Exam Review: Exam 1
Who is considered the father of Microbiology?
Who was the first person to see bacteria using a simple microscope:
What is considered a domain?
What makes a bacterium( prokaryote) different from a animal cell (eukaryote).
Which microorganisms are prokaryotic and which are eukaryotic? Only 1 prokaryote and 3 eykaryotes listed in book.
What environmental factors influence microbial growth? What is the optimum pH, temperature?
What is growth generation time?
What is a biofilm?
What is denature?
What are the 4 main types of growth versus oxygen concentration?
From what are each of the 4 macromolecules constructed?
What are the four types of macromolecules?
What is used for motility in bacteria? What type of movement is observed? What is the movement toward? What is this called?
What are transport molecules that requires channel proteins and a chemical reaction?
What is transport that requires a channel but no reaction or energy?
What is transport that requires energy?
How is prokaryotic cellular reproduction performed?
What are the main parts of the bacterium and what are they used for? What are the characteristics of the different parts?
What are the differences between the gram-negative and gram-positive cell walls?
What is a REDOX reaction?
What is an enzyme and what is the most important part of the enzyme?
What is anabolism and catabolism?
Describe bacterial metabolism from substrate phosphorylation (glycolysis) through cellular respiration and the proton motive force and ATP synthesis. (as described in class) from glucose to ATP synthase.
What is the purpose of ATP? How is this accomplished?
What are the electron carriers and their purpose?
What are the 4 stages of the bacterial growth curve? What happens during each stage?
What are the organisms called that obtain carbon from CO2 or other biosynthetic sources ?
What are organisms that obtain nutrients from organic sources?
What are organisms that obtain nutrients from both inorganic and organic sources?
What are the enzymes common to the replication of "leading” and “lagging” DNA strands ?
What do DNA and RNA have in common?
What are the 4 types of RNA? What are each used for?
What are the four nucleic acids found in RNA and DNA?
What part of the gram-negative bacillus that is responsible for endotoxic shock ?
Where are codons and anticodons found?
What are the different types of enzyme inhibition? (3) Page 136-137
What is a type of extrachromosomal DNA in the bacterial cell ?
What is proton motive force?
What is selective media?
What is differential media?
What is a colony forming unit?
Tuesday, January 27, 2009
Sunday, January 25, 2009
Preliminary Exam 1 Review
Review may be updated if needed.
Exam 1 review-You are responsible for the information discussed in class and for any other information if specifically asked to review it for exam. Review Key terms in the back of each chapter as a study aid.
You can also access the textbook’s website for other study assistance. www.microbiologyplace.com.
1. Know the 4 most important men in micro history and what they did.
2. Know the 3 Domains and binomial nomenclature definition
3. Know Koch's postulates
4. Know difference between Eukaryotic and Prokaryotic
5. Know the environmental factors that influence microbial growth and what the organisms are called in reference to pH, temperature, Oxygen,
6. Know the 4 Macromolecules and their monomers.
7. Know the main bacterial structures, membrane, cell wall, appendages, capsules, slime layers, motility and chemotaxis, including runs and tumbles (what direction does a flagellar turn?) nucleus and plasmids.
8. Know Simple transport, Group Translocation and ABC and basic bacterial transport
9. Know oxidation/reduction
10. Know the basic steps of Bacterial metabolism, glycolysis, citric acid cycle, chemoosmosis and fermentation.
11. Know difference between catabolism and anabolism
12. Know what the proton gradient is and how it works.
13. Know how the electron carriers NAD/FAD and the carriers in the membrane work.
14. Know the stages of microbial growth and what they mean. Know the different environmental definitions concerning how microbes live pointed out in class i.e. temperature, pH, oxygen etc. Know about bacteriological media.
15. Know the enzymes involved in DNA replication and the basic steps in DNA replication. What is a leading and lagging strand etc. How does DNA replication occur?
16. Know the 4 nucleotide bases for DNA and RNA. What bond is responsible for the double helix?
17. Know the 3 stages to protein formation: Replication, transcription and translation. What are the three types of RNA. What are their function? What subunit makes a protein? How do replication, transcription and translation work together to make a protein? What are the steps in order?
18. Know codon vs anticodon
19. Know what an enzyme is and about feedback inhibition, isoenzymes and covalent modification
20. Know operon induction and attenuation
21.Know enzyme repression and induction
Exam 1 review-You are responsible for the information discussed in class and for any other information if specifically asked to review it for exam. Review Key terms in the back of each chapter as a study aid.
You can also access the textbook’s website for other study assistance. www.microbiologyplace.com.
1. Know the 4 most important men in micro history and what they did.
2. Know the 3 Domains and binomial nomenclature definition
3. Know Koch's postulates
4. Know difference between Eukaryotic and Prokaryotic
5. Know the environmental factors that influence microbial growth and what the organisms are called in reference to pH, temperature, Oxygen,
6. Know the 4 Macromolecules and their monomers.
7. Know the main bacterial structures, membrane, cell wall, appendages, capsules, slime layers, motility and chemotaxis, including runs and tumbles (what direction does a flagellar turn?) nucleus and plasmids.
8. Know Simple transport, Group Translocation and ABC and basic bacterial transport
9. Know oxidation/reduction
10. Know the basic steps of Bacterial metabolism, glycolysis, citric acid cycle, chemoosmosis and fermentation.
11. Know difference between catabolism and anabolism
12. Know what the proton gradient is and how it works.
13. Know how the electron carriers NAD/FAD and the carriers in the membrane work.
14. Know the stages of microbial growth and what they mean. Know the different environmental definitions concerning how microbes live pointed out in class i.e. temperature, pH, oxygen etc. Know about bacteriological media.
15. Know the enzymes involved in DNA replication and the basic steps in DNA replication. What is a leading and lagging strand etc. How does DNA replication occur?
16. Know the 4 nucleotide bases for DNA and RNA. What bond is responsible for the double helix?
17. Know the 3 stages to protein formation: Replication, transcription and translation. What are the three types of RNA. What are their function? What subunit makes a protein? How do replication, transcription and translation work together to make a protein? What are the steps in order?
18. Know codon vs anticodon
19. Know what an enzyme is and about feedback inhibition, isoenzymes and covalent modification
20. Know operon induction and attenuation
21.Know enzyme repression and induction
Chapter 6
Many definitions for the exam.
Chapter 6
Microbial Nutrition and Growth
Metabolism Results in Reproduction
Microbial growth – an increase in a population of microbes rather than an increase in size
Discete Colonies: cells arising from single parent cell
Reproduction = growth
Sources of Carbon, Energy, Electrons
Organisms categorized into groups
Autotrophs: use an inorganic carbon source (carbon dioxide) are autotrophs
Heterotrophs: catabolize reduced organic molecules (proteins, carbohydrates, amino acids, and fatty acids) are heterotrophs
Chemotrophs: acquire energy from redox reactions involving inorganic and organic chemicals are chemotrophs
Phototrophs: use light as their energy source are phototrophs
Bacterial Cell Division Cell Growth and Binary Fission
Microbial Growth
Microbial growth involves an increase in the number of cells.
Growth of most microorganisms occurs by the process of binary fission
FTS Proteins
Fts proteins regulate cell division and chromosome replication
Fts proteins interact to form a division apparatus in the cell called the divisome.
The protein FtsZ defines the division plane in prokaryotes
Mre proteins help define cell shape
Peptidoglycan Synthesis and Cell Division
New cell wall is synthesized by inserting new glycan units into preexisting wall material
Cell lysis called autolysis can occur unless new cell wall precursors are spliced into existing peptidoglycan
Bactoprenol facilitates transport of new glycan units through the cytoplasmic membrane to become part of cell wall
Transpeptidation bonds the precursors into the peptidoglycan fabric
Growth of Bacterial Populations
Exponential Growth: Microbial populations show a characteristic type of growth pattern which is best seen by plotting the number of cells over time on a semilogarithmic graph
The Growth Cycle
Microorganisms show a characteristic growth pattern (Figure 6.8) when inoculated into a fresh culture medium.
Lag, Stationary, Death Phases
lag phase, then exponential growth commences. As essential nutrients are depleted or toxic products build up, growth ceases, and the population enters the stationary phase. If incubation continues, cells may begin to die (the death phase).
Direct Measurements of Microbial Growth: Total and Viable Counts
Growth is measured by the change in the number of cells over time. Cell counts done microscopically measure the total number of cells in a population,
viable cell counts (plate counts) measure only the living, reproducing population.
