Biology lab 111

Experiment 3: the microscope: - The unaided eye has a resolving power of about 0.1mm - Light microscope has a resolving power of about 2 - Light microscope can improve resolution as much as 1000 times, compared to the unaided eye - Contrast means increasing differences between the lightest and the darkest parts of an image - The microscope is carried by holding the arm with one hand and supporting the base with the other

hand

Light microscope systems: 1- Mechanical 2- Illuminating 3- Imaging

Mechanical parts: 1- Tube 2- Arm 3- Nosepiece 4- Base 5- Stage 6- Focusing knob

Imaging parts: 1- 3-4 objective lenses 2- 1-2 ocular lenses

Illuminating parts: 1- Light source 2- Condenser lens 3- Iris diaphragm - Focusing knobs are coarse adjustment knob and fine adjustment knob - If air bubbles present in wet mount preparation, such bubbles appear as circles of various sizes with

dark edges - Always start your microscopic study with the 4X objective lens - Never use coarse adjustment knob when you view a specimen with the 40X objective lens

Total magnification = objective lens magnification * ocular lens magnification

- The image of the specimen in the light microscope is inverted

Types of microscopes:

1- Light microscope 2- Dissecting microscope 3- Phase contrast microscope 4- Transmission electron microscope 5- Scanning electron microscope

Dissecting microscope: - Has two oculars and two tubes

Disadvantages: 1. Limited magnification and resolution

Advantages: 1- 3D image 2- Larger working distance 3- Viewing large objects

Phase contrast microscope: - Studying alive specimen without killing them

Transmission electron microscope: - Electron beams are used as a source of illumination instead of light waves - Operated under vacuum - Has electromagnetic lenses - Magnification can reach 1,000,000 - Resolution may reach 0.2nm - Specimen has to be cut into sections as thin as 60-100nm and must be stained with heavy metals to

make them electron dense

Scanning electron microscope: - The surface of the specimen must be coated with a thin layer of gold - The energy in the electron beam makes the gold emits more electrons which are picked up by a

detector - Results in a picture of the surface of the specimen on a cathode ray tube

Experiment 4: the cell: - All cells have a plasma membrane, a region of DNA or nucleus, and a cytoplasm

Types of cells: 1- Prokaryotic 2- Eukaryotic - Prokaryotic cells are bacteria, compose the domains eubacteria and archeabacteria

Eukarya kingdoms:

1- Animals 2- Plants 3- Protists 4- Fungi - Eubacteria include bacteria and cyanobacteria

Bacteria shape: 1- Bacilli 2- Spirilli 3- Cocci

Bacteria in yoghurt: - Yoghurt contain lactobacillus

- Lactobacillus adapted to live on lactose and converts milk to yoghurt - Methelyne blue pigment used

Cyanobacteria: - Photosynthesis prokaryotes - Exist as colonies and filaments and as a single cells - A slide of anabaena which is a filamentous cyanobacteria is used to observe cyanobacteria

Eukaryotic cells kingdoms: 1- Protists 2- Animalia 3- Plantae 4- Fungi - Nucleus and mitochondria and chloroplast are membrane bound structure

Human cheek cells: - Protection function - Methylene blue is used

Human skin cells: - Methylene blue is used

Onion epidermal cells: - The onion is made up of thickened modified leaves called scales - The onion epidermal cells comes from a thin translucent tissue which lines the scales outer curve - Lugol's stain is used

Experiment 5: biological macromolecules: Classes of macromolecules:

1- Carbohydrate 2- Lipids 3- Proteins 4- Nucleic acids - The chemical properties of classes depend on functional groups - Dehydration is joining building blocks - Hydrolysis are breaking down of polymers

Carbohydrates: - Glucose is a 6 carbon aldose - Fructose is a 6 carbon fructose - Two glucose molecules form maltose - Glucose and fructose form sucrose - Glucose and galactose form lactose

Polysaccharides examples: 1- Starch 2- Glycogen 3- Cellulose 4- Chitin

Benedict's test: - To detect reducing sugars - Reducing sugars have free aldehyde or ketone groups - Benedict reagent consist of CuSO4 making it blue colored - The positive sign is orange-brownish color - This test needs boiling

