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WSU / Biology / BIO 1500 / 1000000/170000

1000000/170000

1000000/170000

Description

School: Wayne State University
Department: Biology
Course: Basic Life Diversity
Professor: William branford
Term: Winter 2019
Tags: Biology
Cost: 50
Name: BIO 1500 Exam 1 Study Guide
Description: These notes cover what is going to be on the next exam.
Uploaded: 01/25/2019
13 Pages 6 Views 5 Unlocks
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BIO 1500: Basic Life Diversity Midterm Exam 1 Study Guide Content 


How species evolved morphologically, genetically, functionally, and ecologically?



I. Section 1: Essential Concepts

A. Biodiversity

B. Naming and Sorting Biodiversity

C. Phylogenetic Approach to Biodiversity

II. Section 2: All living things unicellular or smaller

A. Viruses

B. Bacteria

C. Archaea [notes upload over the weekend after tomorrow’s (1/25) lecture along with the rest of bacteria section]

Section 1 

I. Biodiversity = Basic life diversity

A. Defined as its place within the universe and our place within it If you want to learn more check out sociology 101 midterm

1. The variety and variability of life on Earth

B. History and discovery of the term

1. First used by Raymond F. Dasmann (wildlife specialist and

conservationist) in 1968

2. Term first invented by W.G. Rosen in 1985

3. E.O Wilson was the first to publish the word in 1988

a) Important sociobiologist


Who is the first person to draw a phylogenetic tree?



C. Measures variation at different levels of biological organization

1. Morphological diversity: structural differences in species

a) Ex. arm, mouth, nose, etc. If you want to learn more check out italian 101 study guide

2. Functional diversity: feeding mechanisms and motility

3. Ecology: study of species in a given environment and how they interact a) Species - species (how they interact with each other)

b) Species - environment interactions (how they interact with the

environment)

4. Genetic: number and diversity of genes facilitating diversity of species, morphology, and function

a) Molecular Evolution: have to know differences in genomes

D. Species dimension of biodiversity

1. Estimated number of Earth’s current species ranges from 10 million to 1 trillion

2. Only 1.2 million of those are documented as of 2016

a) In other words only 1% of the planet’s species have been


Consisting of ribosomal RNAs are found in all organisms, is what?



documented

II. Naming and Sorting Biodiversity

A. Linneaus and the origin of taxonomy

1. Taxonomy: defining

thousands of names for

living things and grouping

them into larger and larger

groups

B. Garret Hardin’s 3 Approaches to

Sciences (first 3 can be used to

research anything at all and the 4th Don't forget about the age old question of dinitrogen hexoxide

one makes this the 4 approaches to

studying biodiversity)

1. Literate: assigning names

and groups

a) Backbone of biodiversity

b) Taxonomy cladistics

c) Discovered by Carl Linnaeus (1707-1778)

(1) Known as the father of modern taxonomy

(2) Worked in Sweden as a botanist, physician and zoologist

(3) Famous for…

(a) Normalizing the modern system for the naming of

species through binomial nomenclature → many

long, latin names existed before but he condensed

them into 2 words

(i) Ex. Homo sapiens [Genus species]

(b) Introducing taxonomy: species can be sorted into

small, nested groups, also known as clades/taxa

based on similarities between them

(i) To explain diversity and differential

similarities of species (natural theology)

d) Widely used taxonomic categories

(1) Species: Canis lupis = wolf

(2) Genus: Canus

(3) Family: Canidae

(4) Order: Carnivora Don't forget about the age old question of a felony is an act usually punishable by incarceration for

(5) Phylum: Vertebrates

(6) Kingdom: Animalia

(7) Domain of Life: Eukaryotes

e) Advantages of Taxonomic System

(1) Easier to keep an overview of millions of species

(2) With single words, you can talk about many species at once

because there are over thousands of animal species

(3) You can be identified as an expert in certain groups of

species

(a) Ex. Ornithologist (birder)

2. Numerate (Quantitative approach)

a) Counting species and clades

b) Exploring morphological, functional, genetic, and evolutionary dimensions of biodiversity

c) Major clades of life

d) Terrestrial > Marine

Terrestrial 

Marine

Animals = 1,000,000

= 170,000

Plants = 250,000

= 8,500

Fungi = 40,000

= 1,000

Protists = 8,000

= 8,000

Bacteria = 10,000 Don't forget about the age old question of what encloses the third ventricle

= 650

Archaea = 500

= 1

3. Ecolate

4. Evolutionary/phylogenetic

a) How biodiversity rose and how species evolved morphologically, genetically, functionally, and ecologically

b) “Nothing in biology makes sense except in the light of evolution” C. Biological Species Concept

1. Species are groups of actually or potentially interbreeding natural

populations that are reproductively isolated from other groups → members can reproduce together and are genetically distinct

