BIOL 2053 Test 1

autotrophs

"self-feeders" -can produce their own organic molecule from an inorganic carbon source.

ATP-binding cassette(ABC) transporters

-2 hydrophobic membrane spanning domains -2 cytoplasmic associated ATP-binding domains -subtrate binding domains

Euryarchaeota:

Halophiles -require NaCl concentration greater than 1.5M -high salt environments are fairly rare. -Great Salt Lake in Utah -Dead sea btwn Israel and Jordan

ribozymes

RNA molecule that can act as a catalyst within a cell.

pilli

facilliate transfer of DNA from one cell to another -gliding motility -twitching motility

bacteria/ eukaryotes

fatty acids attached to glycerol by ester linkeages

metabolism

a controlled set of chemical reactions that extract energy and nutrients from the environment, and transform them into new biological materials.

mutation

a heritable change in the base sequence of the genome -alters -can change phenotype. DNA: AT, GC RNA:

microbes

a more general term that includes microorganisms and viruses.

polymerase chain reaction

a technique that amplifies specific pieces of DNA

building blocks for micofilaments

actin

homeostasis

active regulation of their internal environment to maintain relative constancy.

lycostaphin

acts on the crossbridge of certain staphylococcus species only(look at slide 55)

macromolecules

all cells are built from macromolecules. macromolecules- large, complex molecules consisting of simpler subunits. four types: polypeptides, nucleic acids, lipids, polysaccharides

fimbrae

allow attachment

genetic variation

allowing the possibility of evolution, or inherited change within a population, through natural selection over the course of multiple generations.

carboxysomes

key enzymes involved in the conversion of inorganic matter into organic matter.

nucleoid

largest single entity in the cytoplasm -a convoluted mass of DNA coated with proteins and RNA molecules still in the process of being synthesized. -in contrast to the nucleus of eukaryal cells, a membrane does not surround the nucleoid of bacterial cells.

fungi

less likely to cause disease, but can do so in immuncompromised individuals. for ex. epidermophyton floccosum, candida albicans

attractant

alternating runs and tumbles result in no directed movement. -prolonged runs can move a bacterium toward a chemical.

growth

an increase in the mass of biological material.

pastuerization

any technique using mild heating, irradiation, or high pressure to destroy spoilage or pathogenic microrganisms without cooking the food product

protozoa: Giardia lamblia

as a whole, a broad category-- some heterotrophic, some photosynthetic, variable cells walls; different motility strategies; different reproduction strategies -giardia is interesting because it is genetically "old", it lacks mitochondria and it causes human disease. examples: amoeba proteus, tetrahymena thermophilia

hook

attaches filament to the basal body

Type V are sec- dependent

autotransporters- transport themselves out

rod shaped

bacillus(plural, bacilli) examples: e.coli, bacillus anthracis

horizontal gene transfer

bacteria exchanges gene between cells.

C-O-C-double bond- O

bacteria, eukarya

inclusion bodies

bacterial cells store extra carbon, nitrogen, or phosphorous in inclusion bodies. example: PHB

mitosis

basic cell division: copying of one nucleus into two nuclei -followed by cytokinesis to produce two identical cells from one original cell -dipolid

archaea

branched chain hydrocarbons attached to glycerol by ether linkeages. -some have diglyercol tetraethers

peroxisomes

break down of fatty acids

chemoreceptor proteins

by using chemoreceptor proteins to sense changes in concentrations of attractants or repellants, cells can produce more runs to move in a particular direction.

protozoa and fungi

can cause significant diseases in plants(potato blight and the great irish famine 1800s) -phytophora infesans,

photosynthetic algae

cell walls of photosynthetic algae have cellulose, pectin, and silica

algae

cellulose

fungi

chitin

lophotricios

cluster of flagella at one or both ends

spherical shaped

cocus(plural, cocci) example: staphylococcus aureus, streptococcus pyogenes

plasmid(s)

composition: DNA function: variable, encode non-chromosomal genes for a variety of functions.

ribsomes

composition: RNA function: translation(protein synthesis)

enzymes involved in breaking down substrates

composition: protein function: energy production, providing anabolic precursors

cytoskeletal structures

composition: protein function: guiding cell wall synthesis, cell division, and possibly partition of chromosomes during replication.

chromosome- packaging proteins

composition: protein function: protection and compaction of genomic DNA

enzymes involved in synthesis of DNA, RNA

composition: protein function: replication of the genome, transcription.

