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Second Year Biology Semester 2 > Microbiology > Flashcards

Microbiology Flashcards

1
Q

How are relationships identified

A

Evolutionary evidence (fossil records)
Similarity of observable characteristics
genetic similarities and evolutionary relatedness

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2
Q

What are the three domains of life

A

Bacteria, archaea and eukaryotes

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3
Q

What is the order that domains are broken down in

A

Life, Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

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4
Q

What are the rules of binomial nomenclature

A

Genus name is always capitalized, can be abbreviated
Species name is always lower case can not be abbreviated
Always italicised (typescript) or underlined (written text)

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5
Q

What makes up domain eukarya

A

Microscopic algae, microscopic fungi, protozoa, helminths

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6
Q

What makes up domain archaea

A

archaeabacteria

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7
Q

What makes domain bacteria

A

Eubacteria (true bacteria)

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8
Q

what are the problems with algal blooms

A

turns the tide red. Can be harmless but could cause problems from toxins or accumulated biomass

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9
Q

Describe fungi

A

Can be multicellular or single cellular yeasts. Some cause mold or disease

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10
Q

What fungi causes black mold on food

A

Aspergillus niger

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11
Q

Explain how protozoa-1 work

A

Cyst is injected, converts into trophozoite which can be excreted (Giardia lamblia)

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12
Q

Explain what helminths are and how they work

A

Protazoa-2 types of worm and nematodes. They are often parasitic and ingestion of eggs causes diseases

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13
Q

What are archaeabacteria

A

Prokaryotes that are distinguished from domain bacteria. They may be considered ancient organisms and many live in extreme environments

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14
Q

define thermophiles

A

organisms which grow at extremely high temperatures

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15
Q

Define psychorophiles

A

organisms that thrive at extremely low temperatures

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16
Q

Define halophiles

A

organisms which live in conditions of extreme salinities

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17
Q

Describe mathanogens

A

organisms which live in anaerobic conditions and produce methane

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18
Q

How do archaea distinguish from bacteria

A

Their ribosomes structure
types and linkages of lipids
Variations in RNA polymerase
Difference in cell wall
Lack of peptidoglycan

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19
Q

What is the difference between gram positive and gram negative bacteria

A

Gram positive bacteria have a thick layer of peptidoglycan on the outside of the plasma membrane. Gram negative has a thinner layer and an outer membrane

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20
Q

What are some ways bacteria can gain energy

A

photoautotrophs gain energy from light
methanotrophs gain energy from methane
chemolithotrophs gain energy from inorganic molecules
chemoorganotrophs gain energy from organic chemicals

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21
Q

What did Anthony van Leeuwenhoek discover

A

in 1676 he saw animalcules (what we would call microscopic organisms) in a water sample. He made the monocular microscope

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22
Q

What is spontaneous generation and how was it disproven

A

The belief that living organisms could develop from non-living organisms (maggots from rotting meat, fleas from hair etc.)
Francesco Redi disproved it using a 3 jar experiment

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23
Q

What is Lois Pasteur known for

A

Pasteurization (aseptic techniques), showing microbes caused fermentation, developed anthrax and rabies vaccine

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24
Q

what is a simple microscope

A

A microscope with only one lens

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25
Q

What is a compound microscope

A

microscopes that contain an eyepiece and one or more additional lens. Light is directed onto specimen using condenser lens. Can be monocular or binocular

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26
Q

Why is blue light used in microscopy

A

has shorter wavelength and can improve resolution

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27
Q

describe the objective lens

A

Mounted on a rotating head it can provide different magnification

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28
Q

Describe the eyepiece lens

A

A magnifying lens. Usually x10

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29
Q

How do you calculate total magnification

A

Objective lens + eyepiece lens

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30
Q

how does immersion oil improve resolution

A

this is due to oil having the same refractive indices to glass

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31
Q

Describe light field microscopy

A

Specimens are stained with dyes to improve contrast. This allows visualization of specimens showing size and morphology

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32
Q

Describe dark field microscopy

A

Allows image contrast but without using a stain which can introduce artifacts. The specimen causes light to scatter and unscattered light is excluded. Lights specimen from sides and backlights it.

