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UNT / Biology / BIOL 2041 / What if there is no oxygen?

What if there is no oxygen?

What if there is no oxygen?

Description

School: University of North Texas
Department: Biology
Course: Microbiology
Professor: Daniel kunz
Term: Winter 2016
Tags: Biology, Microbiology, test, bundle, and 2041
Cost: 25
Name: Test 1 bundle
Description: This bundle includes all of our notes for the test, our timeline, media tables and stain tables. Hope this helps and good luck on the test
Uploaded: 02/11/2016
33 Pages 36 Views 1 Unlocks
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Chp 1


What if there is no oxygen?



● Fig 1.2 van leeuwenhoek

○ First person to describe an organism by making 1st microscope magnified by 25X coined term “animalcules” aka bacteria

● Microorganisms are ubiquitous

○ Minute living things usually to small to see with unaided eye

○ Maintains balance between organisms and chemicals in our environment ● Pathogenic

○ Disease producing

● Microbiology

○ Bacteria

■ Focus of class

■ simple unicellular organisms

■ Genetic material in a special nuclear membrane Don't forget about the age old question of Maturity is what?

■ Inclosed cell wall with peptidoglycan

■ Produces via binary fission

■ Uses organic chemicals

■ Called prokaryotes

○ Protozoa


How much light passes through the suspension?



■ Unicellular organisms

■ Movement

● Cilia

● Flagella We also discuss several other topics like What do the three main serous membranes consist of?

● Pseudopod

○ False feet We also discuss several other topics like How do we measure uncertainty?

○ Example

■ Amebae

■ Live as free organisms or as parasites

■ Can be photosynthetic

○ Algae

■ photosynthetic eukaryotes

■ Sexual or asexual

■ Composed of carbohydrate known as cellulose

■ Don't need organic compounds from the environment

■ Makes oxygen and carbohydrates used by their organisms

○ Fungi We also discuss several other topics like What was john muir known for?
We also discuss several other topics like What happened at the world's fair in 1939?

■ Cell walls made of chain

■ Eukaryotes

■ Distinct nucleus containing DNA surrounded by nuclear membrane ■ Can't carry out photosynthesis


How do we form macromolecules?



● Can look like plants

■ Examples

● Yeast

● Mold

○ Archaea

■ Considered a prokaryote

■ Made up of prokaryotic cells with a cell wall

■ Lacks peptidoglycan

■ Found in extreme environments

● Methanogens

○ produces methane during respiration

● Extreme halophiles

○ Love extremely salty environments

● Extreme thermophiles

○ Live in hot sulfurous water Don't forget about the age old question of What does people are rational mean?

■ Unknown to cause human disease

○ Virus

■ Only seen with electron microscope

■ Acellular

● Not cellular

■ Contains one type of nucleic acid in a core

● So it contains either DNA or RNA

● Core is surrounded by protein coat

○ Coat is called lipid membrane

● Fig 1.4 important name dates and discovery

○ 1665 Leeuwenhoek

○ 1857 Pasteur

○ 1861 Pasteur

○ 1864 Pasteur

○ 1876 Koch

○ 1884 Gram

○ 1928 Fleming

○ 1973 Berg

○ 1981 Mitchell

○ 1997 Prusiner

■ Golden age of microbiology 1857­1884

■ When we learned the most about microorganism ● Table 1.2 Nobel prize and the discovery

○ 1987 tonegawa

○ 1989 bishop & varmus

○ 1997 prusiner

○ 2005 marshall & warren

○ 2008 barre & montagnier

● Modern day advances

○ Genetic engineering computerized biology

■ Bioinformatics

■ Genomes

● Biology is now tech driven

● Mass of amount of microorganisms is the greatest because all organisms that would recycle all the carbon are in ground not in the sky 10­15% cause disease ● One pound of Microorganism in colon

● Meta genomics

○ complete genome of areas of soil or people

● All organisms classified 3 groups

○ Archaea

■ Primitive bacteria

■ Lacks peptidoglycan

○ Bacteria

■ contains peptidoglycan

○ Eukaryotes

■ Plants

■ Animal

■ Protist

■ Fungi

○ This is determined by organisms RNA and/or DNA it classifies inside domain ● Timeline

