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Microbiology test two
test two
186
Microbiology
Undergraduate 3
11/01/2009

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Term
Six most common elements
Definition
CHONPS, Carbon hydrogen oxygen nitrogent phosphorus and sulfur
Term
definition of catabolism
Definition
breaking down of complex molecules to release energy
Term
Definition of Anabolism
Definition
is the set of metabolic pathways that construct molecules from smaller units.
Term
metabolism
Definition
is comprised of both anabolism and catabolism
Term
Anabolic cell growth is
Definition
turning simple compounds into complex by anabolic processes
Term
Anabolic cell growth is
Definition
turning simple compounds into complex by anabolic processes
Term
Energy used during anabolic process
Definition
ATP
Term
Thermodynamics
Definition
study of energy by the calorie
Term
Calorie
Definition
heat needed to raise on ml of H2O 1 degree celcius
Term
kilocalorie
Definition
temp needed to raise 1000 ml of water one degree celcius
Term
Two laws of thermodynamics
Definition
Energy cannot be created or destroyed but changes forms. energy goes from more concentrated to less concentrated by ways of entropy.
Term
1st law of thermodynamics
Definition
energy cannot be created or destroyed but changes forms.
Term
second law of thermodynamics
Definition
energy goes from more concentrated to less concentrated
Term
exergonic reaction
Definition
reaction that releases energy spontaneous reaction
Term
catalyzed
Definition
reducing activation energy
Term
catalyzation in biological systems is
Definition
enzymes
Term
ribosomes are
Definition
RNA enzymes
Term
Metabolism deals with
Definition
enzymes by speeding up reactions
Term
co-enzyme
Definition
are organic molecules that are required by certain enzymes to carry out catalysis. They bind to the active site of the enzyme and participate in catalysis
Term
co factors
Definition
substance that needs to be present in addition to an enzyme for a certain reaction to take place.
Term
non-competitive inhibitor
Definition
binds to allosteric site and changes shape of active site
Term
factors controlling enzymes
Definition
substrate concentration, heat, ph, salt concentrations, heavy metals
Term
temperature that enzymes work and work the best
Definition
37 degrees centigrade and 40 degrees centigrade
Term
Competitive inhibitor
Definition
binds to active site and will not let the real substrate bind ex penicillin and peptidoglycan cell wall
Term
v max of enzyme activity
Definition
maximum velocity or rate of reaction due to enzyme activity
Term
proteins structure composed of
Definition
primary structure of petide bonds of amino acids, secondary structure of pleated sheet helical structure held by hydrogen bonds, tertiary structure give look of 3D view shape, quaternary structure consist of sub units for a 2 subunit protein
Term
Active site of proteins with enzymes will on have this type of fit
Definition
complimentry fit
Term
Hydrogen bonding is broken by
Definition
heat, salt, ph,substrates and heavy metals such as lead and mercury
Term
Biological pathways allow enzymes to work together in
Definition
chains, substrate 1 to enzyme 1 to substrate 2 to enzyme 2
Term
Feedback inhibition
Definition
enzyme product is materials for enzyme 2
Term
last enzyme can effect first enzyme this way
Definition
the last enzyme can turn of first enzyme by making an allosteric enzyme that allows substrate to be used somewhere else
Term
oxidation
Definition
oxidising material by a molecule losing an electron and losing hydrogen
Term
Benefit to oxidation reaction in microbiology
Definition
electron lost is gained by another molecule
Term
Reduction reaction
Definition
picking up of an electron and hydrogen and called redox reaction
Term
Energy from oxidation reaction will get stored as
Definition
high energy molecule ATP contains adinine and ribose
Term
heterotrophs
Definition
oxidase organic compounds of fats, proteins, sugars
Term
lithotroph
Definition
oxidise reduce forms of inorganic compounds for carbon such as iron oxidizing bacteria sulfure bacteria
Term
photoautotroph
Definition
convert light energy into chemical energy and use co2 as their carbon source
Term
fermentation
Definition
partial oxidation of organic compout with final electron acceptor being another organic compound
Term
steps to fermentation
Definition
ATP by production of glycolysis is split into 2 3 carbon chains to make 2 atp, its transfered to nad+ and reduced to NADH then is oxidised giving up H+ to pyruvate. THis is energy for lactic acid bacteria and yeast
Term
glycolysis ?