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33
Q

Describe phase-contrast microscopy

A

A beam of light is spit in two passed through the specimen and then reunited to form an image. The specimen which has different refraction index causes phase variation

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34
Q

Describe fluorescence microscopy

A

An excitation light is shone on a sample which the itself emits a coloured light. Fluorecent dye molecules that attach to parts of specimen. The microscope uses a laser beam to scan on/through the specimen.
Gives a high resolution visualization and quantification of 3D structures

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35
Q

Describe electron microscopy

A

Electron microscopy can be used to magnify images over 100000 times. Similar to light microscopy but at much higher magnification

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36
Q

Describe scanning microscopy

A

Scanning electron microscopy (SEM) is beams of electrons that scan surface of the specimen making £D images from the scattered electrons and other particles

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37
Q

Describe transmission microscopy

A

TEM is beams of electrons emitted into vacuum and focused on specimen. Electrons pass through or are scattered. Scattering visualised

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38
Q

What are the two types of specimen preparation

A

Wet and hanging drop mounts and fixed mounts

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39
Q

describe Wet and hanging drop mounts

A

Microscopy specimens are mounted
Wet and hanging drop mounts allows live cells to be examined for motility shape and arrangement

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40
Q

Describe fixed mounts

A

A specimen fixed onto a slide by gently heating it. Specimen is stained to allow improved visualization

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41
Q

Why do you stain specimens

A

Most bacterial cells are colourless and detail is hard to see. Provides more contrast. enhances visibility of specimen details

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42
Q

Describe chromophores

A

chromophores have a ring structure with an unbonded electron which can be positively or negatively charged. They are responsible for giving each dye its characteristic colour

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43
Q

What is cationic dyes

A

basic dyes with positive charges on chromophore. Bind to nucleic acids many proteins and cell membrane. The most widely used dye

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44
Q

What are examples of cationic dyes

A

Methylene blue, basic fuchsin, crystal violet

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45
Q

Describe anionic dyes

A

Acidic dyes with negatively charged chromophore. They bind to positively charged structures

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46
Q

Give some examples of Anionic dyes

A

Eosin, acid fuchsin

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47
Q

What are differential stains

A

the use of two or more dyes. These are usually a primary stain and a counter stain.

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48
Q

Describe gram stains

A

Gram stains distinguish the two classes of bacteria based on cell wall structure. They can be positive or negative. The key feature is peptidoglycan that provides rigidity.

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49
Q

How do you do a gram stain

A

Cells are fixed and and first treated with crystal violet, the primary stain, before being washed with iodine. Cells are treated with acetone then counterstained with basic fuchsin or safranin

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50
Q

Describe gram positive cells

A

Cells have a thick layer of peptidoglycan that traps crystal violet. They stay blue/purple

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51
Q

Describe gram negative cells

A

cells that have a thin layer of peptidoglycan and more easily release the CV-mordant complex. They end up with a pink colour

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52
Q

Describe the features of a typical prokaryotic cell

A

2-10um in length, intracellular have a plasma membrane, a nucleoid, pili, flagellum and glycocalyx

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53
Q

Describe the bacterial nucleiod

A

its a single circular chromosome free in cytoplasm. There is no surrounding membrane but genome includes plasmids and extra-chromosomal elements
It complexes with DNA binding proteins

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54
Q

What comprises the bacterial cell envelope

A

The inner plasma membrane, the cell wall and exterior layers including capsule, polysaccharide or slime

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55
Q

Describe bacterial cytoplasmic membrane

A

semi-porous, permeable to specific molecules, has a phospholipid bilayer, hydrophilic to outside hydrophobic to inside

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56
Q

How is movement across membranes done in bacterial cells

A

simple diffusion, facilitated diffusion and active diffusion.

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57
Q

Describe the bacterial cell wall

A

part of the cell envelope, made of peptidoglycan, determines cell shape, prevents osmotic lysis and is target for some antibiotics as its recognized by host system

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58
Q

What are the differences between gram positive and gram negative peptidoglycan

A

Gram negative has a more open structure and fewer bonds than gram positive

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59
Q

describe the gram negative outer membrane

A

unusual and highly complex. It is an asymmetric phospholipid bilayer featuring several surface exposed molecules that play a role in virulence

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60
Q

what is unusual about Mycoplasma

A

It is pleomorphic meaning it has no cell wall. It is parasitic and requires a host to survive

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61
Q

What is lysozyme

A

an enzyme produced by eukaryotic cells and hydrolyses peptidoglycan to protect against bacterial infection

