MBIO-2000 MODULE 1

Study of microbes

-Very small entities
-Viewed by microscope
-Study of non living entities and living organisms

2 major microbes

-Acellular microbes
-Cellular microorganisms

Acellular microbes

Don't have a cell
Ex)
-Virus
-Prions

Cellular microorganisms

Do have a cell
Ex)
-Bacteria
-Archaea
-Algae
-Protozoa
-Fungi

Prokaryotic cell

-Simple cell
-Smaller than eukaryotes
-Circular DNA (no paired chromosomes)
-Contain:
-Cytoplasm
-Cytoplasmic membrane
-Ribosomes
-Nucleoid
-Ribosomes
-Cell membranes/wall
-Flagella
-Pili
-Proteins/enzymes

Eukaryotic cell

-In our bodies
-Complex
-Paired chromosomes
-Contains:
-Nucleus
-Nuclear membrane
-Mitochondria
-Smooth and rough ER
-Golgi
-Plasma membrane
-Lysosomes
-Chloroplasts

Cell

The smallest unit of life that is capable of replication

Bacteria are ______?

-Prokaryotes
-No true nucleus
-Very small 1-3 um

Fungi and protists are ______?

-True nucleus
-DNA in nuclear membrane
-Animal and plant cells 10-30 um

Contributions of microorganisms

-Normal flora of human body (prevent opportunistic pathogens from taking over the body or may become opportunistic pathogens)
-Environment (recycle nutrients by bacterial and fungal decomposition of dead plants and animals)
-Aid in digestion and production of dairy products
-Aid in development of medical treatments

Microbial classification

-Binomial nomenclature:
-First name=genus
-Second name= species

Robert Koch

-Bacillus anthracis
-Discovered understanding of Anthrax

Cytoplasm

-Protein synthesis
-DNA replication
-Cellular metabolism
-Contains: DNA, plasmids, ribosomes
-No membrane-enclosed organells
-No mitochondria
-Generates ATP by floating enzymes in cytoplasm

Nucleoid

-No nuclear membrane
-No organells
-Large bacterial DNA (free floating)
-Closed circle of DNA

Plasmids

-Circular bacterial DNA (transfer genetic material to another bacteria)
-Code for toxins or antibiotic resistance
-Passed along by binary fission (bacterial replication) to daughter cells or sex pilus formation (tube-like structures extending to pass along plasmid)

conjugation:

-Bacteria exchange genetic information
-If capable of conjugation with have a pilus

What enzyme is in cytoplasm

-RNA polymerase

RNA polymerase

-Copies DNA into mRNA during transcription

Bacterial molecular biology

-RNA polymerase copies DNA into mRNA in transcription
-mRNA floats in cytoplasm to ribosome, which reads mRNA and creates amino acid chain during translation
-Amino acids fold up to a metabolic enzyme (make ATP) or a structural enzyme (for cell wall) or a secreted enzyme (destroy tissues)

Genetic information

-Genes in double-stranded DNA
-Transcribed into single stranded mRNA via RNA polymerase

Gene in DNA

-3 base start sequence 'ATG'
-RNA polymerase copies into 'AUG'

RNA codons

-Sequence of 3 mRNA

What is the shape and function of a protein dictated by
?

-Sequence of amino acids (from RNA codons read by ribosomes)

How is an amino acid sequence created?

-mRNA looks for AUG start codon
-Adds other amino acids based on next 3 mRNA bases
-UGA sequence=stop codon

Bacterial cell envelope layers

-Inner membrane
-Cell wall
-Capsule

Inner membrane

-Simple lipid bilayer
-Transport proteins for transporting macromolecules in and out of cells

Cell wall

-Rigid
-Made of peptidoglycan: Thick layer= gram positive, Thin layer= gram negative
-Surrounds cell membrane
-Protects from osmotic stress (pop if not protected) and environment

Capsule

-Not in all bacteria
-Made of polysaccharide layer:
-Lets bacteria stick to surfaces
-Hide bacteria from immune system
-Protects bacteria from phagocytosis