Definition
Glucose phosphoralates by addition of phosphate and HExokinase adds phosphate to Po4 molecule.
Term
atpases
Definition
will phosphoralate ADP and Make ATP and spin at a fast rate with the flow of hydrogen ions from outside to inside
Term
glycolysis step 1
Definition
1. addition of two phosphates to the 6 carbon molecule at the expense of two ATP- producing two ADP and creating 6 carbon sugar diphosphate.
Term
glycolysis step 2
Definition
The six carbon molecule with two phosphates is split into two three carbon molecule in a series of steps to pyruvate. The electrons are transferred to coenzyme NAD+ to form NADH and ATP is formed with 4 molecules of ATP formed. under aerobic conditions the pyruvate goes on to make more ATP and anaerobic to form lactic acid
Term
common fermentation products are
Definition
ethanol and lactic acid.
Term
glycolysis is
Definition
is a catabolic process in which a glucose molecule containing 6 carbons is split into 2 pyruvate molecules( 3 carbon molecule), Electron transfer from phosphate gives the coenyme Nad+ to turn it to NADH, during fermentation NAD+ is generated by the NADH giving up the electron and H+ to pyruvate to form the fermentation product.
Term
lactic acid bacteria
Definition
streptococcus, lactobacillus
Term
yeast(ethanol) bacteria
Definition
sacchromyces.
Term
aerobic respiration
Definition
complete oxidation of glucose to CO2 and H20 and final electron acceptor is 02
Term
Glycolysis yields This
Definition
2 pyruvate(3 carbon chains) 2 Atp and 2 NADH
Term
Kreb cycle yields
Definition
2 ATP
Term
Kreb cycle
Definition
A co2 and NADH is giving off from conversion of Pyruvate to Acetyl-COA. 4 Carbon molecule is starting material and binds with acetylcoa creating a six carbon molecule with COA carrier molecule given off. Now CO2 is given off creating a 5 carbon molecule and a electron is given off to creat NADH. Next second decarboxylation occurs with CO2 and NADH given off with A molecule of ATP and 4 carbon molecule is formed. THe four carbon molecule is further oxidising hydrogens to give off NADH AND FADH2.
Term
How many cycles must kreb cycle perform to yield 4 ATP? why
Definition
The kreb cycle must complete two rotations because the glucose molecule is breaking down two pyruvate and can only break down one molecule at a time making it have to cycle twice producing 4 atp
Term
Properies of enzymes- structure
Definition
most are proteins, they have a tertiary structure thatthat allows for the presence of an active site that binds substrates and possibly co-enzymes (by lock and key) -
Term
enzymes binding structure results in
Definition
enzyme-substrate complex, it reduces the activation energy of a reaction and alllow the reaction to occur very fast. Then releasing changed substrates which are now called products
Term
Enzymes are reused Y or N?
Definition
YES!!
Term
Enzyme specificity
Definition
specific as the reactions they perform and the substrates they will bind at the active site.
Term
Can enzyme reactions reverse?
Definition
if there is not much difference between the energy of the substrates compared to the energy of the products energy difference is not much.
Term
enzyme names end in
Definition
"ASE", protease example
Term
co-enzymes
Definition
A nonprotein and if it is organic then it is a loosely-bound cofactors termed coenzyme. Coenzymes are relatively small molecules compared to the protein part of the enzyme. The coenzymes make up a part of the active site, since without the coenzyme, the enzyme will not function. example coenzyme A (CoA) usually the electron acceptor
Term
co-factor
Definition
A cofactor is a non-protein chemical compound that is bound (either tightly or loosely) to a protein and is required for the protein's biological activity. flavin or heme are example
Term
Decarboxylase involved in
Definition
Kreb cycle enzymes catalyze the decarboxylation of amino acids, beta-keto acids and alpha-keto acids[1].
for example Pyruvate decarboxylase catalyzes the decarboxylation of Pyruvate
Term
dehydrogenase
Definition
is an enzyme that oxidizes a substrate by transferring one or more hydrides (H−) to an acceptor, usually NAD+/NADP+ or a flavin coenzyme such as FAD or FMN.
