BIOLOGICAL

BASICS
 LEARNING OBJECTIVES
• Microbial diversity

• Cell construction

• Cell nutrients
 MICROBIAL DIVERSITY
Are all cells the same?

Where can we find living cells?

Psychrophiles <20 C
Temperature Mesophiles 20-50 C
Thermophiles >50 C

Neutrophiles 6-8
pH Acidophiles 1-2
Alkaliphiles >9
 MICROBIAL DIVERSITY
Aerobic
Oxygen Anaerobic
Facultative

Nutrients Cyanobacteria
Halophiles

Coccus
Shapes Bacillus
Spirillum

Extremophiles
 NAMING CELLS
Taxonomy

Classification

Nomenclature
Latin
Dual name (binary nomenclature)
Genus (related species) + Specie: Escherichia coli
Strains designated by the addition of letters/numbers: E. coli K12

Coronavirus: Family Coronavidae; genus Betacoronavirus (SARS-CoV Tor 2, bat-SL-CoVZC45, etc.)

 CLASSIFICATION
Classification

Nuclear membrane

# chromosomes

Organelles

Virus?
 VIRUSES
Characteristics

Small (30-200 nm)

Parasites of other cells (bacteria, yeast, animal, plant)

Cannot store or capture free energy

Not functionally active except when inside the host

Contain either DNA or RNA; surrounded by the capsid

Biotechnological tools (vaccines, gene therapy, etc.)

 VIRUSES
Infection
Almost all cell types are susceptible to viral infections

Bacteriophage

Lytic cycle
Lysogenic cycle
 PROCARYOTES
Characteristics

Size: 0.5-3 um

Shape: coccus; bacillus; spirillum

Doubling time: < 30 min to several hours

Type: eubacteria and archaebacteria

 PROCARYOTES
Eubacteria

Gram stain (+ and -)

Presence (-) or absence of outer membrane (+)

Archaebacteria

Different membrane composition (peptidoglycan and lipids)

Different ribosomal RNA

Extreme environments (thermoacidophiles, halobacteria…)

 EUCARYOTES
Eucaryotes

Fungi (yeasts, molds), algae, protozoa, animal and plant cells

5x-10x larger than procaryotes (5-20 um)

True nucleus: chromosomes (DNA) surrounded by a

membrane

Cellular organelles in the cytoplasm

 EUCARYOTES
Microscopic eucaryotes

Yeasts: 5-10 um; spherical, cylindrical or oval; S. cerevisiae

Fungi
Molds: 5-20 um; long, highly branched cells; A. niger, P. chrysogenum

Unicellular organisms: 10-30 um

Algae
Photosynthesis (chroloplasts); Chlorella

Unicellular organisms: 5-50 um

Protozoa
Lack cell walls and ingest other organisms; Amoeba
 CELL CONSTRUCTION
Cell components
Elemental composition:

50% C, 20% O, 14% N, 8% H, 3% P, 1% S (small amount salts and vitamins)

Major structural elements:

High molecular weight polymers (protein, nucleic acids, polysaccharides, lipids, storage materials)

Metabolites:

Inorganic salts (K+, NH4+, PO43-, Ca2+, SO42-), metabolic intermediates (acetate), vitamins

They are functional only when in the proper 3D configuration and in its unique microenvironment

A cell like a reactor with 2,000 reactions (metabolic pathways) taking place
 CELL CONSTRUCTION
Amino acids and proteins
Most abundant organic molecules in living cells Structural
(40-70% of dry weight)

Polymers built from amino acid monomers Catalytic

Types: fibrous and globular proteins
Functions

Protective Transport

Regulatory
 CELL CONSTRUCTION
Amino acids and proteins
Enzymes: largest class of proteins (> 2,000) Structural
Catalytic power
Catalytic

Functions

Transport

Regulatory
 CELL CONSTRUCTION
Amino acids and proteins
Common amino acids Structural
L-/D- isomeric forms
Catalytic

Functions

Transport

Regulatory
 CELL CONSTRUCTION
Amino acids and proteins
Acidic/basic groups Peptide bond: Structural

Catalytic

Functions

Zwitterion Polypeptides (< 50 amino acids)

Regulatory
Proteins (> 50 amino acids)
Isoelectric point Prosthetic groups (Hb)
 CELL CONSTRUCTION
Amino acids and proteins
Structure Structural

1 2 3 4
Linear sequence of Hydrogen bonding Interactions Interactions among
amino acids between residues between R groups polypeptide chains

Covalent, disulfide,
Helixes (more or
hydrogen bonds Disulfide bonds or
less rigid) and
Unique and/or other weak
sheets (more
hydrophobic interactions
stable)
hydrophilic
 CELL CONSTRUCTION
Amino acids and proteins
Structure Structural
 CELL CONSTRUCTION
Amino acids and proteins
Lock and key
Antibodies Structural
Bind to particular molecules or portions of molecules
with high specificity

Appear in blood serum in response to foreign

(antigen) macromolecules (pathogen)

Immunotherapy

Immunoglobulins: IgG, IgA, IgD, IgM, IgE

 CELL CONSTRUCTION
Amino acids and proteins
Antibodies Structural
Bind to particular molecules or portions of molecules
with high specificity

Appear in blood serum in response to foreign

(antigen) macromolecules (pathogen)

Immunotherapy

Immunoglobulins: IgG, IgA, IgD, IgM, IgE

 CELL CONSTRUCTION
Carbohydrates
Structural
Key roles: structural and storage compounds

