Bio Practice Test

In SILENCE, we can
experience God.
Be still at heart, in mind, and in action.
Quiz Number 6
Part I. Identification. Name or give what each item
requires. Each item is worth two (2) points.
1. Centrosome is composed of two or three

___________.
2. The nuclear lamina is composed of ___________.
3. The accepting site of a Golgi apparatus is called
__________.
4. Nucleolus is responsible for the production of
__________, which is composed of rRNA.
5. __________ is a part of endomembrane system
that stores calcium in the cell.
Quiz Number 6
6. __________ regulates the entry and exit of
molecules in and out of nuclear envelope.
7. Peptidoglycans is composed of __________ and
__________.
8. The membrane that bounded the central vacuole
is called _________.
9. The semi-liquid where all organelles are bound is
called ___________.
10. Centromere gives rise to the ___________, which
is a part of the cytoskeleton.
Quiz Number 6
BONUS:
What is the difference between

“bound” and “bounded”?
(2 points)
Quiz Number 6
1. Centrosome is composed of two or three

centrioles
___________. intermediate
filament
2. The nuclear lamina is composed of ___________.
3. The accepting site of a Golgi apparatus is called
cis-face
__________.
4. Nucleolus is responsible for the production of
ribosome which is composed of rRNA.
__________,
Smooth ER is a part of endomembrane system
5. __________
that stores calcium in the cell.
Quiz Number 6
6. Pore complex regulates the entry and exit of
__________
molecules in and out of nuclear envelope.
proteins and
7. Peptidoglycans is composed of __________
carbohydrates
__________.
8. The membrane that bounded the central vacuole
tonoplast
is called _________.
9. The semi-liquid where all organelles are bound is
cytosol
called ___________.
microtubule which
10. Centromere gives rise to the ___________,
is a part of the cytoskeleton.
Is it okay to drink five small
bottles of Yakult everyday?
Lactobacillus casei Shirota
Cell Structures & Communication
Mr. Mardocheo Yao Crispino | Oldcorne, Walpole, Xavier, Denn, Grodecky
General Biology 1 | First Semester, School Year 2017 – 2018
Walkthrough:
The Cell Theory
Prokaryotic versus Eukaryotic Cells
Nucleus and Ribosomes
Endomembrane System
Mitochondria, Chloroplast, and Peroxisomes
Cytoskeleton and Extracellular Components
Cell Communication, Membrane, and Transport

M. Y. Crispino (mcrispino@ateneo.edu) General Biology 1 | First Semester, S.Y. 2017 – 2018
The Cell Theory
What is a cell?
The cell is the
simplest collection of
matter that can be
considered a living
entity.
Cancer cells as they divide

The Cell Theory
What is a cell?
All cells are related by
their decent from
earlier cells.
Organelles are
membrane-bounded
structures that have
Cancer cells as they divide specific functions
within cells.

The Cell Theory
Robert Hooke cell walls of a cork

The Cell Theory
Anton van Leeuwenhoek animalcules

The Cell Theory

The Cell Theory
scanning electron microscope (SEM)

The Cell Theory
cryo-electron microscope
The Cell Theory

The Cell Theory
The Three Tenets 1. All organisms are made of
of Cell Theory one or more cells (Schleiden
and Schwann)
2. The cell is the basic unit of

structure for all organisms
(Schleiden and Schwann)
3. Omnis cellula e cellula / All

cells come from existing cell
(Virchow)
The Cell Theory
Modern Addenda
to Cell Theory
1. Energy flow occurs within
cells.
2. Heredity information (DNA)
is passed on from cell to
cell.
3. All cells have the same
basic chemical
composition.

