MCB 3

____ _____ cells are __ ____ than ______(gram negative or positive for options )

is the periplasmic space smaller /narrow in gram positive or negative by abt 20 nm

after the periplasmic space in gram positive cells, we have the ___ ___

gram positive have a ___ layer of peptidoglycan

gram positive, less complex, gram negative

gram positive

cell wall

thick

teichoic acids are present in ___ ____ cells

they interact ____ with _____

they have a ___ ____ ___ which allows for the embedding in the ___ ____

teichoic acids are found in ____ which are found in a. thin layer in the _____

gram posiitve

covalently peptidoglycan.

fatty acid tail, plasma membrane

peptidoglycan, periplasma

which type of gram do you find fewer enzymes in

in the periplasmic space, there are enzymes involved in ___ ____ _____

overlapping layers of peptidoglycan

lipoteichoic acid is good for anchoring ____ to the ____

lipoteichoic acid carries a ____ charge, can act as a ___ ____ to…..

anything up to what kiladoltan can come in

gram positive

cell walll synthesis

peptidoglycan , membrane

negative, can act as a physical barrier preventing things from entering cells

25,000

gram negative

they vary from ___ to ___ nm

____ takes up 20-40 percent of the cell

after the periplasmic space, wa have the ___ ____, which has an inner leaflet and outer leaflet

the inner leaflet has the same ____ in the plasma membrane

the outer membrane is made up of ___

30-70nm

periplasmic space

outer membrane

phospholipid

lipopolysaccharide

there are more enzymes in the periplasmic space for gram ____ than posiitve

enzymes here are involved in ____ ___, ___ ____, enzymes can also hydrolyze them and neutralize them

Braun’s lipoprotein is the most ____ protein in the outer membrane. It’s embedded in the ___ leaflet of the outer membrane and peptidoglycan anchors the outer

what are porins

they allow gram negative bacteria to have more options than gram positivee

negative

nutrient acquisition, toxin modification,

abundant protein, inner leaflet

channel proteins only in gram negative bacteria that allow substances to pass through via facilitated diffusion and active transport across the outer membrane /concentration gradients

3 components of LPS, what are they

explain what each portion that both of them do

lipid A, core polysaccharide, and O antigen

composed of 3 parts: lipsd A-inner most part of LPS, portion that embeds with the inner leaflet lipids

core polysaccharide, smaller part of LPA, connects lipid A to O antigen

the most external section and biggest=O

what is lipid A made up of

what does this help to maintain?

what is the core polysaccharide made up of , around how many, what’s an example of a sugar that would be found here

what Is O antigen made up of, how many, repeating sets of sugars

lipid A: made up of 2 glucose sugar derivatives, 3 fatty acids, phosphate or pyrophosphate

structure and integrity,

sugars, around 10, slightly unusual sugar, might find heptose,

O antigen-made up of sugars, up to 200 sugars, repeating sets of sugars

LPS importances

which part of LPS is responsible for stabilizing the outer membrane structure

____ ___ is sticky and aids in the attachment to surfaces and biofilm formation

LPS contributes to negative charge on cell surface

helps stabilize outer membrane structure, job of lipid A specifically

helps with attachment to surfaces so org can

polysaccharide portion

creates a permeability barrier

prevent host cell immune response

protection from host defenses,

some can modify sugars that are found in O antigen

when host detects gram negative, it amounts an immune response to the O antigen or sugar that it’s seeing

what happens if you can change the O antigen

what is another big importance of the LPS system, due to which part of the LPS

when you treat infection that is gram negative, you don’t want to treat with smth that will cause enzyme to ___ bc lipids will be _____ and acts s an endotoxin

