Mod 3 Pt. I Flashcards by Chloe Rivas

3 Universal Ancestor

Domain Eukarya
Domain Archaea
Domain Bacteria

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Domain Eukaryota or Eukarya; their name comes from the Greek eu__ and karyon ___

“true”
“nut” or “kernel“.

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surrounded by a plasma
membrane and contains many different structures and organelles with a variety of functions.

eukaryotic cell

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used to describe unicellular (single-celled) organisms that lack true nucleus and membrane-bound cell organelles. This means that the genetic material in prokaryotes is not bound within a nucleus.

Prokaryotes or procaryotes

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Prokaryotes or procaryotes is coined from two Greek
words

pro, before, and karyon, nut or kernel.

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(Eukaryotic cell structures & function)
- Strengthen and give shape to the cell

Cell wall and pellicle

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(Eukaryotic cell structures & function)
- Photosynthesis—trapping light energy and formation of carbohydrate from CO2 and water

Chloroplasts

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(Eukaryotic cell structures & function)
- Cell movement

Cilia and flagella

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(Eukaryotic cell structures & function)
- Environment for other organelles, location of many metabolic processes

Cytoplasmic matrix

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(Eukaryotic cell structures & function)
- Transport of materials, protein and lipid synthesis

Endoplasmic reticulum

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(Eukaryotic cell structures & function)
- Packaging and secretion of materials for various purposes, lysosome formation

Golgi apparatus

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(Eukaryotic cell structures & function)
- Intracellular digestion

Lysosomes

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(Eukaryotic cell structures & function)
- Cell structure and movements, form the cytoskeleton

Microfilaments, intermediate
filaments, and microtubules

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(Eukaryotic cell structures & function)
- Energy production through use of the tricarboxylic acid cycle, electron transport, oxidative phosphorylation, andother pathways

Mitochondria

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(Eukaryotic cell structures & function)
- Ribosomal RNA synthesis, ribosome construction

Nucleolus

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(Eukaryotic cell structures & function)
- Repository for genetic information, control centre for cell

Nucleus

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(Eukaryotic cell structures & function)
-Mechanical cell boundary, selectively permeable barrier with transport systems, mediates cell-cell interactions and adhesion to surfaces, secretion

Plasma membrane

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(Eukaryotic cell structures & function)
- Protein synthesis

Ribosomes

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(Eukaryotic cell structures & function)
- Temporary storage and transport, digestion (food vacuoles), water balance (contractile vacuole)

Vacuole

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(Prokaryotic cell structures and functions)
- Resistance to phagocytosis, adherence to surfaces

Capsules and slime layers

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(Prokaryotic cell structures and functions)
Gives bacteria shape and protection from lysis in dilute solutions

Cell wall

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(Prokaryotic cell structures and functions)
Survival under harsh environmental conditions

Endospore

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(Prokaryotic cell structures and functions)
Attachment to surfaces, bacterial mating

Fimbriae and pili

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(Prokaryotic cell structures and functions)
Provides the power of motility or self-propulsion

Flagella

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(Prokaryotic cell structures and functions) - Buoyancy for floating in aquatic environments.

Gas vacuole

(Prokaryotic cell structures and functions) - Storage of carbon, phosphate, and other substances

Inclusion bodies

(Prokaryotic cell structures and functions) - Localization of genetic material (DNA)

Nucleoid

(Prokaryotic cell structures and functions) - Contains hydrolytic enzymes and binding proteins for nutrient processing and uptake’

Periplasmic space

(Prokaryotic cell structures and functions) - Selectively permeable barrier, mechanical boundary of cell, nutrient and waste transport, location of many metabolic processes (respiration, photosynthesis), detection of environmental cues for chemotaxis

Plasma membrane

- unicellular organisms without nuclei * No organelles * Have cell walls * Lacks peptidoglycan * DNA is more similar to eukaryotes, denotes lineage. * Live in extreme environments - No oxygen - hot springs, deep ocean * Energy: Chemosynthesis*

ARCHAEBACTERIA

ARCHAEBACTERIA Biological Functions:

* Protecting cell against ion & pH fluctuations, osmotic stress, degrading enzymes or predacious bacteria. * helps in maintaining shape & envelope rigidity of the cell. * it promotes cell adhesion to surfaces * widely studied recently especially in connection with nanotechnology due to their ability to self assemble protein units without the aid of enzymes.

Major Types of Archaebacteria Cell Wall - Type I - The most common type of archaeal cell wall is an

S layer composed of either protein or glycoprotein.