Walkthrough:
The Cell Theory
Endomembrane System

Prokaryotic vs Eukaryotic
All cells have:
Plasma membrane
the selective barrier that
bounded the cells
Chromosomes
gene carriers in the form
of DNA
plant, animal, and bacteria cells

Prokaryotic vs Eukaryotic
All cells have:
Ribosomes
tiny complexes that make
proteins according to
instructions from the
genes
plant, animal, and bacteria cells

Prokaryotic Cells
Prokaryotic Cells
A typical rod-shaped bacterium (prokaryote)

Prokaryotic Cells
Nucleoid
a not membrane-bounded
region where DNA of the
prokaryotic cell is
concentrated
It contains three layers of
protective media namely:
(1) plasma membrane,
(2) cell wall, and
(3) capsule.
A bacterium under TEM
Prokaryotic Cells
(phospholipid bilayer)
(peptidoglycan: carbs + protein) (outer membrane)

Three layers of protective media for bacteria
Prokaryotic Cells
Gram-positive (left) Gram-negative (right) bacteria

Prokaryotic Cells
Gram-positive versus Gram-negative bacteria

Prokaryotic Cells
Analogy for the Gram-positive bacteria

Prokaryotic Cells
Analogy for the Gram-negative bacteria

Prokaryotic Cells
Which is more resistant to drugs?

Eukaryotic Cells
Eukaryotic Cells
A generalized animal cell

Eukaryotic Cells
A generalized plant cell

Eukaryotic Cells
What is the difference between:
1. kinetocore, telomere, gyrase, telomerase?
2. ribozyme, spliseosome, nucleosome?
3. chromatin, chromatid, and chromosome?
4. centrosome, centriole and centromere?
5. myosin, actin, tubulin, microfilaments, intermediate
filaments, and microtubules?
6. gap junctions, desmosomes, and tight junctions
7. collagen, proteoglycans, fibronectin, and integrins?

Walkthrough:
The Cell Theory
Endomembrane System

Nucleus: Information Central
Structure of the nucleus

Nucleus
contains most of the genes in
the eukaryotic cells
Nuclear envelope
a double membrane that
encloses that nucleus that
separates its contents from
the cytoplasm
Electron micrograph of nucleus

Pore complex
an intricate protein structure
that lines each pore and plays
an important role in the entry
and exit of macromolecules,
RNA, and proteins

Nuclear lamina
netlike array of protein
filaments (intermediate
filaments) that mechanically
support the shape of the
nucleus

Nuclear matrix
a framework of protein
fibers that extend
throughout the nuclear
interior
Chromatin
the complex of DNA
and proteins making
up the chromosomes
Structure of nucleus
Nucleolus
a prominent structure
made up of DNA and
proteins within the
nondividing nucleus;
proteins imported
from the cytoplasm are
assembled with rRNA
into small and large
units of ribosomes
mRNA
a product of
transcrition that carries
genetic message of the
DNA; read by
ribosomes to produce
protein and enzyme as
products.

Chromatin condenses to form chromosomes

Genetic information from nucleus to ribosomes

Ribosome: Protein Factories
Location and structure of a ribosome

Ribosomes
complexes made of
ribosomal RNAs and
proteins; carry out
protein synthesis
They are not
membrane-bounded;
thus they are not
considered organelles*.
mRNA translated into protein

Free ribosomes
function within the
cytosol; examples are
enzymes that catalyze
the first steps of sugar
breakdown

Bound ribosomes
make proteins that are
destined for insertion
into membranes, for
packaging, and
secretion; e.g.
pancreatic cell for
digestive enzymes


Walkthrough:
The Cell Theory
Endomembrane System

Endomembrane System
Functions:
1. Synthesis of proteins
2. Transport of
proteins into
membranes and
organelles
3. Metabolism and
movement of lipids
4. Detoxification of
toxins
Members of the endomembrane system
Endomembrane System
Members:
1. Endoplasmic
reticulum (ER)
2. Golgi apparatus
3. Vacuoles
4. Lysosomes
5. Nuclear envelope
6. Plasma membrane
Members of the endomembrane system

ER: Biosynthetic Factory
ER
Extensive network
of membranes that
it accounts for
more than half of
the total
membranes for
eukaryotic cells
Structure of the ER

ER
consists of network
of membranous
tubules and sacs
called cisternae.
ER lumen
internal
compartment of ER
Structure of the ER

Rough Endoplasmic Reticulum
Functions:
1. Has bound
ribosomes
2. Produces proteins
and membranes,
which are
distributed by
transport vesicles
Rough ER

Smooth Endoplasmic Reticulum
Functions:
1. Synthesizes lipids
2. Metabolizes
carbohydrates
3. Stores calcium
4. Detoxifies poison
and drugs
Structure of the ER

Transport vesicle from transitional ER

From ER to Golgi apparatus to cell membrane



Synthesis and packaging of a secretory protein by the rough ER

What is the difference between

constitutive and controlled exocytosis?
How does ER regulate its processes?

