Scientific Inquiries and Biological Techniques

Wednesday, 1 November 2023 6:22 pm

Dreamer

Biological Techniques
- Methods and procedures used by biologists to study macro- and microorganisms
Microscopy
- Provides a magnified image of organisms or cells
- Classified into different types based on method of magnification, and purpose
- Modern Compound Microscopes are composed of:
○ Ocular Lens
▪ Found inside the eye piece
▪ Where the final magnified image can be viewed
▪ Usually has a magnification of 10x or 15x
○ Objective Lenses
▪ Found attached to the nosepiece
▪ Vairy in levels of magnification from x4 up to x1000 or more
▪ Each objective is represented by a particular color
□ Scanner --> Red
□ Low Power --> Yellow
□ High Power --> Blue
□ Oil Immersion Objective (OIO) --> White (OIL)
○ Condenser & Diaphragm
▪ Responsible for the regulation of light for brightness and contrast
adjustments

Parts of a Microscope

- Eyepiece --> magnifies the image produced by the microscope's objective

- Eyepiece Tube --> holds the eyepiece in place above the objective lens
- Body Tube --> separates the objective and the eyepiece and assures continuous
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 - Body Tube --> separates the objective and the eyepiece and assures continuous
alignment of the optics
- Course Focus --> used to bring the specimen into approximate or near focus
- Fine Focus --> fine tune the focus on the specimen, also used to focus on various
parts of the specimen
- Nosepiece --> circular structure where the various objective lenses are screwed
in
- Objective Lens --> directly observe the object the microscope user is examining
- Arm --> connects to the base and supports the microscope head
- Stage Clips --> hold the slides in place
- Base --> serves as a support for microscopes
- Specimen Stage --> where the specimen is placed for observation
- Condenser & Diaphragm --> concentrate light correctly on the specimen and
direct the light rays into the objective
- Illumination Mirror --> light source used to transmit light
Using a Compound Microscope
1. Set up the light source
2. Ensure that the stage is at the lowest level and objective
3. Ensure that the nose piece and eye piece is locked in place
4. Place the prepared slide (w/ cover slip) onto the stage and center the specimen,
lock it w/ the stage clips
5. Using the coarse focus knobs, slowly bring the stage upward enough to see at
least a blurred version of the specimen, use the fine focus knob to see the
individual structures clearly
6. Move the nosepiece so that you are using the next objective w/ a higher
magnification
7. Repeat step 6 w/ a higher magnification and take notes of the structures
8. Once finished, use the coarse focus to gently lower the stage

Types of Microscopes
- Light Compound Microscope
○ Makes use of light to view section specimen to 200x magnification
○ Can either use a mirror to reflect light from an outside source or has its own built
in light bulb

Magnification Ocular Lens Total Magnification

Scanning 4x 10x 40x
Low Power Objective 10x 10x 100x
High Power Objective 40 10x 400x

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High Power Objective 40 10x 400x
Oil Immersion to 100x
Objective (OIO)
- Transmission Electron Microscope (TEM)
○ Makes use of a stream of electrons
○ Studies the internal structures of section specimen

- Scanning Electron Microscope (SEM)

○ Makes use of a stream of electrons
○ Studies the 3D surface of a specimen
- Dissecting Microscope
○ Also known as "Stereomicroscope"
○ Use angled light to view 3d structures of a specimen
○ Can also use the angled light for low magnification observation of a sample

Slide Preparation
- Wet Mount
○ Fastest and simplest slides to prepare
○ Specimen (usually suspended in liquid) is placed on the slide as a single
drop, sealed with a coverslip, and is ready for examination
- Fixation
○ Adhesion of the specimen to the slide
○ Killing microorganisms to stop their movement (while keeping the structures
intact)
○ Heat Fixation
▪ Thins smears of the specimen are briefly run through a heat source
○ Chemical Fixatives
▪ Ethanol
▪ Formaldehyde
▪ Acetic acid
▪ Denature and stabilize the cell structures
▪ Commonly done in tissue samples
- Staining
○ Method of coloring certain cell structures by applying stains or dyes which
are made of positive/negative ions
○ Dyes are composed of:
▪ Chromophore --> contains the color
▪ Counter Ion --> does not contain the color
▪ Basic Dye --> positive ion is the chromophore
▪ Acidic Dye --> negative ion
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 ▪ Acidic Dye --> negative ion
○ Dyes are selected based on how they react with the specimen
○ Positive Stain --> dye directly interacts w/ the specimen
○ Negative Stain --> reacts with the environment or background
Staining Techniques
- Can be classified into different techniques based on the number of dyes used,
structures it highlights, and what microscope is going to be used
- Simple Stain
○ Colors all structures the same
○ Used to emphasize certain structures
○ Basic Stains
▪ Stains negatively charged molecules (nucleic acids, proteins)
▪ Methylene Blue, Crystal Violet, Malachite Green, Basic Fuchsin, Safranin
▪ Outcome: Positive Stain (color depends on the dye)
○ Acidic Stains
▪ Stains positively charged molecules
▪ Eosin, Acid Fuchsin, Rose Bengal
▪ Outcome: Positive or Negative (depends on cell chemistry if it repels the
stain)
○ Negative Stain
▪ Stains the background, not the specimen
▪ Indian Ink, Nigrosine
▪ Outcome: Dark Background w/ Light Specimen
- Differential Stain
○ Distinguishes organisms or structures based on their interaction of different
dyes
○ Using multiple stains to better differentiate
○ Gram Staining
▪ Distinguishes cells by cell wall composition (gram positive or gram
negative)
▪ Crystal Violet, Gram's Iodine, Ethanol, Safranin
▪ Outcome: Gram (+) becomes violet, Gram (-) becomes pink
▪ Process
1) Primary Dye
2) Decolorizer
3) Counter Stain (must be different from primary dye)
 If accepts primary dye: Gram (+)
 If accepts counterstain after step 2: Gram (-)
▪ Examples
□ Gram - Positive
 Staphylococcus sp. <-- skin
 Streptococcus sp. <-- throat

