introduction to microbes and their building blocks: an...
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Introduction to Microbes and Their Building
Blocks: An Introduction
Chapter 1
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Microbes: Tiny But Mighty •Microbiology deals with living things too small to be seen without magnification
•Microorganisms include - bacteria
- algae
- protozoa
- Helminths
2011
Viruses
•Viruses can infect all living cells, but are not alive themselves
•Viruses are - parasitic - protein-coated genetic elements - dependent on their infected host - connected with the evolution of microbes and
humans
Could a bacteria be infected by a virus?
How about a virus?
Guinea has reported some 396 cases and 280 deaths (71%)
Sierra Leone has 176 cases and 46 deaths (26%)
Liberia reports 63 cases and 41 deaths. (65%)
Ebola 2014
http://www.who.int/mediacentre/news/notes/2014/ebola-response/en/
Características de los seres vivientes :enfoque en Bacterias
1. metabolismo
2. Crecimiento y reproducción
5. Movimiento
6.Evolución
• mutaciones
• perdida de material genético
existente o adquisición
de material genético exógeno
The Nature of Microorganisms •Microbes are very easy and very difficult to study
- reproduce rapidly
- can be quickly grown in large populations in the laboratory
- can’t be seen directly, but we can predict their presence using our senses! Only in special occasions.
Evolutionary Timeline Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Humans
Mammals
Reptiles
Insects
Eukaryotes
1 billion
years ago
2 billion
years ago
3 billion
years ago
4 billion
years ago
Prokaryotes
Probable origin of earth
Present
time
NASA GSFC image by Robert Simmon and Reto Stöckli
Microbes and the Planet (cont’d) •Microbes are ubiquitous
- found in the Earth’s crust, polar ice caps, oceans, and the bodies of plants and animals
- occur in large numbers
- live in places where other organisms cannot survive
Microbial community of in a hypersaline
pond, San Salvador Island, Bahamas
Microbes and the Planet (cont’d)
•Evolution - the accumulation of changes that occur in organisms as they adapt to their environments
•The Theory of Evolution - documented every day in all corners of the planet
- observable phenomenon testable by science
- has undergone years of testing and has not been disproven
- a label for a well-studied and well-established natural phenomenon
Wielgoss, S., J. E. Barrick, O. Tenaillon, M.
J. Wiser, W. J. Dittmar, S. Cruveiller, B.
Chane-Woon-Ming, C. Médigue, R. E.
Lenski, and D. Schneider. 2013. Mutation
rate dynamics in a bacterial population
reflect tension between adaptation and
genetic load. Proceedings of the National
Academy of Sciences, USA 110:222-227.
Richard E. Lenski
Hannah Distinguished Professor
Michigan State University
Email: [email protected]
http://myxo.css.msu.edu/
How Microbes Shape Our Planet
•Anoxygenic photosynthesis
- Light-fueled conversion of carbon dioxide to organic material that does not produce oxygen
•Oxygenic photosynthesis
- Light-fueled conversion of carbon dioxide to organic material that does produce oxygen
- the source of oxygen on the planet
- lead to the use of oxygen for aerobic respiration
- photosynthetic microorganisms account for 70% of the Earth’s photosynthesis
Microbes Harming Humans
•The majority of microorganisms that associate with humans cause no harm •Pathogens: microbes that cause disease •The World Health Organization (WHO) estimates that there are 10 billion new infections caused every year by microbes •Infectious diseases are among the most common cause of death in the U.S. and worldwide •The death toll from infectious diseases is approximately 13 million people per year worldwide •The CDC reports that a child dies from malaria every 30 seconds
Teoría de la generación espontánea: Origen de la vida de objetos no vivientes.
Promulgada por Aristóteles (384-322 B.C.) y aceptada por mas de 1900 años.
Francesco Redi (1629- 1697)
Demostrando que las larvas provienen de las moscas y no de la carne!!
