Biology Exam IV
Final: Monday, 12/9
75% new material
25% old
Self quizes
•
•
•
•
•

22 evolution
27 Bacteria 27
28 protist
31 fungi
viruses
Viruses
Horizontal transmission of
a plant viral disease could
be caused by
Insects as vectors carrying virus
particles between pl...
RNA viruses require their
own supply of certain
enzymes because

Host cells do not have enzymes
available that can replica...
R plasmid
Contains genes for antibiotic
resistance and for sex pili
Transposition differs from
other mechanisms of genetic
recombination because it
Scatters genes to new loci in the
genome
An operon codes for an
amino acid. If the regulation
of this operon is like that of
the trp operon

The amino acid acts as...
A mutation that makes the
regulatory gene of an
inducible operon nonfunction
would result in
Continuous transcription of t...
Which information
transfer is catalyzed by
reverse transcriptase?
RNA -> DNA
Which characteristic is
common to BOTH bacteria
and viruses?
Nucleic acid as genetic material
Which of the following
processes would never
contribute to genetic
variation within a bacterial
population?
meiosis
During conjugation
between an Hfr cell and
an F- cell
Genes from the Hfr cell may replace
the genes of the F- cell by
reco...
Emerging viruses arrive by
All of the above
a)
b)
c)

Mutation of existing viruses
The spread of existing viruses to
new h...
A certain mutation in E coli
makes the lac operator
unable to bind to the active
repressor. How would this
affect the cell...
Gram-negative
• meningococcal
menintus

• Thin cell wall
• outer wall (OM): toxic
to humans
• sensitive to osmotic
pressur...
Gram-positive
• THICK peptidoglycan
layer
• resistant to osmotic
pressure
Classify bacteria by habitat
1. halophile
2. coliform: your
digestive tract
3. thermophile
4. acidophile
Classify bacteria by metabolic pathway
1. obligate aerobe:
require O2
2. anaerobe: O2 kills
anaerobes
3. facultative aerob...
Classify bacteria by metabolic pathway
• M. tuber

1. obligate aerobe:
require O2
Classify bacteria by metabolic pathway
• Cl. tetanic

2. anaerobe
Classify bacteria by metabolic pathway
• E. coli (facultative)

1. obligate aerobe:
require O2
2. anaerobe: O2 kills
anaer...
Classify bacteria by metabolic pathway
• cyanobacteria
(photoautotroph)

1. obligate aerobe:
require O2
2. anaerobe: O2 ki...
capsule: sugar material that covers cell
wall
• Strep pyroxenes, H.
influenza

• protect against
phagocytosis
• protect ag...
fimbriae & pili: attachment purpose
structures
• pile: used for
conjugation (sexual
reproduction)
slime layer: sticky matrix of
polysaccharides that protects the
bacteria

• Streptococcus mutans
cause tooth decays
taxis: movement toward or away from
stimulus
internal/genome structure of bacteria
• one chromosome (DNA)
• no organelles
• plasma membrane
carries out metabolic
proce...
binary fission: similar to mitosis
• one bacteria splits to
two
• mitosis: split nucleus
endospore
• anthrax (Bacillus
anthracis)
endospore
• botulism
endospore
• tetanus
endospore
• gas gangrene
(Clostridium perfringen)
classify bacteria via nutritional intake
1.
2.
3.
4.

photoautotrophy
chemoautotrophy
photoheterotrophy
chemoheterotrophy
photoautotrophy
• energy from sunlight
• carob from CO2
chemoautotrophy
• energy from inorganic
molecules like sulfur
• carbon from CO2
photoheterotrophy
• carbon from organic
sources (other
organisms)
chemoheterotrophy
• energy and CO2 from
organic sources
eubacteria aka “bacteria”
• cell wall made of
peptidoglycan
Archaea
• cell wall made of
pseudomurein
methanogen
• anaerobic Archae
• remove excess
hydrogen, O2
symbiotic categories
1. mutualism
2. commensalism
3. parasitism
Genus of bacterial diseases!
1.
2.
3.
4.
5.
6.