ONLY IN GRAM NEGATIVE

other orgs can’t use it’s immune response correctly allowing the bacteria to escape the immune response

acts as an endotoxin-toxin that is found inside the cell,

lipid A: when lipid A is carried into peptidoglycan, does not trigger septic response, when cell is lysing, it triggers it bc lipid A carries the dangerous lipids

lyse, released

with porin proteins in E.coli for example

they are ____ permeable than plasma membrane due to the presence of porin and transporter proteins

more

do gram posiitve have an outer membrane, if not what is the most external facing layer of the cell

in GP, the peptidoglycan has ___ ____ throughout it’s matrix

gram negative has systems for facilitated diffusion and ____ ____ to move things against concentration

gram neg also havs ___ and ____ ___ in the outer membrane to transfer molecules into the periplasmic space

no, cell wall

large pores

active transport

porin, TonB

__ ___ secretion systems are ____ and specialized type secretion systems and are associated with gram ___ bacteria

they have two domains, the ____ and ___ domain

domain inserts itself into the _ ___, translocates to and then is released

Type V, autotransporters(transport themselves), negative

passenger, barrel domain

barrel domain inserts inteself into outer membrane and then is released

passenger domain is the actual space where the thing that needs to get out sits

for gram positive gram stains, their ___ layer of ___ traps ____t, when adding alcohols you ____ the cells with shrinks the ____ and ___ them shut so crystal violet can’t get out

for gram negative gram stains, have an ___ _____ layer, some crystal violet sticks here, alcoho ____ the _____ out of outer membrane lipids

gram positive-thick, peptidoglycan, violet, dehydrate, pores, seals

outer membrane, crystal violet, pulls, violet

study question, similarities and ddifferences between gram positive and gram negative cell walls

gram posiitve contains ___ ___ in their cell while gram negative does not

____is only present in gram __

____ interacts with plasma membrane so the cell ….

gram ___ has a smaller ___ space

teichoic acids

LPS, negative

techie acid, doesn’t go floating out into space

positive, periplasmic space

blank and blank contribute to the motility of bacteria

what are the three layers thet you might have around a cell wall

flagella, pili

capsule, surface array layer, and slime mold

blank is the most common appendage

do all bacteria have it

they can differentially express their flagella in response to ___

the blank allows it to spin

it’s blank and blank, also a blank

flagella-locomotion

no

enviro

motor

thin and hollow, spiral

note, but don’t memorize: salmonella enteric can only have petrichou’s flagella

spirillum volitions always have polar flagella

salmonella enteric can only have petrichou’s flagella

spirillum volitions always have polar flagella

define

monotrichous, polar flagellum, amphitrichous, lophotrichous, and peritrichous

monotrichous-one flagellium

polar flagellum-F at end of cell

amphitrichous: one F at each end of cell

lopotrichous-cluster of F at one or both ends

peritrichous-come off everywhere on cell surface, surround surface of the cell

what are the three parts of bacterial flagella

blank is the blank and most blank part of flagella

blank is the most blank part, also a blank to the cell envelope

blank protein is a blank coupler, blank sits inside the blank, allows for connection to the bank

from TEM image-3 distinct components

filament, longest, obvious

basal body, internal part, anchor F

hook protein, flexiblee, filament , hook, basal body

gram negative flagella vs gram positive flagella

WHAT are the 3 rings function

is gram negative more or less complex than gram positive and why

P and N is always more ___ which is important for ___

there are also subunits of…

the basal body is embedded in the ….

how many rings are embedded between diff letter of the cell envelope

where is the P line, MS ring, and C ring found/embedded in

which ones actually spin around to support motion

remember that hook must be wider thane element and remember that the central shaft is hollow too

the rings of the basal body that anchor the flagellum into the cell envelope

negative F-more complex,

bc basal body must span a more complex cell envelope

hollow, construction of filament

protein flagellin

cell envelope

4 rings

P ring is embedded in peptidoglycan, MS ring is embedded in plasma membrane, C ring is found in cytoplasmic side of plasma membrane o.