Problem With Plate Counts
"the great plate count anomaly"
occurs because microscopic methods count dead cells whereas viable methods do not
different organisms may have different requirements for growth conditions in culture.
Membrane Filtration
Indirect Measurement of Growth
Turbidity measurements are an indirect but rapid method of measuring growth.
To relate a direct cell count to a turbidity value, a standard curve must be established.
Physical Requirements for Growth
Temperature
pH
Osmolarity
Pressure
Growth and Temperature
Psychrophiles: function best at cold temperatures.
Psychrotolerant: Organisms that grow at 0ºC but have optima of 20ºC to 40ºC are called Mesophiles
Thermophiles: Organisms with growth temperature optima between 45ºC and 80ºC. a
Hyperthermophiles. Organims with growth temperature optima greater than 80°C are called
Microbial Growth and pH
Most organisms grow best between pH 6 and 8.
Acidophiles: Organisms that grow best at low pH
Alkaliphiles: Organisms that grow best at high pH
Growth in High Salt Concentrations
Halophiles: grow best at reduced water concentration and higher salt concentrations
Extreme halophiles: require high levels of salts for growth.
Halotolerant: organisms that tolerate some reduction in the water activity but generally grow best in the absence of an added solute, like salt.
Oxygen and Microbial Growth
Aerobes: require oxygen
Anaerobes: do not require oxygen
Facultative organisms: can live with or without oxygen.
Aerotolerant anaerobes: can tolerate oxygen and grow in its presence even though they cannot use it.
Microaerophiles: aerobes that can use oxygen only when it is present at levels reduced from that in air.
Culture Requirements
Special techniques are needed to grow aerobic and anaerobic microorganisms
Toxic Forms of Oxygen
Several toxic forms of oxygen can be formed in the cell, but enzymes are present in organisms that can neutralize most of them
Superoxide in particular seems to be a common toxic oxygen species.
Growth Requirements
Organisms use a variety of nutrients for energy and to build organic molecules and cellular structures
Most common nutrients: carbon, oxygen, nitrogen, and hydrogen
Four toxic forms of oxygen
Singlet oxygen – molecular oxygen with electrons boosted to higher energy state
Superoxide radicals – some form during incomplete reduction of oxygen in aerobic and anaerobic respiration
aerobes produce superoxide dismutases
anaerobes lack superoxide dismutase and die
Peroxide anion – formed during reactions catalyzed by superoxide dismutase and other reactions
Aerobes contain either catalase or peroxidase
Obligate anaerobes either lack both enzymes
Hydroxyl radical
(Aerobes also use antioxidants such as vitamins C and E to protect against toxic oxygen products)
Classification of Organisms Based on Oxygen Requirements
Aerobes –use aerobic respiration
Anaerobes – no aerobic metabolism
Facultative Anaerobes –use either fermentation, anaerobic respiration, aerobic respiration
Aerotolerant anaerobes – no aerobic metabolism; only some enzymes to detoxify oxygen
Microaerophiles – aerobes that require oxygen levels from 2-10% and have problems with hydrogen peroxide and superoxide radicals
pH
Organisms sensitive to acidity because H+ and OH- interfere with H bonding in proteins and nucleic acids
Neutrophiles: Most bacteria and protozoa grow best around neutral pH (6.5-7.5)
Acidophiles: Some bacteria and fungi grow best in acidic habitats
Acidic waste products can help preserve foods by preventing further microbial growth
Alkalinophiles: live in alkaline soils and water up to pH 11.5
Osmotic Pressure
Hypertonic solutions have greater solute concentrations; cells placed in these solutions will undergo plasmolysis (shriveling of cytoplasm)
This effect helps preserve some foods
Restricts organisms to certain environments
Obligate halophiles – grow in up to 30% salt
Facultative halophiles – can tolerate high salt concentrations
Hydrostatic Pressure
Water exerts pressure in proportion to its depth
For every addition of depth, water pressure increases 1 atm
Organisms that live under extreme pressure are barophiles
Their membranes and enzymes depend on this pressure to maintain their three-dimensional, functional shape
Chapter 6
Microbial Nutrition and Growth
Metabolism Results in Reproduction
Microbial growth – an increase in a population of microbes rather than an increase in size
Discete Colonies: cells arising from single parent cell
Reproduction = growth
Sources of Carbon, Energy, Electrons
Organisms categorized into groups
Autotrophs: use an inorganic carbon source (carbon dioxide) are autotrophs
Heterotrophs: catabolize reduced organic molecules (proteins, carbohydrates, amino acids, and fatty acids) are heterotrophs
Chemotrophs: acquire energy from redox reactions involving inorganic and organic chemicals are chemotrophs
Phototrophs: use light as their energy source are phototrophs
Bacterial Cell Division Cell Growth and Binary Fission
Microbial Growth
Microbial growth involves an increase in the number of cells.
Growth of most microorganisms occurs by the process of binary fission
FTS Proteins
Fts proteins regulate cell division and chromosome replication
Fts proteins interact to form a division apparatus in the cell called the divisome.
The protein FtsZ defines the division plane in prokaryotes
Mre proteins help define cell shape
Peptidoglycan Synthesis and Cell Division
New cell wall is synthesized by inserting new glycan units into preexisting wall material
Cell lysis called autolysis can occur unless new cell wall precursors are spliced into existing peptidoglycan
Bactoprenol facilitates transport of new glycan units through the cytoplasmic membrane to become part of cell wall
Transpeptidation bonds the precursors into the peptidoglycan fabric
Growth of Bacterial Populations
Exponential Growth: Microbial populations show a characteristic type of growth pattern which is best seen by plotting the number of cells over time on a semilogarithmic graph
The Growth Cycle
Microorganisms show a characteristic growth pattern (Figure 6.8) when inoculated into a fresh culture medium.
Lag, Stationary, Death Phases
lag phase, then exponential growth commences. As essential nutrients are depleted or toxic products build up, growth ceases, and the population enters the stationary phase. If incubation continues, cells may begin to die (the death phase).
Direct Measurements of Microbial Growth: Total and Viable Counts
Growth is measured by the change in the number of cells over time. Cell counts done microscopically measure the total number of cells in a population,
viable cell counts (plate counts) measure only the living, reproducing population.
Problem With Plate Counts
"the great plate count anomaly"
occurs because microscopic methods count dead cells whereas viable methods do not
different organisms may have different requirements for growth conditions in culture.
Membrane Filtration
Indirect Measurement of Growth
Turbidity measurements are an indirect but rapid method of measuring growth.
To relate a direct cell count to a turbidity value, a standard curve must be established.
Physical Requirements for Growth
Temperature
pH
Osmolarity
Pressure
Growth and Temperature
Psychrophiles: function best at cold temperatures.
Psychrotolerant: Organisms that grow at 0ºC but have optima of 20ºC to 40ºC are called Mesophiles
Thermophiles: Organisms with growth temperature optima between 45ºC and 80ºC. a
Hyperthermophiles. Organims with growth temperature optima greater than 80°C are called
Microbial Growth and pH
Most organisms grow best between pH 6 and 8.
Acidophiles: Organisms that grow best at low pH
Alkaliphiles: Organisms that grow best at high pH
Growth in High Salt Concentrations
Halophiles: grow best at reduced water concentration and higher salt concentrations
Extreme halophiles: require high levels of salts for growth.
Halotolerant: organisms that tolerate some reduction in the water activity but generally grow best in the absence of an added solute, like salt.
Oxygen and Microbial Growth
Aerobes: require oxygen
Anaerobes: do not require oxygen
Facultative organisms: can live with or without oxygen.
Aerotolerant anaerobes: can tolerate oxygen and grow in its presence even though they cannot use it.
Microaerophiles: aerobes that can use oxygen only when it is present at levels reduced from that in air.
Culture Requirements
Special techniques are needed to grow aerobic and anaerobic microorganisms
Toxic Forms of Oxygen
Several toxic forms of oxygen can be formed in the cell, but enzymes are present in organisms that can neutralize most of them
Superoxide in particular seems to be a common toxic oxygen species.