Term
kinase
Definition
type of enzyme that transfers phosphate groups from high-energy donor molecules, such as ATP, to specific substrates. The process is referred to as phosphorylation.
Term
fermentation atp net gain
Definition
2 ATP
Term
NAD+ regenerated in fermentation by
Definition
The NADH giving up the electron and H+ to pyruvate to form the fermentation product.
Term
ATP formed in Aerobic respiration is
Definition
formed by oxidative phosphorlation by glycolysis, krebs cycle, and ETS
Term
Produced during kreb cycle
Definition
2 NADH FADH2
Term
role of oxygen in electron transport chain
Definition
o2 is the final electron accept to form H2O as the electrons travel through the electron chain protons are pumped across the cell membrane.
Term
ATPase
Definition
catalyzes the formation of ATP by combining(phosphorylating) ADP(adenosine diphosphate) with inorganic phosphate ions to give ATP
Term
glycolysis is found where
Definition
cytoplasm
Term
electron transport chain is found where
Definition
Cell membrane
Term
Glycolysis and kreb cycle is found in
Definition
cytoplasm
Term
eukaryotes have kreb cycle in
Definition
mitochondria
Term
light reaction needs
Definition
light
Term
dark reaction can occur
Definition
w/ or w/o light at anytime
Term
oxygenic photosynthesis
Definition
non-cyclic phosporalation with oxygen produced.
Term
algea and cyanobacteria are able to carry this out
Definition
oxygenic photosynthesis
Term
Nostoc
Definition
rod shape organism in chain, hetercyst and fix nitrogen. and oxygen we breathe first strated from these bacteria
Term
photosystem
Definition
proton pumpes through membrane and electron actually goes back to the photosystem making it a cyclic system
Term
Organism grows faster in fermentation or aerobic respiration
Definition
Aerobic respiration is better due to energy produced of 34 atp produced compared to 2 atp
Term
difference between aerobic respiration and anearobic respiration
Definition
Aerobic respiration is the complete oxidation of glucose and final exctron acceptor is 02, 34 atp compared to 2 in fermenation. fermentation is partial oxydation of glucose with final electron acceptor being another organism. products of anearobic respiration are ethanol and lactic acid. they both share glycolysis
Term
chemoautorophic bacteria
Definition
inorganic energy sources. Most are bacteria or archaea that live in hostile environments such as deep sea vents
Term
chemoautotrophic bacteria
Definition
gain energ by oxidizing inorganic compounds. elements are Fe2, Sulfur, H2S.
Term
sulfur-oxidizing bacteria
Definition
important in symbiotic relationship the surlfure-oxidizing bacteria are found inisde and the worms bring h2s and o2 to provide energy for the worm
Term
oxygenic photosynthesis bacteria
Definition
cyanobacteria
Term
anoxygenic photosynthesis bacteria
Definition
purple bacteria, rhodosprillum, chormatum
Term
light reaction of photosynthesis produces
Definition
Oxygen and Atp
Term
dark reactions need
Definition
Require ATP, NADPH,
Term
dark reactions produce
Definition
glucose by calvin cycle
Term
Dark reaction consist of
Definition
Carbon Fixation, Reduction reactions, and ribulose 1,5-diphosphate (RuDP) regeneration
Term
Fred griffith
Definition
transforming principle, which is today known to be DNA,
Term
fred griffith
Definition
The smooth strain (S strain) had a polysaccharide capsule and was virulent when injected, causing pneumonia and killing mice in a day or two. The capsule is a slimy layer on the cells' surface that allows the bacteria to resist the human immune system. The rough strain (R strain) did not cause pneumonia when injected into mice (it was avirulent), since it lacked a capsule. When the virulent S strain was heated to kill it, and then injected into mice, it produced no ill effects. However, when dead S strain mixed with live R strain was injected into the mouse, the R/S mouse died.
