BIOL Exam 4

Viruses and Viroids

both are nonliving particles with nucleic acid

* require the assistance of living cells to reproduce

Viruses

small infectious particles that consist of nucleic acid @@enclosed in a protein coat@@

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require a host cell to help them reproduce

* DNA or RNA
* Bigger
* Has capsid
* Nucleic acid
* Broad host range

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Viroid RNA

* smaller
* no protein coat
* catalyzed reaction
* tend to affect plants

Host range

the number of species and/or cell types that can be infected

* variety in specifically

Host cell

a cell infected by a virus

* could be general/any cell; or could be a specialized type of cell like a nerve cell, or skin cell

Capsid

protein coat; enclosed the nucleic acid; composed of one or more protein subunits called @@CAPSOMERS@@

* lost of variety in shapes

Viral envelope

encloses the capsid; lipid bilayer (derived from the plasma membrane of the host cell); may have spike glycoproteins; @@not all have an envelope@@

Genome

DNA versus RNA, single-stranded (ss) versus double-stranded (ds)

* linear versus circular
* some have several copies
* vary in size vs thousands

Viral Reproductive Cycle

leads to the production of new virus


1. Attachment
2. Entry
3. Integration
4. Synthesis of viral components
5. Viral assembly
6. Release

Attachment

Specific for cell types

Entry

different mechanisms

* after entry integration occurs quickly

Integration

Integrase (protein) -ase

* cuts host chromosome & inserts viral genome

Synthesis of viral components

uses hosts machinery

Viral assembly

self-assemble or use viral proteins to assemble

Release

virus lyses cells & release

Lysogency

Lysogenic cycle

* integration, replication, and excision
* stays the same

Prophage

viral genome is integrated w/host chromosome

Lytic Cycle

* synthesis, assembly, and release
* breaking cells
* actively spreading

Temperate phages

a lysogenic cycle,

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virulent phages

* __**only have a lytic cycle**__

Latency in humans

similar to lytic

* chicken pox
* shingles
* get infected once and then viruses somewhere in your body
* viruses not moved in your body

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Two different mechanism


1. Virus @@__**integrates into the host genome**__@@ and may remain dormant for long of times


1. ex: HIV
2. Episomes: genetic elements that replicate independently of host DNA
* can be nucleus/nerve cell

Emerging viruses

arisen recently, or are more infectious

* due to mutation

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ex

* HIV/AIDS
* Zika Virus
* New strains of influenza
* SARS-CoV2

Viroids

composed of a single-stranded RNA molecule

* many are ribozymes
* much smaller
* no capsid

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@@__**Not code for proteins**__@@

* disease mechanism not well understood

Prions

__**proteins that affect animals**__

composed entirely made of a protein cause rare fatal brain diseases in animals

* @@induce abnormal protein folding@@

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“infectious” occurs by eating meat of infected animals

* cows
* deers

Genetic properties of bacteria

* usually a single type of circular chromosome
* dsDNA
* chromosomes contain a few thousand unique genes
* single origin of replication

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proteins important for forming @@__**loops and supercoiling the DNA NUCLEOID**__@@

NUCLEIOD

the region where tightly packed bacterial chromosomes found

Plasmids

small, circular pieces of DNA that exist independently of the chromosome

* occur naturally in many strains of bacteria and in a few types of eukaryotic cells such as yeast
* own ORI

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replicated independent

* use in bio technology PCR
* inside the cell of bacteria
* Provides growth advantages

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REMEMBER: OWN origin of replication that allows it to be replicated independently of bacterial chromosome

4 main in nature only for plasmid

1. Resistance plasmids
2. Degradative
3. Virulence
4. Fertility

Resistance plasmids

useful for genetic engineering

* vs. antibiotics

Degradative

help remove unusual substances/pollutants

* remove toxins

Virulence

carries genes for pathogenesis

Fertility

promote gene transfer

Main mechanisms for horizontal gene transfer

* Conjunction
* Transformation
* Transduction

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Conjugation

* direct contact
* “sexual” transfer

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ex: plasmid transfer between strains

* donor/recipient
* donor to the recipient through “appendage”
* could be to same for different species of bacteria

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sex for bacteria

Transformation

* most common
* competent
* released in the environment and taken up by the recipient (nature)
* ex: DNA in soil

Competent cells

naturally, take up naked DNA

ONLY COMPETENT CELLS: are capable of transformation

* can be done artificially

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DOES NOT require direct contact between cells

* cells have genes

Transduction

* “Picks up” some donor DNA
* Phage infects new cells and transfers DNA to the recipient
* The virus takes up DNA from the previous host and injects it into the next host

relates to viruses

uses viruses to infect bacteria

injects to the next host

Recombination DNA technology

use of laboratory techniques to @@__**bring together fragments of DNA from multiple sources**__@@