regulatory factors

composition: protein, RNA control of replication, transcription, and translation

magnetosomes

composition: protein, lipid, iron function: orienting cell during movement

inclusion bodies

composition: various polymers function: storage of carbon, phosphate, nitrogen, sulfur

golgi apparatus

connected to the ER through a series of vesicles

cell walls of fungi

consist of cellulose, chitin, or glucan

nucleus

contains most of cell's DNA, site of transcription

peroxisome

contains various oxidative enzymes, like catalase and oxidase

nitrogen fixiation

conversion of atmospheric N2 into inorganic compounds, such as ammonia for cell use.

hypertonic solution

cytoplasm has a lower solute concentration than the external environment, causing a net loss of water from the cell.

cytoskeletal homolgues

cytoskeletal homologues are found in both Bacteria and Archaea. -Ta0583 is an actin homolog in Thermoplasma acidophilum that resembles eukaryal actin. -cytoskeletal proteins from M. thermoautotrophicum and M. kandleri more closely resemble cytoskeletal proteins.

jonas salk and albert sabin

develop polivirus vaccines

meiosis

different from mitosis(four cells from one original cell, but each has half the original cell's quantity of DNA) -achieved by one round of DNA replication followed by two rounds of cell divisions.

lysosome

digestion of macromolecules

alexander fleming

discovers penicillin

basal body

disk-like structure that produces torque on filament to turn it like a propeller

louis pasteur

disproves idea of spontaneous generation

motors

dyneins, kinesins

O polysaccharide antigen

e.g., E. coli O157:H7 -extends out prevents phagocytosis

mitochondrion

energy production

haploid cell

events ensure each haploid cell is genetically distinct, increases chances for genetic variation in sexual reproduction.

phylogeny

evolutionary history of organisms

pathogens

exploit the cytoskeleton

gas vescles

provide buoyancy to the cells

cytoskeleton

provide the same protection as a cell wall, however.

biosphere

regions on earth supporting life.

central dogma

replication(DNA->DNA) transcription(DNA->RNA) translation(RNA->Protein)

morphology of archaeal cells

rods, spheres, spirals -irregular shapes(sulfolobus spp.) -rectangular shapes(thermoproteus spp.)

rough ER

rough ER has protein- synthesizing ribosomes attached to it

physarum

second slide mold type (physarum), fuses many cells into a multinucleate giant cell.

preproteins

secreted proteins synthesized as preproteins have amino-terminal signal peptide -signal peptide delays protein folding -chaperone proteins(SecB) keep preproteins unfolded Step 1: Protein is synthesized.

plasma membrane permeabilty

selectively permeability -small and uncharged molecules such as O2 and CO2 can diffuse freely across a phospholipid bilayer -larger compounds, or molecules that are more polar or charged cross the membrane less readily

Type VI

similar to bacteriophage genome injection systems

rough ER

site of translation and protein folding

twitching motility

slow, jerky process using fibers(pilli) that can extended, attached to a surface and pulled back to pull along a surface(N. menigitidis, P. geruginosa)

picrophilus oshimae

0.7 pH, sulfur rich volcanic regions

formation of the cell wall

1. NAM is synthesize in the cytoplasm and linked to UDP

steps of ABC transporters

1. solute-binding protein interacts with solute 2. complex interacts with channel 3.channel undergoes conformational change 4.ATP hydrolysis provides energy for opening channel and movement of solute.

pyrococcus furiosis

100 degrees celsius natural habitat: hydrothermal vents

methanogenium frigdum

15 degrees celsus, ace lake, antartcia

nuclear function.

1a. DNA replication 1b. Transcription 2.Processing 3.Translation

structure of microtubules

25 nm 13 protofilaments that form a hollow tube

microfilaments structure

7 mm in diameter, 2 protofilaments twisted around each other in a helix

intermediate filaments structure

8-11 nm in diameter

step 4

Bactoprenol flips NAM-NAG to periplasm

step 6

Bactoprenol flips back to cytoplasm.

ether in archaea

C-O-C in archaea

largest bacteria

Thiomargarita namibiensis- 700 micrometers Epulopiscium fishelsoni- 200-700 micrometersx 80 micrometers

monotrichous

one flagellum

amphitricous

one flagellum at each end of cell

eukaryotes

organism that is composed of cells that contain a membrane- bound nucleus

prokaryotes

organisms that lacks a membrane- bound nucleus; includes bacteria and archea

facilitated difusion+environment

particle is abundant in the environment

chloroplast

photosynthesis

phylum, class, order, family, genus, species

phylum, class, order, family, genus, species.

achae's plasma

plasma membrane can even be a monolayer instead of a bilayer. -in this case, each lipid has a phosphoglycerol molecule on both ends. -this is often seen in archaeons living in high temp. environments due to its stability.

