BIOL 4110 Exam 1 Flashcards: Key Terms & Definitions

Microbial physiology

structure function relationships in microorganisms, especially how microbes respond to their environment

lab setting: petri dish life

Study glycolysis

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Cytoplasm

gel-like network; crowded with proteins and other molecules

Plasma membrane

encloses the cytoplasm

-composed of phospholipids, membrane proteins, and other molecules

Cell wall

covers the cell membrane

-composed of peptidoglycan

Outer membrane (gram-negative)

LPS, phospholipid, proteins

Ribosomes

rRNA + riboproteins

Nucleoid

chromosomal DNA + DNA associated proteins

Flagellum

external helical filament whose rotary motor propels the cell

How do microbes build biomass?

autotrophs: fix CO2 and assemble into organic molecules

heterotrophs: assimilate organic compounds as carbon sources

How do microbes obtain energy?

energy sources (phototrophs and chemotrophs)

electron donors (lithotrophs and organotrophs)

Phototrophs (microbes energy source)

obtain energy from chemical reactions triggered by light (photosynthesis)

Chemotrophs (microbes energy source)

obtain energy from oxidation-reduction reactions

Lithotrophs (microbes electron donor)

use inorganic molecules as electron sources

Organotrophs (microbes electron donor)

use organic molecules as electron sources

Complex media

nutrient rich, but contains poorly defined ingredients (yeast extract or beef extract)

Defined (synthetic) media

precisely defined; used to characterize the phenotype of a mutant

Population growth

not only refers to indiviudals

studied in a batch or liquid culture

shows growth in 4 stages

What are the 4 stages of population growth?

-lag phase

-exponential (log) phase

-stationary phase

-death phase

Calculation of growth rate

Nt = (N0)2^n

Nt = final cell number

N0 = original cell number

n = number of generations

Generation doubling time

the time that takes for a population to double

Eukaryotes development of internal membranes

create internal micro-environments

advantage: specialization = increase efficiency/ natural selection

Endosymbiosis

origin of mitochondria

engulfed aerobic bacteria, did not digest them

mutually beneficial relationship

-natural selection

Evolution of eukaryotes

origin of chloroplasts

engulfed photosynthetic bacteria, did not digest (natural selection)

Abiotic origins process

abiotic origins → origins of life → LUCA → diversification and complexity

origins of life: membranes, electron transport/ATPase, ribosome, nucleotides/nucleic acids

Where did eukaryotes come from?

lokiarchaea

Culturing and counting bacteria

microbes in nature exist in complex, multispecies communities

we have only cultured a small fraction of microorganisms around us

What is so special about glucose?

glucose can be converted to cellulose using cellulolytic enzymes

Enzymes

catalyze all chemistry in the cell

speed up rate of reactions

can be turned off or on

work by lowering the activation energy of a chemical reaction

Glycolysis and energy production in bacteria

glucose (glycolysis/PPP ED) → pyruvate → ethanol/lactate through fermentation → respiration

in between glucose and pyruvate, NAD+ → NADH → NADH + FADH2 → ATP

Preparatory phase

glucose is phosphorylated twice at the expense of 2 ATP and isomerized to fructose

glucose → F-1,6,bp

Allosteric site in phosphofructokinase

activator: ADP

inhibitor: PEP/ATP

What happens after the formation of F-1,6-BP in glycolysis?

it cleaves to G-3-P and dihydroxyacetone-P and later converted by triose phosphate isomerase

Payoff phase in glycolysis

conversion of 2 molecules of G-3-P → 2 pyruvate

4 ATP and 2 NADH are produced per molecule of glucose

What are the major carbohydrate pathways?

glycolysis or EMP: glucose catabolism (hexoses)

PPP: C5 molecule-based catabolism

Entner-Doudoroff: restricted almost entirely to bacteria (gram positive/negative and archaea)

Substrate-level phosphorylation

a high energy phosphate is directly transferred from a substrate molecule to ADP

How is glucose used with other products?

glucose (storage) → glycogen, starch, sucrose

glucose (oxidation via PPP) → ribose-5-phosphate

glucose (oxidation via glycolysis) → pyruvate

PPP

source of cellular NADPH and important precursor of nucleotide and amino acid biosynthesis

20% of g-6-p is directed into PPP

80% is directed into glycolysis

What are the main purposes of PPP?

source of NADPH

precursor formation

Precursors derived from PPP

R-5-P: nucleic acids, histidine, tryptophan

Sedoheptulose-7-P and erythrose-4-P: aromatic amino acids

Entner-Doudoroff Pathway

alternative method for glycolysis, less profitable

some species don't have all enzymes for glycolysis so they take this route

alternative precursor for this cycle: gluconate

Similarities of major glucose pathways

all start from glucose → phosphoglyceraldehyde in different routes

phosphoglyceraldehyde → pyruvate same pathways

Model fermentation

substrate is oxidized to an organic intermediate with oxidizing agent NAD

some energy released is conserved by substrate level phosphorylation

oxidized intermediate is reduced to end products

-NADH2 is the reducing agent

Lactic acid fermentation

lactic acid is the end product

glucose → pyruvate (lactate dehydrogenase) → lactate

-NADH → NAD+

Alcoholic fermentation

yeast possess pyruvate decarboxylase and alcohol dehydrogenase to convert pyruvate to ethanol

glucose → pyruvate (pyruvate decarboxylase) → acetaldehyde (alcohol dehydrogenase) → ethanol

What other processes require NADPH in bacteria?

fatty acid synthesis

nucleotide synthesis

What must be done before you enter the citric acid cycle?

pyruvate → acetyl-coA

catalyzed by pyruvate dehydrogenase → inhibited by acetyl-coA and NADH, only works under aerobic conditions