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62
Q

What are the three outcomes when bacterial cell wall is punctured/removed

A

Hypertonic, isotonic, hypotonic

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63
Q

define protoplasts

A

gram positive cells that have lost their cell walln

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64
Q

define spherolasts

A

gram negative cells that have lost their cell wall

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65
Q

what is the glycocalyx

A

comprised of glycoproteins and proteoglycans that are secreted onto the cell surface

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66
Q

what are flagella

A

whip like organelles specialised to allow motility. Common in all 3 types of life

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67
Q

what is an aflagellate bacteria

A

bacteria lacking flagella (this is typical in cyanobacteria

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68
Q

Define monotrichous

A

one flagellum protrudes from one end

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69
Q

Define Lophotrichous

A

several flagella protrude from one end

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70
Q

define amphitrichous

A

at least one flagellum at each end

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71
Q

Define peritrichous

A

flagella protrude from all over cell surface

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72
Q

How does the flagellum move the cell

A

They rotate in one direction (counterclockwise) and the bacterium moves forward.
Rotation in the opposite direction cause the bacterium to tumble and randomly change direction. Switching back to move forward

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73
Q

describe pili

A

thin protein tubes extending from the cytoplasmic membrane. Not involved in movement. They allow cells to adhere to receptors.

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74
Q

What are endospores

A

gram positive cells with a differentiated life cycle. They can form endospores a highly resistant structures that allow these bacterial species to withstand hostile condition by undergoing dormancy

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75
Q

How do endospores form

A

When nutrients are limited they germinate inside vegetative cells

76
Q

Describe Staphylococcus aureus

A

Gram positive
Facultative anaerobes
Form in clisters
infects digestive tract, lung, urinary tract and skin.
Invasive

77
Q

Describe Streptococcus pyogenes

A

Gram positive
Fermentative
Forms in long chains
Infects respiratory tract, skin
Invasive

78
Q

Describe the 2 types of firmicutes

A

Non sporulating gram positive bacteria.
Endospores forming gram positive bacteria
they have low G+C (35-55%)

79
Q

Describe the 3 types of actinobacteria

A

Rod shaped representatives
Acid fast group
Filamentous actinobacteria
They have high G+C (>65%)

80
Q

Describe the Clostridium genera

A

Rod shaped
Obligate anaerobes
Spore formers

81
Q

Describe the Bacillus genera

A

Rod shaped
Facultative anaerobes
Spore formers
Common in soil

82
Q

Compare obligate anaerobes to facultative anaerobes

A

Obligate anaerobes are organisms that can grow and survive only in the absence of oxygen
Facultative anaerobes can grow with or without oxygen

83
Q

How have Bacilli been used in biotechnology

A

They secrete a wide range of enzymes into their environment some of which have useful properties including serine protease, cellulase and alpha amylase

84
Q

What is the agricultural application of Bacillus

A

they produce a “crystal protein” toxin when it sporulates that can be used as an insect pathogen

85
Q

What is the medical application of Bacillus

A

some produce peptide antibiotics synthesized by a complex enzyme

86
Q

Describe enterobacteriaceae

A

A large homogenous phylogenetic group of gamma proteobacteria
Facultatively anaerobic, gram negative and non sporulating rods
non motile
Oxidase negative and ferment sugars

87
Q

Describe the Enterobacteriaceae family

A

Gram negative microorganisms including Escherichia, Salmonella, Shigella, Yersinia and Proteus

88
Q

Define the term coliform

A

Bacteria with biochemical and morphological traits in common.
Gram negative, facultative anaerobes, non-spore forming rods, and they ferment lactose to acid and gas.

89
Q

Describe E. coli

A

Gram negative, motile, facultatively anaerobic.
They are catalase positive, oxidase negative ad can ferment a range of carbohydrates to acid and gas

90
Q

How are archaeal membranes different from bacteria and eukaryotes

A

Archaea lipids are unique in 4 ways
side chains are not fatty acids (isoprenes)
Ether linked lipids rather than ester linked
Different chiral form of glycerol
Some posses lipid monolayers

91
Q

How is genetic transmission done in bacteria

A

Binary fission is asexual reproduction
Following replication genetic material bacterial cell divides forming two new individual bacteria

92
Q

Describe vertical genetic transmission in eukaryotes (yeast)