○ 4.5 billion years ago

■ Earth born in Big Bang

○ 3.8 billion years ago

■ Archaea microorganism appear

○ 2.7 billion years ago

■ Oxygen appears

○ .7 billion years ago

■ Multicellular organisms appear

○ .2 billion years ago

■ Man appears

● Idea war between Biogenesis and Spontaneous Generation

Biogenesis

Spontaneous Generation

1668 F. Redi ­flys touch meat, maggots appear from eggs therefore it's not spontaneous

1745 John Needham's heated solution set out and organisms appear

1765 Lazzaro Spallanzani ­repeated Needham’s experiment in a closed container no organisms appear

argues that you removed vital force that makes life possible O2 (which is

discovered by lavorisies)

1861 Louis Pasteur ­combines

Spallanzani and Needham's experiment with the S shaped flask (fig 1.3) noticed

law to no growth

○ 1735 Carolus Linnaeus

■ Binomial name system created

■ However not applied to virus do to their inherent lack of life

● Atom structure fig 2.1

○ Electron shells

■ Contain negative electrons

○ Nucleus

■ Contain neutral neutrons

■ Contains positive protons

○ Atomic weight

■ Sum of protons and neutrons

○ Atomic number

■ Number of electrons

○ Different bonds

■ Covalent bonds form between two electrons

● Atoms combine in the outermost shells

● Missing or extra electrons in outermost chill are called valence

■ The number of protons and electrons is equal in the atom

■ Ions are atoms that have gained or lost electrons and then are charged ■ Ionic bonds

● Are attractions between ions of opposite change where one atom

loses electrons and another gains electrons

■ Compounds are made up of molecules that are different

● H2O

● C6H12O6 

■ Molecular weight is the sum of all of the atomic weights

■ Forces holding compounds together are chemical bonds

○ Dimple movement due to unequal sharing of electrons

■ Interactions are determined by the charges

○ Relative bond strengths

■ Covalent

● 125­418 kilojoules/mole

■ Ionic

● 10­20 kilojoules/mole

■ Hydrogen

● 2­10 kilojoules/mole

■ 1 kilojoule is equal to .24 kilo cal

● Lecture 2

○ Important biological molecules

■ Inorganic

● No carbon containing molecules formed by ionic bonding

○ Example

■ Water

● An example polar molecule

● Considered universal solvent

■ Salts

■ Bases

■ Organic

● Carbon and hydrogen containing molecules formed by covalent bonding

○ Example

■ Macromolecules

● Proteins

● Nucleic acids

● Carbohydrates

● Lipids

○ Composition of cells tables 1.1 and 1.2

■ Bulk of cell is water

● 70%

■ Second major part of cell is proteins

● 15%

■ Third

● Monomers

○ Water ­inorganic compound

■ Great solvent

● Polar substances dissociate forming solutes

■ Acids

● H and some negative anion

● Causing a negative pH

○ Less than 7

■ Base

● Dissociate to HO and a cation

● Casing a positivity pH

○ Greater than 7

■ Salts are neutral

● Na and Cl

○ pH equal to ­log[H ion]

○ organic compounds

■ The chain of carbon atoms in an organic molecule known as a carbon Skeleton

■ Functional groups are responsible for most of the chemical properties of. A particular organic compound

■ Table 2.4

● Hydroxyl

○ Lipids and carbohydrates

● Amino

○ Proteins

● Ester

○ Bacteria and eukaryotic plasma membranes

● Ether

○ Archaea plasma membranes

● Sulfhydryl

○ Energy metabolism and protein structure

● Carboxyl

○ Organic acids

● Phosphate

○ ATP, DNA

● We maintain ourselves with a process called homeostasis

○ We maintain at pH 7

○ Archaea like pH 2

○ Some things grow at pH 2 at 100C 

● How do we form macromolecules

○ Monomers Join by dehydration synthesis or condensation reactions ○ Fig 2.8

● Found in all cells that are living

○ Proteins

○ Carbohydrates

○ Lipids

○ Nucleic acids

● Functions and Properties

○ Carbohydrates

■ Starts as a sugar

● Glucose and fructose go through dehydration synthesis to from

sucrose and water

● Can be reversed through hydrolysis

■ Only finding Carbon, hydrogen and oxygen

● In this ratio

○ CH20

● Hexose C6H1206.