MS ring and C ring

positive-so

gram positive

basal Is the same function in which two groups

how many rings are in gram positive

where is the inner ring embedded

where is the outer ring associated with

are there more or less layers here than in gram negative

gram positive

gram P and N

only 2 rings here

plasma membrane

peptidoglycan layer

less layers so less rings

gram positive

how many genes does it take here to build a flagellum

operons are used by which two domains, what does it allow us to do

filament extends to outer entire by using ___ ___. Basal body is modified __ ___ ___ ____.\

making flagellum: we shove them up hollow ___ ____ and they pop out at the top

do flagella grow at the tips or the base

once flagella subunits reach the itpe, they do __ ___, meaning they don’t need external organizing force. Interactions between flagellar subunits allow them to make up the configuration

20-30 diff genes to do this

genes are encoded in operons

bacteria and archaea, allows us to transcribe genes as a single RNA molecule/put multiple genes together at the same time to make the same structure

filament extends to outer enviro by using basal body. Basal body is modified type 3 secretion system.\

making flagellum, we shut them up hollow basal body and they pop out at the top

tips

undergo self assembly-don’t need external organizing force, interactions between flaglellan subunits that allow them to make up the configuration

flagella moves in bacteria by …..

how fast depends on bacteria and ….

E. COLI does 1100 revolutions per sec

counter-clockwise and clockwise rotation is what kind of movement(both each

what direction can most bacteria not do

which kind of bacteria can move backwards

spinning like a propellor

which way your’re spinning

counter-clockwise rotation =directed run=forward -

clockwise rotation=tumble

bacteria can’t do backward movement

Archaea can do backwards though

with tumble remember that something happens and disrupts run causing cell to stop and tumble

chemotaxis

what 2 things do you need to do this

what do chemo repellents bind to

what do chemoreceptors do, what can influence them

directed movement towards or away from chemical attractant

NEED to have a flagella to do this, must also have chemoreceptors-inthe plasma membrane,

chemo repellents bind to chemoreceptors

chemoreceptors sense presence of things, diff in concentration that have influence too

define positive and negative chemotaxis

positive chemotaxis-towards a chemo attractant

negative chemotaxis-running away from a chemo repellent

is chemotaxis a flagellar movement

when chemoattractants are high and chemorepellants are llow what do bacteria do

what does a zone of clearing around a disk mean

no, regulation

high chemoattractants=bacteria move towards it

high chemorepellants mean bacteria moves away from it

bacteria has run away from the thing, chemorepellant concentration is high

high concentration of attractant means

decreasing concentration of attractant means

high concentration of repellant means

decresasing conentration of repellant means

high arts of runs

increased tumbles(reorienting)

more tumbles (need to reorient away)

more running (more running moving away from it successfully keep going

bacteria have blank movement when there isn’t a conc of anything

high conc of repellent means more run and fewer blank, and once you get away you can blank more and less blank

random

chemotaxis system is made from __

what specific thing switches you from running and tumble

what determines whether or not the bacteria runs or tumble

when CheY-P is phosphorylated what happens

what happens when CheY is unphosphorylated

explain the steps of the signaling chain

what happens if CheZ removes the

what happens when there is a high concentration of attractant

what happens when conc of attraction drops,

proteins

molecule switch does this

the phosphorylation state of CheY

it interacts with the motor switch, causing a clockwise rotation/tumble

CheY-P has no interaction with switch and a counter clockwise rotation occurs meaning run

1. chemoreceptor detects a chemical signal in the environment

2. receptor transmits that signal to CHeW

3. CheW passes it to CheA

4. CheA phosphorylates CheY, then it becomes CheY-P

5. CheY-P travels to the motor switch causing a clockwise rotation/tumble

6. cheZ removes the phosphate from CheY-P resetting it back to CHeY and the run resumes

CheA activity is suppressed, less CheYP means that the motor stays CCW so bacteria keeps running toward the attractant

cheap becomes active, phosphorylates CheY, CheY-P hits the switch and tumbles to reorient

flagella is 2 part motor, allows us to produce torque-torque allows us to spin smth

roto part-composed of C ring or MS in gram neg, and inner and outer in gram positive

