Download prokaryotic cell

Chap.2
Basic concepts of Biology
5 basic groups of microbes
• a. bacteria
• Bacteria are typically unicellular, microscopic, prokaryotic organisms that reproduce by bi
nary fission (see Fig. 1 and Fig.2).
• b. fungi: yeasts and molds
• Yeasts are typically unicellular, microscopic, eukaryotic fungi that reproduce asexually by
budding (see Fig. 3 and Fig. 4).
• Molds are typically filamentous, eukaryotic fungi that reproduce by producing asexual rep
roductive spores (see Fig. 5 and Fig. 6)
• c. viruses
• Viruses are typically submicroscopic, acellular infectious particles that can only replicate i
nside a living host cell. The vast majority of viruses possess either DNA or RNA but not bot
h (see Fig. 7 and Fig. 8).
• d. protozoa
• Protozoa are typically unicellular, microscopic, eukaryotic organisms that lack a cell wall (
see Fig. 9 and Fig. 10).
• e. algae
• Algae are typically eukaryotic microorganisms that carry out photosynthesis (see Fig 11 an
d Fig. 12).
Terms
• -phil- (-phile, -philia, -philic) are used to spe
cify some kind of attraction or affinity to somethi
ng, in particular the love or obsession with some
thing.
• They are antonymic to suffixes -phob-.
• Phil- (Philo-) may also be used as a prefix with
a similar meaning.
Microorganism
-temperature
• mesophilia / mesophile: Preference of moderate
temperatures in microorganisms.
• psychrophilia / psychrophile: Preference of cold
temperatures.
• thermophilia: Love of high temperatures; thrivin
g in high temperatures (e.g. microbes).
microorganism
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Biology
acidophilia / acidophile: Preference of acidic conditions
alkaliphilia / alkaliphile: Preference of alkaline environments.
anthophilia / anthophile / anthophilic: Attraction to flowers.
anthrophile / anthrophilic: Attracted to humans (e.g., parasites).
anemophily: a form of pollination whereby pollen is distributed by wind.
cryophilia / cryophilic / cryophile: Preference for cold environments, climates, objects and l
ow temperatures; e.g., Protea cryophila (Snow Protea).
extremophilia / extremophile: Preference of living extremal conditions for some microorga
nisms.
geophilia / geophilic / Geophile Referring to organisms that prefer the soil.
halophilia / halophile: Attraction/attracted to salt or salt-water.
heliophilia / heliophile: Attraction/attracted to sunlight.
hydrophilia: Attraction to water.
hyperthermophilia / hyperthermophile / hyperthermophilic: Describing organisms that thr
ive in extremely hot environments.
limnophilia / limnophile / limnophilic: Preference of ponds or marshes.
lithophilia / lithophile / litophilic: Preference/affinity to stones.
microorganism
• microaerophilia / microaerophile / Microaerophilic: of organisms that can tolerate or requi
re environments containing low levels of oxygen.
• myrmecophilia: in names of orchids of genus myrmecophila, "love of ants"
• nemophilia: Love of the woods/forests, in the name of the genus Nemophilia of flowers.
• nyctophilia: A preference for darkness or night.
• ombrophilia / ombrophile: Affinity/affined to large amounts of rainfall.
• petrophilia / petrophile / petrophilic: Preference of living or spending time in rocky areas.
• photophilia / photophile / photophilic: Preference of living or spending time in lighted con
ditions.
• psammophile: A plant loving sandy areas (psammophyte).
• rheophilia: Preference of living in running water.
• rhizophilia: Preference of living on roots.
• tropophilia / tropophile / tropophilous: Preference of seasonal extremes of climate.
• xerophilia: Love of living or spending time in very dry conditions.
• xylophilia: Love of wood.
• zoophily: a form of pollination whereby pollen is distributed by animals.
Introduction to bacteria
-Morphology and classification
• Bacillus (plural, bacilli): rodlike
• Coccus (plural, cocci):
spherical
-cocci often take on multi-cell
forms:
=two cocci: diplococci
=chains of cocci: streptococci
1. The coccus
• The cocci are spherical or oval bacteria having one of several distinct arrang
ements based on their planes of division.
