a metabolic pathway

building up of biological molecules, produce complex molecules that cytoplasm is made of, consume energy in the form of ATP

release energy that is used to produce ATP

involved in breaking down of complex molecules to yield simple molecules that the cell can use as synthetic raw material

the catalyst of biochemical reactions (specific to substrate it acts on-lock and key model)

most are proteins

a typicla enzyme can make a reaction go 100 million times faster

impairment of just one can cause Xp

cannot make an unfavorable reaction occure-destabilizes chem bonds in substrates, promotes formation activated complex (state between substrates and products)

catalytic site

usually a pocket or cleft where substrates bind

functional groups on amino acids that surround the active site bind the substrate molecules-encourages of new chemical bonds leading to the formation of the product

in medium (outside cell): exoenzymes-secreted, help digest large molecules (starch) to release smaller molecules (sugar) the cell can absorb, some exoenzymes are toxins-disease causers

Embedded in cytoplasm membrane: involved in respiration, some pump ions across mmebrane, otherse pump nutrients in and waste out, or cause metabolic canges inside due to outside signals

in the cytoplasm of bacterial cell: over 1000 different enzymes, synthesize aa, protein, nucleoties, nucleic acids, sugars, etc, or break down nutirents to simple compounds producing ATP

Hydrolytic enzymes

lipase: digest fats

amylase: digest starch

gelatinase: digest protein

1) substrate binds enzyme at activation site

2) flex of enzyme produces strain/distortion of chem bonds found in substrate

3) substrate chem changed into product

4) product released

5) enzyme emerges unchanged ready to bind another molecule

hydrolysis (catabolic)

ex: lipase (break down lipid molecules)

lactose+H2O=Galactose+Glucose

rearrangement of atoms within a molecule (catabolic or anabolic)

Ex: phosphoglucoisomerase-> converts glucose into fructose during glycolysis

joining of 2+ chemicals (anabolic)

ex: acetyl-CoA synthesis (acetate+coenzyme A = acetyl CoA for kreb cycle)

splitting a chemicals into smaller parts without water (catabolic)

ex: fructose-> G3P and DHAP during glycolysis

transfer of e- or H atoms from one molecule to another

ex: lactic acid dehydrogenase (lactic acid oxidized to form pyruvic acid during fermentation)

moving functional group to another

molecule (may be anabolic)

Ex: hexokinase (transfer phosphat form ATP to glucose in glycolysis first step)

6 steps

humans lake the enzyme to make methionine so must consume methionine in diet (also folic acid for women)

has feedback inhibition from formed products

simple: chain of aa

conjugated: proteins + added organic or inoganic moleucles that are closely associate with the protein

can make biochemical reactions progress faster by reducing activation energy barrier by stabilizing transition state

DO NOT

change nature of reactants/products

change chemical potential energy of substances

change free energy of a reaction

make unfavorable reactions favorable

adenosine triphasphate

bonds between phosphates unstable w high chem potential energy

energy released when ATP looses a phosphate (forms ADP)

Drives unfavorable biosynthetic reactions

cell stores energy by trapping energy from catabolic reaction and using it to attach a phosphate to ADP

cell uses for: substrate activation, power cellular motion and pump ions/other molecules across membrane

1 of 2 ways cells make the most of ATP

-energy to form high energy phosph-anhydride bond comes from hydrolysis of higher energy bond

a phosphate group is being added to ADP to make ATP and cell must form a metolic intermediate that has very high energy bond joining the phosphate group to an organic coupound before SLP occurs

the second way cells make the most of ATP

(H+-ATPase)

-uses potential energy of proton motive force. (chemoosmotic theory or oxidative phosphorylation)

requires there to be an intact membrane separating tow comparments of differing proton concentrations, can be established by using chemical reactions of respiration via e- transport chain (redox reactions pump H+ across resultin in electrical charge across membrane)

=oxidation-reduction

reduction=gain of e- (becomes more -)

add 2 H or remove an O

(oxidation is the opposite)

add O or remove 2 H

chemoheterotrophic organisms use redox to make energy

both enegy and C derived from organic compounds

aerobic, anaerobic respiration, and fermentation

achieved by 20 discrete steps allowing energy to be released slowly to be efficiently utilized by the cell

glycolysis, Kreb, and e- transport chain pathways

(difference between fire and the cell: fire released unctontrolled, high ignition temp and dry fuel, uses cellulose a polymer of glucose)