Importance of citric acid cycle

production of immediate compounds of other synthesis pathways

production of large quantities of ATP that require energy for various synthetic processes

Gluconeogenesis

process that allows the cells to form glucose from non-hexose precursors ( glycerol, lactate, pyruvate, propionate, and glucogenic amino acids)

-reverses glycolysis

Oxidative branch of TCA cycle

citrate → succinyl-CoA

Reductive branch of TCA cycle

oxaloacetate → succinyl CoA

Reverse citric acid cycle

-anaerobic

-CO2 fixation

-ATP produced using acetyl-CoA and secreting acetate

What is the difference between bacterial and human ATP synthase?

the opportunity to develop novel antibacterial treatments without affecting human health

What are 2 alternative carbohydrate sources?

lactose (disaccharide)

chitin, cellulose (polysaccharides)

What is the preferred source of energy?

glucose (monosaccharide)

Catabolite Repression (non-glucose metabolizing system)

in the presence of glucose, genes for the utilization of other carbon sources are repressed

What is required in the absence of glucose?

the induction of carbohydrate genes needed for transport and metabolism

What does lactose produce?

Lactose uses beta-galactosidase → galactose + glucose

Organization of an Operon

multiple genes with related functions are transcribed as a single mRNA

What is produced at the level of translation?

individual polypeptides

What do operons allow for?

expression of multiple genes to be regulated by a single mechanism

What does the repressor do?

binds to the operator site and prevents transcription of z,y, and a

What happens when lactose is present?

a small amount gets converted to allolactose

What is the inducer that binds to the lac repressor?

allolactose

IPTG

an analogue of allolactose

What does IPTG do?

it binds to the lac repressor, but is not hydrolyzed by beta-galactosidase

What gene is induced when the cell switches to lactose utilization?

beta-galactosidase (lacZ)

What genes are induced in the presence of galactose?

galactokinase

galactose-1-phosphate uridylyl transferase

UDP-galactose-4-epimerase

Chitin

2nd most abundant biopolymer

found in exoskeletons of crustaceans and insects

mostly produced in the ocean

What are some other uses of chitin?

biomedical devices

drug delivery

water purification

cosmetics

How is chitin degraded?

growth on chitin induces the expression of secreted enzymes

those enzymes (chitinase) are capable of degrading chitin and a chitoporin

When was the oxygenation of Earth's atmosphere?

2.4 billion years ago

Photosynthesis

the reduction of carbon dioxide into biomass using energy derived from light

-process that could produce such large amounts of oxygen

What bacteria can do photosynthesis?

archaea and bacteria by splitting a water molecule and results in oxygen gas

What color is cyanobacteria?

blue-green color that comes from chlorophyll

How do microbes build biomass?

all life on earth is based on carbon, which they acquire in different ways to generate biomass

-when energy is obtained from chemical reactions triggered by light (photosynthesis)

Phototrophy (light eating)

a metabolic mode to convert light energy into chemical energy for growth or the conversion of light energy into chemical energy (ATP)

Photoautotroph (energy source)

uses CO2 as a carbon source

ex: use H2O to reduce CO2 > cyanobacteria

Photoheterotrophs (energy source)

assimilate organic compounds as carbon sources

ex: green non-sulfur bacteria, purple non-sulfur bacteria

Cyanobacteria characteristics

chlorophyll a in thylakoids

reducing power H2O (oxygenic)

aerobic environment

Different wavelength (green and purple) bacteriochlorophylls

No H2O, thus no O2 production (anoxygenic)

anaerobic environment

Green Bacteria (non-sulfur)

carbon source: organic compounds

reducing power: organic compounds

Green Bacteria (sulfur)

carbon source: CO2

reducing power: H2S

Purple Bacteria (non-sulfur)

carbon source: organic compounds

reducing power: organic compounds

Purple Bacteria (sulfur)

carbon source: CO2

reducing power: H2S or S2O3^2- (thiosulfate)

Light harvesting pigments

obtain energy by photoexcitation of chlorophyll or bacteriochlorophyll

Light absorption

electrons flow through electron transfer chain (cyclic or noncyclic) → pump H+ → ATP synthesis

Phototrophy (chlorophyll)

goes through ETC

Phototrophy (carbon source: CO2)

does biosynthesis (production of complex molecules)

What can the absorption of a photon of light do?

it can drive the electrons of certain types of molecules into a higher energy state called an excited state

What happens to the energy from the excited state?

it can be lost by conversion to heat, fluorescence emission, exciton transfer, or electron transfer to another molecule (photooxidation)

Antenna complex

large numbers of light-harvesting chlorophyll and bacteriophyll are grouped together

Functions of the antenna complex

absorbs light

funnels the energy to the reaction center

Reaction center

electron from chlorophyll and bacteriophyll is photoexcited → electron transfer chain

What happens in the reaction center?

energy goes through the electron transport chain → results in the transport of a proton out of the cell

How does energy flow through a photosynthetic antenna complex?

energy flows through the chromophores of the light harvesting complex 1 and 2 (yellow)

-then it becomes trapped at the chlorophyll of the reaction center (light green)

Function of chlorophyll

acts as light harvesting pigment passing energy of absorbed photon between molelcules until it reaches the reaction center

Where does the transformation of light into chemical energy occur?

the reaction centers

What are the types of antennas?

LH1: absorbs light at longer wavelengths than LH2

LH2: absorbs light at shorter wavelengths than LH1

-quickly passes its energy to LH1 where it goes to the reaction center

Photosynthesis (anoxygenic)

oxygen is not involved

energy in light is captured and converted into ATP

purple and green bacteria conduct bacterial photosynthesis or anoxygenic photosynthesis