Microbiology Exam 2

List attributes that all cells share

List attributes that all cells share

1. Plasma membrane (outer covering that separates interior from surround environment)

2. Cytoplasm (jelly-like region w/ other cellular components)

3. DNA (genetic material)

4. Ribosome (particles that synthesize proteins)

Distinguish between prokaryotes and eukaryotes

• Prokaryote do not have nucleus but eukaryotes do

• In prokaryote cells, DNA is stored in the cytoplasm and in eukaryotes cells, DNA is stored in the nucleus

• Prokaryote do not have organelles enclosed in plasma membranes

Compare and contrast the genomic DNA (chromosomes) of prokaryotes vs. eukaryotes

• eukaryotic chromosomes are located within the nucleus and linear where prokaryotic chromosomes are located in the nucleoid (cytoplasm) plants, fungi, bacteria, algae, and archaeaand are circular

List taxa of organisms that have a cell wall

plants, fungi, bacteria, algae, and archaea

Describe the cell walls’ compositions

Contain two layers, the middle lamella and the primary cell wall, and many cells produce an additional layer, called the secondary wall. The middle lamella serves as a cementing layer between the primary walls of adjacent cells

Summarize the central tenet and purpose of the endosymbiont theory.

The endosymbiont theory is that the earliest eukaryotic cells were prokaryotes engulfing and maintaining a symbiotic relationship with other prokaryotes

Explain the broad taxonomy and characteristics of the helminths

• They are in the kingdom Animalia

• multicellular

• eukaryotic

• also belong to group of animals called metazoa

List the general reproduction methods of taxa of eukaryotic microbes

reproduce both asexually (through mitosis) and sexually (through meiosis and gamete fusion)

State the source of agar

from the cell walls of red algae

Differentiate between protozoa and algae

protozoa are heterotrophic (find/ingest their food from environment) while algae are autotrophic (photosynthetic- make their own food)

List examples of protozoas

• Euglena- some have chloroplasts

• Trypanosomes- causes African sleeping sickness

• Giardia- cause a diarrheal illness that is spread through fecal contamination

• Dinoflagellates- cause glowing bays

• Amoeboid- causes amoebiasis

• Nonmotile- causes malaria

• Ciliated- complex, large unicellular organisms

List examples of Algae

• Diatoms- precursors for sand and diatomaceous earth

• Green

• Red

• Brown

Distinguish between organisms (cells) and viruses

• viruses are non-living infectious particles, much smaller than a cell, and need a living host cell to reproduce; cannot produce ATP; cannot independently form proteins from molecules of messenger RNA

• cells can exist by themselves or as a larger organism; genetic material of the cell is DNA, a double stranded helix

List attributes that all viruses share

• small

• have DNA or RNA genomes

• are obligate intracellular parasites

Describe the capsid of a virus

• the protein coating surrounding the nucleic acid of a virus

• encloses the genetic material of the virus

• function is to protect the nucleic acid from the environment

What are other names for virus?

• Infection

• germ

• disease

• pathogen

• illness

List characteristics that are used to classify viruses

• what type of nucleic acid it has

  • double stranded DNA

  • single stranded DNA

  • double stranded RNA

  • single stranded RNA

• present or absent of an envelope

• nucleocapsid structure

  • Isocahedral

  • Helical

  • Complex

• virion (fully-assembled virus)

Describe Isocahedral

• each virus has different variations on how the axes of symmetry can be drawn

• made of 20 facets- not necessarily of equal area)

  • Naked/Enveloped

Describe Helical

• arranged in cork skew structure or rod like

  • influenza → got envelope from the host cell’s plasmid membrane

Describe Complex

• symmetry is poorly understood or a combination of shapes

  • Bacteriophage structure → host cells are bacteria

  • HIV

• “Any or none of the above”

Distinguish between enveloped and naked viruses

• enveloped = extra lipid bilayer membrane surrounding the protein capsid; composed of envelope and nucleocapsid

  • naked = more virulent than enveloped viruses; cause host cell lysis; composed of capsid protein and nucleic acid (DNA/RNA), virion, nucleocapsid

Describe the functions of viral envelopes

• protecting the RNA or DNA molecules

• evading recognition by the immune system

• facilitating virus entry (helps it enter host cell)