C and MS ring turn and stator part-S part is stationary, made from Mot A and Mot B proteins get energy from potential energy stored in proton gradients

motA and motB creates channels so ions can flow down concentration gradient to allow energy for torque

located n basal body

MOT proteins form channel so protons can flow down concentration gradient

gives energy to spin MS ring and C ring

allow spinning of shaft up until filament

FIM and FIN make part of C ring

FLig-believe motB

MOTS not embedded in ring, kind of in the outside

external flagella can def move

other mechanisms of movement though, some that are not external

spirochete-notoruiosu fo rhaing internal flagella

don’t see them externally bc flagella wraps around periplasmic space or organism

when it does movement-it does corkscrew like motions

non flagellar motility

gilding motility-few diff types

performed by orgs that make a slime layer-layer of polysaccharide. orgs producee smooth polysaccharide and then org glides over it

twitching motility-for those that have pili. just bc you have pili does not mean that you can twitch

good for adherence , secondary function that some bacteria have evolve from there I pili

bacteria can extend their pili and those pili stick to surface and retrace their pili. hold them selves along

polymerization of actin

bacteria that will infect eukaryotic cells, like shigella. it will be endocytosedinto host cell, escaped from the endocystic vesicle, it will use the hosts actin to mvke actin tails, uses actin tails to push between eukaryotic cells, don’t have to exit the cell, you can spread from cell to cell

coopting host cellular machinery, and allowing bacteria to spread inside cells

priamary function of pilis is adherence

made out of protein subunit called pillin

have a protein called ashesi-portion of pili that is sticky

fimbriae-structuraly both are the same thing, it is also made of pilling, have same thing at it’s tips,

bacterial cell surface

stalks-made by certain subset of bacteria, low nutrient enviro bacteria

stalk is an extension of cell membrane

tip of stalk is holdfast. fast is composed of polysaccharides,s sticky, allows for sticking to other cells

find steaks in orgs that liven lownutent enviro bc it gives more expansive surface area fr new nutrients

3 layers

capsule, slime layer, or surface array layer or S layer

they’re glycocafyx-layers of polysaccharide that these types of cell secrete, if you secrete capsulee or slime layer

S-layers aren’y glycocalyx bca ren’t yamde up of polysaccharide, made up of proteins and glycoproteins

capsules and slime layers do

both-aid in attachment to solid surfaces, polysaccharide, think sticky

to other cells, help in biofilm formation,

capsules continued

composed of polysaccharides-thick and tightly organized, well organized, adheres very tightly to cell surfaces, aren’t physically removed easily from cells

can see them insight microscope

capsules help protect the cell from essication, bc they have a high water conc

help hide the bacterial cells out in the host cell immune response

ex: smooth strain pathogenic-has a capsule so host immune cell can’t see it, so it won’t have an immune response

, rough strain non pathogenic-don’t contain a capsule and host cells can see them and mount a response on them before they have a chance to do anything

biofilms have glycocalyx later, slime mold or capsule

other cells can stick to other bacteria

form this big 3d community

it’s protected for Theo orgs

single cells can be easily killed, harder to kill the orgs in the inner portion

plaque=a bifilm that hangs out in the tooth

biofilm that contains archaea and bacteria

slime layer

it is much thinner than capsule

it doesn’t adhere as tightly

can’t see a slime layer under a light microscope, yes with electron though

they can protect the cell from desiccation due to high water content, aid in attaching

can protect the cell somewhat form host cell immune response, not as good though

great for gliding motility, capsule cannot do this

capsule-is soft and gel like

slime layers-in gram neg and pos orgs

if you have a capsule you don’t have a slime layer or s layer

if you have slime layer or s layer you don’t have capsule

CHECK THIS

s layers

in gram pos and gram neg

gram neg-S layer sticks to other membrane

gram pro-associated with peptidoglycan surface

S layer functions

acts as a physical layer, makes later highly impenetrable

protect it from ion and pH fluctuations, osmotic stresss, enzymes and predation

-shape and rigidity, highly structured, not softt or flexible

-can protect from host defenses but not as great as capsule or slight-does it by blocking antimicrobial comps from being able to make it’s way into the cell