Glycolysis branches off into either after producing   2 pyruvic acids

respiration: kreb cycle and e- transport chain

fermentation: pyruvic acid used for formation of products

glucose (10 steps) 2 pyruvate (C3H4O3)

"partial oxidation" activated by attachment of two phosphates to form fructose-1,6-bisphosphate

2 ATP required to start

4 ATP produced substrate level phosphorylaation   (2 ATP net gain)

2 molecules NAD+ reduced to 2 NADH and 2 H+

Tricarboxylic acid cycle or citric acid cycle (pyruvate dehydrogenase reaction)

8 reactions resulting in oxidation of 2 pyruvate to 6 CO2

8 NAD+ reduced to NADH + H+

2 FAD reduced to FADH2

2 ATPs made by substrate level phosphorylation

oxidative phosphorylation= series of redox inolving membrane bound enzymes and e- carriers that result in

the reoxidation of NADH + H+ back to NAD+

reduction of O2 to H2O and the production of 34ATPs per glucose

yields Proton Motive Force sufficient to produce 3 ATPs per NADH oxidized at 2 ATPs per FADH2 oxidized

mitocondria in eukaryotes and cytoplamic membrane in bacteria

NADH + H+ is oxidized to NAD+

electrons passed between carriers and protons pumped across the membrane

oxygen reduced to H2O, in aerobic respiration oygen is terminal e- acceptor. Protons flow through ATP synthase and generate ATP from ADP + Pi

oxidation of glucose to CO2 and H2O

uses glycolysis, krebs cycle, e- transport chain and oxidative phosphorylation

yields 38 ATPs per glucose molecule

created by e- transport chain

used for ATP synthesis

active uptake of nutrients

ion pumps

flagella rotation

sufficient to produce 3 ATPs per NADH oxidized and 2 ATPs per FADH2 oxidized

NADH + H+ is still oxidized back to NAD+ using membrane bound e- transfer chain

Terminal e- acceptor not O but instead some oxidized mineral (if proper mineral present bacteria can use respiration to produce energy in absense of air)

PMF generates ATP, can generate 36 ATP per glucose

ATP generated by substrate level phosphorylation

terminal e- acceptors are organic compounds

anaerobic and no light required or oxidized minerals, inefficient, extracts only a fraction of potentail energy in the food molecules

2 ATPs per glucose, lactic acid and ethanol fermentation

glucose partially oxidized to pyruvate (glycolysis)...NADH oxidized back to NAD by reduction of pyruvate to lactic acid

yield 2 ATP per glucose

made by a variety of bacteria (some used in cheese and yogurt production and tooth decay)

glucose->pyruvate via glycolysis

pyruvate decarboxylated to yield acetaldehyde. NADH oxidized back to NAD by reduction of acetaldehyde to ethanol

yield 2 ATPs per glucose

made by bacteria and fungi, especially yeasts

biproduct CO2

made in mixed acid fermentation by many bacteria also by Acetobacter and Gluconobacter wich produces vinegar which is a two step process.

1) yeasts are used anaerobically to produce ethanol from sugar

2) Gluconobacter/Acetobacter used to aerbically partially oxidize ethanol to acetic acid

photosynthesis

energy from light, carbon from CO2

oxygenic (water) and anoxygenic (H2S)

generates ATP (convert CO2 to sugar) & NADPH (reducing agent)

photosynthesis-dark reaction

fixation of C both photoautotrophic and chemoautotrophic (sugar from CO2 requires ATP-energy and NADPH-reducing)

require some reduced compound + some oxidized compund as starting material for redox

yields energy so ATP and NADPH can be made

Used to assimilate CO2

hydrogen sulfide oxidation (H2S is the reducing agent)

uses e- transport chain proton gradient

(deep ocean volcanic vent and tube worms)

fix CO2 using RuBisCo-type enzyme (calvin cycle)

either with or without O2

can use NO3-

DNA to 2 DNA

(DNA reproduction)

mRNA

synthesis of RNA

(DNA=1RNA strand)

(info in mRNA synthesizes a protein)

synthesis of a protein converts info in a nucleotide language into the aa language

G-C

T-A

Helicase-separates strands of old DNA

single-strand binding protein-keeps apart

Primase-makes short RNA primers

DNA polymeraseIII-adds nucleotides to end of primer

DNA polymerase I-removes primers (fill gap)

