Final Exam Study Guide Flashcards
Microscopes increase ________ by increasing ________
resolution, magnification
What is the source of energy for light microscopy? Electron microscopy?
light
electron beams
What is the range of resolution for light microscopy? Electron microscopy?
micrometer (10^-6 m)
nanometer (10^-9 m)
What are the types of light microscopy? Electron microscopy?
bright
dark
phase contrast
fluorescence
SEM
TEM
TEM shows what details of the cell? What is the image in? What about SEM?
internal in 2D
external in 3D
Semi-permeable only to a few small molecules
Cell membrane
What is the Cell Membrane made of
phospholipid bilayer and proteins
What is the cell wall made of
- peptidoglycan (PG), itself made of repeating disaccharide unit of NAM and NAG, and amino acids
The difference in PG of gram-positive and gram-negative (thick/thin) and effect on gram stain
gram-positive has a thick cell wall (10-13 strands) and retains crystal violet stain (purple)
gram-negative has a thin cell wall (3-5 with layers) and does not retain crystal violet stain (pink)
Which envelope appears as a triple layer in TEM pictures (G+ or G-)?
gram-negative
What are the growth phases
- lag - prepare for growth
- log - actual growth
- stationary - no growth, turns on stress response
- death - no nutrients start to die off
The fastest growth would occur under optimal conditions of temp, pH, aerobiosis, etc., when proteins are most functional. And the membranes are intact
Extremophiles
What is DNA made up of?
nucleotides
What are nucleotides made up of
Protein, deoxyribose, N-base,
Leading strand
copied continuously
lagging strand
copied in fragments, Okazaki fragments
What are the enzymes in replication, know their functions
helicase
primase
DNA polymerase
ligase
What is transcription
making mRNA from DNA
Transcription and translation are ________
coupled
The molecules that carry the amino acids
tRNA
Free DNA uptake, requires recipient cells to be competent
transformation
plasmid DNA uptake, requires cell-to-cell contact. Donor has sex pili
conjugation
Bacteriophages carry DNA from one host to the next
transduction
Mutations: point vs. insertion/deletion mutation
point is one based is switched to another
inertion/deletion is when 1 or more nucleotides are added or removed
silent, missense, nonsense, frameshift. know the difference
silent -> no change in amino acid
missense –> changes to different amino acid
nonsense –> changes to a stop codon
frameshift –> changes to completely different amino acid sequences
Control of gene expression; DNA level
mutate gene -> most drastic least reversible
control of gene expression; Transcription level
activators/repressors, and also modify the activity and conc of sigma factors
control of gene expression; Post-transcription level
modify mRNA stability by Rnases
control of gene expression; Translation level
translation repressor proteins
control of gene expression; post-translation level
modify the protein after it if made by chemical modification or cleavage
break down of complex food molecules to smaller ones to make ATP.
catabolism
What will ATP be used for
building
anabolism or biosynthesis
the energy storage molecule in the cell
ATP
NADH or any electron carrier has ___ forms in the cell, an __________ form and a ________ form
2, oxidized, reduced
What does glucose break down to
pyruvate
What happens after glucose breaks down to pyruvate
NADH accumulates.
the cell has to recycle NADH back to NAD to be able to breakdown more glucose
What is the main goal of fermentation or respiration?
recycle NADH to NAD
What is recycling done through?
fermentation or respiration
Is more ATP produced during fermentation or respiration
respiration
in TCA cycle, and by ATP synthase after the completion of ETS
is breakdown of food molecules in fermentation partial or complete?
