DNA to mRNA

protein synthesis

biosynthesis

promoter

RNA (pol)ymerase

Sigma (σ) Factor

RNA pol + σ factor

synthesizes RNA

5 protein subunits

1. RNA Holoenzyme binds to DNA (forms Closed Complex)

2. DNA is unwound

(Start of Open confirmation)

1. Ribosome binds to mRNA at Shine-Delgarno sequence

2. AUG is first codon

1. Aminoacyl-tRNA arrives at A site

2. Transpeptidation reaction occurs between P and A sites

3. Translocation

– Empty tRNA exits from E site

– tRNA with growing chain moves from A to P

– New tRNA comes into the A site

1. E site (exit site)

2. P site (peptidyl, or donor site)

3. A site (aminoacyl, or acceptor)

+lipids= lipoproteins; gram -

+sugars= glycoproteins; gram +

two or more genes transcribed from 

a single promoter

• Regulatory regions are upstream of 

genes; one regulatory region can control grouped genes

Transcriptional-  change in gene expression levels by altering transcription

rates.

Translational - control of the levels of protein synthesized from its mRNA.

Protein- how much the mRNA is translated into proteins.

Diauxic Growth of E. coli-

transition occurs; glucose genes off, lactose genes on

when a regulatory protein promotes transcription initiation; activator protein binds upstream and promotes RNA Holoenzyme binding

when a regulatory protein inhibits transcription initiation; repressor protein binds to operator to prevent transcription

Mutation: induced/spontaneous

Recombination: leads to newcombintations of genes on a chromosome

point mutation

alteration of base pair resulting in SAME amino acid

Prion

infectious proteins that lack nucleic 

acids

mad cow

point mutation

alteration of base pair resulting in DIFFERENT amino acid;

Auxotroph- nutritional mutant that requires an additional growth factor

Prototroph- parent of an auxotroph

Fast, easy to idenitify mutagens; an increase in reversion rate = potential 

mutagen/carcinoge

bacterial sex

plasmid DNA  carries gene for sex pilus; F⁺

cell-cell contact required

– Temperature

– Nutrients

– Water (osmotic balance)

– Appropriate atmosphere

– pH

stops bacterial growth

-static/-stasis = standing still

D value; decimal reduction time

time require to kill 90% of microbes or spores

ribosomes

DNA

Enzymes

Cell wall

Membranes

intensity/concentration- lowers D-value

Microbial load- number of microbes; D-value same rate, increased time to do so

Population Compostition- mixture of microbes

Temperature- increased temperature, more active

Environment- type of material contaminated

autoclave- moist heat, under pressure. More quantity, more time

Boiling- moist heat, not under pressure

pasteurization- sub-boiling temps; high temp short time, ultra high temp,

Hot air

incinteration

physical

DNA damaged

ionzing- gamma rays/xrays

non-ionizing- UV light

physical

seperates bacteria from liquid

HEPA filtration for air

ultra filtration- filters out lipopolysaccharide endotoxins from dead gram -

chemical

Bactericidal or bacteriostatic depending on 

concentration

higher concentration = bacterialcidal

– Increases membrane permeability

– Denatures protein

Chemical

Oxidizing agent, inactivates key proteins

Iodine – very effective germicide

 Chlorine

chemical

• Antibacterial and effective against algae and 

fungi

• Mode of action

– Inactivate enzymes - react with –SH group

toxic

chemical

Surface active compounds (“surfactants”)

– Damage cell membranes

– Denature protein

chemical

disinfecting, sanitizing, and antisepsis

compounds (natural or synthetic) 

that inhibit specific metabolic processes in 

cells

Paul Ehrlich- syphillis antibiotic

Alexander Fleming- penecillin

antibiotic targets

• Cell wall synthesis

• Membrane function

• Protein synthesis

• Metabolite antagonism

Active against Gram positives

– Natural or semi-synthetic

– Allergies and pathogen resistance

ex PENECILLIN 

Quinolones (nalidixic acid, ciprofloxacin) – Inhibit DNA gyrase; Very broad spectrum

Mitomycin – Cross-links with DNA; Induces endonuclease activity

Enzyme inhibitors

ex. Sulfonamide

• Humans and animals

• Plant pathogens

 • Pests

CO2 fixation and O2 evolution on Earth

Lichens

a unique symbiotic life form 

consisting of fungi and algae (actually 

cyanobacteria)

Protozoology: study of protozoa

Eukaryotic, unicellular animals

Motile by cilia, flagella, or amoeboid motility

Require host machinery to multiply

1 nucleic acid- DNA or RNA

acellular

capsid- some have lipid envelope

Nucelocapsid

Virion- complete individual virus

10nm - 300nm

helical- tube shape

polyhedral- multi-sided

• Attachment: adhesion to target site

• Entry: Virus injects nucleic acid into host

• Replication: early viral proteins shut down host metabolism, then replicates

• Maturation/assembly: Capsids/nucleic acids; sometimes host DNA picked up

• Release: Virions are released; Cell lysis; budding

attachment/entry- same; except DNA becomes circular

Repression- phage represses lytic cycle

Integration- phage inserts into host DNA; prophage

attainment- prophage replicates with chromosome; repressor protein blocks lytic

Entry- to lytic cycle; prophage expressed

contain envelopes with Glycoprotein spikes

'naked' virion = non-enveloped

Immune system- immunity from current/previous infection.