A

budding off of daughter cells in yeast and binary fission of certain protozoa

93
Q

What is recombination (bacteria)

A

bacterial genome recombining with DNA from phages and other bacteria

94
Q

What are Amoebozoa

A

Diverse groups of terrestrial and aquatic protists. They move using pseudopodia and feed by phagocytosis. Include the Amoeba genus

95
Q

What are slime molds

A

Originally thought to be fungi as found in habitats of fungi. Found in soil and decaying plant matter and feeds on E.coli

96
Q

What does ‘fruiting bodies’ mean

A

macroscopic reproductive structures produced by some fungi (e.g. mushrooms)

97
Q

Describe fungi

A

chemoheterotrophic
do not perform photosynthesis
Have cell walls that contain chitin

98
Q

what is hyphae

A

network formed by multicellular fungi

99
Q

What are conidia

A

hyphae that extend above the surface can produce asexual spores. They are often pigmented and resisatnt to trying

100
Q

What are mycelia

A

Compact tufts formed by hyphae

101
Q

How do fungi reproduce by asexual means

A

Most reproduce by asexual means
Growth and spread of hyphal filaments
Asexual production of spores
Simple cell division

102
Q

How do fungi reproduce by sexual means

A

Sexual spores can originate from fusion of two haploid cell to form diploid cells

103
Q

Describe fungal phylogeny

A

share a more common ancestor with animals than any other eukaryotic organisms. Estimated to have diverged 1.5 billion years ago

104
Q

Describe Chytridiomycetes

A

the earliest diverging line of fungi. Commonly found in soil and freshwater. Some are colonial and some are unicellular

105
Q

Describe Zygomycetes

A

Known for food spoilage
Enzymes for industry
Commonly found in soil and decaying plant material
All form zygospores

106
Q

Describe Microsporidia

A

Unicellular, obligate parasites of animals and protists. Often infect immune compromised individuals.

107
Q

Describe Glomeromycetes

A

Obligate symbionts
All known species form endomycorrhizae
Forms arbuscular mycorrhiza
Reproduce asexually only

108
Q

Define endomycorrhizae

A

The fungus colonizes the interior of host plant root cells (arbuscular mycorrhizas)

109
Q

What is arbuscular mycorrhizas

A

a form of endomycorrhiza that helps capture nutrients for plants

110
Q

Describe Ascomycetes

A

Highly diverse
Found in aquatic and terrestrial environments. Decompose dead plant materials
Includes bakers yeast and penicillium

111
Q

Describe Candida

A

ubiquitous fungi found throughout the world as normal body flora

112
Q

Describe mushrooms and other basidiomycetes

A

Over 30000 described species
Many are mushrooms/toadstools as well as yeast and pathogens
they undergo both vegetative and sexual reproduction

113
Q

Describe algae

A

Protists with chloroplasts
Most found in freshwater and marine environments
Most photoautotrophs
Reproduce a/sexually

114
Q

How do algae reproduce

A

Asexual - Fragmentation, spores, binary fission
Sexual - gametes fuse to produce diploid zygotes

115
Q

Describe green algae

A

Have chlorophylls a and b as well as carotenoids
Store carbs as starch
Wide variety of forms
cell walls of cellulose
closely related to plants

116
Q

Describe Volvox

A

individual cells that form spherical colonies
Only a few cells are reproductive

117
Q

Describe diatoms

A

Single celled or colonial
Cell wall consists of silica
have bilateral symmetry
major component of phytoplankton

118
Q

Describe dinoflagellates

A

Mostly marine some freshwater
Important primary producers
phototrophic, heterotrophic and mixotrophic
Some bioluminescent
Unicellular
Lists, horns and spines used to identify species

119
Q

What are lists

A

membranous thecal extensions of armored dinoflagellates

120
Q

What are horns

A

contain cytoplasm and are covered in thecal plates and can be hollow or partially solid

121
Q

Describe spines

A

solid projections that taper to a point

122
Q

talk about toxic dinoflagellates

A

75% of worlds toxic marine microalgae are dinoflagellates. Toxins can cause seafood poisoning

123
Q

what are zooxanthellae species

A

A group of dinoflagellates that form symbiosis with for example corals and jellyfish

124
Q

what are the key characteristics of protozoa

A

unicellular
eukaryotic
non phototrophic
heterotrophic
many parasites
diverse life cycles