2. Speciation: reproductive

isolation of one species Don't forget about the age old question of james dow finance 303

from a shared ancestor

in other species

3. Species: base unit of

quantifying/identifying

biodiversity

4. Presence or absence of

gene flow determines

the boundaries between

species

III. Phylogenetic Approach to Biodiversity

A. Charles Darwin (1845)

1. First person to draw a phylogenetic tree

2. Alfred Wallace (1823-1913) and him hypothesized that species

biodiversity is an ongoing process that generates new species from old

ones (descent with modification)

a) First to

hypothesize

that all species

of life have

descended over

time from

common

ancestors

3. Beagle with Charles

Darwin

a) Galapagos

Islands: Beagle

landed here,

tried to salvage

resources (water)

(1) Discovered finches there and thought they were all the

same species

(2) However him and his bird expert (John Gould) identified at

least 14 finch species based on molecular phylogenetic

species tree reconstruction

b) Ultimate version species tree of Darwin’s finches has been

reconstructed using information for whole genome sequences

(1) Phylogenomics: use of whole genome sequences to

reconstruct species phylogenies

(a) New standard for reconstructing phylogenetic

relationships

c) Gave them the idea that these birds had evolved from one common ancestor

4. Darwin’s definition of evolution

a) Descent with modification through natural selection

(1) Species evolved over time as a result of natural changes to

their environment and standards of living

B. Evolution Concept generated by 2 processes

1. Descent with modification

a) Linnaeus’ hypothesis that there were different degrees of

phylogenetic relatedness

2. Diversification of last common ancestors (LCAs)

a) Every clade/taxa has its own LCA

b) Phylogenetic systematics

(1) Monophyletic: include all members that relate back to the

same common ancestor

(2) Paraphyletic: lacks one descendant of equal taxonomic

level of the node representing its LCA

(3) Polyphyletic: lacks more than one descendant of equal

taxonomic level of the node representing its LCA

C. Conclusion

1. Trait similarities can be due to shared descent (homology) or independent evolution (homoplasy)

2. There are no detailed similarities at the level of anatomy for flight, therefore these species relate through their trait of fur even though it seems to be the other way around

a) Fur is related through morphology, cellular organization, structural proteins, genes required for development

b) All animals are multicellular however whether they have fur or fly D. Ribosomes

1. Ribosomes consisting of ribosomal RNAs are found in all organisms (eukaryotes and bacteria)

a) Two large subunits (mix of two types of molecules)

b) Nucleic acid/RNA form the foundation of ribosomes and proteins that surround it

c) Homo sapiens of E coli have similar ribosomal structure meaning they have the same last common ancestor → change is due to

descent with modification

E. Evolutionary Conservation of

human gene content

1. 37% of our genes date

back past the last

common ancestor of

eukaryotes and bacteria

2. Approximately 25,000

genes in our genome

3. 28% date back past the

LCA of humans and

other eukaryotes

4. A total of 65% of our

genes (37+28) are

shared with all other

eukaryotes

5. 16 % are specific for

animals so 81%

(65+16) are shared with

all other animals

F. Ribosomal RNA structure has been conserved for the past 3.5 billion years in 3 main domains of life (Archaea, bacteria, and Eukarya)

1. Genes shared between Eukarya and bacteria are used to reconstruct the tree of life

2. First molecular tree of life dates all three domains back to last universal common ancestor

Section 2 

I. Viruses

A. Rapid evolution of the human gut virome

1. Humans colonized by immense populations of viruses

2. Human virome: collection of all viruses that are found in or on humans including eukaryotic and prokaryotic viruses

3. Human virome includes

a) Both eukaryotic and bacterial viruses

b) Viruses causing acute, persistent, or latent evolution

c) Viruses integrated into our genome such an endogenous

retroviruses

4. Majority of human gut viruses are bacterial viruses (bacteriophages) B. Retroviruses like HIV integrate viral DNA into the host cell genome→ enter by endocytosis

1. Reverse transcriptase converts HIV RNA genome into double stranded DNA

2. DNA is incorporated into host cell genome

3. The host transcription protein machinery produces viral RNA genome copies and proteins

4. Assembly and release of new virus

C. Organization of the human genome

1. In most eukaryotes, genes that code DNA represent usually only a small fraction of genome content (1.5%)

2. A much larger amount is taken by mobile transfer from viruses and bacteria

a) Dead transposons have DNA of bacterial origin

b) SINEs and LINEs have DNA of viral origin

D. Massive amounts of integrated viral DNA is one of the reasons why eukaryotic genomes are so large

1. Viral genomes by comparison are the smallest we know

a) Smallest viral genome: Trichomonas vaginalis (~5000 bp) virus b) Tallest viral genome (~ 2.5 Mb, 2500 genes)

