Rutgers General Biology 116 Final Exam Review

Systematics

study of the diversity of life and the evolutionary relationships between organisms

2 parts: diversity, evolution

Taxonomy

Describing, naming, and grouping

binomial nomenclature

each species is assigned a two-part scientific name

Genus + specific epithet

Hierarchical classification

i. Species = basic levels of classification

ii. Hierarchy = levels of classification

iii. Each level more inclusive than one below

hierarchical classification system

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

Taxa

Grouping of organisms at any of these levels

Clade

group of species that includes ancestral species & all of its descendants -> Monophyletic group

Phylogentics

study of evolutionary relationships in a group of species

evolution

-Accumulation of genetic changes with population over time

-Allele frequencies

natural selection

mechanism - acts on variation

components of a tree

1.Branch points = nodes

-divergence of 2 lineages from common ancestor

2. sister taxa - groups of organisms that share an immediate common ancestor

3. basal taxa - Lineage that diverges early in history of group

4. Polytomy - Branch point from which more than 2 groups emerge

5. Extant species - currently living, tips of branches

Biological diversity (biodiversity)

all living organisms

Virology

study of viruses (not on tree of life)

General Characteristics of Viruses

1. nonliving particles

2. very small

3. Genetic material

Nonliving particles ( not cells)

-no nucleus, no cytoplasm, no organelles

Nonliving particles (Obligate Intracellular Parasites)

-invade susceptible host cells

-cannot carry out metabolic activities on their own

-survive only by using resources of host cell

Nonliving particles (cannot reproduce on their own)

replicate (multiply) only inside living host cell

Virus size

very small 20-300nm, cannot see with light microscope

Genetic material virus

1. either DNA or RNA

2. single stranded or double

3. linear, circular, or segmented

4. 3-100 genes > info to replicate within host

Virus structure

-Capsid

-Envelope (some viruses)

Capsid

1. Protein coat

2. Capsomere - protein subunit

3. Shape of virus

4. Attachment

Envelope (some viruses)

1. From host plasma membrane

-Exocytosis

2. Bilayer membrane

-Phospholipids (host)

-Post membrane proteins (host)

-Proteins + glycoproteins of viral origin

Viral Replication (intro)

1. Host range

a. Host species that can be infected by a particular virus

b. Narrow Ex. Measles (humans)

c. Broad Ex. West Nile virus (humans, birds, horses)

2. Specific tissues

a. Ex. Human cold viruses

i. Only infect cells lining upper respiratory tract

3.. specificity

a. Interaction between viral surface proteins & specific receptor molecules on host cell surface

Viral Replication (Basic features)

Virus binds to a host cell

Viral genome enters cells:

- Injected genetic material

- Material enters via endocytosis

Enveloped virus:

- Fuse with host cell plasma membrane

Viral replication (viral genome direct production of proteins)

- viral genome takes over host cell

Viral replication (host cell copies)

Host cell copies viral genome & produces viral proteins

Viral replication (Viral nucleic acids & capsomeres)

- spontaneously self-assemble of Nucleic acids & capsomeres

Viral replication (exit host cell)

Damages or destroys the host cell (tissue damage)

Lytic cycle

ends in death of host

virulent phage

Bacterial

-some bacteria don't have surface receptors that are recognized by virus

- restriction enzyme recognize foreign DNA (eat & destroy)

-Bacterial DNA methylation

Lysogenic cycle

-replication of phage genome without destroying host cell

- temperate phages

-Phage lambda

temperate phages

lysogenic or lytic

Phage lambda

attaches to host cell + injects DNA

Lambda DNA forms a circle

either viral genome converts host cell into "factory":

- enters lytic cell or

- DNA incorporated into a specific site on host chromosomes

Prophage (phage lambda)

-Integrated virus

Has gene which codes for protein that prevents the transcription of most other viral genes:

-No lytic cycle

-Replicated along with host chromosomes

Cell encounters certain external environmental conditions

cause virus to revert to lytic cycle

Background Prokaryotes

-First organisms on Earth, about 3.5 billion years ago

-Domains (Bacteria and Archaea)

-Dominant and pervasive

-They are everywhere, great diversity

Cellular organization of Prokaryotes (what it lacks)

-Simpler and smaller than eukaryotic cells

-lack membrane-bound organelles

NO: nucleus, mitochondria, chloroplasts

Cellular organization of Prokaryotes

- Nucleoid - region of cytoplasm, not enclosed

- DNA haploid, One set of chromosome

-Many have Plasmid

-Plasmid - small DNA rings, nonessential genes

-Ribosomes- location of protein synthesis

-Plasma membrane - encloses the cytoplasm

-Fimbriae - attachment structures on surface

-Cell wall

-Capsule

-Flagella

cell wall of prokaryotes functions

-maintain the cell shape

-rigid structure

-prevents bursting in hypotonic environment

-Bacilli - Rod-shaped

-Spiral (rigid), Spirochetes (flexible)

