Biology II Lecture 1 exam

What are prokaryotes

• bacteria and archaea

-fully functioning cells

• Extremely diverse group due to varied methods of \n acquiring and using energy

• On the Earth for 3.5 billion years

Prokaryote structure

• Prokaryote means “before nucleus” (Lack a membrane-bound nucleus)

• DNA in nucleoid region

• May have accessory ring of DNA (plasmid)

• Lack membranous organelles

• Outer cell wall containing peptidoglycan

• Some move by means of flagella

Prokaryote Structure

• Cell envelope:

-Glycocalyx (can be organized in a capsule or loosely organized as a slime layer)

-Cell wall

-Plasma membrane

• Cytoplasm:

-Nucleiod (single strand of circular DNA, Plasmids are sings of accessory DNA)

-Ribosomes (synthesize proteins)

-Thylakoids (cyanobacetria)

• Appendages:

-Flagella (can rotate 360, hook inserted in a basal body, Archean flagella lack a basal body)

-Conjugation pilus (used for reproduction to swap genetic information, binary fusion)

-fimbrae (short bristle like hairs that help adhere to surfaces)

what is bacteria

• Bacteria are the more common type of prokaryote

-Over 2,000 different bacteria have been named

• Most bacterial cells are protected by a cell wall

- Contains peptidoglycan (reacts to Gram stain and results used to differentiate bacteria)

Gram stains of Bacteria

• Gram stain procedure:

• When washed after staining:

- Gram- positive bacteria retain dye and appear purple (Thick peptidoglycan layer causes stain to remain)

-Gram- negative bacteria do not retain dye and appear pink (Peptidoglycan layer is much thinner)

Cell wall of Bacteria

• Structure of cell wall also of diagnostic use

-Bacteria can be classified in terms of their three basic shapes

• Spiral (spirilli)

• Rod (bacilli)

• Round (cocci)

Metabolism of Bacteria

• Bacteria are very diverse in their needs for oxygen

• Oxygen requirements:

-Obligate aerobes: UNABLE to grow in the ABSENCE of free oxygen, require oxygen

-Obligate anaerobes: UNABLE to grow in the PRESENCE of free oxygen, “allergic” to oxygen

-Facultative anaerobes: ABLE to grow in EITHER the presence or absence of free oxygen 10

what troph can bacteria be

Bacteria can be autotrophs or heterotrophs

define autotrophic bacteria (2 types)

• Autotrophic means produce their own food

• Photoautotrophs

-Photosynthetic

-Use solar energy to reduce CO2 to organic compounds

• Chemoautotrophs

-Chemosynthetic

-Oxidize inorganic compounds (ammonias) to obtain the necessary energy

-Cycle keeps nitrogen in the ecosystem

-Use it to reduce CO2 to an organic compound

define Heterotrophic bacteria

• Heterotrophs must take in food to get energy

• Most prokaryotes are chemoheterotrophs (take in organic nutrients)

• Aerobic saprotrophs (decompose most large organic molecules to smaller molecules, Essential recyclers in healthy ecosystem)

• May be free-living or symbiotic

What are Symbiotic Relationships formed between

archaea and bacteria

Mutualism

• both species benefit

• EX: Human intestinal bacteria that produce vitamin K and B12

• EX: Nitrogen fixing bacteria live in nodules in plants

commensalism

• One species benefits

• EX: E. coli creates an environment suitable for parasites

parasitism

• one benefits and one is harmed

• EX: Parasitic bacteria cause disease and are called pathogens

Parasitic bacteria and pathogens

• Parasitic bacteria cause disease and are called pathogens

• The deadliest pathogens form endospores

• If environmental conditions are not favorable for reproduction

-Spores are formed and encapsulated to protect them

-Anthrax spores can stay viable for 1,300 years !!