• a. Division in one plane produces either a diplococcus or streptococcu
s arrangement.
• b. Division in two planes produces a tetrad arrangement.
a tetrad: cocci arranged in squares of 4
- photomicrograph of a tetrad
• c. Division in three planes produces a sarcina arrangement.
sarcina: cocci in arranged cubes of 8
- photomicrograph of a sarcina
• d. Division in random planes produces a staphylococcus arrangement.
• staphylococcus: cocci arranged in irregular, often grape-like clusters
- photomicrograph of a staphylococcus
An average coccus is about 0.5-1.0 micrometer (µm) in diameter. (A micro
meter equals 1/1,000,000 of a meter.)
2. The rod or bacillus
• Bacilli are rod-shaped bacteria. Bacilli all divide in o
ne plane producing a bacillus, streptobacillus, or
coccobacillus arrangement.
• a. bacillus: single bacilli
-(eg., Escherichia coli O157H7, a bacillus)
• b. streptobacillus: bacilli arranged in chains
- photomicrograph of a streptobacillus
• c. coccobacillus: oval and similar to a coccus
• An average bacillus is 0.5-1.0 µm wide by 1.0-4.0 µm
long.
3. The spiral
• Spirals come in one of three forms, a vibrio, a spiri
llum, or a spirochete.
• a. vibrio: a curved or comma-shaped rod
- photomicrograph of a vibrio
• b. spirillum: a thick, rigid spiral
- photomicrograph of a spirillum
• c. spirochete: a thin, flexible spiral
- photomicrograph of a spirochete
• Spirals range in size from 1 µm to over 100 µm in len
gth.
1. nuclear body
• eukaryotic cell
• a. The nuclear body is bounde
d by a nuclear membrane havi
ng pores connecting it with the
endoplasmic reticulum
b. It contains one or more pair
ed, linear chromosomes comp
osed of deoxyribonucleic acid (
DNA) associated with histone
proteins.
c. A nucleolus is present.
d. The nuclear body is called a
nucleus
• prokaryotic cell
• a. The nuclear body is not bou
nded by a nuclear membrane.
b. It usually contains one circu
lar chromosome composed of
deoxyribonucleic acid (DNA) a
ssociated with histone-like pro
teins.
c. There is no nucleolus.
d. The nuclear body is called a
nucleoid
2. cell division
• eukaryotic cell
• a. The nucleus divides by mito
sis.
b. Haploid (1N) sex cells in dip
loid or 2N organisms are prod
uced through meiosis
• prokaryotic cell
a. The cell usually divides by bin
ary fission.
• There is no mitosis.
b. Prokaryotic cells are haploid.
• Meiosis is not needed.
3. cytoplasmic membrane
- also known as a cell membrane or plasma me
mbrane
• eukaryotic cell
• a. The cytoplasmic membrane
is a fluid phospholipid bilayer
containing sterols.
b. The membrane is capable of
endocytosis (phagocytosis and
pinocytosis) and exocytosis.
• prokaryotic cell
• a. The cytoplasmic membrane;
is a fluid phospholipid bilayer
usually lacking sterols.
• Many bacteria do contain stero
l-like molecules called hopanoi
ds.
•
b.The membrane is incapable
of endocytosis and exocytosis
4. cytoplasmic structures
•
eukaryotic cell
• a. The ribosomes are composed of a 60
S and a 40S subunit forming an 80S ri
bosome.
b. Internal membrane-bound organell
es such as mitochondria, endoplasmic
reticulum, Golgi apparatus, vacuoles,
and lysosomes are present.
c. Chloroplasts serve as organelles for
photosynthesis.
d. A mitotic spindle involved in mitosi
s is present during cell division.
e. A cytoskeleton is present.
• It contains microtubules, actin micofil
aments, and intermediate filaments. T
hese collectively play a role in giving s
hape to cells, allowing for cell moveme
nt, movement of organelles within the
cell and endocytosis, and cell division.