Growth Requirements
Organisms use a variety of nutrients for energy and to build organic molecules and cellular structures
Most common nutrients: carbon, oxygen, nitrogen, and hydrogen
Four toxic forms of oxygen
Singlet oxygen – molecular oxygen with electrons boosted to higher energy state
Superoxide radicals – some form during incomplete reduction of oxygen in aerobic and anaerobic respiration
aerobes produce superoxide dismutases
anaerobes lack superoxide dismutase and die
Peroxide anion – formed during reactions catalyzed by superoxide dismutase and other reactions
Aerobes contain either catalase or peroxidase
Obligate anaerobes either lack both enzymes
Hydroxyl radical
(Aerobes also use antioxidants such as vitamins C and E to protect against toxic oxygen products)
Classification of Organisms Based on Oxygen Requirements
Aerobes –use aerobic respiration
Anaerobes – no aerobic metabolism
Facultative Anaerobes –use either fermentation, anaerobic respiration, aerobic respiration
Aerotolerant anaerobes – no aerobic metabolism; only some enzymes to detoxify oxygen
Microaerophiles – aerobes that require oxygen levels from 2-10% and have problems with hydrogen peroxide and superoxide radicals
pH
Organisms sensitive to acidity because H+ and OH- interfere with H bonding in proteins and nucleic acids
Neutrophiles: Most bacteria and protozoa grow best around neutral pH (6.5-7.5)
Acidophiles: Some bacteria and fungi grow best in acidic habitats
Acidic waste products can help preserve foods by preventing further microbial growth
Alkalinophiles: live in alkaline soils and water up to pH 11.5
Osmotic Pressure
Hypertonic solutions have greater solute concentrations; cells placed in these solutions will undergo plasmolysis (shriveling of cytoplasm)
This effect helps preserve some foods
Restricts organisms to certain environments
Obligate halophiles – grow in up to 30% salt
Facultative halophiles – can tolerate high salt concentrations
Hydrostatic Pressure
Water exerts pressure in proportion to its depth
For every addition of depth, water pressure increases 1 atm
Organisms that live under extreme pressure are barophiles
Their membranes and enzymes depend on this pressure to maintain their three-dimensional, functional shape
Chapter 5
Chapter 5 is difficult. Read Chapter. Alot of test material.
Chapter 5
Microbial Nutrition, Culture and Metabolism
Biochemical Reactions Within Cells.
Every cell acquires nutrients
Metabolism requires energy (light or nutrients)
Energy stored in adenosine triphosphate (ATP)
Cells catabolize nutrients to form precursors
Precursors +ATP +enzymes =anabolic reactions
Cells grow by assembling macromolecules
Growth Requirements
Organisms use a variety of nutrients for their energy needs and to build organic molecules and cellular structures
Most common nutrients – those containing necessary elements such as carbon, oxygen, nitrogen, and hydrogen
Microbes obtain nutrients from variety of sources
Sources of Carbon, Energy, Electrons
Organisms categorized into groups
Those using an inorganic carbon source (carbon dioxide) are autotrophs
Those catabolizing reduced organic molecules (proteins, carbohydrates, amino acids, and fatty acids) are heterotrophs
Those that acquire energy from redox reactions involving inorganic and organic chemicals are chemotrophs
Those that use light as their energy source are phototrophs
Other Chemical Requirements
Phosphorus: membranes, DNA, RNA, ATP, some proteins
Sulfur: sulfur-containing amino acids, disulfide bonds critical to proteins, and vitamins
Trace elements: tap water
Growth factors: organic chemicals not synthesized by certain organisms (vitamins, some amino acids, purines, pyrimidines, cholesterol, NADH, heme)
Anabolism can cease due to insufficient nitrogen needed for proteins and nucleotides
Nitrogen from organic and inorganic nutrients; cells recycle nitrogen from amino acids and nucleotides
The reduction of nitrogen gas to ammonia (nitrogen fixation) by certain bacteria is essential to life on Earth because nitrogen is made available in a usable form
Iron and other Growth Factor Requirements
Iron needed in cellular respiration. Under anoxic conditions, iron is soluble. Under oxic conditions, siderophore is needed for transport into cell.
Growth factors: Organic compounds needed only in trace amounts; include vitamins and amino acids.
Culture Media
Majority of prokaryotes have never been grown in culture medium
Six types of general culture media
Defined media
Complex media
Selective media
Differential media
Anaerobic media
Transport media
Culture Media:
Chemically defined (defined medium)
Undefined (complex medium).
Selective, differential, and enriched are terms that describe media used for the isolation of particular species or for comparative studies of microorganisms.
Culturing Microorganisms
Inoculum introduced into medium (broth or solid)
Environmental specimens
Clinical specimens
Stored specimens
Culture – refers to act of cultivating microorganisms or the microorganisms that are cultivated
Obtaining Pure Cultures
Cultures composed of cells arising from a single progenitor
CFU: colony forming unit
Aseptic technique: prevent contamination
Two common isolation techniques
Streak Plates
Pour Plates
Culture Media
Culture media: nutrient solutions that supply the nutritional needs of microbes
Streak Plate Method
ENZYMOLOGY
Enzymes regulate metabolic reaction rates
Control metabolism
molecules (mostly protein) that accelerate or catalyze chemical reactions (A--->B) in cells by breaking old covalent bonds & forming new covalent bonds
Biological catalyst
different from a chemical catalyst - have complex structure (sequence of aa’s)
act only upon a specific substrate
do not change direction (energetics) of reactions of catalysis*
Enzymes Catalysts
Enzymes are organic catalysts –help reactions occur but are not permanently changed
Most are protein
Some are RNA-ribozymes
To catalyze a reaction the enzyme must bind the correct substrate and position the substrate relative to the catalytic active site
Enzyme Activity
How is energy produced? Electrons
Electrons transfer from “donor” molecule to “acceptor” molecule
These reactions are always coupled…Meaning what?
EVERY ELECTRON THAT IS GAINED MUST FIRST BE GIVEN
REDOX
Electron Carriers
Cells use electron carrier molecules to carry electrons (often in H atoms) from donors to acceptors. Each carrier transport a pair of electrons.
Three important electron carriers (derived from vitamins)
Nicotinamide adenine dinucleotide (NAD+) → NADH
Nicotinamide adenine dinucleotide phosphate (NADP+) → NADPH
Flavine adenine dinucleotide (FAD) → FADH2
Electron carriers
External carriers
NADH dehydrogenases: 2 e and 2 H+
Flavoproteins: 2 e and 2 H+
Accepts and donates e
Membrane Carriers
Cytochromes: iron containing prophyrin ring, quinone, flavins
NAD as a Redox Electron Carrier
NAD+ and FAD accept electrons and hydrogen during reactions
They become NADH and FADH2
They deliver electrons and hydrogen to the electron transfer chain to make ATP
(Electron Carriers)
NAD+ (Nicotinamide Adenine Dinucleotide)
NAD+ functions in cellular respiration by carrying two electrons. With two electrons, it becomes NADH.
NAD+ oxidizes its substrate by removing two hydrogen atoms. One of the hydrogen atoms bonds to the NAD+. The electron from the other hydrogen atom remains with the NADH molecule but the proton (H+) is released.
NAD+ + 2H ® NADH + H+
NADH then donates the two electrons (one of them is a hydrogen atom) to another molecule. The carrier FAD works in a similar manner.
ATP Production/Energy Storage
Organisms release energy from nutrients
Phosphorylation – organic phosphate is added to substrate; i.e. carbohydrate
Cells phosphorylate ADP in 3 ways:
Substrate-level phosphorylation
Oxidative phosphorylation
Photophosphorylation
Adenosine TriPhosphate
Substrate Level Phosphorylation and Oxidative Phosphorylaltion
Substrate Phosphorylation: ATP is produced during the breakdown of specific substrates in the breakdown of sugar.
Oxidative Phosphorylation: ATP is produced as a result of the proton motive force.
Energy Conservation: Options
Two Options
Fermentation: Produces energy for ATP synthesis with no outside electron acceptors.
Respiration: A electron acceptor is present to act as a terminal electron acceptor.
Glucose
A simple sugar (C6H12O6)
Atoms held together by covalent bonds
Glycolysis-Fermentation
Glycolysis is an anoxic process that occurs in the cytoplasm and can be divided into three major stages:
Preparatory reactions
ATP and pyruvate production
Making fermentation products
Cellular Respiration
Glycolysis (breakdown of glucose)
Produces: PYRUVIC ACID
In Cellular Respiration, pyruvic acid used to produce ATP by a series of reactions
Three stages of cellular respiration
Synthesis of acetyl-CoA
Citric Acid Cycle
Final series reactions -electron transport chain
Anaerobic Pathways
Do not use oxygen
Produce less ATP than aerobic path
Use Fermentation pathways
Fermentation
Essential function – regeneration of NAD+ for glycolysis, so that ADP can be phosphorylated to ATP
Not as efficient as respiration – most of the potential energy remains in the bonds of fermentation products
Fermentation products are waste to bacteria. Many are useful to humans (ethanol, acetic acid, and lactic acid)
Summary: Glycolysis to Krebs Cycle
Starts with Glucose
Breakdown of Glucose to Pyruvic acid (Glycolysis)
Pyruvic Acid converted to Acetyl-CoA (Respiration)
Acetyl-CoA converted to ATP and e- Carriers (Krebs)
CO2 and H2O produced as by products
Purpose?
