L01 Lecture Video 9.30.2021/10.07.

2021
Prof. Ronaldo A. Bigsang || September 2021 BIO107
Transcribers: Loyd Joredell H. Curit
Editors: Loyd Joredell H. Curit Cell and Molecular Biology

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L01 Cells, Genomes, and Model Organisms

Theme 1: Living things, though infinitely varied when viewed from the
outside, are fundamentally similar inside

1.1 All cells store their hereditary information in the form of DNA
 DNA is a long unbranched, double-stranded molecule formed
by four types of nucleotides.
 Each nucleotide has a phosphate, a sugar, and a base.
 Covalent bonds link the nucleotides in each strand, while H-
bonds hold the two DNA strands together.
 The sequence of bases determines the genetic information.
 The information can be read, interpreted, copied by any kind of
cell.
 He was able to established the concept of transformation.
 Transformation is the process of inserting a genetic material
into the cell.
Avery, MacLeod, McCarty Experiment
 Another experiment pointing out to DNA as the transforming
material/principle.
 Got samples from the dead mouse and extract different
components.

 This experiment revealed that in the DNA R exhibited the

phenotype of S – could be the transforming principle.

Hershey-Chase Experiment
 Labelled different components of virus. T2 phages & E. coli

Griffith’s Transformation Experiment

 He was able to transform a strain of streptococcus to another
strain.
 When he used a live R strain with a dead S strain, it should be
expected that the mouse would be alive, however, the mouse
died.
 He got some samples and cultured it, and observed living S
strain.
 He concluded that there was a transforming material which
caused the phenomenon he observed but he has still no idea
about it.
 By labelling the protein coat with radioactive S, sulfur, and the
DNA with P, phosphorous.
 With this experiment they’ve concluded that the transforming
principle is the DNA.
1.2 All cells replicate their DNA by templated polymerization.
 DNA is synthesized using a template formed by a preexisting
DNA strand.
 The nucleotide sequence in one strand is complementary to the
other strand.

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 They labelled E. coli DNA and cultured in a heavy nitrogen

medium.
 DNA is initially labelled N15, N14 is added and observed after 4
generations.
 E. coli grown in heavy nitrogen medium, took some samples.
 Samples grown in light nitrogen, and the density of light
nitrogen label.
Experiment dispelled the conservative model. Since red label is not
evident anymore.
 Templated polymerization of a new strand.
Experiment dispelled the dispersive model. Since there should be more
 New strand is formed from a template of the parent DNA. orange label.
 A = T; C = G
 DNA is replicated in a semi-conservative matter. Straight or Circular?
o When replication from a parent DNA molecule, you
will have a parent strand paired with a daughter
strand.

Three Proposed Models for DNA Replication

A. In prokaryotic, there is one ori site in a circular DNA so

replication forks grow away from each other.
B. In eukaryotic, there are multiple ori sites, and replication forks
move away from each other.

1.3 Gene is a DNA fragment corresponding to one protein or RNA

 Genome dictates the nature of proteins, when and where they
are to be made.
 Gene expression is a regulated process.
 Coding segments specify the transcripts and protein products.
 Non-coding regions serve as punctuation and regulatory
sequences that control the local rate of transcription.
 Conservative model is characterized by the parent strands
always paired together.
 Semi-conservative model is characterized by a parent strand
paired with a daughter strand.
 Dispersive modes is characterized by getting segment of the
parent strands and gets incorporated in the formation of
daughter strand.

The Meselson-Stahl Experiment

 Established that the cells use semi-conservative model in
replicating.

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Long non-codinng RNA is ~1000-10000 nt long with little to no protein-
coding potential.
1.4 All cells transcribe portions of their DNA into RNA
 RNA is a single-stranded polynucleotide closely related to DNA.
o Sugar: ribose
o Bases: A, G, C, U (replacement for thymine)
 RNA molecule is flexible and can fold up into specific shapes
 The shape of RNA may enable it to recognize and selectively
bind molecules, even catalyze some chemical changes.

1. Transcriptional Activation
2. Transcriptional Repression
3. Enhancer RNA
4. Scaffolding Protein for Chromatic Remodeling Complexes
5. Regulation of RNA Splicing
6. Sequestration of mRNA

MicroRNA
 Is a small (18-25 nt) noncoding RNA
 Major regulatory gene families in eukaryotes.
 Silence gene expression post-transcriptionally by binding to the
3’ untranslated regions of target mRNAs
RNA is similar to DNA but some if its properties enables it to perform
other actions.
 Transcription is a form of templated polymerization that faithfully
rewrites DNA to RNA.
 Noncoding strand serves as the template to produce RNA
transcripts.
 These transcripts function as intermediates in the transfer of
genetic information.
 Messenger RNA (mRNA) guides the synthesis of proteins.

 Applications include cancer-prevention mechanism.

