TOPIC 1: CENTRAL DOGMA - The central dogma states that the pattern of

information that occurs most frequently in our cells is:

DNA or Deoxyribonucleic acid
- made-up of nucleotides forming right-handed double  From existing DNA to make new DNA (DNA
helix replication)
- Serves as a common genetic language in all  From DNA to make new RNA (transcription)
kingdoms of life.  From RNA to make new proteins
- PARTS: sugar-phosphate backbone (translation).
 a covalent bond, hard to break
 hydrophilic (loves water) - Reverse Transcription – in HIV. Transfer from RNA
- nitrogenous bases.
to DNA.
 Hydrophobic (hates water)
- Weaker Hydrogen bond, breaks easily.
- 5’ to 3’ direction Replication Process:
- Adenine – Thymine ; Guanine Cytosine. Base pairs
due to compatible Hydrogen Bonding. 1. Separating or Unzipping the two strands by the
- Unstable when heated, strands denature. enzyme Helicase, resulting in replication fork or the
line of separated strands waiting to be paired as
template.

2. Primase enzyme starts the process of pairing. It

releases primer as the marking of starting point where
pairing of new strand begins.

3. DNA polymerase enzyme binds with primer and

At 60 ℃ At 80 ℃
makes the new strands. This can only add new bases
in 5’ to 3’ direction continuously.

4. Leading Strand above starts from 5’ to 3’ direction,

while the other separated stand below, the Lagging
Strand is in 3’ to 5’.

5. This makes the adding of DNA Polymerase only in

small chunks called the Okazaki Fragment.
Side with larger angle Side with smaller angle
6. It still starts with Primer or marking, then DNA
- Major and Minor grooves are where the info content Polymerase releasing new strands in 5’ to 3’ or
of double helix is accessible. opposite direction. It releases more Primer then adds
- Enzymes (restriction or transcription) enters in it. new DNA fragments.

7. Then an Exonuclease enzyme removes the initial

Central Dogma primer that was inserted in. That’s where another DNA
polymerase could insert itself a new base fragment to
- Process where DNA instructions are converted into a makes the process continuous.
functional product. From DNA to RNA, making a
functional protein product. 8. DNA Ligase seals the fragments of both strands.

- suggests that DNA contains the information needed *Replication is conservative because it conserves the
to make all of our proteins, and that RNA is a old strand, and makes a new one.
messenger that carries this information to
the ribosomes. Transcription in Prokaryotes:
- The ribosomes serve as factories in the cell where Both Transcription and Translation
the information is ‘translated’ from a code into the
functional product. Because prokaryotic organisms lack a cell nucleus,
the processes of transcription and translation occur
- The process by which the DNA instructions are
almost simultaneously. Eukaryotic cells, in contrast,
converted into the functional product is called gene
have intracellular organelles and are much more
expression.
complex.
Gene expression has two key stages
- transcription and translation. RNA Polymerase Enzyme reads antisense DNA to
use it as a template in synthesizing RNA Molecule
- In transcription, the information in the DNA of every with complementary sequence. RNA is single
cell is converted into small, portable RNA messages. stranded and uses Uracil instead of Thymine.

- During translation, these messages travel from Prokaryotic RNA Polymerase (a Beta) also contains
where the DNA is in the cell nucleus to the ribosomes smaller protein subunits that catalyzes the covalent
where they are ‘read’ to make specific proteins. bonds of base pairs.
Alpha, Beta and Sigma factors (Prokaryotic RNA Transcription in Eukaryote:
polymerases). Alpha and Beta are sticking together.
PRE-mRNA
The Sigma factor recruits the RNA polymerase to the
promoter where transcription will begin. - DNA to mRNA
- Promoter as recognition site, RNA polymerase
attaches to begin.

- It separate the strand from 5’ to 3’

- Template strand (below) is the strand where the RNA

attaches to encode.

- Coding Strand (above)

- it continuously creates complementary and.

- RNA polymerase reads the template DNA and
moves forward creating a bubble. It reads the - Terminator creates signals to tell mRNA to stop
antisense DNA in 3’ to 5’ direction. coding.
 It could form sorta hairpin signal.
- Then RNA nucleotides are added to the DNA
complementary strand. (A-U ; C-G) mRNA

- Once done, the complex (Alpha and Beta factors - 5’ modified Guanine ; 3’ Poly-A-Tail (many A’s)
Prokaryotic RNA polymerase) dissociates and bubble
closes. Then goes to Ribosome. - Introns ‘nonsense’ sequence, no purpose. Splicing.
- Exons are left, put in mature mRNA.
-mRNA is translated into amino acid sequence by
ribosome (through tRNA). A molecular machine of - Goes to Ribosome to be translated.
protein and RNA is called rRNA, ribosomal RNA.

