GENERAL

BIOLOGY
© hjtlopez
MICROSCOPY Field of View
• Diameter of the cricle of th light
Microscope • Should be in millimeters or mm
• Used to view microorganisms which cannot be seen through the
naked eye such as bacteria, fungi, protists and microscopic Specimen Size
worms • Estimation of how many specimens can fit the diamter
• Anton Van Leeuwenhoek
- Father of Microbiology Measuring with a Microscope
- Animacules- movement of the animals Types of Micrometer
Stage Micrometer and Eyepiece Graticule/Ocular Micrometer
Types of Microscope
Compound, Dissecting, Scanning Electron, and Transmission 1. Stage Micrometer
Electron - Could either be glass or metal
2. Eyepiece Graticule/ Ocular micrometer
1. Compound Microscope - Fits into a microscope eyepiece but it still depends on the
- Magnification can be 1000-1500 times mode
2. Dissecting Microscope
- Magnification can be 40 times FORMULAS
- Used to see frogs and fish Total Magnification: Ocular Lens: 10x
Objective Lens: High Power (40x)
3. Scanning Electron Microscope (Ocular Lens) (Objective Lens) Total Magnification:
- Magnification can be 100,000 times (10x) (40x)= 400x

- Produces 3D images Field of View: 15x / 16
4. Transmission Electron Microscope Field Numberuuu Ocular Lens: 15x
Field Number: 16
- Magnification can be 100,000 times Total Magnification Objective Lens: Scanner (4x)
- Produces 2D images Field of View:
16
(15x) (4x). = 0.27 mm or 270um
Parts of Microscope Specimen Size:
Field of View: .27mm
Ocular Lens, Body Tube, Revolving Nosepiece, Objective Lens, Arm, AaaaaaaField of Viewaaaaaaaaa Estimation: 2
Diaphragm/Iris, Stage, Stage Clips, Coarse Adjustment Knob, Fine Estimated Number of Specimens Specimen Size:
.27mm
Adjustment Knob Base, Light Source/Mirror 2. = .135mm
Calibrating Factor:
1. Body Tube- connects eyepiece and objective lens (Stage Micrometer) (10 microns) Stage Micrometer: 5
Ocular Micrometer: 4 )
2. Revolving Nosepiece- rotate one objective lens to another Ocular Micrometer Constant: 10um
Calibrating Factor:
3. Objective Lenses- vary in terms of magnification (5) (10um)
a. Scanner- magnify up to 4x 4 = 12.5um

b. Low Power- magnify up to 10x
c. High Power- magnify up to 40x Start: 10
End: 62
d. Oil Immersion- magnify up to 100x Actual Size: Actual Size:
4. Stage clips- holds the specimen (End — Start) (Calibrating Factor) (62-10) (12.5um)= 650um

5. Diaphragm/Iris- controls the light coming from the light source
6. Light source/Mirror- illuminator COMPOUNDS
7. Ocular Lens- where you look at that can magnify up to 10 time Inorganic Compounds (no carbon)
or 15 times Water, Salt, Acid and Bases
8. Arm- supports the upper portion and used in carrying
9. Stage- where you put the specimen 1. Water
10. Coarse Adjustment Knob- used for Scanner and Low Power - Two-thirds (60%) of body’s weight
11. Fine Adjustment Knob- used for High Power and Oil Immersion - Properties of Water
12. Base- support or the bottom of the microscope a. Polarity/ Solvent Properties
13. Condenser- focuses the light into the specimen that the user is o It is an excellent solvent
viewing Ø It is a polar liquid in body temperature
14. Collector Lens with Field Diaphragm- controls the light coming o Called as the “universal solvent”
from the condenser Ø Solvent- liquid or gas in which solid amounts
15. Rheostat Control Knob- adjust the amount of light emitted by can be dissolved
the light bulb Ø Solute- any dissolved substance
16. Condenser Control Knob- used to adjust the condenser’s vertical Ø Solution- particles are tiny
height Ø Suspension- particles are large
Ø Colloids- particles are of intermediate size
o Oil and Water (H2O)
Ø Only hydrogen bonds will form excluding the
water
b. High-heat Capacity
o It absorbs and release large amounts of heat
before its temperature changes
o It prevent sudden changes (metabolism and in the
environment) in body temperature
Ø Evaporation of sweat
o Normal body temperature: 37C or 98.6F
o It acts as a transport and exchange medium in the
body
c. Cushioning
o Forms a protective function
o If there is no water, it may cause more ruptures