○ Example:

■ Glucose, fructose and Galactose are isomers they

have the same chemical make up just in a if fervent

orientation

● Pentose C5H10O5 Example: Ribose

● C,H22O11is a disaccharide with two linked sugars know as sucrose ○ Polysaccharide are two linked sugars

○ Oligosaccharides are more than two sugars

● Important note

○ Every time a sugar is added water is formed through the

dehydration synthesis

○ Polymers v.s. macromolecules

■ x­x­x­x­x­x­x­x­x­x­x­x­x­x­x­x­x

● All x are glucose molecules

● Bond formed between them is an ether (C­O­C bond) linkage with a directional linkage

○ Alpha 1­4 linkage

■ An ether linkage between the first carbon on the

first carbon ring and the 4 carbon on the second

carbon ring going on the bottom

● Example

○ Starch and amylose is done only

with alpha 1­4 linkage

○ Beta 1­4 linkage

■ An ether linkage between the first carbon on the

first carbon ring and the 4 carbon on the second

carbon ring going on the top

● Example

○ Cellulose is done only with beta 1­4

linkage

○ We can make fibers with this

○ Lipids

■ Simple lipids

● Fats or triglyceride

○ Glycerol and fatty acids

● Saturated fats have hydrogens on all the carbons

○ Solid at room temperature

■ Example

● Butter

● Crisco, vegetable shortening

● Unsaturated fats have one or more double bonds

○ Causing it to bend at the double bond

○ More liquid and healthy

■ Example

● Olive oil

● Good for storage of energy and also cell walls

● Functional group is a carboxylic acid with. A long carbon structure with an ester linkage between the glycerol fatty acids

