle cells
 nerve cells
 What is the molecular basis of
biological phenomena? ü aging
development
Approaches to Problem 2. Development and Evaluation of
Models
1. Correlation of Structure and
- tentative explanation of how a
Function
system works
Collagen triple aggregate - tested for validity
(tendon stranded for
protein) additional 3. Strong Inference
strength - based on observations, facts and
DNA double- stability data
stranded replicability - inductive methods to draw
specific conclusions
base
pairing Frederick Griffith (1928)
Cell non-polar prevents
membrane fatty polar - Transformation experiment on
acids molecules Diplococcus pneumoniae
to (Pneumococcus)
freely pass Smooth type (S)
through
- thick polysaccharide capsule
- smooth mucoid colonies
2. Physical Measurements
- pathogenic / virulent
Some methods:
Rough type (R)
a. Ultracentrifugation
- no capsule
b. Electrophoresis
- rough colonies
c. Infrared absorption spectroscopy
- non-pathogenic / avirulent
3. In vitro approach a. General Properties of Transforming
- crude extracts and reconstituted Substance
systems
1. viscous, silky sheen
2. loses activity in distilled water
The LOGIC of Molecular Biology 3. activity retained for months in
physiological salt solution
Arguments based on:
4. withstands heating at 65°C for
1. Efficiency 30-60 minutes
- Living cells have had millions of 5. loses activity with increased acid
years to evolve: Competition and concentration
survival selected for efficiency.
- In biological processes, little
energy and material are wasted.
- e.g. gene expression
 Crucial data from other researches:
1. DNA is made of nucleotides
(phosphate, sugar,ATCG)
2. here is a specific base pairing (1
purine: 1 pyrimidine)
3. Helical structure of DNA
4. X-ray diffraction photograph of
Arguments against DNA as the Crystalline DNA
genetic material Properties of Genetic Material
- DNA is too simple; proteins can (FAIRS)
account for more diversity. F = flexible/respond to external signals
- DNA is relevant only to some
bacteria; protein is the more likely A = altered/generate genetic diversity
genetic material.
I = information
- The extract was contaminated /
not pure DNA. R = replicated and transmitted
accurately
Hershey and Chase Blender
Experiment S = stable (very)
- Phage DNA that was injected into
the cell that carried the
NUCLEIC ACIDS
information to produce more
phage particles, thus proving that  Informational molecules of all
DNA, not proteins, was the organisms
source of the genetic material.  Long, chain-like polymers
Use of T2 Phage: assembled from repeating
subunits, the nucleotides
- Lytic phage
- Lyses cell after 30-60 min 2 Types of Nucleic Acids
- Releases new phages  Deoxyribonucleic acid (DNA)
Blender Experiment:  Ribonucleic acid (RNA)

- Phages were labeled Nucleoside - a unit of only the base and

- Phages were allowed to infect the sugar without phosphate
cells
- Shearing done using kitchen
blender 3 Components of nucleotides
- Phages were torn off from
 Nitrogenous base
surface of cells
 Five-carbon Sugar
- Radioactivity measured
 Phosphate Group
 1. Numerous hydrogen bonds
between base pairs in the interior
of the molecule
NITROGENEOUS BASES 2. Covalent bonds
- β-N-glycosidic bond (sugar
a. Pyrimidines
to base)
- 6-membered ring made up of
- Phosphodiester bond (nt to
carbon and nitrogen atoms
nt)
 Uracil (U) – 2,4-dioxypyrimidine
 Thymine (T) – 2,4-dioxy-5-
methylpyrimidine or 5-
methyluracil
 Cytosine (C) – 2-oxy-4-
aminopyrimidine

