microbiology exam 1

why did i choose this major

microbe

microscopic organism

when did microbes first appear on earth?

3.8-4.3 billion years ago

four qualities of life:

metabolism, growth and reproduction, evolution, structure

what do phytoplankton include?

photosynthetic bacteria and single-celled algae

prokaryotic

has absence of nucleus and no membrane-bound organelles

eukaryotic

has nucleus and membrane-bound organelles

benefits of phytoplankton:

cycling O₂, provide O₂ to the ocean, food source, provide nutrients to the ocean

oxygenic photosynthesis

light + 6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂

anoxygenic photosynthesis

light + 6CO₂ + 12H₂S → C₆H₁₂O₆ + 12S + 6H₂O

Anton van Leeuwenhoek

first to describe bacteria under the microscope and is the “father of microbiology”

Robert Hooke

first to describe fruit molding and confirmed Leeuwenhoek’s discoveries

Ferdinand Cohn

found endospores

Louis Pasteur

disproved spontaneous generation and observed that fermentation was done by microorganisms

Robert Koch

one microbe can cause infection

pure culture

grown alone

central dogma: DNA → mRNA → protein

replication, transcription, translation

ribosome

composed of proteins and mRNA

Woese and Fox

compared 16S rRNA in different microorganisms and made a phylogenetic tree where archaea, bacteria, and eukarya are all equally related

Hugs et al.

compared 16S rRNA  and proposed new phylogenetic tree, where archaea and eukarya more closely related

chloroplast endosymbiont hypothesis

chloroplasts arose from symbiotic partnership between ancestral eukaryote and cyanobacteria

mitochondria endosymbiont hypothesis

mitochondria arose from symbiotic partnership between ancestral bacterium and  “alpha proteobacterium”

light microscope

0.2 micrometer resolution, 1000x magnification, can identify shape, arrangement, and size of bacteria

electron microscope

0.1 nanometer resolution, 100,000x magnification, used to see viruses and ultrasmall cells, can identify molecular and surface structures 

coccus

circular

spirochete

worm-like

bacillus

rod-shaped

appendaged

have a tail-like appendage

spirillium

C-shaped

filamentous

long, thread-like, similar to a batch of spaghetti

stain types:

simple, gram positive, gram negative, basic (+), negative (-), fluorescent 

staphylo

cluster

strepto

chain

tetrad

four

how are bacteria always related?

through 16S rRNA

cell envelope

several layers surrounding cytoplasm, including cytoplasm membrane, cell wall, and other structures

what does cell envelope prevent?

osmotic lysis (bursting of the cell due to osmotic pressure)

bacteria cell wall contains

peptidoglycan: G-M, 1,4 glycosidic linkage, 4 amino acids, DAP, D and L conformation, gram positive S-layer 

archaea cell wall contains

pseudomurein: G-T, 3,4 glycosidic linkage, 3-4 amino acids, no DAP, all L, S-layer

metabolism

series of biochemical reactions required to sustain life

catabolic

reactions used to obtain energy and break down complex molecules, exergonic (releases energy)

anabolic

reactions used to synthesize cellular material, endergonic (requires energy)

reducing power

ability to donate electrons during electron transfer reactions (required for catabolic and anabolic reactions)

phototroph

obtain energy from light

aerobic

chemotroph uses O₂ as electron acceptor

anaerobic

chemotroph uses anything besides O₂ as electron acceptor

chemotroph

obtain energy from chemical reactions

chemoorganotroph

energy and reducing power is from an organic molecule

chemolithotroph

energy and reducing power is from inorganic molecule

respiration

form of aerobic or anaerobic catabolism in which electron donor, which can be organic or inorganic, is oxidized using electron acceptor, such as O₂

fermentation

metabolic process that releases energy from sugar or other organic molecule and does not require O₂ or electron transport system; uses organic molecule as final electron acceptor

chemoorganotroph aerobic respiration

C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + 38 ATP

chemoorganotroph anaerobic respiration

C₆H₁₂O₆ + 12NO₃^- → 6CO₂ + 12NO₂^- + 6H₂O + <38 ATP

chemolithotroph aerobic respiration

H₂S + ½ O₂ → S^o + H₂O + <38 ATP

chemoorganotroph anaerobic fermentation

C₆H₁₂O₆ → 2(C₃H₆O₃) + 2 ATP

NADH

nicotinamide adenine dinucleotide 

NADH is good at ______

shuttling electrons around the cell

in respiration, NADH is _____ to _____

oxidized; NAD⁺

• glycolysis stage II

• pyruvate → acetyl coA

• citric acid cycle

in fermentation, NAD⁺ is _____ to _____

reduced; NADH

• glycolysis stage II

NADH → NAD⁺

• fermentation step

what type of carbon do autotrophs use?

CO₂

what type of carbon do heterotrophs use?

organic carbon

initiation of replication in bacteria

DnaA binds to the origin of replication (oriC) and uses ATP to pull dsDNA apart

what is DNA gyrase?

topoisomerase (cut and rejoin DNA strands to relieve tension)

in replication, elongation is catalyzed by _____

DNA polymerase III (synthesizes new DNA strands in 5’-3’ direction)

DNA polymerase I

removes RNA primers (exonuclease) and adds DNA

DNA ligase

seals nicks in DNA

in DNA termination, __ _____ binds to the ter sequence and topoisomerase IV cuts the two genomes apart

Tus protein

what happens when the DnaA protein binds to the origin of replication?

the double helix is pulled apart in an ATP-dependent manner

what direction does DNA polymerase synthesize new DNA in?

5’-3’

what enzyme is required to remove the RNA primer?

DNA polymerase I

initiation in transcription begins with the ___ ____ binding to the ___ ________, which then binds to the DNA strand at the promotor region

sigma factor; RNA polymerase

promotor region

binding site for RNA polymerase

RNA polymerase transcribes in the ______ direction and synthesizes only in the ______ direction

3’-5’; 5’-3’

operon

multiple genes under same promotor in transcription

termination in transcription

rho protein binds to mRNA at rho-dependent termination site, which releases the mRNA and RNAP, then RNAP pauses at stem-loop and weak RNA-DNA binding leads to RNAP due dissociate

transcription in bacteria vs eukaryotes 

bacteria:

• RNA polymerase: 4 subunit core enzyme

• Pribnow sequence in promotor

• coupled translation in cytoplasm

eukaryotes:

• RNA polymerase: 12 subunit core enzyme

• more complex initiation of transcription: TATA box

• transcription & RNA processing: nucleus

Translation: cytoplasm

what is sigma factor?

polypeptide subunit of RNA polymerase

what sequences are required to being translation?

RBS and start codon AUG

which antibiotic stops translation?

streptomycin binds to the 30S subunit and causes a misreading

what are the stop codons in the termination of translation?

UAA, UAG, UGA

which binding is required to initiate translation?

f-methionine tRNA to the start codon