○ Known as a triglycerides due to the three fatty acid chains

■ Phospholipid

● C­H­O­Phosphorus

● Polar heads with nonpolar tail

○ Polar head

■ Hydrophilic

● Likes water

○ Nonpolar tail

■ Hydrophobic

● Hates water

○ Forms lipid bilayers

■ If saturated the membrane is immobile

■ If unsaturated the membrane moves more

● Cholesterol is a Steroid

○ Fig 2.11

○ Found in a eukaryotic beings bacteria don't have much if

any present

○ Protein

■ N­C­C

● Structure, transport, membrane, metabolic enzymes,

● Fig 2.12

● Building blocks are amino acids

○ Table 2.5

○ Glycine

○ Alanine

○ Cysteine

■ Important structure to know

○ Isoleucine

■ Nonpolar

○ Glutamic acid

■ Polar

○ Lysine

● Displays steiro chemistry in the form of chirality aka enantiomers ○ Example

■ Hands

■ L for left and D for right

■ L are more common in biology

■ Figure 2.13

● Peptide bonds formed by dehydration synthesis

○ Fig 2.15

○ Primary

■ Polypeptide strand

● All of the amino acids in a strand

● Example

○ X­y­u­x­t

○ Secondary

■ Comes about from hydrogen bonds

● coil to make alpha helix Or make beta

pleated sheets

○ Tertiary

■ 3D structures

● Fold around self

● Has a directionality

○ One end has an amino end on one

side and a carboxylic Acid on the

other end

● Keeping shape

○ Uses disulfide bonds to make sulfide

bridges

○ Uses ionic bonds

○ Uses hydrophobic interactions

○ Uses Hydrogen bonds

○ Quaternary

■ Two or more polypeptides in their folded states

■ X­X

■ &­%

● Known as a heterodimer

● Hemoglobin is a alpha 2 beta 2 heterodimer

○ With one amino acid change in one

subunit of hemoglobin you have

sickle cell anemia

■ It doesn't always change the

function but it can

■ &­%­&­%

● Known as a heterotetramer

● Conjugated proteins

○ Proteins and small macromolecules

■ Results in glycoproteins and lipoproteins

○ Nucleic acids

■ DNA

● Has thymine not uracil

■ RNA

● Basic elements found

○ C H O N P

● Doesn't have the base thymine it has uracil

■ Basic structure

● Nucleotide

○ Phosphate bonded to a sugar which is bonded to a base

■ If the ribose is missing a OH group it results in

Deoxyribose resulting in DNA

■ This base determines the type of nucleotide

■ Purines­ has two rings

● Adenine

● Guanine

■ Pyrimidines

● Cytosine

● Thymine or uracil

■ Bonding rules

● Apples on Trees

○ Adenine bonds to Thymine

● Gas in Cars

○ Cytosine bonds to Guanine

● Nucleoside

○ Just the base and sugar

● ATP

○ Adenosine Triphosphate

○ Has ribose adenine and 3 phosphate groups

■ The breaking of the phosphate groups results in

energy

● ADP

○ Adenosine Diphosphate

● Lecture 3­chap 3

○ Some metric units of length

■ 1 meter is equal to

● 39.4 inches

● 3.28 feet

■ 1 centimeter

● .01 meter

● .39 inch

■ Millimeter

● 1/100 meter

■ Micrometer

● 1/1000000 meter

○ 10^­6

● .0000394 inch

■ Nanometer

● 1/1000000000 meter

○ 10^­9

○ Figure 3.2

○ Size

■ Tick 1 mm

■ Red blood cell 4. Micrometer

■ E.coli bacteria 1 micrometer

■ Virus 50 nanometer

■ DNA 50 nanometers

○ Microscopy the instruments

■ Magnification =Objective lens X ocular lens

● Max 1­2000X for light microscope

■ Resolution

● The ability of lenses to distinguish fine detail and structure

● Ordinary light microscope Resolution parameter is around .2 um ■ Curtail light

● Bending or refractive index

● Fig 3.3

● This is drones by adding immersion oil

○ Types of microscope

■ Direct light

● Energy

○ White light

● Type

○ Bright field microscopy

● Use

○ Stain specimens

■ Reflective light

● Energy

○ White light

● Type

○ Dark field microscopy

● Use

○ Place an opaque disk so that there is a dark background

allowing more detail to be seen with difficult to be seen

■ EX

● Syphilis

■ Direct and reflective

● Cream of the crop microscope

● Energy

○ White light

● Type

○ Phase contrast

● Use

○ enhances the contrast

○ Has a diffraction plate and annular diaphragm

■ Fluorescence

● Energy

○ Uv light

● Type

○ Fluorescence

● Use

○ Cells stained with dyes know as fluorochromes

■ Confocal

● Energy

○ Laser light

● Type

○ UV

● Use

○ More detail inside

○ 3D image

○ Takes small pictures at various planes that reform later in

the computer

■ Electron microscopy

● Energy

○ Electrons

● Type

○ Transmission, tunneling and scanning

● Use

○ Transmission

■ Magnification 10­100000X

■ Resolution 2.5 nm

● Sees inside

● Has a heavy metal stain to attract the

electrons

○ Scanning

■ 1000­10000X

■ Resolution 10nm

● Sees outside

● Has a heavy metal coating with gold

catching the reflected specimens

○ Staining methods

■ Be familiar with smear and staining procedure

■ Simple stains

● Have one stain added to it

■ Differential

● Used to distinguish groups of microorganisms

○ Gram stain

■ Differentiation between gram positive and gram

negative

■ Crystal violet

● Purple dye

● Gram positive

■ Iodine

● Mordant

○ Forces the dye into the cells

■ Alcohol

● Decolorization

■ Safranin

● Counterstain

○ Gram negative

○ Acid­fast stain

■ Mycobacterium

● Positive acid fast

○ Examples

■ Mycobacterium leprae

■ Causes leprosy

■ Mycobacterium tuberculosis

■ Causes tuberculosis

■ Mycobacterium smegmatis

● Stains positive because of the mycolic acid

in the cell walls

■ Special stains

● Fig 3.14

● Negative staining

○ Good for seeing capsulized cells

● Endosperm staining

○ Makes endospores clearer

○ Common bacteria used in the test

■ Bacillus

● Aerobic

○ Must have oxygen

■ Clostridium

● Anaerobic

○ No oxygen required

● Flagella staining

○ Pronounces the flagella of bacteria

● Lecture 4

○ Prokaryotes

■ Eubacteria

● Know as

○ True bacteria

○ Cyanobacteria (blue­green)

