MODULE 6

Protein and DNA

In the search for genetic material, there were two possible candidate materials

Alfred Hershey and Martha Chase

Confirmed DNA as genetic material

Erwin Chargaff

examined components of DNA from different
species

DNA is a double helix

Significant Discoveries by Watson and
Crick

length of 3.4nm and 0.34nm apart

Each twist of the helix has a length of _____,
with each nitrogenous base stacked at
______ apart (10 nitrogenous bases/turn)

A : T and C : G

Four nitrogenous bases that exhibit specific
base pairing

Hydrogen bonds

Nitrogenous bases of complementary
nucleotides are held by

antiparallel

Arrangement of the two complementary
strands are

carbon, hydrogen, oxygen,
nitrogen, and phosphorus

A nucleotide contains

a. 5-carbon sugar
b. Phosphate group
c. Nitrogenous base: pyrimidine and purines

Components of a Nucleotide

pyrimidine (thymine, cytosine,
and uracil)
purines (adenine and guanine)

Nitrogenous bases

5’ carbon

Phosphate group is attached to the ________ of deoxyribose sugar

3' carbon

phosphate group of the next nucleotide is attached to
the

5’-3’

Elongation of new DNA strand is only in
the _______ direction

Semi-Conservative Model

Model of DNA Replication

Each of the two complementary strands are
templates for the new DNA strands; One old strand acts as a template on which a new strand will form.

Semi-Conservative Model of DNA Replication

Helicase

The unwinding of the DNA helix and breaking of the hydrogen
bonds to expose the nitrogenous bases is catalyzed by?

Singe-strand binding protein

holds the 2-helix strands apart to expose nitrogenous bases

Topoisomerase

relieves the strain in the tightening twist of
DNA helix.

Origin of Replication

special sites where
DNA replication begins

Replication bubble and Replication fork

Two conditions that are created when the DNA Helix unwinds

Primase

RNA nucleotides make PRIMERS (10
nucleotides long), which are catalyzed by?

nucleoside triphosphate

*Polymerization process is driven by __________________; its hydrolysis of
pyrophosphate into two inorganic phosphates (exergonic reaction) provides
energy for addition of new nucleotides.

DNA polymerase III

New nucleotides align with the
complementary DNA template, addition is
catalyzed by ___________

DNA polymerase I

The lagging strand is synthesized by the?

Leading Strand

a continuous strand

Lagging Strand

consists of short
segments of nucleotide later joined to
form a single strand

Okazaki fragments

short segments of nucleotide

1 primer, several primers

Leading strand requires ___ primer, while
lagging strand needs ______ primers, one
per segment

DNA ligase

joins the Okazaki segments

Process of DNA Replication

1. Unwinding of DNA Helix
2. Synthesis is initiated by priming
3. New nucleotides align with the
complementary DNA template
4. The other new DNA strand elongates
in the direction away from the
replication fork.

Telomeres

are added to the end of DNA.
- protects the genes from being eroded in
successive rounds of DNA replication
- prevents the activation of cell’s
monitoring system that could trigger
events leading to cell death

Proofreading and Mismatch Repair

Mechanisms to Repair Damaged DNA

Proofreading

occurs during DNA replication where DNA
polymerase “check on its work” before
adding a new nucleotide. Upon detecting
a wrong nucleotide was added, it will simply
detach and replace with a correct
nucleotide; Exonuclease removes the incorrect
nucleotide

Mismatch Repair

occurs after DNA replication when an error
is detected by recognition of nicks
(single stranded breaks) in the newly
synthesized DNA. The mispaired nucleotide
and its neighboring nucleotides are
removed and replaced with correct
nucleotides by DNA polymerase. The
ligase then seals the gaps to make a
continuous strand.

1. Direct Reversal
2. Base Excision Repair
3. Nucleotide Excision Repair
4. Double Stranded Break Repair

DNA Damage Repair Mechanisms

Direct Reversal

occurs when a nucleotide base
undergoes methylation (-CH3) is added to
the oxygen of an N-base, so a Guanine
becomes paired with thymine (T) instead of
cytosine (C). An enzyme readily removes
this and replaces it with the correct
nucleotide.