Gene cloning

process of making GO multiple copies of a particular DNA

Genomics

the molecular analysis of the entire genome of a species

3 main steps gene cloning

1. @@__**Isolate or obtain DNA**__@@


1. need vector DNA


1. plasmid: small, circular
2. need DNA interest
3. isolating DNA and isolating vectors and DNA of interest

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2. @@__**Insert DNA of interest into the vector**__@@


1. “combine”
2. PCR


1. Polymerase chain reaction


1. exponential amplification of DNA like DNA replication in a tube


3. ligase: combine these two pieces of DNA together to create 1 new piece

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3. @@__**Transform**__@@

a. Host(bacterial) strain to make many copies of the DNA


1. or use to make protein encoded by the DNA

PCR

repeated rounds of denaturing, anneal, and the extension will amplify your DNA of interest

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Polymerase chain reaction

* the enzymatic reaction that makes copies of our DNA of interest

\*exponential amplification of DNA

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@@Denature@@

* separate strands

@@Anneal@@

* complementation
* primers help bind
* temp drops

@@Extend@@

* temp raises
* polymerase finds the primers bound to DNA

Usefulness of PCR

* fast
* little starting amount to get lots of products
* specific for DNA of interest
* add sequencing through primers
* relatively inexpensive

Restriction enezymes

Can cut DNA at specific sequences

* specific known @@__**restriction sites**__@@ in the DNA
* most restriction sites are @@__**palindromic**__@@
* reads the same forwards/backward

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certain restriction enzymes cut, they leave a tiny bit of an overhang;

* it is not blunt cut;
* this can allow complementary base pairing between fragments
* (vector and the DNA of interest)

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Restriction enzyme leaves a short, complementary sequence between the two pieces so that they will be able to bind to each other; the ligase combines/joins the pieces

Electrophoresis

allows “visualizing” DNA in a gel matrix

* agarose gel
* can be used to separate molecules based on their charge. size/length, and mass

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DNA= negatively charged migrated towards +

* larger = not as far
* smaller = farther

DNA sequencing

a special type of PCR and analysis

* dideoxy chain
* termination method
* missing the 3’ -OH group and cause chain to terminate

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Need the OH- to add nucleotide

Genomics

looks at all the genes

* molecular analysis of the entire genome
* use techniques to study a genome
* complete set of DNA of an organism
* all the DNA

importance of studying genomes

* bacteria cause disease
* can apply knowledge to more complex organisms
* origin of the first eukaryotic cell probably involved the union between an archaeal and bacterial cell
* bacteria are often used as tools in research

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Genomes of thousands of bacterial and archaeal species have been sequenfed

* usually a single type of circular chromosome a few million base pairs in length

Archaeal and bacterial genomes less complex than eukaryotes

* lack centromeres and telomeres
* single origin of replication
* relatively little repetitive DNA

Genomics importance

reasons to sequence eukaryotic genomes

* a great benefit from identifying and characterizing genes in model organisms
* more information to identify and treat human diseases
* improved strains of agricultural species
* way to establish evolutionary relationships

Evolution

genetically pass

* heritable change in one or more characteristics of a population or species from one generation to the next

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THEORY: broad explanation of the natural world (makes valid predicitions)

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Microevolution

changes in a single gene

(in a population over time)

Macroevolution

formation of new species or groups of species

Empirical thoughts

the early classification system was developed

Darwin’s influence

Formulated theory of evolution by mid-1840s

* 1859: Darwin’s On the Origin of Species
* based on variation and natural selection

Variation

* traits heritable
* passed from parent to offspring
* the genetic basis was not yet known

Natural selection

* individuals with better traits flourish and reproduce
* more offspring are produced than can survive
* competition for limited resources

Species

groups of related organisms; capable of interbreeding

population

members of same species in the same area

Fossil record

can see a change in fossils when looking directly at the oldest to youngest fossils

Transition form

show an intermediate state between the ancestor & descendants

Biogeography

the study of the geography and distribution of extinct and living species

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ex: islands may have unique species compared to the mainland due to isolation

Endemic

naturally found only in a particular region

Convergent evolution

when 2 species from different lineages have independently evolved similar characteristics

* because they occupy similar environments

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ex:

* shark & dolphins

Selective breeding

procedures used to modify traits in domesticated animals

* aka artificial selection
* traits were chosen by breeders to make more desirable offspring

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ex: poodles

Homologies

fundamental similarity due to descent from a common ancestor

* anatomical
* developmental
* molecular

anatomical

homologous structures

* bones of forelimbs
* related to the study of anatomy/ body structure

Developmental

* embryonic structures
* embryos share similar traits

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ex:

* fish
* salamander
* tortoise
* chick
* human

Molecular

similarities in gene sequences

* 16s 18s

Vestigial structures

* anatomical features w/no current function
* resemble structures of ancestors

molecular changes that reveal evolutionary change

* homologous genes
* paralogous genes

homologous genes

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SIMILAR

function in separate species

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* sequences similar but not identical due to independent/random mutations

