Lecture Quiz #2 Flashcards
Give an example of a solute
Sodium chloride
Define halophile and osmotolerance
Halophile: loves salts
Osmotolerance: has a salt limit
Define acidophile, neutrophil, and alkaliphile
Acidophile: Likes acidic environments
Neutrophil: Likes neutral environments
Alkaliphile: Likes basic environments
Define psychrophile, mesophile, thermophile
Psychrophile: Likes extreme cold
Mesophile: Likes moderate temperatures
Thermophile: Likes extreme heat
Define piezophile (barophile)
Likes high-pressure environments
Define obligate aerobe, obligate anaerobe, and microaerophile
Obligate aerobe: Needs lots of air/ oxygen
Obligate anaerobe: Needs no air/ oxygen
Microaerophile: Likes a little air/ oxygen, but not a lot
Define metabolism
The total of all chemical reactions occurring in the cell
Define anabolism and catabolism
Anabolism: the biosynthesis of new organic molecules from smaller organic and inorganic compounds
Catabolism: breaking down of molecules into smaller units while releasing energy, ‘fueling reactions’
Microbes are big producers of what two elements?
Oxygen and nitrogen
Define and give examples of the 3 types of cellular work
1) Chemical: synthesis of complex biological molecules
2) Transport: taking up nutrients, eliminating wastes, and maintaining ion balances
3) Mechanical: movement of structures that are part of the cell (motility, rotation of flagella, partitioning of chromosomes)
Define chemoorganotroph, chemolithotroph, and phototroph
Chemoorganotroph: energy source is organic molecules
Chemolithotroph: energy source is inorganic molecules
Phototroph: energy source is light
Define autotroph and heterotroph
Autotroph: Carbon source is CO2
Heterotroph: Carbon source is organic molecules
Define organotroph and lithotroph
Organotroph: electron source is organic molecules
Lithotroph: electron source is inorganic molecules
The most commonly used practical form of energy is?
ATP
Give 3 examples of altered ATP, and briefly describe how altering ATP works
-Guanosine, cytidine, uridine
-Enzymes hydrolyze bonds and alter original triphosphate molecule of ATP to make different energy sources
Name the basic purposes of GTP, CTP, and UTP (guanosine, cytidine, uridine)
GTP: protein synthesis
CTP: lipid synthesis
UTP: peptidoglycan, and polysaccharide synthesis
Give 5 examples of cellular processes that are exergonic reactions.
Aerobic respiration
Anaerobic respiration
Fermentation
Phototrophy
Chemolithotrophy
Give 3 examples of cellular processes that are endergonic reactions
Chemical work
Transport work
Mechanical work
Give 4 examples of carbon sources
CO2, sugars, amino acids, and fatty acids
Define substrate level phosphorylation
The generation of ATP (or GTP/UTP, etc)) from ADP (or GDP/ UPT, etc) by chemical reaction
Define oxidative phosphorylation
An alternative way to create ATP generated by a proton gradient
Define oxidation-reduction (redox) reactions
Electrons move from an electron donor to an electron acceptor
The ETC (electron transport chain) of bacteria is very similar to that of what?
Mitochondria
Describe the chemiosmotic hypothesis and how it relates to the ETC
As electrons move through the chain, energy is generated; this energy allows protons to be pumped across the membrane to create electrochemical gradient. This gradient (charge separation) is the energized state called Proton Motive Force
Give a quick 5 bullet-point synopsis of what happens during the ETC
1) NADH is an electron donor
2) A series of redox reactions that pump protons through the membrane
3) The electrochemical gradient is established
4) Oxygen is the final electron acceptor
5) ATP synthase accepts protons to generate ATP
What are the three pathways of glucose catabolism, and which is the most common?
1) Embden-Meyerhof pathway: most common
2) Entner-Doudoroff pathway: only in prokaryotes
3) Pentose Phosphate Pathway
Describe the Embden-Meyerhof pathway of glucose catabolism
-It’s an amphibolic pathway, which means it’s both anabolic and catabolic
-Starts with glucose, 2 ATP are used to generate 3 Glyceraldehyde 3-phosphate
-Fructose 1,6 biphosphate; glucose are involved
-Nicotinamide adenine dinucleotide
-Generates NADH, which is an electron donor
-Redox active coenzyme
-The end product of this pathway is pyruvate
Describe the Entner-Doudoroff pathway of glucose catabolism
-Only found in prokaryotes
-NADPH is generated in this pathway, which is also an electron donor
-The production of KDPG
-Part 1 end products are pyruvate and glyceraldehyde 3-phosphate
-Part 2 end product is pyruvate
-Creates 2 pyruvates, doesn’t create 2 extra ATPs like the embden-meyerhof pathway (but does still generate ATP)
Describe the Pentose Phosphate Pathway of glucose catabolism
-Starts with 3 glucose-6
-Changing the chemistry of sugar, ultimately ending up with pyruvate
-Know that the glyceraldehyde-3-p and 6-phosphogluconate are a part of the pathway
-Ancient origin; may be older than the other pathways. It’s carried out by enzymes in the cells, but can be done without them.