b. Purines
- 6-membered ring fused to a 5-
membered ring
 Adenine (A) - 6-aminopurine
 Guanine (G) - 2-amino-6-
oxypurine
Primary Structure of the DNA
1. Two-stranded
FIVE CARBON SUGAR (PENTOSE) 2. Sugar-phosphate backbone on
the outside
- Links covalently to nitrogenous 3. Bases
bases - specific pairing
- β-D-Ribose
- sequence
- β-D-Deoxyribose 4. Each strand is a string of
nucleotides.
5. Two complementary strands are
PHOSPHATE GROUP held by H-bonds.
- A chain of 1, 2 or 3 phosphates Secondary Structure of the DNA
linked to the pentose sugar at its
5’-carbon 1. Two intertwined antiparallel
- Monophosphate, diphosphate, strands of nucleotides
triphosphate 2. Major and minor grooves
- Essential for binding proteins
3. Right-handed helix
CHEMICAL BONDS IN THE DNA - Looking down on the central
axis, the strands follow a
 clockwise path, away from the
observer
4. Helix has a constant diameter of
20 Å
5. The space separating the sugar-
phosphate backbone of a DNA
double helix is just wide enough
to
accommodate a purine-
pyrimidine base pair.
6. Bases are perpendicular to
helix axis.
- Bases are planar and stacked on
top of each other.
- 10 bp in 1 complete turn
- 3.4 Å distance between base
pairs
7. Hydrophobic associations
between the base pairs in the
interior of the molecule forming a
stable nonpolar environment
RIBONUCLEIC ACID (RNA)
- Exists largely as single-stranded
chains in living cells
- Sugar: ribose
- Bases: C G A U (Uracil)
- Genetic material of some viruses
Segments of RNA molecules may:
- form RNA-DNA hybrid
- pair temporarily in double-helical
form
- fold back on themselves to set up
extensive double-helical regions
- RNA whose single strands are
not perfectly complementary ->
form double-stranded RNA at
certain regions
Peculiar Nucleic Acid Sequences
1. Mirror Repeat- symmetrical
sequence within each strand
2. Inverted Repeats (palindrome)-
two copies of an identical
sequence present in the reverse
orientation
Other Secondary Structures
1. Internal Loops - when there are
bases that cannot pair on both
sides of the helix
2. Bulge Loops - unpaired bases
occur only on one side of the
helix
3. Cruciform - DNA with a region of
dyad symmetry in which the axis
of symmetry separates the
inverted repeats
4. Hairpin
- ssDNA molecule with an
inverted repeat
- RNA molecule copied
from a palindromic DNA
 5. Stem-and-Loop Structure
- Similar with that of the
hairpin occurs when the
loop at the end would have
many unpaired bases
- Role: attenuation
6. Cloverleaf Structure
- Characteristic CHAPTER 3: Nature and Composition
conformation of the tRNA of Plasma Membrane
molecule
- Made up of three stem-  Lipid Bilayer
loops - Major lipids in Cell
- Has four arms Membranes, formation of
bilayers, fluidity of a lipid
bilayer, glycolipids in
Significance of secondary structures eukaryotic Plasma
membrane
1. Means of stabilizing genome  Membrane Proteins
structure - Association of proteins
e.g. the ssDNA of some viruses
with the lipid bilayer,
form hairpins or lollipop
solubilization and
structures
purification of membrane
2. Serve as recognition site for
proteins, functions of
initiation of DNA replication in
membrane proteins
ssDNA viruses
 The Fluid Mosaic Model
~ palindromes at the ori site
- The components and
3. Serve as signals for the initiation
interaction of plasma
& termination of transcription
- membrane molecules
~ operator and terminator regions
have protrusions recognized by WHAT IS PLASMA MEMBRANE?
Proteins
4. Important in the function of the - The limiting membrane
NA made from it that envelop cells
e.g. cloverleaf tRNA complex - Made of phospholipids,
folding of rRNA cholesterol, proteins, and
5. Form the core of catalytic RNA oligosaccharide chains
molecules (ribozymes) linked to phospholipid and
~ as binding sites for substrates protein molecules
and cofactors e.g. self-splicing FUNCTIONS:
rRNA intron from Tetrahymena
(protozoan) - Physical barrier
- Communication
- Selective permeability
 - Electrochemical Gradients
The LIPID BILAYER
- Constitute 50% of the mass of
most animal membranes.
- Provides basic structure for all
cell membranes.
- Can be seen by electron
microscopy (EM)
- Bilayer structure is due to the
properties of lipid molecules,
which spontaneously assemble
into bilayers even under simple
artificial conditions
Characteristic of Lipids:
- Amphiphilic
Major Lipids in Cell Membranes
 STEROLS
- Cholesterol are found in large
amounts in eukaryotic organisms
 PHOSPHOLIPIDS
- Polar head group (phosphate
group)
- Two hydrophobic hydrocarbon
tails
 Phosphoglycerides
 Sphingolipids
GLYCOLIPIDS
- Sugar-containing molecules
- Found exclusively in the
monolayer facing away from the
cytosol
- ~5% of the lipid molecules (in
eukaryotes)
- Gangliosides- most complex
glycolipids
FUNCTIONS OF GLYCOLIPIDS:
- Protects plasma membrane
- Maintains electrical field across
membrane and the concentration
of ions
- Cell-recognition process and
cell-surface receptor
-
MEMBRANE PROTEINS
- Major constituents of
membranes (~50% by weight of
the plasma membrane)
 Integral Proteins
- Directly incorporated within the
lipid bilayer
- Single- and multi-pass
transmembrane proteins
 Peripheral Proteins
- Loosely associated with one of
the two membrane surfaces,
particularly the inner
GLYCOPROTEINS
- Formed from glycosylation
- For cell recognition, protection
for mechanical and chemical
damage and prevents unwanted
interaction of cells.
CELL WALL
- Protective layer that surrounds
some cells and gives them
shape and rigidity.
- Prevents osmotic lysis
- Found in plants, bacteria (varies
between species), and archaea
BACTERIAL CELL WALL
- contain peptidoglycan composed
of polysaccharide chains that are
cross-linked by unusual peptides
 containing both L- and D-amino
ssacids, including D-glutamic
acid and D-alanine
QUIZ
Q. Water has the highest percent
composition of all organic molecules
present in a bacterial cell.
Answer: False
Q. What is the biologically dominant
DNA configuration?
Answer: B DNA
Q. How many base pairs are there in a
single complete turn of the double helix
structure of a C DNA?
Answer: 9.33
Q. This refers to the single stranded of
nucleotides followed downstream by its
reverse complements.
Answer: Inverted repeats & palindrome