DNA ligase-joins DNA pieces

DNA gyrase-controls super twisting

DNA topoisomerase- same as above

copy of info in a gene needed to direct synthesis of a protein (sequence of nucleotides making up codons that will code for aa that will link to make a protein)

single stranded

quickly degraded

structural part of ribosome

ribosome=complex enzyme that synthesizes protein

more stable than mRNA (covered in ribosomal proteins)

regions of double stranding (hairpin-like structures)

brings correct aa into ribosome and positions it in place so the protein strand can grow

clover leaf structure (formed by hairpin formation)

one loop contains the anticodon-segment that complements specific codon in mRNA (64 total)

specific aa on acceptor arm

D-loop/TyC loop bind specific charging enzymes that attach the aa

UAA, UAG, UGA

the 3 nonsense codons

(all the rest are sense codons - 61)

universal

triplet code

64 codons

unambiguous (CUU is always Leucine)

degenerate (6 codons specify Leucine)

not punctuated

stable change, permanent and rare

passed on (inherited)

produces genotypic change

some cause phenotypic change

result of DNA base pairing error in replication

missense mutation: encode diff aa, inactivate the enzyme

nonsense mutation: encodes early stop codon, eliminates enzyme

neutral mutation: minor, no effect to enzyme (change encodes same aa)

uptake of naked DNA

DNA released from donor strain by lysis of dead cell, recipient strain take up the DNA

competent most efficient when size is small

if you shock the  recipient it is more likely to take up DNA

direct cell to cell contact

narrow cytoplasmic bridge, donor cell stays alive, donation of one copy to recipient, use of plasmid F-pilus and sex pilus

F+ strain -copy of F plasmid in cytoplasm (e-coli)

HFT strain-F factor integrated in chromosome

DNA from donor incorporated into a defective virus partical (transducing phage particle) that attaches recipient and injects DNA

Death of donor strain

DNA from donor must integrate into the genome of the recipient

1) autonomous replicon, copied within the host cell and passed to future generations

2) integrates into host chromosome by homologous recombination, crossing-over, must be similar

3) integrates into host chromosome by transposition

bacterial genes organized into physically linked coordinately expressed groups

regulate gene expression

lactose

if lactose then small amount of allolactose

if no lactose the lac repressor protein binds the operon and blocks transcription,

when lactose is present allolactose binds receptor and inactivates it

aa tryptophan synthesis

high tryptophan in cytoplasm represses trp operon.

trp repressor protein is inactive in the absense of tryptophan

prevent the growth of bacteria but wont kill

protect the product but not kill the product

add salt instead of incineration to meat

example is refrigeration

species of microorganism

material protecting

biological factors (age of cells, size of population)

environmental (storage temp, pH, water activity, presence of organic matter)

used in aquarioums and on instrument/lab bench surfaces

causes damage to DNA that increase the frequency of potentially fatal mutations

gamma ray or x-ray

used on food(strawberries, beef, poultry)

less effect on tast vs heat

used on inanimate objects

selective toxicity

good solubility in H2O

stable at room temp

toxicity at room temp

capacity to penetrate

non-corrosive

non-staining

non offensive (smell)

denature protein and disrupt cytoplasmci membrane structure but are weak and mostly just act to help clean a surface

detergent-synthetic derivative of fatty acid (more soluble in H2O-less likely to leave soap scum)

surfactants (reduce surface tension of H2O and increase solubility of oily particles)

soap-salt of fatty acid

selective toxicity

microbicidal

soluble in H2O

potent

stable

unlikely for microbial resistance to develop

complements host's defenses

not inactivated by other metabolites

does not casue allergies

does not increase host susceptibiltiy to further infection

inhibit enzymes one way or another

(antibiiotics kill those important only to the bacteria)

inhibit:

peptidoglycan (cell wall)

translation by 70s ribosomes (protein synthesis)

folic acid biosynthesis

RNA polymerase or DNA polymerase

disrupt cell membrane

binding protein is a bacterial enzyme that forms the peptide bond that cross-links one aa side chain in peptidoglycan to another peptide chains

Penicillin the drug acts a competitive inhibitor of this enzyme

(beta lactam drugs)

competitive inhibitors of penicillin binding proteins

inhibit folic acid synthesis

structural analog of PABA and competetive inhibitor of enzyme that converts PABA to dihydrofolate

