BIOLOGY LAB NOTES

Microscopy
The lenses are the most important part of the microscope
Two lenses (optical lens “eyepiece” )(objective lens which is closer to the
specimen )
Convex Lenses (converging lenses) bend light and focus it(converge) in one
spot(focal point)

The arm and base are the supporting parts of the microscope
The function of the ocular lens is to magnify (10x)
The body tube (connects the ocular lens to the nosepiece (The light rays pass
between the upper and lower lenses )
ILLUMINATOR (sub-stage position )
Condenser is a group of lenses beneath the stage (gather light and concentrate it
Into a cone of light), This illuminates the specimen with uniform intensity
Diaphragm (rotating disc)(vary the intensity and size of the light cone), control the
amount of light and regulates the contrast and resolution
Coarse adjustment (focusing the lenses) Fine adjustment (focusing on the details)
Resolution is the ability to differentiate between very close objects I the image
(ability to measure the separation of mages close together)
Total magn=eyepiece*nosepiece
Microscope lenses sees In 2D,
Fine adjustment knob can be used to build a 3d picture of the specimen
Field of view (magn field of view diameter )
1mm=1000um, object size=(FOV/fit number)*magnification
Oil immersion lens (100x) same refractive index as glass , prevents the scattering
of light , If not used the quality will be poor because air and glass have different
refractive indexes causing light to be scattered
•Light microscope: uses focused light and lenses to magnify a specimen. Image
plane is "flat" (2D)
•Inverted Microscope: is useful for observing living cells or organisms at the
bottom
of a large container
•Scanning Electron Microscope (SEM): have lower magnifying power but can
provide 3 dimensional viewing of objects
•Transmission Electron Microscope (TEM): used for studying cells and tiny
slices of microorganismslike viruses
•Fluorescence microscope: optical microscope that uses fluorescence an
phosphorescence to study properties of organic or inorganic substances
Practical tips (place the cover slip slowly to avid air bubbles, you can control the
amount of light through the diaphragm, Don’t forget to clean the oil lens )

Reproduction
Binary fusion daughter cells are half the size of the parent cell
Budding two different sized cells are made (yeast and hydra)
Spores (specialized reproductive cells with a small amount of cytoplasm ),
surrounded by tough coats, develop in favorbale conditions
Vegetative propagation (naturally by runners, plantelts, tubers and bulbs)
Flowering plants (pollination&fertilization ) the egg inside the stigma is called
ovule
Spermatogenesis is the process of the formation of haploid sperms
Spermatocyte: a male gametocyte, from which a spermatozoon develops
Oogenesis is the process of formation of the ovum
Oocyte: a cell that develops into an egg or ovum; a female gametocyte
What happens in the Prophase?
(chromosome condensation &they become visible ), spindle fibers formation ,
nuclear envelope breaks down and nucleolus disappear
What happens in the prometephase?
(it is like completing the prophase)
Kinetochores are formed, chromosomes condense more, microtubules attach to
kinetochores, centrosomes move to the poles
What happens in themetaphase (alignment in the middle0
Anaphase?
To separate (cohesion proteins break down, sister chromatids are single so we call
them chromosomes, the cell needs to elongate to divide later, the non kinetochore
spindle fibers lengthen to do that )
Telophase? (it’s like a reverse of pro)
Chromosomes decondense, nuclear envelope is formed, mitotic spindles break
down )
Cytokinesis (Animal vs plant )
Cleavage furrow (actin and myosin filaments ) cell plate from vesicles that contain
cell wallmaterial
The difference between meiosis 1 and mitosis is that
IN meiosis (cross over occur in prophase, pairs of homologous chromosomes are
In the equator of the cell instead of sister chromatids )