partial
is breakdown of food molecules in respiration partial or complete
complete
What happens in fermentation
electrons and protons from NADH are dumped on pyruvate. Pyruvate will be reduced by those electrons to fermentation products and NADH will be recycle to NAD when it gets rid of its electrons and protons
What happens in Respiration
steps in order, starting with pyruvate
1. PDC
2. TCA -> most NADH produced here
3. ETS -> here is where the NADH gets recycled
What is the energy source for a chemotroph
chemical energy
What is the energy source for a phototroph
light energy
What is the electron source for a organotroph
organic
ex: NADH
What is an electron source for lithotroph
inorganic
ex: H2, H2S, NH3
usually all autotrophs are also lithotrophs
What is a carbon source for heterotroph
organic
ex: glucose
What is a carbon source for an autotroph
inorganic
ex: CO2
all organisms that fix CO2 are autotrophs
What are the functional components of any ETS in order
- initial substrate oxidoreductase
- mobile electron carrier
- terminal oxidase
The ETS is kick-started when the electron donor donates the ________ to the first component of the ETS
electrons
If the donor is organic; NADH -> ______
respiration
if the donor is inorganic; H2, H2S, NH3 -> ________
Lithotrophy
The ETS ends by movement of electrons from the last component of the ETS to the __________ __________
terminal acceptor
if the acceptor is O2 -> __________ ____ _________
process is aerobic
If the acceptor is not O2; sulfate or nitrate -> ___________
anaerobic
The type of the process is dictated by the nature of the ________ ________, while the _______ /___________ _____________ is decided by the electron acceptor used
electron donor, aerobic/anaerobic nature
Where are the ETS components embedded
in a membrane
What happens during the operation of ETS
the movement from electron from one component to the next leads to the generation of a pmf across the membrane
What can pmf be used to do
- import nutrients - symport
- export toxins - antiport
- rotate flagella
- make ATP by ATP synthase
What is substrate-level phosphorylation
If the ATP production occurred before the ETS, or does not need a functional ETS to occur
What is Oxidative Phosphorylation
If ATP is made after the ETS and needs the ETS to function properly to occur
Reactions or steps in which ATP is being produced
Phosphorylation
What are the requirements for biosynthesis
- essential elements. C, N, O, S, P
- NADPH
- ATP
What are the biosynthetic processes
- CO2 fixation
- N2 fixation
What is CO2 fixation
converting CO2 which is an inorganic form of C to an organic C intermediate
What is the enzyme and cycle used in CO2 fixation
Calvin Cycle
Rubisco enzyme
Who does CO2 fixation
Green plants and cyanobacteria
Where does CO2 occur
carboxysomes
What is N2 fixation
N2-> NH3
- converting N2 to NH3 which is the form of N that all cells can use
What is the enzyme used in N2 fixation
nitrogenase
Who does N2 fixation
Cyanobacteria and Rhizobium
Where does N2 fixation occur
N2ase is highly O2 sensitive
- Heteroxysts protect the N2ase from O2
- Cyanobacteria carry out N2 fixation at night and photosynthesis in the morning.
How does divergence occur between different clades over time?
- random mutations
- natural selection
- reductive (degenerative) evolution
What is the most widely used gene in constructing phylogenetic trees
the gene encoding the small subunit rRNA
What are the three fundamental domains of life
bacteria
archaea
eukarya
The intimate association of two unrelated species
symbiosis
Mutualism
both partners benefit
endosymbiosis
occurs when one partner grows within the body of another
syntrophy
metabolic association where the presence of one partner is needed for the completion of the other’s metabolsim
What are the two types of firmicute
spore formers and non-spore formers
What are the two main types of gram-positive bacteria
firmicutes and actinobacteria
Where do methanogens grow
anaerobic habitats
What are common traits of most fungal cells
- absorptive nutrition
- hyphae
- cell walls containing chitin
process by which organisms acquire an element to build into cells from an inorganic source
assimilation
process of breaking down organic nutrients to inorganic minerals
dissimilation
Termites have __________ ________ and archaea in their gut that help them digest wood polysaccharides such as cellulose
endosymbiotic bacteria
fungal mycelia associating with the roots of plants
Mycorrhizae
What are the two kinds of Mycorrhizae
ectomycorrhizae
endomycorrhizae
What do plants provide fungi with
energy-rich products of photosynthesis
What does Rhizobia do when it enters plant cells
differentiates into bacteroid
