Midterm 1 Flashcards
Who first did microscopic description? (1665)
Robert Hooke
Who first did microscopic organisms description? (1684)
Anthony Van Leeuwenhoek
Who criticized spontaneous generation (end of 19th c.)?
Francesco Redi; Lazzarro Spallanzani
What did Pasteur?
Provided evidence against spontaneous generation (classic experiment of 1861); vaccines
Who is the father of microbiology?
Leeuwnhoek
1847 and 1867: what did Semelweis and Lister can be proud of?
Reduction of spread of disease (hand washing + phenol)
1884: Robert Koch?
Discover of microorganisms : anthrax and tuberculosis are due to microorganisms
Microorganisms in size order
Viroids (100 nm); bacteria/archea (2 um); eukaryotes (2-100 um)
Nuclear membrane of micro?
Bacteria and Archea = no, Eukaryotes = Yes, Viroids = capsid made of capsomeres
Nucleolus in microo?
Not in Bacteria nor Archea nor Viroids, but rDNA in Eukaryotes
How many years of evolution for microo?
4 billions!
Four roles of microo in the environment?
recycling nutrients; detoxifying by metabolism; source of food; genetic diversity provides drugs/antibiotics
Properties of all cells (3)
Compartmentalization; growth and evolution
Properties of some cells (3)
Motility, differentiation, communication
General functions of cells
Genetic + Catalytic = Growth
What sets the size of cell?
S/V ratio : if too big; can still grow; if too small; not enough surface to interact with the environment regarding intern processes
What is the main difference regarding structure of pro vs eukaryotes?
Nuclear membrane
What are the roles of a membrane (3)?
Selective permeability, protein anchor + energy (pmf)
Name types of membrane proteins (4)?
Sensors, adhesins, transporters, enzymes
The membrane of bacteria and eukaryotes?
Phospholipid bilayer composed of glycerol, fatty acids (2) and a phosphorous group
What is the main difference between eukaryotes and archea membrane?
Archea one is composed of isoprene instead of fatty acids, has ether bonds instead of ester (except when it is in water) and can be monolayer in hostile environment
Stabilization of the membrane?
In eukaryotes = sterols (chol for animal, ergo for fungi and stigma for plants and protozoans); in prokaryotes = hopanoids (1 more ring)
Storage of DNA
Pros: circular, ds, haploid, paccked with Histone-like prot to form nucleoid, no compartment, may contain plasmids (extra additions of DNA)
Euk: linear, ds, diploid, packed with histone to form chromatin fibers, in the nucleus
What is protein pathway from DNA?
DNA polymerase (copy); RNA polymerase (transcription); ribosome (translation)
Describe ribosome
Made of 2 subunits :
30S + 50S = 70S, bound to cytomembrane or free in Pros
40S +60S = 80S, bound to ER or free in Euk
Cell walls in Euk is composed of..?
Polysaccharides! Cellulose for plants, chitin for fungi, may also be of galactose or mannose..
Nucleus of Euk is composed of 2 types of chromatin which are..?
Euchromatin: loosely packed, actively transcribed; or heterochromatin: densely packed, low level of transcription
Endoplasmic Reticulum of Euk: two types
System of membrous channels : Rough is for ribosomes, while smooth is for synthesis of lipids
Rough Endoplasmic Reticulum synthesis of proteins: describe pathway (6)
- mRNA leaves nucleus and attaches to ribo = prot synthesis started (signal)
- Signal recognition particules bind to signal (on prot)
- SRPs bind to RER so then prot enters RER
- Signal peptidase
- Ribosome + mRNA break away (poly peptide is done)
- Final preparation of polypeptide before Golgi complex
What is the Golgi complex?
Further processing of proteins, vehiculed in vesicles
Mitochondria and Chloroplasts
Mito: produces ATP, some protozoa do not have it, pourous outer membrane, inner is 75% prot, 25% lipids (not permeable at all!), matrix contains enzymes, DNA and ribosomes 70S (an eaten pro)
Chloro: Inner membrane is made of transport proteins, thylakoids are a closed system of sacks and tubules, while stroma contains circular DNA, 70s ribosomes and enzymes of Calvin cycle.
