Biology 10.1 - Compiled Notes

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Biology 10.1Exercise 1 - Microscopy

I. Three Tasks of a Microscope

a. Magnification – increase image size

b. Resolution – minimum distance between two points that

can be differentiated

c. Contrast – render the image visible to the naked eye,

camera, or any other imaging deviceII. Types of Microscopes

a. Light Microscope – refers to the use of transmitted light to

observe specimens

i. Simple

1. Uses single lens; convex (thicker at the center)

2. Invented 500 years ago

3. Anton van Leeuwenhoek

4. Image

a. Virtual: Upright

b. Real: Inverted

ii. Compound

1.

Uses a set of lenses to magnify objects and

different to stains to provide the image contrast

2. Has a 2-stage magnification: eyepiece x objective

3. Image

a. Virtual: Inverted

b. Real: Upright

4. Image Movement

a. If move slide to the right; image to the left

b. If move slide up; image goes down

5. 2 Magnifying Lenses

a. Ocular Lens

b.

Objective Lens6. 2 Types

a. Binocular microscopes

i. 2 eyepieces

b. Monocular microscopes

i. 1 eyepiece

iii. Other Types:

1. Stereoscopic (Dissecting microscope)

a. Has relatively low magnification

b. Depth of field is greater than the compound

i. Objects can be seen in 3D

c. Light can be directed onto the (from the

top) object and up through (from the

bottom) it

2. Fluorescence

a. Reveals transparent specimens if they are

treated with specific dyes and exposed to

UV light

3. Phase-contrast & Differential Interference

Contrast

a. Converts invisible difference into light-dark

differences

b. Electron Microscope

i. Uses electron beams reflected on electromagnetic

lenses to magnify objects up to 100,000x

ii. Always shows a black and white image

iii. The better resolution is due to shorter wavelengths o

electrons

iv. 2 Kinds

1. Scanning Electron Microscope – details of

surface features2. Transmission Electron Microscope – similar to

compound but magnifies 100,00x closer

III. Parts of the Microscope

a. Optical Parts

i. Mirror or Illuminator

1. The mirror has a concave and plane side

ii. Objectives – most important, gathers light passing

through the specimen to project an accurate, real,

inverted image of the specimen

1. Scanner

2. LPO (10x)

3.

HPO (40x)

4. OIO (Oil Immersion Objective; 100x)

iii. Eyepiece or Ocular Lends

1. Looks at the focused, magnified image projected

by the objective and magnify that image a

second time as a virtual image seen as if 10

inches form the eye.

iv. Condenser

1. Substage component that gathers light from the

light source and concentrates it into a cone of

light that illuminate the specimen with uniform

intensity over the entire field of viewv. Iris diaphragm

1. Substage component that controls the amount o

light that would enter the condenser

2. Closing the iris will increase contrast at the cost

of resolution

b. Mechanical

i. Base, Pillar, Arm

1. Houses electrical components for operating and

controlling the intensity of the lamp – base

2. Supports the stage and substage – pillar

3. Supports the structures that holds the objective

and ocular lenses – arm

4. Provides stability and mechanical support to the

microscope

ii. Stage

1. Supports the specimen to be viewed

2. Has an opening for light to pass through – the

stage aperture

3. Specimens are held in place by stage clips

4. Specimens can be moves using the stage knobs

iii. Nosepiece



1. Holds the objectives of various magnifications

iv. Dust Shied

1. Prevents dirt from settling on the objectives

v. Body Tube

1. Holds the nosepiece and dust shield

vi. Draw Tube

1. Holds the ocular in place

vii. Adjustment Knob

1.

Elevates or lowers the stage in larger (coarse) orsmaller (fine) increments

2. The Coarse AK is used to bring the specimen

into view

3. The Fine AK is used to bring the specimen into

focus

viii. Condenser Adjustment Knob

1. Raises or lowers the condenser to adjust contrast

ix. Iris Diaphragm Lever

1. Controls the diameter of the iris diaphragm

2.

IV. Terms

a.