Lugol's test: - To detect starch - Yellowish-brown color is a negative sign - Bluish-black color is a positive sign - Iodine only interact with coiled molecules - Doesn't need boiling

Proteins: - The building block of proteins are amino acids - Amino acid are linked together by a peptide bonds

Proteins types: 1- Structural 2- Regulatory 3- Storage 4- Contractile 5- Transport

Ninhydren test: - To detect amino acids - Ninhydren reagent reacts with free amino groups - A purple or violet color is the positive sign - Need boiling

The biuret test: - To detect peptide bonds - A violet color is the positive sign - Doesn't need boiling

Lipids: Lipid classes:

1- Neutral fats 2- Phospholipids 3- Steroids

- Cholesterol is an example of steroids

Sudan red test:

- To detect lipids

- A red color is a positive sign

- Doesn't need boiling

- The final step is mixing with vortex

Lipid solubility test:

- Lipids are soluble in nonpolar solvents such as alcohols

- To detect the solubility of lipids

- The final step is mixing

The grease spot test:

- The spread of oil on a paper sheet to give a transparent spot

Nucleic acids: Types of nucleic acids:

1- DNA 2- RNA

Types of nitrogenous bases: 1- Purines 2- Pyrimidines

Purine types: 1- Adenine 2- Thymine 3- Cytosine 4- Guanine

- Uracile is found only in RNA instead of Thymine

- Pyrimidine have only one ring while purine have two

Extraction of DNA:

- The final step is to invert the tube several times

The Dische diphenylamine test:

- To detect DNA

- A blue color is a positive sign

- Need boiling

Experiment 6: enzymes:

- Most enzymes are proteins

Enzyme categories: 1- Hydrolytic 2- Oxidizing 3- Reducing

- Enzymes are categorized depending on the type of reactions they control

- Rennin coagulate milk protein which is casein

- Catechol oxidase react with catechol to give a dark brown color

Factors affecting enzyme activity:

- Rennin alters the 3D structure of casein

- Rennin allows the digestion of milk to be more effective by slowing its passage through the digestion system

Factors affecting enzyme activity:

1- Temperature 2- Ph 3- Enzyme concentration

Temperature:

- High temperatures denaturate the active site of the enzyme

- Low temperature stops the enzyme activity

- Enzyme can survive low temperatures but not the high temperatures

PH:

- Enzyme can't work in acidic or basic solutions

Catechol oxidase test:

- To detect catechol oxidase

- By adding catechol to the reaction mixture

- Dark brown color is the positive sign

- Catechol oxidase forms benziquinone

- Catechol is poisonous

- Phenylthiourea is an inhibitor of catechol oxidase

- Phenylthiourea must be added to solution before the enzyme to inhibit its activity before completing its job

Experiment 7: physical properties of the cell:

- Brownian movement has been discovered by Robert brown

- Diffusion is the movement of molecules from higher concentrations to lower concentrations

- An example of diffusion within liquids is the addition of liquid dye to water

Observing Brownian movement:

- We use carmine dye to observe it

Effect of temperature on Brownian movement:

- Temperature and Brownian movement are proportionally related

- As the temperature increases the Brownian movement increases

Diffusion within solution:

- Starch and iodine = color change inside the bag only

- Iodine move inside the bag where the starch located

- Phenolphthalein and sodium hydroxide = color changes in and outside

Diffusion within semisolid medium:

- The less the molecular weight the bigger the diameter

Osmosis:

- Osmosis is the diffusion of water across a selectively permeable membrane

- Hypotonic means greater concentration in the cell

- Isotonic means equal concentrations

- Hypertonic means less concentration in the cell

Osmosis in plant cell:

- We use elodea or onion epidermal cells to observe the osmosis in the plant cells

Osmotic pressure:

- We will use osmometer

- Osmometer is filled with molasses or sugar solution

- The height of the solute in the tube increases as the concentration of sugar increases