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  Streptococcus sp. <-- throat
□ Gram - Negative
 Escherichia sp. <-- E. Coli, from dirty stuff
 Salmonella sp. <-- raw chickens & eggs
○ Acid-Fast Staining
▪ Distinguishes acid-fast cells from non-acid-fast cells
▪ Basic Fuchsin, Acid Alcohol, Methylene Blue
▪ Acid-fast are red
□ Resists colorizing by acid after accepting stain
▪ Non-Acid-Fast are blue
□ Readily colorized by acid after staining
▪ Process
1) Application of Primary Stain
2) Application of Mordant (heat)
3) Application of Decolorizer
4) Application of Counter Stain
○ Endospore Staining
▪ Distinguish and study the presence of endospores
▪ Malachite Green (Schaeffer-Fulton Procedure), Safranin
▪ Outcome: Endospores are bluish-green, other structures are pink
○ Flagella Staining
▪ View flagella that are present in bacteria
▪ Tannic Acid/Potassium Alum (Mordant), Basic Fuchsin/Pararosaline
▪ Outcome: Visible Flagella
○ Capsule Staining
▪ Identify cells w/ capsules
▪ Indian Ink/Nigrosine (Negative Stain), Methylene Blue (Counter Stain)
▪ Outcome: Capsules are clear or seen as halos

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Scientific Method
Wednesday, 1 November 2023 7:59 pm

Scientific Method
- Process of thinking used by scientists to collect information and
provide scientific explanations

Methods of Reasoning
- Inductive Reasoning/Bottom-Up Approach
○ Based on specific observations which lead to general
conclusions
○ Generalized conclusion based on featured evidences
○ "Organisms A, B, and C all possess same characteristics as X.
Therefore, organisms having the same characteristics as A, B, and
C probably also possess the same X characteristics."
- Deductive Reasoning/Top-Down Approach
○ Based on general principles to explain scientific observations
○ Logical thinking based on testing observed phenomena
○ "Every organism A has the characteristics of X. The organism
under observation is an organism A. Therefore the organism has
the characteristics X."

Experimental Designs
- Controlled observation to test a hypothesis
- Consists of the following
○ Sample Size
○ Variables

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 ○
○ Controls
○ Statistical Analysis
- True Experimental Research Design
○ Complete control over all extraneous variables
○ Predict the effect of the manipulated independent variable
○ Examples: Pretest and post-test only design, Solomon four-group
design, factorial design
- Quasi-Experimental Research Design
○ Independent variable is manipulated to see its effect on the
dependent variable
○ Does not contain either randomization or a control group
○ Examples: Non-randomized control group design, Time Series
Design
- Pre-Experimental Research Design
○ Little to no control over extraneous variables
○ Examples: One-shot case design, one-group pretest design

Origins of the Study of Life

- Theory of Abiogenesis (Spontaneous Theory)
○ Life originates from non-living matter
○ Originated from Aristotle and was believed until the 17th
Century
- Theory of Biogenesis
○ Life originates from pre-existing life
○ Proven by experiments conducted by Red, Spallanzani and Louis
Pasteur

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The Cell
Monday, 2 October 2023 8:32 pm

Nasa end super summarized super ikli super short version

Cell Theory
- Postulated by Schleiden, Schwann, and Virchow
- Composed for three tenets
○ Cells are the smallest & most basic unit of structure and
functions of organism
○ All organisms are composed of cells
○ Cells arise from pre-existing cells

Cells - Identification and Classification

- First record of seeing a cell and identifying it belongs to Robert Hooke
- Cells can differ in number, size, components, and composition
- Based on structural differences, cells can be classified as
○ Prokaryotic Cells
○ Eukaryotic Cells
Cells Share Common Structural Features
- Cell/Plasma Membrane
○ Outer boundary of the cell which separates its contents form the
environment
- Cytoplasm
○ Gel-like substance that constitutes the cells internal environment
○ Holds all the structural components of the cell
- Genetic Material
○ DNA that holds information for cell activities and functions
- Ribosomes
○ Structures that manufacture proteins which are needed for cell
function

Classification of Organisms Based on Cell Structure

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- Pro = before
- Eu = true
- Karyon = kernel
- Main difference is the presence of an enclosed structure to
separate the genetic materials of the cell
○ Prokaryotic has a Nucleoid
○ Eukaryotic has Nucleus

Cell Types
- Membrane-bound organelles
○ Eukaryotic cells
○ Plant & Animal Cells
- Cells that do not have membrane-bound organelles
○ Prokaryotic cells
○ Unicellular organism
○ Bacteria

Prokaryotic Cell
- Earliest and most primitive cells
- Contains only simple structures with very little differentiation
- Size varies from 0.1 - 5 µm (w/ few exceptions)
- Consists of organisms from the Domain Archaea and Bacteria
- Prokaryotes
○ NO nucleus
○ NO membrane-bound organelles
○ ALL are unicellular
○ Smaller than eukaryotic cells
○ Forerunner to eukaryotic cells (smaller & simpler)
○ DNA - Single Strand & Circular
- Structure
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- Structure
○ Capsule --> slimy outer coating
○ Cell Wall --> tougher middle layer
○ Cell Membrane --> delicate inner skin
○ Pili --> used for communication to other cells
○ Cytoplasm --> inner liquid filling
○ DNA --> one big loop
○ Flagella --> for swimming
○ Ribosome --> for building structures
Components of a Prokaryotic Cell

