Micro Bio Exam 2

Antiseptic

kills microbe but safe for living tissue

Aseptic Technique

to not introduce new microbes

Bactericidal

kills bacteria

Bacteriostatic

inhibits new growth while its present

Degerm

get rid of microbes at a site

Disinfectant

kills but not safe for living tissue

Germicide

lower overall # of various microbes

Sterilant

kills everything including endospores

pasteurization

kills harmful organisms responsible for such diseases

most resistant to least microbes

endospores, protozoan cysts, mycobacteria (resistance to drying out and chemicals), pseudomonas (can use disinfectants as nutrients), naked viruses (nucleic acids surrounded by a protein shell), enveloped viruses, vegetative bacteria

d value

time required to kill 90% of the population of bacteria under specific conditions

critical items

direct contact with tissue, like a needle, needs to be sterile because it is going below the mucus membrane which is sterile

semi-critical

direct contact with mucous membranes, camera for colonoscopy

non-critical

contact with unbroken skin, blood pressure cuff

moist heat

denatures protein, examples include boiling and pasteurization, high temp. short time (HTST), ultra high temp. shorter time (UHT), autoclave which is faster because it is pressurized, not sterile but safe for consumption

filtration

pores need to be 0.2 micrometers for bacteria to be trapped, can’t catch viruses, used for heat sensitive liquids or gases

radiation as a physical germicide

use short energy waves to create ions (ionization) that chop up DNA

ultraviolet wave as a physical germicide

lead to mutations in microbes on the surface of objects

high-level disinfectants

all microbes except endospores

intermediate-level disinfectants

all vegetative microbes and most viruses

low-level disinfectants

fungi, vegetive bacteria except mycobacteria, enveloped viruses

factors affecting choice of a chemical

toxicity, does it get confused by other organic matter that is not dangerous, safe on the material being treated, residue that could still be toxic to tissue, cost and availability, storage, environmental risk

alcohols

antiseptics so its safe for tissue, dehydrate cells when more than 70%, dissolves membranes, does a little protein denaturing

aldehydes

disinfectant, sterilant, inactivates proteins and nucleic acids

halogens

oxidation (takes away electrons) of proteins so they are inactive, chlorine and iodine

ethylene oxide

sterilant used in chemiclave, stronger oxidizer of proteins

metal compounds as germicides

ions slowly leak out and attach to SH group on proteins to inactivate them, not safe to us

phenolics

disinfectant (not safe for tissue), destroy cell membrane and proteins, Lysol

biguanides

affects cellular proteins, chlorhexidine is the most effective, low toxicity, broad range of microbes affected

Quaternary ammonium compounds as germicides

positively charged detergents attracted to bacterial surface and destroy cell membrane, Pseudomonas are resistant

weak organic acids for preservation

benzoic, sorbic, propionic, used for bread, cheese, and juice, interfere with cell membrane of bacteria

nitrates and nitrites

in bacon, prevents endospore germination

lyophilization

freeze-drying, microbes can be revived when water is reintroduced

importance of studying metabolism

products can be useful to humans (ethanol from plants, antibiotics from viruses), can cause disease (products could be toxic), use different substrates making bacteria unique, target or antimicrobial therapies using bacteria specific pathways

catabolic pathways

breaking down “food” and harvesting its energy to make ATP, also produces precursor metabolic for biosynthesis

anabolism

use energy and percussor metabolites to synthetize polymers into cellular structures (macromolecules) needed to survive

metabolism

sum of total of all catabolic and anabolic reaction

radiant energy

sun energy harvested by plants and bacteria to synthesize organic compounds

chemical energy

energy in the form of organic compounds

enzymes

specific to each step in a pathway, turns one substate into one product (final or intermediate), proteins, forms or breaks bonds or transfers electrons between atoms by bending, can be reused because they are not altered when catalyzing a reaction

cofactors

non-protein component associated with the active site of the enzyme, promotes or facilitates enzyme function, metal ions such as magnesium which is needed for DNA and RNA polymerase

coenzyme

organic cofactor that acts as carriers of molecules or electrons, most are synthesized from vitamins

allosteric regulation of enzyme activity

positive and negative effectors that bind to the allosteric site, end product can be the inhibitor and detaches when concentrations are too low, allosteric inhibitor or activator changes the enzyme shape, the first enzyme in a pathway is usually affected

non-competitive inhibition

inhibitor that binds to a site that is not the active site, reversible includes allosteric inhibition, non-reversible (mercurochrome) forms a covalent bond between the inhibitor and enzyme that is non-reversable

competitive inhibition

competes with substrate for enzyme active site, plugs the active site because it looks like the substrate (structural analogs), sulfa drugs fill the active site so PABA can not attach and kills the bacteria

oxidative phosphorylation

glucose’s electrons are moved to the electron transport chain to make proton motive force making ATP via NAD and FAD, most used pathway to make ATP

substrate level phosphorylation

ATP is made when an enzyme directly transfers a phosphate group onto ADP, occurs during glycolysis and Krebs cycle

photophosphorylation

producing ATP during photosynthesis from light energy using proton motive force

reduced state

has the electron to donate, reducing agent, NADH, FADH2, NADPH

oxidized state

doesn’t have the electron but is ready to accept one, oxidizing agent, NAD+, FAD+, and NADP+

glycolysis

produces lots of precursor metabolites

aerobic respiration

includes ETC, O2 is the terminal electron acceptor, 4 (2 from glycolysis and 2 from TCA) total ATP from substrate-level phosphorylation, 34 ATP from oxidative phosphorylation