-When conditions are favorable they will resume normal bacterial cell functions

Sexually transmitted bacterial diseases in humans

• Syphilis

• gonorrhea

• Chlamydia

Respiratory bacterial diseases in humans

• Strep throat

• tuberculosis

• whooping cough

bacterial skin diseases in humans 

• Carbuncle

• impetigo

• wound infections

• leprosy

Digestive tract bacterial disease in humans 

• Food poisoning

• dysentery

• cholera

• pepetic ulcers

Nervous system bacterial disease in humans 

• Botulism

• tetanus

• meningitis

Systemic bacterial disease in humans  

• Plague

• typhoid fever

• diphtheria

Other bacterial disease in humans   

• Lyme disease

• Tularemia

Cyanobacteria

• Formerly called the Blue-Green algae (Cyanophyta)

• Cyanobacteria are Gram-negative bacteria that photosynthesize

• Believed to be responsible for introducing oxygen into the primitive atmosphere

-Lack visible means of locomotion

-Can live in extreme environments

-When commensals with fungi, form lichens

Archaea

• Archaea were once considered bacteria

• Carl Woese discovered that the base sequence of their rRNA differs from Bacteria

• Other differences:

-Archaea do not have peptidoglycan in their cell walls like the Bacteria

-Archaea biochemically are more like Eukarya than Bacteria

Archaea Metabolism

• Most are chemoautotrophs

• Some mutualistic

• Some commensalistic

• None known to be parasitic

• None are photosynthetic

• Many live in harsh conditions

Archaea habitats

• Anaerobic marshes: methanogens

- Produce methane from hydrogen gas and CO2

• Salty lakes: halophile

- Require high salt concentrations for growth

• Hot sulfur springs: Thermoacidophiles

-Reduce sulfides and survive best at temperatures above 80ºC (176oF)

-Plasma membranes contain unusual lipids

6 protist supergroups

1\. Archaeplastids

2\. Chromalveolates

3\. Excavata

4\. Amoebozoa

5\. Opisthokonts

6\. Rhizaria

Protist Supergroup Archaeplastids

• Green Algae

-Chlorophytes

-Charophytes

• Red Algae

Protist Supergroup Chromalveolates

• Stramenopiles

- Brown algae

- Diatoms

-Water molds

• Alveolates

- Dinoflagellates

- Ciliates

- Apicomplexans

Protist Supergroup Excavata

• Euglenids

• Parabasolids

• Diplomonads

• Kinetoplastids

Protist Supergroup Amoebozoa

• Amoeboids

• Slime Molds

Protist Supergroup Opisthokonts

• Choanoflagellates

• Nulceariids

Protist Supergroup Rhizaria

• Foraminiferans

• Radiolarians

what domain is Protists in and what types of organelles do they have

• eukarya

• membranous organelles

how are protists classified

by supergroups

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Endosymbiotic hypothesis of protists

• Aerobic bacteria became mitochondria

• Cyanobacteria became chloroplast

both have their own DNA

both have double membrane because vesicles is used to prevent from rejection

General Biology of Protists

• Many are unicellular

• Highly complex

• Unique organelles, such as contractile vacuoles

-Amoeboids and ciliates

• Most are free-living

• Some are colonial

• Single cell or huge

  -200m long

Protists consumption

• Very diverse in how they acquire food

-Parasitic (ex: malaria)

-Autotrophic (make their own food) (Photosynthetic)

• Heterotrophic (consume food)

-Engulf by endocytosis (eating)

• Mixotrophic (both auto and hetero trophic)

life cycles of protists

• Asexual reproduction by mitosis is most common

• Sexual reproduction may occur in unfavorable conditions (bad environment and share info by assexual reproduction)

• Spores allows protists to survive hostile environments

- A cyst is a dormant cell with a resistant outer covering

- Helps certain parasitic species survive the host’s digestive juices

what does endo, eco, and pinto mean

releasing, entering, and drinking like liquid

Ecology of Protists

• Protists are of enormous ecological importance

• Photoautotrophic forms:

- Produce oxygen

- Function as producers in both freshwater and saltwater ecosystems

• Major component of plankton:

- Organisms that are suspended in the water

- Serve as food for heterotrophic protists and animals

Complexity and diversity of protists

* Complexity and diversity of protists makes them difficult to classify

• Many classification schemes proposed

• None has broad support

• Cannot be classified as plants ( bc they do not protect their gametes and zygote)

• Cannot be classified as animals ( bc they Do not undergo embryonic development)

• Cannot be classified as fungi ( bc they Do not have chitin in their cell wall)

• Could be split into as many as a dozen kingdoms

Protists SUPERGROUP Archaeplastida

• Photosynthetic

• Have plastids (chloro plast )derived from cyanobacteria

• Includes land plants:

• Green Algae:

1. Chlorophytes

-Chlamydomonas

-Volvox

2. Charophytes

• Red Algae:

•Porphyra

Protists Supergroup Archaeplastids: Green Algae

• Contain chlorophyll a and b

• Variety of environments from oceans to snow banks

• Form symbiotic relationships

• Majority are unicellular but can be colonial or filamentous

• Not always green

• Chlorophytes

-Chlamydomonas

-Volvox

• Charophytes

-Spirogyra

-Chara

Protists Supergroup Archaeplastids: GreenAlgae: Chlorophytes

• Chlamydomonas

• Single, large chloroplast with a pyrenoid to synthesize starch

• May have a bright red eyespot

• Light-sensitive to find locations for photosynthesis

• Two long, whip-like flagella

• Volvox

• Colonial – loose association of independent cells

• hollow sphere of thousands of cells arranged in a single layer surrounding a watery interior

• Some cells are specialized for reproduction

Protists Supergroup Archaeplastids:GreenAlgae: Charophytes

• Spirogyra

• Filamentous green algae: end-to-end chains

• Ribbon-like, spiraled chloroplasts

• Sexual reproduction by conjugation:

- Contents of one filament move into cells of other filament

-Forms diploid zygospores

• Chara

• Most closely related to land plants

• Freshwater lakes and ponds

• Commonly called stonewort

• Encrusted with calcium carbonate deposits

Protists Supergroup Archaeplastids: Red Algae

• Multicellular seaweeds

• Red and blue pigments in addition to chlorophyll

• Mostly in warm seawater

• Economically important

• Agar: capsules; dental impressions; cosmetics; culture medium; electrophoresis; food prep.

• Carrageen: an emulsifying agent used in chocolate, low-fat foods, & cosmetics

• The reddish-black wrappings around sushi rolls consist of processed Porphyra blades

• Porphyra

Protists SUPERGROUP Chromalveolates

Two large subgroups (members):

• Stramenopiles

Have flagella or are descended from a flagellated ancestor

- Brown algae

- Diatoms

-Water molds

• Alveolates

Have alveoli (air sacs) that lend support

-Dinoflagellates

-Ciliate

-Apicomplexans

Protists Supergroup: Chromalveolates: Stramenopiles

1. Brown algae

• Most in cold ocean waters along rocky coasts

• No unicellular or colonial brown forms

• Chlorophylls a and c

• Laminaria (Kelp)

• Fucus (rockweed)

2. Diatoms

• Have ornate silica shell

• Large portion of plankton

• Diatomaceous earth used in industry

• Cyclotella

3. Water mold

• Filamentous

• Form furry growths

• Some live on land

• Responsible for the potato famine in Ireland

• Saprolegnia

 Protists Supergroup: Chromalveolates: Alveolates

1. Dinoflagellates

• Unicellular

• Protected by cellulose plates

• Two flagella

• Cause red tide

• Ex: Gonyaulax, Ceratium

2. Ciliates

• Unicellular

• Move by cilia

• Trichocysts for defense

• Ex: Paramecium, Stentor

3. Apicomplexans (Sporozoans)

• Nonmotile

• Parasitic

• Spore forming

• Apical complex of organelles at infective end

• Mosquito parasite Plasmodium causes one type of malaria

• Ex Toxoplasma is found in cat feces

Protists SUPERGROUP: Excavates

• Include zooflagellates

• Atypical or absent mitochondria

• Most are symbiotic and many parasitic

• Distinctive flagella

• Members:

• Euglenids

• Parabasalids

• Diplomonads

• Kinetoplastids

Protists SUPERGROUP: Excavates

1. Euglenids: (eat others that have chloroplasts)

• Small freshwater unicellular organisms

• Difficult to classify

• Have two flagella and an eyespot (shades a photoreceptor)

• EX: Eulgena

2. Parabasalids

• Single celled

• Survive in low oxygen

• Fibrous connection between Golgi apparatus and flagella

• Ex: Trichomonas

3. Diplomonads

• Single celled

• Survive in low oxygen

• Common beaver ponds

• Two nuclei and two sets of flagella

• Ex: Giardia

4. Kinetoplastids

• Single celled

• Have mitochondria with kinetoplasts

• Large DNA mass in mitochondria

• Ex: Trypanosoma (sleeping sickness)