Vaccination: exposure to virus (inactivated or 

portion of virus)

Fever: increased temp inactivates some viral 

proteins

Interferon: antiviral produced by the body, blocks viral protein synthesis

anti parallel

(5’ - 3’ and 3’- 5’)

2 consesus sequences

-35 (TTGACA)

-10 (TATAAT) = Pribnow box

first nucleotide to be transcribed

Stem-loop of A-U bound by 2 H-bonds

RNA pol and transcript fall off then Termination occurs

1. Rho factor binds to mRNA and moves along until stem-loop reached

2. Helicase unwinds RNA-DNA complex then RNA pol dissociates

• Synthesis stops at nonsense codon

– UAA, UAG, UGA

• Release factors aid in termination

• Final peptide bond made, peptide released

• Ribosomes dissociate from mRNA

sense environmental changes

can change 3D confirmation

• Transcriptional control based on DNA 

sequence/folding

ex. trp operon

Two-Component 

Phosphorelay System

 Link events outside of the cell to expression 

inside of the cell

1. sensor

2. response regulator

Increased substrate = increased velocity

End product may inhibit biosynthesis

Bind effector molecule to protein's allosteric site

point mutation

alteration in base pair that results in a STOP CODON

– Capsule

– O-antigen of LPS (“rough” mutant)

– Fimbriae

– Pigmen

Histidine auxotroph- mutant bacteria with histidine nutritional requirement

1/1,000,000,000 colony will grow on non nutritional medium

Mutagen introduced to increase mutation rate

• New, foreign DNA is incorporated into 

the chromosome

• Once foreign DNA is incorporated, the 

organism is called a recombinant 

organism

Transfer 'naked' DNA from one bacterium to another

Frederick Griffith- Transforming principle

fragments of DNA are join in vitro

new DNA are expresses in vivo

AKA recombinant DNA

study of molecular properties of entire genome (overall sequence)

interdisciplinary work involving:

– Genomics (genes expressed)

– Proteomics (proteins made)

– Computing (computer analysis)

Sterilize

disinfectant

antiseptic

sanitize

sterilize- kill all forms of life including endospores

disinfectant- kills vegetative cells

antiseptic- disindfection for animate objects

sanitize- reduce microbial population to a safe level

refridgeration- bacteriastatic; food preservation

remove water; canning/curing

not affective against mold

have microbial activity

solubility

stability

non-toxic

uniform composition

not inactivated by other materials

active a room temp

ability to penetrate

non-damaging

deoderizing ability

detergent ability

low cost

– Dissolve lipids

– Denature protein

cell membrane

proteins

mitochondria

lowest concentration of an antibiotic that 

inhibits growth of an organism

kirby-bauer technique

lowest concentration of antibiotic that kills 

test organism

AKA  minimal lethal concentration

– Polymyxins – toxic, for P. aeruginosa infections

– Polyenes – antifungal, targets sterol-containing 

membranes

– Azoles – antifungal, block synthesis of membrane sterol 

Translation inhibitors- RNA misreading

• Inactivation of antibiotics– β-lactamase

• Blocking entry of antibiotic

• Pumping antibiotic out of cell

• Altering target enzyme so it is unaffected

mycology- study of fungi

• Fungi are not photosynthetic; heterotrophs

• Most have cell wall

two organisms interact, one benefits 

while the other is harmed

Fungal

Decomposition

Decompose complex organic material

Fungi

Industrial

1. Fermentation and distilling industries

– Ex. Citric acid used for cleaners

2. Production of enzymes

– Ex. Cellulase used for stone-washed 

jeans

Fungi

antibiotics

Fungi 

Plant Nutrition

• Some fungi associate with roots

– Help them obtain nutrients from soil

– Called mycorrhizae

Algae and Protozoa

• Phycology: study of algae

• Unicellular and multicellular plants

moist habitats 

aerobic or anaerobic

resting stage called cyst -not as resistant as endospore

Protozoa

Disease

• Amoebic dysentery 

• African sleeping sickness

• Malaria

Protozoa

Digestion

lack enzymes for protein synthesis/ATP generation

uses host cell machinery

Host type

Nucleic acid type

capsid symmetry

size

nuclear envelope

replication

gene number

disease caused

differ from bacteria

based on- mechanisms of penetration, mode of transmission, strategy andlocationof replication

Bacteriophages

lytic- virulent

lysogenic- temperate

Single stranded viruses ex. HIV

enzyme reverse transcriptase RNA to DNA

DNA incorporates into host genome

plant “virus” that consists only of 

ssRNA (lack capsid!)