Midterm 1 Flashcards
1
Q
Who first did microscopic description? (1665)
A
Robert Hooke
2
Q
Who first did microscopic organisms description? (1684)
A
Anthony Van Leeuwenhoek
3
Q
Who criticized spontaneous generation (end of 19th c.)?
A
Francesco Redi; Lazzarro Spallanzani
4
Q
What did Pasteur?
A
Provided evidence against spontaneous generation (classic experiment of 1861); vaccines
5
Q
Who is the father of microbiology?
A
Leeuwnhoek
6
Q
1847 and 1867: what did Semelweis and Lister can be proud of?
A
Reduction of spread of disease (hand washing + phenol)
7
Q
1884: Robert Koch?
A
Discover of microorganisms : anthrax and tuberculosis are due to microorganisms
8
Q
Microorganisms in size order
A
Viroids (100 nm); bacteria/archea (2 um); eukaryotes (2-100 um)
9
Q
Nuclear membrane of micro?
A
Bacteria and Archea = no, Eukaryotes = Yes, Viroids = capsid made of capsomeres
10
Q
Nucleolus in microo?
A
Not in Bacteria nor Archea nor Viroids, but rDNA in Eukaryotes
11
Q
How many years of evolution for microo?
A
4 billions!
12
Q
Four roles of microo in the environment?
A
recycling nutrients; detoxifying by metabolism; source of food; genetic diversity provides drugs/antibiotics
13
Q
Properties of all cells (3)
A
Compartmentalization; growth and evolution
14
Q
Properties of some cells (3)
A
Motility, differentiation, communication
15
Q
General functions of cells
A
Genetic + Catalytic = Growth
16
Q
What sets the size of cell?
A
S/V ratio : if too big; can still grow; if too small; not enough surface to interact with the environment regarding intern processes
17
Q
What is the main difference regarding structure of pro vs eukaryotes?
A
Nuclear membrane
18
Q
What are the roles of a membrane (3)?
A
Selective permeability, protein anchor + energy (pmf)
19
Q
Name types of membrane proteins (4)?
A
Sensors, adhesins, transporters, enzymes
20
Q
The membrane of bacteria and eukaryotes?
A
Phospholipid bilayer composed of glycerol, fatty acids (2) and a phosphorous group
21
Q
What is the main difference between eukaryotes and archea membrane?
A
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
22
Q
Stabilization of the membrane?
A
In eukaryotes = sterols (chol for animal, ergo for fungi and stigma for plants and protozoans); in prokaryotes = hopanoids (1 more ring)
23
Q
Storage of DNA
A
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
24
Q
What is protein pathway from DNA?
A
DNA polymerase (copy); RNA polymerase (transcription); ribosome (translation)
25
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
26
Cell walls in Euk is composed of..?
Polysaccharides! Cellulose for plants, chitin for fungi, may also be of galactose or mannose..
27
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
28
Endoplasmic Reticulum of Euk: two types
System of membrous channels : Rough is for ribosomes, while smooth is for synthesis of lipids
29
Rough Endoplasmic Reticulum synthesis of proteins: describe pathway (6)
1. mRNA leaves nucleus and attaches to ribo = prot synthesis started (signal)
2. Signal recognition particules bind to signal (on prot)
3. SRPs bind to RER so then prot enters RER
4. Signal peptidase
5. Ribosome + mRNA break away (poly peptide is done)
6. Final preparation of polypeptide before Golgi complex
30
What is the Golgi complex?
Further processing of proteins, vehiculed in vesicles
31
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
32
Thylakoids in details
Contains pigments and enzymes that harvest light - ATPases are bound to membrane
33
Eukaryotic skeleton has three types of filaments
Microtubules (formed out of a and b-tubulin subunits); actin; intermediate filaments (keratin, desmin, vimentin)
34
Microtubules in details
Highways to travel among the cell : kinesin and dynein are attached to vesicles and walk on microtubules (driven by ATP breakdown)
35
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
36
Are cillia and flagella covered by plasma membrane in euk?
Yes
37
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))
38
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
39
Gram + cell wall
90% peptidoglycan: 10% is teichoic or lipoteichoic acid and wall-associated proteins attached by sortase
40
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
41
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
42
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 -)
43
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
44
Surface appendages of prokaryotes
Fimbriae and Flagella
45
Three types of flagella
Monotrichous, peritrichous and lophotrichous
46
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.
47
Flagellum biosynthesis of Bacteria
Build the base and put a cap. Then build from the top with a channel
48
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)
49
Flagellum structure of Archea
Grows from the base (pushing the top out)
50
Description of the actual mvt
Goes from a physical/chemical gradient to another: light, nutrient, oxygen.. random vs directed mvt
51
Frimbriae of Bacteria
About 4 um long; principally for attachment to surfaces
52
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
53
Gram + fimbriae
Surface adhesins (only one prot); by sortases, attached to peptidoglycan (covalent)
54
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
55
Formation of endospore
Asymetric cell division; prespore and septum (separation); cortex, cell wall; coat; when fully mature, cell die
56
What are cell inclusions?
Reserves, but not organelles (maybe one layer) for nutrients and magnetosomes
57
What does drive flagella of Euk.?
ATP
58
Viruses, what are they?
Obligate intracellular parasites that affect one type of host; can't replicate itself, but can be killed..
59
What is a virion?
Outside-of-a-host viruses
60
Physics of a virus?
Nucleic acid (one type: RNA or DNA) + capsid of proteins (made of capsomeres) + envelope (lipids); can be ss or ds
61
What is a complex virus?
Around 100 proteins
62
Types of viruses?
Helical, polyhedral, complex virus (attack bacteria)
63
What is a viroid?
Closed circles of ss RNA (240-380 nucleotides); replication depends on host machinery
64
What are prions?