Both organelles make most of their prot, but some imported
Thylakoids in details
Contains pigments and enzymes that harvest light - ATPases are bound to membrane
Eukaryotic skeleton has three types of filaments
Microtubules (formed out of a and b-tubulin subunits); actin; intermediate filaments (keratin, desmin, vimentin)
Microtubules in details
Highways to travel among the cell : kinesin and dynein are attached to vesicles and walk on microtubules (driven by ATP breakdown)
What are centrioles and basal bodies?
Organizing centers for microtubules : 9 sets of a complete microtubule + 2 halves, no center
Basal bodies are centrioles that have migrated to membrane (their own microtubules are flagella or cillia) : 9 sets of 1 microtubule and 1 half + 2 centers
Are cillia and flagella covered by plasma membrane in euk?
Yes
Cell walls of bacteria: 2 types
Cell walls allow structure by withstanding osmotic pressure
Gram + : Large peptidoglycan layer that binds crystal violet (purple)
Gram - : thin peptoglycan + outer membrane (loose crystal violet, only keep counterstain (pink))
What is peptoglycan layer?
Short polypeptide side chain containing D-aminoacids (NAM and DAP have never been found in Archea or Euk)
2 sugars: NAG and NAM
Lysosomes target the glycosidic bond
This membrane is solid due to transpeptidation (solid cross linking stabilization: in +, it is interbridge)
Penicillin inhibits transpeptidation
Gram + cell wall
90% peptidoglycan: 10% is teichoic or lipoteichoic acid and wall-associated proteins attached by sortase
Cell walls of Gram -
Cell wall = outer membrane (lipopolysaccharides + phospho in the outer, phospho in the inner side) + peptido (5%), periplasm = space between cyto and outer (contains a lot of prot = protein gel)
LPS layer protects the bacteria against outside
Outer membrane contains porins and lipoproteins
LPS in details
From the outside : O-specific prot (for family, 2-5 monosaccharides) - core polysaccharide -(KDO) lipid A (6 lipid tails)
Lipid A has a major role in pathogenesis of bacteria
Cell wall of Archea
No peptido, no outer membrane; diverse and may contain prot/polysacc/glycoprot (pseudopeptidoglycan: different but similar, no D aa) and no glycosidic bond (lysosymes cant target it, b1-3)
Paracrystalline surface layers (S-layers may also be found in the out side of bacteria + or -)
One another type of layers : capsule
Capsule and slime = polysaccharides layer on Archea or Bacteria (xtra defence against host defence system)
Hetero or homo (only few gram-), covalently bond to the external layer
Surface appendages of prokaryotes
Fimbriae and Flagella
Three types of flagella
Monotrichous, peritrichous and lophotrichous
Physics of flagellum with Pros
Embated into cyto membrane + cell wall; mot proteins create a pmf in the periplasm (as a rotor: electricity); as much rings as layers, so Gram - have C for cytoplasm, Ms for membrane superficial, P for peptidoglycan and L for LPS layer.
Flagellum biosynthesis of Bacteria
Build the base and put a cap. Then build from the top with a channel
3 ways to move with a flagellum
CCW is a direction, CW is a stoping; CCW is a direction, CW is another (reversible); CCW is a direction, the cell stops, reorients, and starts again (unidirectional)
Flagellum structure of Archea
Grows from the base (pushing the top out)
Description of the actual mvt
Goes from a physical/chemical gradient to another: light, nutrient, oxygen.. random vs directed mvt
Frimbriae of Bacteria
About 4 um long; principally for attachment to surfaces
Gram - fimbriae
Attached to the outer membrane; grow from the base with to prot: chaperone and usher; stand exchange; adhesion with subunits or specialized subunits
Gram + fimbriae
Surface adhesins (only one prot); by sortases, attached to peptidoglycan (covalent)
Endospore
Dormant stage for bacteria: exosporium (proteins), spore coat (spore-specific proteins), core wall (cytoplasm, Ca2+, DPA: they both capt water to rehydrate when time comes, SASPs), cortex (proteins needed for germination) and DNA
Formation of endospore
Asymetric cell division; prespore and septum (separation); cortex, cell wall; coat; when fully mature, cell die
What are cell inclusions?