Borelia
Treponema
Staphylococcus
Mycobacterium
Yersinia
Neisseria

1.
2.
3...
Lyme
• Borelia
syphilis
• Treponema
MRSA
• Staphylococcus
tuberculosis
• Mycobacterium
plague
1. Bubonic
2. pneumonic

• Yersinia
gonorrhea
• Neisseria
exotoxin
• G positive
botulin
• exotoxin
• Gram positive
tetanus
• exotoxin
• Gram positive
endotoxin
• Gram negative
• you get more sick
• bacteria has outer
membrane
Gram-positive
• EXOtoxin
Gram-negative
• ENDOtoxin
• have outer membrane
Gram
• exotoxin
– made of G positive
– botulin and tetanin are
examples
– can elicit immune
response 
– can be vaccinated...
Chlamydomonas
• eyespot
• pyrenoid
• protist
Diatom
• protist
Algae
• photosynthetic protist
Protists
• Lecture: Thursday
11/21

•
•
•
•

Cercozoans
Forams
Radiolarians
Amoeba
– 4 clades

• Rhodophyta (red algae)
• ...
Cerocozoans
• Amoeba-looking cells
• Clade foraminiferans
(“forams”)
• Feed by pseudopodia
Phylum: Forams
• shrimp

• Porous, multichambered calcium
carbonate shells called
tests
• Pseudopodia extend
through the p...
Forams (importance)
• layers of foram tests in
marine sediments from
limestone and oil deposits
– Egyptian pyramids

• act...
forams
• limestone cliff in Dover
England
Kingdom: radiolarians
• have silica tests fused
into one piece (like
diatoms)
• pseudopodia are called
axopodia, which rad...
Kingdom: amoeba
• have lobe-shaped
pseudopodia (false feet)
rather than threadlike
• do not have tests and
have no shape
•...
Four Clades of Amoeba
1.
2.
3.
4.

Gymnanoebas
Entaamoeba
plasmodial slime mold
cellular slime mold
Gymnanoebas
1.
2.
3.
4.

Gymnanoebas
Entaamoeba
plasmodial slime mold
cellular slime mold

• free living (not disease
caus...
Entaamoeba
1.
2.
3.
4.

Gymnanoebas
Entaamoeba
plasmodial slime mold
cellular slime mold

• generally parasitic 
– ex. En...
plasmodial slime mold
1.
2.
3.
4.

Gymnanoebas
Entaamoeba
plasmodial slime mold
cellular slime mold

• spend most life cyc...
plasmodial slime mold
1.
2.
3.
4.

Gymnanoebas
Entaamoeba
plasmodial slime mold
cellular slime mold

• Life cycle
1. fruit...
cellular slime mold
1.
2.
3.
4.

Gymnanoebas
Entaamoeba
plasmodial slime mold
cellular slime mold

• cells do NOT fuse; bu...
cellular slime mold
• life cycle
– fruiting bodies
– amoebas
– signal: cells aggregate
and form plasmodium
slime mold; the...
kingdom: Rhodophyta (red algae)
• phycoerythrin (red
pigment) which allowed
Rhodophyta to live in
deeper waters
• Most are...
kingdom: Rhodophyta (red algae)
• Uses
– eaten as food
– agar: food, petri dish
– coralline algae secrete
shells of calciu...
kingdom: chlorophyta (green algae)
1. chlorophylls
2. charophyceans

• have chloroplasts
– chlorophyll a and b
– store sug...
Slides: slime mold
1. endamoeba histolytica
2. foraminisera
3. trypanosome
gambienso nasco
4. paramecium
5. plasmodium
6. ...
Biology exam iv for dec 9-2013 monday [self quizzes] [all lecture notes]
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Biology exam iv for dec 9-2013 monday [self quizzes] [all lecture notes]