Historia de la Microbiología: rutas de descubrimiento
Antoni van Leeuwenhoek (1684) : primero en observar una bacteria y
describir las células rojas de la sangre
“…tho my teeth are keep usually very clean, nevertheless when I view them in a
magnifying glass, I find growing between them little white matter as thick as wetted
flower: in this substance tho I do not perceive any motion, I judged there might
probably be living Creatures...”
Philosophical Transactions of the Royal Society of London 14(159):568-574 [May 20, 1684].
generación espontánea: En microorganismos?
John T. Needham (1713-1781)
Varios
días
Lazzaro Spallanzani (1729-1799)
Varios
días
sellada
Lazzaro Spallanzani (1729-1799)
Concluye lo siguiente:
1) Needham no sello las botellas herméticamente bien o no las calentó
lo suficiente.
2) Existen microorganismos en el aire y pueden contaminar experimentos.
3) La generación espontánea de microorganismos no existe, todos los seres
vivos surgen de otros seres vivos.
Esto no fue suficiente.. 1) demasiado calor y destruyo la “fuerza de la vida”
2) No permitió que entrara el aire esencial para la vida.
Historia de la Microbiología: rutas de descubrimiento
Louis Pasteur (1822- 1895): prueba que la teoría de generación espontánea es
incorrecta, técnicas de esterilización, vacunas, fermentación, teoría del germen
de enfermedad..
Eduard Buchner (1860-1917)
La fermentación alcohólica puede llevarse acabo sin células vivas
Solo con la presencia de enzimas. Su trabajo da origen a la bioquímica.
Fig. 1.15
sellado
No fermentación
sellado
fermentación
levadura
Historia de la Microbiología: rutas de
descubrimiento
Robert Koch (1843-1910): prueba que los
microorganismos pueden causar
enfermedades (teoría del germen de la
enfermedad),
•catapulta el desarrollo de la microbiología.
Bacillus anthracis
Postulados de Kock
Descubrimiento
de Mycobacterium
tuberculosis
Ignaz Semmelweis (1818-1865)
Joseph Lister (1827-1912)
phenol Heridas, cirugías, gasas, etc.
Observar, hipótesis, experimento, resultados
Mortandad de 18.3% a 1.3%
Florence Nightingale (1820-1910)
Documento e implemento reglas de limpieza en los hospitales.
Además fundo la primera escuela de enfermería.
Libro: Notes on nursing (1859) by Florence Nightingale
Biblioteca UPRM: RT40 .N5 1992 C.1
En circulación
John Snow (1813-1858)
Documento los casos de cólera e hipotetizo
Que estos se debían al agua contaminada
Otras personas importantes:
Albert Neisser
Shibasaburo Kitasato
Kiyoshi Shiga
Martinus Beijerinck
Alexandre Yersin
Edward Jenner
Alexander Flemming
Que hicieron? Cual fue su contribución? Esta es su asignación para la próxima clase!
Descubrimiento e
inicio: Microbiologia
Medica y General
Era de la Biologia Molecular y
la Microbiologia General
Microbiologia Molecular,
Genomica y Proteomica
Nursing
tamaño de una bacteria comparable al de organelos como el mitocondrio,
cloroplastos e hidrogenosomas
Five Types of Microorganisms
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Fungus
Human hair
Bacterium
Virus
200 nm
Fungus:
Syncephalastrum
Bacterium:
E. coli
Helminth: Head (scolex)
of Taenia solium
Protozoan:
Vorticella
Bacteria
Helminth is visible
to the naked eye.