List several factors that determine a virus’ host range

1. Does the virus have the right proteins to attach to proteins on the cell membrane?

2. Once inside, does the host cell have the right stuff for the virus to survive and replicate?

   1. Does host cell have right machinery in place?

   2. Does host cell have correct starting materials

      1. amino acids

      2. nucleotides

3. Once replicated, are the new virions able to somehow fully assemble and leave the host cell to infect others?

   1. What is the exit strategy? Exocytosis, bursting the cell (lysing host cell), budding?

Recognize the importance of the lysogenic cycle of some viruses

Allows a phage to reproduce without killing its host

Summarize the six steps of viral replication, and describe each step

1. absorption → attachment to victim cell

2. penetration → entry into host cell

3. uncoating → to release the genetic material (DNA or RNA) into the host cell

4. synthesis/replication → the host cell’s machinery is tricked into making new virus parts (DNA/RNA and proteins)

5. assembly → new parts are put together to make nucleocapsids

6. release → virions are released via host cell lysis or budding

Contrast anabolic versus catabolic chemical reactions

• anabolic reaction → use energy to build complex molecules from simpler organic compounds (proteins from amino acids, carbohydrates from sugars)

  • Bone development and mineralization

  • muscle mass gain

• catabolic reaction → break complex molecules down into deeper into simple ones, releasing chemical energy

  • breakdown of proteins into amino acids, glycogen into glucose, and triglycerides into fatty acids

Describe the three chemical reactions that make up aerobic cellular respiration

• Glycolysis

• Krebs Cycle

• Electron Transport Chain

Differentiate between aerobic and anaerobic respiration processes

• Aerobic respiration takes place in presence of oxygen; carbon dioxide and water are end products; releases more energy

• Anaerobic respiration takes place in absence of oxygen; alcohol is end product

Explain the purpose of fermentation

List possible products of fermentation

• ethanol

• lactic acid

• carbon dioxide

• hydrogen gas

What the importance and general definition of oxidative phosphorylation

• provides most of the ATP that higher animals and plants use to support life and is responsible for setting and maintaining metabolic homeostasis

• a cellular process that harnesses the reduction of oxygen to generate high-energy phosphate bonds in the form of adenosine triphosphate (ATP)

List waste products of aerobic respiration, and state which reaction(s) produce them.

• Carbon dioxide

  • the pyruvate dehydrogenase reaction that converts pyruvate to acetyl CoA

  • the isocitrate dehydrogenase reaction that converts isocitrate to alpha-ketoglutarate

  • the alpha-ketoglutarate dehydrogenase reaction that converts alpha-ketoglutarate to succinate.

• Water

  • the electron transport chain reaction in complex 4 where the electrons from the cytochrome C are used to reduce oxygen to form water.

State the reactants and products of glycolysis

• reactants = glucose

• products = molecule of pyruvate, 2 ATP, and 2 NADH

Understand how ATP is formed in cells which use oxygen

• Glucose reactions with oxygen, forming ATP that can be used by the cell

• cellular repatriation, glucose and oxygen react t form ATP

Compare and contrast aerobic respiration in prokaryotes versus eukaryotes

• in eukaryotic cells, the majority of the process of cellar respiration except glycolysis occurs in the mitochondria

• in prokaryotic cells the process occurs on the inner surface of the cell membrane or in the cytoplasm because they do not have membrane-bound organelles such as mitochondria

Where does organisms get energy?

• Phototrophs: Light

  • Plants

  • Alge

• Chemotrophs: Chemicals; covalent bonds

  • Where humans get their energy

    • Glucose (in our diets) to create ATP

What carries electrons during cellular respiration?

• Organotrophs: organic compounds

• Lithotrophs: inorganic molecule OR single ion/atom

Where does organisms get their carbon?

• Carbonfixation

  • Autotroph: fixation carbon (usually from inorganic carbon)

    • Heterotroph: Eat organisms

What microbial metabolism uses light, organic compounds, and carbon fixation?

Photoorganoautotroph

What uses chemicals, organic compounds, and eat organisms

Chemoorganohetrotrophs

What are the common types of microbial metabolism?

• Photoautotrophs

• Chemoautotroph

• Chemoheterotrophs

What is the microbial metabolism, Photoautotrophs?