-potential uses in nanotechnology

come together via self assembly

helps to prevent with damage

bacterial endospore

dormant structure formed by some bacteria

not metabolically active

very resistnat

desiccation, heat, chemicals, radiation, antibiotics

hard to get things through an endospore

some endospores are some of the most nasty toxins,

majority are soil dwelling, bc soil is a dynamic enviro, nutrients washed out and washed into it

spore is made and then released into the enviro by bacteria

spores are made in the mother cell

central=bacillus subtillius

bacillus anthracis=subterminal

terminal=all the way at the end

clostridium tetani do swollen sporangium

where spores sporm are characteristic of the org that forms

core is where DNA is found, doe snot have water, has calcium dipicenoic acid, CaDPa, double membrane structure inner and outer membrane

inner membrane of spore =highly impermeable, proteins are tightly crossed here, phospholipid bilayer, germinate receptors are located here

core wall/cell wall

then cortex-can occupy half of cell volume, has ppetidoglycan, they are not fully crossliknked though it’s kind of weekend, difference in cross linking contributes to heat resistant properties

then outer membrane-slightly more impermeable than inner membrane

then we have inner coat and outer coat-made out of 70 diff inner proteins, tightly cross linked, some orgs have. a layer made up of glycoproteins-epsosporeum, bacillus and anthracite have this

outer membrane act as physical Barries due to cross linked barriers

why they’re so resistant

have a low metabolic activity

during sporulation calcium DPa moves into core, displaces water so water moves out, causes enzymes not to function,

they are resistant to ___ due to The actions of SASPS, small acid soluble DNA, they physically bind to DNA, proteins block DNA forms being damaged by the UV

dehydrated core

specialized cross inking of cortedxt which contributes to heat reisstnace

spore coats and exosporium=just physically barriers to prevent things form moving across it

how to make a spore-sporulation

triggered by nutrient deprevaition, doesn’t have orgs to. eat can either dye or hang around and make spores, that’s what they do

long process, can take 10 hours, all or nothing, can’t stop in the middle or go back, it’s tightly controlled

controlled by master orgs Spore 0a, once it’s phosphorylated it starts the response and edouens’t stop

lack of nutrients trigger sporulation.

500 proteins that are involved

megatherium is the largest of bacillus species

cell division-cell divides in step 1-also have axial filament formation-DNA stretches out the length of the cell,

step 2: septum formation, forming a wall int he cell, turning it into 2 separate compartment, 1 compartment will be smaller, another will be larger

spore develoeps n smaller comportment

step 3: mother cell membrane comes down and circulates around, engulfing of spore by membrane of mother cell, smth of DNA to spore foremother cell

step 4: core is formed in the middle, membrane is 4, laying down our cortex here

step 5: synthesis of coat synthesis inner and outer

step 6: complete spore coat formation nd exosporium formation

we''ve made out spore

step 7: lysis of the mother spore, spore produces enzymes that lyse the mother cell so that it can be released into the enviro

germination

happens when we hav enough nutrients in enviro

we unwind everything that we did in sporulation

complex process, all or nothing response, multi stage process as well, not as many as sporulation,

last stage is outgrowth

fully developed vegetative org is cracking spore so bacteria can come out

activation -process where you wake yourself up, not germinating here, allows cell to response appropriately to nutrients when nutrients are present in the enviro

ex: temp rises, triggering activation, if nutrients come into our enviro we can do germination:

nutrients bind to germination receptors-inner membrane which triggers germination, opposite steps of sporulation. water rushes into the cell, calcium DPa rush out, metabolic activity increases, activation of diff enzymes, which degrade the coats and exosporium, water rushing in breaks peptidoglycan

germination

outgrowth-acitv enzymes degrade the spore codes allowing bacteria to be released into the enviro

species: groups of strains sharing common features, while differing considerably from other strains

domain is broadest, work our way down to genus species, which is more narrow

gram positive is more related to itself than gram neg

if you’re likely to form nasty groups colonies, more to look like one that forms that too

spore forming orgs are more related then non spore forming

similar metabolic pathways

culture collections to store diff organisms

store it in -80 for sleep

ppl like to store strains so everyone can u

archaea have both eukaryotic and bacterial factors

they liv win some of the most inhospitable places on earth-what they’re characterized as

e

methanogens-first area-can produce methane in a way that is unique to Archeaa

halo bacterium salinarium-it is an archaea, it likes salt-between 3-5 molar

prococcus furiosus-likes intense heat, hydrothermal vents

picrophilus oshimae-bitter loving-loves sulfur ph of .7

methanogenium frigidum-loves chilly enviro

A things similar in bacteria

.5-5 micrometers in diameter

similar shapes, cocci, rod shapes, spirals, also some that are unique to them

singular, circular chromosome, rods, spheres too

lacks a true membrane bound nucleus-DNA is in area but not constrained by membrane

eukaryotic structures

how DNA is organized-DNA is complexed with histones, wrapping DNA around them

transcription and translation machinery is highly conserved, homologues of DNA replication enzymes

their plasma membrane-organization-HAVE monolayers, not in eukaryotes or bacteria

cell wall-composition

archaea has irregular shapes

they have rectangular shapes like in thermoproteus spp

squared too-not present in bacteria

cell envelope-plasma membrane and everything outside of that

has 6 organizations of envelope-start with plasma membrane but diff organizations

majority have a cell wall

temp determines what the bilayer or monolayer will look like

hydrocarbon tails don’t have fatty acids, they use isoprene unit-five carbon molecule with short branched chains-makes the tail portion of lipids in plasma membrane

-iso unit links to glycerol-we’ll see Ether linkages in archaea-less impacted by temp changes, more stable at higher or colder temps in comparison to ester in bacteria and eukarya

bilayer for archaea-use isoprene unit for 20 carbon molecules called phytanyl, linked to. glycerol via Esther linkage, connected via 1 carbon

phytanyl groups interact with each other

monolayer -2 hydrophilic head groups, isoprene units connected from one to the other

more likely to find monolayers for orgs that like high temps-ex those that can survive autoclave

Rachael cell wall

5 distinct configurations

most have s layer, it’s part of the cell wall

configuration e does not have an s layer, but others do

if you have f configuration for Racheal cell envelope you ve two lipid layers so no celll wall

archael cell walls provide the physical barrier, preventing things from making way into archaean cell walls, help us maintain our cellular shape

help in osmotic protection

configuration e-have pseudo marry, look like murine but is not murine. lots of similarity in the structure of both and differences

NAT in pseudomary and NAM in peptidoglycan

archaea have beta 1-3 linkage and pseudomurien have beta 1-3

penta peptide that gets cut off in both archaea and bacteria

L and D form in bacteria no D form in archaea

lysosome won’t work against archaea bc it’s beta 1-3 not beta 1-4

beta lactic work yes or no

archaea have plasmids and inclusions

dna in cytoplasm nuclear region

how DNA is packaged is diff in archaea bc it gets wrapped around

DNA is neg charged and histones are pos charge, wrapping prevents it being exposed to nucleases hanging out in enviro

diff in archaea nucleosome, it’s a 6 length pair not 8 bc genome in archaea is smaller than eukaryotes

cytoskeletal for cell division, cell wall support for shape, organizing internal space of cell

