Bio Unit 2

What is a capsid?

A protein shell that encloses the viral genome.

What is a retrovirus?

An RNA virus that uses reverse transcriptase to integrate its genome into the host's DNA.

What is the Baltimore classification system?

A system that classifies viruses based on their method of mRNA synthesis.

What are prions?

Infectious proteins that cause diseases like mad cow disease.

What are viroids?

Infectious RNA molecules that affect plants.

What is phagocytosis?

The process by which protists engulf food particles.

What are charophytes?

A group of green algae most closely related to land plants.

What is a cuticle in plants?

A waxy layer covering plant surfaces to reduce water loss.

What are stomata?

Pores on plant surfaces that regulate gas exchange.

What is sporopollenin?

A tough polymer that protects plant spores from desiccation.

What are the three types of body symmetry in animals?

Asymmetry, radial symmetry, and bilateral symmetry.

What are germ layers?

Embryonic layers (ectoderm, mesoderm, endoderm) that give rise to different tissues.

What is a protostome?

An organism in which the mouth develops before the anus during embryonic development.

What is a deuterostome?

An organism in which the anus develops before the mouth.

What is cephalization?

The concentration of sensory organs at the front end of the body.

What is an amniotic egg?

An egg adapted for land, containing membranes that protect the embryo.

regressive hypothesis

suggests that viruses evolved from free living cells

progressive hypothesis

suggest the viruses evolved from RNA and DNA molecules

virus first hypothesis

suggests that viruses may have been the first self-replicating entities before the first cells

capsid

outer protein coating of virus

outer-envelope

envelope some viruses have made up of protein and phospholipid membranes derived from the host cell

bacteriophages

viruses that infect bacteria

capsomeres

proteins of the capsid encoded in the viral genome

virus core

contains the genome (total genetic content of the virus)

endocytosis

when a cell engulfs a particle or another cell/organism

3 ways a virus can exit the host cell

1. lysis

2. exocytosis

3. budding

lysis

the cell bursts and the virus can now find a new host

budding

a section of the cell membrane forms an envelope around the virus as it leaves the cell

exocytosis

the virus leaves via the cells transport system

lytic cycle

the bacteriophage infects the cell, replicates multiple times, and then the cell bursts releasing the phage

lysogenic cycle

the phage enters the cell, incorporates its DNA into the host cell, cell divides passing on DNA of phage (under stressful conditions phage DNA is excised; goes into lytic cycle)

why are viruses difficult to treat

• viruses don’t metabolize or reproduce on their own

• viruses are often spread before the infected individual realizes they are sick

• viruses are highly variable

• viruses evolve rapidly

characteristics of the LECA

• cells with nuclei surrounded by a nuclear envelope with nuclear pores

• mitochondria

• cytoskeleton with microtubules and microfilaments

• flagella and cilia

• linear DNA organized around histones

• mitosis

• sexual reproduction

endosymbiosis

when one cell engulfs but does not digest another cell, they end up in a symbiotic relationship, engulfed cell evolves into an organelle within the larger cell

secondary endosymbiosis

occurs when a cell engulfs a cell that has already undergone primary endosymbiosis

autogeny

theory proposed for the origination of of ER and nucleus: may have evolved within the cell as opposed to being a result of endosymbiosis

plastid

organelle responsible for manufacturing and storing food, often via photosynthesis

6 major protist clades

• archaeplastida

• amoebazoa

• opisthokonta

• rhizaria

• chromalveolata

• excavata

archaeplastida key characteristics

red algae and green algae, photosynthetic capability, generally non-motile, convert sunlight into matter contributes to ecosystem

amoebazoa key characteristics

move with pseudopodia, amoebas and slime molds, heterotrophs (engulf organic debris), regulate bacterial populations in soil and water

opisthokonta key characteristics

singular posterior flagellum, heterotrophs (consume organic matter)

chromalveolata key characteristics

cilia, flagella, consists of alveolate and stramenopiles, photoautotrophic and heterotrophic,

rhizaria key characteristics

move with pseudopodia or flagella, mostly heterotrophic, contribute to nutrient cycling

excavata key characteristics

move with flagella, most are heterotrophic, some can cause diseases in humans

binary fission

the circular chromosome is replicated as the cell splits

mitosis

chromosomes are replicated, the nucleus breaks down, and spindles are involved in division of cell

when does sexual reproduction occur?

when conditions are unfavorable

allows populations to evolve and adapt more quickly to their environment

when does asexual reproduction occur?

when conditions are favorable

uses less energy and allows populations to grow quicker

diploblast

animal with two germ layers

includes radial, biradial, and asymmetrical symmetry (sea stars, jellyfish)

triploblast

animals with three germ layers

includes animals with bilateral symmetry

endoderm

usually develops into digestive and respiratory systems (internal organs and tissues)

ectoderm

develops into skin/outer covering of animals and nervous system

mesoderm

develops into muscle tissues, skeleton, blood cells, many organs, body cavity (column)

ediacaran period

likely beginning of animals

cambrian explosion

relatively rapid diversification of animals

Ordovician period

animals came ashore

protostome vs deuterostome

cells divide/cleave different at different angles

mouth and anus develop at different sides of the embryo

at cleavage, protostomes cells are determined while deutorostome cells are not

what does a virion consist of?