• Uses light and carbon fixation to make their own organic compound and energy

  • Plants

What is the microbial metabolism, Chemoautotroph

• Uses inorganic chemicals (methane, ammonia, sulfur, carbon dioxide) to make organic compounds and energy

  • Pompeii worm with a “fleece” of bacteria

What is the microbial metabolism, Chemoheterotrophs?

• Most bacteria get their carbon and energy by consuming other organic compounds

  • Humans

Summarize the sequence of events involved in binary fission

1. a young cell

2. chromosome is replicated and new and old chromosomes move to different sides of cell

3. protein band forms in center of cell

4. Septum formation begins

5. When septum is complete, cell are considered divided. Some species will separate completely as shown here, while others remain attached, forming chains or doublets

What is commensalism?

• One organism benefits, and the other is unaffected

What is mutualism?

• Both organisms benefit

What is parasitism?

• One organism benefits at the expense of the other (the other one is injured)

What is symbiosis?

• Two organisms living together

What is a hypothetical scenario involving symbiosis with a parasitism relationship?

• Any infectious disease because you are loosing homeostasis

What is a hypothetical scenario involving symbiosis with a commensalism relationship?

• Trees; they are home to animals (animals benefit)- the tree do not benefit but are not damaged

What is a hypothetical scenario involving symbiosis with a Mutualism relationship?

• The relationship between clownfish and sea anemones because both benefit from each other

List five bacterial aerotolerance categories

1. Obligate Aerobes

2. Facultative Anaerobes

3. Oblique Anaerobes

4. Aerotolerant Anaerobes

5. Microaerophiles

Define Obligate Aerobes

• Only aerobic growth, oxygen required

• Growth occurs where high concentrations of oxygen have diffused into the medium

• Presence of enzymes catalase and superoxide dismutase (SOD) allows toxic forms of oxygen to be neutralized; can use oxygen

Define Facultative Anaerobes

• Both aerobic and anaerobic growth; greater growth in presence of oxygen

• Growth is best where most oxygen is present, but occurs throughout tube

• Presence of enzymes catalase and SOD allows toxic forms of oxygen to be neutralized; can use oxygen

Describe Oblique Anaerobes

• Only anaerobic growth; ceases in presence of oxygen

• Growth occurs only where there is no oxygen

• Lacks enzyme to neutralize harmful forms of oxygen; cannot tolerate oxygen

Describe Aerotolerant Anaerobes

• Only anaerobic growth; but continues in presence of oxygen

• Growth occurs evenly; oxygen has no effect

• Presence of one enzyme, SOD, allows harmful forms of oxygen to be partially neutralized; tolerates oxygen

Define Microaerophiles

• Only aerobic growth'; oxygen required in low concentration

• Growth occurs only where a low concentration of oxygen has diffused into medium

• Produce lethal amounts of toxic forms of oxygen if exposed to normal atmospheric oxygen

What does obligate mean?

• MUST have something

What are mesophiles?

• thrive in mild conditions

What are extremophiles?

• thrive in extreme conditions (obligate- MUST have extreme conditions)

What are examples of extremophiles?

• Osmophile

• Halophile - able to thrive in high-salt conditions

• Methaotroph - uses methane as an energy soruce

• Psychrophile - able to thrive in low temperatures (cold)

• Thermophile - able to thrive in high temperatures (hot)

• Acidophile - able to thrive at low pH

• Alkaliphile - able to thrive at high pH

• Anaerobe - able to. thrive in the absence of oxygen

• Xerophile - able to thrive in very dry conditions

• Barophile - required pressure up to 100 times atmospheric pressure

What is a Osmophile?

• able to thrive in high solute concentrations

What is a Halophile?

• able to thrive in high-salt conditions

What is a Methaotroph?

• uses methane as an energy source

What is a Psychrophile?

• able to thrive in low temperatures (cold)

What is a Thermophile?

• able to thrive in high temperatures (hot)

What is a Acidophile?

• able to thrive at low pH

What is a Alkaliphile?

• able to thrive at high pH

What is a Anaerobe?

• able to thrive in the absence of oxygen

What is a Xerophile?

• able to thrive in very dry conditions

What is a Barophile?