Major Types of Archaebacteria Cell Wall - Type 2 - Additional layers of material are present outside the S-layer. In Methanosprillum, there is a

protein sheath external to the S-layer.

Major Types of Archaebacteria Cell Wall - Type 3, In Methanosarcina,

S-layer is covered by a chondroitin like material called as methanochondroitin.

Major Types of Archaebacteria Cell Wall - Type 4 - S-layer is the outermost layer and is separated from the plasma membrane by a peptidoglycan-like molecule called

psuedomurein.

Major Types of Archaebacteria Cell Wall - Type 5

- S layer is absent. cell wall is single thick, homogenous layer - Gram positive bacteria. These archaea often stain Gram positive. This type is present in Methanobacterium, Halococcus etc.

It is a thin layer lining the inner surface of the cell wall. * Semipermeable membrane controlling the flow of metabolites * Chemically, consists of Lipoprotein and carbohydrates. Sterols are absent

Cell Membrane

Differences between bacterial and archaeal phospholipids:

* chirality of glycerol – the glycerol used to make archaeal phospholipids is a stereoisomer of the glycerol used to build bacterial and eukaryotic membranes * linkage (ester vs. ether linkage) * side chains (fatty acids vs. isoprenoid chains) * branching of side chains – different physical structures; can form carbon rings

embedded in or loosely attached to the cell membrane

Cell Membrane Proteins

Prokaryotic Cell membrane Functions

* permeability barrier * regulate movement of materials into and out of cell * contains proteins that transport nutrients into the cells and eliminate waste materials * synthesizes cell wall components * assist with DNA replication (anchors DNA) * secretes proteins * carries on cell respiration (ATP synthesis) * contains bases of flagella * proteins respond to chemical substances in the environment

Transport Systems 1. Rarely used by prokaryotes; no energy expenditure (i.e. glycerol) 2. Movement is against a concentration gradient; requires energy expenditure - Uses proton motive force (i.e. lactose and waste products; efflux pumps) - Uses ATP; extremely high substrate affinity of the periplasmic-binding proteins (i.e. maltose) 3. Chemically alters (phosphotransferase system) a molecule as it passes through the cell membrane; uptake does not affect the concentration gradient (i.e. glucose, mannose, fructose)

1. Facilitated diffusion (Passive transport) 2. Active transport - Major facilitator superfamily - ABC transporters 3. Group Translocation

used to actively move out certain proteins synthesized by the cell – i.e. proteins used to make up structures like flagella; enzymes to break down substances too large to transport into the cell – distinguishes proteins based on characteristic sequence of amino acids that make up one end (signal sequence) – uses ATP – still poorly understood

Transport System (SECRETION) general secretory pathway

semifluid substance inside the cell membrane * 4/5 water + 1/5 dissolved substances (enzymes, proteins, carbohydrates, lipids, salts, vitamins and various inorganic ions) * where chemical reactions take place

Cytoplasm

Colloidal system of variety of organic and inorganic solutes in viscous watery solution * No ER and Mitochondria * Contains mesosomes, inclusions, and vacuoles

Cytoplasm

Vesicular, convoluted invaginations of the plasma membrane * Prominent in GM+ bacteria * Principal sites of Respiratory enzymes * Analogous to mitochondria in Eukaryotes

Mesosomes

chromosome region * gel-like region containing the chromosomes and plasmids

Nucleoid

single, circular, double-stranded DNA molecule that contains all genetic information required by a cell * 1 mm long * 10% of cell’s total volume – supercoiled chromosomal DNA * Archaea chromosome: complexed with proteins; resembling histone proteins

Chromosomes

* accessory genetic information * circular, supercoiled, double stranded DNA molecules * 0.1 – 10% of chromosome size * contains hundreds of genes (5-100 genes) * can be of many types per cell * not required but may provide bacteria with genetic advantage * may contain genes for antibiotic resistance (R), disease production * can be transferred and spread to other bacterial cells * replicate independently from chromosome

Plasmids

* sites for protein synthesis – protein – 50% of bacterial cell dry weight – 90% of cell energy is for protein synthesis * the faster the cell is growing, the faster proteins are produced, the greater the number of ribosomes * site for antibiotic action (streptomycin and tetracycline)

Ribosomes

Subunit Ribosome

Prokaryotic Ribosome - 30S; 50S = 70S Eukaryotic Ribosome - 60S; 40S = 80S

contain the pigments used to capture light energy for synthesis of sugars

Chromatophores/ chlorosomes

convert nitrogen compounds into plant-useable form – house the enzymes used in deriving energy from oxidation of nitrogen compounds

nitrifying bacteria

* variety of small bodies within the cytoplasm * storage of materials that are later use as source of nutrients * reservoir of structural building blocks * granules; vesicles