-Cocci - spherical, single, Diplococcus (pairs), streococcus (chain), staphylococcus (clumps)

Peptidoglycan (polymer)

Consists of sugars and polypeptides that crosslink those sugars

Peptidoglycan (only found in the domain, Bacteria)

NOT found in Archaea

NOT found in eukaryotic cells

Organisms that do not have peptidoglycan

Plants = cellulose

Fungi = chitin

Peptidoglycan (differences in bacterial cell wall composition)

-Basis of Gram stain → 2 categories of Bacteria

-2 stains

1st crystal violet → turns cells purple

2nd safranin → turns cells pink (lighter color)

If together, the purple dominates over the pink

Penicillin

Interferes with peptidoglycan synthesis

Gram-negative bacteria has an _________?

outer membrane

-Contains lipopolysaccharides (LPS)

-A toxin that causes fever

-Gram-negative is more likely to cause serious disease

Capsules and slime layers

-Surrounds cell wall

-Capsule layers are organized and tight, whereas slime layers are more loose

-Protection against dehydration and phagocytosis (Maintain water levels)

Motility (taxis)

-Taxis - directed movement in response to a stimulus

-Positive Taxis (Towards stimulus)

-Negative (Away from stimulus)

-Ex. - phototaxis goes toward/away from light

Motility (flagella)

-Found in Bacteria, Archaea, and some eukaryotic cells

-Perform similar functions, but arose independently (NOT related by common descent/ancestor)

-Analogous structures - whip like structure which allows the cell to move

Comparison of Prokaryotic and Eukaryotic Flagella

Prokaryotes:

-1/10 as wide as eukaryotic flagella

-NOT covered by extension of plasma membrane

-Differs from eukaryotes in mechanism of propulsion and molecular composition

Comparison of Bacteria and Archaea

-Similar in size and propulsion mechanism

-Composed of different proteins

Prokaryotic Flagella parts

3 main part:

-Motor (series of rings embedded in the cell wall and plasma membrane

-Hook (curved part of the flagellum

-Filament (rotates and propels the cell, looks like a tail/hair)

Prokaryotic Flagella function

- H+ pumped out across the plasma membrane by ETC (forms gradient)

- H+ diffuses through the motor, produces force (hook turns, flagellum rotates)

Reproduction: Binary Fission

Asexual process

Reproduction: Evolution

-Must have genetic variation

-Sexually reproducing organisms (meiosis, fertilization)

-Prokaryotes (reproduce asexually, producing exact copies, high levels of genetic diversity among the prokaryotes)

Genetic diversity

Rapid reproduction and mutation

EX: E. coli found in the human intestine

genetic diversity (mutation)

error

-same offspring are different

-Probability of mutation in a gene is about 1 in every 10 million per cell division

-Rare on a per gene basis

-Among the 2x10^10 new cells produced in one intestine, 2000 cells will have a mutation in that particular gene

EX: E. coli is about 4300 genes, so the end of results is that about 9 million mutations occur per day per human host generation times

Genetic Diversity (Sig of mutation)

Increases genetic variation quickly in species that have short generation times

Genetic recombination

combining of DNA from 2 sources

Genetic recombination (eukaryotes)

- through meiosis and fertilization

Genetic recombination (prokaryotes)

- through transformation, transduction, and conjugation

-Processes bring together DNA from different individuals (different cells) of the same species

Horizontal gene transfer

Movement of genes from one organism to another of a different species

Transformation

-Process where prokaryotic cells take up foreign DNA from its surroundings

-Griffith's experiment

(R and S strains)

Transduction

-When a phage (virus) transfers prokaryotic genes from one host cell to another of the same species

Transduction (viral replication)

-Fragment of the host DNA will by accidentally packaged into a new viral particle

-Host DNA can be transferred to another host cell when the virus infects it

Conjugation

-Genetic material is transferred between living prokaryotic cells

They are still alive

F (fertility) factor

-A plasmid (ring of DNA), Differs from bacterial chromosomes

-Present in F+ cell (Donor cell)

-Contains DNA required for production of pilus

F+ cell uses _____ to attach to a F- cell (recipient)

pilus

-The pilus pulls the recipient close to the donor cell

-A mating bridge is produced, which allows the DNA to transfer to the recipient

-Recipient is now a F+ cell, which is a donor

Energy sources

Phototrophs - energy comes light

Chemotrophs - energy from chemicals

Carbon sources

Autotrophs - inorganic

Ex. - carbon dioxide

Heterotrophs - organic

Ex. - glucose

Ex. - chemoheterotrophs

Role of oxygen (obligate aerobes)

Organisms that MUST use oxygen for cellular respiration

Role of oxygen (obligate anaerobes)

-Poisoned by oxygen and die

-Some organisms live by fermentation (Produce ATP without an ETC)