Signal Sorting

Signal sorting by ER
Golgi Apparatus: Shipping &
Receiving Center
Golgi Apparatus: Shipping & Receiving Center
Structure of Golgi apparatus

Golgi apparatus
consists of
flattened
membranous
sacs called
cisternae

Functions:
1. Modifies products
of the ER
2. Manufactures
certain
macromolecules
3. Sorts and packages
materials into
transport vesicles

Coatomer
a protein complex
that coats the
transport vesicle;
has three types:
1. COPI
2. COPII
3. Clathrin-coated

COPI
retrograde transport;
from trans-face to
cis-face to ER
COPII
anterograde
transport; from ER to
cis-face to trans-face
COPI
Clathrin-coated vesicles
Lysosome: Digestive Compartments
Lysosome: Digestive Compartment
Lysosome
a membranous sac of
hydrolytic enzymes
that can digest
macromolecules;
works best in an
acidic environment
Structure of lysosome

Some types of cell

can engulf another
cell by phagocytosis;
this forms a food
vacuole.

Lysosomes also use

enzymes to recycle
the cell’s own
organelles and
macromolecules, a
process called
autophagy.

Phagocytosis

Autophagy

Phagocytosis by macrophage

Autophagy of a mitochondria

Lysosome formation
Vacuole: Maintenance Compartments
A plant cell or fungal

cell may have one or
several vacuoles,
derived from
endoplasmic
reticulum and Golgi
apparatus
Structure of vacuoles

Food vacuoles
are formed by
phagocytosis.

Contractile vacuoles pump excess water out of the cell.
Paramecium sp., a common freshwater protozoa

Central vacuole are found in plant cells. It holds reserves

of organic compounds and water.

Vacuole of Paramecium sp.

Walkthrough:
The Cell Theory
Endomembrane System

Mitochondria & Chloroplasts
Endosymbiont Theory
Evidences of endosymbiont theory:
1. Mitochondria and chloroplasts have two

membranes surrounding them.
2. Like prokaryotes, mitochondria and chloroplasts
contains ribosomes as well as circular DNA
molecules like that of a bacteria.
3. Mitochondria and chloroplasts are autonomous
organelles that grow and reproduce within the cell.

Mitochondria and chloroplasts have

similarities with bacteria:
1. Enveloped by a double membrane
2. Contain free ribosomes and
circular DNA molecules
3. Grow and reproduce somewhat
independently in cells
Mitochondria and Chloroplast

Mitochondria: Powerhouse of the Cell
Mitochondria are in
nearly all eukaryotic
cells.
They have a smooth

outer membrane and an
inner membrane folded
into cristae.
Structure of Mitochondria
The inner membrane
creates two
compartments:
intermembrane space and
mitochondrial matrix.
Some metabolic steps of

cellular respiration are
catalyzed in the
mitochondrial matrix.
Structure of Mitochondria
Network of mitochondria of Euglena sp.

Mitochondria in animal cell

Chloroplast: Capture of Light Energy
Chloroplast
structure includes
thylakoids,
(membranous sacs)
stacked to form a
granum in
stroma (the internal
fluid).
Structure of chloroplast
There are three
compartments:
1. intermembrane
space
2. stroma
3. thylakoid space.
Chloroplast belongs
to general group of
plant organelles
Structure of chloroplast plastids.
Network of chloroplasts of Spirogyra sp.