- Ribosomes have small and large units. DNA to Protein:

- RNA attaches first to the Aminoacyl site (A), then the Nucleus contains genome with 24 pair of
Peptidyl site (P), exits in Exit (E) site. This allows chromosomes. It has a long strand in its ends which is
tRNA to connect different amino acids to form the DNA, being held together by a protein called
polypeptide chain. Histone.

DNA has genes with instructions containing intructions

for making protein. RNA polymerase when gene swith
on, attaches to DNA creating base pairs. Transcription
happens.

Process of mRNA being a template needs

Nucleus to Cytoplasm. Ribosome in Cytoplasm, reads

it to produce a chain made up of Amino Acid. tRNA
transfers amino acids in the chain.

- Ribosome read rRNA sequence 3 nucleotides Genetic Mutations

(codon) at a time. A universal code to determine
sequence if Amino Acids. CRISPR

- Start codon initiates translation (Methionine) DNA coding is transcribes into mRNA by condons,
then is translated into a specific Amino Acid.
- Stop codon signals the end

- After translated, it moves to 5’ direction through

ribosome. Amino acids are added one by one in TOPIC 2: MOLECULAR BIOLOGY
polypeptide chain. Peptide bond is covalent.
DNA Structure
- After translation of chain, mRNA and polypeptide
chain or protein are released from ribosome. - Linus Pauling discovered secondary structure of
Protein using x-ray crystallography. A method for
- Chaperones – helper of protein in folding. investigating molecular structure observing patterns
formed by x-ray through crystal of substance.

- Rosalind Franklin used x-ray crystallography to

understand its structure.
- James Watson and Francis Crick and Maurice 3. Termination
Wilkins awarded for DNA structure discovery. - DNA primase of lagging strand removed,
complementary bases added.
- Chargaff’s rule – 4 kinds of monomers (nucleotides).
2 types are always present in equal amounts. A-T
(purines); G-C (pyrimidine) complimentary. Telomere Replication

- Telomere - ends of linear chromosome that has

RNA Structure repetitive sequences that do not code for gene. In
lagging strand, it is shortened.
- Has a nitrogenous base, five-carbon sugar, and
phosphate group. - on the lagging strand there is no place for a primer
to be made for the DNA fragment to be copied at the
- Ribose sugar and hydroxyl group at 2’ carbon. DNA end of the chromosome. This presents a problem for
has hydrogen atom. the cell because the ends remain unpaired.

- Uracil instead of Thymine. Single stranded. - Telomerase enzyme are found to be ac5ive in germ
cells, adult stem cells, and some cancer cells.
- mRNA, tRNA, rRNA.
- Telomerase enzyme in maintaining chromosome
ends as it attaches to it and complementary bases of
DNA in Cell RNA are added to the ends of DNA strand.

- In Prokaryotes, circular chromosome is found in area - Once lagging strand is elongated, DNA polymerase
of cytoplasm called nucleoid. can add to nucleotide that are complimentary.

- DNA replication is much studied in prokaryotes

because they are small sized with large variants. DNA Repair

- Supercoiling – DNA twisted beyond double helix. DNA Polymerase Proofreading – editing DNA by
They keep on twisting to fit DNA in small bacterial cell proofreading newly added bases. Incorrect are
removed and replaced.
- In Eukaryotes, linear DNA molecule fits inside
nucleus. DNA strands are bounded by protein Mismatch Repair – In replication, this enzyme
histones forming nucleosomes. Like a “beads on a recognizes wrong bases. Excise it, then replacing
string.” correct base.

- Metaphase stage in mitosis, chromosomes are most Nucleotide Excision Repair – DNA strand is unzipped,
intact at the center. then incorrect bases are removed along with feew
new bases, and replaced by copying the template with
- In interphase, chromosomes are condensed. When help of DNA polymerse.
staining, the darkly stained region ore not active and
found in telomere and centromere regions. Lightly - This is also important in correcting Thymine Dimers
stained contains active genes. that are caused by UV light. That if not removed,
causes mutation, With sensitivity to sunlight and
develops cancer.
DNA REPLICATION

- occurs in S or Synthesis phase in cells cycle. DNA TRANSCRIPTION

- Elucidation structure how DNA copying happens. 1. Initiation

- Unwinding region of mRNA creates that bubble
- 2 strands of double helix separares in this part, and called Transcription Bubble”
these strand serves as the template for new strand.
- Promoter – DNA sequence which proteins and
- DNA replication is Semiconservative. enzymes bind to initiate the process. It determines
wehter the corresponding gene is transcribed .
In Eukaryotes…
2. Elongation
1. Initiation - Template Strand – one of unzipped DNA strand
- DNA is made accessible for the proteins and
enzymes - Nontemplate strand – mRNA product is cmplementry
- There is a specific nucleotide called ‘origins of to the template strand and almost identical to other
replication’ where this begins. DNA strand.