Protists SUPERGROUP: Amoebozoans

• Protozoans that move by pseudopod

• False foot

• Pseudopods form when cytoplasm streams forward in aparticular direction

• Usually aquatic

• Members:

1. Amoeboids

2. Slime molds

• Plasmodial

• Cellular

Protists SUPERGROUP: Amoebozoans: Amoeboids

• Move

• Ingest food with pseudopod

• Phagocytize prey

• Food vacuoles digest prey

• Contractile vacuoles removed excess water

• Can be parasitic

• Ex: Ameoba

Protists SUPERGROUP: Amoebozoans: Slime molds

1. Plasmodial slime mold

• Body in the form of a plasmodium

• Diploid, multinucleated, cytoplasmic mass

• Enveloped by a slimy sheath

• Produce sporangium which in turn produces spores

• Ex: Physarum

2. Cellular Slime Mold

• Body in the form of individual amoeboid cells

• Later aggregate into pseudoplasmodium

• then forms sporangium & spores

Protists SUPERGROUP: Opisthokonts

• Unicellular and multicellular protozoans.

• Includes animals and fungi

• Members:

1. Choanoflagellates

2. Nucleariids

Protists SUPERGROUP: Opisthokonts: Choanoflagellates

• Animal-like protozoans that are close relatives of sponges

• Include unicellular as well as colonial forms

• Ex: Codonosiga

Protists SUPERGROUP: Opisthokonts: Nucleariids

• Rounded or slightly flattened cell body

• Threadlike pseudopods called filopodia

• Close fungal relatives due to molecular similarities

• Ex: Nuclearia

Protist SUPERGROUP: Rhizarians

• Organisms with fine, threadlike pseudopods.

• Previously classified along with Amoebozoans

• New molecular data indicate the two groups are not closely related

• Skelton (like a starfish) called a test

• Fossil test are used to index rock

• Egyptian species found world wide

• Members:

1. Foraminiferans

2. Radiolarians

Protists SUPERGROUP: Rhizarians: Foraminiferans

• Calcium carbonate test is often multichambered

• Pseudopods extend through openings in the test

• Fossilized tests make up White Cliffs of Dover

Protists SUPERGROUP: Rhizarians: Radiolarians

• Glassy silicon test is internal and has a radial arrangement of spines

• Pseudopods are external to the test

Characteristics of the Fungi

• Kingdom Fungi contains over 100,000 species

• Mostly multicellular eukaryotes that share a common mode of nutrition

• Heterotrophic

- Cells release digestive enzymes and then absorb resultant nutrient molecules

• Absorption rather than ingestion of food makes fungi saprotrophs

• Some are parasitic

• Several have mutualistic relationship

Evolution of Fungi

• Protists evolved some 1,500 mya

• Plants, animals, and fungi trace their ancestry to protists

• Molecular data tells that animals and fungi shared a common ancestor after plants evolved

• Flagellated unicellular protist, was most likely the common ancestor

• Animals and fungi are more closely related to each other than either is to plants.

• Description of fungal structure applies best to the zygospore fungi, sac fungi, and the club fungi.

• Fungal anatomy doesn’t lend itself to becoming fossilized

• Probably evolved earlier than the earliest known fungal fossil dated 450 mya

Structure of Fungi

Body (thallus) of most fungi is a multicellular mycelium

• Consists of a vast network of thread-like hyphae

• Hyphae grow at their tips

• Give the mycelium a large surface area to volume ratio

•Some have cross wallscalled septate

• Aseptate fungi are multinucleated

Fungal cells difference from plants:

• Cell walls of chitin, like insect exoskeleton

• Lack chlorophyll

• Excess food stored as glycogen as in animals

• Lack motility

• Grow toward a food source

• Possibly evolved from red algae - both lack flagella

Fungi reproduction

Both sexual (in most) and asexual reproduction:

• Asexual reproduction usually involves the production of windblown spores

• Unicellular yeasts reproduce by budding

• Sexual reproduction involves three stages:

1. Haploid Hyphae

2. Dikaryotic Stage

3. Diploid Zygote

What happens during Sexual Reproduction in fungi 

• During sexual reproduction, hyphae from two different mating types fuse

• Hyphae that contain paired haploid nuclei are said to be Dikaryotic (The two nuclei are NOT fused at this point)