Noncoding regions can also be useful especially in gene regulation.

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1.5 All cells translate RNA into protein in the same way.
 Proteins are long, unbranched polymers of amino acids and are
the main molecules that put the cell’s genetic information into
action.
 DNA sequence specifies the amino acid sequence, which in
turn determines the function of the protein product.
 There are 20 types of amino acids, each built around the same
core structure where a specific side chain attaches giving the
protein distinct chemical property.

Amino acids  Peptide  Protein

Side chain attaches amine group and acid group.
Whatever is encoded in the DNA is followed to produce protein.

Cells acquire free-energy from various sources.

 Living organisms obtain their free energy in different ways.
 Organotrophic organisms feed on other living things or the
organic chemicals they produce.
 Phototrophic organisms harvest sunlight and convert it into
forms that can be used by the cell (photosynthesis)
 Lithotrophic organisms capture their energy from energy-rich
systems of inorganics chemicals in the environment.

1.8 All cells function as biochemical factories dealing with the same
basic molecular building blocks.
 The cell is a big biochemical factory producing proteins, lipids,
and other molecules by the use of the energy acquired from the
environment.
1.6 All cells use proteins as catalysts
 Catalytic protein folds into a specific conformation forming
reactive sites --- enzymes.

1.9 All cells are enclosed in a plasma membrane across which

nutrients and waste materials must pass.
1.7 All cells acquire and utilize energy
 Cells are the basic unit of life exhibiting characteristics of life.
 Cells acquire energy to sustain all cellular processes from its
environment.
 ATP (Adenosine triphosphate) main energy currency of the cell
 Plasma membranes acts as a selective barrier (semipermeable)
 Membrane transport proteins determine which molecules enter
the cell.
 Amphiphilic (phospholipid) molecules aggregate spontaneously
to form bilayer in water. (water-loving/ lipid-loving)
 Cells produce molecules whose chemical properties cause
them to self-assemble into the structure that a cell need.

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1.10 Cells respond to stimuli and self-regulate
 Cells are covered with receptors (located inside or outside the
cell) that interact with substances in the environment in highly
specific ways.
 Receptors provide pathways through which external stimuli can
evoke specific responses in target cells. (receptors exhibit
different responses to signals and influence how the cell acts)
 Cells may respond to specific stimuli by altering their metabolic
activities, moving from one place to another, or activating death
pathways.
 Cells are robust, under constant regulation.
 Cells use specific feedback circuits to regulate cellular
responses to maintain homeostasis.
Theme 2: Living things are related in a family tree through evolution.
Diversity of genomes and the tree of life
 Traditionally, living things were classified based on morphology.
 In microbes, biochemistry and nutritional requirements were
considered.
 Genomic analysis is a simpler, more direct, and more powerful
way to determine evolutionary relationships. (OMICs
technology)
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Organisms now are classified into 3 domains: Bacteria, Archaea, &
Eukaryotes
By utilizing genomic analysis in looking at genomes is much more
accurate way.
The nuclear genome of a eukaryotic cell evolved from an ancient
archaeon.
 Prokaryotes comprise two distinct groups – bacteria and
archaea – that diverged early in the history of life on earth.
 Eukaryotes diverged later on from an ancient archaeal cell.
 At the molecular level, archaea seem to resemble eukaryotes
more closely in their machinery for handling genetic information,
but bacteria more closely in their apparatus for metabolism and
energy conversion.
Some parts of the genome will change more easily than others.
 Highly conserved genes cannot alter so easily as they often
code for highly optimized essential protein or RNA and
molecule.
Genes or cells that are highly conserved are present in every cell or
common as they possess important characteristics that is useful and
beneficial to the cell. Encodes for an essential function and removal would
be disadvantageous. Altering the genome would alter the product. A
change in the gene would affect product and function.

 Genomic mutation may be [1] beneficial, [2] selectively neutral,
or [3] fatal.
o [1] mutation is perpetuated because of increased
likelihood of reproduction
o [2] mutation may be perpetuated or not as it becomes
a matter of chance whether the altered cell will
succeed when it competes for limited resources.
o [3] mutation leads nowhere as the cell dies without
progeny.
Mutations may be beneficial and fatal depending on its effect on the cell.
Mutation may or may not increase the fitness of the cell/organism.
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Mutations are alteration of genomic sequence in the DNA. The diversity of More than 200 gene families are common to all 3 domains of life
mutations may result to various products including cell death.
Common genes are possibly highly conserved genes. These genes
 Through endless repetition of this cycle of mutation and natural above are identified through genomic analysis.
selection, organism evolves. Researches on genome and DNA sequences still are conducted to reveal
more of the benefits by having the knowledge on genomic analysis.
Humans are actually more related to methanococcus (archaeon), than to
bacteria as presented in genomic analysis between the organisms. There are two fundamentally different classes of cell.
DNA barcoding – use the DNA or genomic sequence as barcodes to
easily identify organisms more easily and specific.
Microevolution – occurs in a short period of time; usually in prokaryotic
cells.