For Structure
○ Capsule
▪ Outermost layer that encases the entire cell for additional
protection
▪ Usually composed of polysaccharides
□ Form of carbohydrate
□ Monosaccharide; sugar, one
□ Disaccharide; sugar, two
□ Polysaccharide; sugar, many
○ Cell Wall
▪ Rigid case that encloses the entire cell
▪ Gives shape
▪ Bacteria: Peptidoglycan
▪ Archaea: NO Peptidoglycan
○ Plasma Membrane
▪ Semi-permeable membrane that encloses the internal
structures of the cells
▪ Regulates the passage of the molecules in & out of the cell
▪ Bacteria: Fatty Acid
▪ Archaea: Non-Fatty Acid Lipids

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 ▪ Archaea: Non-Fatty Acid Lipids
○ Mesosome
▪ Folded part of the plasma membrane that enters the area
of the cytoplasm
▪ Where the electron transport system for the creation of
energy is located
○ Cytoplasm & Cytosol
▪ Gel-like substance that fills the interior of the cell
▪ Cytosol --> liquid substance
For Activities and Function
- Ribosome
○ Scattered throughout the cytoplasm
○ For protein synthesis
- Pili
○ Functions for attachment
○ Cell-to-cell communication
○ Passing of genetic material
- Flagellum
○ For movement
○ Tail-like appendage anchored to the cell membrane and wall
- Fimbriae
○ Bristle - like fibers used for attachment
○ Primary functions for attachment
○ Thinner than Pili
For Genetic Material
- Nucleoid
○ Region of the cell where DNA is present
○ Do not have an enclosed structure for its genetic material
○ Ribosomes and enzymes are seen near this region
- Plasmid
○ Small independent loops of DNA which are separate from the
chromosomal DNA

Eukaryotic Cells
- Highly evolved, complex structures, and larger size compared to
prokaryotes
- Size varies from 10 - 100 µm (w/ few exceptions)
- Exhibits heavy Compartmentalization of internal structures known
as Organelles
○ Organelles are mini-organs for the cell that has its own
functions and purposes
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 functions and purposes
- Divided into:
○ Protista
○ Fungi
○ Plantae
○ Animalia
- Derivations vary per classification, but all have the general components
of a typical eukaryotic cell
- Cell structures can be categorized for:
○ Structures for Protection
○ Genetic Control Organelles
○ Manufacturing, Storing, Distributing and Breakdown Organelles
○ Energy Processing Organelles
○ Organelles for Structural Support, Movement and communication
between cells
Structures for Protection
Cell Membrane
○ Functions as a barrier to separate the environment and
internal structures of the cell
○ Regulates the passage of molecules to and from the cell
○ Composed of two sheets of phospholipids, hence the name
Phospholipid bilayer
▪ Phospholipids
□ Organic molecules that exhibit both polar (hydrophilic) and
non-polar (hydrophobic) ends
 Hydrophilic --> Loving of water
 Hydrophobic --> Resists water
▪ Cause of its bipolar nature is due to its 3 key structures
□ Charged Phosphate Group
□ 3 Carbon Glycerol Molecule
□ Two Fatty Acid Tails
▪ Charge Phosphate Group and the Glycerol Molecule
□ form the phospholipids polar head
▪ 2 Fatty Acids
□ makeup the non-polar hydrophobic tail
▪ Hydrophobic tails move away from the environment and
cluster together forming the middle portion of the lipid bilayer
▪ Hydrophilic heads are faced toward the environment
▪ Because the middle portion of the membrane is non-polar, this
causes it have selective permeability
□ Non-polar molecules such as glucose can't pass freely
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 □ Non-polar molecules such as glucose can't pass freely
through the cell
Fluid Mosaic Model

▪ Fluid because of the hydrophilic heads

▪ Mosaic because it's like a form of art; it's composed of
different structures
Membrane Proteins
- Cell membrane is composed of proteins and other molecules which
are randomly scattered
- Presence of membrane proteins and other molecules is why the cell
membrane is termed as Fluid Mosaic
Structures Embedded in the Cell Membrane
- Transport Proteins
○ Creates passageways for ions and non-polar molecules to pass
freely through the cell membrane
○ Channel Proteins
▪ Forms tunnels for the import and export of materials and
wastes
○ Receptor Proteins
▪ Works by recognizing and binding to specific ligands
(signaling molecules)
▪ Initiates a series of biochemical events that ultimately lead
to a cellular response
- Cell Recognition Proteins
○ Distinguishes cells by recognizing and binding to specific
molecules/structures present on the surfaces of other cells
- Junction Proteins
○ Assists in cell-to-cell adhesion and communication between cells
- Enzymatic Proteins
○ Participates in metabolic reactions such as degradation and
synthesis to sustain life in the cell
○ Degradation = "break down"
○ Synthesis = "creation"
○ Speeds up a chemical reaction
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 ○ Speeds up a chemical reaction
○ Catalysts doesn't get all used up
- Carbohydrate Chains
○ Serves as identification tags for cell recognition proteins
- Cholesterol
○ Makes the cell membrane flexible and less fluid
○ Strengthens the membrane
○ Makes it less permeable to water soluble substances
Cell Wall
- Additional boundary between the cell membrane and the environment
for added structural support and protection
- Only found in plant cell (also present in prokaryotic bacteria)
- Composition Varies
○ Plants & Algae: Polysaccharide Cellulose
▪ Cellulose is rigid and does not allow free passage of
molecules, plants and algae have openings which allow water
an molecules to diffuse
○ Fungi: Chitin
Cytoplasm
- Jellylike substance contained within the cell membrane
- Generally composed of the cell organelles (not including the nucleus)
and cytosol
- Cytosol is the liquid component of the cytoplasm and is largely
composed of water
- Organelles are compartmentalized structures which offer
efficiency and provides the cell the ability to do different complex
metabolic reactions in localized areas
○ Membranous Organelles (Single membrane)
▪ Golgi body
▪ Lysosomes
▪ Smooth and Rough Endoplasmic Reticulum
▪ Vesicle
▪ Vacuole
○ Membranous Organelles (Double Membrane)
▪ Nucleus
▪ Mitochondria
▪ Plastids
○ Non-Membranous Organelles
▪ Ribosome
▪ Centriole

