BIOTECH

 The science of using living organisms, or the products of living organisms, for human
benefit or to benefit human surroundings

HISTORY

 Classical biotechnology
o domestication of animals as livestock
o Microorganisms to make breads, cheeses, yogurts, beer and wine
 Selective breeding – organisms w/ desirable features are purposely mated to produce
offspring w/ same desirable characteristics
 Zebrafish mutant – lacked reflective pigment + lacked black pigment
 Antibiotic
o 1982 – Alexander Fleming – Penicillium inhibited the growth of Staphylococcus
aureus; Penicillin G(parenterally) and Penicillin V(oral)
o 1940 – penicillin was available to treat bacterial infections
o 1950-1960 – batch large-scale processes
o 1960 – gene cloning; genetic engineering; recombinant DNA technology
o 1990 – human genome project
 Pharmaceutical production – Genentech by Eli Lily

PRODUCTS OF MODERN BIOTECH

 Recombinant proteins – proteins that are produced by gene-cloning techniques

 Cloning – growing large number of genetically identical cells from a single cell
 Cell culture – cells are grown in dishes or flasks within liquid culture media designed to
provide the nutrients necessary for cell growth
 Fermenters or bioreactors – mass produce cells containing the DNA of interest

TYPES

 MICROBIAL BIOTECH
o Use of yeast for beer and wine making
o Created better enzymes and organisms for making many foods, simplifying
manufacturing and production processes and treatment of industrial wastes
o Make vaccines, produce recombinant proteins and diagnostics purposes
 AGRICULTURAL BIOTECH
o Genetically engineered, pest resistant plants
o Solutions for today’s farmers in the form of plants that are more environmentally
friendly while yielding more per acre
o Removal of tumor-causing gene in Ti plasmid (causes crown gall-disease
characterized by large bulbous tumors in tomatoes, tobacco, and soybean)
o Climate change-ready rice
 ANIMAL BIOTECH
o Bioreactors to produce important products, e.g. antibodies
 oGene knockout experiments (used in basic research as model organisms, e.g.
mice)
o Animal cloning
 FORENSIC BIOTECH
o Dna fingerprinting – collection of methods for detecting an organism’s unique
DNA pattern
 BIOREMEDIATION
o To process and degrade a variety of natural synthetic substances
o Stimulated the growth of oil-degrading bacteria to clean up the oil spills in Africa
 AQUATIC BIOTECH
o Aquaculture – raising finfish or shellfish in controlled conditions for use as food
sources
 MEDICAL BIOTECH
o Gene therapy – genetic disease conditions can be treated by inserting normal
genes into a patient or replacing diseased genes with normal genes
o Stem cell technology – used for immature cells that have potential to develop and
specialize into nerve cells, blood cells, muscle cells, and virtually any other type
of cell in the body

BIOMOLECULES

Life is characterized by:

 Biological diversity
 Chemical unity – obey the rules of physical and organic chemistry; common biological
reactions occur inside living systems

LIFE’S UNITY

 Organization
 Reproduction
 Growth and development
 Metabolism
 Irritability and responsiveness
 Movement
 Adaptation

CHARACTERISTICS AND MANIFESTATION OF LIFE

 ORGANIZATION
o Atom, molecule, cell, organ, organ system, organisms, population, community,
ecosystem, biosphere
 REPRODUCTION – parents produce offspring
 GROWTH AND DEVELOPMENT
o Growth – increase in cell number, size, and volume in multi-celled species
o Development – first cell of a new individual becomes a multi celled adult
  TRANSFER AND TRANSFORMATION OF ENERGY AND MATTER;
 ACQUIRE MATERIALS AND ENERGY
o Metabolism – sum of all biochemical processes in a cell
 SENSE AND RESPONSE TO CHANGE
o Receptor – molecule that responds to a specific form of stimulation
o Thigmotropism – directional growth in response to touch
o Homeostasis – keeps its internal conditions within tolerable changes
 Temperature
 Moisture level
 Acidity
 Physiological factors
 MOVEMENT
o Cilia – back and forth
o Flagella – undulating or snakelike motion
 ADAPTATION

COMPOSITION OF LIVING MATTER

 30 or naturally occurring chemical elements (92) are essential to living systems

 Composed mostly of LIGHTER ELEMENTS
 4 most abundant – CHON 99%

BIOMOLECULES

 Non-carbon containing substances

o Water (~70%); - influences the shape and function of biomolecules; acts as
reaction medium of most biochemical processes
o ions; small molecules
 Carbon containing substances (bioorganic)
o Proteins; carbohydrates; lipids; nucleic acids