Reserves, but not organelles (maybe one layer) for nutrients and magnetosomes
What does drive flagella of Euk.?
ATP
Viruses, what are they?
Obligate intracellular parasites that affect one type of host; can’t replicate itself, but can be killed..
What is a virion?
Outside-of-a-host viruses
Physics of a virus?
Nucleic acid (one type: RNA or DNA) + capsid of proteins (made of capsomeres) + envelope (lipids); can be ss or ds
What is a complex virus?
Around 100 proteins
Types of viruses?
Helical, polyhedral, complex virus (attack bacteria)
What is a viroid?
Closed circles of ss RNA (240-380 nucleotides); replication depends on host machinery
What are prions?
One single protein
How do prions act?
Prions can’t replicate; they induce misfolding of other prot
What are the two components of life that are difficult to metabolize?
Carbon and energy: lots of transfo
What is anabolism?
Use of energy and reducers to oxidyze
What is catabolism?
Use of precursors to produce energy and oxidizers to be reduced
What is an electron donor?
A reducer
What is an electron carrier?
Can easily be reduced or oxidized
The basic metabolic pathways
Glycolysis, penthose phosphate pathway and TCA cycle
Glycolysis in short
One glucose = 2 pyruvate 2 ATP (substrate-level phosphorylation), 2 NADH
What is substrate-level phosphorylation?
The synthesis of energy-rich phosphate
bonds through reaction of inorganic phosphate with an activated
organic substrate.
What is oxydative phosphorylation?
Formation of ATP via ETC
TCA cycle in short
Pyruvate is oxidized to CO2 and water (gives 2 electrons) via pyruvate dehydrogenase complex and Acetyl-CoA
One net turn: 2+1 CO2, 1 GTP (ATP), 3 + 1 NADH, 1 FADH2
Can other compounds then pyruvate undergo TCA cycle?
Yes
Aerobic respiration vs anaerobic respiration?
Oxygen is used as a final acceptor
Name an hydrogen carrier?
FMN
What if there is no FMN?
When H and its electrons are accepted in a complex with no FMN, only the electrons continue, proton is used to produce pmf
What is the final step of aerobic respiration?
Two protons and two electrons from the inner space are used to reduce oxygen to water
What does influence ATP production?
Environmental conditions, like pH (no pmf if no gradient..)
How many protons for 1 ATP?
3 to 4
Glycolysis + TCA cycle = how many ATP?
38
When does fermentation occur?
When there is no final acceptor.. TCA stops (succinate cannot be oxidized). Only glycolysis
Fermentation in short
Electron donor is organic compound; final electron acceptor is a organic product
Net yield of ATP throught fermentation?
2 ATP/glu
What is the penthose phosphate pathway?
It leads to many sugars; it produces reducing power
Most cells can convert NADH to…
NADPH
Net yield of penthose pathway?
2 NADPH + CO2 + sugar
In Euk, where are the enzymes of TCA, of glycolysis and fermentation?
TCA and respiratory: mitochondria membrane
Glycolysis and fermentation: cytoplasm
In Pros, where are the enzymes of TCA, of glycolysis?
Respiratory chain in cyto membrane; the rest in cytoplasm
3 types of transport
Passive, facilitated (down a gradient), active (against a gradient - ATP)
Transport vs Simple diffusion?
Biosynthesis of transport system is controlled; can be saturated
When is active transport the most used pathway?
Unicellular, for nutrients
In multicellular organisms, which tranport type and why?
Facilitated diffusion from blood or plasma
Types of transporters?
Uniporter, antiporter (one’s out to let one in), symporter (two needed to enter)
When there is no oxygen, how to create a pmf?
ATPases are inverted
Why inverting ATPases?
To produce a pmf that will produce a Na+ gradient
ABC transporters:
Made of a transporter, a ATP-hydrolyzing prot ans a specific receptor.
