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GSU / Biology / BIOL 3880 / What is the definition of metabolism in the cell?

What is the definition of metabolism in the cell?

What is the definition of metabolism in the cell?

Description

School: Georgia State University
Department: Biology
Course: Microbiology
Professor: Crow
Term: Spring 2016
Tags:
Cost: 50
Name: Test 1 Study Guide
Description: Chapters 1-3, & 5.
Uploaded: 01/31/2017
18 Pages 46 Views 1 Unlocks
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Chapter 1


What is the definition of metabolism in the cell?



Leeuwenhoek: early microscope development & Hooke a s protist 11674) & selenomonads(1676)

Microdes: can be harmfuldor helpful; ubiquitous Dexiprokaryotes, eukaryotes, viruses : angle

bacteria


What is the definition of growth in the cell?



& archaea

fungi

GROWTH nutrients converted

into newcell materials used to make new cells We also discuss several other topics like What does a mission statement tell you about a company?

METABOLISM

Takeup nutrients

4 transform them

4 expel

•genetic:

transcnption

translation

•catalytic:

biosynthesis

EVOLUTION evolving cells display new characteristics Phylogenetic trees: Show relationship of evolution


What is the definition of evolution in the cell?



Properties of cells If you want to learn more check out What is the formula for finding a rectangle?

DIFFERENTIATIONA

form new cell structures

• ex: spore Don't forget about the age old question of How to increase objectivity?

MOTILITY some are capable of self propulsion

Some Cell Properties

COMMUNICATION using chemical messengers to interact

GENETIC EXCHANGE exchange qenes by different mechanisms

LUCA

BACTERIA

ARCHAEA

EUKARYA

Tots

Li Tgeneration of phylogenetic tree:

Disolate DNA from

each organism We also discuss several other topics like What is the prohibition in congress?

@Make rRNA copies

using PCR

3 Sequence

Sanalyze sequence

5 Gjenerate phylogenetic tree

U Most microbes'habitat is the marine subsurtacel661.) & terrestriar con If you want to learn more check out What are the major themes of hesiod’s theogony?

U humans are no longer dying from bacterial infection bic of vaccines

and antibiotics. No gastroenteritis bic meat is cooked better & handwashing. » 19008 Top 3: Influenza & pneumonia;Tuberculosis; Gastroenteritis

Today's Top 3: Eorteer; Heart clisease; cancer; stroke U Bacteria in the gut breakdown foocl to gain nutrientsproduce gas We also discuss several other topics like What are the four competing philosophies?

U Pasteur:disproved spontaneous generation theory through exps

Dheat non sterile liquid UPRIGHT

microbes and

dust trapped in to sterilize liquid in

- liquid remains -

bend while the S-neck glassware

Liquid couled

Sterile

FLASK TIPPED

liquid contaminated

microbes & dusthave access to the liquid

O koch's postulate

» Isolate blood & pathogen from sick animal. Cynow pathogen

in pureculture. Intect healthy animal wi pathogen. Reisolate pathogen from previously healthy animal & it must be shown

to be the same pathogen from the original sick animal.

> Causative Agent Identification by Koch: Anthrax & TB

O Beijerinck: formulated the ennchment culture technique Dmicrobes

are isolated from natural samples using selective nutrient & incubation conditions to favor a particular metabolic group of organisms. > Meisulated Actobacter cuerobic nitrogen-fixing bacterium)

O Winogradsky: studied nitrifying bacteria & sultur bacteria, showing

that they catalyze specific transformations » Chemolithotropny: oxidation of inorganic compounds to yield energy

"earth eaters" that get carbon from coa » Winggradsky isolated Clostridium pasteurianum lanaerobic

nitrogen fixing bacteria).

si

lifferent

Study Sou

Study Souto

Chapter 2&3

Olight Microscopy: bright field

clarkfield

phase contrast-light passes through cells light approaches to flourescence & surroundings at different

from the sicle &

on rates is scattered by

for to

the specimen

visualization based onlight emission

Inatural or staining) Staining steps:

Smear sample on slide airdry @ Pass Slide lusing tongs & gloves) over flame (fanning motion) © Stain Slide wi crystal violet for 1 min

Add lodine timin) to lock in violet color 5 Decolorire using alcohol (205) © tainterstain using satranın (1-2 min) & visualize using microscope

>Egram(+): purple thick peptidoglycans

>Egram(-): pink tored thin peptidloglycan O Differential Interference contrast (010) Microscopy 1300 Visualization):

polarized light passes through apnism that generates a different beams. The beams pass through the specimen & recombine into I When they enter the objective uns » The beams have clifferent refractive index & are out of phase-> Specimen

appears 3-0.

Ci confocal Scanning Laser Microscopy (320 visualization):

microscope that couples a laser & fluarescent microscope Donly a particular layer within a speamen is in perfect focus aranny

Illuminating one plane & eliminating stray lights from the other planes, Tells in various layers can be observed by adjusting the plane of focus of the laser beam. » Viewer accesses several planes of focus in specimen

sin specimen

d

M Electron Microscopy:electromagnets function as lenses & the whole

system operates iña vacuum. » Transmission Electron microscope (TEM):examine cells & their

Structure at high magnification &resolution, Resolving power > light micro Dwavelength of e shorter than wavelength of visible light a san view structures at the molecular level

Transmission: e-can't penetrate easily. Use stains to visualize external features :

» Scanning Electron Microscopy: Speamen coated within tilmofa

heavy metallex:gold). Electron beams back &forth across the speumen. Electrons scattered from metal coating are collected & projected on a monitor to produce an image.

O Cell Morphology:

COCCUS

ROD

SPIRILLUMI

SPIROCHE TE

BUDDING &r APPENDAGED BACTERIA

FILAMENTOUS

BAC TERJAD . The o Surface Area to volume (SIV) advantages higher for smallest celis

sable to exchange nutrients and wastes withe environment more efficie O tell membrane:surrounds and separates cell fromexternal environment

> Bacteria: strengthened by repanoids (Sterol-like);

minded toglycerol) þesterlinicages lfatty acids bonded to glycerol)

i

l

cell

O-CH2

CHA

P

i

SUOSU

10

PO - CH2

12

DArchaea:lipid monolayers-theatresistant Ino breaks between layer.

Lipidsmay contain ring structures and sugars

Ether linkages between glycerol & hydrophobic side chains

R-C-O-CH2

halk. 60-CH

2

Do

in

Be

to LÀ

V

-o-p-o- CH, NÓ

Q Membrane functions: permeability; transportjenzymatic function

> permeability barrier:prevents leakages. Egateway for nutrients in of waste out. sprotuin anchor:membrane is the site of proteins that participate

in transport, chemotaxis energy conservation: site of generation & dissipation of the proton motive force

o simple transport: driven by energy from proton motive force U ogroup translocation: Chemical modification of substance during

transport lex: phosphorylation), A TP lor similar) is required. s In E.coli phosphotransferase system, glucose enters cell through

transporter & 15 phosphorylated, trapping glucose inside the cell. O ABC (ATP Binding cassette ) Transporter: periplasmic binding up

proteins involved. Energy from ATP. SABC has high substrate binding affinity Deram 1-) Bacteria: uses periplasmic binding proteins

-> periplasm:space between theceu membrane drouter membrane Cyraml+):cloesn't use periplasmic binding proteins bic no space between cell membrane & outer membrane

Llegram(+) Cell wall: 901. Of cell wall is peptidoglycan >technoid acids & lipoteichnoic acid may be present

Daldin 1-1 charge for cell surface w ogram 1) Cell wall: little peptidoglycanın cell membrane (CM)

Large Outer crembrane LOM)

( Lipid A core Polysaccharide-to-specific polysaccharide LPS3 -> Lipid & core can be similar between bacteria, but O-specific

l varies-unique toxins O byrami+) has only.cytoplasmic membrane

Ojrami-) has cytoplasmic membrane & outer membrane Darchaeal twino peptidoglycan &typically no on

cw changes &varies between archaeal type &type of environment »S-layer: used in archaealitypes that have osmotic Stress