homologs of bacteria and some homologs to eukaryotic , depends where you are in evolutionary timeline, further you are the more closer they are to eukaryotes, earlier on you’ll find cytoskeletal elements somewhere in the middle you have some that have cytoskeletal elements of both bacterial and eukaryotic, play the same role though

slime layers and capsule are rare in bacteria, mostly just s layer in archaea

unique: have cannulae-hollow glycoprotein tubes that link cells together to form a complex network, allows them to communicate maybe, sharing of nutrients, surface structures that we only find in archaea

another surface structure-hami or hamus-filamentous structures coming off surface of the cell they aid in archael attachment, grappling hook configuration that helps aid in attachment

great for biofilms bc you have to have cells that attach to each other

helps preventing archaea from being removed from enviro

flagella in Arachne or archella

appendage of locomotion

rotate like propellar

differences-they are thinner, not hollow like bacterial ones, -that’s what causes differences

they are built at the base here

2 or more diff versions of flagella protein, only 1 in bacteria

movement is diff

archaea have forward and backward not spin or tumble like bacteria

bacteria gets energy from ion gradients to move rotors

archaea hydrolyzes ATP and uses that to spin

eukarya have flagella but they don’t spin around,

metabolism is the sum of all the chemical reactions in an organism (catabolic and anabolic)

catabolism is the energy releasing processes -gives fuel for rxns

anabolism is the energy using processes

enzymes mediate each step in reactions

metabolic p

laws of thermodynamics

1-energy can’t be created or destroyed, only converted from one to another

2-physical and chem processes happen, and randomness occurs-universe tends to go to disorder, higher to lower energy state causing disorder

entropy-measure of randomness or disorder in system

free energy

free energy change =delta G

exothermic=neg delta G, spontaneous -don’t add energy in system for it to happen

pos delta G-endergonic, non spontaneous, need to add energy to system to make it start

transition state-energy peak of reaction, most unstable point of reaction, right before we have bonds break

activation energy-the amt of energy it takes to hit the transition state

ushe absorbs energy from enviro to hit this peak

the more activation energy you need, the slower ithe reaction will run

not every reaction need san enzyme to run

enzymes speed up rate of a rxn,. some actions w/o enzymes are so slow it wouldn’t even be useful,

enzymes lower the Ea to make it quicker

non spontaneous reaction-adding an enzyme won’t make it spontaneous

enzymes don’t change the freee energy that is available in system

free energy is determined by free energy available in reaction and product

converting reactant to product MUST:

enzyme and substrate must encounter each other in prop orientation, enough force, enough energy, when adding enzyme in you take the chance that this will all happen out of the equation

enzymes have an affinity for the substrate , increase the concentration of substrates ou are promoting the likelihood that they will enocounter each other, enzymes grab the substrate, orient them properly, and bring them together with enough force to do bond breaking

take chance out of equation

one enzyme have one specific substrate

confirmation of active site, structure component of substrate confirms this

lock and key model-now we use induced fit model, better and uses things form lock and key

lock and key model-have to have substrate with specific confirmation to fit,

diff-lock and key is rigid model, doesn’t allow for any flexibility in structure of enzyme itself

but there IS some flexibility

induced fit model-there is still specificity, specific confirmation of active site,o only specific substrate will fit, when substrate bind to active site, the enzyme active site binds to it and changes the final confirmation of it a bit

enzymes are catalysts, don’t get modified or used int he process

they have a turnover number that is associated with it

can be anywhere from 1-10,000 mols

hturnover number=how fast can enzyme grab a substrate and convert it to product

active site=where substrate bonds to on enzyme , is very specific to substrate

substrate is unique to active site too, they fit together great

some enzymes are only made up of polypeptides-only protein component

some enzymes need non proteins components, it’s gnats be essential for it’s function, if you do not have it , it won’t work

cofactors=non protein components

coenzyme MUSt bind to enzyme to create active site that has a structure that is complimentary to substrate