CARBOHYDRATES

 Most abundant organic molecule in the biosphere (protein most abundant in living)
 FUNCTIONS:
o Storehouses of chemical energy
o Supportive structural components
o Essential components of genetic materials
o Ligands and receptors in chemical communication
 CLASSES:
o Monosaccharides (simple) (3-7C)
 Aldoses (carbonyl carbon = 1)
 Glyceraldehyde
o Erythrose and threose
o Ribose, arabinose, xylose, lyxose
 o Allose, altrose, glucose, mannose, gulose, idose,
galactose, talose
 Ketoses (carbonyl carbon = 2)
 Dihydroxyacetone
 Erythrulose
 Ribulose, xylulose
 Psicose, fructose, sorbose, tagatose
 Cyclization = reversible = preferred in aqueous sol’n
o Dissacharides; (fructose, sucrose, glucose, maltose, galactose, lactose)
 Reducing – free anomeric carbon (carbonyl carbon)
 Lactose = beta 1,4 galactopyranose + glucopyranose
 Maltose = alpha 1,4 glucopyranose glucopyranose
 Non-reducing
 Sucrose = alpha 1 glucose, beta 2 fructose
o Oligosaccharides
 Melezitose - honey
 Dextrantriose – sake and honeydew
o Polysaccharides
 Homopolymer
 Cellulose – beta 1-4 glycosidic bonds; can’t be digested by
humans (lack of cellulose); dietary fiber, hydrophilic bulking agent
for feces
 Starch
o Amylose (10-20%) = linear (12-13 units then branching)
o Amylopectin (80-90%) = branched polymer
 Glycogen = higher degree of branching; energy storage in animal
cells
 Heteropolymer
 Chitin
 Hyaluronic acid = imparts high viscosity; lubricant and shock
absorbers in joint tissues and eyes
 Carrageenan
o Hydrocolloid from red algae; gelling properties

LIPIDS

 Insoluble in water; soluble in polar solvents; yields large amounts of energy

 BIOLOGICAL FUNCTIONS
o Store chemical energy
o Insulate vital organs
o Components of cell membranes
o Chemical messengers (hormones)
o Covering of nerve fibers
 CLASSIFICATIONS
o Saponifiable lipids – contains fatty acids; produces fatty acid salts upon base
hydrolysis
 Triacylglycerols/triglycerides
 has glycerol as backbone w/ 3 fatty acids; neutral fat; esters of
glycerol and fatty acids
 main storage form of fatty acids in cells
 FATTY ACIDS – saturated (fats) and unsaturated (oils)
o Monocarboxylic acids that contain long unbranched
hydrocarbon chains
o 12-26 carbon atoms in length; (saturated,
monounsaturated, polyunsaturated)
o Essential FA: polyunsaturated
 FA that mammals cannot synthesize
 Linoleic (omega 6), gamma linolenic,
Eicosapentaenoic acid, docosahexanoic acid
 Essential in normal visual and central nervous
system development
o Modified FA: lactobacillic acid, tuberculostearic acid; (from
bacteria)
 Phospholipids- glycerophospholipids, sphingolipids, glycolipids
 Glycerophospholipids
o Common constituent of cellular membranes
o Triesters of Glycerol(backbone) wherein: 2 FA, and
phosphate group
o Has polar head (in phosphate group) and non polar tail
(hydrocarbon chain in FA)
 Sphingolipids
o Derivatives of lipid sphingosine (18C alcohol); has amino
group, CH2(CH2)12CH(triplebond)CHCHOHCHCH2
o Found in plasma membranes, e.g. sphingomyelin
o Highest concentration in cells of central nervous sytem
o Amino group usually forms an amide bond between a FA
o OH group carbon 1 attached to a group via ester linkage
o FA – (amide linkage second to last carbon) – sphingosine
– (phosphoester bond on last carbon) – phosphate group –
polar group (attached to O of the phosphate)
 Glycolipids
o Contain monosaccharide bonded to the OH of sphingosine
by a glycosidic bond
o Monosaccharide (Glc/Gal) or oligosaccharide (up to 7
monosacch.) – glycosidic linkage (last C) – sphingosine –
amide linkage(2nd to last C) – FA
o Cerebroside – nerve cell membrane
 Contain only 1 monosacch., galactocerebroside
 o Gangliosides – cell surface markers
 Contain 2 or more monosacch.
 GM3 – ABO blood types; GM2 and GM1 – neural
membranes
 Waxes
 Esters of long chain alcohols with long chain fatty acids
o Non-saponifiable lipids
 Steroids
 Contain steroid nucleus (4 fused rings, 3 cyclohexane, 1
cyclopentane)
 Cholesterol
o Most abundant steroid in the body
o Important constituent of cell membranes
o Synthesized in liver and obtained from foods
o Inserts into bilayer membranes
o Hydroxyl group oriented toward the aqueous phase (w/
phospholipid)
o Hydrophobic ring system adjacent to FA chains of
phospholipids
 Bile salts
o Synthesized from cholesterol and released by the
gallbladder
o Emulsify fats and oils to give greater surface area for lipid
digesting enzyme
 Hormones
o Produced from cholesterol
 Sex hormones: Androgens – testosterone;
Estrogens – estradiol
o Adrenal corticosteroids – adrenal glands in the kidneys
o Anabolic steroids – derivatives of testosterone
o Progestins – progesterone; control of menstrual cycle and
pregnancy
o Glucocorticoids – cortisols; control of carbohydrate,
protein, and lipid metabolism
o Mineralocorticoids – aldosterone; regulate salt balances in
tissues
 Vitamins
 Eicosanoids
 Signaling molecules derived from C20 Essential FA
 Messengers in the central nervous system
 Prostaglandins – intensifies pain, enhancing inflammation reponse
 Thromboxane – promotes formation of blood clot
 Leukotrienes – inflammatory and hypersensitivity reponse
 Terpenes (5C)
  hydrocarbon derivaties constructed from recurring isoprene units
 produces scents and tastes of plant products