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 Genetic Control Organelles
- Nucleus
○ Storehouse of genetic information (DNA)
○ Functions to prevent damage to the DNA and direct all cell activity
○ Numerous proteins are needed for genetic function, so nucleus has
specialized structures to facilitate their entry:
▪ Nuclear Envelope
□ 2 membrane structures that encloses the nucleus and
separates it from the cytoplasm
▪ Perinuclear Space
□ Space between 2 membranes of the nuclear envelope
▪ Nucleoplasm
□ Semifluid substance inside the nucleus
▪ Nuclear Pores
□ Perforations in the nuclear envelope
□ Regulates the passage of materials (usually proteins,
ribosomes, and RNA)
▪ Nucleolus
□ Condensed region of the nucleus where synthesis of
ribosomal RNA (rRNA) and ribosomal subunits are
centralized
□ rRNA is combined with imported proteins to form the large
and small ribosomal subunits
□ These subunits exit through the nuclear pores and
combine once within the cytoplasm
- Deoxyribonucleic Acid (DNA)
○ Long-chain molecule of inheritance made of segmented portions
called genes
○ Contains the information needed for cell activities (such as
protein synthesis)
○ Compacted by proteins called histones
▪ forms a condense structure called chromatin and
condenses further into chromosomes when cell division is
occurring
○ 2 Types of Chromatin in the Nucleus
▪ Euchromatin
□ Contains active DNA
□ Stains slightly when view under microscope
▪ Heterochromatin
□ Contains inactive DNA

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 □ Contains inactive DNA
□ Stains deeply when view under microscope
Manufacturing, Storing, Distributing, and Breakdown
Organelles
- Endoplasmic Reticulum (ER)

○ Extensive folded membrane

○ occupies a large space in the cytoplasm
○ Folded like a maze where the membranous tubules and flattened
sacs are called cisternae, while the spaces between them are the
cisternal space
▪ Cisterna is continuous with the nuclear envelope, and so the
perinuclear space is also continuous with the cisternal space
▪ This connection allows the synthesized ribosomes from the
nucleolus to be transported directly to the ER
2 Regions of the Endoplasmic Reticulum
▪ Rough Endoplasmic Reticulum (RER)
□ Closest to the nucleus
□ Cisternae are flattened sacs
□ Studded with ribosomes
□ Gives it a rough appearance when viewed
□ Proteins are formed and temporarily stored in the
cisternal space
□ Short carbohydrate attaches to the formed protein
(converting it into a glycoprotein, a secretory protein)
thereby making it ready for cell use
□ Secretory proteins are moved to the specialized
Transitional ER, where transport vesicles take them to the
Golgi body for further packaging
□ Secretory proteins made from the RER are typically used
by specialized cells
 Pituitary Glands
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  Pituitary Glands
 Hormones
□ Can also be secreted outside the cell
 Mammary Glands
 Milk Proteins
▪ Smooth Endoplasmic Reticulum (SER)
□ Region adjacent to the RER
□ NO Ribosomes
□ Cisternae are membranous tubules
□ Involves metabolic processes:
 Synthesis and Transport of Lipids
 Metabolism of Carbohydrates
 Detoxifications of Drugs and Poisons
□ Specialized form of SER in muscle cells is the
sarcoplasmic reticulum
 Calcium ions are stored and released
 When a nerve signal stimulates the muscles the
release of ions triggers a contraction
- Protein Synthesis Process
1. Ribosome (proteins)
2. Rough Endoplasmic Reticulum (RER)
3. Golgi Bodies
- Ribosomes
○ Sites of protein synthesis
○ Spherical granules composed of 2 subunits; Large and Small
Subunit, synthesized in the nucleolus
▪ Subunits exit the cytoplasm and combine to form ribosomes
○ Each ribosome consists of ~70 proteins and several ribosomal
RNA (rRNA)
○ Either bound ribosomes attached to the RER and nuclear
membrane, or free ribosomes suspended in the cytosol
▪ Structurally identical and can alternate roles depending on the
needs of the cell
○ Proteins synthesized by free ribosomes functions as enzymes or
structural proteins
○ Proteins synthesized by bound ribosomes function as secretory
proteins or hormones
- Golgi Apparatus/Body
○ Stacks of cisternae which acts as a processing system that sorts,
modifies, and packages products from the ER
○ Proteins finish their folding here to become functional

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 ○ Proteins finish their folding here to become functional
○ Enzymes in the Golgi Body manufacture and attach
carbohydrates that serve as name tags for the cell
○ Has specialized regions that interact with the ER, the rest of the cell,
and with each other through vesicles budding off from the Golgi
cisternae
Golgi Body Regions

▪ Cis-face
□ At the Top
□ Receiving end of the Golgi
□ Transport vesicles from the ER are fused with the cisterna
of the Golgi
□ Responsible for returning incorrectly sent proteins back to
the ER
▪ Dictyosome/Medial-face
□ At the Middle
□ Bulk or main stacks of cisternae
□ Responsible for processing proteins and lipids and
directing them to their destinations
□ Packs and prepares proteins
▪ Trans-face
□ Shipping end of the Golgi
□ Sorts and directs the modified proteins to their destination
by budding off secretory vesicles
- Lysosomes
○ Acts like a digestive system for a cell
○ Free floating organelles
○ Contains enzymes that dismantle and recycle food particles,
captured bacteria, worn-out organelles, and debris
○ Enzymes, known as lysozyme, originates from the RER
▪ Recognized, refined and packaged by the Golgi body where it
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 ▪ Recognized, refined and packaged by the Golgi body where it
fuses with transport vesicles carrying cell debris
○ Main function is intracellular digestion by means of autophagy
- Peroxisome
○ Structurally identical to lysosomes however, the enzymes present
are from the Golgi body
○ Have much higher concentrations than lysosomes
○ Mainly function to dispose of toxic substances and lipids
Energy Processing Organelles
- Mitochondria