Mendelian genetics
Allele is an alternative form of a gane , They work in pairs, one allele at one
homolgous chromosome
Why pisum sativum?
Easy to fertilize, recognize and grow fast
YY*yy=F1 (Yy), (Yy*Yy= 3:1 ratio)
Dominant (green inflated pod , yellow round seeds , purple axial flower, tall plant)
Not dominant then it’s recessive
Mendel’s laws
Law of segregation (gametes have one allele for each gene )(meiosis)
Law of independent assortment (traits are not linked and genes of different trait
segregate independently)
Law of dominance (dominant is always expressed)
Linked genes (deviate the independent assortment)
Genes close on the same chromosome are inherited together , Crossing over
(recomination) may cause them to be inherited independently ,
The closer the two genes get the less likely they would be inherited together,
Higher recombination rate indicates bigger distance
Deviation of Mendel’s laws
Incomplete dominance (blending)(no allele dominates)
Co-dominance (both are dominantly expressed and appear together)
Dominant traits
Cleft chin, free earlobes (the ear isn’t flat ), dimples, freckles,no hitchhiker’s
thumb
most lethal diseases are recessive.
Huntington’s disease (autosomal dominant disorder) progressive chorea, rigidity,
and dementia
Sickle cell anemia (autosomal recessive Disease)(early onset) (mutation in the
gene coding for hemoglobin )
Practical tips (Questions about punnett squares and inheritance patterns )
Chromosomal basis of inheritance

• Centromere – contains recognition sites for kinetochore proteins

Telomeres – specialized repetitive sequences that “cap” each end(maintained by

telomerase) (unexpressed repetitive sequences)
Satellite chromosome (SAT-chromosomes), Exist in 13,14,15,21,22, (secondary
constriction (NOR nucleolar organizing region) -important in nucleoli formation
Morphology Function Banding characteristics
(Metacentric Autosomes (22 pairs, Chromosomal banding
)(centromere is centered somatic ) (alternating light and
)normal (p and q arms are Allosomes (1 pair, sex) dark regions along the
equal) chromosome,after
Submetacentric (not staining with dye.)
centered)
Seven groups
calssification
(Denver group)

Heterochromatin (packed , high DNA density and AT content, appear dark)

• Facultative (can be loosened and expressed)(survival genes )
• Constitutive (never opens )
Euchromatin (less condensed, less DNA density and less AT content expressed
,appear light )
G-banding technique
Giemsa stain (acidic), AT rich are dark because the stain attach to the regions , GC
rich regions appear light
Trypsin enzyme 9digest histones so the Giemsa dye access the DNA)
Abnormalities
Numerical (whole chromosome )
• Polyploidy (failure of separation of chromosomal sets usually during
meiosis) (•Happens in plants, in some pathologies, cancers.)
• Aneuploidy(Non disjunction ) (due to loss or duplication.)( trisomy,
monosomy(turner (45,x))
• Edwards syndrome (18)( low set ears, unusual fingerprint )
• , Patau syndrome (13) (palate or cleft lip),(polydactyly (something like an
extra finger)
• Down syndrome ( Trisomy 21) (symptoms (Flattened Facial Profile, Upward
Slanting Eyes: Almond-shaped eyes that slant upward, Small Ears, short
fifth finger, separated toes )

Structural (parts )
Translocation occur between two non-homologous chromosomes
Deletions (Commonly occurs in telomeric regions during cell division)
Karyotyping (cytogenetic testing) is the process of pairing and ordering all the
chromosomes of an organism (•Detection of chromosomal aberrations (Size and
Shape) and The loss or addition of chromosomes)
Limitations:rely on G-banding quality (blood samples are the best
)(chromosomes from he amniotic flid give poor quality)
Bacterial staining

Outer membrane (lipopolysaccharides and proteins)

Iodine (I- or I3 - ) interacts with crystal violet (+) to form large and an insoluble
complex
The decolorizing agent, (ethanol or an ethanol and acetone solution), interacts with
the lipids of the membranes of both gram-positive and gram-negative bacteria
(ippoly scharrides of garm negative are removed to expose the peptidoglycan layer
, gram negative cell wall becomes leaky and allow the dye to wash off
In gram positive it dehydrates the peptidoglycan layer ( the dehydration and the
thick peptidoglycan traps the stain)
Counter stain (sufranin or carbl-fuchsin)