Describe the TCA Cycle (Aka Krebs Cycle, Aka Citric Acid Cycle)
-NADH is made right when it enters the cycle
-Acetyl-coenzyme A plays a large role
-GDP is broken down into GTP, which are the high-energy molecules
-FAD and FADH2 are and NAD and NADH are electron donors; there are 5 electron donors in the cycle
-The process oxides pyruvate into 3 carbon dioxides
-Generates GTP
Describe what happens to the ETC if we grow bacteria with low aeration in the stationary phase
Then there’s only a certain amount of oxygen to help the ETC run, so they generate less hydrogen and have to conserve
What is proton motive force driven by?
The proton gradient and active transport
What is the ATP yield from aerobic respiration, and what kind of phosphorylation do these ATP come from?
-Yields 32 ATP
-Primarily from oxidative phosphorylation, but also uses some substrate-level phosphorylation.
Define chemorganotropy
Anaerobic glucose metabolism
What is anaerobic glucose metabolism called?
Chemorganotrophy
Describe the diversity of electron acceptors and why it’s important
-There’s a huge diversity of electron acceptors, which is important for the diversity of microbes in general.
-Diversity is impacted by nitrate waste that leaks from farms, factories, etc into the environment; nitrate occurs in oxygen depleted sediments and soils.
What type of reaction is chemorganotrophy
A dissimilatory nitrate reduction (denitrification)
What does chemorganotrophy break down, and what does three things does it break down into?
Nitrate > nitrite > nitric oxide > nitrogen gas
Nitrites oxidate iron atoms in hemoglobin, which means _____ nitrite consumption can lead to poor oxygen
high
What are the four unifying themes of fermentation?
1) NADH is oxidized to NAD+
2) Oxygen is not needed
3) Electron acceptor is pyruvate
4) ETC cannot operate, which leads to reduced ATP production
What happens to pyruvate during fermentation, and why do people find this valuable?
Pyruvate is converted to lactate and/or X (which is then turned into Y); X & Y can be used in weapons production
True or false: A lot of fermenters can be explosive, so they’re often used to manufacture weapons
True
List 4 types of fermentation
1) Lactic acid fermentation (has two types)
2) Alcohol (ethanol) fermentation
3) Complex fermentation
4) Other fermentation substrates: variety of sugars, amino acids, and organic acids
List and describe the two different types of lactic acid fementers
1) Homolactic fermenters: use the Embden-Meyerhof pathway to reduce pyruvate to lactate (lactate dehydrogenase). (tldr: only make lactate)
2) Heterolactic fermenters: also produce ethanol and CO2
Briefly describe reactants and products of alcohol (ethanol) fermentation
Sugars > ethanol + CO2 (enzyme: alcohol dehydrogenase)
Briefly describe the components of complex fermentation
Mixed acid (#1, 5, 6, 8, 9)
Butanediol (#1, 4, 5, 6, 9)
Give examples of monosaccharides and disaccharides, and describe what monosaccharides do
Monosaccharides such as: lactose, mannose, fructose are modified by enzymes to make the sugar the enzyme wants to carry down the pathway
Disaccharides such as: maltose, sucrose, lactose, cellobiose
List 4 other types of catabolism not otherwise talked about
Lipid catabolism, protein catabolism, fatty acid beta oxidation, and transamination
Describe what happens in lipid catabolism and protein catabolism
1) Lipids: Tricylglycerols and other lipids are broken down with lipases into fatty acids
2) Proteins: Polypeptides are broken down by proteases into amino acids
Describe what happens in fatty acid beta oxidation and transamination
1) Fatty Acid Beta Oxidation: 2 carbons are broken down for every fatty acid broken down because they’re good sources of electron donors, as well as acetyl-Coa.
-The fatty acid carbon sources can be extremely beneficial to the cell.
2) Transamination: If the cell is starving and needs pyruvate, they can take an amino acid and a-Ketoglutarate to for pyruvate and glutamate
-Intermediates of the krebs cycle are produced
What are the energy and carbon sources in phototrophy?
Light is a source of energy; the pigments in the cell (chlorophyll b and bacteriochlorophyll a) trap light energy
Carbon source is often CO2
Describe how pigments are important to phototrophy
-Alternating/ conjugated double bonds of the pigments allow for the generation of electron resonance (meaning they bounce from double bond to double bond)
-The types of chlorophyll have a great versatility in wavelength absorption
In what types of organisms does oxygenic photosynthesis occur, and briefly describe its two stages
1) Occurs in plants, eukaryotic algae, and cyanobacteria
2) Photons initiate the transfer of electrons, then:
-Photosystem 1 traps light at longer wavelengths
-Photosystem 2 traps light at shorter wavelengths
Photosystem 1 traps light at _____ wavelengths, and photosystem 2 traps light at ______ wavelengths
longer; shorter
Give 5 examples of internal structures found in bacteria
Gas vacuole, ribosomes, inclusions, nucleoid, endospore
What is the purpose of a gas vacuole?