■ Updated name for algae

■ Archaebacteria

● Known as

○ Ancient bacteria

○ Differentiation of prokaryotes

■ Morphology

● Coccus

○ sphere

● Rod

● Spirillum

● Spirochete

● Budding and appendaged bacteria

● Filamentous

■ Chemical composition

■ Nutrient requirements

■ Biochemical activities

○ Comparison of prokaryotes and eukaryotes

Thing

Prokaryotes

Eukaryotes

DNA surrounded by

membrane

NO

YES

Membrane bound

organelles

NO

YES

Histones associated with DNA

NO

YES

Cell wall with

peptidoglycan

YES

NO

Mitosis

NO

YES

Size

.2­2 um

10­100 um

○ Bacterial structures

■ Fig 4.6

■ Structures unique to bacteria

● Glycocalyx

○ Sugar coat around cell

○ Capsule

■ When it's firmly attached around the cell

■ Protects pathogenic bacteria from phagocytosis by

the cell of the host

○ Slime layer

■ When it is unorganized around the cell

○ Function

■ Makes it sticky

■ Resists and makes it difficult to proceed with

phagocytosis

● Example

○ Plaque

● Flagella

○ Function

■ Allows propulsion

○ Made of protein called flagellum

○ Anchored to cell wall and membrane by basal body

○ The hook rotates circularly

■ Different from eukaryotes where it undulates

○ Arrangements can be different around the cell

■ Fig 4.7

■ Atnichois

● Without flagella

■ Polar

● Both ends of the cell

● Monotratus

○ On one pole (one end of the cell)

● Lophotrichous

○ Tuff coming from one pole

● Amphitrichous

○ Flagella on both poles

■ Periatratus

● Many flagella all over the cell

○ Parts

■ Filament

● Contains flagellum around a hollow core

■ Hook

■ Basal body

● Anchor to the cell

○ Movement aka bacterial taxis

■ Fig 4.6

■ Run

● When flagella rotate in a clockwise motion

■ Tumble

● When flagella stop rotating

● Axial filament

○ Called endoflagella

○ Rotation causes cell to move in a twisting motion

■ Spirochete bacteria

■ Treponema pallidum

● Fimbriae

○ Can be all over surface

○ Smaller than flagella

○ Function

■ Attachment

● Pili

○ Longer than Fimbriae

○ 1 to 2 per cell

○ Involved in DNA transfer between cells

● Cell wall

○ Made of peptidoglycan

■ Repeating N­acetylglucosamine (NAG) a​nd

N­acetylmuramic acid (NAM)

■ Linked by short peptides chains in the D the type

■ Linkages between NAM and NAG

● Ether linkage with a Beta 1­4 linkage

● The peptide bond attaches to the NAM

● Fig 4.12

○ Lysis

■ Destruction of cell due to cell rupture

○ Protoplast

■ Wall­less cell where plasma membrane may remain intact if lysis doesn't occur

○ Difference between gram negative and gram positive cells ■ Fig 4.13

■ Gram negative

● Above the double layer plasma membrane

the peptidoglycan rest with (10­20%) with a

outer membrane above that. Sticking out of

this is LPS

○ Remember it's a sandwich

■ Gram positive

● Right above the double layer plasma

membrane is Peptidoglycan (60­90%) with

polysaccharide teichoic acids

○ Remember it's a chunk of meat on a

piece of bread

■ Acid­fast cell wall

● 60% lipid membrane prevents uptake of dye

● Cell membrane

○ Also known as inner membrane

○ Inside cell wall in casing the cytoplasm

○ Breakdown of nutrients and production of ATP

○ Where moment across the layer occurs

○ The plasma membrane

■ Phospholipid bilayers

■ Peripheral proteins

■ Integral and transmembrane movement

○ Fluid mosaic model

■ Membrane is viscous

■ Membrane moves unilaterally

■ Made up of phospholipids and proteins

○ Passive­downhill

■ Along the gradient

■ Simple diffusion

● Just crosses the membrane

○ Slower and linear

■ Facilitated diffusion

● Uses protein in the membrane to change or add to item before entering the cell

○ Not necessary

● Rate of entry it quick but eventually settles

out as the concentration gradients equalize

as all carrier proteins are in use

○ Active ­up hill

■ Against the gradient

■ ATP dependent

■ Requires energy but not ATP directly

● Something other than ATP used

○ Transporters or permeases

■ Simple diffusion

● Doesn't use ATP

○ Driven by energy in the proton

motive force

● Uses membrane charge gradient

● Used to maintain equilibrium

● Uses first law of thermodynamics

○ Energy can not be created or

destroyed only transformed

● 2nd law of thermodynamics

○ Trendcy for things is to favor entropy

● Symporter

○ Transports in

● Antiporter

○ Transport out

■ Group translation

● Mainly seen in bacteria

● Chemical modification of transported

substance driven by phosphoenolpyruvate

○ R­P

■ ABC transporter

● Periplasmic binding proteins are involved

and energy comes from ATP

○ ATP­> ADP + Pi 

■ Facilitating diffusion

● Proteins in the membrane function as

spaces for things to pass when the

corresponding receptors are present

■ Osmosis

● Net movement of solvent across membrane

● Cytoplasm

○ 70% water

○ No cytoskeleton

○ Has things suspended inside

● Inclusions

○ Ribosomes

■ Fig 4.19

■ Has a defined structure

● Consists of a large subunit (50S) and small

subunit (30S)