-->protects it from osmotic lysis

->transport

Touter layer cell structures: used for attachment & virulence

Dcapsules:firmiy attached to cwinot harmful to you)

Slime layers: 100 sely attached.-> gained or lost dueto environment

r

O Fimbriae: used for attachment using adhesion a Pili (pulus): vinilence ria adhesion genetic exchange

D Endospores:produced by bacteriaduring sporilation.

»Highly differentiated cells that are extremely resistant to heat,

harsh chemicals,& radiation

Sp o rt >survival structures that enable bacteria to endure unfavorable

growth conditions > dormant stage of a bacterial life cycle:

vegetative cell tendospore → vegetative cell D Dipicolinic acid accumulates incore of bacteria when the endospore

15 cteveloping a Sporulation:

DActivation- eyermination outgrowth

D vegetative cell

undergoes assymmetric

Engulfmenta

Spure 3

STAGE I

Cortex

Formation

STAGE TIL

Prespure clevelops cell wall & cytoplasmic membrane STAGE IV

Germination

Spore coat

Maturation & cell lysis

STAGE VI, VI

&

forms

STAGE V

O Flagella: Whipping motion

peritrichous: distribuition of flagella over the body

surface

Aloola slophotrichous: having 2 +

flagella at Iend or both ends

DMonotrichous: Single flagellum

at one end

SD Amphitrichaus: single or multiple

flagella extend from both ends of the cell

mon

O Flagella anchored in CW & CoM:

P » Zring anchor in LPS » Pring anchorin peptidoglycan D4S & Erings anchor in CM & cytoplasm

> Flagellar motor: rotor Irod & rings ) -> basal body Li agliding Motility: slower & smoother form of movement than flagell

> Tyllde proteins anchor and pull organisms -> extend through multiple - layers D themotaxis: "chemo"schemical utaxis" directed movement

s positivermove towards

012

D

o negative: move away

t O Tumble: flagella separated; organism reonents itselftoget to desired

destination tattractant o Run: movement; flagellatogether O Macronutrients for Microorganisms

scarbon (C) 50%. Dhydrogen lnl) Selenium (Se) Doxygen (0) 777.

phosphorus LP) s nitrogen (N)

osulfur(s)

a complex a culture Media

» Complex: a lot of food sources:microbal, animal, plant product digest s Selective: allow some bacteria lor specificone) to grow & notothers

->ex: salt, sugar, alter temp., antibiotics on media. Some bacteria cant

live in these conditions DDefined: know different components & how much of each is needed fora

bacterium to grow (replicate natural environment). Speutic recipe. Deitterential dyedia: indicate specific bacteria using dyes, sugars, etc. D Aseptic technique & plating Ibacteria swabbing on media): Slide 35

Tenapa-3 PPT)

Sad Soup

o latabolism & Energy Classes

ENERGY SOURCE Light

Chemical Photoautotropn | Chemoautotroph

CARBON SOURCE

Organic ù compounds

Photoheterotroph

Themo heterotroon

[ Aerobes: obtain energy in the presence of oxygen O chemotrophs: use oxidation of compounds (chemical energy)

schemoorganotrophs: use organic compounds to get carbon schemolithotropns: use inorganic carbon (Hz. H2S, NH3...)

Phototrophs:convert light chemical energy Energy: capacity to dowork

Free energy loy):energy avallable to do work

in

OLEAST Energy source: oxygen, nitrate, inon, carbon

Catalysts: speed up the rate of areaction by lowering the activation energ sprosthetic groups: tightly bound to enzyme lex: heme)

coenzymes: 100 sely bound to enzymelex: FALO)

EL

o catalytic Cycle:

E + S Substrap Eis complex -

T enzyme enzyme. Substrate

E+ P

complex -

o

û

bindsto

product

o Redox Reactions:

e

REDUCING

AGENTA

• loses e sont

• Oxidized by Y more pos.