○ Double membranous structures that supply energy to the cell by

means of cellular respiration
○ Consists of their own ribosomes and DNA
▪ Basis of the endosymbiotic theory
○ Space between the double membranes is called the
intermembrane space
○ 2 membranes of the mitochondria allow it to perform functions for
cellular respiration
▪ Outer Membrane
□ Smooth continuous boundary
□ Encapsulates all the contents of the mitochondria
▪ Inner Membrane
□ Intricately folded structures called cristae
□ Enzymes responsible for cellular respiration are located
□ Number of cristae is proportional to the energy
requirements of the cell in between these folds is the
mitochondrial matrix
□ Contains DNA and ribosomes for genetic function
▪ Sites of energy production where adenosine triphosphate
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 ▪ Sites of energy production where adenosine triphosphate
(ATP), the cell's source of chemical energy, is synthesized
▪ Process of converting energy-rich molecules (e.g pyruvate)
is known as the Kreb's Cycle which makes use of pyruvate
oxidations and produces carbon dioxide as a waste product
▪ Considered as semi-autonomous organelles because they
can grow and divide on their own
- Plastids
○ Group of large organelles only found in plant cells
○ Chloroplasts
▪ Green colored plastids due to the green pigments: chlorophyll A
and B
▪ Sites of energy production in plants
▪ Where photosynthesis occurs
□ Makes use of solar energy and transforms it into energy-
rich molecules
▪ Parallel to the mitochondrion due to their double membrane
features and the presence of their own DNA
▪ Other Specialized Structures
□ Outer Membrane
□ Inner Membrane
□ Thylakoid
 Third membrane system folded into flattened sacs
 Photosynthetic pigments such as chlorophyll A and B
are found here
 light-dependent reactions occur here
 Thylakoid Membrane separates the stroma and the
grana
□ Granum
 Stacks of thylakoids the increase the surface area for
the attachment of chlorophyll
 Each chloroplast has around 50 grana
 Each granum is made of around 50 thylakoids
 Each granum is connected to the other by an
intergranal lamellae
□ Stroma
 Enzyme-rich gel-like matrix
 Found inside the chloroplast
 Contains DNA, Ribosomes, Photosynthetic Enzymes,
Lipid Droplets and Starch
 Where light-dependent reactions occur via the

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  Where light-dependent reactions occur via the
enzymes present
○ Chromoplasts
▪ Colored plastids rich in pigments such as carotenoids
▪ Gives fruits, flowers, and leaves their orange, yellow, and red
colors
▪ Can arise from chloroplasts that have lost their chlorophyll
(i.e. ripening of fruits)
○ Leucoplasts
▪ Non-colored plastids
▪ Do not contain pigments
▪ Function mainly as storage for nutrients
▪ Amyloplasts --> Starch filled leucoplasts
▪ Elaioplasts --> stores oil
▪ Aleuroplasts --> stores proteins
Organelles for Structural Support, Movement, and
Communication Between Cells
- Cytoskeleton
○ Flexible network of protein threads and fibers
○ Provides mechanical and structural framework of support
○ Helps in directing cell movement, transport, and responses
○ 3 Major Protein Components
▪ Microtubule
□ Thickest and longest filament
□ Composed of tubulin assembled into hollow tubes that can
rapidly add or remove tubulin molecules
□ Functions as a trackway where specialized proteins use
it as a path to carry cargo such as vesicles
▪ Intermediate Filament
□ Smaller than microtubules
□ Appears ropelike
□ Provides the cell tensile strength
□ Allows it to stretch without breaking
□ Composed of multiple protein subunits
▪ Microfilament
□ Thinnest filament composed of actin
□ Present in nearly all cell types of eukaryotes
□ Can provide strength to resist stretching,
compression, and assists in anchorage
□ Actin filaments are especially notable in muscle cells

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 □ Actin filaments are especially notable in muscle cells
□ Works together with myosin to produce muscle contractions
- Centrosomes and Centrioles
○ Small dense region in the cytoplasm
○ Microtubules are assembled and arranged
○ Termed the Microtubule Organizing Center (MTOC)
○ Inside the centrosome are two hollow cylinders made of filaments
(microtubule triplets) called centriole
○ Centriole is composed of 9 filaments arranged in a circular pattern
○ Centrosome division is crucial in preceding and stimulating cell
division
▪ Division of Centriole
□ Each centriole will divide into two, and each two pairs will
move into opposite poles of the cell
▪ Formation of Asters and Spindle Fibers
□ From the pair of centrioles, asters will form
□ Source of a system of microtubules called spindle fibers
where chromosomes can attached and be pulled toward
respective poles
□ Plant cell do not form asters when dividing
□ Centrioles can also divide to form basal bodies where cilia
and flagella are formed
□ Cilia
 Both cilia and flagella have a 9+2 pattern regarding
the microtubules that compose them
 Short, numerous extensions that move in a
coordinated to propel the cell
□ Flagella
 Longer extensions which occur singly or in pairs
 Movement is done by propeller motion
- Cell Surface and Junctions
○ Cells are joined to each other by structures called junctions
○ In plants, the plasma membrane and cytoplasmic fluid extend
specialized structures between cell called plasmodesmata to
communicate and pass molecules effectively
○ Animal cells have different types of junctions depending on
their location and function
▪ Tight Junctions
□ Fuses cells together to form an impassable barrier using
actin fibers
□ Attaching to membrane-anchored proteins, forming cell
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 □ Attaching to membrane-anchored proteins, forming cell
sheets
□ Important in controlling biochemical movements
▪ Adhesion Junctions
□ Connects 2 neighboring cells together or a cell to the
extracellular matrix
□ Acts like screws using cytoskeletal fibers to form strong
sheets with spaces between them
▪ Gap Junctions
□ Similar to plasmodesmata
□ A channel protein links with the cytoplasm of an adjacent
cell to allow exchange of ions and nutrients