Buoyancy for floating in aquatic environments
What is the purpose of ribosomes?
Protein synthesis
What is the purpose of inclusions?
Storage of carbon, phosphate, and other substances
What is the purpose of the nucleiod?
Localization of genetic material (DNA)
What is the purpose of an endospore, and in what type of bacteria are they found?
-Survival under harsh environmental conditions; only observed in bacteria
-Specifically only some gram-positive bacteria
What are the 3 main components of the bacterial cytoskeleton, and what do they do?
1) FtsZ: A division protein widely observed in bacteria; forms a disc shape in the center of the cell
2) MreB: maintains cell (rod) shape, localizes proteins
3) Crescentin: introduces crescent-shaped morphology
Name and briefly describe the density of 3 storage inclusions found in bacteria
1) Glycogen (sugar)
2) Polyhydroxyalkanoate granules: Very light
3) Polyphosphate granules: Very dense; store phosphate
What is the purpose of vacuoles?
To store gas for buoyancy in an aquatic environment
What do magnetosomes do?
Aid in orientation to seek nutrients; based on earth’s magnetic poles
What is the purpose of carboxysomes?
A specialized site for CO2 fixation (a protein coat with an enzyme inside)
There are as many as ________ ribosomes growing in a bacterial cell, whereas eukaryotes have up to ________
70K; 10 million
Why is the difference in size and composition between a prokaryote and eukaryote important?
It’s important for antibiotics; they can pick out bacterial ribosomes and keep them from synthesizing proteins
Describe bacterial nucleiods
-Most are circular
-No membrane
-Have proteins and histone-like proteins that interact and organize things
Name 3 types of bacterial plasmids and briefly describe what they do
1) Conjugative plasmids: the F factor; transfers copies of themselves into another bacteria
2) R (resistance) plasmids: can be conjugative (transfered through bacterial “sex”); delivers antibiotic resistance genes
3) Virulence plasmids: encode genes for pathogenicity
Some Gram-_________ bacteria are spore-formers
positive
What is the purpose of sporulation, and what do spores contain?
1) Spores represent a dormant state for long-term survival; formation (sporulation) is induced by harsh environmental conditions
2) Spores contain the entire chromosome enveloped by a membrane, peptidoglycan and an outer protein coat (keratin-like)
Certain conditions will cause spores to become activated; this is called _____________
germination
What aspect of sporulation is useful in diagnosis?
The location of endospores
Name 4 locations of endospores
1) Central
2) Swollen sporangium (makes cell somewhat sperm-shaped)
3) Terminal (at the end of a rod-cell)
4) Subterminal (almost at the end of a rod-cell)
Why do we typically set autoclaves to 121 degrees celcius?
That’s the temperature that can kill endospores
Briefly describe the morphology of protozoa, amoeba, and algae
Protozoa: motile due to cilia that cover their surface, heterotrophs
Amoeba: has a pseudopod and a contractile vacuole to control movement; prevents excess water inside the cell
Algae: have stored starch grains so they have carbon on-demand, use sunlight’s energy or can use organic compounds, extreme diversity, extremely abundant
Describe the differences between passive and facilitated diffusion
1) Passive diffusion: Non-polar lipid-soluble substances diffuse passively from high to low concentration
2) Facilitated diffusion: can control specific (sugars, ions, charged polar molecules, ATP, etc) or nonspecific transport (water, glycerol, urea, etc), allows nutrients in and out.
What are the two types of facilitated diffusion?
Specific and nonspecific transport
Describe the rates of diffusion in passive and facilitated diffusion
The rate of transport is rather linear in passive diffusion, whereas the rate of transport in facilitated diffusion is very quick, but plateaus due to the saturation effect.
Define active transport
Transport of a substance through a concentration gradient
Define primary and secondary transport
Primary active transporters: use ATP for energy
Secondary transporters: use gradient for potential energy
What does primary active transport utilize to move substances?
Uniport transport: The one-way transport of a single molecule
Uniport transport is an example of __________ _______ transport, whereas antiport and symport transport are examples of _________ ________ transport.
Primary active transport; secondary active transport
List and describe the two types of secondary transports
1) Antiport: 2 molecules are transported in different directions
2) Symport: 2 molecules are transported in the same direction
(Can be very complicated and involve multiple subunits or phosphate transfer)
What do phosphotransfer systems (group translocations) require?
Has to have a series of phosphate handoffs, which generates energy and the ability to phosphorylate the sugar.
Define siderophore and what it allows bacteria to do
-A molecule that binds to various forms of iron and makes it available to the cell
-This allows bacteria living in an animal to steal that creature’s iron