Gram -: free in the periplasm
Gram +: anchored to the cyto membrane
What is group translocation?
Use of a chain to finally have a compound that can activate the transporter
Type of ATPase and efficiency
Euk: 1 H+/ATP, P-type
Pros: 3 H+/ATP, F-type
What is endocytosis?
Use of vesicles (in Euk)
About oxygen requirements: three types of microo?
Aerobes, anaerobes and facultative aerobes
About sources of energy, electrons and carbon types of microo?
Energy: chemicals or light
Electrons: organic or not
Carbon: organic or not
What is a chemoorganotroph?
Needs organic chemicals as energy
What is chemolitotroph?
Needs inorganic chemicals as for energy
What is a phototroph?
Needs light for energy
Heterotroph stands for..?
Organic chemicals needed
Autotrophs stands for..?
Inorganic chemicals needed
Anaerobic respiration vs fermentation?
Anaerobic respiration means ETC with other final acceptors
What is a denitrifying bacteria?
Chemoheterotroph that produces gas from nitrogen source
In phototroph, light energy is used to produce..?
Pmf, which will be used in Calvin Cycle to produce sugar
Phototrophs can be oxygenic and..?
Anoxygenic
Light is harvested by..?
Pigments (color = differentiation of nm)
Pigment diversity has ecological significance because..?
Bacteria on top absorb lenghts that the ones below don’t
Reaction center
In the choroplast: flower shape; light harvesting peripheral pigments + rc pigments: P680/700/840
What is the role of carotenoids?
Pigments that protect others against toxic oxydation
What is the role of phycobilins?
They harvest different wavelenghts than the others
Describe a chloroplast
Double membrane; stroma (cytoplasm); thylakoids and their membrane
How can we explane the pmf provided by the thylakoid membrane?
The stroma is alkaline and negative while the intrathylakoid space is acid and positive
4 sites of photosynthesis for pros
cyto membrane: heliobacteria; intracyto membranes: purple bacteria; thylakoid membrane: cyanobacteria; chlorosome (green non/sulfur bacteria)
Which of the 4 types of site for photosynthesis in Pros is the best for low density of light?
Chlorosome
How to produce anoxygenic photosynthesis with purple bacteria?
1- Cyt get electrons from a donor (sulfur or succinate)
2- Pigments P870, receiving electrons, are excited by light
3- ETC (pmf) to produce ATP and NADH
What is the issue with purple bacteria and NAD reducing?
P870* is not enough, so NAD enters the ETC Complex 1, which uses pmf to reduce it (less ATP produced, very low yield, reverse utilization)
With green bacteria, we do anoxygenic photosynthesis
Cyclic photophosphorylation with P840; no need for electron donor to produce ATP (use sulfur products), but use ferredoxin to reduce NAD
What is oxygenic photosynthesis?
Produces pmf with PS11 (P680) and Reducing power with PS1 (P700): Non cyclic (only cyclic if NADH is sufficient: no NADH produced)
What produces pmf among oxygenic photosynthesis?
Quinones
Anoxygenic photosynthesis with sulfide
Cyclic; only PS1 (P700)
What is a chemoautotroph?
Uses inorganic compounds
What are nitrifying bacteria?
They use inorganic nitrogen compounds to produce nitrate. Oxygenic.
Very low yield because reverse electron flow is used to produce ATP.
What are sulfur bacteria?
Chemoautotroph using sulfur compounds to produce pmf and sulfuric acid. NADH is produced with reverse electron flow. Oxygenic.
What are methanogens?
Bacteria producing methan; anaerobes
What is a methanotroph?
Uses the by-products of methanogens to produce energy. Oxygenic.
What is the Calvin cycle?
The reverse ETC cycle that produces sugar from energy of light. Euk enzymes are found in the stroma while Pros enzymes are found in the cytoplasm
What is the total Calvin cycle yield?
6 CO2 + 12 NADPH + 18 ATP = 1 sugar + 12 NADP + 18 ADP + 17 Pi