polypeptides

polymers of amino acids -the most abundant class of macromolecules -often referred to as "proteins" -fold into elaborate structures and can execute a vast array of important jobs. -

joseph lister

practices infection control

hydrogenosome

production of H2 and ATP

repellant

prolonged runs can also move a bacterium away from a chemica.

lynn margulis

proposes endosymbiotic theory

craig venter

proposes first complete bacterial genome sequence

Carl Woese

proposes three- domain classification of living organisms

aquaporins

protein channel in the plasma membrane that facilliates passage of water.

preprotein and sec

the preprotein is taken to a channel in the membrane formed by secY, secE, and secG -secA translocates preprotein through the plasma membrane -when preprotein emerges from plasma membrane a signal peptidase removes the signal peptide. Step 2: SecB prevents new protein from folding. Step 3: SecE, SecG, and SecY form channel. Step 4: Signal peptide is removed by peptidase.

reproduction

the production of new copies of the organism.

microbiology

the study of microorganisms

biogeochemical cycling

the transition of various chemical between organic and inorganic forms.

capsules

thick layer of polysaccharides surrounding some cell -can provide adhesion, form biofilms, defense against immunity, protection against drying out) -examples of biofilms include dental plaque and mold on bathroom surfaces.

gram- positive

thick peptidoglycan layer -comprises 40-80% of the cell wall dry weight -surface of peptidoglycan layer decorated by teichoic acid

gram-negative bacteria

thin peptidoglycan layer(~2 nm) comprises 5% of cell wall dry weight -outer membrane has phospholipid inner leaflet and lipoplysaccharide outer leaflet

flagella

three parts: filament,hook, basal body

Type I pathways

transport proteins across outer membrane that were first translocated across plasma membrane by Sec-dependent pathway.

motility of fungi, protozoa, slime molds, algae

typically non motile, varied: (swimming: cilia/ flagella, amoeboid: psuedopods), amoeboid: psuedopods, non-motile or swimming: flagella

cell wall of fungi, protozoa, slime molds, and algae

typically yes: chitin, typically no, typically no, typically yes: cellulose

eukaryotic cell envelopes- cell walls

unlike the peptidoglycan in the cell wall of bacteria and archaea, many eukaryotes lack or have a chemically distinct cell walls

anton von leeuwenhoek

use microscope to see, microorganisms

sex pilus

used to join bacteria for DNA transfer -longer, thicker, less numerous

taxon

used to name a group

Facilitated diffusion

using a protein channel to move particles WITH a concentration gradient(no energy)

active transport

using energy to move particles against a concentration gradient -co-transport mechanisms(symptom/ antiport) -ATP-binding cassette(ABC transporters)

building blocks for intermediate filaments

varied; lamin, keratin, vimentin

cytoskeleton

vast network of interconnected filaments within the cytoplasmic matrix.

curved rod

vibrio example: vibrio cholerae

chloroplast

when an early eukaryal cell engulfed a cyanobacteria like bacterium capable of photosynthesis.

hypotonic solution

when the cytoplasm has a higher solute concentration than the external environment, causing water to move into the cell.

mitochondria in fungi, protozoa, slime molds, algae

yes, typically yes, yes, yes, yes

nucleus in fungi, protozoa, slime molds, algae

yes, yes, yes, yes

building blocks

α- and β-tubulin

S- layers

"armors" -crystalline array of interlocking proteins -found in gram-positive and gram-negative bacteria -can act as a armor, protecting a cell against predation or infection with bacteriophages.

heterotrophs

"other feeders" -organism that obtain carbon from organic molecules such as sugar, obtained from the environment.

Can the CW structure be degraded? YES!

-Artificially by B-lactam antibodtics -these work by preventing peptidoglycan crosslinking, weakening the cell wall structure.(look at slide 56).

step 3- joining of subunits to existing cell wall

-Autolysis- degrade the new existing peptidoglycan wall to allow the new NAM-NAG subunits to be incorporated. -Transglycosylation and transpeptidation reactions, resulting in the respective polymerization and crosslinking of the glycan strands via flexible peptides.

LPS- Lipopolysaccharise parts

-O side chain(O antigen) -core polysaccharide -lipid A(toxin)

Step 1: Synthesis of precursors of NAG and NAM

-Peptidoglycan synthesis begins in the cytoplasm. -UDP is added to N-acetyl muramic acid

central dogma 2

-RNA is synthesized from a DNA template during the process of transcription and delivers instructions to the ribosome for the production of a specific chain of amino acids. -Ribosomes are the protein synthesis factories of the cell. -During translation, transfer RNA delivers amino acids to the ribosome. DNA-> transcription->RNA->translation->polypeptide(amino acids).

what are the critical structural and functional properties of the bacterial cell envelope?