coenzyme-organic, more loosely attached to enzyme

prosthetic groups=inorganic, ex zinc or magnesium, ore firmly attached ot enzyme

important coenzymes

NAD+

NADP+

FAD

coenzyme A

coenzymes again

they give us active site

coenzymes acts as carriers

it pops off a functional group, and it shuffles over functional group to substrate to, modifies substrate and modifies it so it can be released into the enviro

two factors effecting enzyme function

temperature

pH

when enzyme denatures ad unfolds, substrate can’t find an active site

all enzymes have a. temp range that they are optimal in, you can get too high or too low

too high or too low will cause enzyme function loss

too high-you’re denaturing,

too low-you’re loosing function for a diff reason, bc enzyme and substrate need to encounter each other and when there’s barely heat it sows down rate of motion decreasing the chance for them toe nocunter each other, also won’t have energy we need to reach transition state

ph-you’r loosing function too high vs too low the same way, it’s not like temp ewer it’s diff you’re loosing structure both ways

concentration of substrate-the more substrate available, the faster you’re products gnats form, increase product formation until hint v max

v max is where you plate bc enzyme is saturated, won’t matter if you grab more enzyme is grabbing as much as they can

affinity-being able to grab and pull the substrates to them

km-substrate concentration required by the enzyme to operate at half of it’s maximum velocity

low km means high affinity for substrate, need ton of substrate around , has low affinity for substrate

enzyme that has high km needs not art of substrate b it has a high affinity for substrate

competitive inhibitors-will compete directly at the active site for binding with he substrate, look a lot like the natural substrate , it binds to active site

noncompetitive inhibitor-don’t compete at active site of enzyme, bind at a diff site somewhere on enzyme that’s not active site, causes a conformational change that changes site of the active site, natural substrate won’t be able to fit into site

affinity for substrate vs how much affinity for competitive einhibitor

concentration-overcome it by dumping more natural substrate into enviro, increases likelihood that enzyme will encounter the one with higher concentration

sulfahydomite-bacteria static-prevent cell form replicating DNA,

folate is used to make DNA -improtant to be able to make this

PABA-binds to dihydroxate synthase,

enzyme promotes change of PABA to product to be used to make folate

Sulfa drug looks like PABA and goes there to bind

enzyme makes a product, but product can’t be used by the cell to make folate, isn’t the correct product

this targets folate synthesis pathway

we get folate from food, we don’t have to worry about disrupting our folate pathway

ways to regulate

metabolic channeling focused on where intermediates and end products are located into cell, moving them from one pallete to the other , ore important tin eukaryotic bc don’t have tons of compartment in prokaryotic, gram neg periplasmic to eukaryotic

regulate synthesis of enzyme-don’t make an enzyme, can’t use it to make product,

direct stim ulation or inhibition enzyme- do you want to turn enzyme on or off,

metabolic channeling

regulating by moving things around to diff places in the cell

compartmentation

used more in eukaryotic cells bc they’re more complex, higher level of compartmentation

bacteria still use it, bu not as frequently, ushe gram negatives

you can have diff distribution of enzymes and metabolites-creates variation of enzyme concentrations and metabolite concentrations within diff compartments

channeling allows us to operate similar pathways simultaneously and independent of each other

allows us to coordinate diff activities via transport of themselves

post translational regulation of enzymes activity

turn the enzyme on or off

2 ways-

allosteric regulation or covalent modification, allows us to turn enzyme on

allosteric regulation

you havve allosteric effector

binds to enzyme on allosteric site -NONcovalently, reversible binding, can come off

when it binds there it changes shape of enzyme

change reaches all the way to the active site

positive efector increases enzyme activity while negative effector inhibits the enzyme

it is VERy specific bindingng to a SPECIFIC site, it’s purposefully, , we can not only inhibit enzyme activity, we can turn on enzyme activity, diff form noncompetitive inhibition-smth form enviro is effecting enzyme, only turning enzyme off non specifically activating enzyme ,