Bacterial cell wall

-Crucial for:
-Osmotic stress resistance
-Protect against attack by the immune system

Types of bacterial cell walls

-Gram positive (stain)
-Gram negative (don't stain)

Gram positive cell wall

-Massive block-like layer of cross-linked peptidoglycan molecules (protects against complement attack and detergents)

Gram negative cell wall

-Thinner peptidoglycan layer (resist osmotic stress)
-Lipopolysaccharide layer (lipids with chains of sugar)
-Lipopolysaccharides are negatively charged=negatively charged molecules are repelled
-Hides bacteria from immune system

Cocci

Round spheres

Bacilli

Rod-like shapes

Helical

Curved or spiral shapes

How are bacteria shapes determined?

How peptidoglycan layer assembled suring its production

Bacterial capsule

-Organized layer of polysachharides excreted to the outside of bacteria
-Gram negatives=second layer of lipopolysaccharides help hide bacteria from immune system
-Gram positives= lipopolysachharides hide armoured gram positive from the immune system
-Assists adhesion of a microbe to a surface and form a biofilm

What happens when you inhibit the synthesis of the capsule of pathogenic bacteria?

-The immune system rapidly destroys potentially fatal microbes

Pili

-Small hair-like structures on outside of bacteria
-Allows bacteria to attach to surfaces such as teeth or intestines

Flagella

-Whip-like structures providing motility for certain bacteria
-Propeller like motion to drive bacteria towards food sources and away from toxic compounds

Biofilm

-Diffused
-Unorganized extracellular layer of polysaccharides and glycolipids (help hide from immune system and stick to difficult surfaces such as polystyrene)
-Protects bacteria from antibiotics
-Sticks to surfaces longer and after being washed
-Streptococcus mutans use it to colonize and cause cavitities

Bacterial cell division

-By binary fission (mother cell divides into 2 daughter cells)
-Cleavage of cell membrane and cell walls= two smaller bacteria
-Take in nutrienes, grow, copy DNA, then divide
-Simple compared to eukayotes

Generation time

-Time it takes for one bacteria to duplicate
-10 min to 24 hours
-effect in disease development
-Ex):
-Mycobacterium tuberculosis=weeks to months
-Staphylococcus aureus (flesh eating disease)= hospital within hours

Factors that influence bacterial growth and generation time

-Availability of nutrients
-Moisture
-Temperature
-Ph
-Gaseous atmosphere

Nutrients

-Energy source for microorganisms
-Sources of: carbon, oxygen, hydrogen, nitrogen, phosphorous, and sulfur

Essential nutrients

-Organisms unable to synthesize but are required for building macromolecules and supporting life
-Ex):
-Amino acids
-Essential fatty acids

Cells consist of ____% of water?

-75-90%

Why is water important for bacterial growth and generation time?

-To carry out metabolic processes
-Required to form cytoplasm

Temperature

-Each organism has an optimal growth temp
-Thermophiles: 50-60 Celsius, up to 113 Celsius
-Mesophiles: 37 Celsius
-Psychrophiles: 10-20 Celsius, low as 4 Celsius

Ph

-Hydrogen ion concentration of a solution
-Acidophiles: ph less than 7 (usually 3-4)
-Ex):
-Helicobacter pylori (love acidic environmrnt of stomach and cause ulcers
-Alkaliphiles: ph greater than 7 (usually 9 or greater)
-Ex):
-Vibrio cholerae

Obligate aerobes

-Require 20-21% O2
-Found in lungs
-Ex):
-Mycobacterium tuberculosis

Microaerophiles

-Require reduced oxygen (5%)
-Found in small and large intestinal lumen
-Ex):
-Campylobacter jejuni= severe gastroenteritis

Obligate anaerobe

-Can't survive in oxygen
-Found in the deep intestinal lumen

Facultative anaerobe

-Live in presence or absence of oxygen but prefer low oxygen and high carbon dioxide
-Most common
-Ex):
-Staphylococcus
-Streptococcus
-E.coli
-Listeria
-Enterobacteriacea