-The PM can also be used for capturing energy. -embedded electron transport chains can help create proton motive force(PMF) -can be used for respiration/ photosynthesis -can be used to derive energy for motion(flagella)

progenote

-Woesse -a cell hypothesized to store info in genes not yet linked linked together on chromosomes.

gram-positive cells have:

-a thick outer layer of peptidoglycan -a very narrow periplasmic space -teichoic acids in the peptidoglycan(negatively charged)

gram-negative cells have:

-a varying- width periplasmic space containing a very thin layer of peptidoglycan -an outer membrane composed of lipopolysaccharide(LPS)

gram negative

-additional outer layer membrane not found on gram-positive bacteria -lipopolysaccharides and proteins are examples of gram-negative bacteria

besides motility, what other stuff is still left on the outside of bacterial cells?

-adherence molecules to stick to surface(pilli, fimbrae)

the cell envelope

-all archaeons have a plasma membrane. -most archaeons have a cell wall. -both structures are different from their equivalents in Bacteria and Eukarya.

sec-dependent pathway

-also called general secretion pathway -highly conserved in all domains

plasma membrane

-bilayer composed of phospholipids -amphipathic= polar and non polar portion -bacterial membranes lack sterol lipids, such as cholesterol, which are major components of eukaryal membranes.

Can the CW structure be graded? YES!

-can be degraded naturally by lysozyme and lysostaphin secretions. -Lysozyme cleaves back of peptidoglycan.

protozoa

-can cause significant human diseases. for ex. giardia lamblia, trypanosoma brucei, plasmodium flaciparum, toxoplasma gondii

microtubules

-cell division is assisted by spindle fibers. -as spindle fibers depolymerize, chromosomes move apart.

cell wall: a role in cell support

-cellulose and chitin in eukaryal cells use speicific B-1,4, glycosidic bonds between sugars for strength and rigidity

phylogeny of archaea

-comparisons of rRNA gene sequences can establish phylogenetic trees. -woese and Fox began these studies in the 1970s. -the first portion terms "archaeons" were the methanogens-- a poorly characterized group of microbes capable of producing methane as a byproduct.

flagellar synthesis

-complex process involving many genes/ gene products -new flagellin molecules transported through the hollow filament using Type III-like secretion system -filament subunits self-assemble with help of filament cap at tip, not base.

lysosome

-contains digestive enzymes

morphology of eukaryal cells

-defined by the presence of a membrane- bound nucleus -usually larger than bacterial/ archaeal cells -contains organelles -many possess a cell wall structure -complex internal cytoskeleton in place

archaeal cell envelopes

-differ from bacterial envelopes in the molecular makeup and organization. -S layer may be only one component outside plasma membrane. -some lack cell wall -capsules and slime layers are rare.

archaeal membrane lipids

-different from Bacteria and Eukarya in having branched chain hydrocarbons attached to glycerol by ether linkages. -polar phospholipids, sulfolipids, glycolipids and unique lipids are found in archaeal membranes.

mitochondrion

-double membrane -contains DNA -independent replication -not present in amitochondriates

chloroplast

-double membrane -contains DNA -independent replication -unique to photosynthetic organisms

hydrogenosome

-double membrane -found in some amitochondriates -may be remnant of mitochondrion

interesting feature about nucleus

-double membrane containing spores -outer membrane continuous with ER -contains DNA

Lipid A

-embedded in OM -induces inflammation

motility from flagella

-energy to spin flagella dericed from proton motive force(PMF) -complex structures with up to 40 different proteins -spinning one way produces a "run"(directional movement) while spinning the other way produces a "tumble"(nondirectional movement.)

disctyostelium

-even more complex -it exists in a haploid unicellular form until conditions worsen. then a multicellular "slug" is formed with a stalk and then a fruiting body -spores form in the fruiting body, restarting the life cycle of haploid cells. -these haploid cells can fuse into a diploid macrocyst form. -the macrocyst form undergoes meiosis to generate more haploid cells.