To produce energy to fuel reactions
Electron Transfer Phosphorylation
Occurs in the bacterial membrane
Coenzymes deliver electrons to electron transfer chains
Electron transfer sets up H+ ion gradients
Flow of H+ down gradients powers ATP formation
Chemiosmosis-Electron chain
H+ ions,
propelled by proton motive force
flow down electrochemical gradient
Through ATP synthases (protein channels) that phosphorylate ADP to ATP
Called oxidative phosphorylation because proton gradient created by oxidation of components of ETC
A total of ~34 molecules of ATP are formed from one molecule of glucose
Biosynthesis of Sugars
Polysaccharides are biosynthesized from activated forms of their monomers.
Monomers: hexoses or pentoses
If unavailable, gluconeogenesis occurs.
Breakdown of different substances to make sugars
Anabolic Pathways – Carbohydrate Biosynthesis
Anabolic Pathways – Amino Acid Biosynthesis
Nucleotides and Lipids
Nucleotides (purines and pyrimidines) are biosynthesized using carbon from several sources
Fatty acids are synthesized two carbons at a time and then attached to glycerol to form lipids
Anabolic Pathways – Lipid Biosynthesis
Anabolic Pathways – Nucleotide Biosynthesis
Know Enzyme Regulation by Feedback inhibition, Isoenzymes, Covalent Modification
Chapter 5
Microbial Nutrition, Culture and Metabolism
Biochemical Reactions Within Cells.
Every cell acquires nutrients
Metabolism requires energy (light or nutrients)
Energy stored in adenosine triphosphate (ATP)
Cells catabolize nutrients to form precursors
Precursors +ATP +enzymes =anabolic reactions
Cells grow by assembling macromolecules
Growth Requirements
Organisms use a variety of nutrients for their energy needs and to build organic molecules and cellular structures
Most common nutrients – those containing necessary elements such as carbon, oxygen, nitrogen, and hydrogen
Microbes obtain nutrients from variety of sources
Sources of Carbon, Energy, Electrons
Organisms categorized into groups
Those using an inorganic carbon source (carbon dioxide) are autotrophs
Those catabolizing reduced organic molecules (proteins, carbohydrates, amino acids, and fatty acids) are heterotrophs
Those that acquire energy from redox reactions involving inorganic and organic chemicals are chemotrophs
Those that use light as their energy source are phototrophs
Other Chemical Requirements
Phosphorus: membranes, DNA, RNA, ATP, some proteins
Sulfur: sulfur-containing amino acids, disulfide bonds critical to proteins, and vitamins
Trace elements: tap water
Growth factors: organic chemicals not synthesized by certain organisms (vitamins, some amino acids, purines, pyrimidines, cholesterol, NADH, heme)
Anabolism can cease due to insufficient nitrogen needed for proteins and nucleotides
Nitrogen from organic and inorganic nutrients; cells recycle nitrogen from amino acids and nucleotides
The reduction of nitrogen gas to ammonia (nitrogen fixation) by certain bacteria is essential to life on Earth because nitrogen is made available in a usable form
Iron and other Growth Factor Requirements
Iron needed in cellular respiration. Under anoxic conditions, iron is soluble. Under oxic conditions, siderophore is needed for transport into cell.
Growth factors: Organic compounds needed only in trace amounts; include vitamins and amino acids.
Culture Media
Majority of prokaryotes have never been grown in culture medium
Six types of general culture media
Defined media
Complex media
Selective media
Differential media
Anaerobic media
Transport media
Culture Media:
Chemically defined (defined medium)
Undefined (complex medium).
Selective, differential, and enriched are terms that describe media used for the isolation of particular species or for comparative studies of microorganisms.
Culturing Microorganisms
Inoculum introduced into medium (broth or solid)
Environmental specimens
Clinical specimens
Stored specimens
Culture – refers to act of cultivating microorganisms or the microorganisms that are cultivated
Obtaining Pure Cultures
Cultures composed of cells arising from a single progenitor
CFU: colony forming unit
Aseptic technique: prevent contamination
Two common isolation techniques
Streak Plates
Pour Plates
Culture Media
Culture media: nutrient solutions that supply the nutritional needs of microbes
Streak Plate Method
ENZYMOLOGY
Enzymes regulate metabolic reaction rates
Control metabolism
molecules (mostly protein) that accelerate or catalyze chemical reactions (A--->B) in cells by breaking old covalent bonds & forming new covalent bonds
Biological catalyst
different from a chemical catalyst - have complex structure (sequence of aa’s)
act only upon a specific substrate
do not change direction (energetics) of reactions of catalysis*
Enzymes Catalysts
Enzymes are organic catalysts –help reactions occur but are not permanently changed
Most are protein
Some are RNA-ribozymes
To catalyze a reaction the enzyme must bind the correct substrate and position the substrate relative to the catalytic active site
Enzyme Activity
How is energy produced? Electrons
Electrons transfer from “donor” molecule to “acceptor” molecule
These reactions are always coupled…Meaning what?
EVERY ELECTRON THAT IS GAINED MUST FIRST BE GIVEN
REDOX
Electron Carriers
Cells use electron carrier molecules to carry electrons (often in H atoms) from donors to acceptors. Each carrier transport a pair of electrons.
Three important electron carriers (derived from vitamins)
Nicotinamide adenine dinucleotide (NAD+) → NADH
Nicotinamide adenine dinucleotide phosphate (NADP+) → NADPH
Flavine adenine dinucleotide (FAD) → FADH2
Electron carriers
External carriers
NADH dehydrogenases: 2 e and 2 H+
Flavoproteins: 2 e and 2 H+
Accepts and donates e
Membrane Carriers
Cytochromes: iron containing prophyrin ring, quinone, flavins
NAD as a Redox Electron Carrier
NAD+ and FAD accept electrons and hydrogen during reactions
They become NADH and FADH2
They deliver electrons and hydrogen to the electron transfer chain to make ATP
(Electron Carriers)
NAD+ (Nicotinamide Adenine Dinucleotide)
NAD+ functions in cellular respiration by carrying two electrons. With two electrons, it becomes NADH.
NAD+ oxidizes its substrate by removing two hydrogen atoms. One of the hydrogen atoms bonds to the NAD+. The electron from the other hydrogen atom remains with the NADH molecule but the proton (H+) is released.
NAD+ + 2H ® NADH + H+
NADH then donates the two electrons (one of them is a hydrogen atom) to another molecule. The carrier FAD works in a similar manner.
ATP Production/Energy Storage
Organisms release energy from nutrients
Phosphorylation – organic phosphate is added to substrate; i.e. carbohydrate
Cells phosphorylate ADP in 3 ways:
Substrate-level phosphorylation
Oxidative phosphorylation
Photophosphorylation
Adenosine TriPhosphate
Substrate Level Phosphorylation and Oxidative Phosphorylaltion
Substrate Phosphorylation: ATP is produced during the breakdown of specific substrates in the breakdown of sugar.
Oxidative Phosphorylation: ATP is produced as a result of the proton motive force.
Energy Conservation: Options
Two Options
Fermentation: Produces energy for ATP synthesis with no outside electron acceptors.
Respiration: A electron acceptor is present to act as a terminal electron acceptor.
Glucose
A simple sugar (C6H12O6)
Atoms held together by covalent bonds
Glycolysis-Fermentation
Glycolysis is an anoxic process that occurs in the cytoplasm and can be divided into three major stages:
Preparatory reactions
ATP and pyruvate production
Making fermentation products
Cellular Respiration
Glycolysis (breakdown of glucose)
Produces: PYRUVIC ACID
In Cellular Respiration, pyruvic acid used to produce ATP by a series of reactions
Three stages of cellular respiration
Synthesis of acetyl-CoA
Citric Acid Cycle
Final series reactions -electron transport chain
Anaerobic Pathways
Do not use oxygen
Produce less ATP than aerobic path
Use Fermentation pathways
Fermentation
Essential function – regeneration of NAD+ for glycolysis, so that ADP can be phosphorylated to ATP
Not as efficient as respiration – most of the potential energy remains in the bonds of fermentation products
Fermentation products are waste to bacteria. Many are useful to humans (ethanol, acetic acid, and lactic acid)
Summary: Glycolysis to Krebs Cycle
Starts with Glucose
Breakdown of Glucose to Pyruvic acid (Glycolysis)
Pyruvic Acid converted to Acetyl-CoA (Respiration)
Acetyl-CoA converted to ATP and e- Carriers (Krebs)
CO2 and H2O produced as by products
Purpose?