Antibiotic resistance
Antibiotic vs antimicrobials
Derived from (Mold or fungi Bacteria, Synthetic or semi-synthetic compounds)
Antiseptics are antimicrobial agents that can be applied on living
tissue(chloroxylenol)
Disinfectants are meant to destroy microorganisms which contaminate nonliving
objects(formaldehyde)
•Narrow spectrum antibiotics: •Broad spectrum antibiotics:
penicillin and rifamycin. cephalosporines
and tetracyclines.

Bactericidal antibiotics: Bacteriostatic antibiotics:

Fast killing targets cell wall and DNA Slow killing and inhibit growth
(aminoglycosides, β-lactams, and targeting protein synthesis and essential
vancomycin.) enzymes,
tetracycline, erythromycin,
clindamycin, and
chloramphenicol.
Intrinsic Resistance Acquired Resistance
Bacterial natire and genetic Due to antibiotics
makeup 9mutation or gene transfer

Antibiotic sensitivity test, called Kirby-Bauer or disc diffusion test

Bacteriophages
Named after the group they infect (Coliphages for Escherichia coli)

Both base plate and tail fibers help phage attach to the cell
Virulent (lytic) Temperate (lysogenic)
Phage typing (identifying pathogenic bacteria)( Both base plate and tail
fibers)
The titer for (HTL)=the number of plaques/(The spotted volume(ml)of
phage lysate we platted)*conversion factor(1000)*The dilution factor
(10^7)) exp: (22/10)*1000*10^7
100Ml bacterio+900Ml(PBS &TSB)

Algae
Algae are photoautotrophic organisms. They have photosynthetic pigments.
Thallus (body) (composed of filaments or cells)( lacks specialized tissues)
live in aquatic environments: Red algae, brown algae, and green algae.
Chlamydomonas (unicellular) Spirogyra (green Algae)
• Cell wall: Glycoprotein only. Ex. Multicellular Algae
• Flagella are present. Cell wall: Glycoprotein and cellulose.
• A single, cup-shaped chloroplast. • No flagella.
• Reproduction is asexually by binary • Many, spiral-shaped chloroplasts.
fission. • Reproduction is sexually by
conjugation and
asexually by fragmentation.
Asexual (by one organism) Vegetative (from Sexual
(favorable conditions ) vegetative parts ) (During
the protoplast of a cell divides into several • Fragmentation unfavorable
protoplasts (Zoospores) (The body is conditions)
broken down
into several • Any vegetative
parts cell can produce
(fragments) and gametes or a
each fragment specialized
develops into a gametangium
thallus.) may be
developed.
• fission (mitotic • The gametangia
division and may be
cells get morphologically
separated by similar (iso
septum ) gametangia) or
Zoospores (are unicellular, flagellated
dissimilar(hetero
reproductive cells)
gametangia).
Produced from (vegetative cells or in
specialized cells (Sporangium)
Gametes are
habloid

Conjugation
Once the zygotes are released, the parent filaments die. The
zygotes wait for favorable conditions to germinate.
3