external structures

-extended beyond the cell envelope in bacteria -function in protection, attachment to surfaces, horizontal gene transfer, cell movement -pilli and fimbriae -flagella

filament

-extension outside cell wall -hollow, rigid cylinder of flagellin protein

transpeptidation

-final step in cell wall synthesis -forms the peptide cross- links between muramic acid residues in adjacent glycan chains. -inhibited by the antibiotic penicillin. -has glycine, d-alanine, l-lysine, d-glutamate, l-alanine

archaeal flagella

-flagella thinner -more than one type of flagellin protein -flagellum are not hollow -hook and basal body difficult to distinguish -more related to type IV pilli, which are involved in twitching motility in that Domain -growth occurs at the base, not the end

bacterial flagellar movement

-flagellum rotates like a propeller -run: CCW rotation causes forward motion. -tumble: clockwise rotation(CW) disrupts run causing cells to stop and tumble.

vacoule

-food vacoule serve as sites of digestion -contractile vacuoles help maintain water balance

FtsZ protein

-forms a ring, the Z-ring -evolutionarily related to tubulin

Par-M

-forms actin- like filaments -responsible for moving copies like plasmids to opposite sides of the cell

archaea and eukarya

-gene encoding protein: replication, transcription, translation features in common with Bacteria: genes for metabolism other elements are unique to Archaea -unique rRNA gene structure. -capable of methanogenesis

evolution of archaea

-genetic sequence analyses indicate both Archaea and Eukarya may have branched off from bacteria. -development of histones may have been an early "branch-point- event" in the evolution of Archaea and Eukarya -the unique plasma membrane is also interesting but it is not required to thrive in harsh environments.

intermediate filaments

-heterogeneous elements of the cyto-skeleton - ~10 nm in diameter -keratin and vimentin classes -role in cell is unclear -play structural role -some shown to form nuclear lamina -other help link cells together to form tissues

lipids

-hydrophobic hydrocarbon molecules -form the foundation of the plasma membrane, a barrier surrounding the cell, that quite simply, separates inside from outside. -restricts the movement of materials into and out of the cell, thereby allowing the cell to capture and concentrate nutrients for metabolism and growth and prevent the products of metabolism from escaping -organic macromolecule that does not dissolve in water; important component of cell membranes.

mycoplasms

-lack cell walls -sterols in plasma membrane

atypical cell walls- acid-fast cell walls

-like gram-positive cell walls -waxy lipid(mycolic acid) bound to peptidoglycan -mycobacterium -nocardia

cells

-living organisms are composed of cells simplest structure capable of carrying out all of the processes of life.

distinctive properties of archaea

-look like bacteria -however, genetic analyses show them to be different. -they live in some of the most inhospitable places(for humans) on earth.

microfilaments

-maintain cell shape -create division furrow in cytokinesis -cell movement

functions of cell wall

-maintains shape of the bacterium, almost all bacteria have one. -helps protect cell from osmotic lysis and toxic materials -may contribute to pathogenicity

FtsZ

-many bacteria -involved in cell division -forms ring during septum formation in cell division -tubulin homolog

Crenarchaeota

-many members are thermophiles or hyperthermophiles(growing at temperatures greater than 55 degrees celsius or 88 degrees celsius, respectively). -many are also acidophiles(thriving in low pH) -some also are barophiles(thriving in high pressures, e.g. at the bottom of the ocean) -to survive in these conditions, these microbes possess multiple adaptations to survive.

MreB

-many rods -maintains shape -chromosome alignment -polarity -actin homolog

endosymbiosis

-most biologists now agree that mitochondria and chloroplasts, two of most distinctive organisms in the eukaryal cells are derived from bacterial cells through a process known as endosymbiosis. -have their own circular genome. -include a gene encoding 16S rRNA, the SSU rRNA molecule present in bacterial ribosomes. -related to specific groups of bacteria.

flagella

-motility -may be part of virulence functions.

chemotaxis

-move toward chemical attractions such as nutrients, away from harmful substances. -move in response to temperature, light, oxygen, osmotic pressure, and gravity. control>attachment>repellent

archaeal size, shape, arrangement

-much like bacteria, cocci and rods are common shapes -other shapes can also exist: no spirochetes or mycelial forms yet, branched/ flat shapes -sizes varied(typically, 1-5 micrometers, N.equirans= 0.4 micrometers, Thermoproteus= 100 micrometers long)

gram-positive

-multiple layers of peptidoglycan -thicker cell wall than gram-negative bacteria -peptidoglycan, teichoic acids, and proteins are examples of gram-positive bacteria

motility from flagella

-not all cells have external flagella! -some spirochetes have flagella in the periplasm. -as they spin, they rotate the entire cell body like a corkscrew.