OXIDIZING

GENT gainse reduced by X

. more neg.

Reduction potential: determine energetics & likelihood of metaboli reactions » Large 1-) changes in free energy + greater energy release

> Largelt) changes in free energy+more energy required Ogglycolysis:universal process, dore across species. In cytosol.

> 10 Steps (I) Energy investment

(2) Energy payoff

(1) Energy Investment:

• ATP Usedin steps I & 3

hexo kinase (I) & PEK13) enzymes

(2) Energy payoff

• (Step 5: Timenzyme convert DHAP+ GAP)

•Make NADH in Step 6 LUAPDH Enzyme) .myake ATP @STEPS 7 & 10

[17 Cylucose Hexo kina G6Pd Y 3) 007

MS o SUSE ATP: [3] Fructose 6-pt Fructose 1,6-

p

10:22

Decora

PFK

GAPDH

[6] GAP GAPDH 1,3-BPZY

MAKE NADH

MAKE NADH

3

[7] 1,3-BPG Como pinay 3;P-Oglycerate

SMAKE ATP

[10] Pep Pyruvate Pyruvate

kinase

UNAD used as an e-carrier that is recycled to maintain reclox balance

D Oxidative Phosphorylation:

» NADH + H+ transfers 2e-+23+ to complex I (NADH hydrogenase) DFlavoproteins & quinones + accept de- & 231+ but only donate er.

Iron sulfur proteins & cytochromeste only > Comprex I apart of TCAIXreb Cycle: sin mitochondria matrix for

Leukaryotes; in prokaryotes (6) Succinate and Tumarate

lacking mitochondria, TCAIN denydrogenase

(cytosol wl H+ gradient

Succinate

Quinone brings er to complex III

Leaminler IT

Di

olyt c brings e- to complex IV BATP у

DATP Synthase: uses H1+gradient to make ATP as 'Wtenters the cell

Hitenters FO & causes To to rotate, which makes Fz turn, DADP+ Pi +ATO o the synthase can work in reverse if Uitgradient & ATP cunc. A

TO

Stuch SOUD

•ake

turate

geitric Acid Cycle

sin mitochondria matrix ceukaryotes) p pyruvate dehydrogenos acetyl.com t renters cycle Des Remove carbons & release as tos:

isoCitrate socitrato a-ketoglutarate [make NADIP)H]

a clenydrogenase

the a-ketoglutarate

ute denudrocenate sucuny?- cox make NADH D Convert 6-carbon compound Ithrough oxidations &

transformations) backinto oxaloacetate during a

into oxalvacetate during and half of cycle Sir Gopi

2 succinate substrate-level

phosphorylation synthetase obylucose. Catabolism:

Beglycolysis: 2 ATP-> Substrate-level phosphorylation

6 ATP → Oxidative phosphorylation

SATP GDP > Citric Acid: 1 o TP> Substrate-level phosphorylation

Cycle

74 ATP-s ocidative phosphorylation TEATPixa) ISTAN

» Suce

succinyl-Cox

38 ATP per glucose Blog La-ketoglutarate & Koce oxaloacetate are Mitrogen detectors

for cell sbotn serve in metabolism (TCA) & biosynthesis (precursors for amina

acids A

d otto

i isoatrates alyboxylate O eglycoxylate cycle: Isocltrates

1) srly ase

malate synthasen

malate

malate I denydrogenase Oxaloacetate

O chemoorganotrophy: sembor source

e donor organic compound Te-acceptors + bitrate (NO3-)

sulfate LS04) a chemolithotrophy:

Organic e acceptors) De-donors : 712, 7125, Teat, NH4

en acceptors: sulfate (S042-) ?

