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