Cytoplasmic streaming
Peroxisome: Oxidation
Peroxisomes: Oxidation
Peroxisome is a
specialized metabolic
compartment
bounded by a single
membrane.
It detoxifies alcohol
and other harmful
compounds by
producing hydrogen
Structure of peroxisomes
peroxide and
converting it to water.
Peroxisomes: Oxidation
This organelle uses
oxygen molecule or
ROS to remove
hydrogen from organic
substrate (R) to form
hydrogen peroxide,
which is further used
by catalase to produce
water as the end
product. Defect may
Structure of peroxisomes lead to VLCFA.
Walkthrough:
The Cell Theory
Endomembrane System

Cytoskeleton: Support and Motility
Cytoskeleton
Network of fibers
extending throughout
the cytoplasm
Colorized micrograph of cytoskeleton

Functions:
1. Organizes cell’s
structure and
activities
2. Interacts with motor
proteins to produce
motility
Types:
1. Microtubules
2. Microfilaments
3. Intermediate
filaments
Microtubules

Microfilament
Intermediate filament
Centrosome and Centriole

In many cells, microtubules grow out from a
centrosome (composed of two or three
centrioles) near the nucleus. The centrosome is
a “microtubule-organizing center”
Centrosome and Centriole

In animal cells, the centrosome has a pair of
centrioles, each with nine triplets of
microtubules arranged in a ring

Microtubules
control the
beating of cilia
and flagella,
locomotor
appendages of
some cells.
They differ in
their beating
patterns
Cilia and Flagella

Paramecium sp. Cilia

Chlamydomonas sp.
Extracellular Components
Plant cell walls and Plasmodesmata

Tight Junction
prevents leakage of fluid
across a layer of cells.
Desmosome
“clips“ cells into strong
sheets
Gap Junction
behaves like
plasmodesmata of plant
cells

Extracellular matrix of animal cells

Walkthrough:
Cell Transport
Endomembrane System
Cell Membrane, Transport, and Communication

Cell Membrane
Cell Membrane
Properties:
1. Selective permeability
2. Fluid mosaic
3. Has functional Proteins
4. Can fuse and form vesicles
5. Asymmetrical
6. Has different functions

Cell Membrane
The phospholipid
is an amphipathic
molecule.

Cell Membrane
The phospholipid
is an amphipathic
molecule.
Most of the
membrane
proteins are
amphipathic, as
well.

Cell Membrane
What makes the
cell membrane
semi-permeable?

Cell Membrane
2. Fluid Mosaic Model The cell membrane is not
an instant knowledge
because scientists used
models as hypotheses to
the structure of the cell
membrane.
 Hugh Davson and James
Danielli: Sandwich Model
S. J. Singer and G.
Nicolson: Fluid Mosaic
Model
Cell Membrane
2. Fluid Mosaic Model
What are the factors that affect the fluidity of the cell membrane?
Cell Membrane
2. Fluid Mosaic Model
What are the factors that affect the fluidity of the cell membrane?
Cell Membrane
3. Has functional proteins
Integral versus Peripheral Proteins

Cell Membrane
Protein that
spans the
entirety of the
biological
membrane.
Many of these
functions as
gateways.
Transmembrane Protein
Cell Membrane
Transport Proteins
Cell Membrane
Aquaporins
Cell Membrane
4. Can fuse and form vesicles

Cell Membrane
5. Asymmetrical

Cell Membrane
5. Asymmetrical
Freeze-fracturing technique

Cell Membrane
6. Has different functions Selective permeable
membrane
Keeping the cytoplasm
compact
Allows communication with
other cells
Allows recognition of
external substances
Allows mobility of
organisms (Amoeba sp.)
Site of various chemical
reactions
Cell Membrane
What is the difference between the composition of

cell membrane and the extracellular matrix?
What is the role of carbohydrate attached to the cell
membrane proteins?
What is the difference between plasmodesmata, gap
junctions, tight junctions, and desmosomes?

Cell Transport
Cell Transport
What is the difference between active and passive
transport?
What is the role of gradient concentration in cell
transport? How about electrochemical gradient?
What is the difference between diffusion and osmosis?
What are hypertonic, hypotonic, and isotonic
conditions?
What is the difference between simple and facilitated
diffusion?
What is the difference between Na-K pump and Co-
transport proteins?
Passive Transport
1. Diffusion
concentration gradient

Passive Transport
1. Diffusion

Passive Transport
2. Osmosis

Passive Transport
2. Osmosis

Passive Transport
2. Osmosis

Passive Transport
2. Osmosis

Active Transport

Active Transport
1. Na+ - K+ (Sodium-Potassium) pump

Active Transport
2. Cotransport Proteins

Active Transport
2. Cotransport Proteins

Active Transport
3. Bulk Transport
Exocytosis
Active Transport
3. Bulk Transport
Endocytosis

Cell Communication
A. Cell Messaging
How does your body process this image?