○ 50 and 30 equals 70S

■ S is a suedberg

■ Is the rate of sedimentation a

in an ultracentrifuge

○ This differentiation is good for

antibiotics to fight bacteria and not

fight your own cells

■ Composed of RNA and proteins

○ Granular storage

■ Phosphate

■ Lipid

■ Sulfur

■ Specialized compartment

● Carboxysome

○ Involved in photosynthesis

● Magnetosome

○ Magnets to help orientation and

move

■ Gas vacuoles

○ Endospore

■ Fig 4.21

■ Makes a large structure and loose main part of cell (vegetative cell)

○ Tolerant to heat and drought can last

up to 75 years

○ Know structure of eukaryotic cell

● Only plants have cells walls

● In the cytoplasm there is the apprentice of a cytoskeleton ○ Microtubules

○ Actin and myosin

● Are continuous not each other

○ Nucleus /

○ Endoplasmic reticulum

■ Detoxification Lipid and CHO

○ Golgi complex

■ Pick up proteins

■ Protein synthesis

■ Distributed system

○ Lysosomes

■ Destruction

○ Plasma membrane

● Mitochondrian

○ has to own matix

○ Endosymbiosis theory

■ We have 70s mitochondria and chloroplast inside eukaryotic cells

■ The antient cell absorbs this bacteria and both

benefit from being present in the cell

● The bacteria can not replicate on their wn

■ Figure 10.2

● Chloroplast

● Table 4.2 differences between prokaryotic and eukaryotic cells

● Cultivation and growth

○ Minimum requirement for growth

■ Chemical

● Carbon,

○ Biomass and energy

● Nitrogen,

○ Biomass and other cell components

● Hydrogen,

● Phosphorus

● Sulfur

● Water

● Trace metals

○ Fe Mg Ca K Mo

● Growth factors

○ Vitamins

● Oxygen

○ Toxic oxygen species

■ H2O2 

● Catalase

● 2H2O2­­>2H2O+ O2 

■ O2­

● Attacked by superoxide dismutase

● 2H+ 2O2­ ­­­> H2O2 +O2 

■­OH

● Most toxic

microbe

catalase

superoxide dismutase

relations to oxygen

aerobes

and

facultative

anaerobes

yes

yes

tolerate

required/not required

obligate

anaerobes

no

no

not

tolerated

not required

aero

tolerant

no

yes

some

tolerance

not required

microaerop

no

yes

some

hile

tolerance

Required

■ Physical requirements

● Temperature

○ Figure 6.1

○ Hyperthermophiles

■ 95C 

○ Thermophiles

■ 60C 

○ Mesophists

■ >35C 

○ Psychotropics

■ Food spoilers

■ 20C 

■ Grow in the cold

○ Psychrophiles

■ Oceans and Arctic regions

■ 10C 

● pH

○ Acidophiles

■ acid loving

■ Grows around pH2

○ Alkalophiles

■ base loving

■ Grows around pH9

● Osmoticum

○ Salt concentration

○ Moderate halophilic

○ Halophiles

■ Think the Dead Sea

■ Culture media

● Types of media

○ Artificial media

■ Complex

● Nutrient agar

■ Chemically defined

■ Selective or differential

● Blood agar

● Mannitol­salt Agar

○ Live

■ Needs a live specimen to cultivate organism

● M. Leprae grows on armadillo

● Table 6.2

○ Chemically defined

■ We know all the things in it to the chemical

composition

● Table 6.4

○ Complex media

■ There is one unknown in the media in which we

don't know the chemical makeup of

● Cultivation methods

○ Mixed vs pure cultures­ what’s a colony?