Inclusion Bodies

is responsible for the rigidity of the bacterial cell wall and for the determination of cell shape

Peptidoglycan

subunits are covalently joined to one another to form a glycan chain * high molecular weight linear chain * serves as backbone of the peptidoglycan molecule

N-acetylglucosamine (NAG) N-acetylmuramic acid (NAM)

characterized by the presence of a very thick peptidoglycan layer (≈30 layers) * 20-80 nm thick * Cell wall contains 90% Peptidoglycan and 10%Teichoic acid * fully permeable to many substances (sugars, amino acids, ions)

Gram Positive Cell Wall

Interwoven in the cell wall of Gram-positive are

Teichoic acids and lipoteichoic acids (covalently bonded to NAM)

contains a thin peptidoglycan layer adjacent to the cytoplasmic membrane - also contains an additional outer membrane composed by phospholipids and lipopolysaccharide (LPS) which face into the external environment and periplasmic space

Gram Negative Cell Wall

Outer Membrane has: 1. specialized channel-forming proteins – channels for low molecular weight substances 2. translocate proteins produced to the outside of outer membrane

1. porins 2. secretion systems

The LPS (in outer membrane) present on the Gram negative cell wall consists of 3 regions:

* Polysaccharide determining O antigen * Core Polysaccharide * Glycolipid portion /Lipid A

causes a form of Septic shock for which there is no direct treatment.

LPS or endotoxin

Lipopolysaccharide (LPS) PARTS: - responsible for toxic properties of G- bacteria (endotoxin) – anchors the LPS in the bilayer – composition recognizable by body as presence of invading bacteria – small amounts may elicit defense system response enough to effectively eliminate the pathogen

Lipid A

Lipopolysaccharide (LPS) PARTS – side chain portion of LPS directed away from the membrane – chains of sugar molecules with varying composition and lengths – used to identify certain species or strains – i.e. E. coli O157:H7

O-specific polysaccharide (O-antigen)

* most observed among G- bacteria, rarely in G+ bacteria * gel-like fluid (periplasm) and protein-filled (secreted proteins) * very active area of cell metabolism (i.e. nutrient degradation and transport) * contains 1. digestive enzymes (destroy potentially harmful substances), 2. transport proteins (transport metabolites into the bacterial cytoplasm)

Periplasmic Space

____ constitute for the major surface antigens. e.g.: In Streptococcus pneumoniae (Gram positive) Teichoic acid bears the antigenic determinants called the ___

Teichoic acids; “Forssman antigen”

one of the most important sites for attack by antibiotics compounds that interfere with the synthesis of peptidoglycan or alters its structural integrity

– penicillin – enzyme lysozyme

– interfere with peptidoglycan synthesis – binds to proteins involved in cell wall synthesis – prevents cross-linking of glycan chains – more effective against G+ bacteria – modified to create derivatives that can pass through porin channels

penicillin

(Targeting the Peptidoglycan – found in many body fluids – breaks bond between the NAM and NAG molecules

lysozyme

Differences of Cell Wall gram positive vs. gram negative (LONG PPT)

Lipopolysaccharide Outer membrane Negative Gram Positive Peptidoglycan (thick) Teichoic acid

The Gram staining method, named after the Danish bacteriologist who originally devised it in 1882 (published 1884), ___ is one of the most important staining techniques in microbiology.

Hans Christian Gram,

reflects fundamental differences in the biochemical and structural properties of bacteria.

The Gram reaction

Gram Stain 1. Crystal violet 2. Iodine 3. 95% ethanol 4. Safranin

1. Primary stain 2. Mordant 3. Decolorizer 4. Counterstain

Mycoplasma species * variable shape * have sterols in their cell membranes (stability)

Cell Wall-Less Bacteria

“Parts of the body that protrude out from the main body

Appendages; Cell wall appendages

a general term for any network of polysaccharide (and small proteins) lying outside the cell. * bacteria may appear moist and glistening * thick or thin; flexible or rigid * few have repeating units of one or two amino acids (D-amino acids)

GLYCOCALYX

Glycocalyx Type 1. less discrete structure or matrix which embeds the cell ; diffuse and irregular 2. discrete detectable layer of polysaccharides deposited outside the cell wall; distinct and gelatinous (thicker and more rigid)

1. Slime Layer 2. Capsule

Capsule and slime layers: In most species, the solid material is a ____ though in some species _____

complex polysaccharide polypeptide or protein

Glycocalyx Type When glycocalyx is tightly bound to the cell wall of bacteria, it is referred to as capsule. It is gelatinous in nature and cannot be easily stained and removed from the bacterial cell wal

Capsule

The glycocalyx is called “slime layer” if it is loosely bound to the cell wall of bacteria. Slime layer is irregular and can easily be removed from the bacterial cell wall.