Numerical Aperture

i. Width of the cone of light that can enter the objective

lens

ii. NA = n (sinµ)

1. n – refractive index of the medium

a. Air = 1.00

b. Water = 1.33

c. Glycerine = 1.47

d. Oil = 1.515

2. µ - half of the angular aperture

b. Resolving Power and Resolution

i.

Resolving Power - Ability of a microscope to distinguishclose objects as separate and distinct

ii. Resolution – check tasks

1. Limit - diameter of the airy disks of a single spot

iii. Factors that affect resolving power and resolution

1. Numerical Aperture of the Objective

2. Wavelength of light

iv. R = ! / 2NA = 0.61! / NA = 1.22! / (NAob + NAcond )

c. Magnifying power

i. The ability of a lens to magnify an object

ii. Magnification

1.

The degree by which an object isenlarged/reduced in size

2. 2 Types:

a. Linear Magnification

i. = magnification x magnificationocular

Objective Mobj Mocular

LM

Scanner 4x 10x 40x

LPO 10x 10x 100x

HPO 40x 10x 400x

OIO 100x 10x 1000x

*Depends on the ocular

b. Magnification of Illustration

i. = sizedrawing/sizeactual

d. Working distance

i. Distance between the tip of the objective and the

specimen

e. Relationships

i. " resolution # contrast

ii. " resolution # resolving power

iii.

" resolution " working distanceiv. " resolution " wavelength

v. " numerical aperture " magnifying power

vi. " numerical aperture " resolving power

vii. " magnification # working distance

V. Path of Light

a. Lamp/Mirror $ Condenser $ Specimen $ Objective $

Eyepiece

VI. Calibration of the Ocular Micrometer

a. Calibration constant = (stage units / ocular units) x 0.01mm

VII. Actual Size of Specimen

a.

Actual Size = Ocular Units x C.C.Exercise 2 – The Cell

I. Basic structural (all living things are made up of cells) and

functional (Exhibits all properties and activities of life) unit.a. Anton van Leeuwenhoek – protozoa, spermb. Robert Hooke – cork cells (cellula)

c. Theodore Schwann – all animal are made up of cells

d. Matthias Schleiden – all plants are made up of cellse. Rudolf Virchow – cells arise from the division of pre-existing

cells

f. Felix Dujardin – sarcodeII. The Cell Theory

a. All living things are composed of cells (X.c. and X.d.)

b.

Cells are the basic unit of structure and function in livingthings

c. All cell come from pre-existing cells. (X.e.)

III. Two Types:

a. **Viruses – can’t reproduce outside a host

i. An obligate parasite w/ a protein coat and nucleicacid (DNA and RNA)

b. Eukaryotes have compartmentalization via and

endomembrane system and specialization of functionsbought about by the presence of membrane-boundorganelles

c. Organellesi. Only in animals

1. Centrioles2. Lysosomes – digestive organelle where

macromolecules are hydrolyzedii. Only in plants

1. Vacuoles – storage tanks of the cell

a. S: membrane – enclosed sacb. F: store H2O, salts, proteins, CH2O

Eukaryotic Prokaryotic

0.1 – 10 µm 10 – 100 µm

No membrane boundorganelles; no nucleus

Organelles are membranebound; true nucleus



2. Cell Walls3. Chloroplasts – plastid: organelles that store food

and pigment

IV. Cell Structure and Functiona. Cell Membrane (Singer or Nicholson)

i. Fluid Mosaic Model1. Fluid – phospholipid bilayer: a trilaminar structure

a. e- dense protein – clear structure of lipids –

e- dense proteinb. Bilipid layer – allows only uncharged, non-

polar, small molecules and waterc. Oligosaccharides – glycoproteins and lipids

i. Cell wall recognition/communication

ii. Molecular ID of the celld. Proteins – extrinsic, integral and trans-

proteins that transport molecules in and outof the cell

2. Mosaic – integrated proteins and moleculesa. Extrinsic – proteins are outsideb. Integral – proteins are inside

ii. Functions:

1. Separates cells from surroundings2. Regulates the entrance and exit of substances

3.