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d. Biochemical Reactions Neutralization reaction- acids and bases interact
o Peptide bonds- protein pH Concentration
o Glycosilic linkage- carbohydrates • Measures the hydrogen ion concentration of a solution
o Dehydration Reaction (monomer to polymer) • Ranges from 0-14
Ø ATP is required a. Acid- Lower than 7
Ø Water removal: to give way for bonds b. Base- Higher than 7
Ø Bigger c. Neutral- Exactly 7 (10-7 moles per liter)
Ø Monomer 1 + Monomer 2= Dimer • Each successive change of 1 pH represents a tenfold change
o Hydrolysis Reaction (polymer to monomer) a. pH 3 to pH 7= (10 x 10 x 10 x 10)
Ø Release ATP: to break molecules • Normal blood pH- 7.35 to 7.45
Ø Needs water
Ø Simpler Buffer system
• Any substance that tends to minimize the changes in pH that
might occur when an aid or base is added to a solution
• Highly essential to maintain homeostasis that are usually
regulated by kidneys and lungs
• Carbonic acid- donates hydrogen when blood becomes too
alkaline
• Bicarbonate acid- accepts hydrogen when blood becomes too
acidic

Organic Compounds (with carbon)
Carbohydrates, Proteins, Lipids and Amino Acids

2. Salts Carbon
- Involves sodium, phosphorus, potassium and calcium • The backbone of amino acids, the building blocks of protein
- Dissociation: process when salt dissolves in body fluid and • Accounts 18% of body weight in humans
separate easily in their ions
• Forms four covalent bonds that are single or double bonds
- Electrolytes: electric current in solution that is mainly used
• It can build macromolecules
for buffer system
• Contains carbon except for carbon dioxide and carbon monoxide
- Salt is formed through ionic bonds
because organic molecules don't just contain carbon, they
- Water keeps the ions dissolved
contain hydrocarbons or carbon bonded to hydrogen.
- The slightly negative ends (O-) of polar water molecules are

attracted to positive ions (Na+), whereas the slightly positive
1. Carbohydrates (monosaccharide)
(H+) end of water are attracted to negative ions (Cl-)
- Immediate source of energy
- Important for:
- Contains carbon, hydrogen, and oxygen
a. Nerve impulses- sodium and potassium
- Excess carbohydrates turn into fats
b. Hemoglobin- iron
- 1-2-1 CHO ratio (generalized structure: CH2O)
- Too much:
- Electroneutral- shares neutrons, never gains or loses them
a. Fat- gall stones
- Types of Carbohydrates:
b. Calcium- calcium stones
a. Monosaccharide
3. Acids and Bases
o For cellular respiration
- Also considered as electrolytes
o Contains five or six carbon atoms arranged in
- Acids
either five or six membered ring
a. Give up or proton donors/naked protons
o Can be either an aldose or ketose
b. Hydrogen ions and anions are released
o Anions determines the acid’s effects on the
environment
c. Higher hydrogen concentration
d. Strong acids- ionize completely and liberate all their
protons; dissociate from original compound
o HI- hydoriodic acid
o HCl- hydrochloric acid (produced by the stomach) o Contains carbonyl group and hydroxyl group
o HBr- hydrobromic acid o Number of carbons- prefix + “ose”
o HNO3- nitric acid o It includes:
o HClO4- perchloric acid Ø Ribose- structure of nucleic acids
o H2SO4- sulfuric acid Ø Deoxyribose- structure of nucleic acids
e. Weak acids- ionize incompletely Ø Glucose- blood sugar (6 carbon rings)
o H2CO3- carbonic acid (carbonated drinks) Ø Fructose- fruits (5 carbon rings)
o C2H3O2- acetic acid (vinegar) Ø Galactose- dairy products (6 carbon rings)
f. Includes black coffee, orange, etc.
- Bases
a. Combine with or proton acceptors
b. Hydroxyl ions and cations are released
c. Lower hydrogen concentration (alkaline)
d. Strong bases
o LiOH- lithium hydroxide
o NaOH- sodium hydroxide
o KOH- potassium hydroxide b. Disaccharide
o Ca(OH)2- calcium hydroxide o Two monosaccharides joined by glycosidic linkage
o Sr(OH)2- strontium hydroxide o It includes:
o Ba(OH)2- barium hydroxide Ø Sucrose- glucose + fructose (cake sugar)
e. Weak bases Ø Lactose- glucose + galactose (nido)
o H2CO3- bicarbonate ion (important base in blood) Ø Maltose- glucose + glucose (milo)
f. Includes baking soda, detergents, drain cleaner, etc.
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b. Phospholipids
o Composed of 2 fatty acids and 1 glycerol
o Cell membrane structure
o Semi-permeable
Ø Hydrophilic- water-soluble, head, glycerol
Ø Hydrophobic- water-insoluble, tail, 2 fatty
acids
c. Steroids
o Composed of four carbon rings
o Lipids that contain cholesterol
o Common steroids:
Ø Cholesterol- basis of all body steroids
Ø Bile salts- breakdown product of cholesterol
released by the liver that is used for fat
digestion and absorption
c. Polysaccharides
Ø Vitamin D- produced in the skin on exposure
o Many sugars (polymers of monosaccharides)
to UV which is necessary for bone growth
o Because of their large size, they lack the
and function
sweetness of single and double sugars
Ø Sex hormones- estrogen and progesterone
o Used for:
(female) and testosterone (male)
Ø Storage
Ø Corticosteroids- a long-term anti-stress
v Starch (Plants)
hormone
§ Joined by 1-4 linkage
- Other lipid substances:
§ Structures known as plastids
a. Prostaglandins- derivatives of fatty acids in cell
§ Amylose- simplest form
membranes; functions in regulation of blood pressure,
§ Flour
uterine contractions and motility of gastrointestinal
v Glycogen (Animals)
tract
§ Liver
b. Glycolipids- determine the blood type and helps in cell
§ Muscle cells and fat cells
recognition
§ Systematic and cellular energy
c. Vitamin A- vision
source
d. Vitamin E- wound healing and contribute to fertility
Ø Structure
e. Vitamin K- necessary for proper clotting of blood
v Cellulose (Plants)
3. Proteins (amino acids)
§ Most abundant organic compound
- Contains carbon, oxygen and hydrogen
§ Major component of the tough
- Also contain nitrogen and sulfur
walls that enclose plant cells
- Comprised of 20%-30% cell mass
§ Includes fiber
- Produced in ribosomes
v Chitin (Animals)
- Forms peptide bonds during dehydration synthesis
§ Major constituent in exoskeleton
- Denaturation: unfolding of tertiary and quaternary
(arthropods)
structure that can cause them to be dysfunctional due to
2. Lipids (fatty acids and glycerol)
change in temperature and body pH
- Contains carbon, hydrogen and oxygen but less than in
- Generalized structure:
carbohydrates
a. NH2 (Amine group)
- Sometimes contains phosphorus
b. COOH (Acid group/Carboxylic group)
- Main source of energy
c. R group- makes the amino acid unique
- Insoluble in water