Soaper Duper Summarized Version

Cell Theory
- Composed of 3 tenets
○ Cells are the smallest & most basic unit of structure and functions
of an organism
○ All organism are composed of cells
○ Cells arise from pre-existing cells

Common Structural Features of Cells

- Cell/Plasma Membrane --> outer boundary
- Cytoplasm --> gel-like substance
- Genetic Material --> information for cell activities
- Ribosomes --> Manufactures proteins

Prokaryotic Cell
- Earliest and most primitive
- Simple structures
- 0.1 -5 μm
- NO nucleus
- NO membrane-bound organelles
- DNA --> single strand & circular
- For structure
○ Capsule --> encases the entire cell
○ Cell Wall --> rigid case that encloses the entire cell
○ Plasma Membrane --> encloses the internal structure; semi-
permeable
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 permeable
○ Mesosome --> folded part of the plasma membrane
○ Cytoplasm & Cytosol --> gel-like substance
- For Activities and Function
○ Ribosome --> for protein synthesis
○ Pili --> for attachment to other cells; passing of genetic material
○ Flagellum --> for movement; tail-like appendage
○ Fimbriae --> used for attachment; thinner than pili
- For Genetic Material
○ Nucleoid --> where DNA is present
○ Plasmid --> small independent loops of DNA
Eukaryotic Cells
- Highly evolved, complex structures, and larger size
- 10 -100 μm
- ORGANELLES (mini-organs) --> Heavy compartmentalization of internal
structures
- Structures for Protection
○ Cell Membrane --> barrier to separate the environment and
internal structures; regulates the passage of molecules
○ Cell Wall --> additional boundary; only found in plant cells
○ Cytoplasm --> jellylike substance;
▪ Cytosol --> liquid component of the cytoplasm
- Genetic Control Organelles
○ Nucleus --> storehouse of genetic information (DNA)
○ Deoxyribonucleic Acid (DNA) --> information needed for cell
activities
- Manufacturing, Storing, Distributing, and Breakdown
Organelles
○ Endoplasmic Reticulum (ER) --> extensive folded membrane
▪ Rough Endoplasmic Reticulum (RER) --> stores protein made
by attached ribosomes
▪ Smooth Endoplasmic Reticulum (SER) --> builds lipids &
carbohydrates; detoxification of drugs & poison
○ Protein Synthesis Process
1. Ribosomes (proteins)
2. Rough Endoplasmic Reticulum (RER)
3. Golgi Bodies
○ Ribosomes --> sites of protein synthesis; builds proteins from
amino acids
○ Golgi Apparatus/Body --> processing system that sorts, modifies,
and packages products from the ER
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 and packages products from the ER
▪ Cis-Face --> receiving end
▪ Dictyosome/Medial-Face --> packs and prepares proteins
▪ Trans-Face --> shipping end
○ Lysosomes --> digestive system of the cell
○ Peroxisome --> disposes of toxic substance and lipids
- Energy Processing Organelles
○ Mitochondria --> powerhouse of the cell
○ Plastids --> only found in plant cells; group of large organelles
▪ Chloroplasts --> green colored; sites of energy
▪ Chromoplasts --> colored plastids
▪ Leucoplasts --> non-colored; storage for nutrients
- Structural Support, Movement and Communication Between
Cells
○ Cytoskeleton --> mechanical and structural framework of support
○ Centrosomes and Centrioles --> microtubules are assembled and
arranged
○ Cell Surface and Junctions --> cells are joint to each other by
structures called junctions
○ Plasmodesmata --> transport, communication & signaling between
cells; cytoplasmic "bridges"
○ Vacuole --> food storage in plants

Structures Embedded in the Cell Membrane

- Transport Proteins --> passage way for ions and non-polar
molecules
- Channel Proteins --> forms tunnels for import and export
- Receptor Proteins --> recognizing and binding to specific
Ligands (signaling molecules); initiates a series of biochemical
events
- Cell Recognition Proteins --> recognizing and binding to specific
molecules/structures
- Junction Proteins --> cell-to-cell adhesion and communication
- Enzymatic Proteins --> metabolic reactions such as degradation
and synthesis
- Carbohydrate Chains --> identification tags
- Cholesterol --> strengthens the membrane

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Plasma Membrane and Transport Mechanisms
Thursday, 2 November 2023 6:00 pm

Plasma Membrane
- Boundary between the cell's internal and external environments
- Regulates all substances that enter and exits the cell
- Has SELECTIVE PERMEABILITY, which makes it a semi-permeable membrane

Structure and Organization

- Composed of amphipathic molecule known as a Phospholipid

○ Amphipathic are those that has unique characteristics:

▪ Hydrophilic (water-loving)
▪ Hydrophobic (water-fearing)
- Allows the plasma membrane to adopt a bilayer structure:
○ Hydrophilic surface is facing both the aqueous external environment and
cytosol
○ Hydrophobic tails forms an internal layer
Structures of the Membrane
- Represented using a model known as FLUID MOSAIC MODEL

○ Mosaic --> derived from the diverse proteins and other macromolecules
embedded within the membrane
○ Fluid --> embedded macromolecules are able to move along and across the
membrane regularly and also because of the hydrophilic heads
- Transmembrane Proteins
○ Regulate the movement of molecules across the membrane