Fungi
Cell wall is composed of chitin and lacks motility
 • Areial mycelium produce reproductive spores
• Hyphae may be coenocytic with no septums(cell walls) or septated
• Spores growing into fungus is called germination
• Plasmogamy (haploid cells fuse together to form a heterokaryotic
cell(with 2 or more nucleus) that forms a diploid zygote which
undergoes meiosis to produces spores)
• Karyogomy (fusion of the nucleus inside the heterokaryotic cell)
Fungal classification
Kigndom fungi= 5 phyla according to the sexual reproduction
Chytridimycota the simplest and most primitive fungi (Marine). Most
chytrids are unicellular and few form coenocytic fungi (sexually and
asexually(diploid zoospores), flagellated gametes
Glomeromycota coenocytic fungi and mutualist with plant roots
(asexually)
Zygomycota (conjugated)(bread mold)(Rhizopus)coenocytic hyphae
(1n)(asexually by sporangiospores)(soil,plants and animals)(sparophytes
and parasites)(sexual and asexual)
Ascomycota (sac)(asci special elongates sacs that produce spores
(peants and serial grains)(saprophytic and parasite)(sexual and asexual)
Basidiomycota (club) (mushroom )(agaricus)
Gills are lined with basidia which form basidispores
Grow on organic materials (staw,grains and dead
bodies)(sparophyte)(sexual)
Deuteromycota: The Imperfect Fungi (penicillum)(don’t have sexual
phase) (saprophytic )feed on oragnic stuff (asexual conidiospores.)
Plants
Roots, Stems, and Leaves (have different tissues and cell types )
Roots store carbohydrates
• Tap root( embryonic root gives rise to lateral roots (bean plant)dig deep in
soil
• Fibrous root (embryonic root dies and small roots from the stem emerge )
Stem (transport and support), aids in photosynthesis by growin towards
sunlight
Epidermis layer in plants secrete the cuticle layer , and among the
epidermal cells stomata exist
Open (blue light) (turbud)
Close (dark, drought (ABA ABSICIC ACID)(shrinked)
All three tissues (dermal, vascular, and ground tissues) are found in all
plant organs (roots, stems, and leaves)

Periderm: replaces the epidermis in older regions of stems and roots,

found mainly in woody plants.
Ground tissue can be internal (pith)or external(cortex) to the vascular
tissue. cells help in storage, photosynthesis, and support.
Parenchyma cells: Collenchyma Cells: Sclerenchyma cells:\
storage , support, elongated cells with (dead) (the cell dies
photosynthesis. irregular thick cell after its cell wall is
walls fully formed),
structural support the cytoplasm is
growing rapidly and missing, leaving an
need to be empty central cavity.
strengthened such as
the petiole ("stalk") of
leaves.
Cotyledon (seed leaf) the first leaf of a plant to develop
• Dicot plants that have two cotyledons
• Monocot plants have one cotyledon
Reproduction in flowering plants (angiosperms)
Frog anatomy
• The eggs hatch into aquatic larvae, known as tadpoles,( specific rasping
mouthparts
• appropriate for herbivorous diet(Metamorphosis))(2), then tadpoles develop
a lung and hind legs (3), tail disappear , change deit (insects) (2-4 year to be
an adult)(4)
• Third eyelid (nictitating membrane: thin transparent, movable membrane)
• •Tympanic membrane: Located behind each eye, it is for hearing,
Tympanum (1 pair)
• Buccal Cavity: contains mucous glands that produce mucus that aids in the
lubrication of food. Frogs don’t have salivary glands.
• Tongue (attached to the front of the mouth which is extended to catch insects
(food))
• Eustachian tube openings: Openings in the mouth lead to tubes connecting to
the middle ear to equalize air pressure.
• Glottis: The opening from the mouth into the respiratory system
• internal nostrils: Just in front of vomerine teeth,(anteriorly opening of nares),
they serve in respiration
 •
Digestive system
• small intestine (A small anterior duodenum, A much longer
posterior ileum)
• •Liver and pancreas bring bile and pancreatic juice(mainly
trypsin, lipase, and amylase)
• Liver (3 loops, pile, detoxification,NH3=urea)
• Gall bladder (at the liver) It’s a sac-like structure that is
responsible for the storage of bile
Circulatory System
3 chambers; 2 atria and a ventricle
•Spleen: Organ responsible for breaking down of aged RBCs and storage of a
reservoir of blood cells
Chest muscle (rectus abdominis)