PROTEINS 1

 hairs and nails – alpha-keratin

 muscle – actin and myosin  enable body movement
 blood – hemoglobin
 enzyme – saliva, small intestines, stomach  helps digest food
 major constituent of most cells
 very diverse molecules
 defines what an organism is, what it looks like, how it behaves (responsible for most
phenotype) phenotype  genotype  protein  peptides  amino acids
 made up of 20 standard amino acids
 BASIC AMINO ACID STRUCTURE
o Central carbon
 Alpha carbon
 Tetrahedral geometry
 Surrounded by 4 different groups (except glycerine)
 Chiral (except glycerine)
 Enantiomers exist
 Only L-enantiomers occur naturally (NH2 is LEFT)
 D-enantiomers – found in antibiotics and bacterial cell walls
 D and L does not indicate the direction in which the molecule rotate plane
polarized light
o Carboxylic group
o Amino group – left for L configuration
o R group
 AMINO ACID CLASSIFICATIONS
o Alkyl/ Aliphatic (nonpolar)
 Glycine, Gly, G
 ALANINE, Ala, A
 Leucine, Leu, L
 Isoleucine, Ile, I – 2 chiral carbons
 Proline, Pro, P
 Valine, Val, V
o Sulfur-containing
 Methionine, Met, M
 Cysteine, Cys, C – sulfur in form of sulfhydryl, important in disulfide
linkages
o Acids – contains carboxyl groups (weaker acids than alpha-carboxyl group);
negatively charged at physiological pH (-ate, not –ic acids)
 Aspartate, Asp, D, Aspartic Acid, asparDate
  Glutamate, Glu, E, Glutamic Acid, glutEmate
o Base – hydrophilic nitrogenous bases; positively charged at physiological pH
 Histidine, His, H – imidazole ring protonated/ionized
 Lysine, Lys, K – diamino acid, protonated at pH 7
 Arginine, Arg, R – guanidinium ion always protonated; most BASIC amino
acid
o Aromatics – very hydrophobic, contain aromatic group, absorb UV at 280 nm
 Phenylalanine, Phe, F
 Tyrosine, Tyr, Y – OH ionizable
 Tryptophan, Trp, W – bicyclic indole ring
o Alcohols – polar side groups, hydrophilic, can for H-bond
 Serine, Ser, S – looks like Ala w/ -OH
 Threonine, Thr, T – 2 chiral carbons
o Amides – polar side groups, hydrophilic, can form H-bond
 Asparginine, Asn, N – amide of D (aspartate)
 Glutamine, Gln, Q – amide of E (glutamate)
 PROTONIC EQUILIBRIA OF AMINO ACIDS
o Exhibit acid-base properties due to their alpha-COO and alpha-NH2 groups
o Additional acidic/basic group may be present in the side chain
o pKas of amino acids are known; alpha-COO pKa~2; alpha-NH3+~9
o have characteristic titration curves
 AMINO ACIDS AS BUFFERS
o When pH=pKa  amino acids act as a buffer
o When pH=pKa1  equal amounts of form 1 and 2 exists and so on…
o Isoelectric point (IpH)  Zwitterion exists; neutral charge; glycine exists
predominantly in dipolar form
 IpH = average of pKa  wherein Zwitterion is in between
 Proteinogenic amino acids
o Amino acids that are included in the genetic code and incorporated into proteins
o ESSENTIAL AAs – proteinogenic AAs that cannot be synthesized by humans
and have to be supplied from the diet
 HILL VTMRFY
 PVT MAT HILL
 Non-proteinogenic amino acids
o Result of enzymatic modifications (ex: post translational modification)
o Synthesized from alpha-amino acids by decarboxylation (biogenic amines)
o Rare amino acids
 Ornithine, citrulline
 L_dopamine
 Seleno-cysteine