One single protein
65
How do prions act?
Prions can't replicate; they induce misfolding of other prot
66
What are the two components of life that are difficult to metabolize?
Carbon and energy: lots of transfo
67
What is anabolism?
Use of energy and reducers to oxidyze
68
What is catabolism?
Use of precursors to produce energy and oxidizers to be reduced
69
What is an electron donor?
A reducer
70
What is an electron carrier?
Can easily be reduced or oxidized
71
The basic metabolic pathways
Glycolysis, penthose phosphate pathway and TCA cycle
72
Glycolysis in short
```
One glucose = 2 pyruvate
2 ATP (substrate-level phosphorylation), 2 NADH
```
73
What is substrate-level phosphorylation?
The synthesis of energy-rich phosphate
bonds through reaction of inorganic phosphate with an activated
organic substrate.
74
What is oxydative phosphorylation?
Formation of ATP via ETC
75
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
76
Can other compounds then pyruvate undergo TCA cycle?
Yes
77
Aerobic respiration vs anaerobic respiration?
Oxygen is used as a final acceptor
78
Name an hydrogen carrier?
FMN
79
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
80
What is the final step of aerobic respiration?
Two protons and two electrons from the inner space are used to reduce oxygen to water
81
What does influence ATP production?
Environmental conditions, like pH (no pmf if no gradient..)
82
How many protons for 1 ATP?
3 to 4
83
Glycolysis + TCA cycle = how many ATP?
38
84
When does fermentation occur?
When there is no final acceptor.. TCA stops (succinate cannot be oxidized). Only glycolysis
85
Fermentation in short
Electron donor is organic compound; final electron acceptor is a organic product
86
Net yield of ATP throught fermentation?
2 ATP/glu
87
What is the penthose phosphate pathway?
It leads to many sugars; it produces reducing power
88
Most cells can convert NADH to...
NADPH
89
Net yield of penthose pathway?
2 NADPH + CO2 + sugar
90
In Euk, where are the enzymes of TCA, of glycolysis and fermentation?
TCA and respiratory: mitochondria membrane
| Glycolysis and fermentation: cytoplasm
91
In Pros, where are the enzymes of TCA, of glycolysis?
Respiratory chain in cyto membrane; the rest in cytoplasm
92
3 types of transport
Passive, facilitated (down a gradient), active (against a gradient - ATP)
93
Transport vs Simple diffusion?
Biosynthesis of transport system is controlled; can be saturated
94
When is active transport the most used pathway?
Unicellular, for nutrients
95
In multicellular organisms, which tranport type and why?
Facilitated diffusion from blood or plasma
96
Types of transporters?
Uniporter, antiporter (one's out to let one in), symporter (two needed to enter)
97
When there is no oxygen, how to create a pmf?
ATPases are inverted
98
Why inverting ATPases?
To produce a pmf that will produce a Na+ gradient
99
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
100
What is group translocation?
Use of a chain to finally have a compound that can activate the transporter
101
Type of ATPase and efficiency
Euk: 1 H+/ATP, P-type
Pros: 3 H+/ATP, F-type
102
What is endocytosis?
Use of vesicles (in Euk)
103
About oxygen requirements: three types of microo?
Aerobes, anaerobes and facultative aerobes
104
About sources of energy, electrons and carbon types of microo?
Energy: chemicals or light
Electrons: organic or not
Carbon: organic or not
105
What is a chemoorganotroph?
Needs organic chemicals as energy
106
What is chemolitotroph?
Needs inorganic chemicals as for energy
107
What is a phototroph?
Needs light for energy
108
Heterotroph stands for..?
Organic chemicals needed
109
Autotrophs stands for..?
Inorganic chemicals needed
110
Anaerobic respiration vs fermentation?
Anaerobic respiration means ETC with other final acceptors
111
What is a denitrifying bacteria?
Chemoheterotroph that produces gas from nitrogen source
112
In phototroph, light energy is used to produce..?
Pmf, which will be used in Calvin Cycle to produce sugar
113
Phototrophs can be oxygenic and..?
Anoxygenic
114
Light is harvested by..?
Pigments (color = differentiation of nm)
115
Pigment diversity has ecological significance because..?
Bacteria on top absorb lenghts that the ones below don't
116
Reaction center
In the choroplast: flower shape; light harvesting peripheral pigments + rc pigments: P680/700/840
117
What is the role of carotenoids?
Pigments that protect others against toxic oxydation
118
What is the role of phycobilins?
They harvest different wavelenghts than the others
119
Describe a chloroplast
Double membrane; stroma (cytoplasm); thylakoids and their membrane
120
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
121
4 sites of photosynthesis for pros
cyto membrane: heliobacteria; intracyto membranes: purple bacteria; thylakoid membrane: cyanobacteria; chlorosome (green non/sulfur bacteria)
122
Which of the 4 types of site for photosynthesis in Pros is the best for low density of light?
Chlorosome
123
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
124
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)
125
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
126
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)
127
What produces pmf among oxygenic photosynthesis?
Quinones
128
Anoxygenic photosynthesis with sulfide
Cyclic; only PS1 (P700)
129
What is a chemoautotroph?
Uses inorganic compounds
130
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.
131
What are sulfur bacteria?
Chemoautotroph using sulfur compounds to produce pmf and sulfuric acid. NADH is produced with reverse electron flow. Oxygenic.
132
What are methanogens?
Bacteria producing methan; anaerobes
133
What is a methanotroph?
Uses the by-products of methanogens to produce energy. Oxygenic.
134
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
135
What is the total Calvin cycle yield?
6 CO2 + 12 NADPH + 18 ATP = 1 sugar + 12 NADP + 18 ADP + 17 Pi