■ Mixed culture

● More than one organism

■ Pure culture

● Just one culture

■ Streak­plate

● Diluting the culture so that there is isolated

colonies formed by “cloning”

■ Spread­ plate

○ Anaerobic cultivation techniques

■ Works inside a glove bag or glove box

● There is no oxygen inside the area to do the

experiment

■ Gas­Pak anaerobic jar

● Put plates inside a jar with bags of gas

inside

■ Candle jar

● When the candle no longer burns there is

no more oxygen

■ CO2 packet

● Much like the Gas­Pak the Petri dish is

inside a package preventing oxygen from

entering

○ Maintenance and preservation

■ Using an agar slant

● Can keep for about a year

■ Cryogenic freezing

● Mix your culture with something like glycerol

● Freeze at ­20C 

○ Other agent can allow it go as cold

as ­80C 

■ Lyophilization

● Freeze dried

● Create a vacuum at a cold temperature and seal it

● Can keep till rehydrated

○ Bacterial growth

■ Fig 6.15

● Lag phase

○ Cells are adapting to the new

medium

● Log phase

○ Exponential growth phase

○ Binary fission

■ Grown is 2n 

■ One cell splits to 2

■ This causes a geometric

growth

○ Growth rate constant represented by

μ

■ Ln 2 equal to .693

○ Generation time is represented by t

gen

■ μ equal (ln2)/t gen

■ ___ generations per hour

● Stationary phase

○ Inhibitors (lack of nutrients,

overpopulation) max out the growth

of bacteria

● Death

○ Logarithmic decline

■ Measuring growth

● Direct

○ Count the actual numbers of cells

○ Weigh the biomass that is present

○ Microscope measurement

■ A grid is placed below slide

to directly count the cells

■ Gives total not the viable

cells

● Indirect

○ Turbidity

■ How much light passes

through the suspension

○ Oxygen consumption

○ Carbon dioxide production

■ Isolation and counting

● Pour plate method

○ Swirl agar and culture

■ Count growth in and on the

plate

● Spread plate method

○ Spread liquid across

■ Count what is on top

● Serial dilution

○ 1:1,000,000 and plate it out

● Lecture 5

○ Microbial metabolism

○ Figure 5.1

■ A driving force for the cell to want to reproduce

■ Metabolism equal to Catabolism plus anabolism

● Catabolism

● Anabolism

■ Organisms

○ Chemotrophs

■ Uses chemicals as an energy source

● Organotrophs

● Lithotrophs

○ Phototropism

■ Uses sunlight as an energy source

● Enzymes

○ Speed up chemical reactions

○ Types

■ Oxidation

● Removal of electron

● Aka take hydrogen away

● Also know as dehydrogenation

■ Reduction

● Gain electron

● Aka take Oxygen away

■ Redox reaction

● Oxidation Paris with reduction

● 5.9 figure

■ Cofactors

● Things used to activate an enzyme before

the substrate

■ Dehydrogenases

● Needs a protein & a cofactor (nonprotein)

and then a substrate forming a holoenzyme

(whole enzyme)

○ If it's tightly bound its know as a

prosthetic group

■ Doesn't like to leave

● Figure 5.3

○ Denaturation

■ Loss of tertiary structure isn't the primary structure ■ Happens due to temperature and pH

● Conservation of energy

○ Mechanisms of generating ATP

■ Substrate­level phosphorylation

● P­diphosphoglyceric acid­P ­­­>

3­phosphoglyceric acid

○ 1,3­DPGA­­­>3­PGA

■ Oxidative phosphorylation

● Figure 5.14

● Involves ETC

○ Electron transport chain

■ Bound to the mitochondrial

membrane

■ In bacterial this occurs on the

plasma membrane

○ Enzymatic complexes

■ NADH dehydrogenase

(flavoprotein)

■ Cytochrome b­c1(Fe)

■ Cytochrome oxidases (Fe)

■ Photophosphorylation

● Light­driven

○ Glycolysis

■ 4 ATP produced

■ 2NADH produced

● Aerobic respiration

■ C6H12O6 + 6O2­­­> 6CO2+ 6H2O

■ Emben­Meyerhof pathway

○ Pre­TCA

■ Occurs in cytoplasm

■ Everything after occurs in the mitochondria

○ KRebs cycle, TCA

■ Fig 5.13

■ produces ATP via oxidative phosphorylation

■ Malic acid picture

○ Table 5.3 keeps track of the energy bookkeeping ○ Chemiosmosis

■ Peter Mitchell Nobel 1978

■ . Fig 5.16

■ Yields 3 ATP per 1 NADH

● What if there is no oxygen?