Protects and supports the cellb. Cell Wall (only in plants)

i. Has three (3) layers1. Primary Cell Wall

a. Thin and flexible; fibrous and elastic cellulose2. Middle lamella

a. Thin layer; rich in polysaccharides calledpectin; Acts as the glue

3. Upon maturation cells strengthens its cell wallsa. Secretion of hardening substances into the

Primary C.W.b. Addition of a Secondary Cell Wall

i. Plants = cellulose + lignin

ii.

Fungi = chitiniii. Prokaryotes = CH2Os + polypeptides

c. Nucleus

i. Enclosed by a nuclear envelope1. Double-membrane with pores

a. 2 bilipid layers with a space of 20-40 nmb. Pores are 100 nm in diameter

2. Nuclear side is line with a Nuclear Laminaa. Netlike array of protein filament for shape

and supportb. Nuclear Matrix (?) – network of protein

fibers3. Chromosomes (carry genetic info) made of

chromatin (complex of DNA and protein)a. 46 in somatic cells; 23 in sex cells

ii. Nucleolus1. Mass of densely stained granules and fibers

adjoining part of the chromatind. Cytoplasmic Organelles

i. Ribosomes1. RNA + protein

2. Protein factoriesii. Endoplasmic (w/in the cytoplasm) Reticulum (network)

1. Extensive internal membrane2. Rough ER

a. Rough due to the presence of ribosomes;connected to the nuclear envelop

b. Protein synthesis and modification

3. Smooth ERa. Smooth walls

b. Synthesis of lipids, packaging of proteins intovesicles, metabolism of carbohydrates,

detoxification (for the liver), storage ofcalcium ions

iii. Golgi Apparatus – shipping and receiving center1.

Packages and distributes synthesized molecules2. Has a cis face (the receiving; located near ER)

and a trans face (the transporting)

3. Cisternal Maturation Model

iv. Lysosome1. Membranous sac of hydrolytic enzymes use for

digestion of macromolecules

a.

Endocytosis: cells engulf microscopicparticles

b. Phagocytosis: cell engulfs particle by

wrapping pseudopodia around it and taking into the cell

c. Autophagy: cell recycles its own materials

v. Vacuoles1. Membrane enclosed sac for storage

e. Mitochondria and Chloroplastsi. Mitochondria’s 2 Layers

1. Outer layer – acts as envelope2. Inner layer – has many folds to increase surface

area3. Site of cellular respiration

a. Glucose + 6 O2 ! 6 CO2 + 6 H2O + ATP

i. ATP: Adenosine Triphosphate4. The power house of the cell



ii. Chloroplasts are plant organelles (plastids) that storefood and pigment1. Site of photosynthesis

a. 6 CO2 + 6 H2O + light ! Glucose + 6 O2 f. Cytoskeleton

i. Made up of microtubules1. Hollow tubes made of protein

2. Cilia – short thread-like structure for cellmovement and movement of substances alongcell surface

3. Flagellaii. Supports cell structure and drives cell movements



Exercise 3 – Mitosis

I. The Cell Cyclea. Important Terms:

i. Cell division – the basis of the continuity of lifeii. Genome – a cell’s endowment of DNA

1. Prokaryotic – single DNA molecule2. Eukaryotic – multiple DNA molecules

iii. Chromosomes – structures DNA are packaged into

iv.

Chromatin –

complex of DNA and proteins; is thebuilding material of chromosomes.v. Somatic Cells – human body cells except reproductive

cells

1. Gametes – reproductive cells; egg and sperma. Chromosomes are half of somatic cells

vi. Sister Chromatids – duplicated chromosome; attached

by cohesins1. Centromere – point of greatest attachment

vii. Mitosis – division of genetic material in nucleus

1. Cytokinesis – division of the cytoplasmviii. Meiosis – a variation of cell division where the number

of chromosomes is reduced to half

b.