•
Prokaryotic cell
• a. The ribosomes are composed of a 50
S and a 30S subunit forming an 70S ri
bosome.
b. Internal membrane-bound organell
es such as mitochondria, endoplasmic
reticulum, Golgi apparatus, vacuoles,
and lysosomes are absent
b. There are no chloroplasts. Photosyn
thesis usually takes place in infoldings
or extensions derived from the cytopla
smic membrane.
c. There is no mitosis and no mitotic s
pindle.
d. They may contains only actin-like p
roteins that, along with the cell wall, c
ontribute to cell shape.
5. respiratory enzymes and electron
transport chains
• eukaryotic cell
• - The electron transport syste
m is located in the inner memb
rane of the mitochondria
• prokaryotic cell
• - The electron transport syste
m is located in the cytoplasmic
membrane
6. cell wall
• eukaryotic cell
• a. Plant cells, algae, and fungi
have cell walls, usually compos
ed of cellulose or chitin. Eukar
yotic cell walls are never comp
osed of peptidoglycan
b. Animal cells and protozoans
lack cell walls
• prokaryotic cell
• a. With few exceptions, memb
ers of the domain Bacteria hav
e cell walls composed of peptid
oglycan
b. Members of the domain Arc
hae have cell walls composed o
f protein, a complex carbohydr
ate, or unique molecules resem
bling but not the same as pepti
doglycan.
7. locomotor organelles
• eukaryotic cell
• - Eukaryotic cells may have fla
gella or cilia. Flagella and cilia
are organelles involved in loco
motion and in eukaryotic cells
consist of a distinct arrangeme
nt of sliding microtubules surr
ounded by a membrane.
• prokaryotic cell
• - Many prokaryotes have flagel
la, each composed of a single, r
otating fibril and usually not s
urrounded by a membrane.
8. representative organisms
• eukaryotic cell
• - The domain Eukarya: animal
s, plants, algae, protozoans, an
d fungi.
• prokaryotic cell
• - The domain Bacteria and the
domain Archae.
Since viruses are acellular and possess both living and nonliving characteristics,
they are considered neither prokaryotic nor eukaryotic.
Learning Objectives for "Prokaryotic Cell
Structure: The Cytoplasmic Membrane"
• 1. State the chemical composition and major function of the cytoplasmic membrane in bact
eria.
• 2. Briefly describe the fluid phospholipid bilayer arrangement of biological membranes.
• 3. State the net flow of water when a cell is placed in an isotonic, hypertonic, or hypotonic e
nvironment and relate this to the solute concentration.
• 4. Define the following means of transport:
• a. passive diffusion
b. osmosis
c. channel proteins
d. uniporter
e. antiporter
f. symporter
g. facilitated diffusion
h. active transport
i. the ABC transport system
j. group translocation
• 5. State how the antibiotic polymyxin and disinfectants such as orthophenylphenol, chlorhe
xidine, hexachlorophene, zephiran, and alcohol affect bacteria.
• 6. Define binary fission and geometric progression and relate this to bacteria being able to a
stronomically increase their numbers in a relatively short period of time.
• 7. Briefly describe the process of binary fission in bacteria.
Plasmids and Transposons
• In addition to the nucleoid, many bacteria often
contain small nonchromosomal DNA molecules
called plasmids.
• Plasmids usually contain between 5 and 100 gen
es.
• Plasmids are not essential for normal bacterial g
rowth and bacteria may lose or gain them withou
t harm.
• They can, however, provide an advantage under
certain environmental conditions. For exampl
e, under normal environmental growth conditions, b
acteria are not usually exposed to antibiotics and ha
ving a plasmid coding for an enzyme capable of dena
turing a particular antibiotic is of no value.
• However, if that bacterium finds itself in the body w
hen the particular antibiotic that the plasmid-coded
enzyme is able to degrade is being given to treat an i
nfection, the bacterium containing the plasmid is abl
e to survive and grow.
A. Structure and Composition
• Plasmids are small molecules of double strande
d, helical, nonchromosomal DNA.
• Like the nucleoid, the two ends of the double-str
anded DNA molecule that make up plasmids cov
alently bond together forming a physical circle.
