MIC 230 Final

What cell structure/layer do all bacteria cells contain?

Cytoplasmic membrane (cell membrane)

What is the cell membrane composed of?

Highly selective permeable barrier

What is the cell envelope? What is always included in it and what is sometimes included?

Refers to all layers of prokaryotic cell. Always includes inner membrane and cell wall, sometimes included outer membrane if present

What are hopanoids?

lipids found in some bacteria, there function is stabilizing the membrane

What does the fluid mosaic model tell us?

Cell membranes are much more fluid than we often picture them

What are prokaryotic cell walls made of and what is their function?

Made out of peptidoglycan and function to protect the cell from osmotic pressure

What is peptidoglycan made of?

Repeating units of NAG and NAM amino acids that are in a cross linking pattern

What types of bonds are between layers of NAG and NAM?

peptide bonds

What type of bonds are in between NAG and NAM within a layer?

glycosidic bonds

What is the s-layer?

A protein layer found in some bateria that is made of proteins sticking out and covering cell

What are characteristics of gram + peptidoglycan layer?

very thick, and contains teichoic and lipteichoic acids

What purpose do teichoic and lipteichoic acids in the peptidoglycan layer of gram + bacteria?

to make the cell more hydrophilic and stabilize the cell wall under changing ionic environments

What is the “most outside” part of the cell envelope for gram + bacteria?

the cell wall

What are characteristics of gram - peptidoglycan

thin layer

Does gram - bacteria have an outer membrane?

Yes

What is the outer membrane of gram - bacteria composed of?

lipopolysaccharide (LPS) and phospholipid layer

What is the periplasm?

Space between the outer membrane and cytoplasmic membrane in gram - bacteria

What are some characteristics of LPS

* has polysaccharide repeats pointing away from the cell surface
* stabilizes outer membrane
* extra permeability layer
* increases hydrophilic nature of the outside of the cell

What are the functions of the cell membrane?

* permeability barrier
* protein anchor
* energy conservation

What are porins?

channels in the peptidoglycan layer of gram - bacteria that allow the diffusion of hydrophilic small molecular substances through the outer membrane

Why are porins necessary?

Because the outer membrane of gram - bacteria is extremely impermeable

What are some bacterial cell surfaces?

capsule and slime layer

What is a capsule and what purpose does it serve?

a polysaccharide layer that surrounds the cell and prevents water loss

What is a slime layer and what is its purpose?

Thin layer that is loosely attached to the cell wall, is used to prevent water loss and being eaten

What are the extracellular appendages of bacteria cells?

Pili or fimbriae

What is the cytoplasm and what takes place there?

it is the liquid inside the cell and the place where the vast majority of cellular activities take place

What can be found in the cytoplasm of prokaryotes?

DNA, RNA, proteins, DNA poly, RNA poly, ribosome, cytoskeleton structures, and inclusion bodies

What are cytoskeleton structures

cell wall synthesis, cell division, chromosome partitioning

What are inclusion bodies?

crystals (or other chemical form) of energy producing molecules

What are lipid bodies?

found in some cells and made up of triacylglycerol and acts as storage of high energy lipids for long term survival

What are gas vesicles?

protein shells filled with gas and used by microbes to position themselves in a water column

What are magentosomes

A membrane enclosed organelles that allows movment toward a magnetic field

What are endospores?

highly differentiated cells that are resistant to heat, harsh chemicals, and radiation

What are the three main types of motility?

Gliding, pili-dependent, and flagella dependent

How does gliding motility work?

snowmobile-like inner motor

How does pili motility work?

requires repetitive extension and retraction of pili, ATP dependent

How does flagella based motility work>

Uses a biological rotary motor powered by proton motive force, often can only move in one direction and a time so the “tumble and run” model is used

Taxis

the directed movement toward and attractant or away from a repellent

What are the 6 essential macronutrients?

Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur

Where do bacteria get carbon?

amino acids, fatty acids, sugars, nucleotides, aromatic compounds, and CO2

Where do bacteria get nitrogen?

proteins, nucleic acids, NH3, NO3, and N2

Where do bacteria get phosphorus?

phospholipids, nucleic acids, and PO4

Where do bacteria get sulfur?

Amino acids, vitomes, and SO4

What are other required elements for growth?

* major ions such as Fe, Mg, Na, Cl, Ca, K
* trace elements (micronutrients) such as copper, zinc, nickle, tungsten, and others

What are growth factors?

Molecules needed for growth that are made by the cell, such as vitamins, amino acids, purines, pyrimidines, etc.

Prototroph

a microbe that can synthesize necessary molecules required for growth

Auxotroph

a microbe that is not able to synthesize a molecule required for growth, instead must acquire that molecule

Is it possible to be both a prototroph and an auxotroph?

Yes, can be one for one nutrient and one for another

True or false: All organisms have the same optimal temperature

False, each organism will have an optimal temperature for growth, although can group these together

What temp do psychophiles perfer?