○ Glucose fermentation

■ Yeast

■ Forms lactic acid and or ethanol

■ only forms via substrate level phosphorylation ■ fig 5.18b

■ Wiseman process

● How we make acetone

■ Fig 5.27

■ Doesn't use electron transport chain ○ E.coli can live theses ways:

■ Aerobic

● Glucose

○ Electron donor

● NH3 

● S

● P

● TM

● O

○ Electron acceptor

■ Anaerobic

● Glucose

○ Electron donor

● NO3­

● S

● P

● TM

● He

○ Electron acceptor

■ Fermentation

● Glucose

○ Electron donor

● N­3 

● S

● P

● TM

● He

○ Electron acceptor

Stain type

Purpose

Dyes

Concept

Gram stain

Differentiate between gram negative​and gram positive​cells

1. Crystal violet

2. Iodine

3. 95% alcohol

4. Safranin

Developed by Christian Gram 1884

Gram positive​items will be purple​while gram negative​items will be red

Negative stain

To see morphology Size, shape, and

arrangement

Nigrosin

The negative charge stain is repelled from the

negative charge bacteria causing the background to be black and the cells to appear a purple white

Simple stain

To see the cell

morphology

Basic stains such a s methylene blue

The negative charged cell takes in the positive

charged dye

Endospore

stain

Used to see the

endospores around cells

Schaeffer­Fulton

method

1. Malachite

green

2. Water

3. Safranin

The constant heat breaks down the protein coat around the Endospore and will take the green dye everything else will appear pink

Acid­fast stain

Differential stain

identifies the

members of

Mycobacterium

Kinyoun stain

1. Carbolfuchsin

2. Acid alcohol

3. Methylene

blue

The red ​rods will be the bacterium in the Genus Mycobacterium whereas everything else will be blue

Remember Golden age of microbiology was 1857­1884 ● 4.5 billion years ago

○ Earth is formed in the Big Bang

● 3.8 billion years ago

○ Archaea appear

● 2.7 billion years ago

○ Oxygen appears

● .7 billion years ago

○ Multicellular organisms appear

● .2 billion years ago

○ Man appears

● 1665

○ Leeuwenhoek

■ Makes first microscope

■ Makes first observation of microorganisms

● 1735

○ Carolus Linnaeus

■ Makes official two part naming system

● 1857

○ Pasteur

■ Fermentation

● 1861

○ Pasteur

■ Disproves spontaneous generation

● 1864

○ Pasteur

■ Pasteurization

● 1876

○ Koch

■ Germ theory of disease

● 1884

○ Gram

■ Gram­stain procedure

● 1928

○ Fleming

■ Penicillin

● 1973

○ Berg

■ Genetic engineering

● 1975

○ Mitchell

■ Chemiosmotic mechanism

● 1987

○ Tonegawa

■ Described genetics of antibody production

● 1989

○ Bishop & Varmus

■ Discovered oncogenes, cancer causing genes ● 1997

○ Prusiner

■ Prions

● 2005

○ Marshall & Warren

■ Peptic ulcers caused by Helicobacter pylori

● 2008

○ Barre & Montagnier

■ Discovered HIV

Media

Organism

Inhibitor

Indicator

Result

CNA Agar

Promotes

growth of gram positive material

Colistin

Nalidixic acid

Growth of gram positive

organism

MacConkey

Agar

Selective and

differential

Growth of gram negative

organism

Bile salts­ inhibit Gram positive

Neutral red​color will come to the colonies

Lactose

fermenting gram negative

colonies will

appear pink

Lactose non

fermenters will turn clear

Mannitol Salt

Agar

Selective and

differential

Growth of

Staphylococcus spp

Sodium chloride 75%

Phenol red

S.

Saprophyticus produces white color colonies

and turns media yellow

S. epidermidis doesn’t have a color change

Tryptic Soy Agar

Grows most

things

Growth of the

majority of

organisms

Blood Agar Plate

Enriched and

differential

media

Growth of most gram­positive

and

Gram­negative

Blood

Hemolytic

patterns

Alpha, Beta,

gamma, and non hemolysis

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