Experiment 8: metabolism: Examples of photosynthetic autotrophs:

1- Green plants 2- Some monera 3- Some protists

Examples of heterotrophs: 1- Most monera 2- Some protists 3- All fungi 4- All animals

- Anabolism is synthesis reaction

- Catabolism is breaking down reaction

Respiration: Alcoholic fermentation:

- Carried out by yeast in an anaerobic process

- Oxygen-stressed muscles of animals carry out lactic acid fermentation

Measuring yeast fermentation:

- Baker's yeast, sacharomyces cerevisiae is used

- Starch is converted to glucose

- Respirometer is a set to see fermentation

Cellular respiration:

- Respiration is a catabolic reaction

Ways to measure cellular respiration: 1- Consumption of O2

2- Production of CO2

3- Release of energy during cellular respiration

Production of CO2during aerobic respiration:

- The change in the volume of gas in the respirometer will be directly related to the amount of oxygen consumed

- During respiration, oxygen will be consumed and its volume will be reduced because carbon dioxide produced is being converted to a solid

Iodoform test:

- To detect alcohol

- Secondary alcohols with an adjacent methyl group react with iodine in alkaline medium

- A yellow precipitate is a positive sign

Photosynthesis:

- Carbon dioxide from the atmosphere provides the carbon source for photosynthesis

- Water provides the hydrogen source for photosynthesis

- Chlorophyll pigment are necessary to trap the light

Demonstration of photosynthesis:

- We use elodea to demonstrate photosynthesis

- As we increase the light intensity the photosynthesis reaction increases

- If we add a source of CO2 the photosynthesis reaction increases

- The source that we use is sodium bicarbonate

Extraction and separation of photosynthetic pigments:

- The most polar pigment will be the lowest

- We use a paper chromatography

- We use a pencil and aceton

- The highest pigment is carotenes the xanthophylls pigment then chlorophyll a and the lowest is chlorophyll b pigments

Experiment 9: cell division:

- Cells have many specialized functions one of which is division

- Dividing cells undergo a repeated sequence of events called cell cycle

Cell cycle stages: 1- Interphase 2- Mitosis 3- Cytokinesis

Interphase phases: 1- Gap 1 G1

2- Synthesis S 3- Gap 2 G2

- Mitosis results in two nuclei containing identical chromosomes

- Mitosis is called equational division, because the resulting cells have equal number of chromosomes

- In interphase the cellular material is being doubled

Mitosis stages: 1- Prophase 2- Metaphase 3- Anaphase 4- Telophase

- Meiosis or reductional division, resulting in cells have half the chromosomes in the mother cell

- In prophase the chromosomes is being condensed

- In metaphase the chromosomes are aligned to the center of the cell

- In anaphase the each centromeres split

- In telophase the cytoplasm is being constricted and split into half

Mitosis in animal cells:

- A slide of white fish blastula is used in this experiment

Mitosis in plant cells:

- A slide carrying a longitudinal section of an onion root tip is used in this experiment

- Mitosis is active at apical meristem

The differences between mitosis in animal and plants: 1- Cytokinesis in plant cell takes place by formation of a cell plate, and not by construction as in

animal cells 2- Lack of centroiles, and consequently astral rays in plant cells

Meiosis in animal cells:

- Occurs in reproductive organ

- It involves prophase, metaphase, anaphase, and telophase

- It happens in two stages meiosis I and meiosis II

- Homologues are chromosome pairs found in body cells

- Diploids have all homologues in it

- Haploids have half the homologues in it

- Meiosis I involves the reduction

- Meiosis II ends up in daughter

- Nematode worm called ascaris is used in this experiment

- Oogenesis is egg formation in ascaris

- Meiosis II doesn't consist of prophase

Experiment 10: Genetics:

- Genes are units of DNA which is located in chromosomes

- Alleles are genes that occupy identical positions on the homologues

- Meiosis produce gametes with 23 chromosomes

- The process that happens during meiosis is called segregation

- Homozygous have two similar alleles

- Heterozygous have two different alleles

- The dominant allele hides the recessive allele

- Codominant are two dominant allele

- Incomplete dominance is intermediate between two homozygotes

- Autosomes are 22 pair of chromosomes

- Sex chromosomes are the last pair of chromosomes

- The genes located on the X chromosome are called sex linked genes

Dominant and recessive traits in humans:

- You only need one copy of a dominant gene in order to see a dominant phenotypic trait

- You need two copies of a recessive gene in order to see a recessive phenotypic trait

Working with human phenotypes: Examples of human phenotypes:

1- PTC tasting 2- Tongue rolling 3- Thumb binding 4- Hair texture 5- Ear lobes 6- A-B-O Blood types

PTC tasting:

- Tasting PTC is determined genetically, its harmless and produces a very bitter taste

- Its dominance

Tongue rolling:

- Tongue rolling is dominant

Thumb binding:

- The hitchhikers thumb is recessive

- Thumb tip bends backward more than 60o

Hair texture:

- Curly hair is incompletely dominant to straight hair

- Wavy hair is intermediate

Ear lobes:

- The detached lobes are dominant

A-B-O blood types:

- Type A contains B antigens

- Type B contains A antigens

- Type O contains Both

- Type AB contains neither A nor B

- The allele of A and B are codominant

- The blood types are detected by mixing drops of the blood with sera containing the A antibody and the B antibody

- Clumping A antibody indicates A type

- Clumping B antibody indicates B type

- No clumping indicates O type

Drosophila melanogaster genetics:

- Drosophila melanogaster is the fruit fly

- Complete its life cycle in 10 to 12 days

- It contains 4 pairs of chromosomes

Differences between male and female fruit flies: 1- Only males have a sex comb 2- The tip of the abdomen is more rounded in males 3- Posterior part of the abdomen is more darker in males and lighter in females 4- Females are larger than males

Examining mutant flies:

- The normal fly is called a wild type

- A mutant fly is any fly exhibiting a phenotypic mutation

- The mutant ebony has a much darker body

- Flies with vestigial wings can't fly they have a defect in the vestigial wings and is called melanogaster mutant

- Yellow flies have a complete yellow body

- White eyed flies have white eyes and are called white eyed mutants

Chi square goodness of fit test:

- Used to compare the observed result with the theoretically expected distribution

Experiment 11: plant tissue: Plant tissue groups:

1- Meristematic 2- Permanent

- Meristematic tissue go through division

- Permanent tissue doesn’t go through division

Types of permanent tissue: 1- Simple 2- Complex

Types of simple permanent tissue: 1- Parenchyma 2- Collenchymas 3- Schlerenchyma 4- Epidermis

Types of complex permanent tissue: 1- Xylem 2- Phloem

Meristematic tissue:

- Composed of embryonic undifferentiated cells

- Apical meristem found at the growing tips

- Apical meristem is responsible for the sustained increase in length of the plant body

- Primary tissue are produced by the apical meristem

- Lateral meristem such as vascular cambium and cork cambium are responsible for the sustained increase in diameter

- After each cell division one of the two daughter cell stays meristematic and the other becomes a part of the plant body

- Tissues produced by the lateral meristem are secondary tissue

Shoot and root apical meristem:

- We use a slide of longitudinal section of coleus shoot tip and a slide of longitudinal section of an onion root tip

Permanent plant tissue Simple permanent tissue: Parenchyma tissue:

- Thin walled (primary and secondary cell walls) and have inter cellular spaces

- Parenchyma are alive at maturity

- Parenchyma is the most common ground tissue

Parenchyma functions: 1- Photosynthesis 2- Respiration 3- Storage 4- Secretion

- We use a cross section of helanthus stem to see parenchyma tissue

Areas of parenchyma: 1- Cortex 2- Pith

- The cortex is the area between the epidermis and the vascular bundles

- The pith is the area in the center of the stem

- Chlorenchyma is a parenchyma cell that contain chloroplast

Collenchyma tissue:

- Consist of living elongated cells

- Irregularly thickened primary walls

- Structural support function

- They are flexible

- Cell walls are thinner than sclerenchyma cell walls

Sclerenchyma tissue:

- Composed of rigid cells that have lignified secondary walls

- Dead at maturity

Sclerenchyma types: 1- Sclereids 2- Fiber

- Sclereids are small irregularly shaped

- Fibers are long and thin and occur in strands

Sclerenchyma functions:

1- Protection 2- Mechanical support

- Internal spaces are nearly obliterated

Epidermal tissue:

- Forms a protective outer covering of the plant body

- 1 cell thick but may be thicker in species that live in very dark habitats and where protection against water loss is critical

- Epidermal cells on the shoot are covered with cuticle

- Cuticle is waxy water resistant material

Complex permanent tissue:

- Composed of more than one type of cells

- Including vascular tissue and periderm

Vascular tissue:

- Vascular tissues are xylem and phloem

- Xylem conduct water and minerals

- Phloem conduct photosynthesis products

- Xylem is composed of parenchyma, fibers, vessels, and trachieds

- Phloem is composed of parenchyma, fibers, sieve tubes, and companion cells

The periderm:

- Located at the outer most layers of woody stems and roots

- Forms the bark

- Composed of cork cells, cork cambium, and phelloderm

- Cork cells is toward outer side, and phelloderm is toward inner side

- We use a slide of tilia

Experiment 12: animal tissues:

- Cells makes tissue, and tissue make organs, and organs make system, and systems makes organism

Example of organs:

1- Stomach 2- Nose 3- Limbs 4- Heart

Example of systems:

1- Reproductive 2- Digestive 3- Nervous 4- Circulatory

- Histology is the science which deals with the study of tissue

Types of tissues: 1- Epithelial 2- Connective 3- Muscular 4- Nervous

- Tissue sections are stained with hematoxylin which gives nuclei dark blue color and eosin which stains cytoplasm in light red color

Epithelial tissue:

- Covers body surfaces as in epidermis or line tubular organs as in the small intense

Function of epithelial tissues: 1- Protection 2- Secretion 3- Absorption 4- Sensation 5- Reproduction

Epithelial tissue features: 1- One free surface 2- Lack blood vessels 3- Very little intercellular spaces 4- Attach to a basement membrane

Simple squamous epithelium:

- Comprised of flat cells with a wide central part which contains a nucleus

- Involved in exchange of materials

- Location in alveoli of lungs and capillaries

Simple cuboidal epithelium:

- Consist of cells with almost equal sides

- Found in kidney tubules and thyroid follicles

- Involved in secretion or absorption

Connective tissues: Connective tissue functions:

1- Connection 2- Defense 3- Cushioning 4- Support 5- Protection 6- Storage of energy

- Comprised of cells, fibers, and ground substance

Types of fibers: 1- Collagen fibers 2- Elastic fibers

- Collagen fibers are tough and flexible

- Elastic fibers can stretch when pulled

- Ground substance may be hard as in bone, semihard as in cartilage, or liquid as in blood

- Connective tissue are highly vascular and lots of intercellular spaces

Types of connective tissue: 1- Proper 2- Special

Types of proper: 1- Loose 2- Dense

Types of special: 1- Blood 2- Adipose 3- Cartilage 4- Bone

Connective tissue proper: Loose connective tissue:

- Also called areolar connective tissue

- Consist of cells scattered in a matrix contains collagen and elastic fibers

- Have an important role in defense

- Found in mesentry

Dense connective tissue:

- Consist of tightly packed collagen fibers

- In regular shape the fibers are arranged parallel to each other

- A slide of longitudinal section of tendon

Special connective tissue: Blood:

- Platelets are the major component of blood

- Platelets are plasma and cellular materials

Types: 1- Leukocytes 2- Erythrocytes 3- Platelets

Leukocytes:

- White blood cells

- Have a defensive function

Types of leukocytes: 1- Neutrophile 2- Lymphocytes

Neutrophile:

- Granular cell with 3-5 lobed nucleus

Lymphocytes:

- Agranular cell with large round nucleus

Erythrocytes:

- Red blood cells

- Have a function in transport of O2 and CO2

- Hemoglobin is an example

- Its nonnucleated small red color cell

Platelets:

- Involved in blood clothing

Adipose: Adipose functions:

1- Storage of fat for energy 2- Thermal isolation 3- Protection

- Found under the skin and around internal organs

- Have no fibers

- An example of its cells is the adipocyte which is large cell with peripheral nuclei

- Have no intercellular spaces

Cartilage:

- Found in the end of long bone and respiratory tubes (trachea)

- Have a function of support

- It connects bone to bone

- Lack blood vessels

- Consist of semisolid gelatinous matrix called chondrin

- The cells of it is chondrocytes

- Chondrocytes cavities are lacunae

- One type of cartilage is hyaline which can be found in trachea and have no fibers

Bones:

- Has a function in support

- It’s a solid matrix from calcium phosphate salts called hydroxyapitite

- The matrix are called lamellae

- Compact bone found in long bone

- Compact bone are made by haversian systems

- Haversian systems cells are osteocytes

Haverisan systems consist of: 1- Osteocytes 2- Haversian canal 3- Lamellae

- Haversian canal consist of blood vessels and nerves

- Volkman's canal are made up by interconnected heversian canals

Muscular tissue:

- Contractile proteins are actin and myosin

- The cells of muscle tissue are either muscle cell or muscle fiber

Skeletal muscle:

- Have a function of movement

- Found in voluntary control organs

- They are striated and have multi peripheral nuclei

Nervous tissue:

- Found in brain, spinal cord, nerves and reach all organs

- The cells of it are nerve cell or neurons

- Neurons are specialized for transmitting impulse

Neuron types: 1- Axon 2- Dendrites

- Axon is long and carries impulses away from the cell body

- Dendrites are short and carries impulses toward the cell body

Experiment 13: vertebrate anatomy: Features that rats share with other mammals:

1- The prescence of hair on most parts of the body 2- The prescence of milk producing glands 3- Endothermy 4- Prescence of placenta and diaphragm

- Only study pictures

Experiment 16: plant anatomy: Groups of flowering plants:

1- Dicot 2- Monocot

Differences between dicots and monocots: 1- Leaf venation is usually parallel in monocots and net like in dicots 2- Flower parts are multiple of 3 in monocots and multiple 4 or 5 in dicots 3- The primary vascular bundles are scattered in stems of monocots and organized in dicots in a circle

The roots: Root functions:

1- Anchor 2- Absorption 3- Storage

- Absorption of water is done by lateral roots and root hairs

- Adventitious roots develop from the base of the stem

- The surface of young roots is formed of epidermis

- Under the epidermis is cortex

- Roots lack cuticle

- Endodermis is the intermost layer of the cortex

- Endodermis has secondary cell walls with lignin and suberin

- Lateral roots comes from the pericycle

- Vascular cylinder is in the middle of the root and consist of xylem and phloem

Internal anatomy of roots: Herbaceous dicots:

- We use a slide of cross section of ranunculus

Herbaceous monocots:

- We use a slide of cross section zea maize

Lateral roots:

- We use a slide of cross section zea maize

The stems:

- The main function is support

Leaf phyllotaxy types: 1- Alternate 2- Opposite 3- Whorled

- Alternate is one leaf at each node

- Opposite is two leaves at each node opposite to each other

- Whorled is three or more leaves at each node

- The internode space is the distance between two successive nodes

Modification of the stem: Modified stem types:

1- Stolons 2- Tubers 3- Rhizomes 4- Bulbs

- Stolons are the running stem horizontally above the ground

- An example of stolons is strawberry or spider plant

- Rhizomes are the horizontally running stem below the ground

- Bulbs are underground structure of shortened stem with modified fleshy leaves

- An example of bulbs is onion

The leaf:

- Consist of a petiole and a lamina

- Leaf venation is the vascular veins within the lamina

Leaf blades types: 1- Simple 2- Compound

Leaf venation types: 1- Parallel 2- Reticulate