1) produce an enzyme that degrades/modifies the antibiotic. genes often located on plasmids (transferable)

2) alter pore protein may slow diffusion of drug into cell

3) gene for drug receptor mutated so receptor no longer binds antibiotic

4) resistant cell alter metabolism so can by-pass inhibited step

5) resistant cell aquire a gene for active transport protein that pumps antibiotic out of cell using ATP (can be found on plasmid/transposon)

lowest concentration of anitbiiotic to inhibit a pathogen

low MIC indicates potent drug

Kirby-Bauer test-used to predict effectivness of antibiotics in treatment of patient

toxic dose/effective dose

the higher the result the safer the drug

low indicates smaller margin of error as try to give enough to kill the infectious microorganism but not enough to hurt host

are eukaryotic organisms so have 80s ribosomes not 70s so antibiotics inhibiting 70s wont work...

they also dont have cell walls of peptidoglycan so penicillins and cephalosporins wont work either

(most drugs that will work have toxic side effects and low therapeutic index)

harder b/c inside cell

must inhibit certain enzyme found only in that virus

occurs in th food processing plant or later

botulism in improperly canned food

protein (C & N source also casein, immunoglobulins)

carbohydrates (lactose)

lipids (butterfat)

vitamins (B, A, (D added))

minerals (calcium)

trace elements

water

pH 7

isontonic salt concentration

form of heat treatment

does not kill all the microorganisms in the product like sterilization would

temps below 100celcius used

(Milk: 63 c for 30 min or 72 c for 15 seconds)

used for beer, wine, juice before fermentation step

(juice is pasteruized then incoulated with starter culture to insure consistent production of good wine)

started in 1900s to kill TB in milk

Low temp holding: heated to 62.8 for 30 min

high temp: heated to 70 for 15 sec (flash pasteurization)

ultra high temp: 149 for a few seconds, well above boiling...no refrigeration of product till it is opened...loss of nutrients and taste and is more expensive than otheer techniques

standard plate count

breed smear

methylene blue test

phosphatase test

acid production: oxidize lactose to produce acid, sour, done to make yogurt and cheese

...

gas production: clostriduim, e coli, yeasts, stormy fermentation: produce acid and CO2 or H2 causing casein to precipitate and produce curds that float from the gas in them or explode

...

Ropy fermentation: produce capsular polysaccharides and grow inlong chains, stringy curds

progein digestion: degrade aa from casein to produce bitter taste, putrifaction, these bacteria are often thermoduric

...

Lipoltic: break down lipids in butter fat, rancid

...

alcoholic fermentation: yeast convert lactose to ethyl alcohol and CO2

...

Sweet curdlers: excrete enzyme rennit, curd form at neutral pH, bittering milk

sugar from barely converted to ethanol by yeast fermentation

Malting: barley moistened to germinate, seed enzymes begin breaking down starch into simple sugars, then grind into powder or malt

Mashing: malt+grains mix with H2O dissolving sugars. ENzymes from seeds still convert amylose to maltose (sugary liquid=wort)

spen grain, remove wart, hops added to wart and boiled

wort cooled yeast added, incubated with air bubbles allowing yeat to grow, then air shut off and anaerobic fermentation occurs

aged at low temp

primary: remove coarse solids

secondary: digestion of solid and dissovle nutrients by aerobic microorganisms

chem disinfection: kill pathogenic bacterial and solids

want to reduce BOD: measure of amount of oxygen used up by aerobic bacterail in water in a 5 day period

imhoff tank: anaerobic, bacteria/archaea bread down organic matter producing CO2 and methane, methane is burnt off for fuel)

indicator organism

small gram- that ferment lactose, non-spore forming and produce acid/gas in 24 hours

always present in large intestine/fecal material

present in large numbers thatn pathogenic bacterial in contaminated water

generally survive in water longer than pathogenic bacteria

easy to cultivate

fecal strptococci

small gram+ cocci found in the intestine

help conversion of an element from one form to another by living organisms and non-biological chem reactions in the the environment (typically invovle redox)

sulfur cycle

nitrogen cylce

carbon cycle

salmonella typhi

shigella dysenteriae/ e. coli

vibrio cholerae

campylobacter jejuni

helicobacter pylori

polio

hep A

rotoviruses (diarrhea)

giardia lamblia (dysentery)

entamoeba histolytica (dysentery)

balantidium coli (dysentery)

crtptosporidium parvum (dysentery)