PEPTIDES

 Formed by condensation reaction of amino acids with the removal of water

 Polymers of amino acids (linked by peptide bonds)
 Most are linear, some are cyclic
 OLIGOPEPTIDES  <15 amino acids (residue)
 POLYPEPTIDES  15-50 residue
 PROTEIN  >100 amino acids (usually composed of 1 or more polypeptides)
 MONOMERIC PROTEINS  only one peptide chain
 MULTIMERIC PROTEINS  more than one polypeptide chain
 HOMOMULTIMERIC  only one kind of polypeptide
 HETEROMULTIMERIC  several different kinds of polypeptide chains
 MOIETY or RESIDUE  each amino acid in a peptide
 N-TERMINAL RESIDUE  free alpha-amino group
 C-TERMINAL RESIDUE  free alpha-carboxyl group
 NAMING
o Replace suffic w/ -yl
 ACIDITY AND BASICITY of PEPTIDES
o All alpha-NH2 and alpha-COOH involved in peptide bonds are no longer
acidic/basic
o Ionizable groups
 N and C terminals
 Acidic/basic R groups
 PEPTIDE BOND
 Peptide bond (C-N) length = 0.133 nm
 C-N bond = 0.145 nm (non peptide bond; not carbonyl carbon, but central carbon)
 C=O = 0.123nm
 Lack of rotation around a bond
 Partial double bond character
 Rigid and planar
 Partial (40%) double bond character due to resonance structure
 Due to resonance structure: cis and trans
 Stable  peptide bond is not chemically reactive; cannot be easily cleaved
 Peptide bond retained during chemical reactions (except harsh conditions, i.e, acid or
base hydrolysis)
 ASPARTAME – dipeptide aspartylphenylalanyl methyl ester  NutraSweet
 VASOPRESSIN – nanopeptide; prevents urination at night
 Polypeptide chain – linear polymer of amino acids
PROTEINS 2

 Made up of one or more polypeptides folding in specific conformations

 CLASSIFICATIONS
o According to composition
 Simple proteins
 Consist of polypeptide chains
 Albumins, globulins, glutelins, albuminoids, prolamins
 Conjugated proteins
 Simple proteins + non-protein substances
 Nucleoproteins = nucleic acid + protein
 Glycoproteins = carbohydrate + protein
 Lipoproteins = lipid + protein
 Phosphoproteins = phosphate groups + protein
 Hemoproteins = heme + protein
 Flavoproteins = flavin nucleotide + protein
 Metalloproteins = metal ion +protein
o According to function
 Enzymes – catalyze biological reactions
 Transport proteins – bind and carry specific molecules/ions from one
organ to another
 Nutrient and storage proteins – mobilized by the organisms to derive
building blocks or energy
 Contractile or motile proteins – allows cells & microorganisms to contract,
change shape or move about
 Structural proteins – supporting filament, cables or sheets for strength
protection of biological structures
 Defense proteins – defend organisms against invasion by foreign
substances
 Regulatory proteins – regulate cellular or physical activities
 Scaffold proteins – proteins that bind to other proteins, causing them to
associate with other structures in the cell; e.g. kinase anchoring protein
 Exotic proteins – EXOTIC;
 Monellin  protein from African plant with a very sweet taste
 Resilin  protein with exceptional elastic properties found in
hinges in insect wings
o According to solubility
o According to shape
 Globular
 polypeptide chain coiled into compact spherical shape
 soluble in water
 mobile within cells
 amylase, hemoglobin
  fibrous
 polypeptide chains arranged side by side in long filaments
 mechanically strong
 water insoluble
 structural and protective functions; e.g. collagen
 STRUCTURE AND FUNCTION
o function depends on structure
o all proteins have at least 3 levels of organization
 Primary structure
o Amino acid sequence
o Lineaer order of amino acids from N-terminus to the C-terminus
o Dictates the structure and function of the proteins
 Secondary structure
o Regular repetitive conformation along short sections of the polypeptide
o Formed by H-bonding between carbonyl group of one peptide bond and the
amino group of another
o Alpha-helix
 Right handed helix with 3.6 aa/turn ~4
 Stabilized by H-bonding (parallel to backbone)
 Side chain groups point outwards from the helix
 AA with bulky side chains are less common
 Glycine and proline destabilize the alpha helix
 Destabilized by: charged R-group, branched R-group,
o Beta-pleated sheet
 Repeating units of AA w/ small compact R groups
 Stabilized by H-bonds between peptide chains (portions of 1 more
polypeptide)(perpendicular to backbone)
 Parallel and anti parallel
 Beta turns  often connects successive strands of anti-parallel beta-
sheets; gives flexibility
 Loops  do not have regular periodic structures, gives flexibility
 Tertiary structure
o 3D structure
o INTERACTIONS:
 Disulfide bonds (cysteine)
 Hydrogen bonds (C=O and NH or peptide backbone)
 Hydrophobic interactions
 Ionic/electrostatic interactions (acidic and basic)
o Myoglobin  O2 binding protein in muscles
o FIBROUS
 Polypeptide chains arranged in long strands or sheets
 Provides support, shape, external protection
 Mechanically strong and resistant to solubilization
 Alpha-keratin, collagen, silk fibroin
 o GLOBULAR
 Contains substantial amounts of alpha-helices and beta-sheets
 Includes enzymes, transport proteins, motor proteins, regulatory proteins;
e.g. myoglobin bovine ribonuclease A, lysozyme