Protozoan
Fungus
Red blood
cell
20 microns
Virus:
Herpes simplex
A single
virus particle
(taenia, herpes): Centers for Disease Control; (vorticella ): © Carolina Biological Supply/Phototake; (e. coli): CDC/Janice Haney Carr;
(syncephalastrum): © Dr. Arthur Siegelman/Visuals Unlimited
Macromolecules: Superstructures of Life •Macromolecules: very large molecules •Four main macromolecules
- carbohydrates
- lipids
- proteins
- nucleic acids
•Monomers: subunits of macromolecules •Polymers: chains of various lengths made up of monomers
Macromolecules and Their Functions Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Table 1.3 Macromolecules and Their Functions
Notes About the Examples Examples Macromolecule Description/Basic Structure
Carbohydrates
Monosaccharides
Disaccharide
Polysaccharides Chains of monosaccharides
Two monosaccharides
3- to 7-carbon sugars Glucose, fructose
Major component of cell membranes; storage
Nucleic acids
Proteins
Ribonucleic acid
(RNA)
Deoxyribonucleic
acid (DNA)
Lipids
Fatty acids + glycerol
Fatty acids + glycerol + phosphate
Fatty acids, alcohols
Ringed structure
Cell wall of mycobacteria
In membranes of eukaryotes and some bacteria
Sugars involved in metabolic reactions; building
block of disaccharides and polysaccharides
Composed of two glucoses; an important breakdown
product of starch
Composed of glucose and galactose
Composed of glucose and fructose
Cell wall, food storage
Maltose(maltsugar)
Lactose (milk sugar)
Sucrose (table sugar)
Starch, cellulose, glycogen
Fats, oils
Membrane components
Mycolic acid
Cholesterol, ergosterol
Chains of amino acids
Pentose sugar + phosphate
+ nitrogenous base
Purines: adenine, guanine
Pyrimidines: cytosine, thymine,
uracil
Contains deoxyribose sugar and
thymine, not uracil
Contains ribose sugar and uracil,
not thymine
Chromosomes; genetic material of
viruses
Ribosomes; mRNA, tRNA, small
RNAs, genetic material of viruses
Facilitate expression of genetic traits
Mediate inheritance
Serve as structural components and perform
metabolic reactions
Enzymes; part of cell membrane, cell
wall, ribosomes, antibodies
Triglycerides
Phospholipids
Waxes
Steroids
Polysaccharides •Contribute to structural support and protection •Serve as nutrient and energy stores •Cellulose: found in plants and algae •Agar: polysaccharide used in preparing solid culture media for microbes •Peptidoglycan: polysaccharides linked to peptide fragments; found in bacterial cell walls •Lipopolysaccharide: complex of lipid and polysaccharide responsible for symptoms of fever and shock •Glycocalyx: outer surface of many cells; functions in attachment or as a receptor that receives external stimuli
Lipids: Fats, Phospholipids, and Waxes
•Triglycerides: storage lipid including fats and oils •Glycerol: 3-carbon alcohol with 3 OH groups that serve as binding sites •Fatty acids: long-chain hydrocarbon molecules with a carboxyl group (COOH) that binds with glycerol
- saturated fatty acids: solid at room temperature
- unsaturated fatty acids: liquid at room temperature
•In most cells, tryglycerides are stored in long-term concentrated form as droplets or globules
(b)
Fatty Acids
(1) Palmitic acid, a
saturated fatty acid
(2) Linolenic acid, an
unsaturated fatty acid
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
H H
H H
H H
H H
H H
H H
H H
H H
H H
H H
H H
H H
H H
H H
H
C H H
O HO O
C
C
C
C
C
C
C
C
H H
H H
H
H
H H
H
H
H
C
H
H
H
H
HO
b(right): © Stockbyte/PunchStock (RF)
C
C
C
C
C
C
C
O
H H
H H
H H
H H
H H
H H
C
C
C
C
C
C
C
O
H H
H H
H H
H H
H H
H H
C
C
C
C
C
C
C
O
H H
H H
H H
H H
H H
H H
C H C
H
H C
H H
+
C H C
H
H C
H H
O
O C
R
O
O C
R
O
O C
R
s 3
Triglyceride
H2O
HO HO HO
OH OH OH
Fatty Acids Triglycerides
Ester
bond
Hydrocarbon
chain
(a)
Fatty
acid
Carboxylic
acid
Glycerol
R hydrocarbon
chain
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Membrane Lipids •Hydrophilic (“water-loving”) region from the charge on the phosphoric acid-alcohol “head” of the molecule •Hydrophobic (“water-fearing”) region in the long, uncharged “tail” of the molecule formed by fatty acids