Term
Avery,mcleod, mcarty 1944
Definition
dead s. pneunomae break it apart by lysis Avery and his colleagues showed that DNA was the key component of Griffith's experiment, in which mice are injected with dead bacteria of one strain and live bacteria of another, and develop an infection of the dead strain's type.
Term
hershey chase
Definition
use of bacteriophage In a first experiment, they labeled the DNA of phages with radioactive Phosphorus-32 (the element phosphorus is present in DNA but not present in any of the 20 amino acids from which proteins are made). They allowed the phages to infect E. coli, then removed the protein shells from the infected cells with a blender and separated the cells and viral coats by using a centrifuge. They found that the radioactive tracer was visible only in the pellet of bacterial cells and not in the supernatant containing the protein shells.
Term
DNA is
Definition
helical shaped and comped of deoxyribose sugar as strands and phosphate bons that keep these together.
Term
semiconservative dna means
Definition
Semiconservative replication would produce two copies that each contained one of the original strands and two new strands.
Term
Dna polymerase bind at this site
Definition
to DNA at origin site.
Term
to replicate DNA
Definition
Dna polymerase bind to dna at origin site, dna molecule fits right into the grooves becasue of its shape and hydrogen bonds break, strands are kept seperated by use of single strand binding proteins, Dna helicase(gyrase) unwind DNA ahead of Dna polymerase to get rid of tosional tension, Dna polmerase(primase) intitial start dna replication
Term
Single strand binding proteins
Definition
come into play by keeping strands seperated
Term
DNA helicase(gyrase)
Definition
unwind DNA ahead of Dna polymerase, actually cuts and flips dna and put its back together so dna is in straight line
Term
What nucleotide bases are easiest to replicate
Definition
Origins tend to be "AT-rich" (rich in adenine and thymine bases) to assist this process, because A-T base pairs have two hydrogen bonds (rather than the three formed in a C-G pair)—strands rich in these nucleotides are generally easier to separate due to the few=flexibilty/many=durability relationship found in hydrogen bonding.
Term
DNA Polymerase
Definition
"reads" an intact DNA strand as a template and uses it to synthesize the new strand. The newly-polymerized molecule is complementary to the template strand and identical to the template's original partner strand. Codes from a 5' end to 3' on leading strand
Term
Dna replicates at this end
Definition
DNA polymerase can add free nucleotides to only the 3’ end of the newly-forming strand.
Term
Laggin strand
Definition
gaps where dna is not copied 5' to 3'
Term
how Laggins strand is copied
Definition
Also needs to have 5' to 3' and Rna polymerase lays down RNA primer then DNA polymerase comes in to lay down dna from the RNA fragments. Then DNA ligase links the fragments together
Term
Leading strand
Definition
Leading strand of continues replication 5' to 3' direction
Term
DNA ligase
Definition
connect Po4 to hydroxyl when runs into new strand after exonuclease replaces RNA w/ DNA then 5' and 3' join together
Term
exonuclease
Definition
replaces RNA w/ DNA
Term
Eukaryotic things have this to make DNA replication run faster
Definition
multiple sites of Origin to allow DNA to be copied faster
Term
Every replication the chromosomes
Definition
get shorter
Term
Telomerase
Definition
repeats ("TTAGGG" in all vertebrates) to the 3' end of DNA strands in the telomere regions, which are found at the ends of eukaryotic chromosomes. adds telomere each time
Term
telomere
Definition
A telomere is a region of repetitive DNA at the end of a chromosome, which protects the end of the chromosome from destruction.
Term
cells that constantly divide
Definition
sperm, white blood cells, cancer cells
Term
Proof reading dna
Definition
Makes a mistake and moves about 1,000 bases a second, WHen a mistake is made DNA polymerase goes backward to fix it.