125
Q

How to protozoa move

A

cilia, flagella, pseudopodia (can be non motile)

126
Q

What is the distribution of protozoa like

A

free living in marine and freshwater environments, decaying organic matter in soil, moisture is a necessity. Some are parasites

127
Q

what is a trophozoite

A

any stage in a protozoans life cycle which can injest food

128
Q

What are cysts

A

non motile form which is protected by a distinct membrane or cyst well

129
Q

what is a definitive host

A

where parasite reaches sexual maturity

129
Q

what is an intermediate host

A

required by parasite to complete its life cycle. Usually undergoes morphological and physiological change in it

130
Q

What is a vector

A

host that plays an active role in transmission can be a definitive or an intermediate host

131
Q

Describe Sporozoa

A

All members are endoparasites. Apical complex. They have complex life cycles

132
Q

Describe Ciliophora

A

Body covered in cilia arranged in rows or spiral
Appearance varies greatly
Most are fee living

133
Q

define catabolism

A

breakdown of complex organic molecule into simpler compounds and releases energy

134
Q

define anabolism

A

the building of complex organic molecules from simpler ones, requires energy

135
Q

define autotrophic organism

A

organism that can make organic molecules from inorganic nutrients

136
Q

define heterotrophic organisms

A

an organism that cannot make organic molecules from inorganic nutrients. Depends on organic molecules for energy generation and precursors for cell material

137
Q

define phototrophs

A

photosynthetic - gets energy from sun

138
Q

define chemotrophs

A

energy from oxidation of chemicals

139
Q

what are redox reactions

A

= energy from oxidation - reduction reactions
Redox reaction occur in pairs
Electron donor (substance oxidized)
Electron acceptor (substance reduced)

140
Q

explain catabolism

A

the breakdown of foodstuffs into small molecules. Has many pathways. Dependent on organism and environment

141
Q

What are the 2 main energy generation strategies

A

Respiration and fermentation

142
Q

Describe respiration

A

aerobic or anaerobic catabolic where electron donor is oxidized

143
Q

Described fermentation

A

anaerobic catabolism where organic compound is both electron donor and acceptor

144
Q

describe cyanobacteria

A

Photoautotrophs that use atoms from water to reduce dioxide to form carbohydrates. First organism to photosynthesize

145
Q

what are lichens

A

an association between fungus and cyanobacterium/algae

146
Q

what is the biogeochemical cycle

A

flow of essential elements of living matter between abiotic and biotic components of Earth

147
Q

How does carbon exists in the non-living environment

A

Carbon dioxide, carbonated rocks, deposits of coal petroleum and natural gas, dead organic matter

148
Q

What is the carbon cycle

A

how carbon moves between the atmosphere, soils, living creatures, the ocean, and human sources

149
Q

what is bioremediation

A

the use of microbes to restore stability or clean e.g. oil spills, chemical spills, water and sewage treatment)

150
Q

describe co-metabolism

A

contaminants not used as a food source by transformed to less hazardous chemicals

151
Q

mineralisation/oxidation

A

contaminants used as a food source and destroyed

152
Q

describe biodegradation of hydrocarbons

A

respiration of the hydrocarbons to carbon dioxide - can be aerobic or anaerobic

153
Q

describe anaerobic biodegradation

A

breakdown of organic compounds in the absence of oxygen. uses alternative electron acceptors.

154
Q

describe biostmulation

A

adding nutrients to the contaminated soil or groundwater in order to enhance the biodegradation of hydrocarbon contaminants

155
Q

describe bioaugmentation

A

microbial cultures are added to the contaminated site in order to have appropriate metabolic capability to degrade hydrocarbon contaminants

156
Q

what are bioplastics

A

biodegradable plastics - potential answer to plastic waste

157
Q

how is waste water treated

A

Stage 1 - screens trap rubbish
stage 2 - stones and grit are removed
Stage 3 - water rest in tanks where any solids sink to bottom becoming sludge which is pulled out to be treated
Stage 4 - good bacteria are grown in the tanks to eat potentially harmless chemicals
Stage 5 - water allowed to rest again. Water is mixed and left over bits sink to bottom

158
Q

Name some examples of biofuels

A

ethanol - from microbial fermentation of glucose
natural gas CH4 from anaerobic metabolism
conversion of waste product to ethanol/methanol
oil from soybeans