- Helicase, unzipping. - RNA Ploymerase enzyme goes along DNA template

and adds nucleotides by base pairing.
2. Elongation
- Adding of Primase, DNA polymerase then 3. Termination
complimentary stands and fragments.
- Prokaryotic Polymerase enzyme is instructed to Cell Signaling
dissociate from the DNA template, freeing mRNA. - communication is also important for cells. Almost
every cells depends on their ability to sense
environment, by sending and receiving signals.
Eukaryotic RNA Processing
- Eukaryotic mRNA maturation crates a , molecule Cells communicate to:
that’s much more stable than Prokaryotic mRNA.  Regulate its own or another cells growth
By: altering gene expressions
- The regulation of gene expression can occur at all
stages of the process. Regulation may occur when  Coordinate movements with other cells.
the DNA is uncoiled and loosened from nucleosomes By: Remodeling cytoskeleton
to bind transcription factors (epigenetic level), when
the RNA is transcribed (transcriptional level), when  Alter its own or another cells metabolism
RNA is processed and exported to the cytoplasm after By: alter the concentration of cellular ions and small
it is transcribed (post-transcriptional level), when the molecules (metabolites).
RNA is translated into protein (translational level), or
after the protein has been made (post-  Cause another cell to die.
translational level). By: altering biological catalyst (de/activating enzyme)

- cell signaling types depend on their gap w/ each

other:

 Juxtacrine Signaling.
- direct contact to exchange proteins on surface.
- ‘juxta’ Latin meaning near/close to.

Ex: E-cadherin:E-cadherin neighboring epithelial cells.

The binding initiates signals causing both cells to stop
growing, by the signal transmitted in each cell’s
surface to nucleus where gene for growth turns off.
Preventing neighboring cells from growing and
dividing. Leading to skin cancers, cell proliferation. E-
- Alternative RNA Splicing allows different protein
products to be produced from one gene when Tumor suppressors – proteins involved in suppressing
different combinations of introns and sometimes
exons are removed from the transcript.

- can be Haphazard, but more often controlled.

SUMMARY:
- Prokaryotes contain a single, double-stranded
circular chromosome. Eukaryotes contain double-  Paracrine Signaling
stranded linear DNA molecules packaged into - cells are not touching but still in same local are.
chromosomes. - ‘para’ Greek meaning alongside.

Ex. Neurons signaling with target neuron releasing

neurotransmitters in the synapse (space between 2
TOPIC 3: CELL COMMUNICATION cells). This is called synaptic signaling. Serotonin is a
neurotransmitter. High serotonin, happy mood. Less
Biological Pathway causs depression.
- series of actions among molecules in a cell that
leads to a certain product or a change in the cell  Endocrine Signaling
- some pathways helps to discover roots f some
disorder

 Metabolic Pathway
- chemical reactions that occur in our body.
- cell breaking down food into energy for later use

 Gene-regulation Pathway
- turns genes on and off. - Hormone-producing cells located far away in body.
- vital because genes provides the recipe by which
cell produce proteins. Endocrine Glands:

 Signal Transduction Pathway

- from cell’s exterior to its interior.
- receptors helps signal to travel into cell where the
message is transmitted by special protein that triggers
specific reaction in the cell.
Ex. Epinephrine hormones for adrenaline are secreted - interacts with the receptor, activates interacts with G-
into the bloodstream and carried throughout the body protein.
to target cells. Only cells with receptors to epinephrine - if ir could not interact, activation in would not be
could bind and receive signal. happening or not as strong.

Epinephrine signals in the liver to break down - A specific molecule binding with receptor can disrupt
glycogen into glucose that elevates blood glucose signal transduction activating another G-protein
levels. It also stimulates target cells in lungs and heart preventing the bad or worse effect of the toxin.
to increase respiratory and heart rate.
- Sometimes, not all molecules binds well with the
receptor. This will not disrupt the STP, same effect.

Propagation of Cell Signal

The epidermal growth

 Autocrine Signaling factor (EGF) receptor
- Target cell and signaling cell can be the same or (EGFR) is a receptor
similar cell. tyrosine kinase involved in
- auto means self, it sends signal to itself. the regulation of cell
- occurs during the early development of organism to growth, wound healing, and
make sure cells develop into the correct tissues and tissue repair. When EGF
functions properly. binds to the EGFR, a
cascade of downstream
 Direct Signaling through Gap Junctions events causes the cell to
- Intracellular mediators – fluid-filled channel allowing grow and divide. If EGFR is
small signaling molecules. Only small molecules can activated at inappropriate
fit and flow. times, uncontrolled cell
- For neighboring cells, between plasma membrane. growth may occur.