A. Cell Messaging
Why do you blush when you see your crush?

A. Cell Messaging
Why do you have this unbelievable energy when cramming?

A. Cell Messaging
When it is a life and death situation, how does your body react?

A. Cell Messaging
Epinephrine, also known as Adrenaline

B. Evolution of Cell Signaling
Yeast cells use chemical
signaling to identify
cells of opposite mating
type and initiate mating
process.
Early versions of cell

communication evolved
even before the
multicellular organisms.
The mating of Saccharomyces cerevisiae
These bacteria use
chemical signals to
share about nutrient
availability.
Quorum sensing
ability of the
prokaryotes to
coordinate their
behaviors that require a
given number of cells.
Communication of Myxococcus xanthus
Production of biofilm as one consequence of quorum sensing

Bioluminescence of Vibrio fischeri

of as one consequence of quorum sensing

C. Local Signaling
Paracrine signaling (left) versus Synaptic signaling (right)

D. Long-distance Signaling
Endocrine (hormone) signaling

E. Signal Transduction Pathway
Overview of cell signaling

E. Signal Transduction Pathway
Dominoes falling as an analogy for cell communication

F. Reception
There are three major
types of cell membrane
receptors:
1. G protein-coupled
receptors (GPCR)
2. Receptor tyrosine
kinases (RTK)
3. Ion channel
receptors
Ligand and Receptor

F. Reception
1. G Protein-Coupled Receptors (GPCR)
GPCR is a cell surface receptor that works with the
help of G protein, a protein that binds the energy-
rich GTP (guanosine triphosphate).

F. Reception

F. Reception

F. Reception

F. Reception

F. Reception
2. Receptor Tyrosine Kinases
RTK is a protein kinase, an enzyme that catalyzes the
transfer of phosphate groups from ATP to another
protein.

F. Reception

F. Reception

F. Reception

F. Reception

F. Reception
What is the difference between G Protein-

Coupled Receptor (GPCR) and Receptor
Tyrosine Kinases (RTK)?

F. Reception
3. Ion Channel Receptors

F. Reception
3. Ion Channel Receptors

G. Transduction
Protein Phosphorylation and Dephosphorylation
 Transduction happens when the receptor changes
in various forms. This change is very often brought
about by phosphorylation and dephosphorylation.
 Protein kinases, group of enzymes that transfer
phosphate groups from ATP to a protein, thus
activating the protein.
 Protein phosphatases, enzymes that remove
phosphate group from a protein, making the
protein inactive again.
G. Transduction
Phosphorylation
cascade
a sequence of
steps that can be
understood as
falling dominoes.

H. Response
Cell signaling leads to regulation of:
(1) transcription and (2) cytoplasmic activities.

I. The case of LuxO gene
LuxO is the gene code responsible for luminescence

of some organisms including Vibrio.
When phosphate is bound to LuxO, there is

light inhibition. There is no luminescence.
When phosphate is not bound to LuxO, there is

no light inhibition. There is luminescence.





J. Microbial Conversations
1. Chemical Language
Gram Positive Bacteria Gram-Negative Bacteria
Short peptides Acyl homoserine lactones
All chemical communications require mechanisms

for making and detection of signals.
Vibrio fischeri (Gram negative): LuxI (autoinducer)
and LuxR (detection)
Gram positive: two component signal transduction
system

1. Chemical Language
An hybrid of Gram
positive and
negative bacteria
when it comes to
chemical
communication
Different AI1 and
AI2 autoinducers.
AI2 serves as the
Vibrio fischeri universal language
for bacterial world.
2. Electronic language
This species
produces nanowires,
a pilin that lacks
carboxyl group.
Geobacter sulfurreducens

Nanowires function in Geobacter sulfurreducens:
1. Bind to and conduct electron to soluble metals
such as uranium
2. Reductively precipitate the soluble metal
3. Protect the cell from the toxic effects of
uranium
4. When cell densities are low, the nanowires
form electronic networks (contrasting to
quorum sensing).
Shewanela oneidensis
Bacillus cells can be stimulated by sound waves.