O2 laenbic respiration) nitrate (NO, -j Sanaerobic

So Oxygen Lainbic)

respiration

anaerobic

so

o Cylucosc 6-p can be used in the Pentose Phosphate Pathway

Dhexose spentose

Dused to make ribosel ueluconeogenesis: formation of glucose from a carbon source

sused in cell wall synthesis

uoglycolysis & TIA cycle intermediates can be used to make amino

acids

Eylycoysis:Alanine, Serines & Anomatic Family DText: glutamate, de aspartate family

O Fatty Acid Synthesis: add ae at a time using Acyl carrier Protein Il Lupid Synthesis: Cy?ycerol + Fatty Acid ONitrogen Fixation; majority of organisms can't do this

Dreduction of N2 + NH3 >> Nitrogenase-a protein subunit

clinitrogenase (reduction occurs here) dintor

= dinitrogenase reductase Dinactivated by On Up »makes ? la the ATP of cellular respiration (approx.) L u

-> 16 A TP from Nitrogen Fixation

D Binary fission:producing generations of cells through cellular grow

Igrowth in number of cells.); parent cell splits in a > Generation time (doubling time):time it takes to go from 1+2 cell

CHAPTER 5 o The Divisome

Studio

» Zip x anchors Fts Z Itubulin-like) ning to EM

DFsts A: aidsin connecting ring & recruits divisome proteins

(actin-like) > Fts proteins aldinpeptidoglycan synthesis BOIVISION septum: synthesis of new CM &Cwmaterial

Openicillinused on grami+) bacteria->taminhibits proteins that

Cross peptidoglycans in cell wall

O Min C, D, & E guide Fts Z to midpoint

DMinelo: oscillating spiral->inhibits division & ring formation Domin E oscillates poletopoze & sweeps Min CID aside to permit

Fts Z binding »Min proteins ensure that cell division is at center point

ng

Ulenome replication: some prokányotes have multiple replication forks

for faster cell division

>bidirectional replication forks seen in plasmid

[lore B clistribution shapes cell structure

DarreB recruits CW synthesizing proteins to specific regions de

Default Shape:cocci (known from Knockout exp.)

possibly

Specitic gene no longer works A Peptidoglycan made of NACH & NAM connections. Autolysins create

gaps between ty & ch for new cell wall material > Bactoprenol interacts wl transglycoslyases in periplasm insert new

CW precursors & catalyze glycosidic bonds Transpeptidation:peptide cross links between adjacent muramic acid

residues -> Eyram(-) : between DAP & Alanine

Llegrowth Curve: 2.119 TO

P

L ESS to o Lag:turnon parts involved in metabolism used for breakdown » Exponential: exponential growth of organism'lcell #increases) > Stationery: food starts to run out. Law nutrients & alot of

organisms present »Death: no microbial growth bic of lack of nutrients > Optical density: light reflected us. light absorbed toreflect how

many cells there are

Study Soup

» Viable cell counti who's alive? >Turbidity: total cell count.

D Batch culture:grow microbes using a limited supply of nutrients s Exponential growth can't be maintained bic nutrients deplete or

the organism's waste products accumulate D Environment charges continually. Delosed system

o continuous culture: a known volume of fresh medium is added at

a constant rate while an equal volume of spent culture medium is removed at the same rate > In equilibrium; growth vessel volume, cell number, nutrient I waste

product status remain constant. & the culture attains steady state,

u Themostat: most common type of continuous culture.

Da device where both growth rate & nutrient can't be transported

into the cell fastenough to meet metabolic clemands »growth rate controlled by dilution rate; cell yield controlled by

concentration of limiting nutrient. ;.

Sorte GAC

Codi 6.)