Term
Direction exonuclease activity runs and why
Definition
3'to 5' to elimnate bases until it feels right and goes forward again
Term
transcription
Definition
copying
Term
messenger rna
Definition
working copies of a gene
Term
Gene expression / protein syn
Definition
dna, transcrption, messenger rna, translation, to protein
Term
how to write out gene name
Definition
Italisized or underlines with 3 letter designation
Term
Gene
Definition
sequence of DNA that codes for a protein or trait
Term
DNA
Definition
double stranded made of deoxyribose
Term
RNA
Definition
single stranded, nucliotide of ribose, No T's in RNA and replaced with U's, functional working copy
Term
RNA polymerase
Definition
makes transcription enzyme and looks for start of the gene
Term
start of the gene
Definition
promotor region
Term
Single strand binding proteins
Definition
Protein that binds to single-stranded DNA usually near the replication fork to stabilize the single strands.
Term
sense strand
Definition
dna of trait needed
Term
Summary of Dna Replication at the fork
Definition
enzymes unwind the parental double helix, proteins stabilize the unwound parental DNA, the leading strand is ynthesized continously by dna polymerase, the laggin strand is synthesized discountinously. and rna polymerase synthesizes sshort rna primer, which is then extended by dna polymerase and dna polymerase digest RNA primer and replace it with dna, dna ligase joins the discontinous fragments of laggin strand.
Term
promotors are
Definition
full of a's and t's and are promotor sequence that are 10 sequence from start and 35 from the start.
Term
Sigma factors
Definition
factors that enable rna polymerase to bind to specific promotor sites
Term
transcription factors
Definition
transcription factor is a protein that binds DNA at specific sites where it can regulate transcription.
Term
cimplementary base pairing between sense strand of dna and resulting messenger RNA
Definition
3' ATGCAT to 5' UACGUT
Term
Primase
Definition
adds a short piece of RNA called an RNA primer at which DNA can synthesize the 3 prime end
Term
Rnase
Definition
removes RNA primers and leaves a gap that is filled by DNA polymerase
Term
Three processes in transcrption
Definition
Initiation, Elongation, termination
Term
intiation
Definition
The RNA polymerase binds to promotr site and replicates at the 3' end
Term
template strand
Definition
serves as one copy for transcription and RNA has a complimentary strand to this
Term
elongation
Definition
forms a bubble and rna polymerase adds bases to 3' prime end of growin rna transcript and continues until it hits a terminator site
Term
terminator site
Definition
at this site rna polymerase and new rna transcript are released from dna, and can occur for self termination, and enzyme termination
Term
self termination
Definition
the rna sequence transcribe at the terminator makes it bind to hydrogens to itself making a loop structure pushes rna polymerase of dna
Term
enzyme dependant determination
Definition
a termination protein enzyme binds to terminator releasing rna polymerase
Term
translation
Definition
uses a mRNA to synthesize a protein, ribosomes read along a mRNA reading the genetic code to aminoa acid sequence in the protein and in bacteria can happen before transcription is completed
Term
Codons
Definition
64 three letter words and genetic code. and 61 of 64 code for genetic material and 3 of 64 code to stop translation
Term
start codon
Definition
shows where to start the translation to the tRNA
Term
Start codon needs
Definition
Anti codon on each tRNA is complimentary to the Codon on the mRNA in translation
Term
tRNA
Definition
goes from sequence to sequence to to create the polypeptide site,
Term
A or amino acid site of tRNA
Definition
amino acid site hold new tRNA with new amino acid attached
Term
E site allows
Definition
used tRNA to exit from ribosome
Term
Stop codon
Definition
a protein called release factor binds in a site and new rna and polypetide are released, the ribosomes are recycled to continue the process
Term
operon in bacteria
Definition
promotor, operater, structural genes
Term
structural genes
Definition
transcribed into mRNA
Term
operons need
Definition
inducer while repressible operons are always to be able to transcribe
Term
control region
Definition
promotor, operator region
Term
lac operon
Definition
is an induced operon meaning genes are not really transcribe but induced to produce the proteins of catabolism when present in the cell
Term
lactose produces allolose that
Definition
blocks the repressor and alows for transcription of lactose
Term
regulatory gene produces repressor until
Definition
the lactos or co repressor is present in the cell letting transcription take place
Term
repressor proteins
Definition
create a block on the operator preventing Rna polymerase from going
Term
inducer and example
Definition
inducer inactivates the repressor and example for lactose is allolactose
Term
bacteria transcription occurs
Definition
cytoplasm and transcription and translation can occur at the same time
Term
In eukaryotes
Definition
transcription occurs in Nucleas and messenger rna leaves through nuclear pores
Term
Rna in eukaryotes has sequences that
Definition
code for nothing to interrupt gene sequence.