• When nuclear fusion occurs, diploid nucleus is formed, which produces haploid windblown spores by meiosis

• Spores germinate directly into haploid hyphae without embryological development

4 Phylum of Fungi

• Fungal phylogeny is under debate

• Zygomycota

• Glomeromycota

• Ascomycota

• Basidiomycota

Fungi: Zygomycota

• Over 100 species

• Bread mold is a common example

• Rhizopus stolonifera

• Forms zygospore during sexual reproduction

•Results from fusion of hyphae from two different mating types

• Zygospore is diploid – undergoes meiosis to produce haploid sporangium filled with spores

• spores is in sexual and asexual reproduction

Fungi: Basidiomycota

• Over 30,000 species

• Familiar species

• Toadstools, mushrooms, bracket fungi, puffballs, stinkhorns– some deadly poisonous

• Also plant diseases such as the smuts and rusts

• Mycelium composed of septate hyphae

Fungi: Basidiomycota reproduction

Usually reproduce sexually

• Haploid hyphae fuse, forming adikaryotic (n + n) mycelium

• Dikaryotic mycelium forms fruitingbodies called basidiocarps (mushrooms)

• Basidiocarps form basidia

• Nuclear fusion happens in the basidia followed by meiosis

• Produces spores (up to 40,000,000 per hour)

Fungal Symbiosis: Lichens

• Symbiotic association between a fungus and a cyanobacterium or green alga.

• Specialized fungal hyphae penetrate the photosynthetic symbiont.

• Nutrients are transferred by the hyphae directly tothe fungus.

• Three morphological types:

1. Crustose – often located on bare rocks or tree bark

2. Fruticose – shrublike

3. Foliose – leaflike

Fungal Symbiosis: Mycorrhizae

• Mutualistic relationships between soil fungi and the roots of most plants.

• Give plants greater absorptive surface

• Help plants acquire mineral nutrients in poor soil

• Hyphae may enter cortex of roots, but not the cytoplasm

• Ectomycorrhizae exterior to the root and grow between cell walls.

• Endomycorrhizae penetrate the cell walls

What makes prokaryotes so divers are a group?

The varied methods of acquiring and using energy

What does the term prokaryote mean? What do these organism lack? Where is there DNA contained? What is a plasmid? What is the cell wall composed of?

• Prokaryote means before nucleus.

• These organisms lack a nucleus.

• The DNA is contained in the nucleoid region.

• A plasmid is an accessory ring of DNA.

• The cell wall is composed of peptidoglycan.

What are the three main structural components of a prokaryote? What features are present in each component?

1. Cell envelope: glycocalyx, cell wall, plasma membrane

2. Cytoplasm: nucleoid, ribosomes, thylakoids (cyanobacteria)

3. Appendages: flagella, conjugation pilus, fimbriae

What are the two type of glycocalyx?

1. Capsule (well organized)

2. Slime layer (loosely organized)

What are three features found in the cytoplasm of a prokaryote? 

The cytoplasm contains a Nucleoid. There is a single strand of circular DNA and often plasmids (accessory rings of DNA). The cytoplasm also contains ribosomes to synthesize proteins. 

How are flagella attached? What type of movement are they capable of?

Flagella’s are attached by a hook inserted in a basal body. They are capable of rotating 360 degrees

What is a conjugation pilus used for? What process follows the use of a conjugation pilus?

• Conjugation pilus are used for reproduction to swap genetic information.

• Binary Fission follows the use of a conjugating pilus.

What do fimbriae help prokaryote to do?

Fimbrae help prokaryotes adhere to the surfaces.

What is the more common type of prokaryote? What do most of these organisms have in their cell walls?

• Bacteria

• Peptidoglycan

What are the different categories of bacterial metabolism? Define each of these categories

1. Obligate aerobes: Require oxygen and cannot without it.

2. Obligate anaerobes: Require the absence of oxygen to grow.

3. Facultative anaerobes: Can grow in an environment with or without free oxygen.

What are the six ways that bacteria can obtain food? Define each

1. Autotrophs: produce their own food

2. Photoautotrophs- use photosynthesis to reduce carbon dioxide to organic compounds

3. Chemoautotrophs: oxidize inorganic compounds to obtain necessary energy. It keeps nitrogen in the atmosphere while reducing carbon dioxide

4. Heterotrophs: must take in food to gain energy

5. Chemoheterotrophs: consume organic nutrients

6. Aerobic saprotrophs: decompose large organic molecules to smaller ones

What are the three symbiotic relationships that bacteria enter? Give an example of each? 