Base Excision Repair

occurs when a chemical reaction called
deamination converts a cytosine base
into a uracil, such that when uncorrected
can lead to mutation.
An enzyme, glycosylases detects and
removes the damaged base. The remaining
DNA backbone is then removed, and the gap
sealed by enzymes

Nucleotide Excision Repair

damage due to ultraviolet exposure of skin
results to covalent bonding of thymine bases
(thymine dimers).
This involves a helicase to open up DNA and
make a bubble; enzymes cut out the
damaged portion, DNA polymerase replaces
the missing DNA and ligase seals up the
gap.

Double Stranded Break Repair

can occur when exposed to high
radiation. This results in the splitting of
chromosomes

Non-homologous end joining and Homologous end joining

Two types of repair mechanisms in Double Stranded Break Repair

Non-homologous end joining

the cut chromosome is joined to a nonhomologous chromosome which
involves a large segment of the
chromosome is missing. This causes
mutation.

Homologous end joining

the sister chromatid of the broken
chromosome provides the template
to replace the damaged
chromosome. Repair results to
normal condition

Production, growth and development, repair and replacement, and reproduction

Cell reproduction refers to:

Somatic Cells

make up all the body cells
that perform all daily functions

Germ Cells

are reproductive cells e.g.,
sperms and eggs; also known as gametes or
sex cells

Apoptosis

A series of events leading to the cell’s
death

Mitosis and Meiosis

Two types of Cell Division

Mitosis

a nuclear division that produces
two daughter nuclei, each with the same
number of chromosomes (diploid (2n)) as
the original; occurs in all somatic cells

Meiosis

a special type of cell division that
produces four daughter cells (sex
cell/gametes). Each cell has a unique set
of genetic material but contains only half of
the set of chromosomes and is a haploid
(n); occurs only in sex cells

Chromosomes

DNA molecules are organized into
compacted structures called?

46

Most human cells contain ____ chromosomes

XY
XX

2 sex chromosomes (X, Y)
__ – in males.
__ – in females

autosomes diploid chromosome (2n)

22 pairs of chromosomes named

a. Autosomes
b. Sex chromosomes

Two types of Homologous Chromosomes:

Karyokinesis

involves the condensation of the nuclear
material and its equal distribution to the two
daughter cells

1. Interphase
2. Prophase
3. Metaphase
4. Anaphase
5. Telophase & Cytokinesis

Stages of Mitosis

Interphase

Characterized by having a distinct nucleus bounded by a nuclear membrane. Nucleolus is readily identifiable, and immediately adjacent to the nuclear membrane is the centrosome, which contains the centrioles
• The cell prepares for division
• DNA replicated
• Organelles replicated
• Cell increases in size

Prophase

Chromosomes appear as thin, coiled filaments but gradually shorten and thicken as mitosis progresses; Centrioles migrate until they reach the
opposite sides of the cell. Their positions mark the poles toward which the
chromosomes will move.
• The cell prepares for nuclear division
• Packages DNA into chromosomes

Metaphase

Chromosomes move toward the middle of
the cell called the equator, through spindle
fibers attached at the centromere of each
chromosome; The cell prepares chromosomes for
division

Anaphase

Centromeres of the doubled chromosome
divide and the 2 sister chromatids separate
and become daughter chromosomes
when they finally reach the opposite poles of
the cell; The chromosome divides

Telophase & Cytokinesis

The spindle disappears, 2 daughter nuclei are reorganized, nucleoli and nuclear membrane reappear. The cytoplasm also becomes divided by a cell plate, which gives rise to a new cell wall when the telophase is complete. In animal cells, the cytoplasm becomes pinched in the middle, and the cleavage furrow thus formed progressively deepens until 2 daughter cells are formed.

replicates once and divides twice

During meiosis, DNA replicates _____, but
the nucleus divides ______.