To produce energy to fuel reactions
Electron Transfer Phosphorylation
Occurs in the bacterial membrane
Coenzymes deliver electrons to electron transfer chains
Electron transfer sets up H+ ion gradients
Flow of H+ down gradients powers ATP formation
Chemiosmosis-Electron chain
H+ ions,
propelled by proton motive force
flow down electrochemical gradient
Through ATP synthases (protein channels) that phosphorylate ADP to ATP
Called oxidative phosphorylation because proton gradient created by oxidation of components of ETC
A total of ~34 molecules of ATP are formed from one molecule of glucose
Biosynthesis of Sugars
Polysaccharides are biosynthesized from activated forms of their monomers.
Monomers: hexoses or pentoses
If unavailable, gluconeogenesis occurs.
Breakdown of different substances to make sugars
Anabolic Pathways – Carbohydrate Biosynthesis
Anabolic Pathways – Amino Acid Biosynthesis
Nucleotides and Lipids
Nucleotides (purines and pyrimidines) are biosynthesized using carbon from several sources
Fatty acids are synthesized two carbons at a time and then attached to glycerol to form lipids
Anabolic Pathways – Lipid Biosynthesis
Anabolic Pathways – Nucleotide Biosynthesis
Know Enzyme Regulation by Feedback inhibition, Isoenzymes, Covalent Modification
Saturday, January 24, 2009
Wednesday, January 21, 2009
Chapter 4
Resolution
Resolution: The ability to distinguish two adjacent objects as distinct and separate.
Light microscopes optimize image resolution by using lenses with high light-gathering characteristics (numerical aperture).
Contrast
Differences in intensity between two objects, or between an object and background
Total Magnification
Product of the magnification of the objective and ocular lenses.
Upper limit=1500
Lenses
Ocular: magnify 10-15X and objective of 10-100X
At 1000 x objects 0.2 um in diamater can just be resolved.
Immersion oil increase the light gathering ability of a lens by allowing rays emerging from the specimen at angles that would otherwise be lost to the objective lens to be collected and viewed.
Simple Stains
Gram Stain and Cell Wall
The structural differences between the cell walls of gram-positive and gram-negative Bacteria are responsible for differences in the Gram stain reaction.
Alcohol can readily penetrate the lipid-rich outer membrane of gram-negative Bacteria and extract the insoluble crystal violet-iodine complex from the cell.
The Gram Stain
Electron microscopy
Two major types of electron microscopy are performed: transmission electron microscopy, for observing internal cell structure down to the molecular level, and scanning electron microscopy, for three-dimensional imaging and examining surfaces.
Cytoplasmic : Part 4.5
A highly selective permeability barrier
Constructed of lipids and proteins
Forms a bilayer with hydrophilic exteriors and a hydrophobic interior.
Permeability Layer
The attraction of the nonpolar fatty acid portions of one phospholipid layer for the other layer helps to account for the selective permeability of the cell membrane.
Transport: Simple, Group translocation and the ABC system.
Translocases
Proteins are exported out of prokaryotic cells through the actions of proteins called translocases, which are specific in the types of proteins exported.
Bacterial Cell Wall: Part 4.8
There are two types of cell walls: Gram-positive and Gram-negative
The wall consists of the following:
Alternating repeats of N-acetylglucosamine and N-acetylmuramic acid
N-acetylmuramic acid is cross-linked between strands by short peptides.
Cross-Linkage
Each peptidoglycan repeating subunit is composed of four amino acids:
L-alanine,
D-alanine,
D-glutamic acid
Either lysine or diaminopimelic acid)
Two N-acetyl-glucose-like sugars.
Gram stain reaction.
The structural differences between the cell walls of gram-positive and gram-negative Bacteria are thought to be responsible for differences in the Gram stain reaction.
Alcohol can readily penetrate the lipid-rich outer membrane of gram-negative Bacteria and extract the insoluble crystal violet-iodine complex from the cell.
Protoplasts
Some prokaryotes are free-living without cell walls
They have unusually tough membranes
Or live in osmotically protected habitats, such as the animal body.
Surface Structures- Part 4.10
Prokaryotic cells often contain various surface structures, including fimbriae and pili, S-layers, capsules, and slime layers. A key function of these structures is in attaching cells to a solid surface.
Capsule: Part 4.10
Composed of repeating units of molecules
Attached to cell surface
Protects from drying
Hides bacteria from host
Slime Layer: Part 4.10
Loosely attached to cell surface
Water soluble
Protects cells from drying
Sticky layer that allows attachment
Fimbriae Versus Flagella
Pilus Versus Fimbriae
Cell Inclusions: Part 4.11
Prokaryotic cells often contain internal granules that function as storage materials or in magnetotaxis.
Some gram-negative prokaryotes can store elemental sulfur in globules in the periplasm
Gas Vesicles: Part 4.12
Gas vesicles are small gas-filled structures made of protein that confer buoyancy on cells.
Gas vesicles contain two different proteins arranged to form a gas-permeable, but watertight, structure .
Cyanobacteria.
Gas vesicles
decrease the density of cells
allow a means of motility
allows organisms in water to position themselves for optimum light harvesting.
they are common in many species of cyanobacteria.
Endospores: Part 4.13
The endospore is a highly resistant differentiated type of bacterial cell produced by certain gram-positive Bacteria.
Endospore formation leads to a highly dehydrated structure that contains essential macromolecules and a variety of substances.
Endospores can remain dormant indefinitely but germinate quickly when the appropriate trigger is applied.
Endospores differ significantly from the vegetative, or normally functioning, cells
Endospore Stain
Motility : Part 4.14
Bacterial Flagella
Motility in most microorganisms is accomplished by flagella.
In prokaryotes, the flagellum is a complex structure made of several proteins, most of which are anchored in the cell wall and cytoplasmic membrane.
Flagella move the cell by rotation. A speed of about 60 cell lengths/second achievable.
Gliding Motility: Part 4.15
Prokaryotes that move by gliding motility do not employ rotating flagella They creep along a solid surface by gliding using the slime layer
or by a ratchet-protein mechanism that moves the outer membrane of the cell.
TAXIS: Part 4.16 Chemotaxis
Motile bacteria can respond to chemical and physical gradients in their environment.
In chemotaxis and phototaxis, random movement of a cell is biased either toward or away from a stimulus by controlling the degree to which runs or tumbles occur
Taxis: Part 4.16
The latter are controlled by the direction of rotation of the flagellum, which in turn is controlled by a network of sensory and response proteins.
Counterclockwise rotation moves the cell in a direction called a run. Clockwise rotation causes the tuft of flagella to spread, resulting in tumbling of the cell
Resolution: The ability to distinguish two adjacent objects as distinct and separate.
Light microscopes optimize image resolution by using lenses with high light-gathering characteristics (numerical aperture).
Contrast
Differences in intensity between two objects, or between an object and background
Total Magnification
Product of the magnification of the objective and ocular lenses.
Upper limit=1500
Lenses
Ocular: magnify 10-15X and objective of 10-100X
At 1000 x objects 0.2 um in diamater can just be resolved.
Immersion oil increase the light gathering ability of a lens by allowing rays emerging from the specimen at angles that would otherwise be lost to the objective lens to be collected and viewed.
Simple Stains
Gram Stain and Cell Wall
The structural differences between the cell walls of gram-positive and gram-negative Bacteria are responsible for differences in the Gram stain reaction.
Alcohol can readily penetrate the lipid-rich outer membrane of gram-negative Bacteria and extract the insoluble crystal violet-iodine complex from the cell.
The Gram Stain
Electron microscopy
Two major types of electron microscopy are performed: transmission electron microscopy, for observing internal cell structure down to the molecular level, and scanning electron microscopy, for three-dimensional imaging and examining surfaces.
Cytoplasmic : Part 4.5
A highly selective permeability barrier
Constructed of lipids and proteins
Forms a bilayer with hydrophilic exteriors and a hydrophobic interior.
Permeability Layer
The attraction of the nonpolar fatty acid portions of one phospholipid layer for the other layer helps to account for the selective permeability of the cell membrane.
Transport: Simple, Group translocation and the ABC system.
Translocases
Proteins are exported out of prokaryotic cells through the actions of proteins called translocases, which are specific in the types of proteins exported.