O C C
O O
H
H
O
O
P O O
R
O
Variable alcohol group
Polar lipid molecule
(a)
Phosphate
polar head
(b)
Water Water
(2) Phospholipid bilayer
Glycerol
Water
(1) Phospholipids in single layer
Charged
head
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HC
HCH
CH
Fatty
acids
Nonpolar
tails
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
View of a Membrane Bilayer of Lipids
H C
C
C C
Cell
membrane
Protein
Cholesterol
Glycolipid
Phospholipids
Site for
ester bond
with a fatty
acid
Cholesterol
HO
CH2
CH2
CH2
CH2
CH
CH3 CH3
CH
H2C C
H2C
CH3
CH3
CH3 CH
CH
HC
HC CH
H2C
H2
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Steroids and Waxes •Steroids: complex ringed compounds commonly found in cell membranes and animal hormones
- cholesterol: reinforces the structure of the cell membrane in animal cells and mycoplasmas
•Waxes: esters formed between a long-chain alcohol and a saturated fatty acid
- fur, feathers, fruits, leaves, human skin, and insect exoskeletons are naturally waterproofed with waxes
- bacteria that cause tuberculosis and leprosy contain a unique wax in their cell wall that contributes to their pathogenicity
Proteins •Predominant organic molecule in cells •Amino acids: building blocks of proteins •Peptide: a molecule composed of short chains of amino acids •Polypeptide: contains an unspecified number of amino acids but usually has more than 20 and is often a smaller subunit of a protein
Protein Structure and Diversity •Primary structure (1°): the type, number, and order of amino acids in the chain •Secondary structure (2°): arises when functional groups exposed on the outer surface of the molecule interact by forming hydrogen bonds
- alpha helix
- beta-pleated sheet
•Tertiary structure (3°): created by additional bonds between functional groups •Quaternary structure (4°): formed when more than one polypeptide forms a large, multiunit protein
Stages in the Formation of a Functioning Protein
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Beta-pleated sheet Random coil Alpha helix
Secondary Structure
(b)
Primary Structure
(a)
Amino acid
sequence
Tertiary Structure
(d)
Quaternary Structure
Alpha helix
Folded polypeptide chain
Two or more
polypeptide chains
Lys
Ph
e
(c)
Protein Bonding and Folding
•Each protein develops a unique shape with a distinctive surface pattern •Creates a functional diversity required for thousands of cellular activities •Enzymes: protein catalysts for chemical reactions in cells •Antibodies: complex glycoproteins with specific attachment regions for bacteria, viruses, and other microorganisms •Native state: the functional three-dimensional form of a protein •A protein becomes denatured if the •protein structure is disrupted for some •reason
The Nucleic Acids: A Cell Computer and Its Programs •DNA: contains the special coded genetic program with detailed and specific instructions for each organism’s heredity •RNA: “helper” molecules responsible for carrying out DNA’s instructions and translating the DNA program into proteins
The Double Helix of DNA •Formed by two very long polynucleotide strands linked by hydrogen bonds between complementary pairs of nitrogen bases •Adenine pairs with thymine •Guanine pairs with cytosine
RNA: Organizers of Protein Synthesis •Often a long, single strand of nucleotides •Contains ribose instead of deoxyribose and uracil instead of thymine •Three major types:
- messenger RNA (mRNA)
- ribosomal RNA (rRNA)
- transfer RNA (tRNA)
.
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
A T
C G
G C
T A
A T
C G
U
A
C
G
C
A
D
D
D
D
D
D
D
D
D
D
D
D
R
R
R
R
R
R
(a) A nucleotide, composed of
a phosphate, a pentose
sugar, and a nitrogen base
(either A, T, C, G, or U) is
the monomer of both DNA
and RNA.
DNA
(b) In DNA, the polymer is composed
of alternating deoxyribose (D) and
phosphate (P) with nitrogen bases
(A,T,C,G) attached to the deoxyribose.