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  • A virus containing RNA as its genetic material. The RNA may be single stranded or double stranded. Examples of RNA viruses include Reoviruses, Picornaviruses, Togaviruses, Orthomyxoviruses, Rhabdoviruses, etc.
  • R plasmids can contain genes that confer resistance to antibiotics such as ampicillin.When antibiotics are used, they only kill those bacteria without resistance to that antibiotic. This causes resistant bacteria populations to increase. This is the reason that we see more and more antibiotic resistant strains of bacteria.Many R-factors can pass from one bacterium to another through bacterial conjugation and are a common means by which antibiotic resistance spreads between bacterial species, genera, and even families. For example RP1, a plasmid that encodes resistance to ampicillin, tetracycline, and kanamycin originated in a species of Pseudomonas, from the Family Pseudomonadaceae, but can also be maintained in bacteria belonging to the family Enterobacteriaceae, such as Escherichia coli.
  • corepressor:any substance that reacts with a genetic repressor in order to activate it and decrease gene expressionAPPEARS IN THIS RELATED CONCEPT:Operonscorepressor:any substance that reacts with a genetic repressor in order to activate it and decrease gene expressionAPPEARS IN THIS RELATED CONCEPT:Operons
  • An operon can be repressible or induciblelac operonThe lac operon is an operon required for the transport and metabolism of lactose in Escherichia coli and other enteric bacteria. It consists of three adjacent structural genes, lacZ, lacY and lacA. The lac operon is regulated by several factors including the availability of glucose and of lactose.inducera molecule that starts gene expressioninducible operonIn negative inducible operons, a regulatory repressor protein is normally bound to the operator, which prevents the transcription of the genes on the operon. If an inducer molecule is present, it binds to the repressor and changes its conformation so that it is unable to bind to the operator. This allows for expression of the operon.
  • reverse transcriptase, also called RNA-directed DNA polymerase, an enzyme encoded from the genetic material of retroviruses that catalyzes the transcription of retrovirusRNA (ribonucleic acid) into DNA
  • Hfr cell: A high-frequency recombination cell (Hfr cell) (also called an Hfr strain) is a bacterium with a conjugativeplasmid (often the F-factor) integrated into its genomic DNA.The Fertility factor (first named F by one of its discoverers Esther Lederberg) allows genes to be transferred from one bacterium carrying the factor to another bacterium lacking the factor by conjugation. The The episome that harbors the F factor can exist as an independent plasmid or integrate into the bacterial cell's genome. There are several names for the possible states:Hfr bacteria possess the entire F episome integrated into the bacterial genome.F+ bacteria possess F factor as a plasmid independent of the bacterial genome. The F plasmid contains only F factor DNA and no DNA from the bacterial genome.F' (F-prime) bacteria is formed by incorrect excision from the chromosome, resulting in an F plasmid carrying bacterial sequences that were next to where the F episome was inserted.F- bacteria do not contain F factor. Will act as the recipient.
  • Operon - a cluster of structural genes that are expressed as a group and their associated promoter and operator How does the system work? Without lactose in the cell, the repressor protein binds to the operator and prevents the read through of RNA polymerase into the three structural genes. With lactose in the cell, lactose binds to the repressor. This causes a structural change in the repressor and it loses its affinity for the operator. Thus RNA polymerase can then bind to the promoter and transcribe the structural genes. In this system lactose acts as an effector molecule. lac Operon - an inducible system
  • endo-end of the world
  • 11/21
  • Biology exam iv for dec 9-2013 monday [self quizzes] [all lecture notes]