Meiosis I and II

Divisions of Meiosis

1. Prophase 1
2. Metaphase 1
3. Anaphase 1
4. Telophase 1

Stages of Meiosis I

Prophase 1

Each chromosome duplicates and remains
closely associated. These are called sister
chromatids

Metaphase 1

Chromosomes align at the center of the cell

Anaphase 1

Chromosome pairs separate with sister
chromatids remaining together

Telophase 1

Two daughter cells are formed with each
daughter containing only one chromosome
of the chromosome pair.

1. Prophase 2
2. Metaphase 2
3. Anaphase 2
4. Telophase 2

Stages of Meiosis II

Prophase 2

Stage where DNA does not replicate

Metaphase 2

Chromosomes line up at the center of the
cell

Anaphase 2

Centromeres divide and sister chromatids
move separately to each pole.

Telophase 2

Cell division is complete

cell cycle

Every cell undergoes a ____ ______, an
ordered sequence of events in
preparation for the cell to reproduce or
undergo cell division

G1, S, G2, M

Four Phases of Cell Cycle

G1 phase

the cell
increases in size due to duplication of
cellular contents

S Phase

copies its genetic material

G2 Phase

grows and prepares to divide by
developing organelles and proteins

M Phase

divides producing two
similar daughter cells

interphase

The G1, S, and G2 phases make up
_________, which accounts for the span
between cell divisions

Cell Cycle Regulation

During the cell cycle, there are
“checkpoints” to ensure that a normal and
healthy cell is produced

Cell Cycle Control system

operates cyclically using a set of molecules in the cell
that both promotes and coordinates key events.

Checkpoint

stop and go-ahead signals
that regulate the cell cycle

Quiescent

occurs outside of cell cycle;
Cells that never enter the G1 phase as
they become terminally differentiated at
maturity. E.g., nerve and heart muscle cells.
These cells continue to perform their
function until the organism's death.

G0 Phase

”resting phase”; cell does not
divide or prepare to divide

G1, G2, M Checkpoints

Main Control Checkpoints

G1 Checkpoint

main control, also referred
as “Restriction Point”; either prevents
progression or cause the cell to enter G0
phase

G2 Checkpoint

assessment of DNA
replication and sufficient supply of proteins

M Checkpoint

attachment of chromosomes on spindle fibers and
chromosome alignment during metaphase

Protein kinases and Cyclins

Two Regulatory Proteins in the cells

p53

tumor suppressor gene that stops
the progression of the cell cycle and
starts repair mechanisms for the damaged
DNA.

Retinoblastoma protein (Rb)

a tumor suppressor protein that restricts the ability
of a cell to progress from G1 to S phase in the cell cycle. CDK phosphorylates Rb to pRb, which prevents it to restrict cell proliferation. This allows cells to divide normally in the cell cycle.

Protein kinases

enzymes that
activate/inactivate by phosphorylating;
generally present in constant concentration
in growing cells, but in inactive form

Cyclins

a protein attaching on kinase to
get it activated; varying concentrations in
the cell

Cyclin-dependent kinases (Cdks)

complex formed between kinase &
cyclin

Maturation-promoting factor (MPF)

phosphorylates proteins as levels of
cyclin –Cdk molecules increases,
initiating start of mitosis

a. Platelet-derived growth factor (PDGF)
b. Anchorage dependence
c. Density-dependent inhibition

Examples of External Factors Controlling
Cell Cycle

Gametogenesis

Reproduction is one of the important
properties of life because it is linked to
evolution whereby the predecessors’
(parents) traits are constantly replaced by
those that are adapted to the
environment. Preparation of gametes
required for sexual reproduction is a crucial
step in introducing variances or
differences of traits among members of
the interbreeding population

differentiating germ cells

Walls of the seminiferous tubules contain
________________. These germ
cells develop in close contact with large
Sertoli cells, which extend from the periphery
to the lumen.