intermediate filaments function

-nuclear structure -cell-cell interaction

how organisms make and use energy

-one of the simplest means of acquiring energy from organic molecules is glycolysis, the reaction in which glucose is converted to pyruvate, with the subsequent generation of two ATP molecules. Glycolysis->Glucose-> Pyruvate Glucose+2ADP+2Pi+2NAD+-> 2 Pyruvate+2ATP++2NADH+2H+

polysaccharides

-polymers of monosaccharides or sugars -combed of carbon, hydrogen, oxygen, with general CmH2O, -used in structure or for energy storage.

nucleic acids

-polymers of nucleotides composed of a sugar, phosphate moiety, and a nitrogen- containing base, DNA and RNA -make up most of the remainder of the macromolecules within a cell.

secretory pathway

-protein secretion occurs through the plasma membrane -making proteins and shipping them outside the cell. -uses ATP energy! -ships out toxins, siderophores, enzymes, etc.

PM can hold sensory functions

-proteins in the PM can be used to detect environment changes. -the cell can use the detected changes to alter gene expression to respond.

CreS

-rare, maintains curve shape -lamin, keratin

MreB protein

-related to actin -universal in nonspherical, but never seen in cocci -forms long helical bands underlying the plasma membrane -helps guide cell wall formation to produce an elongated cylinder, rather than a spherical shape.

peptidoglycan(murein)

-rigid structure lying just outside the cell plasma membrane. -two types based on Gram stain

the plasma membrane

-saturation levels of membrane lipids reflect environmental conditions such as temperature -bacterial membranes lack sterols but do contain sterol- like molecules, hopanoids -stabilize membrane -found in petroleum

Type III pathway

-sec independent -forms injectisomes -transports virulence factors and other proteins

chances for genetic recombination

-segregation of maternal/ paternal chromosomes -"crossing over" between chromosomes prior to segregation

microtubules

-shaped like thin cylinder ~25 nm in diameter of α- and β-tubulin -each individual tubulin is approx. 4 to 5 nm in dimater. -help maintain cell shape -involved with microfilaments in cell movements -participate in intracellular transport processes

archaea structure

-size is usually btwn 0.5-5 micrometers in diameter -similar shapes to Bacteria/ Eukarya -both Archaea and Bacteria usually possess singular, circular chromsomes, and lack membrane- bound nucleus -archaeal DNA is complexed with histones(like Eukarya) -many of the DNA replication enzymes of Archaea look like those of Eukarya -the archaea plasma membrane structure is unique to this domain

actin filaments

-small protein filaments, 4 to 7 nm in diameter. -scattered within cytoplasmic matrix or organized into networks and parallel arrays -involved in cell motion/ shape changes

holdfast

-some microbes(coloubater hypomonas) will use an extension of the cell envelope tipped by a "holdfast" of polysaccharides -these extensions provide extra surface area for nutrient absorption as well as the adherence capability

how can molecules get out of a Gram-negative cell's periplasmic space then?

-some move from the periplasm to outside directly(these are known as autotransporters and are rare). -some use single-step(never entering the periplasm) transport system.

enzymes

-some proteins function as enzymes -enzymes: macromolecules that act as a catalyst to speed up chemical reactions within the cell by lowering activation energy. -other proteins facilitate the movement of materials into our out of the cell.

crenarchaeota adaptations for survival

-tetraether lipids/ lipid monolaters -more α-helical regions in proteins -more salt bridges/ side chain interactions in proteins -more arginine/ tyrosine, less cysteine/ serine -strong chaperone protein complexes -thermostable DNA-binding proteins -reverse DNA gyrase enzyme to increase DNA supercoiling

why do the gram positive cell envelope allow bacteria to retain the crystal violet, even after being washed with ethanol, but the gram- negative cell envelope does not?

-the alcohol probably acts a solvent to dissolve the outer membrane of gram-negative bacteria, helping the crystal violet to leach out of the thin peptidoglycan layer. -although there is no outer membrane to protect the gram-positive cell, the cell wall is much thicker, and the alcohol may toughen it by dehydrating the structure, helping to trap enough crystal violet that the cell retain the intense purple color.

what happens when you weaken the CW?(step 1)

-the cell cant resist osmotic pressure changes. 1. Lysozyme cuts peptidoglycan. Rod shaped initially. -> isotonic conditions-> 2. without an intact cell wall, the rod shape is lost. -> protoplast-> 3. in hypotonic conditions, water rushes in. ->4. ruptured protoplast, internal pressure causes cell lysis.

Transpeptidase(penicillin binding proteins)

-the periplasm contains enzymes needed to continue wall synthesis -Transpeptidase(penicillin binding proteins)- link peptidoglycan strands via the pentapeptides and catalyze controlled degradation for new growth.