    1. 1. Biology Exam IV Final: Monday, 12/9 75% new material 25% old
    2. 2. Self quizes • • • • • 22 evolution 27 Bacteria 27 28 protist 31 fungi viruses
    3. 3. Viruses
    4. 4. Horizontal transmission of a plant viral disease could be caused by Insects as vectors carrying virus particles between plants
    5. 5. RNA viruses require their own supply of certain enzymes because Host cells do not have enzymes available that can replicate the viral genome
    6. 6. R plasmid Contains genes for antibiotic resistance and for sex pili
    7. 7. Transposition differs from other mechanisms of genetic recombination because it Scatters genes to new loci in the genome
    8. 8. An operon codes for an amino acid. If the regulation of this operon is like that of the trp operon The amino acid acts as a corepressor
    9. 9. A mutation that makes the regulatory gene of an inducible operon nonfunction would result in Continuous transcription of the operon’s genes
    10. 10. Which information transfer is catalyzed by reverse transcriptase? RNA -> DNA
    11. 11. Which characteristic is common to BOTH bacteria and viruses? Nucleic acid as genetic material
    12. 12. Which of the following processes would never contribute to genetic variation within a bacterial population? meiosis
    13. 13. During conjugation between an Hfr cell and an F- cell Genes from the Hfr cell may replace the genes of the F- cell by recombination
    14. 14. Emerging viruses arrive by All of the above a) b) c) Mutation of existing viruses The spread of existing viruses to new host species Broader dissemination of an existing virus within the current host population
    15. 15. A certain mutation in E coli makes the lac operator unable to bind to the active repressor. How would this affect the cell? The cell would wastefully produce the enzymes for lactose metabolism continuously, even in the absence of lactose
    16. 16. Gram-negative • meningococcal menintus • Thin cell wall • outer wall (OM): toxic to humans • sensitive to osmotic pressure • antibiotic tolerant • thin peptidoglycan layer
    17. 17. Gram-positive • THICK peptidoglycan layer • resistant to osmotic pressure
    18. 18. Classify bacteria by habitat 1. halophile 2. coliform: your digestive tract 3. thermophile 4. acidophile
    19. 19. Classify bacteria by metabolic pathway 1. obligate aerobe: require O2 2. anaerobe: O2 kills anaerobes 3. facultative aerobe: can live with O2 and not 4. heterotroph v photoautotroph
    20. 20. Classify bacteria by metabolic pathway • M. tuber 1. obligate aerobe: require O2
    21. 21. Classify bacteria by metabolic pathway • Cl. tetanic 2. anaerobe
    22. 22. Classify bacteria by metabolic pathway • E. coli (facultative) 1. obligate aerobe: require O2 2. anaerobe: O2 kills anaerobes 3. facultative aerobe: can live with O2 and not
    23. 23. Classify bacteria by metabolic pathway • cyanobacteria (photoautotroph) 1. obligate aerobe: require O2 2. anaerobe: O2 kills anaerobes 3. facultative aerobe: can live with O2 and not 4. heterotroph v photoautotroph
    24. 24. capsule: sugar material that covers cell wall • Strep pyroxenes, H. influenza • protect against phagocytosis • protect against desiccation • allow adherence
    25. 25. fimbriae & pili: attachment purpose structures • pile: used for conjugation (sexual reproduction)
    26. 26. slime layer: sticky matrix of polysaccharides that protects the bacteria • Streptococcus mutans cause tooth decays
    27. 27. taxis: movement toward or away from stimulus
    28. 28. internal/genome structure of bacteria • one chromosome (DNA) • no organelles • plasma membrane carries out metabolic processes • Some bacteria have additional genomes, circular DNA, plasmids
    29. 29. binary fission: similar to mitosis • one bacteria splits to two • mitosis: split nucleus
    30. 30. endospore • anthrax (Bacillus anthracis)
    31. 31. endospore • botulism
    32. 32. endospore • tetanus
    33. 33. endospore • gas gangrene (Clostridium perfringen)
    34. 34. classify bacteria via nutritional intake 1. 2. 3. 4. photoautotrophy chemoautotrophy photoheterotrophy chemoheterotrophy
    35. 35. photoautotrophy • energy from sunlight • carob from CO2
    36. 36. chemoautotrophy • energy from inorganic molecules like sulfur • carbon from CO2
    37. 37. photoheterotrophy • carbon from organic sources (other organisms)
    38. 38. chemoheterotrophy • energy and CO2 from organic sources
    39. 39. eubacteria aka “bacteria” • cell wall made of peptidoglycan
    40. 40. Archaea • cell wall made of pseudomurein
    41. 41. methanogen • anaerobic Archae • remove excess hydrogen, O2
    42. 42. symbiotic categories 1. mutualism 2. commensalism 3. parasitism
    43. 43. Genus of bacterial diseases! 1. 2. 3. 4. 5. 6. Borelia Treponema Staphylococcus Mycobacterium Yersinia Neisseria 1. 2. 3. 4. 5. 6. Lyme syphilis toxic shock (MRSA) tuberculosis plague gonorrhea
    44. 44. Lyme • Borelia