o STRUCTURAL MOTIFS
 Stable arrangement of several secondary structures and the connections
between them (NOT TERTIARY STRUCTURE!!) (SUPERSECONDARY)
 Indicative of a particular 3D architecture and associated w/ specific
function
 Leucine zipper, zinc finger, helix-turn-helix
 Quaternary structure
o FOR MULTIMERIC ONLY
o Describes the organization of subunits in a protein w/ multiple units (oligomeric
protein)
o Homo-multimers or hetero-multimers
o Subunits are held together by non-covalent interactions
o Oligomeric protein is more stable than disassociated subunits  made up of 4
polypeptide chains and a heme group
o Active site often made up of AA residues from different subunits
o Often affected by ligand(substrate or inhibitor) binding
 PROTEIN FOLDING
o Process wherein a protein assumes it proper conformation
 Determines how it works
 Function of a protein depends on its ability to recognize and bind to other
molecule
o Can be spontaneous or can occur with the aid of molecular chaperones
o Molecular chaperones  proteins that interact with partially folded or improperly
folded polypeptides, facilitating correct folding pathways or providing
microenvironments in which folding can occur
 Hsp70  first class of chaperones
 Binds to regions of unfolded polypeptides that are rich in
hydrophobic residues, preventing inappropriate aggregation
  Block the folding of certain proteins that must remain unfolded
until they have been translocated across the membrane
o In an aqueous environment
 Hydrophobic side chains are buried
 Polar and charged side chains on the surface
o Chaperones assist in protein folding; they segregate protein from ‘bad influences’
in the cell
 PROTEIN MISFOLDING
o Prion Protein (PrP)  proteinacious infectious only protein
 Causative agent of Creutzfeldt-Jakob disease in humans, scrapie in
sheep, and bovine spongiform encephalopathy in cattle (mad cow
disease)
 PROTEIN DENATURATION
o Destruction of protein’s proper conformation
o Disruption of forces that stabilize the secondary, tertiary, and quaternary
structures; retains the primary structure or the polypeptide chain
o Denatured proteins are often insoluble
o Denaturing agents
 Strong acids and bases
 Heavy metal cations
 Inorganic salts
 Organic solvents
 High temperature
 Detergents
 Alkaloidal reagents
o TYPES
 IIREVERSIBLE
 REVERSIBLE