New genes are generated from preexisting genes.

 Intragenic mutation randomly modifies the DNA sequence
through various types of errors during DNA replication
 Gene duplication creates a pair of identical genes within a
single cell, which may then diverge in the course of evolution.
 DNA segment shuffling occurs when two or more existing
genes break and rejoin to make a hybrid gene.

DNA polymerase check for errors; acts like proofreading looking for
mistakes.
By these mutations other genes are formed which may or may not be
advantageous to the cell.
 Horizontal (intracellular) transfer introduces a piece of DNA
from the genome of one cell to that of another. (usually in
prokaryotes)
Prokaryotic cells have a relatively simple structure.
 2 distinct kingdoms: Eubacteria and Archaea
 Commonly 1-2 um in size and consist of a single closed
compartment containing the cytoplasm and bounded by the
plasma membrane.
 Genome is composed of a single circular DNA molecule
 Many prokaryotes contain additional small and circular DNA
molecules called plasmids.

Plasmids are very important in recombinant DNA technology.

Prokaryotes are used as model organisms in observing due to their rapid
generation time.

Most eukaryotic cells contain extensive internal membranes that

enclose specific subcellular compartments.

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ENDOMEMBRANE SYSTEM
 Network of membranes related through direct physical contact
or by vesicles
 Divides the cell into structural and functional compartments
 Includes nuclear envelop, ER, Golgi complex, transport and
secretory vesicles, lysosomes, peroxisomes, vacuoles, plasma
membrane

Compartmentalization allows many processes to maximize activity.

ENDOPLASMIC RETICULUM
 Membranous network of tubular and sac-like structures
(cisterna) close to the nucleus
 2 regions:
o Rough endoplasmic reticulum (RER); rough due to
ribosomes attached on it
o Smooth endoplasmic reticulum (SER); no ribosomes
 Compartmentalization is very important. attached
 Compartmentalization of cell allows conduct of several action at
the same time.
 Maximizes space between cell, time for cell to process., and
effort.
 Removing compartment affects the whole of the cell.

ORGANELLES
 Membrane-bound structures
o Single membrane – i.e. ER, vacuole, lysosome,
peroxisome
o Double membrane – i.e. nucleus, mitochondrion,
chloroplast.
 Non-membrane bound organelles (i.e. biomolecular complexes)
o Ribosome, proteasome, nucleosome, centriole and
MTOC, cytoskeleton, flagellum
 Performs specific function in eukaryotic cell Rough ER is involved in protein synthesis due to ribosome attached.
Smooth ER is involved in carbohydrate and lipid metabolism, and
detoxification.

ROUGH ENDOPLASMIC RETICULUM

 Extension of the outer nuclear membrane
 Ribosomes attached to the membranes
 FXN: synthesizes proteins
 Protein products are wrapped in transport vesicles that bud
from the ER

SMOOTH ENDOPLASMIC RETICULUM

 No attached ribosomes
 FXN: synthesis of lipids, processing of sugars, detoxification of
drugs and poison, store calcium for muscle contraction.
NUCLEUS  Lipid and sugar products are wrapped in transport vesicles that
 Usually located at the center of the cell bud from the ER.
 ‘command center’ of the cell
 Contains the genetic material organized into chromosomes GOLGI BODIES
 Controls the activities of the cell  Flattened stack of sac-like membranes (cisterna) that are
 PARTS: scattered throughout the cytoplasm
o Nuclear envelope (surrounding)  Called dictyosomes in plants
o Nuclear pore (opening)  Cis face – receiving side
o Nucleoplasm (cytoplasm-like; chromatin)  Trans face – releasing side
o Nucleolus  FXN: sorts, modifies, packages cellular products and secrete
them out to their destinations.

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 Liver cells (more in in liver cells due to detoxifications)

VACUOLES
 single membrane organelle separated from the cytoplasmic
contents by tonoplasts
 in animals:
o small but several vacuoles
 in protists: (paramecium; aquatic protists)
o contractile vacuoles are used to pump excess water
TRANSPORT AND SECRETORY VESICLES  in plants:
o one large central vacuole (turgidity)
 FXN: storage of water, ergastic substances, inclusions etc.

Transport vesicles hold and transfers products from the ER to the Golgi
bodies into respective destinations.