E. Why study viruses?

1. Have been associated with bacteria, eukarya, and archaea since the beginning of organismal evolution (important part of the tree of life) a) Homoplasy (being infected by different viruses)

b) Viruses do not have ribosomal RNAs

c) Mediate horizontal gene transfer between the 3 domains

d) Bacteria and eukaryotes evolved defense mechanisms

(1) Eukaryotes: small interfering RNA (siRNA) interference

which degrades the dsRNA of invading retroviruses

(2) Bacteria

(a) Peptidoglycan: containing cell walls that are

difficult to penetrate for viruses

(b) Clustered Regularly Interspaced Short Palindromic

Repeat (CISPR) which degrades the genomes of

invading phages and plasmids

2. Many viruses impact human health

a) Through symptoms caused by infection

b) Viruses have been estimated to contribute to about 15% of all human cancers

3. Some viruses benefit their hosts

a) Ex. D. pulchellus reovirus 2(DpRV2) triggers beetles after being parasitized by D.coccinellae wasps

4. Viruses go viral

a) Characterized by extremely fast replication rates

F. Top facts about viruses

1. All require an intracellular environment for protein synthesis thus acting as obligate intracellular parasites

a) Life cycle of bacteriophage

(1) Lytic cycle: bacteriophage induces production of new

phages after infection of host cell

(2) Lysogenic cycle: bacteriophage genome integrates into host

genome and stays dormant

2. Viruses lack their own ribosomes and enzymes for protein and nucleic acid synthesis

3. Viruses hijack the cell’s transcription and translation machineries to express their own proteins and eventually replicate

4. Viruses all have the same basic structure

a) Consist of nucleic acid core surrounded by capsid

b) Lack cytoplasm

c) However, some viruses store specialized enzymes with nucleic core →

reverse

transcriptase enzyme of retroviruses not found in host

d) Many

animal

viruses

have an

envelope

layer that is

derived

from host

cell

membrane

with viral

proteins

(1) Ex.

Influenza virus

5. Viral genomes can consist of

a) DNA or RNA

b) Circular or linear

c) Single or double stranded

6. Viruses are therefore classified by genomes as

a) DNA viruses

(1) Group I: dsDNA viruses

(2) Group II: ssDNA viruses

b) RNA viruses

(1) Group III: dsRNA viruses

(2) Group IV: (+) ssRNA viruses → viral RNA genome serves

as mRNA

(3) Group V: (-) ssRNA viruses → viral RNA genome is

complementary to the viral mRNA

c) Retroviruses

(1) Group VI: ssRNA-RT viruses → HIV included here

(2) Group VII: dsDNA -RT viruses

G. Known Viruses

1. International Committee on taxonomy of viruses

a) 3200 viral species known at this point

b) Morphologically and genetically diverse

H. Diversity of viral morphologies sorted by host ranges

1. Bacterioviruses = phages

a) No unique morphology

b) Mostly restricted to the head-tail Caudovirales

c) Not characterized by a type of capsid

2. Archaeoviruses

a) Infect Archaea

b) Many complex morphotypes

3. Eukaryoviruses

a) Infect eukaryotic species

b) Many complex morphotypes

II. Bacteria

A. E. coli (Escherichia coli)

1. Discovered in 1884 by Theodore Eschrich

2. Resides in human and animal gut as normal part of microbial

populations→ thus referred to as coliform

3. E. coil must release toxins which allow bacterium to bind to the lining of the gut and cause symptoms of disease

4. Example of morphological variation in the same species

a) E. coli B strain REL606 a laboratory strain with a typical

sausage-shaped morphology

b) E. coli 0119: HND strain A111, an enteropathogenic strain that produces hair-like pili

B. Why study bacteria?

1. Tell us about ourselves because they 37% of our gene content 2. Bacteria play key roles

in recycling key

chemicals of life

a) Carbon

b) Sulfur

c) Nitrogen: key

component in

proteins, DNA,

ATP, chlorophyll

3. There are many of them:

present a significant

amount of the biosphere

a) 40 million bacterial cells in a gram of soil

b) 1 million bacterial cells in a mL of fresh water

c) Approximately 5*10^30 on Earth forming a biomass that exceeds that of all plants and animals

d) Ten times more bacterial cells than human cells in the body

(1) Largest number in gut but also large number in skin and

other areas which all make up our microbiome

4. We need them to be functional: evidence that gut microbiota affect brain physiology and animal behavior

a) Germ free mice have defects in brain regions that control anxiety b) Feeding probiotic bacteria to normal mice reduces depressive-like behaviors

c) Specific receptors on gut neurons respond to signals from gut bacteria revealing one mechanism by which microbiota can

communicate with the central nervous system through the

brain-gut

axis

5. Radiation of several

animal groups were

enabled by

symbiosis

gut-associated

bacteria

a) Ex. Ruminants

6. We could NOT live without them

a) Animal survival depends on healthy microbiota

b) The survival of any eukaryotic organism (animals, plants, fungi, protists) depend on specialized bacteria like the mitochondria (1) Have bacterial circular genomes

(2) Have bacterial ribosomes with ribosomal RNAs

c) The survival of any plant depend on another type of specialized bacteria called chloroplasts

(1) Have nucleoids (DNA rings)

(2) Have bacterial ribosomes with ribosomal RNAs

d) Molecular

genetic proof

in the

ribosomal

DNA tree of

life that these

two are

indeed

bacteria

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