Critical role: modulating chemical signaling in animals and plants

Synthesized through photosynthesis

Formula: (CH2O)n n>3

Classification?
 CELL CONSTRUCTION
Carbohydrates
Structural
Monosaccharides: 3-9 carbon atoms; aldehydes or ketones
 CELL CONSTRUCTION
Carbohydrates
Structural
Monosaccharides: 3-9 carbon atoms; aldehydes or ketones

D-ribose and deoxyribose: 5 carbon ring-structured sugars essential for DNA/RNA

 CELL CONSTRUCTION
Carbohydrates
Structural
Disaccharides: Condensation of 2 monosaccharides
 CELL CONSTRUCTION
Carbohydrates
Structural
Polysaccharides: Condensation of >2 monosaccharides by glycosidic bonds

Amylose (α-1,4 bond; starch) Cellulose (β-1,4 bond)

Polysaccharides: Attached to other molecules by glycosylation  Diverse functions

 50% of eucaryotic proteins are glycosylated
 70% of therapeutic proteins are glycoproteins
 CELL CONSTRUCTION
Lipids, fats and steroids
Structural
Lipids: fatty acids are major components

Hydrophobic (soluble in non-polar solvents)

Present in plasma membranes (non-aqueous phases)
Fuel-storage molecules
 CELL CONSTRUCTION
Lipids, fats and steroids
Structural
Lipids: fatty acids are major components

Hydrophobic (soluble in non-polar solvents)

Present in plasma membranes (non-aqueous phases)
Fuel-storage molecules
 CELL CONSTRUCTION
Lipids, fats and steroids
Structural
Fats: esters of fatty acids with glycerol
 CELL CONSTRUCTION
Lipids, fats and steroids
Structural
Phosphoglycerides: Steroids:

Hormones

Regulate animal development and metabolism at

low concentrations (10-8 M)

Cholesterol, cortisone, testosterone, estrogens,

progesterone…
 CELL CONSTRUCTION
Biological membranes
Structural
Selective permeability is key

Phospholipids and proteins

Integral/peripheral proteins

Lipid bilayer

Active and passive transport

Endocytosis and exocytosis

 CELL CONSTRUCTION
Nucleic acids
Structural
Central role: reproduction of living cells

DNA stores and preserves genetic information

RNA plays a role in protein synthesis

Nucleotides: building blocks of nucleic acids and also

molecules to store energy

Nitrogenous bases: A, G, T, C, U

DNA: A, G, T, C

RNA: A, G, U, C
 CELL CONSTRUCTION
Nucleic acids
Structural
Cellular energetics

Adenosine and guanosine:

triphosphates, high energy bonds

Energy currency of cells

Energy use to create a compound that is

thermodynamically unfavorable

Energy storage from reactions that are favorable

 CELL CONSTRUCTION
Nucleic acids
Structural
Polynucleotides DNA

Large molecule, double-helical 3D structure

Base sequence carries genetic information, sugar

and phosphates perform a structural role

Base sequence written in the 5’->3’ direction

 CELL CONSTRUCTION
Nucleic acids
Structural
DNA
Two helical chains form the double-helical DNA,
running in opposite directions (5’->3’ and 3’->5’)

Bases are on inner surface and phosphate and pentose

are on outer surface

Hydrogen bonds: A -> T (2 bonds)

G -> C (3 bonds)

Each strand is complementary to the other

Transcription (RNA synthesis using DNA as template)
Translation (protein synthesis using RNA as template)
 CELL CONSTRUCTION
Nucleic acids
Structural
DNA
DNA replication

One strand comes the parent DNA, the other is

synthesized using the parent as template

Chromosomes: single DNA associated with proteins in the

nucleus of eucaryotes (human genome— 3.2 × 109
nucleotides—is distributed over 24 chromosomes)

Plasmids: circular DNA segments

Separate from chromosomal DNA and self-replicate
Carry small number of genes (antibiotic resistance)
 CELL CONSTRUCTION
Nucleic acids
Structural
RNA

Long, single stranded molecules (70-104 of nucleotides)

RNA content is 2-6X higher than DNA

Certain RNA molecules are double-helical (hairpin loops)

In these: A U; GC

Carry information or involved in protein synthesis

 CELL CONSTRUCTION
Nucleic acids
Structural
Synthesis in chromosome
Carries information to ribosomes mRNA
Short half-life
Carries amino acid from cytoplasm to ribosome
tRNA Small (70-90 nucleotides) and stable
Each of 20 amino acid has one tRNA
65% of ribosomes
Specified based on sedimentation rate rRNA
4 different types in eucaryotes
Not translated into a protein
ncRNA tRNA and rRNA
Regulatory RNA (miRNA, etc.)
 CELL NUTRIENTS
Composition Function of age, type,
nutrient media
Structural
Lipids (5-15% dw)

Nucleic acid (10-20% dw)

Protein (50% dw)

Water (80%)
 CELL NUTRIENTS
Nutrients

Macronutrients (>10-4 M) Structural

• Carbon
• Nitrogen
• Oxygen
• Hydrogen
• Sulfur
• Phosphorus
• Mg, K

Micronutrients (< 10-4 M)

• Trace elements: Mo, Fe, Zn, Cu, Mn, Ca, Na, vitamins, hormones
 CELL NUTRIENTS
Nutrients
Structural