Phases of the Cell Cyclei. Interphase

1. G 1 (1st gap)

a. Cell grows; Duplication of organelles,components, centrosomes

2. S (synthesis)

a. Duplication of the chromosomes (DNA)3. G 2 (2

nd gap)

a. More growth in preparation for M phaseb. Complete duplication of centrosomes

c. Synthesis of tubulins, aster, and histoneproteins

d. Nuclear envelope Is developedii. Mitotic (M) Phase / Mitosis

a.

Prophaseb. Chromosomes become so tightly packed

they can be seenc. Nucleoli disappearsd. Mitotic spindle begins to form

i. Made of fibers of microtubules and

associated proteinsii. Centrosomes are driven apart

2. Prometaphasea. Nuclear envelope fragments

b. Chromatids each has a kinetochorec. When a microtubules attaches to the

kinetochore, the kinetochore becomes akinetochore microtubules

3. Metaphasea. Centrosomes are opposite poles

b. Chromosomes have arrived at themetaphase plate – equidistant to bothcentrosomes

4. Anaphase

a. Starts when cohesion proteins are cleavedb. Each chromatid, due to separation, becomes

a chromosome

c. Cell elongates as non-kinetochoremicrotubules continue to lengthen

5. Telophasea. 2 daughter nuclei form

b. 2 Nuclear envelope form from the previousenvelope’s fragments

c. Chromosomes become less condensedd. Spindle is depolymerized

Interphase and M Phase in Plant Cel

Interphase, M Phase, and Cytokinesis in Animal Cel

iii. Cytokinesis

1. In Animals, formation of a cleavage furrow whichpinches the cell into 2. While in plants, the

formation of a cell plate.



Cytokinesis in Plant Cells

c. Cell Cycle Control System

i. Checkpoint – stop and go signals regulate the cell

cycle1. G 1 Checkpoint – checks cell size, nutrients,

growth factors, DNA damage

2. G 2 Checkpoint – checks cell size and success of

DNA duplication3. Spindle Assembly Checkpoint – checks

chromosomes and spindle attachmentii.

Factors that help control the Cell Cycle

1. Telomeresa. Repeated DNA sequences at the tops of

chromosomesb. TTAGGG sequence lost at every cell

divisionc. Once depleted cell cycle stops

d. Can be restored by telomerase found ingametes

2. Anchorage dependencea. Cell must be attached to a substrate to

grow3. Density Dependence

a.

Cell stop dividing once it is crowded4. Regulatory Proteins

a. Cyclinsi. A protein whose concentration cyclically

fluctuatesii. Peaks during mitosis

b. CDK (Cyclin dependent Kinasesi. Activated by presence of cyclins

ii. Activates other necessary proteinsc. Growth Factors

i. Proteins that stimulates cells to divide

ii. Promotes CDK – cyclin binding (MPF(maturation promoting factor) – theCDK – cyclin complex)

Exercise 4 – Cell Transport

Cell Membrane Transporta. Non-mediated / Passive

i. Movement of small molecules from a region of highconcentration to a region of lower concentration

ii. Energy is not required1. Diffusion – dependent on concentration gradient2. Osmosis – movement of water across cell

membranesa. In animals

i.

Hypertonic –

high concentration of saltoutside of cell ! influx of water;causes lysis

ii. Isotonic – cell is normaliii. Hypotonic – high concentration of salt

inside the cell! water rushes out;

shriveledb. In plants

i. Hypertonic – turgid (normal)ii. Isotonic – flaccid

iii. Hypotonic - plasmolysis

3. Dialysis



b. Mediated / Activei. Movement from low concentration region to a higher

concentration

ii. Energy is used upiii. Requires a carrier protein

iv. Types5. Uniport – 1; one direction Symport – 2; one

direction6. Antiport – 2; two directions

d. Facilitated – requires transport proteinse. Bulk Transport – movement of large molecules with the

use of vesicles

i. Endocytosis1. Phagocytosis – cell-eating

2. Pinocytosis – cell-drinking3. Receptor-mediated endocytosis

ii. Exocytosis

Exercise 5 – Animals and Plant TissuesI.