159
Q

how is drinking water treated

A

Stage 1 - surface water is stored in reservoirs to meet demand
Stage 2 - water is passed through mesh screens to remove debris
Stage 3 - impurities in water are removed
Stage 4 - water run through filtration
Stage 5 - disinfection is vital to ensure diseases are eliminated.
Stage 6 - pH level is controlled

160
Q

describe water purification

A

removal of disease causing organisms from waste water
Chlorination
UV light radiation
Ozonation

161
Q

How do we detect pathogens in water supplies

A

we use indicator organisms coliforms and E. coli as they are indicators of fecal contamination

162
Q

how are microbes associated with crops

A

soil microbiomes
nitrogen
fertilisers
biological nitrogen fixation

163
Q

what is the rhizosphere

A

zone around plant roots where there is an increase in organic carbon called rhizodeposition

164
Q

what promotes rhizobacteria

A

pathogen suppression, fixation of nitrogen, solubilization of mineral

165
Q

what is nitrogen fixation

A

energy intensive process.
atmospheric - spontaneous (lighting)
industrial - Haber-Bosch process
biological - nitrogen fixing bacteria

166
Q

What are ectomycorrhizae structures

A

fungal cells that form an extensive sheath around the outside of the root with only a little penetration into root tissue

167
Q

what is the rumen

A

a special digestive organ possessed by certain herbivorous mammals.

168
Q

describe fermentation in the rumen

A

rumen microbes hydrolyze cellulose to fee glucose that is fermented producing fatty acids that pass through into bloodstream and utilized for energy.

169
Q

describe general features of viruses

A

they reproduce at high rate only in living host cells
their genome can mutate
they have no cytoplasm or organelles
they can grow or divide independently
usually have DNA or RNA but not both

170
Q

describe size and shape of viruses

A

smallest are about 20nm largest 200-300nm
can be helical, icosahedral, or polyhedral

171
Q

how are viruses classified

A

their geometry
whether they have an envelope
what organism they infect
their genome
how they transmit
what they cause

172
Q

describe the core of virus structure

A

nucleic acid genome (RNA or DNA)

173
Q

describe the protein caspid of virus structure

A

often made up of many copies of small proteins. provides protection and directs attachment to host cell

174
Q

describe the helical virus structure

A

simplest way to arrange many copies of identical proteins.
Basic design RNA genome acting as a structure that basic binding proteins condense onto

175
Q

describe icosahedral virus structure

A

rounded structure in which 20ntriangular faces form an icosahedron

176
Q

how is the viral envelope formed

A

derived from host cell by budding
matrix proteins glue the capsid to the membrane
glycoproteins are anchored in the membrane which are essential for recognition/attachment

177
Q

describe lytic growth

A

virus grows in its preferred site
After a few days host responds
immune response gathers momentum and the virus is removed from the system
or virus wins and the hist dies

178
Q

describe lytic growth with latency

A

some viruses can remain dormant in nerve cells
a lytic episode such as the cold sore on the mouth is followed by immune response
virus remains latent and reappears in future

179
Q

describe slow growth viral replication

A

slow diseases are typically characterized by slow development over many years
They often cause progressive neural damage and a fatal outcome and include immunodeficiency virus (HIV)

180
Q

name modes of viral replication in humans

A

lytic growth, lytic growth with latency, slow growth, cancer

181
Q

what does the infectious cycle typically include

A

attachment, penetration, uncoating, transcription/translation, replication, assembly, release

182
Q

describe antibiotics

A

Natural anti-microbial substances produced by fungi and bacteria to compete with other micro-organisms for space and nutrients in soil - they kill them or stop them growing

183
Q

Why are antibiotics important to humans

A

They can be used as drugs (e.g. penicillin)
Before antibiotics simple infected cuts or infections could go systemic and kill

184
Q

describe genetic variation in bacteria

A

mutation - due to rapid division mutations can spread quickly
recombination - genome can recombine with DNA
Can lead to new strains with increased virulence or resistance

185
Q

how are we going to combat antimicrobial resistance

A

Improve knowledge and understanding of AMR
Conserve ad steward the effectiveness of existing treatments
stimulate the development of new antibiotics, diagnostics and novel therapies

186
Q
A

Second Year Biology Semester 2 (3 decks)

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