Term
removal of lactos from around cell
Definition
the repressor stops RNA transcrption
Term
Repression
Definition
the Rna polymerase constantly produces its gene of tryptophan. the regulatory gene produces repressors that are inactive until too many tryptophan are produce that induce the repressor to bind to the operator stoping RNA polymerase
Term
induction
Definition
uses for ex. allolase as an inducer to the lac operon because the repressor is always attached to the operator region. When the lactose is in the cell its allolase inducer binds to the repressor making a substance to break down lactose. The lactose must be present to knock off the repressor
Term
framshift mutations
Definition
Term
basesubstitution mutations
Definition
when a single nucliotide substitutes for another. nonuse mutation, silent mutation, missuse mutation
Term
missuse mutation
Definition
single amino acid substitution can be harmful, beneficial, or nuetral
Term
silent mutation
Definition
just a change in base pairing and nothing is affected
Term
nonsense mutation
Definition
changes codons to make a stop codon which causes early termination of the protein and can be very harmful
Term
framshift mutation
Definition
nucliotides are inserted into or removed from dna sequence, lead to non functional proteins
Term
framshift insertion
Definition
one or more bases added to dna sequence and cause non functioning protein
Term
framshift deletion
Definition
one or bases are removed from dna squence cause non functioning protein
Term
chemical mutations
Definition
mutation are called mutagens. Most of them are also carcinogens.
Term
uv light mutations are by
Definition
UV light can induce adjacent thymine bases in a DNA strand to pair with each other, as a bulky dimer.
Term
radation mutagens
Definition
ionizing radiation xrays and gamma rays cause molecules to lose electrons becoming free radicles and highly radioactive to combine to bases on dna and result in errors and can react to phosphate backbone causeing breaks.
Term
non ionizing radiation
Definition
cause thyamine dymers to attach to one another and prevent cell from copying dna
Term
chemical mutagens
Definition
nucliocide analogs, different base pairings and come incorporating into dna and cause dna to not be able to be copied later, nitrous acid can cause adinine bases to pair to cyctocine bases, cause small insertions or small deletions, acridine, benzopyrine = from soot and smoke
Term
biological mutation
Definition
mutation of DNA during replication
Term
horizontal gene transfer
Definition
conjugation, transformation, transduction
Term
competent bacteria
Definition
are able to pick up dna from their environment and are stapholococcus pnumonia and ecoli(through lab work)
Term
transformation
Definition
bacteria is able to pick up dna from its environment. rough live and dead smooth come together to kill the mouse showing they incorporate from environment.
Term
transduction
Definition
a virus(bacteriophage) injects dna into the bacteria to replicate new viruses and the bacteria is transferred into the new virus being produced this virus then goes and infects bacteria and its dna is incorporated into the bacterias dna causing recombination.
Term
control of gene expression
Definition
negative control = repression
Term
A or amino acid site
Definition
holds new tRNA with amino acid attached
Term
p or polypeptide site
Definition
hold previous tRNA with growing polypeptide attached
Term
avery
Definition
Avery and his colleagues suggest that DNA, rather than protein as widely believed at the time, may be the hereditary material of bacteria, and could be analogous to genes and/or viruses in higher organisms
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