Animal Tissues

a. Epithelial

* covers body surfaces and lines body cavities

b. Connective

* sparse population of cells on an extracellular matrix; cells are called fibroblasts which s r t fiber proteins and macrophages

i. Types of Connective Tissue Fibers

1. Collagenous – for strength and flexibility

2. Reticular – attachment of connective tissue to adjacent tissues

3. Elastic – increase connective tissue elasticity

ii. Types



1. Fibrous – have cells called fibroblasts located some distance from each other; fibroblasts are separated form each other by a

jelly-like ground substance (with white collagen fibers and yellow elastic fibers); Matrix is a term that includes both ground

substance and fibers

a. Loose

i. Also called as Areolar tissue

ii. Supports epithelium and many internal organs

iii. Forms a protective covering.

iv. Its presence allows organs to expand, like the lungs, arteries, and bladder

v.

Adipose tissue –

a special type1. Cells enlarge and store fat – called adipose cells

2. Releases leptin (a hormone) that regulates appetite-control centers in the brain

b. Dense

i. Contains many collagen fibers that are tightly packed

ii. Found in:

1. Tendons – connects muscle to bone

2. Ligaments – connects bones to other bones at joints

iii. Types

1. Regular Dense

2. Irregular Dense

2. Specialized

a.

Cartilage

i. Cells lie in small chambers called lacunae (sing. Lacuna) and are separates by a solid but flexible matrix

ii. Cells are called chondrocytes and chondroblasts

iii. Lacks a direct blood supple (heals slowly)

iv. 3 Types

1. Hyaline

a. Most common type

b. Contains only fine collagen fibers

c. Matrix – glassy and translucent

2. Elastic

a. Contains mote elastic fibers than the hyaline; flexible

3.

Fibrocartilagea. Strong collagen fibers

b. Found in structures that need to withstand great pressure and tension

b. Bone

i. Most rigid connective tissue

ii. Consists of a hard inorganic matrix of salts (the inorganic salts makes it rigid)

iii. Protein fibers provide elasticity and strength (much like a reinforcement)

iv. 2 Types:

1. Compact bone

a. Makes up the shaft of the bone

b. Composed of cylindrical structures called osteons

c. Cells called osteoblasts (bone-forming cells) and osteoclasts make the matrix

d. Bone cells are located in lacunae

e. Has a central canal where blood passes to transport nutrients and where nerves are placed to relay impulses

called the Haversian canal

2. Soft bone

a. Composes the end of long bone

b. Appears as an open bony lattice with many bony bars and plates

c. Blood

i. A fluid connective tissue

ii. Consists of formed elements and plasma; located in blood vessels

iii. Transports nutrients and oxygen to tissue fluid



iv. Formed elements

1. Red blood cells (RBC) or Erythrocytes

a. Transport oxygen; has no nucleus, biconcave in shape, and colored red due to hemoglobin (red pigment)

2. White blood cells or Leukocytes

a. Has a nucleus and without staining are transparent

3. Platelets or Thrombocytes

a. Fragments of giant bone cells present only in bone marrow; incomplete cells

d. Lymph

i.

Fluid connective tissue that is a clear (or faintly yellow) fluidii. Contains leukocytes



c. Muscular

i. Moves the body and its parts;

ii. Contractile tissue composed of cells called muscle fiber

1. Muscle fibers contain filaments made of proteins, actin and myosin

iii. 3 Types

1. Smooth (visceral) – involuntary and has no striations; fusiform in shape

a. One cell one nuclei

2. Skeletal – voluntary and has striations

a.