Microscopic cell count: place x mL of sample on slicle & use grid w/ Known volume per square to count ! » #of cells per unit area of gnd can be counted under the microscope,

giving a measure of the #of cells per small chamber volume. I Aspecial Staining techniques needed to distinguish dead ceris from

live cells DOAPI stains all cells in sample blc it reacts w/ DNA

SUSO

peng

li Bosnia

o Spread Plate crethod:

>Pipette sample onto plate of agar > Spread it evenly over agar surface > Incubate->results: Surface colonies

O Pour Plate Method: This time

> Ripette sample onto sterile plate » Add sterile medium to plate & miwo well wlinoculum > Solidification & incubation

IS

O count by using serial dilutions gives a bettercount, but a higher

risk of lab error such as contamination

s cell count includes live & dead ceus o count using spectrophotometry: measure optical density, how well

light moves through sample & is scattered : > compare to s blank isolution to use the same media to serve as blanc)

How cloudy is sample >Turbidity:totect teltcount cloudiness

Dl Each organism has optimal temp. where they thrive-renzymes

most active, etc. nmin. temp.: transport slows down, organism can't get nutrients Dmax. temp.: organism wil die @ higher temp.

O Psychophile: likes cold temp.

Mesophile: likes room temp. Thermophile; likes hot temp. ->valcanoes, thermalvents, etc. Hyperthermophile:likes extremely hut temp.ex:-88; -10600

188-106°C s

Sporobold

Day To 1932

193) Contos

O Psychrophiles adapt to temp.blc they have cold shock proteins fa

antifreeze proteins. Their CM have more unsaturated & shorter chains

of fatty acids. O Thermophiles | Hypothermophies adapt to temp. blc they have heat

Stabilizing proteins & they produce soltes that aldin resisting unfolding of proteins

Q Acidophiles: grow below 5.5 pH

> 21+ conc.changes canlyse CMIM tolerance is critical) O Alkaliphiles: grow at pH 8 or above

s live in high carbonate soils

some use rat motive forceinstead of PMF

07 Nalophiles: inhabit manne environments & have a Nall requirement

Dhonhalophile: can't survivein salty environments

halotoleranti tolerate some level of dissolved solutes, but grow best

in the absence of the soute Dextreme halophues: grow in very salty environments

( Aerobes:growin presence of Oz

Anaerobes: killed in the presence of Oz Facultative: can grow wlo Oz Microaerophuic: some Oz Sensitinties Aerotolerant anaerobes:can tolerate Oz & grow in its presence (not respuning

storelimination

:

o catalase Test:can a microbe convert hydrogen peroxide into water & Oxyge

'roz can be converted ) 1

H2O2 + H2O2 2H2O + O2

Lunto toxic oxygen ? » Oz can cause oxidative stress on microbe lo

>superoxide dismutase converts superoxide ions-+ peroxide Inot favorable Doecontamination: safe to handle Doisinfect:targets pathogens forelimination

O Heat sterilization: Kill microbes using high heat

DAutoclave (120°C): pressurized Steam

->microbes de all, but they're still present > Pasteurization: controlled heat used to significantly reduce

to total #of microbes in milk +microbial load reduction D Radiation is also used to kill microbes bicit damages ONA

Ionizing kills cells using radicals & damaging ONA.

O chemical controls:

Bacteriostatic:use agent to inhibit growth of microbe, once

agentis removed microbial growth continues

> Bacteriocidal: Kills bacteria->lowers cell viable) count, but

total cell count is stagnant bic the agent kills,

but doesn't remove cells > Bacteriolytici agent that kills & destroys ceus, plummeting

total cell count & viable cell count + Lyse produces toxin do DNA release

Agents that kill organisms end in -cidal. Dagents that inhibit growth end in-static.

OdMinimum Inhibitory concentration (MIC): smallest amount

of agent needed to mhibit growth of organism >test agent boy having series of tubes inoculated wltest organism & a given amount of agent lalso can bedone using solid media) solid media: antimicrobial agent added to disks —discs arranged on inoculated agar plate. Agent cliffusses from discs into agar creating

gradient. The farther the chemical diffuses away from the filter paper, the lower is the concentration of the agent. > Zone ofinnibition: area around bacteria where it hasn't grown

enough to be visible -> large zone of growth innibution + good antimicrobial agent

D Disinfectant: use on surface I may not address spores) QAntiseptic:use on skin

Along wl germicidesnontoxic to animals sterilizers: destroy microbes, including spores Sanitizers: reduce microbial load, but not all

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