DNA almost always exists in pairs of
strands, oriented so that the bases
are paired across the central axis of
the molecule.
(c) In RNA, the polymer
is composed of
alternating ribose (R)
and phosphate (P)
attached to nitrogen
bases (A,U,C,G), but
it is usually a single
strand
Backbone
Backbone
RNA
N base
Pentose sugar
Phosphate
H bonds
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
ATP: The Energy Molecule of Cells •Adenosine triphosphate (ATP): a nucleotide containing adenine, ribose, and three phosphates •Belongs to a category of high-energy compounds that give off energy when the bond between the second and third (outermost) phosphate is broken •This releases energy to do cellular work •Also generates adenosine diphosphate (ADP) that can be converted back to ATP
H
H
N N
N N
NH2
Adenosine
Triphosphate
(ATP)
Adenosine
Diphosphate
(ADP)
Adenosine
–O
OH OH
CH2
O –
(b)
(a)
O– O–
O O O
P P P
O O
O
O
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Fundamental Characteristics of Cells •Cells tend to be spherical, polygonal, cubical, or cylindrical •Protoplasm is encased in a cell or cytoplasmic membrane •Have chromosomes containing DNA and ribosomes for protein synthesis •Exceedingly complex in function
Fundamental Characteristics of Cells (cont’d) •Eukaryotic cells
- found in animals, plants, fungi, and protozoa
- contain organelles that perform useful functions
•Prokaryotic cells
- have no nucleus and generally no other organelles
- complex structure that engages in nearly every activity that eukaryotes can, and many can function in ways that eukaryotes cannot
Nomenclature
•The assignment of scientific names to various taxonomic categories and to individual organisms •Binomial nomenclature
- scientific name is a combination of the genus and species names
- scientific names are italicized when they are written in print and underlined when they are written by hand
- when the name is abbreviated, the genus name is abbreviated to the first initial followed by a period and the full species name is written
Classification •Organized into descending ranks, beginning with a general all-inclusive taxonomic category and ending with the smallest and most specific category •Categories
- domain
- kingdom
- phylum or division
- class
- order
- family
- genus
- species
Sample Taxonomy Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
DOMAIN: Eukarya (all eukaryotic organisms)
Eukaryotic, heterotrophic
and mostly multicellular
Possess notochord, dorsal
nerve cord, pharyngeal slits
(if only in embryo)
Possess hair,
mammary glands
Digital dexterity,
large cerebral
cortex, slow
reproductive rate,
long life span
Large brain, no tail,
long upper limbs
Kingdom: Animalia
Phylum: Chordata
Class: Mammalia
Order: Primates
Family: Hominoidea
Genus: Homo Erect posture, large
cranium,
opposable thumbs
Species: sapiens Humans
Genus: Paramecium Pointed, cigar-shaped cells with
macronuclei and micronuclei
Species: caudatum Cells cylindrical,
long, and pointed
at one end
Cells rotate while
swimming and have
oral grooves
Elongated oval cells
with cilia in the oral
cavity
Single cells with
regular rows of cilia;
rapid swimmers
Only protozoa with
cilia
Includes protozoa
and algae
Kingdom: Protista
Phylum: Ciliophora
Class: Hymenostomea
Order: Hymenostomatida
Family: Parameciidae
A Universal Web of Life
•Darwin and Haeckel proposed two kingdoms: plants and animals •Haeckel later added Protista to the first two kingdoms •In the 1870s, Haeckel added the kingdom Monera
•Whittaker added the kingdom fungi during the period of 1959 – 1969, and the 5 kingdom system became the standard
- animals
- plants
- protists
- monera
- fungi
The Woese-Fox System
•Based on conserved small subunit ribosomal RNA sequences (ssu rRNA)
•Analysis of these sequences revealed a separate group for the archaeabacteria called Archaea
•An entirely new system was proposed based on domains - Bacteria
- Archaea
- Eukarya