LYSOSOMES
 Produced by the Golgi complex
 Contain digestive (hydrolytic) emzymes – ‘demolition sites’ or
‘suicidal bags’
 FXN: digests macromolecules, cellular debris, old organelles
and foreign substances.
 Macrophage (more lysosomes; related to job in immunity)

PEROXISOMES
THE ENDOMEMBRANE SYSTEM
 Contains enzymes produced by cytoplasmic ribosomes
 Peroxidases and catalases
 FXN: detoxify toxins and free radicals, breakdown fats, produce
bile salts

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 “powerhouse of the cell”
 Sausage-shaped organelle about the size of a bacterial cell
 Has its own set of circular DNA and may divide by simple
fission.
 Parts:
o Outer membrane
o Intermembrane space
o Inner membrane fold into crista
o Matrix
 FXN: ATP production via cellular respiration (energy extraction
process)
Folding inside the mitochondria maximizes the surface area for ATP
production to take place.

CHLOROPLAST
 Energy-capturing centers in photosynthetic eukaryotes
 Circular DNA; may divide by simple fission
 PARTS:
o Outer membrane
o Inner membrane
o Thylakoid sacs – granum
o Stroma
 FXN: food production via photosynthesis (energy-storing
process) ATP production

OTHER ORGANELLES

PLASTIDS
 Organelles containing pigments and food materials
 3 Types based on pigments contained:
o Chromoplasts – colored plastids containing
carotenoids; present in fruits, flowers and leaves
o Leucoplasts – colorless plastids which store food
materials
 Amyloplasts – store starch
 Aleuroplasts – store proteins
 Elaioplasts – store lipids
o Chloroplasts – green-colored plastids containing
chlorophylls and carotenoids (carotene and
xantophyll)
GLYOXYXOMES
 Microbodies that store and convert fats into carbohydrates

INCLUSIONS
 Temporary, non-membranous structure – ergastic substances
 INCLUDE:
o Food resrves – starch, protein, oils
o Secretory products – nectar, pigment, enzymes
Ribosome: Free floating in cytoplasm & ER bounded o Excretory products – alkaloids, resins, latex, tannins
o Mineral crystals – crystoliths, raphides, druses
MITOCHONDRION
CYTOSKELETON
 Dense network of protein fibers present in 3 different kinds:
o Microfilaments – cell motility
o Intermediate filaments – provide interna; guy-wire to
resist pulling force
o Microtubules – overall shape and distribution of
organelles
 FXN: supports the shape of the cell; anchors organelles; cell
movement

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CENTRIOLES
 Found in animals but not in plants and fungi
 FXN: anchor and assemble microtubules; give rise to spindle
fibers during cell mitosis

FLAGELLUM
 Consists of a 9+2 arrangement of microtubules
 Anchored in the cell by a basal body OCCLUDING JUNCTIONS
 Long but few in number  Tight junction (zonula occludens)
 FXN: cell movement  Seal cells together in an epithelium in a way that prevents even
CILIUM small molecules from leaking from one side of the sheet to the
 Consists of 9+2 arrangement of microtubules other.
 Anchored in the cell by a basal body  Confine the transport proteins to their appropriate membrane
 Short but numerous domains by acting as diffuson barriers within the lipid bilayer of
 FXN: cell movement; propel substances across a cell’s surface the plasma membrane
 Block the backflow of glucose from the basal side of the
KINESIN AND DYNEIN epithelium into the gut lumen
 Eukaryotic cells have developed high speed locomotives that
run along microtubular tracks ANCHORING JUNCTIONS
 Kinesin – motor protein that moves vesicles to the cell’s  Mechanically attach cells (and their cytoskeletons) to their
periphery neighbors or to the extracellular matrix
 Dynein – motor protein that moves vesicles to the cell’s interior  adherens junctions (zonula adherens) and desmosomes
(macula adherens) hold cells together; cadherin is major
transmembrane adhesion protein
 focal adhesions and hemidesmosomes bind cells to
extracellular matrix; integrin is the major transmembrane
adhesion protein
 adherens junction and focal adhesiosn serves as connection
sites for actin filaments
 desmosomes and hemidesmosomes serve as connection sites
for intermediate filaments

COMMUNICATION JUNCTIONS – GAP JUNCTION

 mediate the passage of chemical or electrical signals from one
interacting cell to its partner
 spanned by channel-forming proteins (connexins) that allow
inorganic ions and other water-soluble molecules to pass
directly from the cytoplasm of one cell to the cytoplasm of the
other, thereby coupling the cells both electrically and
metabolically

In plant cells…

Plasmodesmata are direct links between two adjacent cytoplasm.

Occluding

Anchoring

CELLULAR JUNCTIONS

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Communication

PLASMODESMA

Outside the Plasma Membrane

CELL WALL
 FXN: offer added protection and support to the cell
 Plant cells have cellulosic cell wall (made of cellulose)
 Fingal cells have chitinous cell wall (made of chitin)

EXTRACELLULAR MATRIX
 A mixture of proteins, fibers, and sugar chains secreted by
animal cells
 FXN: helps coordinate the behavior of all cells in a tissue

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