- Hydrpgenation- addition of hydrogen

- Types of Lipids

a. Triglycerides or Neutral fats

o Composed of 3 fatty acids and 1 glycerol

o Energy storage molecules

o Also known as fats and oils

o Stored in adipose tissue
- 20 amino acids are naturally occuring
o Makes up to 75% of the body fats
a. 9 amino acids- produced by the bofy
o Types of Fatty Acids:
b. 11 amino aids- we can get it from the proteins that we
Ø Saturated Fats (Fats)
eat
v Low-density lipoproteins
- Structures of Protein:
v Bad for the body
a. Primary
v Single bonds between carbons
o Amino acid sequence
v Solid at room temperature
o Stabilized by peptide bonds
v Long fatty acid chain
b. Secondary
v Trans fats such as margarine and baked
o Can be alpha-helix or beta-
products
pleated
Ø Unsaturated Fats (Oils)
o Stabilized by hydrogen bonds
v High-density lipoproteins
and peptide bonds
v Good for the body
c. Tertiary
v Double bonds between carbons
o Three-dimensional
v Liquid at room temperature
o Stabilized by hydrogen
v Short fatty acid chain
bonds, peptide bonds and
v Omega-3 fatty acids, olive oil
disulfide bonds

d. Quaternary

o Differs in numbers of

polypeptide chains
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GENERAL BIOLOGY
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- Types of Proteins DNA RNA
a. Fibrous Proteins (Structure) - Deoxyribonucleic Acid - Ribonucleic Acid
o Strand-like, water soluble and stable - Extra hydrogen bond - Extra hydroxyl bond
o Provides mechanical support and high tensile - Base Pairs - Base Pairs
strength a. A-T (2 hydrogen bonds) a. A-U (2 hydrogen bonds)
o It involves: b. G-C (3 hydrogen bonds) b. G-C (3 hydrogen bonds)
Ø Collagen- most abundant; bones, cartilage - Deoxy: no sugar - Ribose: sugar
Ø Keratin- hair, skin, nails - Ribose: sugar - Nitrogenous bases:
Ø Elastin - Nitrogenous bases: a. Purines (2 rings)- A and G
b. Globular Proteins (Functional) a. Purines (2 rings)- A and G b. Pyrimidines(1 ring)- U and C
o Compact, spherical, water soluble, sensible to the b. Pyrimidines(1 ring)- T and C - Single- stranded
environmental changes - Double- stranded - Helical structure
o Mainly functions in biological process - Double-helix structure - Involves in protein synthesis
o It involves: - Genetic blue print - Exists as:
Ø Hormones - Replicates itself exactly before a. mRNA- contains the codon
Ø Antibodies- immunity Acell divides (interphase) For for synthesis
Ø Actin and Myosin- movement of muscles; -aProvides instructions for b. tRNA- anti-codons
contractile aabuilding every protein in the c.rRNA- overlooks the
Ø Enzymes aabody aaatranslation
- Enzymes
a. Most are made up of proteins (tertiary and quaternary ATP (Adenosine Triphosphate)
strcutures) • Without ATP, molecules cannot be made or broken down
b. Acts as catalyst • It is consists of
c. Not permanently changed in the process - Adenine base
d. Usually ends with -ase - Ribose sugar
e. They weakened the bonds in order to lower the - Three phosphate groups
activation energy • Universal energy source
f. Induced Fit- change in shape • Chemical work- energy-absorbing chemical reaction
g. What affects the Enzyme Activity: • Transport work- gate across cell membranes
o Environmental Changes • Mechanical work- ADP to ATP; activates contractile proteins in
Ø Denaturation muscle cell to shorten mechanical work
Ø pH level • Sodium-Potassium Pump
Ø Ionic concentrations
- Sodium out
o Co-factors and Co-enzymes
- Potassium in
Ø Inorganic substances such as zinc, iron and