1. Mutualism: intestinal bacteria in humans that produce vitamin B12 and K.

2. Commensalism: E. coli creates environment suitable for parasites

3. Parasitism: parasitic bacteria (pathogens) cause diseases

What is a pathogen? What is an endospore? When do endospores form? 

• Parasitic bacteria that cause diseases are called pathogens.

• Endospores are spores that are formed within the interior of the cell. Endospores are formed by the deadliest pathogens when the environment are not favorable for reproductions. They are formed to protect and encapsulate them.

What is unique about cyanobacteria? What role are they thought to have played in the Earths primitive atmosphere? Where can they live? How are they related to lichens?

• They are unique because they photosynthesize.

• They are believed to be responsible for the original oxygen levels in the atmosphere.

• They can live in extreme environments.

• Commensals with fungi to form lichens

Who determined that Archaea were separate from bacteria? What did he base his conclusion on? What do Archaea lack in their cell walls? What domain are Archaea most like biochemically?

• Carl Woese determined that arcahae is separate from bacteria based on the base sequence of their rRNA.

• Archaea lacks peptidoglycan in their cell wall.

• Archaea are more likely eukarya than bacteria.

What type of Archaea are not known to exist, yet? What are the three environments listed in your slides that Archaea can inhabit? What are the conditions of these environments?

• Archaea are not known to be parasitic, photosynthetic.

1. Anaerobic marshes: methanogens (uses carbon dioxide and hydrogen to produce methane)

2. Salty Lakes: halophile (require high salt concertation for growth)

3. Hot sulfur springs: Thermoacidophiles (reduces sulfides and survive better at least 80 Celsius, Plasma membranes contains unusual lipids)

What are the various ways that protists can acquire food? What are mixotrophs?

.Parasitic, autotrophic, photosynthetic, heterotrophic, and engulf by endocytosis 

. Mixotrophs are ones that are autotrophic and heterotrophic.

What is the most common form of reproduction in protists? When does asexual reproduction occur? Why?

Asexual reproduction by mitosis is most common in protists. It occurs in unfavorable conditions to share information from one to the other.

What advantages do spores provide? What is a cyst? What advantage does it provide to parasitic protists?

• Spores help protists survive in hostile environment.

• A cyst is a dormant cell that has an outer covering resistance. It helps specific parasitic species survive the host’s digestive juice.

What are some ways that photoautotrophic protists are ecologically important?

Photoautotrophic protists are ecologically important in producing oxygen and in functioning as producers in salt and fresh waters.

Why are protists difficult to classify?

• Protists are difficult to classify because of their complexity and diversity without broad support.

• They can’t be grouped with animals because they don’t undergo embryonic development

• They can’t be grouped with plants because they don’t have protection for their zygotes and gametes.

• They can’t be grouped with fungi because they don’t have chitin in their cell wall.

Explain how fungi are both heterotrophic and saprotrophs. 

Fungi are heterotrophic since the cells release digestive enzymes to break it down and aboard the resultant nutrients. They are also saprotrophs since they abort food rather than ingesting it.

What type of organism is the common ancestor to fungi? What organism group are fungi most closely related to?

• Flagellated unicellular protists are the common ancestor to fungi.

• Animals and fungi are most closely related.

How old is the earliest know fungal fossil? Why do scientists think fungi evolved earlier than the date of this fossil?

The earliest known fungal fossil is dated 450 mya. Scientists think that fungi evolved earlier because fungal anatomy does not lend itself to become fossilized. 

What is a thallus? What is the thallus made of? What is a mycelium made of?

A thallus is the body of fungi that is a multicellular mycelium. Mycelium is made of a network of thread-like hyphae.

Where does growth occur in hyphae? What are septa? 

• In the hyphae, growth occurs at the tip.

• Septa are crosswalks of the hyphae

What are the cell walls of fungi made of? What do fungi lack in their cells? How do they store excess food? What causes the direction of growth in fungi?

• The cell walks of fungi are made of Chitin.

• Fungi lack chlorophyll.

• They store excess food as glycogen.

• The direction of growth in fungi is caused by the location of the food source