Bacterial Cell Wall: Part 4.8
There are two types of cell walls: Gram-positive and Gram-negative
The wall consists of the following:
Alternating repeats of N-acetylglucosamine and N-acetylmuramic acid
N-acetylmuramic acid is cross-linked between strands by short peptides.
Cross-Linkage
Each peptidoglycan repeating subunit is composed of four amino acids:
L-alanine,
D-alanine,
D-glutamic acid
Either lysine or diaminopimelic acid)
Two N-acetyl-glucose-like sugars.
Gram stain reaction.
The structural differences between the cell walls of gram-positive and gram-negative Bacteria are thought to be responsible for differences in the Gram stain reaction.
Alcohol can readily penetrate the lipid-rich outer membrane of gram-negative Bacteria and extract the insoluble crystal violet-iodine complex from the cell.
Protoplasts
Some prokaryotes are free-living without cell walls
They have unusually tough membranes
Or live in osmotically protected habitats, such as the animal body.
Surface Structures- Part 4.10
Prokaryotic cells often contain various surface structures, including fimbriae and pili, S-layers, capsules, and slime layers. A key function of these structures is in attaching cells to a solid surface.
Capsule: Part 4.10
Composed of repeating units of molecules
Attached to cell surface
Protects from drying
Hides bacteria from host
Slime Layer: Part 4.10
Loosely attached to cell surface
Water soluble
Protects cells from drying
Sticky layer that allows attachment
Fimbriae Versus Flagella
Pilus Versus Fimbriae
Cell Inclusions: Part 4.11
Prokaryotic cells often contain internal granules that function as storage materials or in magnetotaxis.
Some gram-negative prokaryotes can store elemental sulfur in globules in the periplasm
Gas Vesicles: Part 4.12
Gas vesicles are small gas-filled structures made of protein that confer buoyancy on cells.
Gas vesicles contain two different proteins arranged to form a gas-permeable, but watertight, structure .
Cyanobacteria.
Gas vesicles
decrease the density of cells
allow a means of motility
allows organisms in water to position themselves for optimum light harvesting.
they are common in many species of cyanobacteria.
Endospores: Part 4.13
The endospore is a highly resistant differentiated type of bacterial cell produced by certain gram-positive Bacteria.
Endospore formation leads to a highly dehydrated structure that contains essential macromolecules and a variety of substances.
Endospores can remain dormant indefinitely but germinate quickly when the appropriate trigger is applied.
Endospores differ significantly from the vegetative, or normally functioning, cells
Endospore Stain
Motility : Part 4.14
Bacterial Flagella
Motility in most microorganisms is accomplished by flagella.
In prokaryotes, the flagellum is a complex structure made of several proteins, most of which are anchored in the cell wall and cytoplasmic membrane.
Flagella move the cell by rotation. A speed of about 60 cell lengths/second achievable.
Gliding Motility: Part 4.15
Prokaryotes that move by gliding motility do not employ rotating flagella They creep along a solid surface by gliding using the slime layer
or by a ratchet-protein mechanism that moves the outer membrane of the cell.
TAXIS: Part 4.16 Chemotaxis
Motile bacteria can respond to chemical and physical gradients in their environment.
In chemotaxis and phototaxis, random movement of a cell is biased either toward or away from a stimulus by controlling the degree to which runs or tumbles occur
Taxis: Part 4.16
The latter are controlled by the direction of rotation of the flagellum, which in turn is controlled by a network of sensory and response proteins.
Counterclockwise rotation moves the cell in a direction called a run. Clockwise rotation causes the tuft of flagella to spread, resulting in tumbling of the cell
Sunday, January 18, 2009
Chapter 3
Chapter 3
Macromolecules
Macromolecules
Four classes of cellular macromolecules:
Proteins-amino acids-polypeptides-protein
Nucleic acids-DNA and RNA
Lipids- fatty acids, fats, sterols, waxes,
Saccharides (carbohydrates)
Protein Structure
Lipids: Fats, Waxes, Steroids, Phospholipids
Saccharides
Weak bonds—such as hydrogen bonds van der Waals forces, and hydrophobic interactions—also affect macromolecular structure, but through more subtle atomic interactions.
A variety of functional groups containing carbon atoms are common in biomolecules and in the folding of complex biomolecules.
The bacterial cell is about 70% water, with over one-half of the dry portion being made up of protein and one-quarter being made up of nucleic acids.
Proteins are polymers of monomers called amino acids.
Nucleic acids are polymers of nucleotides and are found in the cell in two forms, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).
Lipids have both hydrophobic (nonpolar) and hydrophilic (polar) properties. They play crucial roles in membrane structure and as storage depots for excess carbon.
Polysaccharides are polymers of sugars and are present primarily in the cell wall.
The relatively simple structure of the polysaccharides and their derivatives makes them:
the most abundant natural polymer on Earth and
allows them to be used for metabolism, as a component of information transfer molecules, and for cellular structure.
Combine monomeric units (monosaccharides) into polymers (polysaccharides)
All with a carbon-water (carbohydrate) chemical composition approaching (CH2O)n.
The two different orientations of the glycosidic bonds that link sugar residues impart different properties to the resultant molecules. (isomers)
Polysaccharides can also contain other molecules such as proteins or lipids, forming complex polysaccharides.
Lipids
Lipids are amphipathic—they have both hydrophilic and hydrophobic components.
This property makes them ideal structural components for cytoplasmic membranes.
The fourth bond can be one of 21 common side groups, which may be ionic, polar, or nonpolar. It is the heterogeneity of these side groups that defines the properties of a peptide or protein.
Proteins: Primary and Secondary Structure
The sequence of covalently linked amino acids in a polypeptide is the primary structure.
When many amino acids are covalently linked via peptide bonds, they form a polypeptide.
Secondary structure
Hydrogen bonding that produces an alpha-helix ("corkscrew") or beta-sheet ("washboard") formation, or domain
Proteins may have an assortment of either or both domains.
Quaternary Structure
Association of several polypeptides results in quaternary structure
Protein Structure
The final orientation and folding dictates the usefulness of a protein.
Destruction of the folded structure by chemicals or environmental conditions is called denaturation
Macromolecules
Macromolecules
Four classes of cellular macromolecules:
Proteins-amino acids-polypeptides-protein
Nucleic acids-DNA and RNA
Lipids- fatty acids, fats, sterols, waxes,
Saccharides (carbohydrates)
Protein Structure
Lipids: Fats, Waxes, Steroids, Phospholipids
Saccharides
Weak bonds—such as hydrogen bonds van der Waals forces, and hydrophobic interactions—also affect macromolecular structure, but through more subtle atomic interactions.
A variety of functional groups containing carbon atoms are common in biomolecules and in the folding of complex biomolecules.
The bacterial cell is about 70% water, with over one-half of the dry portion being made up of protein and one-quarter being made up of nucleic acids.
Proteins are polymers of monomers called amino acids.
Nucleic acids are polymers of nucleotides and are found in the cell in two forms, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).
Lipids have both hydrophobic (nonpolar) and hydrophilic (polar) properties. They play crucial roles in membrane structure and as storage depots for excess carbon.
Polysaccharides are polymers of sugars and are present primarily in the cell wall.
The relatively simple structure of the polysaccharides and their derivatives makes them:
the most abundant natural polymer on Earth and
allows them to be used for metabolism, as a component of information transfer molecules, and for cellular structure.
Combine monomeric units (monosaccharides) into polymers (polysaccharides)
All with a carbon-water (carbohydrate) chemical composition approaching (CH2O)n.
The two different orientations of the glycosidic bonds that link sugar residues impart different properties to the resultant molecules. (isomers)
Polysaccharides can also contain other molecules such as proteins or lipids, forming complex polysaccharides.
Lipids
Lipids are amphipathic—they have both hydrophilic and hydrophobic components.
This property makes them ideal structural components for cytoplasmic membranes.
The fourth bond can be one of 21 common side groups, which may be ionic, polar, or nonpolar. It is the heterogeneity of these side groups that defines the properties of a peptide or protein.
Proteins: Primary and Secondary Structure
The sequence of covalently linked amino acids in a polypeptide is the primary structure.
When many amino acids are covalently linked via peptide bonds, they form a polypeptide.
Secondary structure
Hydrogen bonding that produces an alpha-helix ("corkscrew") or beta-sheet ("washboard") formation, or domain
Proteins may have an assortment of either or both domains.
Quaternary Structure
Association of several polypeptides results in quaternary structure
Protein Structure
The final orientation and folding dictates the usefulness of a protein.