Paralogous genes

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SIMILAR

within a single organisms

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* homologous genes within a single species
* frequently arise due to duplication event
* two genes in the same organisms
* similar function

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myoglobin

hemoglobin

Horizontal gene transfer

* passing genes to non-offspring/different species


* medical relevance acquired antibiotic resistance

Gene pool

all the alleles for every gene in a given population

frequency allele number of allele

Natural Selection

when beneficial heritable traits become more common in successive generation

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overtime, natural selection results in adaptions

* changes in the population that promote survival and reproduction

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Different types

* directional selections
* stabilizing selection
* disruptive/diversifying selection
* balancing selection

Reproductive success

likelihood of an individual contributing fertile offspring to the next generation

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* certain characteristics make organisms better adapted and more likely to survive to reproductive age
* traits directly associated with reproduction, such as the ability to find a mate and the ability to produce viable gametes and offspring

A modern take on natural selection

* reproductive capability compared to other members of the population
* individual with beneficial alleles are more likely to survive and contribute their alleles to the gene pool of the next generation
* may change through natural selection, thereby significantly altering the characteristics of the population

Fitness

How likely it’s going to pass its genes to an offspring

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Fitness=1 good

Fitness < 1

* genotype less likely to be passed to the next generation

Directional selection

* the phenotypic range has a greater reproductive success in a particular environment

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ex:

* fur color in mice
* giraffe neck length
* Black & white moth

Stabilizing selection

* in the middle
* intermediate phenotypes
* ex birth weight in humans

Diversifying/Disruptive Selection

favors the survival of two or more different genotypes that produce different phenotypes

* likely in populations that occupy heterogeneous environments
* beak size of finches

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Balancing selection

favoring the section of multiple alleles (genetic diversity)

* 2 or more alleles are kept in balance
* ex: malaria and sickle cell trait

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All multiple alleles

Sexual selection

directed at certain traits of sexually reproducing species that make it more likely for individuals to find or choose a mate and/or engage in successful mating

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How members of one sex chose who to mate with

* reproductive success influenced by specific traits

INTRA-sexual selection

* males directly compete for mating opportunities or territories
* BETWEEN members of the same sex

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Choosing the female

competing

WITHIN 1

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playing sports WITHIN the same school or university

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ex:

horns in male sheep

antlers in male moose

male fiddler crab enlarged claws

INTER-sexual selection

* one chooses its mate from the other sex based on desirable characteristics
* Cryptic female choice
* females can use chemical or physical mechanisms to control mating success
* Control by women
* who they mate with

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BETWEEN

* playing with different school

Genetic drift

changes allelic frequencies due to random chance (affects gene pool)

Random events

Unrelated to fitness

Organisms

* may die before reproduction no success @ finding a mate

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Overtime, favors either loss or fixation of an allele

* loss
* NO allele 0%
* Fixation
* 100% see all the time

Larger population

takes more time to see the drift

small population

affected quickly

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small changes/affects

* have a drastic change in population

Bottleneck effect

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* population reproduced drastically, then rebuilds
* randomly eliminates members without regard to genotype
* natural disasters
* surviving members may have allele frequencies different from the original population
* Allele frequencies can drift substantially when the population is small
* new population/less diverse

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Large population → small population

* less genetic diversity
* new population less than the original
* ex: frogs in little colors

Founder effect

founding fathers

* a small group of individuals leaves a large population & establishes a new colony
* small group → large population
* small founding population expected to have a less genetic variation
* building within population

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population doesn’t die off

small groups migrating

assertive meetings

Geneflow

occurs when individuals migrate between populations having different allele frequencies

* gene move between population

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migration tends to reduce differences in allele frequencies between the 2 population

* tends to enhance genetic diversity within a population
* introducing
* deer

Nonrandom mating

mating that has not occurred due to chance

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2 main types: seeking mates

* Assortative mating
* Disassortative mating

Assortative mating

* individuals with similar phenotypes or genotypes are @@more likely to mate@@
* increases the proportion of homozygotes

Disassortative mating

* dissimilar phenotypes mate preferentially
* favors heterozygosity (choosing someone different)

Inbreeding

choice of mate based on genetic history

Systematics

* combination taxonomy + phylogeny
* study of biological diversity & evolutionary relationships

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based on morphological and/or genetic homology

* common ancestor

Taxonomy

* giving organisms names
* describing characteristics
* science of naming/describing/classifying living & extinct organisms (and viruses)
* Hierarchical (domain through species)
* A hierarchical system involving successive levels

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Each group at any level is called a @@taxon@@

Taxonomic group

* Domain, phylum, genus, or supergroup
* The highest level is a domain
* All of life belongs to 1 of 3 domains
* Bacteria
* Archaea
* Eukarya

Phylogeny

relationship of organisms

look at the evolutionary relationships/history of a group or species

* ex trees

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The purpose

* biologist uses the tools of systematics
* trees are usually based on morphological or genetic data
* represents relationships