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 ○ Regulate the movement of molecules across the membrane
○ Forms the transport mechanisms of the cell
○ Composed of:
▪ Carriers Proteins
▪ Channels Proteins
▪ Receptor Proteins
- Interior Protein Network
○ Determines and maintains the structure and form of the plasma membrane
○ Responsible for the shape of the cell
○ Attachment of macromolecules in the membrane
○ Spectrins and Clathrins
- Cell-Surface Markers
○ Recognition of foreign and local cells and tissues
○ Markers are crucial for histocompatibility of the immune system
○ Glycoproteins and Glycolipids
Proteins and Protein Complexes
- Transporters (Channels/Carriers)

○ Responsible for the movement of molecules/solutes across the membrane

○ May come in the form of:
▪ Open channels that is selective to a particular molecule
▪ Carrier that shuttles the molecule across by changing its shape
- Enzymes

○ Specialized proteins that are needed by metabolic functions for chemical

reactions
○ Have active sites exposed to the environment to react w/ substances which triggers

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 ○ Have active sites exposed to the environment to react w/ substances which triggers
a chemical reaction in the cell
- Cell-Surface Receptors

○ Detects chemical messages from the environment to trigger reactions

○ Messages come as molecules and attach to the binding site shaped specifically for
the signal
- Cell-Surface Identity Markers

○ Combinations of surface proteins and proteins complexes

○ Specify the type and origin of the cell
○ Markers bind to each other for recognition purposes
- Cell-to-Cell Adhesion Proteins

○ Bonds and junctions between cells

○ May be permanent or temporary
- Attachment to the Cytoskeleton
○ Responsible for anchoring other surface proteins to the cytoskeleton and
extracellular matrix
○ To maintain shape, stability, and coordinate chemical/mechanical changes
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 ○ To maintain shape, stability, and coordinate chemical/mechanical changes

Transport Mechanisms
Passive Transport
- NO energy will be spend to move the solutes across

Simple Diffusion

○ movement of ions and molecules from high concentrations to low

concentrations
○ Diffusion = spread
○ Applies to lipid soluble molecules and ions that can pass freely through the
membrane
○ Applies to small, non-polar molecules such as oxygen and hormones
○ Gases, hydrophobic molecules, and small polar molecules can pass

Facilitated Diffusion

○ Proteins manage and assist the movement of solutes across the membrane
○ Makes use of channel proteins or carrier proteins
○ Channel Proteins
▪ Provides a small hydrophilic passageway for specific molecules and ions
▪ Leak Channels --> remains open
▪ Gated Channels --> can be opened or closed depending on the presence of
a stimulus
○ Carrier Proteins
▪ Requires the molecule being transported to attach itself to the carrier protein
○ Requires 3 conditions to be met
▪ There should be a concentration gradient on either side of the membrane

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 ▪ There should be a concentration gradient on either side of the membrane
▪ The channel must be open or a carrier must be available
▪ There must be a stimulus (chemical/electric) to open a channel
- Osmosis
○ Movement of water from high concentrations of solutes to low concentration
across membranes
○ Diffusion of water molecules across a selective permeable membrane
Tonicity & Types of Solution
▪ Hypotonicity/Hypotonic Solution

□ High = "hyper"
□ Concentration gradient formed by the solutes side the cell would cause
water from the environment to rush inside
□ Swollen cell
▪ Hypertonicity/Hypertonic Solution

□ Water inside the cell would rush out

□ Causes the cell to shrivel and "dry"
▪ Isotonic Solution
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 ▪ Isotonic Solution

□ Concentration of solute outside the cell is equal to the concentration of

inside
□ Equal :D
- Aquaporins
○ Water is facilitated by specialized protein channels
○ ONLY allows water molecules to move across the membrane in large quantities

Active Transport
- Relies on the expense of cell energy, ATP
- Adenosine Triphosphate (ATP)
- Needed to move molecules against their concentration gradient to maintain internal
conditions
Active Transport According to Energy
- Primary Active Transport
○ Intentional and uphill mode of transport
○ Transport protein directly uses energy from ATP phosphorylation
- Secondary Active Transport
○ Seen as the aftermath of primary active transport
○ Molecule is transported due to the difference in energy from the
phosphorylation of energy
Active Transport According to Direction
- Coupled/Co-transport
○ One protein shuttles two different molecules across the membrane in the
same direction
○ Both molecules must have an affinity for the transport protein, which is now
referred to as a symporter
- Counter-Transport
○ One transporter moves two different molecules across the membrane in
different directions
○ Often a combination of primary and secondary active transport
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 ○ Often a combination of primary and secondary active transport
○ Movement may be simultaneous or in sequence
○ Both molecules must have an affinity for the transport protein, which is now
referred to as a antiporter
○ A protein may transport a single molecule against its concentration gradient,
it's referred to as a uniporter regardless of the direction
Bulk/Vesicular Transport
- Endocytosis
○ Endo means "into"
○ Cells engulf large particles by extending their cytoplasm around the particles
○ Ingested particle is trapped within a pouch or vacuole inside the cytoplasm
○ Enzymes from the lysosomes are used to digest the molecules absorbed
○ Phagocytosis --> large/solid particle; "cell eating"
○ Pinocytosis --> small/liquid particle; "cell drinking"
- Exocytosis
○ Exo means "exits"
○ Exit digested stuff

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Energy Transformation
Sunday, 5 November 2023 3:17 pm

Chemical Energy and ATP

- All cells use chemical energy carried by ATP
- Adenosine Triphosphate (ATP)
○ Molecule that transfers energy from the breakdown of food
molecules to cell processes
○ A wallet that carries money
○ Carries chemical energy that all cells can use
○ Used for functions such as building molecules and moving
materials by active transport
Process of Releasing Energy