anaerobic respiration

molecular other than O2 is the terminal electron such as NO3- or SO4-2, ATP generated various but is more than fermentation but less the aerobic

fermentation

no ETC, organic molecule such as pyruvate is the terminal electron acceptor, 2 ATP from glycolysis

amphibolic pathways

includes catabolic and anabolic processes, makes precursor metabolites

glycolysis

used in nearly all organisms to convert glucose (6 carbon molecule) to pyruvate, source of precursor metabolites, anaerobic, 2 ATP, 2 NADH, 2 pyruvate, in the cytoplasm of prokaryotic and eukaryotic cells

entner-doudoroff pathway

alternative to glycolysis used by some bacteria, only makes 1 ATP, 1NADH, 1 NADPH (needed for some anabolic pathways), and 2 pyruvates, aerobic

pentose phosphate pathway

use by many prokaryotes concurrently as glycolysis or E-D, starts with 3-7 carbon sugar to make precursor metabolites and some NADPH

TCA, CAC, and Krebs cycle

8 step cycle that oxidizes pyruvate (from glucose) using CoA to make acetyl-CoA, 2 turns, each turn makes 4 CO2, 2 ATP, 6 NADH, 2 FADH2, and precursor metabolites, in the cytoplasm of prokaryotes, pyruvate moves from the cytoplasm to the mitochondria of only eukaryotes, aerobic

electron transport chain

only step to use oxygen, used to generate proton motive force, transmembrane proteins are reduced by NADH but is oxidized when the electron goes to the next protein, outside the cell membrane but in the cell wall in prokaryotes and between the mitochondria membranes in eukaryotes

ATP synthase

enzyme/transmembrane protein that uses energy from PMF to synthesize ATP by forming a channel that the H+ can go back with their concentration gradient

fermentation

keeps glycolysis going (so it can keep producing a few ATP) by emptying NADH to another electron acceptor (not ETC because there is no oxygen), makes acids or gases (lactic acid for food preservation, ethanol in alcohol, acetone)

exoenzymes

enzymes that are created in the cell but their function is outside the cell, break up debris to monomers small enough for them to bring in through active transport

DNA replication

only happens when the cell is ready to divide, passing encoded information to the next generation, each replication fork had a leading and lagging strand(discontinuously synthesized as Okazaki fragments), from 5’ to 3’

Central dogma

theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein

characteristic of RNA

single-stranded polymer of nucleic acid, ribose sugar

regulation of gene expression

depends on environment, low levels of transcription generates little gene product (protein or RNA)

DNA gyrase

enzyme that temporarily breaks DNA strands ahead of the helicase to prevent supercoiling

DNA ligase

enzyme that joins two DNA fragments by forming a covalent bond between the sugar and phosphate of adjacent nucleotides

DNA polymerase

enzyme that synthesizes DNA by using one strand as a template, adds nucleotides to the 3’ end, works in a 5’ to 3’ direction

helicase

enzyme the unwinds DNA that the replication fork, makes the double strand into a signal strand

Okazaki fragment

nucleic acid fragment produced during discontinuous synthesis of the lagging strand

origin of replication

distinct region of DNA molecule at which replication if initiated, can have multiple for large DNA strands

primase

enzyme that synthesizes small fragments of RNA to act as primers for DNA synthesis

primer

existing fragment of nucleic acid to which DNA polymerase can add nucleotides

replisome

complex of enzymes and other proteins that synthesize DNA

tanscription

first step in gene expression, produces RNA

- (template) strand

RNA is copied from this strand

+ (non-template) strand

strand not used for transcription

promoter

nucleotide sequence that RNA polymerase binds to initiate transcription, not translated but required for translation to begin

RNA polymerase

enzyme the synthesizes RNA, always in the 5’ to 3’ direction

sigma (σ) factor

specific part of RNA polymerase the recognizes a specific promoter regions, allows the cell to transcribe specialized genes as need, only on to innate transcription

terminator

sequence at which RNA synthesis (transcription) stops, not translated, tells the polymerase to fall off the DNA and release the RNA

polycistronic message

many coding regions between the promoter and terminator on bacterial mRNA

cistron

coding region

stop codon

on mRNA and stops translation, signals the end of the protein because not tRNA recognize the codon

tRNA

reads the mRNA, carries a specific amino acid

anticodon

sequence of three nucleotides in the tRNA that is complementary and antiparallel to a particular mRNA codon, allow tRNA recognition and binding to the appropriate codon

codon: 5’ AUC 3’ anticodon: 3"‘ UAG 5’

mRNA

RNA that carries the genetic information that is deciphered during translation

polyribosome (polysome)

multiple ribosome can attach to a single mRNA to make multiple proteins at once

ribosome RNA

facilitates joining of amino acids, targeted by several antibacterial drugs

ribosome-binding site

sequence of nucleotides in mRNA that the ribosome first binds to, translation start after the start codon

rRNA

RNA in ribosomes

start codon

codon that initiates translation, first AUG after the ribosome-binding site

untranslated region (UTR)

promoter region, any codons between the ribosome-binding site and the start codon, codons after the stop codon

E-site

where the empty tRNA will exit once it’s amino acid has been connected

p-site

holds the tRNA that carries the protein (peptide) being built, amino acid from the a-site will be joined to the chain in this one by a peptide bond

a-site

where the new tRNA recognizes the next codon and with enter (accepted), the amino acid in this site will be attached to the one in the p-site by a peptide bond

mRNA processing before translation in eukaryotes

cap is added to the 5’ end and a poly A tail to the 3’ end, introns are removed by splicing, transported out of the nucleus to cytoplasm, monocistronic