Step 2: UDP- NAM associated with a transport lipid in the membrane

-the second stage takes place at the cytoplasmic membrane -UDP-NAM- pentapeptide precursor is linked to the transport lipid(bactoprenol) -NAG is then added to the NAM -bactoprenol flips sides

Euryarchaeota: methogens

-they reduce CO2 with H2 to produce methane and water in an unusual reaction. -energy released can be used to fix carbon. -all identified methanogens are strict anaerobes -found in human gut and swamp sediments.

archaea

-varied -methanogens: glycopeptides or psuedopeptidoglycan -halogens and hyperthermophilic: glycopeptides

archaea

-wall-less or walls of psuedomurein(lack NAM and D-amino acids)

mitochondrion

-which may have originated when a developing eukaryal cell engulfed another bacterial cell capable of undergoing efficient aerobic respiration.

average size of bacteria

0.5- 5 uM -smaller than eukaryal cells, cannot be seen with the naked eye.

recombinant DNA

DNA sequences linked together to form a single molecule that never existed previously in the natural world.

step 5

Disaccharide added to existing chain. Crosslinking of chains also occurs.

Harald zur Hausen

Discovers that human papillomaviruses cause cervical cancer, leading to development of the HPV vaccine

two groups of arhaeons

Euryarchaeota, Crenarchaeota -two other phyla have been proposed.

how do nutrients cross the PM?

Facilitated diffusion and active transport

Z-ring

FtsZ monomers polymerize into filaments that bundle together to form Z-rings -formation of Z-ring is a fundamental step in cell division -ring interacts with membrane proteins that direct synthesis of the bacterial cell wall. -dissapears after synthesis, rebuilt from cytoplasmic FtsZ during the next cell cycle.

Glucose

Glucose->Glycolysis-> pyruvate -no oxygen= fermentation and lactate or ethanol +CO2 -oxygen= aerobic respiration, CO2+ H2O, ATP

Euryarchaeota: Halophiles

Halobacterium. -produces energy through an odd form of phototrophy. -doesnt use chlorophyll or an electron transport chain. -uses bacteriorhodopsin to harness light energy and produce a proton motive force(then used to make ATP) -Bacteriohodospin gives off redish hue.

smallest bacteria

Mycoplasma- 0.2 micrometers

step 3

NAG is added to NAM

step 2

NAM is linked to bactoprenol

peptidoglycan disaccharide subunit

NAM(N-acetylmuramic acid) has a small peptide chain -peptide varies by species, has HCCH3CO NAG(N-acetylglucosamine) NAG

autolysis

PBP enzymes that degrade peptidoglycan at site where new units are added

microtubules

function: intracellular transport separation of chromosomes in mitosis and meiosis -cell movement

four types of model organisms

fungi, protozoa, slime molds, algae

transglycosylation

glycolases catalyzes glycosidic bond formation forming a unique B-14 glycosidic bond.

bacteria

gram positive, gram negative.

Listeria monocytogenes

gram-positive bacterium that can cause food poisoning, have evolved a strategy for hijacking the mammalian actin cytoskeleton. -when they invade cell, they induce actin polymers to form at one end of bacterium. -polymerization of actin propels the bacterium through the cytoplasm of the host cell and the force generated can actually shoot the bacterial cell through the host membrane into an adjacent cell, which may be the real purpose of this actin- based motility. -when they take up residence within intestinal cells, they bacteria are protected from antibodies produced by the immune system. -by spreading directly from cell to cell, they effectively evade the host immune response, thereby taking full advantage of this shelled habitat.

genus

group of closely related species

species

groups of strains sharing common features while differing considering from other strains.

cell function of fungi, protozoa, slime molds, algae

heterotrophic, heterotrophic, heterotropic, phototrophic

fungi: saccharyomyces cerevisiae

heterotrophic; cells walls of chitin; used to make bread, beer, wine -easy, cheap tool to study eukaryotic structure/ gene expression examples: penicillum sp. aspergillus niger, rhiozopus nigricans, saccharomyces cerevisiae

robert koch

identifies bacillus anthracis as cause of anthrax

psuedomurein

in archaea, cell wall may be composed of psuedomurein(slightly from peptidoglycan structure). -some archaea lack a cell wall(cytoskeleton?)

obtaining energy from glucose

in some cases, glycolysis is coupled with fermentation, a process in which NADH+ produced by glycolysis is converted back to NAD+ and the pyruvate molecules are converted to a waste product, such as ethanol or lactate.

kary mullis

invents PCR

cytoskeleton

involved in intracellular trafficking, motion, and cell division. -this can be observed with fluorescent microscopy.