-Anaerobic respiration

(ETC uses substance other than oxygen to act as an electron acceptor)

Ex. - NO3-

Role of Oxygen (Facultative anaerobes)

-If an aerobic environment, they will use oxygen as an electron acceptor

-If an anaerobic environment, the will fermentation or anaerobic respiration

Prokaryotic Diversity (molecular evidence)

rRNA sequence

-2 domains in prokaryotes existed, Bacteria and Archaea

-Horizontal gene transfer is not common

-Archaea are more closely related to Eukarya than to Bacteria

Proteobacteria

- Alpha - (Rhizobium, Nitrogen fixation)

-Beta - (neisseria gonorrhoeae)

- Gamma - (E. coli, intesine)

- Delta - (Bdellovibrio, predator that attacks other bacteria by drilling into that cell)

-Epsilon - (Campylobacter, which causes diarrhea)

Chlamydias

-all parasites

-infect animal cells in order to survive

-ex: chlamydia trachomatis, causes blindness and STIs

Spirochaetes (Bacteria)

Ex: Borrelia burgdorferi, causes lyme disease

Ex: Treponema pallidum, causes syphilis

Cyanobacteria

-Gram-negative bacteria

-Photoautotrophs - produces oxygen

-Chloroplasts evolved from this group

Gram-positive bacteria

-Thick peptidoglycan layer

-Enormous diversity

Ex. - Streptomyces, where soil bacteria

Ex. - staphylococcus aureus, which causes skin infection

Archaea

-Extremophiles

-loves extreme conditions

-Extreme halophile, loves salt

-Thermophiles, loves hot environment

-Methanogens, release of methane, strict anaerobes, lives in marshes and swamps

Excavata

-many have excavated (deep) feeding groove on one side of cell body

-derived character - genetic similarities

Diplomonads

Mitosomes - modified mitochondria

- lacks functional ETC

-E from anaerobic pathways

-lack plastids

Parabasalids

Hydrogenases - modified mitochondira

-anaerobic metbolism

-release H2 as by-product

-lack plastids

Euglenozoans

-Spiral or crystalline rode inside each flagellum

-great diversity

Euglenozoans: kinetoplastids

-Single, large mitochondrion

-contains kinetoplast (organized mass of DNA)

Euglenozoans: Euglenids

-1 or 2 flagella emerge from pocket at one end of cell

-some are mixotrophs

SAR Clade: Stramenopiles

Derived character:

- 1 flagellum with hair-like projections

-often paired with "smooth" flagellum

-3 main groups

-all photosynthetic

-Secondary endosymbiosis of red algae

SAR Clade: Stramenopiles: Diatoms

-unicellular algae

wall:

-Silicon dioxide embedded in organic matrix > glass-like

-2 overlapping parts

-Protection

Diatomaceous earth:

-filter, absorb, medicinal

SAR Clade: Stramenopiles: Golden algae (features)

-Yellow & brown carotenoids (photosynthetic pigments)

-Most unicellular

-Tiny scales of silica or calcium carbonate

SAR Clade: Stramenopiles: Golden algae (freshwater & marine)

-Nanoplankton

Nano - extremely small

Plankton:

-diverse group of organisms

-live in water column

-cannot swim against current

SAR Clade: Stramenopiles: Brown algae (features)

-most complex protists

-multicellular

-large (few cm to 75m)

-seaweed

SAR Clade: Stramenopiles: Brown algae (marine)

-cold waters

-kelp form underwater forests

-habitat for marine organisms

SAR Clade: Stramenopiles: Brown algae (commercial)

-some edible

Algin - polysaccharide in cells walls, thickener

SAR Clade: Alveolates: Dinoflagellates (features)

-most unicellular

-many have cellulose plates inside plasma membrane

-2 flagella, spinning movement

-plankton

SAR Clade: Alveolates: Dinoflagellates (bloom)

-occasional population explosion

-carotenoids

ex: red ocean tides

SAR Clade: Alveolates: Apicomplexans

Apical complex: penetrates host cells

ex: plasmodium - malaria

SAR Clade: Alveolates: Ciliates

cilia - move & feed

SAR Clade: Rhizarians

derived character:

-protective shell of calcium or silica

SAR Clade: Rhizarians: Radiolarians

-internal skeletons made of silica

SAR Clade: Rhizarians: foraminiferans (forams)

-calcium carbonate tests (porous shells)

-die, sink to bottom, form thick sediments

Archaeplastida (derived character)

-chloroplasts (primary endosymbiosis) - all photosynthetic

-monophyletic group

-Ancestral archaeplastids participated in secondary endosymbiosis

Archaeplastida: Red Algae

Phycoerythrin:

-red photosynthetic pigment

-absorbs blue & green light (penetrates deep into water)

multicellular:

highly branched

warm tropical ocean