• B. Functions
• Plasmids code for synthesis of a few proteins not c
oded for by the nucleoid. For example, R-plasmids,
found in some gram-negative bacteria, often have genes
coding for both production of a conjugation pilus
• http://student.ccbcmd.edu/courses/bio141/lecguide/uni
t1/prostruct/r.html
• Through a process called conjugation, the conjugation pi
lus enables the bacterium to transfer a copy of the R-plas
mids to other bacteria, making them also multiple antibi
otic resistant and able to produce a conjugation pilus.
• C. Transposons (transposable elements or "ju
mping genes") are small pieces of DNA that enco
de enzymes that transpose the transposon, that i
s, move it from one DNA location to anoth
er. Transposons may be found as part of a bacte
rium's nucleoid (conjugative transposons) or
in plasmids and are usually between one and twe
lve genes long.
• Plasmids can also acquire a number of different
antibiotic resistance genes by means of integrons
. Integrons are transposons that can carry mul
tiple gene clusters called gene cassettes th
at move as a unit from one piece of DNA t
o another. An enzyme called integrase enables
these gene cassettes to integrate and accumulate
within the integron. In this way, a number of diff
erent antibiotic resistance genes can be transferr
ed as a unit from one bacterium to another.
• Plasmids and conjugative transposons are very i
mportant in horizontal gene transfer in bacteria.
Horizontal gene transfer, also known as late
ral gene transfer, is a process in which an org
anism transfers genetic material to anoth
er cell that is not its offspring. The ability of
Bacteria and Archaea to adapt to new environm
ents as a part of bacterial evolution, most freque
ntly results from the acquisition of new genes thr
ough horizontal gene transfer rather than by the
alteration of gene functions through mutations.
• A transposon contains a number of genes, codin
g for antibiotic resistance or other traits, flanked
at both ends by insertion sequences coding for a
n enzyme called transpoase.
• Transpoase is the enzyme that catalyzes the cutti
ng and resealing of the DNA during transpositio
n. Thus, such transposons are able to cut themse
lves out of a bacterial nucleoid or a plasmid and i
nsert themselves into another nucleoid or plasmi
d and contribute in the transmission of antibioti
c resistance among a population of bacteria.
Biomolecules
• any organic molecule that is produced by a living
organism, including large polymeric molecules s
uch as proteins, polysaccharides, and nucleic aci
ds as well as small molecules such as primary me
tabolites, secondary metabolites, and natural pro
ducts. A more general name for this class of mol
ecules is a biogenic substance.
• L-type amino acids present in
nature
• Zwitterion:have both positive a
nd negative charges
Carbohydrates
• are organic molecules with the general formula
of CHO in 1:2:1 ratio. Although carbohydrates
constitute only 1 to 2 percent of cell mass, they
provide the raw fuel for cellular energy
production.
• Carbohydrates are classified according to
molecular size and solubility. In general, the
smaller molecules are more soluble than the
larger ones.
Based on McMurry’s Organic Chemistry, 6
th
edition
42
Importance of Carbohydrates
•
•
•
•
Distributed widely in nature
Key intermediates of metabolism (sugars)
Structural components of plants (cellulose)
Central to materials of industrial products: pape
r, lumber, fibers
• Key component of food sources: sugars, flour, ve
getable fiber
• Contain OH groups on most carbons in linear ch
ains or in rings
Chemical Formula and Name
• Carbohydrates have roughly as many O’s as C’s (highly o
xidized)
• Since H’s are about connected to each H and O the empi
rical formulas are roughly (C(H2O))n
▫ Appears to be “carbon hydrate” from formula
• Current terminology: natural materials that contain ma
ny hydroxyls and other oxygen-containing groups
H OH
HO
HO
HO
H
H OH
OH
H
D+ Glucose C6H12O6
43
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Sources
• Glucose is produced in plants through photosynt
hesis from CO2 and H2O
• Glucose is converted in plants to other small sug
ars and polymers (cellulose, starch)
• Dietary carbohydrates provide the major source
of energy required by organisms
45
Classification of Carbohydrates
• Simple sugars (monosaccharides) can't be converted into
smaller sugars by hydrolysis.