Capnophile

-Prefers increased carbon dioxide usually 5-10%
-Many microaerophiles are also capnophiles
-Ex):
-Campylobacter jejuni

4 phases of a growth curve

-Lag phase
-Log phase
-Stationary phase
-Death phase

Bacterial growth curve

-The curve represents the number of bacteria present over time
-Y-axis=logarithmic

Lag phase

-Bacterium introduced to environment where it takes advantage of nutrients and resources
-No cell division
-Bacterium absorbs nutrients, synthesize enzymes, and prepare for cell division
-Length is dependant on time for synthesis of coemzymes or division factors and time for synthesis of new enzyme to metabolize

Log phase

-Growth is at its maximum
-Exponential rate
-Growing and dividing via binary fission
-Using more nutrients

Stationary phase

-Nutrients are heavily depleted
-Toxic waste products accumulate d/t bacterial metabolism
-Rate of division slows down
-Bacteria diving=bacteria dying
-Greatest accumulation of bacteria

Death phase

-Overcrowding
-Nutrients used up
-Toxic metabolites accumulate
-Bacteria die or are dormant

Virulence

-A measure of pathogenicity of a microorganism
-avirulent strains=don't cause disease

Virulence factors

-Microorganism that contributes to ability to cause disease

Receptors

-Molecules on the surface of a host cell that a pathogen is able to recognize
-Only a specific pathogen can recognize a specific pathogen
-Ex):
-Microbes that cause respiratory disease recognize and attach to receptors on respiratory tract

Adhesins/ligands

-Molecules on the surface of the pathogen that -Recognize and attach to receptors on a host cell's surface
-Ex):
-Haemophilus influenzae= bind to respiratory tact by adhesins called hemagglutinin
-Chlamydia trachomatis= bind to genital tract

Capsules

-Help bacteria attach to surfaces that unencapsulated bacteria can't
-Protects from phagocytosis= allows capsulated bacteria to multiple in bloodstream and tissue causing damage
-Bacterial species that can cause disease d/t capsules:
-S. pneumoniae
-H. influenzae
-N. meningitidis

Flagella

-Enable bacteria to invade areas of body that non-flagellated bacteria can't
-Allow bacteria to swim into junctions

Exoenzymes

-Small molecular machine
-Released to evade host defenses
-Damage host tissue
-Enzymes secreted outside of bacterial cell
-Breakdown nutrients to absorb and use to grow

Necrotizing enzymes

-Tissue destruction
-Breakdown plasma membrane
-Ex):
-S. pyogenes
-S. aureus
-Clostridium

Coagulase

-Able to clot plasma
-Binds prothrombin=fibrinogen to fibrin in bacteria (staphylococcus aureus)

Kinases

-Breaks down blood clots
-Staphylokinase=plasminogen to plasmin, which digest fibrin clots to spread throughout body

Hyaluronidase

-Allows pathogens to spread through connective tissue by breaking down hyaluronic acid
-Connective tissue as food source
-Allow bacteria to spread deeper into tissues
-Ex):
-Staphylococcus
-Streptococcus
-Clostridium

Hemolysin

-Damage host red blood cells
-Red blood cell damage (a-hemolysis)
-Complete red blood cell destruction (b-hemolysis)

Toxins

-Poisonous substances carried or released by a pathogen
-No metabolic activity
-2 types:
-Endotoxins
-Exotoxins

Endotoxins

-A component of the cell wall of gram negative bacteria (sloughed off bacteria)
-Can cause septicemia (d/t accumulation of bacterial lipopolysaccharides in the bloodstream)

Exotoxins

-Poisonous proteins secreted by a pathogen
-Small molecules secreted to bind to receptors on cells and cause damage
-Named based on organ system they target

Diphtheria toxin

-Produced by virulent strains of corynebacterium diphteriae
-Inhibits protein synthesis
-Kills mucosal epithelial cells and damages heart and nervous system

Shiga toxin

-produced by shigella and certain e.coli
-Inhibits protein synthesis
-Causes clot formation
-Results in hemolytic uremic syndrome

Viruses

-Small infectious agent only able to replicate in the living cell host
-10-300 nm
-Only viewed via electron microscope
-Contains DNA or RNA
-Obligate intracellular pathogens (viral replication by viral nucleic acid)
-Can't do anything outside of cell
-Surrounded by an envelope

Simplest virus is composed of?