Immune System – Bacterial Infection

- First Barrier: Skin Intracellular Signaling.

Guard Cells/Macrophages  Phosphorylation – in/activate enzyme

- guards border region of body. - addition of phosphate group (PO4-3)
- can devour 100 bacteria each, release enzyme to kill - Kinase – enzyme that catalyzes phosphate transfer
- causes inflammation, orders blood vessels to - Phosphorylates PI to form PI-phosphate
release water. (PIP) and PI-biphosphate (PIP2).
- releases messenger proteins to call back-up - Serine and Threonine – residues activate enzymes
- Tyrosine – affects either activity of enzyme or create
Neutrophils binding site.
- leaves through blood. - Dephosphorylation reverse effect.
They fight heavily, killing healthy cells.
- have barriers to trap and kill bacteria  Second messengers
- they suicide after 5 days to prevent much damage - small molecules that propagate a signal after
initiated by the binding of ligand to receptor.
Brain of Immune system - spread signals through cytoplasm altering behavior
- Dendritic cell reacts to the signals and starts of certain proteins.
collecting samples from enemies.
- piece put as their outer layer 1. Ca2= or Calcium ion as second messngr.
2. cyclic AMP (cAMP) synthesized by adenylyl cyclase
enzyme from ATP. They bind to activate cAMO-
COVID dependent-kinase (A-kinase) enzyme for regulating
many vital metabolic pathway.
 Without vaccination, COVID could easily
absorbed by receptor, penetrate, and divide. - Inositol Phospholipids are lipids that can be
converted into second messengers, located near
 With antibodies, it surrounds the COVID membrane bound receptors.
cells preventing it to attach to the receptor, so - Phospholipase C cleaves PIP2 (this serves as
it would not go any further. second messenger) to form diacylglycerol (DAG) and
Inositol triphosphate (IP3)
 With vaccination, the COVID cell with
antibodies is devoured by the immune cell,
killing it.

Signal Transduction Pathway

- releases toxin
Types of Receptors (where ligand binds) transmembrane domain, but each has specific
extracellular domain and G-protein binding site.
= Internal Receptors = -

 Internal Receptors
- intracellular or cytoplasmic receptor found in
cytoplasm & respond to hydrophobic ligand molecules
that can travel across plasma membrane.
- this cells will bind to the cells inside acting as a
regulator of mRNA synthesis (transcription) to mediate
gene expression.
- Gene Expression – cellular process of transforming
info in cells’s DNA of amino acids that forms protein.

= Cell-Surface Receptors =

 Cell-Surface Receptors
- Transmembrane Receptors are cell surface
membrane-anchored proteins that binds to external
 Enzyme-Linked Receptors
ligand. Ligands do not have to enter.
- cell surface receptors with intracellular domains that
- extracellular signal is converted into intracellular
is also the enzyme itself, and interact directly with
signal.
enzyme.
- they are cell-specific proteins or markers because
thay are specific to an individual cell. A receptor tyrosine kinase is
- errors could cause hypertension, asthma, heart dis. an enzyme-linked receptor
- three main components: an external ligand-binding with a single transmembrane
domain, a hydrophobic membrane-spanning region, and extracellular and
region, and an intracellular domain inside the cell. intracellular domains. Binding
of a signaling molecule to the
extracellular domain causes
the receptor to dimerize.
Tyrosine residues on the
intracellular domain are then
autophosphorylated, triggering
a downstream cellular
response. The signal is
terminated by a phosphatase
that removes the phosphates
from the phosphotyrosine
residues.

 Ion-linked receptors Signaling Molecules

- binds a ligand through an open channel allowing
ions to enter.  Small Hydrophobic Ligands
- When a ligand binds to the extracellular region of the - directly diffuse through the plasma membrane and
channel, there is a conformational change in the interact with internal receptors
proteins structure that allows ions such sodium, - steroid hormones
calcium, magnesium and hydrogen to pass through - In order to be soluble in blood, hydrophobic ligands
must bind to carrier proteins while they are being
transported through the bloodstream

 Water Soluble Ligands

 G- - cannot pass through plasma membrane, or too large
to pass through.
- Binds with extracellular domain of cell surface
receptors.
- small molecules, peptide, proteins.

 Other Ligands
Linked - Nitric oxide (NO) gas, could diffuse across plasma
Protein membrane and interact with receptor in smooth
Receptors muscle.
- binds to - has a very short life, so only in short distances.
active membrane - Nitroglycerin for heart disease triggers release of NO
G- Protein. It causing blood vessels to dilate, restoring blood flow.
has 7