hyphae

irregular branching filaments found in most fungi and some bacteria

cytoplasm of Archaea

like bacteria, a diverse mixture of molecules. -histones form structures that DNA wraps around -histone structure/ wrapping is different in Archaea from Eukarya. -inclusion bodies such as gas vacuoles have been observed in some Archaea.

active transport+environment

low amounts of nutrients in environment

chalamydomas

maintains a motile haploid state -when conditions become back, haploid cells differentiate and fuse into a diploid form, generating a hardier spore form.

yeast and chlamydomonas

may alternate btwn haploid/ diploid stages -allows for better survival and genetic variation

saccharyomyces

may undergo meiosis to form an ascus -haploid mating types can fuse to reproduce sexually or be maintained by asexual mitosis

living organisms are capable of:

metabolism, growth, reproduction, homeostasis, genetic variation, response to external stimuli and adaptation to the local environment

filaments that form the cytoskeleton

microfilaments(actin), microtubules, intermediate filaments, and motor proteins. -plays role in both cell shape and cell movement

microorganisms

microscopic forms of life, organisms that are too small to see with the unaided eye. -usually consist of a single cell and include bacteria, archaea, fungi, protozoa,and algae.

golgi apparatus

modifies, sorts, and transports proteins

motors for microfilaments

myosins

chloroplast in fungi, protoa, slime molds, algae

no, no, no, yes

motors for intermediate filaments

none

protozoa

none

saccharomyces

not limited to ascus formation -budding off of smaller cells can occur, or fission of identically sized cells.

Halobacterium salinarum

notable growth requirement: 3.0- 5.0 M NaCl Natural habit: Dead sea, salted food

gliding motility

smooth sliding over a surface, not well understood(mycobacteria, cyanobacteria)

algae: chalmydomonas

some algae are single cell, but many are multicellular -all are photosynthetic with cellulose cell walls -chlamydomonas has two-flagella form good for studying eukaryal flagella biogenesis/ function -chlamydomonas is also studied because of its ease of growth and durability

Giardia, Entamoeba

some eukaryal cells only create cell walls at specific points in their life.

cannulae

some form cannulae, hollow glycoprotein tubes that link together to form a complex network.

S- layer

some use an S-layer(single layer of many identical armor- like subunits) to protect against predation/ viruses and to mediate adhesion.

spiral shaped

spirillum example: trepenoma pallidum

petritrichous

spread over entire surface of cell

gram negative

stain pink or red, peptidoglycan and outer membrane

gram positive

stain purple, thick peptidoglycan

origin of life

sterile earth: -prebiotic soup yields synthesis of proteins and RNA. RNA-> Self- replicating RNA-> vesicle generated abiotically-> early cellular life uses RNA for catalysts and coding-> protein synthesized using info in RNA-> proteins assume catalytic functions-> developed of DNA from RNA-> DNA replaces RNA as a coding molecule leading to: DNA->RNA->PROTEIN

hopanoids

sterol- like molecule believed to stabilize the plasma membrane of some bacteria

slime molds: Dictyostelium discoideum

still protozoan! model for studying ecology, cell motility, and cell-cell communitaton

vacuole

storage and structure

how do these cells deal with the osmotic shock and loss of water?

studies on Halobacterium salinarum show they maintain a very high intracellular K+ concentration to offset the very high Na+ concentration. -this solution can cause its own problems, denaturing proteins and splitting dsDNA. -How do such cell overcome these problems? DNA denaturing-> higher GC content(stronger bonds)) Protein denaturing-> highly acidic proteins that remain more stable in high salt environments.

genomics

study of genomes

peptidoglycan synthesis

synthesis of peptidoglycan, the major constituent of the bacterial cell wall, takes place in three stages that occur at three different locations in the cell. 1. Synthesis of NAM and NAG UDP- precursors in cytoplasm 2. Transferring precursors to bactoprenol and joining NAG to NAM 3. Adding new NAG-NAM subunits to cell wall via Pencillin binding proteins.

cell wall

the cell wall provides physical and osmotic protection.

cell wall

the cell wall: A role in cell support -eukaryal cells can be broadly separated into those with and those without cell walls. -cells wall can vary widely between the domains.

how can nutrients get through the cell walls? gram negative.

the gram-negative cell has porin and TonB proteins in its outer membrane to transfer molecules into the periplasmic space. -once there, active transports can move the molecule into the cytoplasm.

How can nutrients get through the cell walls? gram positive.

the gram-positive peptidoglycan layer has large pores throughout its matrix.