-Nucleic acid (strand of DNA or RNA) surrounded by capsid

Capsid

-Protein coat
-Composed of small proteins called capsomeres
-Can be helical, isosahedral, or bullet shaped

Envelope

-protect virus from host immune system
-More easily destroyed during sterilization (d/t membrane coating damaged)

Non-enveloped virus

-Center is DNA or RNA
-Surrounded by protective capsid of capsomeres
-Glycoprotein spikes are adhesins and allow virus to bind to host cell

Enveloped virus

-RNA
-Lipid envelope layer around capsid=hiding virus from immune system and regulating virus entry and exit
-Glycoprotein spikes are adhesins and allow virus to bind to host cell

Replication of an animal virus

-Attachment (adsorption)
-Penetration
-Uncoating
-Replication/ synthesis of viral genes for viral DNA/RNA and protein production
-Assembly
-Release

attachment

-Uses glycoprotein spikes to bind to receptors on a specific cell

Penetration

-Trigger endocytosis in host cell (used for non-enveloped viruses)
-If virus is enveloped it uses membrane fusion to merge envelope with host cell

Uncoating

-Virus sheds capsid once inside the cell
-Shed via:
-Right cellular conditions (ph, osmotic pressure, etc)
-Cleavage enzymes (breakdown capsid and release viral genome)

Replication/synthesis

-Uses ribosomes, ATP and nutrients to copy genome and proteins

Assembly

-In host cell cytoplasm,E.R, or golgi
-Uses specific host cell enzymes to regulate assembly
-Self-assemble when enough viral genome meet up with enough capsomeres

Release

-2 types:
-Lysis:non-enveloped viruses use up nutrients and make copies of themselves that cause them to burst open or explode releasing new virions into environment
-Budding:enveloped viruses bud off E.R, golgi, or plasma membrane stealing cells own membrane everytime a new virus is made and released

Central dogma of biology

-RNA polymerase: enzyme that recognizes ATG bases in the sense strand of DNA and copy to mRNA replacing T with U
-RNA-dependant RNA polymerase: not normal to cells

mRNA produced begins with?

-AUG
-AUG is what the ribosome uses to recognize mRNA and to make protein

Virus with DNA-based genome

-If DsDNA, will treat it like DNA
-If DsDNA in cytoplasm our cells think its our own DNA that got out of nucleus and imports it there
-RNA makes new viral proteins and uses own proteins or your cell protein machinery to copy genomes

What happens if a virus genome is RNA and wants to copy itself

-Make antisense strands of RNA (makes complimentary RNA strand)
-Makes double stranded RNA
-Uses complimentary RNA to copy genome

Readable (sense) DNA

-Positive DNA or RNA

Complimentary strands (antisense)

-Negative DNA or RNA

Baltimore classification system of viruses

-Class 1: Double-stranded DNA viruses
-Class 2: Single-stranded DNA viruses
-Class 3: Double-stranded RNA viruses
-Class 4: Positive single-stranded RNA viruses
-Class 5: Negative single-stranded RNA viruses
-Class 6: Single-stranded RNA viruses that replicate through a DNA intermediate
-Class 7: Double-stranded DNA viruses that replicate through single-stranded RNA intermediate

Class 1: dsDNA viruses (double stranded DNA viruses)

-Genome replicated in the nucleus
-Require host DNA polymerase for replication and are dependant on cell cycle while others code for their own DNA polymerase

Class 2: ssDNA viruses (single stranded DNA virus)

-Genome replicated in the nucleus
-Go through dsDNA intermediate for replication to continue