Slime Layer

Functions of Glycoclayx

- Virulence factor; Cause disease in their host - Protects bacteria from antibiotics, chemicals etc - Adherence to surface - Avoidance of desiccation - In cell-cell recognition

some enables bacteria to adhere to specific surfaces and grow as a - polysaccharide-encased mass of bacteria coating a surface

a BIOFILM; streptococcus mutans - Production of dextran or lactic acid within the biofilm

is a sharply defined, organized structure (e.g.: Pneumococcus)

Capsule

Some bacterial species are mobile and possess locomotory organelles - consist of a number of proteins - responsible for bacterial motility/locomotion (pushes bacterium through liquid) - spins like a propeller (rotates both clockwise and counterclockwise)

Flagella; (protein: flagellin)

Flagella * Found in all motile bacteria except ___ * Flagella are highly ___ * Termed as the ____

Spirochetes antigenic, ‘H’ Antigen.

Structure and Arrangement of Flagella has three basic parts – twisted but with hollow core – anchored in cell membrane and cell wall; rings and rod – wide region at the base of flagella; connects the two parts

– filament (flagellin) – basal body (motor) – hook

Types of Flagellar Arrangement 1. Single flagellum at one pole 2. Tuft of flagella at one pole 3. Flagella at both poles 4.Flagella all over 5. Tuft of flagella at both ends

1, Polar/Monotrichous (Vibrio cholerae) 2. Lophotrichous (Spirillum) 3. Amphitrichous (Alkaligenes faecalis) 4. Peritrichous (E.coli) 5. Amphilophotrichous

– bacterial behavior in seeking out favorable environments and avoiding harmful ones

taxis

taxis - sense chemicals and move toward regions that contain more nutrients (attractant) and away from regions with toxic materials (repellant)

chemotaxis

taxis -swim to regions that contain favorable concentrations of dissolved oxygen

aerotaxis

taxis - movement to regions of optimal light intensity and quality

phototaxis

taxis - response to Earth’s magnetic field

magnetotaxis

Flagella are ____ helices, and bundle and rotate together only when _____. When some of the rotors reverse direction, the flagella unwind and the cell starts ____ (may happen occasionally, leading to the cell seemingly thrashing about in place, resulting in the reorientation of the cell. )

left-handed; rotating counterclockwise. "tumbling".

is mediated by the activity of hair-like filaments called type IV pili which extend from the cell's exterior, bind to surrounding solid substrates and retract, pulling the cell forwards in a manner similar to the action of a grappling hook

Twitching

Movement on a solid surface. Cells produce, move in slime trails.

Gliding Motality

Mechanism of sliding motility, the expansion powered by the pushing force of dividing cells

Sliding

tiny, hollow projections not involved in movement * shorter, thinner, and straighter than flagella * made up of pilin proteins – helical structure around a central hollow core

Pili

2 types of Pili 1. with adhesins 2. * longer than attachment pili * DNA transfer from one cell to another

attachment pili (fimbriae) conjugation pili/ sex pili/ F pili

* Hair like surface appendages * 0.5-10 nm thick * Shorter and thinner than flagella * Formed of protein subunits – Pilin * Organs of adhesion * Forms “Pellicles” * Hemagglutination –Clumping of RBCs (Escherichia, Klebsiella) * Special type of Fimbriae called sex pili, help in attachment to other bacteria

Fimbriae

* Organs of adhesion * Forms “Pellicles” * Hemagglutination –Clumping of RBCs (Escherichia, Klebsiella) * Special type of Fimbriae called sex pili, help in attachment to other bacteria

Fimbriae

* similar in structure to fimbriae but are generally longer * one or few per cell * functions in gene transfer * may serve as specific receptors for certain types of virus particles * some are involved in attachment to human tissues

Conjugation Pilus

* resting (dormant) stages of vegetative cells of some bacterial species (Bacillus and Clostridium) * very resistant to heat and harmful agents (drying, cold, radiation, acids, bases, chemical disinfectants) * produced through sporulation * spores may remain dormant for 100 years

Endospores (SPORES)