    45. 45. syphilis • Treponema
    46. 46. MRSA • Staphylococcus
    47. 47. tuberculosis • Mycobacterium
    48. 48. plague 1. Bubonic 2. pneumonic • Yersinia
    49. 49. gonorrhea • Neisseria
    50. 50. exotoxin • G positive
    51. 51. botulin • exotoxin • Gram positive
    52. 52. tetanus • exotoxin • Gram positive
    53. 53. endotoxin • Gram negative • you get more sick • bacteria has outer membrane
    54. 54. Gram-positive • EXOtoxin
    55. 55. Gram-negative • ENDOtoxin • have outer membrane
    56. 56. Gram • exotoxin – made of G positive – botulin and tetanin are examples – can elicit immune response  – can be vaccinated against  • endotoxin – made of G-negative – made of outer membrane (OM) – are released when bacteria die – does NOT elicit an immune response  – you get more sick  – vaccination is difficult 
    57. 57. Chlamydomonas • eyespot • pyrenoid • protist
    58. 58. Diatom • protist
    59. 59. Algae • photosynthetic protist
    60. 60. Protists • Lecture: Thursday 11/21 • • • • Cercozoans Forams Radiolarians Amoeba – 4 clades • Rhodophyta (red algae) • Chlorophyta (green algae) • Lab 26: slime molds
    61. 61. Cerocozoans • Amoeba-looking cells • Clade foraminiferans (“forams”) • Feed by pseudopodia
    62. 62. Phylum: Forams • shrimp • Porous, multichambered calcium carbonate shells called tests • Pseudopodia extend through the pores • ocean pH environmental problem: acidity dissolves tests
    63. 63. Forams (importance) • layers of foram tests in marine sediments from limestone and oil deposits – Egyptian pyramids • act as carbon reservoir • used by geologists to locate oil reserves (oil explorer) • used to determine age of rocks and pas climate
    64. 64. forams • limestone cliff in Dover England
    65. 65. Kingdom: radiolarians • have silica tests fused into one piece (like diatoms) • pseudopodia are called axopodia, which radiate from central body • only ONE clade
    66. 66. Kingdom: amoeba • have lobe-shaped pseudopodia (false feet) rather than threadlike • do not have tests and have no shape • The Blob (film)
    67. 67. Four Clades of Amoeba 1. 2. 3. 4. Gymnanoebas Entaamoeba plasmodial slime mold cellular slime mold
    68. 68. Gymnanoebas 1. 2. 3. 4. Gymnanoebas Entaamoeba plasmodial slime mold cellular slime mold • free living (not disease causing) • found in damp, environmental conditions (in your guts, soil, bottom of lakes)
    69. 69. Entaamoeba 1. 2. 3. 4. Gymnanoebas Entaamoeba plasmodial slime mold cellular slime mold • generally parasitic  – ex. Entaamoeba histolytica: causes dysentery and organ damage – Naegleria: cause fatal encephalitis • found in warm fresh waters in southern states • infections occur via nose and in summer months • very rare: you’re more likely to win the lottery – E. histolyta in stool: cyst, trophozoite – N. fowleri in brain
    70. 70. plasmodial slime mold 1. 2. 3. 4. Gymnanoebas Entaamoeba plasmodial slime mold cellular slime mold • spend most life cycle as a unicellular plasmodium • made up of thousands of cells that fuse to ONE giant cell with many nuclei • When stressed, plasmodium develop to sporangia and produce spores. • Spores germinate into biflagellated cells, which act as gametes or as amoeboid cells. • Syngamy of gametes produce new plasmodium.
    71. 71. plasmodial slime mold 1. 2. 3. 4. Gymnanoebas Entaamoeba plasmodial slime mold cellular slime mold • Life cycle 1. fruiting body 2. spores released 3. signal: cells come together and fuse 4. form plasmodium
    72. 72. cellular slime mold 1. 2. 3. 4. Gymnanoebas Entaamoeba plasmodial slime mold cellular slime mold • cells do NOT fuse; but they act as one organism • spends most life cycle as feeding individual protist cells • form pseudopodia (slug) when food is depleted • slug develops to fruiting body to produce spores
    73. 73. cellular slime mold • life cycle – fruiting bodies – amoebas – signal: cells aggregate and form plasmodium slime mold; they do NOT fuse – they move as one
    74. 74. kingdom: Rhodophyta (red algae) • phycoerythrin (red pigment) which allowed Rhodophyta to live in deeper waters • Most are large and multi-cellular • store sugar as floridean starch (glycogen) like humans • found in tropical waters
    75. 75. kingdom: Rhodophyta (red algae) • Uses – eaten as food – agar: food, petri dish – coralline algae secrete shells of calcium carbonate, which form coral reefs. Algae are NOT coral. They are part of the ecosystem that supports corals.
    76. 76. kingdom: chlorophyta (green algae) 1. chlorophylls 2. charophyceans • have chloroplasts – chlorophyll a and b – store sugar in the form of starch – have accessory pigments and stacked thylakoids – ex. Volva – ulva (sea lettuce) – calberna (sea feather)
    77. 77. Slides: slime mold 1. endamoeba histolytica 2. foraminisera 3. trypanosome gambienso nasco 4. paramecium 5. plasmodium 6. radiolarian ooze tropical pacific
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