• required pressure up to 100 times atmospheric pressure

Define each of the four main phases of a typical growth curve of a bacterium in culture

1. Lag phase → getting used to environment

   1. occurs between hours 1 and 5

2. Exponential growth phase → more growth than death of cells

   1. occurs between hours 5 and 15

3. Stationary phase → “platoe”

   1. occurs between hours 15 and 30

4. Death phase → running out of resources (food, space) and so death begin to out number the number of viable cells in the culture

   1. occurs between hours 30 and 45

What is the purpose of fermentation?

• allows the presentation of substantial amounts of food through lactic acid, alcohol, acetic acid, and alkaline fermentations

• to regenerate NAD+ to allow glycolysis to continue to happen

Describe the chromosomes of prokaryotes and eukaryotes

• Eukaryotic chromosomes are located within the nucleus

• contain free-floating linear chromosomes within nucleus

• Prokaryotic chromosomes are located in the nucleoid

• have a single circular chromosome attached to cell membrane

Describe the structure of a plasmid

• small, circular, double stranded DNA molecule

Describe the location of a plasmid

• Usually found in bacteria

• Sometimes found in eukaryotic and archaea organisms

Describe the purpose of plasmids

• act as delivery vehicles, or vectors, to introduce foreign DNA into bacteria

• Eukaryotes try to wrap their DNA around proteins called histones to help package the DNA into smaller spaces

  • free floating

• Prokaryotes do not have histones

  • bound to an organelle

What is Chargaff’s rule?

• A always pairs with T

• C always pairs with G

Describe the process of DNA replication

• **copying one double-stranded DNA molecule to get two new DNA molecules

• Origin of replication

• Unwinding of DNA double helix

• Stabilization of unwound template strands

• Synthesis of RNA primers

• Synthesis of DNA

• Removal of RNA primers

• Replacement of RNA with DNA

• Joining of Okazaki fragments

• Removal of positive supercoils ahead of advancing replication forks

• Synthesis of telomeres

What does DNA polymerase do?

• After DNA is split, DNA polymerase will pair nucleoide with right pairing base

• It checks it’s work to make sure pairing errors are corrected (mismatch repair)

What are differences between DNA replication in prokaryotes vs. eukaryotes

• prokaryotes = only one point of origin → replication occurs in two opposing directions at the same time and takes place in cytoplasm; posses 1 or 2 polymerase; happens much faster

• eukaryotes = have multple points of origin and use unidirectional replication within the nucleus; have 4 or more polymerase

Relate the components of the central dogma of biology

• DNA (TRANSCRIPTION occurs) → mRNA (TRANSLATION occurs) → Protein

What is transcription?

• The process by which DNA is coped to RNA

What is translation?

• converting the mRNA transcript to a chain of amino acids; occurs at the ribosome

Describe the steps of transcription

1. Initiation → RNA polymerase binds to the promoter of a gene and “unzips” the DNA

2. Elongation → One by one, in sequence, RNA polymerase reads the DNA template and pastes the complementary RNA nucleotides onto a growing mRNA transcript (instead of T, RNA polymerase adds U)

3. Termination → RNA polymerase dissociates, the new mRNA transcript detaches, and the DNA “re-zips” The transcript (mRNA) then finds a ribosome in the cytoplasm)

What is a codon?

• a sequence of three mRNA nucleotides

Describe the steps of translation

1. Entrance of tRNA 1 and 2

2. Formation of peptide bond

3. Discharge of tRNA 1 at E site

4. First translocation

5. Formation of peptide bond

6. Discharge of tRNA 2; second translocation; enters tRNA 4

7. Formation of peptide bond

What is a mutation?

• A change in the DNA nucleotide sequence

What are the types of mutations?

• Substitution

• Point Mutation

• Silent

• Missense

• Nonsense

What is a Substitution mutation?

• One sequence is replaced with another

What is a point mutation?

• (Type of substitution)

• One base pair is replaced with a different one

What is a silent mutation?

• Encodes the same amino acid

What is a missense mutation?

• Encodes a different amino acid

What is a nonsense mutation?

• Makes a new stop codon

What is a insertion?

• one or more nucleotide added

What is a deletion?

• One of more nucleotide removed

A (adenine)

• One of the nitrogen bases found in DNA and RNA, with a purine form

Acidophile

• Staining readily with acid stains