Q. All are components of a nucleotide

Q. The biomolecule that comprised the
except______.
major component of the cell membrane.
a) Phosphate
Answer: Lipids
b) Sugar
c) Base
d) Carboxyl group
Q. Which molecule plays a central part
in energy-transfer reactions?
Answer: Nucleotide Q. Adhesion and cohesiveness are two
(2) essential emergent properties of
water responsible for the movement of
Q. The molecule that is present in a water molecules in the xylem of the
nucleotide and nucleic acid but absent in giant red woods.
a nucleoside is _______. Answer: True
Answer: phosphate group

Q. All are pyrimidines except

__________.
a) Thymine
b) Guanine
c) Uracil
(AMINO ACID)
d) Cytosine
 (RNA)
Q. Ethanol has a higher specific heat
and rate of heat of vaporization
compared to water.
Answer: False

(ADENOSINE TRIPHOSPHATE) Q. All helix rotations of DNAs are right

rotation except for Z DNA.
Answer: True

Q. During translation, segments of RNA

molecules may form RNA-DNA hybrid.
Answer: False

Q. Which of the ff. molecule/s do/es not

belong in the group?
a. Glycerol
b. Nucleotides
c. Amino acids
d. Monosaccharides
e. RNA
(THYMINE)

Q. All elements are present in the

structures of the four (4) types of
biomolecules except_____.
a) C
b) H
c) O
d) N