NUCLEIC ACIDS

 Chemical carriers of genetic information

 Biopolymers made up of nucleotides linked by PHOSPHODIESTER LINKAGES
 2 FORMS: DNA (2-deoxyribonucleic acid) and RNA (ribonucleic acid)
 FUNCTIONS
o As repeating units/ precursor of genetic material
o In energy metabolism (ATP, GT)
o Components of coenzymes and reductants (NAD+, FAD, etc)
o Carriers of activated molecules (UDP-glucose)
 NUCLEOSIDE (w/o phosphate group); NUCLEOTIDE (w/ phosphate group)
 STRUCTURE (COMPOSITION)
o Aldopentose sugar  RIBOSE OR DEOXYRIBOSE
o Phosphate group
 o Heterocyclic base (amine)
 Purine  adenosine & guanine
 Pyrimidine  thymine, cytosine, uracil
 Flat, basic, aromatic rings, conjugated double bonds, capable of H-
bonding
o DNA  AGCT
 Deoxyadenosine
 Deoxyguanosine
 Deoxycytidine
 deoxythymidine
o RNA  AGCU
 Adenosine, guanosine, cytidine, uridine
o Phosphodiester linkage and beta-N-glycosidic bond
 DNA primary structure
o Genetic material
o Stores biological information that governs cellular activites
o Polymer of four nucleotides
o ALTERNATING SUGAR-PHOSPHATE GROUPS FROM BACKBONE
 Nucleotideds oriented in the same direction
 3rd carbon sugar 1 and to 5th carbon of sugar 2
o BASES
 Attached to carbon 1 of sugar
 Order is important
 Determines the genetic information of the molecule
 Conventionally on top of the sugar
 DNA secondary structure
o Composed of 2 strands held together by H-bonding between bases
o A&T  two hydrogen bonds  weaker  where replication starts
o C&G  three hydrogen bonds  higher melting point and energy need to
denature
o Antiparallel  one strand with 5’ to 3’- direction and the other with 3’ to 5’-
direction
o complementary
o double helical structure
 outer
 sugar P-backbone
 P groups are charged
 Very polar
 Protects the inner portion from hydroxides?
 Stability
 inner
 N-bases stacked on top of one another
 Maximizes hydrophobic interactions
 Stabilizes DNA
  DNA tertiary structure
o Chromatin  consist of fibers containing proteins and DNA in approximately
equal proportions (by mass) along with a small amount of RNA
o Chromosome  Chromatin  nucleosomes
 HISTONES  proteins in which the DNA in the chromatin is very tightly associated

LIVING CELL
HISTORY

 Anton van Leeuwenhoek

o Observed living cells and animalcules
o Looked at blood, rainwater, scrapings from teeth through a simple microscope
lens
 Hans and Zacharias Janssen
o First compound microscope
 Robert Hooke
o Thin slice of cork (oak cork) through compound microscope
o Observed tiny, hollow, roomlike structures
o Only saw the outer walls (Cell walls) because cork cells are not alive
 Matthias Schleiden
o View plant parts under a microscope
o Discovered that plant parts are made up of cells
 Theodor Schwann
o Animal parts are made up of cells
 Rudolph Virchow
o All living celles only come from other living cells

THE CELL

 Structural and functional units of all living organisms

 1665 by Robert Hooke plant tissues were divided into tiny compartments called
cellulae (cells)
 1840 by Theodor Schwann --? All organisms exist as either single cells or aggregate of
cells

LIFE’S THREE DOMAINS

 DOMAIN BACTERIA (EUBACTERIA)  prokaryotes  nucleoid region  fatty acids

 DOMAIN ARCHAEA (ARCHAEABACTERIA)  prokaryotes  nucleoid region 
nonfatty acid lipids
 DOMAIN EUKARYA  eukaryotes  nucleus  fatty acid

PROKARYOTES
  Primitive, simple, versatile, ubiquitous, unicellular form
 Easily cultured in lab
 Spherical (cocci), Rod-shaped (bacilli), spiral
 ARCHAEA (ARCHAEABACTERIA)  extremophiles  can live in harsh environments
o Acidophiles  sulfolobus acidocaldaries; pH<5; sulfur springs
o Alkalophiles  natranobacterium gregoryi; pH>9; soda lakes
o Halophiles  Halferax volcanii; salt loving, Dead Sea and Great Salt Lake
o Methanogens  Methanococcus; converts CO2 (+ H2) to CH4
o Psychrophiles  Polaromonas vacuolata  cld loving; Antarctic ice and seas
o Thermophiles  heat loving; acid hot springs, deep ocean geysers
 BACTERIA (EUBACTERIA)
o Pathogenic and may cause disease
 Bacillus antracis = anthrax
 Clostridium botulinum = botulism
 Staphylococcus aureus = sepsis, endocarditis, nosocomial(hospital-
borne) infections
 Salmonella = food poisoning & typhoid; raw eggs
o Antibiotics
 Streptomyces = streptomycin (1943); tetracycline, erythromycin
 Bacillus = bacitracin, polyxyxin
 Penicillium = staphylococcus
 Lysozyme  enzyme in human tears capable of destroying bacteria
 Inhibiting the growth of harmless bacteria
o CYANOBACTERIA  photosynthetic eubacteria; blue-green algae

EUKARYOTES

 Protists  single celled eukaryotes

 Fungi
 Plants
 Animals

PROKARYOTES EUKARYOTES
Almost all small unicellular organisms Both unicellular and multicellular
10^-6 m Much larger in size (2000:1)
Nucleoid region nucleus
Metabolic functions are organized in simpler Greater specialization and complexity in
fashion structure and functioning
Spatially closely related Structured into compartments
(COMPARTMENTALIZATION)
Membrane bound organelles
DNA is ring-shaped Very long linear DNA
No introns (genetic info) Has introns (genetic info)
Genetic info in cytoplasm Genetic info in nucleus
FEATURES OF PROKARYOTIC CELL