nucleic acid core

outer protein coating or capsid

sometimes an outer envelope made of protein and phospholipid membranes from the host cell

homeotic genes

DNA sequences that control embryonic development

hox genes

type of homeotic genes

determine body plan, turn on/off sets of genes

homologous across the animal kingdom

invertebrates = 1 set of hox genes

vertebrates = 4+ sets of hox genes

alternation of generations

plants alternate between two life stages:

sporophyte (2n) and gametophyte (n)

both stages multicellular, both can live independently

Dicot

2 seed

Monocot

seed

gametophyte

multicellular stage of the plant the gives rise to gametes

5 key chordate synapomorphies

1. Notochord - support

2. Dorsal hollow nerve cord → CNS

3. Pharyngeal arches → gas exchange and feeding efficiency

4. Post-anal tail → power

5. Endostyle/thyroid gland secretes iodinated hormones

notochord

forms from mesoderm, located between digestive tube and nerve cord, provides skeletal support, attachment location for some muscles

dorsal hollow nerve chord

formed from the ectoderm, located along the backside of chordates, helps with coordination of movement via nervous system

pharyngeal arches/slits

openings in pharynx that connected to exterior of organism,

aquatic organisms - provide exit water for water from the mouth during feeding

non aquatic animals - have evolved into other features including ears, tonsils, and thymus glands

post-anal tail

aquatic species: used for locomotion

terrestrial species: used for many things (balance, courting, communication)

endostyle/thyroid gland

primitive chordates: secretes mucus that helps trap food particles

vertebrates: endostyle evolved into the thyroid gland, secretes iodinated hormones that regulate metabolism, growth and development

gnathostomes

vertebrates with jaws

chondrichthyes

cartilaginous fish, skeletons made up of cartilage (sharks, rays, skates)

vertebrates

chordates with a skull and spine

osteichthyes

“bony fish” → gnathostomes with “bony” skeletons

largest vertebrate class

actinopterygii

50% of living vertebrate species, no fleshy appendages, slender bones in fins

sarcopterygii/lobe-finned fish

fleshy, bony fins/appendages

humans and other tetrapods evolved from lobe-finned fishes

describe a typical virus “life” cycle

attatchment, entry, reproduction, exit

what attributes of viruses would qualify them to be considered living?  What attributes would qualify them to be considered not living?

living: contain DNA, able to evolve and adapt

nonliving: noncellular, no energy sourcing/producing, cannot reproduce alone

how are eukaryotic cells different in size, structure and components than prokaryotic cells?

eukaryotic cells: larger in size, complex cell structure, nucleus, membrane-bound organelles, linear chromosomes, reproduce by mitosis or meiosis

prokaryotic cells: smaller in size, simple cell structure, no nucleus, circular DNA, no membrane-bound organelles, reproduce by binary fission

when/in which clades did multicellularity evolve? 

multicellularity evolved in the common ancestor of animals, evolved once in plants, animals, and red, green and brown algae, evolved around a dozen times in fungi

what are three benefits of multicellularity as compared to unicellularity? 

enables cells to work together as functional unit, increased body size and cellular efficiency, larger range and size of potential prey, better able to avoid getting eaten

how are mitosis and meiosis similar and how are they different?

diploid vs haploid, one results in identical cell and one results in genetically unique cell

which clades reproduce via binary fission?

bacteria and archaea

which clades reproduce by mitosis and meiosis? 

eukaryotes

what are the three key components of sexual reproduction?

recombination, gamete production, and gamete fusion

what are the costs and benefits of sexual reproduction?

benefits: brings together good alleles faster, can free beneficial mutations (increased chance of survival), shuffles genetic diversity, creates genetically variable offspring

costs: can cause disease/infection, energy costs finding mate, fitness costs if death before finding mate, offspring only have 50% of mother’s DNA, only allows production of ½ as many daughters

what are the costs and benefits of asexual reproduction?

benefits: faster reproduction, less energy cost, increase in population (under favorable conditions), mutations can be directly passed to offspring

costs: limited adaptability (no genetic variance), competition for resource overtime due to overcrowding, vulnerability to to disease/environmental changes

how are haploid and diploid organisms/life stages different (in terms of ploidy levels)?

haploid: one set of chromosomes, produced by meiosis, dominant in fungi

diploid: two sets of chromosomes, produced by mitosis or fertilization, dominant in animals and plants

when do mitosis and meiosis occur in life cycles? 

mitosis: occurs continuously throughout life cycle

meiosis: occurs at reproductive maturity for gamete production

what is heterokaryosis and in which type of organism does this occur? 

heterokaryois = 2 nuclei with different genomes existing within a cell

occurs in: fungi

what animal clades are diploblasts?

cnidaria, ctenophora, porifera, acoelomorpha

what animal clades are triploblasts?

rotifera, annelida, molluska, echinoderma, chordata, arthropoda, nematoda, platyhelminthes

how are chordates and vertebrates similar and different?

All vertebrates are chordates, but chordates also include simpler organisms that lack a backbone

how are ray-finned and lobe-finned fish different? 

ray finned fish: no fleshy appendages

lobe-finned fish: fleshy bony fins

what are the key characteristics of protists?

• high variability, mainly microscopic and unicellular

• some can be bigger or multicellular

• most are motile

• mostly asexual but some sexual

• generally require moist to wet environments

• can be anaerobic or aerobic, and heterotrophic or photoautotrophic