Destruction of the folded structure by chemicals or environmental conditions is called denaturation
Wednesday, January 14, 2009
Chapters 1 and 2
Biology 2400 Dr Krisher or Dr. K (Rhymes with Fisher) email: krisherk@macomb.edu Blog for class info, slide info, exam reviews: macombbio2400.blogspot.com
Attendance and Participation: Mandatory. I will point out in lecture what is important for the exam!
Rules: BE ON TIME. Notify me if you need to leave or will miss class. Do not walk out of lecture: disruptive
Makeup exam-only if arrangements made PRIOR to exam and only if reason is valid and at my discretion.
Lecture: Pay attention, must take notes and keep up. No sleeping, talking, text-messaging, playing on computer. Class discussions.
Lab: Participation is important; Quiz points and take home questions
Chapter 1 PART I Introduction to Microbiology
Science of Microbiology
Microorganisms are central to the functioning of the biosphere
The science of microbiology is the foundation of all the biological sciences
Microorganisms as Cells
The cell is a dynamic entity that forms the fundamental unit of life
The cell can exist alone: macroorganism vs. microorganism
Carry out process of growth, energy generation, and reproductions independently of other cells.
All life began as a microorganism
Basic biological science versus applied biological science
Basic Biological science: processes of microbial life
Applied Biological science: practical uses of microbes
Microbial Cell
Think of Microbe as Compartment
The cell has a barrier, the cytoplasmic membrane, that separates the inside of the cell from the environment.
The nucleus or nucleoid
The cytoplasm
Possibly a cell wall outside the cytoplasmic membrane
Cellular Characteristics
Six features associated with organisms:
metabolism
reproduction
differentiation
communication
movement
evolution
Cellular Functions
Metabolism: use of nutrients to make energy to operate cell functions
Reproduction: Growth and division into two or more daughter cells
Differentiation: process forming new substances or structure
Role of Enzymes
Microbes are machines that carry out chemical transformation.
Enzymes are the catalysts of this chemical machine, greatly accelerating the rate of chemical reactions.
Cells as Coding Devices
Cells are also coding devices that store and process information that is eventually passed on to offspring during reproduction through DNA (deoxyribonucleic acid).
The link between cells as machines and cells as coding devices is growth.
Habitat and Ecosystem
Habitat is the location where a microbial population lives.
Microbial populations can interact and cooperate with each other and environment
Ecosystem: organisms together with the physical and chemical constituents of their environment
Importance of Microbes
Estimates of the total number of microbes on Earth is ~ 5 1030 cells.
The total carbon present in microbes equals that of all plants on Earth
(plant carbon > animal carbon).
Most microbes reside in oceanic and terrestrial subsurfaces.
Most of biomass on Earth is microbial.
Microorganisms change the chemicaland physical properties of their habitats
Removal of nutrients from environment
Excretion of waste products.
Microorganisms are both beneficial and harmful to humans. Pathogens versus Saprophytes
Agricultural Microbiology
Microorganisms are important in the agricultural industry.
Legumes, which live in close association with bacteria that form structures called nodules on their roots,convert atmospheric nitrogen into fixed nitrogen that the plants use for growth.
Bacteria reduce need for plant fertilizer.
Fathers of Microbiology
Robert Hooke was the first to describe microorganisms
Antoni van Leeuwenhoek was the first to describe/see bacteria
Ferdinand Cohn founded the field of bacteriology and discovered bacterial endospores
Louis Pasteur
Spontaneous generation: hypothesis that living organisms can originate from nonliving matter.
Pasteur disproved this idea by comparing:
the growth of microorganisms in one flask containing sterile broth that was exposed to the air
the growth of microorganisms in flask containing sterile broth that was not exposed to the air.
Pasteur’s Experiments
Robert Koch
Koch’s Postulates
The suspected pathogenic organism should be present in all cases of the disease and absent from healthy animals.
The suspected organism should be grown in pure culture—that is, a culture containing a single kind of microorganism.
Cells from a pure culture of the suspected organism should cause disease in a healthy animal.
The organism should be reisolated and shown to be the same as the original
General Microbiology
Culture Media Enrichment Cultures
Beijerinck: Winogradsky: use of inorganic compounds for production of energy by microbes
Early Prevention of Disease
Semmelweis and Handwashing
Lister’s Antiseptic Technique
Nightingale and Nursing
Snow and Epidemiology – infection control and epidemiology
Jenner’s Vaccine – field of immunology
Ehrlich’s “Magic Bullets” – field of chemotherapy
Applied Microbiology
Some subdisciplines of applied microbiology:
medical microbiology,
immunology,
agricultural microbiology,
industrial microbiology,
aquatic microbiology,
marine microbiology, and
microbial ecology
Basic Microbiology
Some subdisciplines of basic microbiology:
microbial systematics,
microbial physiology,
cytology,
microbial biochemistry,
bacterial genetics,
molecular biology.
Chapter 2An Overview of Microbial Life
Cell Structure and Evolutionary History
Elements of Cell and Viral Structure,
Arrangement of DNA in Microbial Cells
The Tree of Life
PART II Microbial Diversity
Physiological Diversity of Microorganisms,
Prokaryotic DiversityEukaryotic Microorganisms
PART I Cell Structure and Evolutionary History Elements of Cell and Viral Structure
Structural Types of Cells
Two structural types of cells are recognized:
The prokaryote and the eukaryote.
Prokaryotic cells have a simpler internal structure than eukaryotic cells, lacking membrane-enclosed organelles
Basic Structures
All microbial cells share certain basic structures in common, such as
cytoplasm
cytoplasmic membrane
ribosomes
a cell wall (usually)
Viruses are not Prokaryotes
Viruses are not cells but depend on cells for their replication
Ribosomes
Functions:
The cell's protein-synthesizing factories—
are particulate structures composed of RNA (ribonucleic acid)
various proteins suspended in the cytoplasm.
Ribosomes and Proteins
Ribosomes interact with cytoplasmic proteins and messenger and transfer RNAs in the key process of protein synthesis (translation)
Arrangement of DNA in Microbial Cells
Genome: The genes that govern the properties of cells, and a cell's complement of genes.
Chromosomes.
DNA is arranged in cells to form chromosomes
Prokaryotes: usually a single circular chromosome
Eukaryotes: several linear chromosomes exist.
Plasmids
Plasmids are circular extrachromosomal genetic elements (DNA)
nonessential for growth
found in prokaryotes.
Nucleus
The nucleus is a membrane-enclosed structure that contains the chromosomes in eukaryotic cells.
The nucleoid, in contrast, is the aggregated mass of DNA that constitutes the chromosome of cells of Bacteria and Archaea
The Tree of Life
Comparative ribosomal RNA sequencing has defined the three domains of life:
Bacteria, Archaea, and Eukarya.
Eukarya from Bacteria
Molecular sequencing has also shown that the major organelles of Eukarya have evolutionary roots in the Bacteria and has yielded new tools for microbial ecology and clinical microbiology.
Evolution
Evolution is the change in a line of descent over time leading to new species or varieties.
The evolutionary relationships between life forms are the subject of the science of phylogeny.
Plus the genome in the chromosomes in the nucleus:
Mitochondria and chloroplasts of eukaryotes contain their own genomes
(DNA arranged in circular fashion, as in Bacteria) and ribosomes.
Ribosomal RNA Sequencing
Using ribosomal RNA sequencing technology, these organelles have been shown to be highly derived ancestors of specific lineages of Bacteria
Mitochondria and chloroplasts were thus once free-living cells that established stable residency in cells of Eukarya eons ago.
The process by which this stable arrangement developed is known as endosymbiosis.
PART II Microbial Diversity, Physiological Diversity of Microorganisms
All cells need carbon and energy sources
Chemoorganotrophs obtain their energy from the oxidation of organic compounds.
Chemolithotrophs obtain their energy from the oxidation of inorganic compounds.
Phototrophs contain pigments that allow them to use light as an energy source.
Autotrophs use carbon dioxide as their carbon source, whereas heterotrophs use organic carbon
Extremophiles thrive under environmental conditions in which higher organisms cannot survive.
Prokaryotic Diversity
Several lineages are present in the domains Bacteria and Archaea, and an enormous diversity of cell morphologies and physiologies are represented there.
Retrieval and analysis of ribosomal RNA genes from cells in natural samples have shown that many phylogenetically distinct but as yet uncultured prokaryotes exist in nature.
Eukaryotic Microorganisms
Algae,
Protozoa,
Fungi, slime molds
Plant and animal cells
Collectively, microbial eukaryotes are known as the Protista. Some protists, such as the algae, are phototrophic.