 Single membrane (cell membrane)

 Nuclear area (nucleoid region)
 Cell wall (only for prokaryotes and plants)
 Ribosomes  for protein synthesis
 Storage granules
 Cytosols  aqueous portion of cytoplasm; water soluble
 Lacks cytoskeleton
 Surface of cell may carry pili (cell adhesion) and flagella (movemement and motility;
microtubules)

Part Function
Fimbriae/pili Attachment structures on the surface of some proakryotes
Nucleoid Region where DNA of cell is located
Plasmid Extrachromosomal piece of circular DNA
Ribosome Complexes that synthesize protein
Plasma membrane (cell Enclosing cytoplasm
membrane)
Cell wall Rigid structure outside plasma membrane
Capsule Jellylike outer coating of many prokaryotes
Flagella Locomotory organelle

Cilia

 Hair-like projections that functions for movement

 9+2 pattern of microtubules (eukaryotic)
 Move when the microtubule doublets slide past one another
 Back and forth motion

Flagella  undulating or snakelike motion

FEATURES OF EUKARYOTIC CELL

 Subdivided by membranes  membrane bound organelles; compartmentalization

 Enclosed by a plasma membrane  a phospholipid bilayer with proteins that
separates the cell from the surrounding environment and functions as a selective barrier
for the import and export of materials; semi-permeable cell membrane

PARTS OF A EUKARYOTIC CELL

 CYTOPLASM  large space containing numerous components in solution

 ORGANELLES  well defined compartments inside the cell; dedicated to important
cellular task; this allows for separate incompatible chemical and physical conditions
(simultaneous reactions done inside the cell)  ADVANTAGE OF
COMPARTMENTALIZATION
 Cytosol  water solution (salts and organic molecules) where organelles are suspended
 Nucleus  largest organelle; contains the genetic material of the cell; site of DNA and
RNA biosynthesis; located at the center typically
 Endoplasmic reticulum and ribosomes (has large and small subunit)  closed network
of shallow sacs and tubules linked with the outer membrane of the nucleus; processes
and transports proteins
o ROUGH ER  transport to golgi apparatus
o SMOOTH ER  lipid synthesis; hydrolysis and folding
 Golgi complex  resembles a bundle of layered slices; sorts and transports molecules
for export; sorts waste and transports them; packaging
 Endosomes and exosomes  bubble-shaped compartments that are involved in the
exchange of substances between the cell and its surroundings
 Mitochondria  double membrane-bound organelle
o Site for cellular respiration
o Produces ATP
o Interspace (space between inner and outer membrane)
 Lysosome  small globular organelle; contains hydrolytic digestive enzymes for
intracellular digestion
o Waste can be used to form another cell
o Eto ba yung suicidal part of the cell? Phagosome??
o PHAGOCYTOSIS  digesting food
o AUTOPHAGY  breaking down damaged organelles due to hydrolytic enzyme
pa rin
 Peroxisome  smaller than lysosome; contain oxidative enzymes and destroy
peroxides; fights free radicals
 Cytoskeleton  framework of proteins; determines the shape of cells and gives its ability
to move
o Microfilaments (actin filaments; 2 strands of actin; muscle contraction;
cytoplasmic streaming)  intermediate filaments (fibrous and supercoiled;
anchorage of nucleus and certain other organelles; formation of nuclear lamina)
 microtubules (hollow tubes, walls consist of tubulin molecules; maintenance of
cell shape; cell motility)
 Cell wall  found in plants only (for eukaryotes); composed of polysaccharides and
proteins; rigid support structure surrounding plant cells that provide protection against
osmotic or mechanical rupture
 Chloroplast or Plastids  where photosynthesis takes places; chlorophyll, Light reaction
and calvin cycle (in stroma)
 Vacuoles  membrane bound found in the cytoplasm; serves as reservoir for food and
waste products
 ANIMAL CELLS PLANT CELLS
LYSOSOMES CHLOROPLASTS
CENTRIOLES  CENTRAL VACUOLE AND TONOPLAST
cell division; formation of cilia, flagella CELLWALL  carbohydrates
FLAGELLA PLASMA MEMBRANE  lipids and proteins
 Centrioles  composed mainly of proteins called tubulin; 9 + 0 pattern of
microtubules triplets
o Help cell division in animals
o Help form centrosome, cilia and flagella