Escherichia coli can be stimulated by microwaves.

Rhodobacter sphaeroides can be stimulated by magnetic fields.

Saccharomyces cerevisiae vibrates to send signals to each other.

Walkthrough:
The Cell Theory
Endomembrane System
Cell Membrane, Transport, and Communication


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In SILENCE, we can

1. Centrosome is composed of two or three

What is the difference between

1. Centrosome is composed of two or three

Prokaryotic versus Eukaryotic Cells

Nucleus and Ribosomes

Mitochondria, Chloroplast, and Peroxisomes

Cytoskeleton and Extracellular Components

Cell Communication, Membrane, and Transport

Cancer cells as they divide

M. Y. Crispino (mcrispino@ateneo.edu) General Biology 1 | First Semester, S.Y. 2017 – 2018

M. Y. Crispino (mcrispino@ateneo.edu) General Biology 1 | First Semester, S.Y. 2017 – 2018

Robert Hooke cell walls of a cork

Anton van Leeuwenhoek animalcules

M. Y. Crispino (mcrispino@ateneo.edu) General Biology 1 | First Semester, S.Y. 2017 – 2018

scanning electron microscope (SEM)

M. Y. Crispino (mcrispino@ateneo.edu) General Biology 1 | First Semester, S.Y. 2017 – 2018

2. The cell is the basic unit of

3. Omnis cellula e cellula / All

M. Y. Crispino (mcrispino@ateneo.edu) General Biology 1 | First Semester, S.Y. 2017 – 2018

Prokaryotic versus Eukaryotic Cells

Nucleus and Ribosomes

Mitochondria, Chloroplast, and Peroxisomes

Cytoskeleton and Extracellular Components

Cell Communication, Membrane, and Transport

plant, animal, and bacteria cells

plant, animal, and bacteria cells

A typical rod-shaped bacterium (prokaryote)

(peptidoglycan: carbs + protein) (outer membrane)

Gram-positive (left) Gram-negative (right) bacteria

M. Y. Crispino (mcrispino@ateneo.edu) General Biology 1 | First Semester, S.Y. 2018 – 2019

Gram-positive versus Gram-negative bacteria

Analogy for the Gram-positive bacteria

Analogy for the Gram-negative bacteria

Which is more resistant to drugs?

M. Y. Crispino (mcrispino@ateneo.edu) General Biology 1 | First Semester, S.Y. 2018 – 2019

A generalized animal cell

A generalized plant cell

M. Y. Crispino (mcrispino@ateneo.edu) General Biology 1 | First Semester, S.Y. 2018 – 2019

Prokaryotic versus Eukaryotic Cells

Nucleus and Ribosomes

Mitochondria, Chloroplast, and Peroxisomes

Cytoskeleton and Extracellular Components

Cell Communication, Membrane, and Transport

Structure of the nucleus

Electron micrograph of nucleus

Electron micrograph of nucleus

Electron micrograph of nucleus

M. Y. Crispino (mcrispino@ateneo.edu) General Biology 1 | First Semester, S.Y. 2017 – 2018

Chromatin condenses to form chromosomes

Genetic information from nucleus to ribosomes

Location and structure of a ribosome

M. Y. Crispino (mcrispino@ateneo.edu) General Biology 1 | First Semester, S.Y. 2017 – 2018

mRNA translated into protein

M. Y. Crispino (mcrispino@ateneo.edu) General Biology 1 | First Semester, S.Y. 2017 – 2018

mRNA translated into protein

M. Y. Crispino (mcrispino@ateneo.edu) General Biology 1 | First Semester, S.Y. 2017 – 2018

M. Y. Crispino (mcrispino@ateneo.edu) General Biology 1 | First Semester, S.Y. 2017 – 2018

Prokaryotic versus Eukaryotic Cells

Nucleus and Ribosomes

Mitochondria, Chloroplast, and Peroxisomes

Cytoskeleton and Extracellular Components