≤15º C

What temp do mesophiles prefer?

20-45º C

What temp do thermophiles prefer?

>45º C

What temp do hyperthermophiles prefer?

\+80º C

What temp do hyperthermophiles prefer?

106º

Do acidophiles prefer acidic or basic conditions?

acidophiles

Do alkaliphiles prefer acidic or basic conditoins?

basic

What type of environment do halophiles prefer?

high salt

What type of environment do osmophiles prefer?

high sugar

What type of environment do xerophiles prefer?

arid, low water

What is an obligate aerobe?

A microbe that must be in an aerobic envi

What is a tolerant anaerobe?

A microbe that can survive in an anaerobic envi

What is a facultative aerobe?

A microbe that can grow in aerobic or anaerobic envi

What are the phases of microbial growth?

Lag, exponential, stationary, and death

What are the effects of catalysts?

* lowers activation energy of a reaction
* increases reaction rate
* does not affect energetics or eq of a rxn (can’t make something non-spontaneous spontaneous)

Characteristics of enzymes?

* vast majority are proteins
* highly specific
* lowers the activation energy to increase the reaction rate
* are recycled because they are unchanged in the reaction
* often regulated (not always “on”)

Steps of an enzyme reaction?

1. the enzyme binds the substrates at binding sites within the active site
2. binding brings the substrates into close proximity with one another to form the enzyme substrate complex
3. bond rearrangement forms a transition-state complex
4. the transition-state complex decomposes, releasing final produces and the enzyme returns to initial state

What do some enzymes require to complete their task?

cofactors

What does it mean if a reaction is coupled?

A reaction requiring energy and a reaction producing energy are done at the same time

What are the two categories/ways to obtain energy

Chemicals (chemotrophy)

Light (phototrophy)

What are the two categories/ways to obtain electrons?

organic molecules (organotrophs)

inorganic molecules (lithotrophs)

What are the two categories/ways to obtain carbon?

organic molecules (heterotrophs)

CO2 (autotrophs)

What is an organism that is a chemo-organo-heterotroph?

Humans

What is an organism that is a photo-litho-autotroph?

Plants and photosynthetic bacteria

What is an oxidation reaction?

loss of electrons, electron donors get oxidized, after they are oxidized they are more likely to be electron acceptors

What is a reduction reaction?

gain of electrons, electron acceptors get reduced, after they are reduced they are more likely to be electron donors

Where are reduced molecules on the redox tower?

top (-V)

Where are oxidized molecules on the redox tower?

Bottom (+V)

What happens the further the electron “falls” down the tower?

More energy is released

How can energy be preserved in the cell?

* coupling exergonic reactions directly to ATP synthase (substrate level phosphorylation)
* electron transport chain (generates proton motive force)

Inputs and outputs of glycolysis

input: glucose, 2 ATP

output: 4 ATP, 2 NADH, and 2 pyruvate

How does glucose produce energy?

Via glycolysis and SLP

What are the steps of fermentation?

Starts with glycolysis, then pyruvate is used to make whatever the name of the fermentation is (lactose, ethanol, etc.)

What are the steps of respiration?

1. glycolysis
2. pyruvate dehydrogenase
3. citric acid cycle
4. electron transport chain

Major inputs and outputs of cellular respiration?

Oxygen + glucose → Carbon dioxide + water + ATP

Why can more energy be produced with aerobic respiration?

because O2 has much more positive redox potential than other e- acceptors

What is the cateogory of an organism that uses glucose as the e- donor?

chemoorganotroph

What does a chemolithotorph do?

inorganic molecules are oxidized and their e- are donated to a membrane associated with ETC for the generation of PMF

Phototrophy

use of light as an energy source

Oxygenic phototrophs

* light provides energy to maintain the flow of e- in the chain
* produces ATP
* produces reducing molecules
* PS II is very P so H2O (normally a very poor e- donor) can still be a donor

Anoxygenic photorophs

* does not use O2
* not super efficient so a constant flow of e- is required

Autotrophy

carbon fixation = “dark reactions”

CO2 → organic molecules

Calvin cycle

Inputs and outputs of calvin cycle

CO2 + NADPH + ATP → Glucose + NADP+ + ADP

Metabolism for most eukaryotes

1. glycolysis
2. citric acid cycle
3. ETC
4. very limited fermentation

What are the 4 repair mechanisms

Photoreactivation, excision repair, SOS repair, homologous recombination

What does photoreactivation repair

repairs thymine dimers

What does excision repair?

general response to damage

base or nucleotide excision

What does SOS repair?

* response to severe DNA damage
* goal is to get genome replicated and repair enough so the cell can divide
* very error prone

What does homologous recombination repair?

* DSBs
* used to repair strands perfectly

Transformation

transfer of free “naked” DNA from environment

What experiment displayed transformation

Griffth’s