UNIVERSAL FEATURES OF CELL

 NUCLEUS OR NUCLEOID REGION

 PLASMA MEMBRANE
 CYTOPLASM
MITOSIS
 cell division
 to grow and develop
 to repair tissues
 to regenerate lost body parts (e.g. liver)
 some organism reproduce asexually via mitosis
 GOAL: to distribute a complete set of genetic instructions to two daughter cells (one
copy of each chromosome)
 30 days  life of RBC

Apoptosis  programmed cell death; carves out distinctive structures

Binary Fission  for bacteria and archaea;

 Parent cell contains one chromosome

 DNA replicates and attaches to cell membrane
 Membrane growth between two attachments points moves the
DNA molecules apart as new cell wall material is deposited
 RESULT: two daughter cells, each identical to the original

Identical DNA  the cell must first replicate its genome

PHASES of the CELL CYCLE

 INTERPHASE  normal cell activity

i. the cell grows during all three phases, but chromosomes are duplicated
only during S phase
o G1 (1 gap)  primary growth phase; preparation for DNA synthesis and cell
st

growth
o S  synthesis; DNA replicated
o G2 (2nd gap)  secondary growth phase; preparation for mitosis and cell growth
 MITOTIC PHASE  cell division; M Phase
o Includes mitosis (nuclear division) and cytokinesis (division of cytoplasm)
o Daughter chromosomes are distributed by the mitotic spindle to two daughter
nuclei
o When division of cytoplasm is complete, two daughter cells are present
o CONTINUOUS PROCESS; NO CLEAR BEGINNING OR END TO EACH
PHASE
o PROPHASE
i. Chromatin (loose complex of DNA and protein molecules in the nucleus)
becomes more condensed  CHROMOSOME (condensed form of
chromatin)
ii. Breakdown of nuclear membrane
iii. TWO Centrosomes (in animals; microtubules organizing centers) begin
to move apart; forms a mitotic spindle
 iv. Microtubules begin to grow from each microtubule organizing center
extending toward the opposite pole
o METAPHASE
i. Spindle fibers attached on to the kinetochore pull the chromosome
toward the microtubule-organizing center
ii. Tug-of-war between the opposing forces drives the chromosomes into the
middle of the cell lining up on a plane (METAPHASE PLATE) equidistant
from each microtubule organizing center
iii. Period when chromosomes are aligned
iv. DOESN’T LAST LONG; AS SOON AS CHROMOSOMES ARE IN
POSITION, ANAPHASE BEGINS
o ANAPHASE
i. COHESIN  protein that keeps the sister chromatids tightly paired until
anaphase
ii. Cohesin breaks down at the start of anaphase and the sister chromatids
separate
iii. Microtubules attached to each kinetochore are exerting force and the
separated sister chromatids are quickly dragged toward opposite poles of
the cell  responsible for the V-shaped appearance of the chromatids
(considered as chromosome) as they move to the ends of the cell
iv. Microtubules  highly dynamic structures: they can lengthen as
individual tubulin proteins are added to one or both ends, and they can
shorten as tubulin proteins are shed from one or both ends
Animal Cells Plant cells
some microtubules that run from Don’t change their overall shape
pole to pole during anaphase due to rigid cell wall surrounding
makes the cell more elongated the plant cells
o TELOPHASE
i. Two sets of chromosome approach the cell poles and events of prophase
occur in reverse
ii. Spindle fibers disintegrate (mitotic spindle)?
iii. Nuclear envelopes (nuclear membrane) form around the separated
chromosomes
iv. Chromosomes begin to uncoil into masses of chromatin
v. Nucleolus reappear
vi. Two identical daughter nucleic form
o CYTOKINESIS
i. Contractile ring in the equatorial region  constricts the cell membrane
and forms a cleavage furrow (indentation of the cell’s surface ; pinching
of cells)
ii. not complete until cytoplasm divides
iii. typically begins during anaphase or telophase
iv. IN ANIMAL CELLS  a ring of microfilaments (thin strands of actin
protein that help determine cell shape) contracts around the center of the
 dividing cell; the microfilament ring pinches the cell roughly in half,
forming a cleavage furrow
v. Each daughter cell receives a portion of the parent cell’s plasma
membrane and cytoplasm (which contains organelles, e.g. mitochondria,
ER, lysosome, etc.)
vi. IN PLANT CELLS  can’t pinch in half because of rigid cell wall; CELL
PLATE forms midway between 2 daughter nuclei;
vii. Vesicles in cytoplasm deliver cell wall material to the cell plate which
becomes the new cell wall between the daughter cells; also supplies the
lipids that form a plasma membrane on each side of the cell plate
enclosing each daughter cell
 G0 phase  cells exist in a quiescent stage (resting period, period of inactivity); cells are
neither dividing nor preparing to divide