• Carbohydrates are made of two or more simple sugars co
nnected as acetals (aldehyde and alcohol), oligosaccharid
es and polysaccharides
• Sucrose (table sugar): disaccharide from two monosacch
arides (glucose linked to fructose),
• Cellulose is a polysaccharide of several thousand glucose
units connected by acetal linkages (aldehyde and alcohol)
Aldoses and Ketoses
46
• aldo- and keto- prefixes identify the nature of the carb
onyl group
• -ose suffix designates a carbohydrate
• Number of C’s in the monosaccharide indicated by roo
t (-tri-, tetr-, pent-, hex-)
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The D-Sugar Family
• Correlation is always with
D-(+)-glyceraldehyde
• (R) in C-I-P sense
48
D, L Sugars
• Glyceraldehyde exists as two enantiomers, first identifi
ed by their opposite rotation of plane polarized light
• Naturally occurring glyceraldehyde rotates plane-polar
ized light in a clockwise direction, denoted (+) and is d
esignated “(+)-glyceraldehyde”
• The enantiomer gives the opposite rotation and has a (
-) or “l” (levorotatory) prefix
• The direction of rotation of light does not correlate to
any structural feature
Cyclic Structures of Monosaccharides:
Hemiacetal Formation
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• Alcohols add reversibly to aldehydes and ketone
s, forming hemiacetals
Fischer Projection Structures of Anomers: All
opyranose from Allose
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Glycosides
• Carbohydrate acetals are named by first citing th
e alkyl group and then replacing the -ose ending
of the sugar with –oside
• Stable in water, requiring acid for hydrolysis
52
Disaccharides
• A disaccharide combines a hydroxyl of one mono
saccharide in an acetal linkage with another
• A glycosidic bond between C1 of the first sugar (
 or ) and the OH at C4 of the second sugar i
s particularly common (a 1,4 link)
A growth medium or culture medium is a liquid or gel designed to support t
he growth of microorganisms or cells [1], or small plants like the moss Physcomit
rella patens [2]. There are different types of media for growing different types of c
ells.[3]
There are two major types of growth media: those used for cell culture, which us
e specific cell types derived from plants or animals, and microbiological culture,
which are used for growing microorganisms, such as bacteria or yeast. The most
common growth media for microorganisms are nutrient broths and agar plates;
specialized media are sometimes required for microorganism and cell culture gro
wth.[1] Some organisms, termed fastidious organisms, require specialized enviro
nments due to complex nutritional requirements. Viruses, for example, are oblig
ate intracellular parasites and require a growth medium containing living cells.
macronutrients
The chemical elements consumed in the greatest quantities by plants are carbon,
hydrogen, and oxygen. These are present in the environment in the form of wate
r and carbon dioxide; energy is provided by sunlight. Nitrogen, phosphorus, pota
ssium, and sulfur are also needed in relatively large quantities. Together, these a
re the elemental macronutrients for plants, often represented by the acronym
CHNOPS. Usually they are sourced from inorganic (e.g. carbon dioxide, water, ni
trate, phosphate, sulfate) or organic (e.g. carbohydrates, lipids, proteins) compo
unds, although elemental diatomic molecules of nitrogen and (especially) oxygen
are often used.
CO2: 탄소공급원
유기화합물: 탄소공급원
Chemo- :무기화합물의 산화:에너지 공급원
Photo-: 빛:에너지 공급원
C. HOPKiN'S CaFe Mg (to be used as C. Hopkins coffee mug) : carbon, hydro
gen, oxygen, phosphorus, potassium, nitrogen, sulfur, calcium, iron, and ma
gnesium.
micronutrients
micronutrients because they are needed only in minuscule amounts, th
ese substances are the “magic wands” that enable the body to produce
enzymes, hormones and other substances essential for proper growth a
nd development.
As tiny as the amounts are, however, the consequences of their absenc
e are severe.
Iodine, vitamin A and iron are most important in global public health t
erms; their lack represents a major threat to the health and developme
nt of populations the world over, particularly children and pregnant w
omen in low-income countries.