1. Energy carried is released when a phosphate group is removed

from the molecule
2. When the phosphate is removed, energy is released and ATP
becomes Adenosine Diphosphate (ADP)
○ Adenosine Diphosphate
▪ Lower-energy molecule that can be converted into ATP by
addition of a phosphate group
▪ ADP is a nearly empty wallet
Amount of Energy from Macromolecules
Molecule Energy
Carbohydrates 4 calories per mg
Lipids 9 calories per mg
Proteins 4 calories per mg
- Breakdown of the simple sugar glucose yields about 36 molecules of
ATP

Chemosynthesis
- Process by which some organisms use chemical energy instead of
light energy to make energy-storing carbon-based molecules
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 light energy to make energy-storing carbon-based molecules
- Sample of Chemosynthesis

- Some Inorganic Oxidation Reactions

Photosynthesis
- Comes from the Greek words:
○ "Photo" = "light"
○ "synthesis" = "putting together"
○ Using light to put something together, specifically carbohydrates
- Chloroplasts: The Sites of Photosynthesis in Plants
○ Found mainly in the cells of the mesophyll, the tissue in the
interior of the leaf
○ Carbon dioxide (CO2) enters the leaf, and exits by way of
microscopic pores called stomata
○ Water (H2O) absorbed by the roots is delivered to the leaves in
veins
○ Leaves also use veins to export sugar to roots and other non-
photosynthetic parts of the plant
- Photosynthetic Pigments: The Light Receptors
○ Pigments are substances that absorb visible light
○ Types of Pigments in Chloroplasts
▪ Chlorophyll A (blue green)
□ Participates directly in the light reactions
□ Suggests that violet-blue and red light work best for
photosynthesis; green is the least effective color
▪ Accessory Pigment Chlorophyll B (olive green)
▪ Carotenoids
□ Group of accessory pigments
□ Hydrocarbons that are various shades of yellow and
orange because they absorb violet and blue-green light
□ Important function is photoreception
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 □ Important function is photoreception
□ Absorb and dissipate excessive light energy that would
otherwise damage chlorophyll or interact with oxygen,
forming reactive oxidative molecules that are dangerous
to the cell
○ Why Leaves are Green?

▪ Chlorophyll molecules of chloroplasts absorb violet-blue and

red light
▪ Reflects or transmits green light
Two Stages of Photosynthesis
- Light Dependent Reaction (photo part of photosynthesis)
○ Converts light energy into chemical energy
○ Collects energy from the sun and break down water molecules to
produce ATP and NADPH
○ Nicotinamide adenine dinucleotide phosphate (NADPH)
- Calvin Cycle (synthesis part)
○ Uses ATP and NADPH from the light-dependent reactions to
produce high-energy sugars
○ Named after the American scientist Melvin Calvin
○ Light-independent reactions

Cellular Respiration
- Glycolysis is needed for cellular respiration
○ Takes place in the cytoplasm before cellular respiration and it
does not require oxygen
○ Makes a small number of ATP molecules
○ If oxygen is available, the product is used to produce many more
ATP molecules through cellular respiration
○ Process in which glucose is broken down to produce energy
○ Products of Glycolysis
▪ 2 ATP
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 ▪ 2 ATP
▪ 2 NADH
▪ 2 pyruvate
○ ATP = energy for cell
○ NADH & Pyruvate = needed for cellular respiration when oxygen is
present
- The Krebs Cycle is the 1st main part of cellular respiration
1. Pyruvate from glycolysis is broken down
2. Coenzyme A bonds to the two-carbon molecule. This
intermediate molecule enters the Krebs cycle
3. Citric acid is formed
4. Citric acid is broken down and NADH is made
5. The five-carbon molecule is broken down, NADH and ATP are
made
6. The four-carbon molecule is rearranged. NADH and FADH2 are
formed
○ For each pyruvate, the Products of Krebs cycle are
▪ 3CO2 (waste product)
▪ 1 ATP
▪ 4 NADH (to the electron transport chain)
▪ 1 FADH2 (to the electron transport chain)
- Electron Transport Chain is the 2nd main part of Cellular
Respiration
1. Electrons removed from NADH & FADH2
2. Hydrogen ions transported across the membrane
3. ADP is changed into ATP when hydrogen ions flow through ATP
synthase
4. Water is formed when oxygen picks up electrons and hydrogen
ions
- Products of the Whole Process of Cellular Respiration
○ Carbon dioxide (CO2)
▪ Waste product from the Krebs cycle and from the
breakdown of pyruvate before the Krebs cycle
○ Water (H2O)
▪ Waste product from the electron transport chain
○ Net gain of up to 38 ATP molecules for every glucose molecules
▪ 2 from glycolysis
▪ 2 from Krebs cycle
▪ Up to 34 from electron transport chain
Fermentation
- Does not make ATP
-
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- Allows glycolysis to continue
- Removes electrons from NADH molecules and recycles NAD+
molecules for glycolysis
1. Pyruvate and NADH from glycolysis enters the fermentation process. 2
NADH molecules provide energy to convert pyruvate into lactic acid (for
lactic acid fermentation) or alcohol and carbon dioxide (alcoholic
fermentation). As the NADH molecules are used, it is converted back into
molecules of NAD+
2. 2 molecules of NAD+ are recycled back to glycolysis. The recycling of
NAD+ allows glycolysis to continue.
Two Types of Fermentation
- Lactic Acid Fermentation

○ Anaerobic respiration in which pyruvate is converted into

lactic acid
○ Anaerobic = process without the presence of oxygen
- Alcohol Fermentation
○ Aerobic respiration used by many yeasts and some types of
plants
○ Aerobic = process with the presence of oxygen

Alas Dose - Cup of Joe

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