vitamins

o Enzyme Inhibitors

Ø Competitive Inhibitors: chemicals that

resemble an enzyme’s normal substrate and

compete with it for an active site

Non-competitive Inhibitors: inhibitors that

do not enter the active site but bind to

another part of the enzyme causing it to

change its shape










CENTRAL DOGMA OF LIFE

Chromosomes
• A molecule of DNA together with associated proteins

• Carries part or all of a cell’s genetic information



Discovery of DNA
4. Nucleic Acids (nucleotides)
• Rosalind Franklin
- Contains carbon, hydrogen, nitrogen, oxygen and
phosphorus - Discovered the basic structure of DNA by x-ray
- Largest molecule in the body crystallography and said that DNA is a double-helix
- Make up the genes structure
- Direct the growth and development by directing protein • James Watson and Francis Crick
structure - Built the first accurate model of DNA molecule
- It is composed of:
a. Nitrogen-containing base Replication (DNA to DNA)
o Adenine • Happens inside the nucleus
o Guanine • Semi-conservative- the old and new strand are complementary
o Cytosine • The two strands of DNA acts as a template for building a new
o Thymine strand in replication
o Uracil • Replication fork- when the double-helix unwind
b. Pentose sugar - Topoisomerase- relaxed DNA in super-coiling
c. Phosphate group - DNA Helicase- remove the hydrogen bonds
- Single-strand binding proteins- bind and stabilize single-
stranded DNA
- DNA Polymerase- assembles new strand of DNA in leading
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GENERAL BIOLOGY
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• Process:
- Helicase- unzipping or unwinding
- Primase- initiating; primers
- Polymerase- builds nucleotide (base pairing)
a. Leading strand- 5’ -> 3’
b. Lagging stand- 3’ -> 5’
o Formation of okazaki fragments
- Ligase- gluing

Transcription (DNA to RNA)
• The synthesis of RNA in the nucleus under the direction of DNA
• Produces mRNA (messenger)
• Process:
- Initiation
a. Promoter (Tata Box)
b. RNA Polymerase
o 3’ -> 5’
o Breaking of bonds
o T -> U
- Elongation (Pre-mRNA -> splicing -> Mature mRNA)
a. Pre-mRNA
o Coding region
Ø Exons
Ø Can produce amino acids
Ø 200-300 nucleotides
o Non-coding region
Ø Introns
Ø Cannot produce amino acids
Ø 1000 nucleotides
Ø Removed during spliicing
- Termination
a. Goes back to original structure

Translation (RNA to Protein)
• The synthesis of polypeptide chain (proteins) which occurs under
the direction of mRNA in the ribosomes
• mRNA is translated to codons (3 nucleotides)
• Start codon: AUG (Methionine)
• Stop codon: UGA, UAA, UAG
• Ribosomes
a. rRNA- large and small substrate
b. mRNA- codon
c. tRNA- anti-codon
• Process:
- Initiation (Aminoacyl Entrance Site)
a. Start codon
b. tRNA will initiate
c. mRNA will enter
- Elongation (Peptidyl Binding Site)
a. Anti-codons attach
b. Translation in the middle (mRNA to tRNA)
- Termination (Exit Site)
b. Stop codon

Checking for mistakes:
• DNA repair mechanism for damage DNA- any of several
processes by which enzymes repair DNA damage
• Proofreading by DNA Polymerase corrects the base-paring errors
• Mutation- a permanent change in DNA sequence; uncorrected
errors in DNA replication may become mutation