Striations are due to the placement of actin and myosin; One fiber with multiple nuclei (Cells have fused)3. Cardiac – involuntary and has striations

a. Cardiac muscle cells are separate but connected via intercalated disks

d. Nervous

* receives stimuli and transmits nerve impulses

i. Neurons

1. Dendrites – an extension that receives signals for the cell

2. Cell body – contains most of the cell’s cytoplasm and the nucleus

3. Axon – an extension that conducts signals away from the cell body

a. Usually covered by myelin (a white fatty substance); once covered it is usually called a fiber

b. Spaced between the myelin sheath are called Node of Ranvier

ii. Neuroglia – primary function is to support and nourish the cell

1. Microglia – Supports neurons, engulf bacteria, and debris

2. Astrocyte – Provides nutrients to neurons and produce glial-derived neutrophic factor (a hormone)

3. Oligodendrocytes – Forms the myelin sheath around fibers in the brain and spinal cord

4. Schwann cells – Forms the myelin sheath around fibers outside the brain.



e. Reproductive

II. Plant Tissues

a. Meristematic

i. 3 Processes

1. Cell Division – results in increase in number of cells

2. Cell Elongation – as the cytoplasm grows and the vacuole fills with water, there is an increased pressure on the cell walls causing

it to expand.

3. Cell Differentiation – specialization

ii.

Apical1. Primary growth – lengthening of plant

2. Root Primary Growth or Shoot Primary Growth

a. Parts

i. Root cap – protects the apical meristem as it pushes against abrasive soil

ii. Leaf Primordia – developing leaves

iii. Bud Primordia – developing buds

1. Primodium is singular

b. Produces: ground, vascular, and dermal tissues

c. Primary Meristems – immature tissues

i. Protoderm – gives rise to the epidermis

ii. Procambium – develops into vascular tissues

iii.

Ground meristem –

gives rise to ground tissues

d. Shoot development (also applicable to root)



iii. Lateral

1. Secondary growth – increase in plant girth

2. 2 Lateral Meristems (secondary growth is due to cell division in lateral meristems)

a. Vascular Cambium

i. Forms a thin, continuous cylinder within the root and stem

ii. Located between the wood and bark

iii. As it divides it adds more cells to the wood (secondary xylem) and inner bark (secondary phloem)

b. Permanent – tissue systems

i. Dermal

1. Epidermis

a. In herbaceous plants; a layer of cells

b.

Unspecialized, living cellsc. Guard Cells

d. Trichomes

e. Stomata – facilitates the diffusion of CO2

i. Between 2 guard cells

2. Periderm

a. Several layers thick; the replacement of the epidermis

b. Mainly cork cells and cork parenchyma cells

ii. Ground

* Cell wall structure is the main difference – a growing cell first has a primary cell wall; once it stops growing the cell secretes a

secondary cell wall between the cytoplasm of the cell and the primary cell wall



1. Parenchyma

a. Has thin primary cell walls

b. Has the ability to differentiate into other plant cells

2. Sclerenchyma

a. Has both primary and hard secondary cell walls

b. At functional maturity (when it is used as support) the cell is dead

c. 2 Types

i. Sclereids

1.

Short cells that are variable in shapeii. Fibers

1. Long, tapered cells

2. Occur in groups or clumps

3. Collenchyma

a. Unevenly thickened primary cell wall; extra thick at corners

b. Flexible tissue; main support for soft, nonwoody plants

c. Usually elongated

iii. Vascular

1. Xylem

a. Tracheid – chief water conductor of gymnosperms and seedless vascular plants

b. Vessel Elements – chief water conductor in angiosperms (flowering plants)

c.

Xylem Parenchyma –

perform storage functions

d. Xylem fibers – act as support

2. Phloem

a. Sieve Tube Elements

i. When stacked together ! sieve tube

ii. Have sieve plates at the ends connecting them to the next sieve tube element

iii. One of the few eukaryotic cells that can survive without a nuclei; usually up to a year but some survive to their

hundreds

b. Companion Cells

i. Adjacent to the sieve tube elements and assists in it’s functioning

ii. Living cell with a nucleus; possible to be directing both sieve tube element and companion cell

iii.

Numerous plasmodesmata (cytoplasmic channels through the cell wall) occur between the two cellsc. Phloem Parenchyma

d. Phloem fibers

i. Frequently extensive in flowering plants

Biology 10.1 - Compiled Notes

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