Cells of algae and fungi have cell walls, whereas the protozoa do not.
Some algae and fungi have developed mutualistic associations called lichens.
Attendance and Participation: Mandatory. I will point out in lecture what is important for the exam!
Rules: BE ON TIME. Notify me if you need to leave or will miss class. Do not walk out of lecture: disruptive
Makeup exam-only if arrangements made PRIOR to exam and only if reason is valid and at my discretion.
Lecture: Pay attention, must take notes and keep up. No sleeping, talking, text-messaging, playing on computer. Class discussions.
Lab: Participation is important; Quiz points and take home questions
Chapter 1 PART I Introduction to Microbiology
Science of Microbiology
Microorganisms are central to the functioning of the biosphere
The science of microbiology is the foundation of all the biological sciences
Microorganisms as Cells
The cell is a dynamic entity that forms the fundamental unit of life
The cell can exist alone: macroorganism vs. microorganism
Carry out process of growth, energy generation, and reproductions independently of other cells.
All life began as a microorganism
Basic biological science versus applied biological science
Basic Biological science: processes of microbial life
Applied Biological science: practical uses of microbes
Microbial Cell
Think of Microbe as Compartment
The cell has a barrier, the cytoplasmic membrane, that separates the inside of the cell from the environment.
The nucleus or nucleoid
The cytoplasm
Possibly a cell wall outside the cytoplasmic membrane
Cellular Characteristics
Six features associated with organisms:
metabolism
reproduction
differentiation
communication
movement
evolution
Cellular Functions
Metabolism: use of nutrients to make energy to operate cell functions
Reproduction: Growth and division into two or more daughter cells
Differentiation: process forming new substances or structure
Role of Enzymes
Microbes are machines that carry out chemical transformation.
Enzymes are the catalysts of this chemical machine, greatly accelerating the rate of chemical reactions.
Cells as Coding Devices
Cells are also coding devices that store and process information that is eventually passed on to offspring during reproduction through DNA (deoxyribonucleic acid).
The link between cells as machines and cells as coding devices is growth.
Habitat and Ecosystem
Habitat is the location where a microbial population lives.
Microbial populations can interact and cooperate with each other and environment
Ecosystem: organisms together with the physical and chemical constituents of their environment
Importance of Microbes
Estimates of the total number of microbes on Earth is ~ 5 1030 cells.
The total carbon present in microbes equals that of all plants on Earth
(plant carbon > animal carbon).
Most microbes reside in oceanic and terrestrial subsurfaces.
Most of biomass on Earth is microbial.
Microorganisms change the chemicaland physical properties of their habitats
Removal of nutrients from environment
Excretion of waste products.
Microorganisms are both beneficial and harmful to humans. Pathogens versus Saprophytes
Agricultural Microbiology
Microorganisms are important in the agricultural industry.
Legumes, which live in close association with bacteria that form structures called nodules on their roots,convert atmospheric nitrogen into fixed nitrogen that the plants use for growth.
Bacteria reduce need for plant fertilizer.
Fathers of Microbiology
Robert Hooke was the first to describe microorganisms
Antoni van Leeuwenhoek was the first to describe/see bacteria
Ferdinand Cohn founded the field of bacteriology and discovered bacterial endospores
Louis Pasteur
Spontaneous generation: hypothesis that living organisms can originate from nonliving matter.
Pasteur disproved this idea by comparing:
the growth of microorganisms in one flask containing sterile broth that was exposed to the air
the growth of microorganisms in flask containing sterile broth that was not exposed to the air.
Pasteur’s Experiments
Robert Koch
Koch’s Postulates
The suspected pathogenic organism should be present in all cases of the disease and absent from healthy animals.
The suspected organism should be grown in pure culture—that is, a culture containing a single kind of microorganism.
Cells from a pure culture of the suspected organism should cause disease in a healthy animal.
The organism should be reisolated and shown to be the same as the original
General Microbiology
Culture Media Enrichment Cultures
Beijerinck: Winogradsky: use of inorganic compounds for production of energy by microbes
Early Prevention of Disease
Semmelweis and Handwashing
Lister’s Antiseptic Technique
Nightingale and Nursing
Snow and Epidemiology – infection control and epidemiology
Jenner’s Vaccine – field of immunology
Ehrlich’s “Magic Bullets” – field of chemotherapy
Applied Microbiology
Some subdisciplines of applied microbiology:
medical microbiology,
immunology,
agricultural microbiology,
industrial microbiology,
aquatic microbiology,
marine microbiology, and
microbial ecology
Basic Microbiology
Some subdisciplines of basic microbiology:
microbial systematics,
microbial physiology,
cytology,
microbial biochemistry,
bacterial genetics,
molecular biology.
Chapter 2An Overview of Microbial Life
Cell Structure and Evolutionary History
Elements of Cell and Viral Structure,
Arrangement of DNA in Microbial Cells
The Tree of Life
PART II Microbial Diversity
Physiological Diversity of Microorganisms,
Prokaryotic DiversityEukaryotic Microorganisms
PART I Cell Structure and Evolutionary History Elements of Cell and Viral Structure
Structural Types of Cells
Two structural types of cells are recognized:
The prokaryote and the eukaryote.
Prokaryotic cells have a simpler internal structure than eukaryotic cells, lacking membrane-enclosed organelles
Basic Structures
All microbial cells share certain basic structures in common, such as
cytoplasm
cytoplasmic membrane
ribosomes
a cell wall (usually)
Viruses are not Prokaryotes
Viruses are not cells but depend on cells for their replication
Ribosomes
Functions:
The cell's protein-synthesizing factories—
are particulate structures composed of RNA (ribonucleic acid)
various proteins suspended in the cytoplasm.
Ribosomes and Proteins
Ribosomes interact with cytoplasmic proteins and messenger and transfer RNAs in the key process of protein synthesis (translation)
Arrangement of DNA in Microbial Cells
Genome: The genes that govern the properties of cells, and a cell's complement of genes.
Chromosomes.
DNA is arranged in cells to form chromosomes
Prokaryotes: usually a single circular chromosome
Eukaryotes: several linear chromosomes exist.
Plasmids
Plasmids are circular extrachromosomal genetic elements (DNA)
nonessential for growth
found in prokaryotes.
Nucleus
The nucleus is a membrane-enclosed structure that contains the chromosomes in eukaryotic cells.
The nucleoid, in contrast, is the aggregated mass of DNA that constitutes the chromosome of cells of Bacteria and Archaea
The Tree of Life
Comparative ribosomal RNA sequencing has defined the three domains of life:
Bacteria, Archaea, and Eukarya.
Eukarya from Bacteria
Molecular sequencing has also shown that the major organelles of Eukarya have evolutionary roots in the Bacteria and has yielded new tools for microbial ecology and clinical microbiology.
Evolution
Evolution is the change in a line of descent over time leading to new species or varieties.
The evolutionary relationships between life forms are the subject of the science of phylogeny.
Plus the genome in the chromosomes in the nucleus:
Mitochondria and chloroplasts of eukaryotes contain their own genomes
(DNA arranged in circular fashion, as in Bacteria) and ribosomes.
Ribosomal RNA Sequencing
Using ribosomal RNA sequencing technology, these organelles have been shown to be highly derived ancestors of specific lineages of Bacteria
Mitochondria and chloroplasts were thus once free-living cells that established stable residency in cells of Eukarya eons ago.
The process by which this stable arrangement developed is known as endosymbiosis.
PART II Microbial Diversity, Physiological Diversity of Microorganisms
All cells need carbon and energy sources
Chemoorganotrophs obtain their energy from the oxidation of organic compounds.
Chemolithotrophs obtain their energy from the oxidation of inorganic compounds.
Phototrophs contain pigments that allow them to use light as an energy source.
Autotrophs use carbon dioxide as their carbon source, whereas heterotrophs use organic carbon
Extremophiles thrive under environmental conditions in which higher organisms cannot survive.
Prokaryotic Diversity
Several lineages are present in the domains Bacteria and Archaea, and an enormous diversity of cell morphologies and physiologies are represented there.
Retrieval and analysis of ribosomal RNA genes from cells in natural samples have shown that many phylogenetically distinct but as yet uncultured prokaryotes exist in nature.
Eukaryotic Microorganisms
Algae,
Protozoa,
Fungi, slime molds
Plant and animal cells
Collectively, microbial eukaryotes are known as the Protista. Some protists, such as the algae, are phototrophic.
Cells of algae and fungi have cell walls, whereas the protozoa do not.
Some algae and fungi have developed mutualistic associations called lichens.
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