Endospore Function

- Protection for the bacterial genome

* Dormant cell * Resistant to adverse conditions - high temperatures - organic solvents * Produced when starved * Contain calcium dipicolinate DPA, Dipicolinic acid ⚫ Identification of Bacteria ⚫ Pathogenesis ⚫ Resistance

Endospores (spores)

Endospores consists of

core, cortex, spore coat, exosporium

[endospore part] thin, delicate covering made of protein

exposporium

[endospore part] – composed of spore-specific proteins – “sieve” – excludes substances such as lysozyme

spore coat

[endospore part] – loosely cross-linked peptidoglyan – maintains core in a dehydrated state – protects core from effects of heat

cortex

[endospore part] – has small, acid-soluble proteins that bind DNA – contains the core wall, cell membrane, cytoplasm, nucleoid, etc. – rich in ____ acid and ___ ions; partially dehydrated (10-30% water) – contains core-specific proteins (small acid-soluble spore proteins) * bind tightly to core DNA and protect it from UV radiation, dessication, dry heat * carbon and energy source during germination

core (spore protoplast) - dipicolinic acid; calcium

In the bacterial endospore Which may occupy as much as half the spore volume, rests beneath the spore coat.

The cortex

complex, yet highly ordered sequence of changes that initiates when cells are grown in low amounts of carbon or nitrogen * ≈8 hours

Sporulation

triggered by brief exposure to heat or certain chemicals

Germination

A differential staining technique is used to distinguish between the vegetative cells and endospores - Designed by:

The endospore stain; Alice B. Schaeffer and Macdonald fulton

: a thin, clear, gel-like outer layer that acts as a membrane (ectoplasm); and an inner, more watery grainy mass (endoplasm) containing structures called organelles.

Amoeba

food synthesis; takes place; & food is stored in the form of glycogen or protein called ___.

in the endoplasm; chromatoidal bodies.

envelopes the cell; fxns as the locomotor apparatus for the procurement & ingestion of food, in respiration, discharge of metabolic wastes & protection of the org.

ectoplasm

locomotory organelles arising from the ectoplasm may vary from: a) numerous short threads distributed over the surface of the body. b. false feet; in Amoebae (crawling movement) c. in flagellates; hair-like projections

1. Cilia 2. Pseudopodia 3. Flagella

Absorb liquid nutrients from the medium or ingest bacteria & cells at any site of the body surface.

PROTOZOANS

Protozoans: Others have specialized cell mouth called ____ usu. located in anterior end of the body.

CYTOSTOME

Protozoans: Ciliates have in addition a cell anus or ____ at the posterior end of the body & through which particulate food wastes are discharged.

CYTOPYGE

The typical life stages of protozoans

Cyst and trophozoite

Is the small reproductive nucleus of ciliate protozoa

Micronucleus

Is the large non-reproduuctive nucleus of ciliate protozoa

Macronucleus

are vegetative or feeding forms

Trophozoites

- A more or less central body in the vesicular nucleus of certain protozoa (for example, trypanosomes, parasitic amebae), with the chromatin.

Endosome/ Karyosome

Flagellate move by help of ___ Example of Flagellates ar: (3)

Flagella - Trypnosoma, Leshmenia (blood pathogen) - Giardia (intestinal parasite) - Trichomonas (reproductive tract pathogen)

Characteristic features of the stained trophozoite include:

1) two nuclei (Nu) with central karyosomes (k), 2) fibrils running the length of the parasite – axonemes (Ax), and 3) Median Bodies (MB)/ Parabasal bodies

The function of the median bodies are not known, but most believe they are somehow involved with the - plays a role in the attachment of the trophozoite to the intestinal epithelium

*adhesive disk* and its formation.

The three major groups of fungi are:

* multicellular filamentous molds * macroscopic filamentous fungi that form large fruiting bodies. Sometimes the group is referred to as ‘mushrooms’ * single celled microscopic yeasts

Structures that help fungi absorb and digest food 1. the body of a typical fungus; consisting of many tiny tubes 2. hyphase tangled into a thick mass

1. Hyphae 2. Mycelium

the first Penicillium fungi used for the isolation of penicillin antibiotics, which is used for the treatment of Gram-positive bacteria. It is also used in the production of other β-lactam antibiotics

Penicillium chrysogenum is also known as Penicillium notatum

are small, lemon-shaped single cells that are about the same size as red blood cells. They multiply by budding a daughter cell off from the original parent cell

Yeasts

Structure of Viruses: 1. Protective Shell 2. A lipid containing membrane that surrounds some virus particles

1. Capsid 2. Envelope

Parts of Viruses

Fatty Envelope Capsid Shell Proteins sticking out of fatty envelope Instruction booklet genes